Multiple sequence alignment - TraesCS5A01G131600

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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 TraesCS5A01G131600 chr5A 100.000 3736 0 0 1 3736 296467202 296470937 0.000000e+00 6900.0
1 TraesCS5A01G131600 chr5B 94.225 3273 101 32 512 3736 247667394 247664162 0.000000e+00 4916.0
2 TraesCS5A01G131600 chr5B 86.335 483 52 9 4 484 247667861 247667391 7.160000e-142 514.0
3 TraesCS5A01G131600 chr5D 93.085 2849 107 36 961 3736 223887609 223890440 0.000000e+00 4087.0
4 TraesCS5A01G131600 chr5D 93.240 858 47 6 85 941 223886770 223887617 0.000000e+00 1253.0
5 TraesCS5A01G131600 chr3D 82.727 110 15 3 1226 1332 95482322 95482430 1.100000e-15 95.3
6 TraesCS5A01G131600 chr4D 81.443 97 16 2 18 113 56951585 56951680 1.110000e-10 78.7


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 TraesCS5A01G131600 chr5A 296467202 296470937 3735 False 6900 6900 100.0000 1 3736 1 chr5A.!!$F1 3735
1 TraesCS5A01G131600 chr5B 247664162 247667861 3699 True 2715 4916 90.2800 4 3736 2 chr5B.!!$R1 3732
2 TraesCS5A01G131600 chr5D 223886770 223890440 3670 False 2670 4087 93.1625 85 3736 2 chr5D.!!$F1 3651

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
997 1025 0.250727 GCACACACCTCCTGCCTTAA 60.251 55.0 0.0 0.0 0.0 1.85 F
2432 2532 0.531532 GCGATACCATCAGCAGCAGT 60.532 55.0 0.0 0.0 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2654 2754 0.036388 TGGTCGACTGGATTCAAGCC 60.036 55.0 16.46 0.0 0.0 4.35 R
3364 3465 0.037975 CCCTTGTTGTGCTTGGATGC 60.038 55.0 0.00 0.0 0.0 3.91 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
33 34 8.614346 TCGGAAATATTAAAAATCTAACGGTGG 58.386 33.333 0.00 0.00 0.00 4.61
35 36 9.726232 GGAAATATTAAAAATCTAACGGTGGAC 57.274 33.333 0.00 0.00 0.00 4.02
44 45 4.339872 TCTAACGGTGGACTTTTAAGCA 57.660 40.909 0.00 0.00 0.00 3.91
63 64 3.501062 AGCATGTCAAATATGATGCTCGG 59.499 43.478 0.00 0.00 44.63 4.63
77 78 7.984422 ATGATGCTCGGAATGACAAATTATA 57.016 32.000 0.00 0.00 0.00 0.98
122 123 3.920231 TCAGCAAGCATATCAAGTCCT 57.080 42.857 0.00 0.00 0.00 3.85
154 156 4.018960 AGACTAAGCACATCAGGGATTTGT 60.019 41.667 0.00 0.00 0.00 2.83
161 163 4.201657 CACATCAGGGATTTGTCATGCTA 58.798 43.478 0.00 0.00 0.00 3.49
162 164 4.275196 CACATCAGGGATTTGTCATGCTAG 59.725 45.833 0.00 0.00 0.00 3.42
205 207 1.336702 GCAAAACATCATCGCCCACAA 60.337 47.619 0.00 0.00 0.00 3.33
216 218 0.310854 CGCCCACAACCTTTCAAGAC 59.689 55.000 0.00 0.00 0.00 3.01
224 226 5.530915 CCACAACCTTTCAAGACACAATCTA 59.469 40.000 0.00 0.00 36.27 1.98
226 228 5.531287 ACAACCTTTCAAGACACAATCTACC 59.469 40.000 0.00 0.00 36.27 3.18
263 265 7.587629 CCATACTCGCAACATCATAAATTGAT 58.412 34.615 0.00 0.00 46.27 2.57
265 267 9.533983 CATACTCGCAACATCATAAATTGATAC 57.466 33.333 0.00 0.00 43.40 2.24
269 271 5.009510 CGCAACATCATAAATTGATACCCCA 59.990 40.000 0.00 0.00 43.40 4.96
270 272 6.460814 CGCAACATCATAAATTGATACCCCAA 60.461 38.462 0.00 0.00 43.40 4.12
271 273 6.925165 GCAACATCATAAATTGATACCCCAAG 59.075 38.462 0.00 0.00 43.40 3.61
299 301 6.580041 GTCAGATTTGCTATGTTTGTTCACTG 59.420 38.462 0.00 0.00 0.00 3.66
302 304 3.902261 TGCTATGTTTGTTCACTGCAG 57.098 42.857 13.48 13.48 0.00 4.41
359 361 2.880268 TCAAGTGAACTGCCACTGATTG 59.120 45.455 0.00 0.00 45.82 2.67
377 379 2.411628 TGGCAACACCGCATACTATT 57.588 45.000 0.00 0.00 46.17 1.73
378 380 3.545366 TGGCAACACCGCATACTATTA 57.455 42.857 0.00 0.00 46.17 0.98
379 381 4.079980 TGGCAACACCGCATACTATTAT 57.920 40.909 0.00 0.00 46.17 1.28
426 428 1.976728 CGTAACACGTCTGTACTGCAG 59.023 52.381 13.48 13.48 38.48 4.41
484 511 5.393027 GCACCACCAACAGATTTTATACAGG 60.393 44.000 0.00 0.00 0.00 4.00
485 512 5.125417 CACCACCAACAGATTTTATACAGGG 59.875 44.000 0.00 0.00 0.00 4.45
486 513 5.014755 ACCACCAACAGATTTTATACAGGGA 59.985 40.000 0.00 0.00 0.00 4.20
487 514 5.949354 CCACCAACAGATTTTATACAGGGAA 59.051 40.000 0.00 0.00 0.00 3.97
488 515 6.095440 CCACCAACAGATTTTATACAGGGAAG 59.905 42.308 0.00 0.00 0.00 3.46
489 516 6.095440 CACCAACAGATTTTATACAGGGAAGG 59.905 42.308 0.00 0.00 0.00 3.46
490 517 5.594317 CCAACAGATTTTATACAGGGAAGGG 59.406 44.000 0.00 0.00 0.00 3.95
491 518 6.423182 CAACAGATTTTATACAGGGAAGGGA 58.577 40.000 0.00 0.00 0.00 4.20
492 519 6.652205 ACAGATTTTATACAGGGAAGGGAA 57.348 37.500 0.00 0.00 0.00 3.97
493 520 7.039722 ACAGATTTTATACAGGGAAGGGAAA 57.960 36.000 0.00 0.00 0.00 3.13
494 521 7.119387 ACAGATTTTATACAGGGAAGGGAAAG 58.881 38.462 0.00 0.00 0.00 2.62
495 522 6.547510 CAGATTTTATACAGGGAAGGGAAAGG 59.452 42.308 0.00 0.00 0.00 3.11
496 523 6.450352 AGATTTTATACAGGGAAGGGAAAGGA 59.550 38.462 0.00 0.00 0.00 3.36
497 524 6.471942 TTTTATACAGGGAAGGGAAAGGAA 57.528 37.500 0.00 0.00 0.00 3.36
498 525 5.710409 TTATACAGGGAAGGGAAAGGAAG 57.290 43.478 0.00 0.00 0.00 3.46
499 526 1.076438 ACAGGGAAGGGAAAGGAAGG 58.924 55.000 0.00 0.00 0.00 3.46
500 527 0.332972 CAGGGAAGGGAAAGGAAGGG 59.667 60.000 0.00 0.00 0.00 3.95
501 528 0.851332 AGGGAAGGGAAAGGAAGGGG 60.851 60.000 0.00 0.00 0.00 4.79
502 529 0.849540 GGGAAGGGAAAGGAAGGGGA 60.850 60.000 0.00 0.00 0.00 4.81
503 530 1.081481 GGAAGGGAAAGGAAGGGGAA 58.919 55.000 0.00 0.00 0.00 3.97
504 531 1.431633 GGAAGGGAAAGGAAGGGGAAA 59.568 52.381 0.00 0.00 0.00 3.13
505 532 2.158219 GGAAGGGAAAGGAAGGGGAAAA 60.158 50.000 0.00 0.00 0.00 2.29
506 533 3.583228 GAAGGGAAAGGAAGGGGAAAAA 58.417 45.455 0.00 0.00 0.00 1.94
525 552 5.712152 AAAAACCAACAGATGAGATGGAC 57.288 39.130 9.79 0.00 36.75 4.02
575 602 5.486775 TGTGGAAGATCTCCTCATCTTTTCT 59.513 40.000 0.00 0.00 45.64 2.52
598 625 2.476185 CGCTTTACCAAATCGCCAGAAG 60.476 50.000 0.00 0.00 0.00 2.85
650 677 0.959372 CAAGCAAGAGGACAGGCCAG 60.959 60.000 5.01 0.00 40.02 4.85
669 697 3.496160 CCAGGAAACGAGAAAGAAAGGGA 60.496 47.826 0.00 0.00 0.00 4.20
737 765 2.289945 GGCCTGCCAGGTCTATTCTATG 60.290 54.545 13.35 0.00 36.93 2.23
886 914 3.379688 GGAATCCTTTCTCATGTGCTTCC 59.620 47.826 0.00 0.00 32.16 3.46
931 959 2.930562 ACGCTCCTGGAAAGCCCT 60.931 61.111 0.00 0.00 36.36 5.19
932 960 2.124942 CGCTCCTGGAAAGCCCTC 60.125 66.667 0.00 0.00 36.36 4.30
933 961 2.664081 CGCTCCTGGAAAGCCCTCT 61.664 63.158 0.00 0.00 36.36 3.69
934 962 1.223211 GCTCCTGGAAAGCCCTCTC 59.777 63.158 0.00 0.00 33.53 3.20
935 963 1.271127 GCTCCTGGAAAGCCCTCTCT 61.271 60.000 0.00 0.00 33.53 3.10
936 964 0.829990 CTCCTGGAAAGCCCTCTCTC 59.170 60.000 0.00 0.00 35.38 3.20
937 965 0.415429 TCCTGGAAAGCCCTCTCTCT 59.585 55.000 0.00 0.00 35.38 3.10
938 966 0.829990 CCTGGAAAGCCCTCTCTCTC 59.170 60.000 0.00 0.00 35.38 3.20
939 967 1.622173 CCTGGAAAGCCCTCTCTCTCT 60.622 57.143 0.00 0.00 35.38 3.10
940 968 1.756538 CTGGAAAGCCCTCTCTCTCTC 59.243 57.143 0.00 0.00 35.38 3.20
941 969 1.360852 TGGAAAGCCCTCTCTCTCTCT 59.639 52.381 0.00 0.00 35.38 3.10
942 970 2.031870 GGAAAGCCCTCTCTCTCTCTC 58.968 57.143 0.00 0.00 0.00 3.20
943 971 2.358195 GGAAAGCCCTCTCTCTCTCTCT 60.358 54.545 0.00 0.00 0.00 3.10
944 972 2.736670 AAGCCCTCTCTCTCTCTCTC 57.263 55.000 0.00 0.00 0.00 3.20
945 973 1.898863 AGCCCTCTCTCTCTCTCTCT 58.101 55.000 0.00 0.00 0.00 3.10
946 974 1.771255 AGCCCTCTCTCTCTCTCTCTC 59.229 57.143 0.00 0.00 0.00 3.20
947 975 1.771255 GCCCTCTCTCTCTCTCTCTCT 59.229 57.143 0.00 0.00 0.00 3.10
948 976 2.224402 GCCCTCTCTCTCTCTCTCTCTC 60.224 59.091 0.00 0.00 0.00 3.20
949 977 3.312890 CCCTCTCTCTCTCTCTCTCTCT 58.687 54.545 0.00 0.00 0.00 3.10
950 978 3.323403 CCCTCTCTCTCTCTCTCTCTCTC 59.677 56.522 0.00 0.00 0.00 3.20
951 979 4.222336 CCTCTCTCTCTCTCTCTCTCTCT 58.778 52.174 0.00 0.00 0.00 3.10
952 980 4.280677 CCTCTCTCTCTCTCTCTCTCTCTC 59.719 54.167 0.00 0.00 0.00 3.20
953 981 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
954 982 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
955 983 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
996 1024 1.374947 GCACACACCTCCTGCCTTA 59.625 57.895 0.00 0.00 0.00 2.69
997 1025 0.250727 GCACACACCTCCTGCCTTAA 60.251 55.000 0.00 0.00 0.00 1.85
1007 1035 3.070302 CCTCCTGCCTTAACTCTACCATC 59.930 52.174 0.00 0.00 0.00 3.51
1016 1044 5.586643 CCTTAACTCTACCATCCTTGCTTTC 59.413 44.000 0.00 0.00 0.00 2.62
1205 1237 7.528481 TCAATCAATTTCATTTGCAGCATAC 57.472 32.000 0.00 0.00 0.00 2.39
1343 1377 2.353889 CTCCATTTCTTCTGTCCATGCG 59.646 50.000 0.00 0.00 0.00 4.73
1370 1404 6.084821 CCAACTGGTAAGAAGACAGATGGTC 61.085 48.000 10.80 0.00 45.00 4.02
1407 1441 4.238514 CCACAGTACTAGTGCTCTGAAAC 58.761 47.826 15.95 0.00 35.69 2.78
1536 1570 3.582647 TGCTCAAGAAGATCAAGGTACCA 59.417 43.478 15.94 0.00 0.00 3.25
1540 1574 1.840635 AGAAGATCAAGGTACCAGCCC 59.159 52.381 15.94 0.00 0.00 5.19
1748 1812 9.271828 GTTTGTTTTGGAAACCAGATTGATTAT 57.728 29.630 1.53 0.00 33.81 1.28
1754 1818 7.350744 TGGAAACCAGATTGATTATTGATGG 57.649 36.000 0.00 0.00 0.00 3.51
1942 2006 2.807045 CCAGCTCACGTCGTGCTC 60.807 66.667 20.56 13.53 42.49 4.26
2012 2076 4.809426 GGAATGATACGGTTGTCGATCTTT 59.191 41.667 0.00 0.00 42.43 2.52
2013 2077 5.050972 GGAATGATACGGTTGTCGATCTTTC 60.051 44.000 0.00 7.45 42.43 2.62
2064 2128 4.727507 ATAGTAGCAGACAACTCACCAG 57.272 45.455 0.00 0.00 0.00 4.00
2086 2150 5.233050 CAGTGCCACTTGTCTATTTCTATCG 59.767 44.000 0.00 0.00 0.00 2.92
2096 2160 4.504461 GTCTATTTCTATCGGCGCATATGG 59.496 45.833 10.83 3.77 0.00 2.74
2121 2185 9.143155 GGAGTAAAAACCCAAATATATGGACAT 57.857 33.333 0.00 0.00 43.54 3.06
2174 2271 9.823647 GGATCTTAGAATGAACTCTGACAATTA 57.176 33.333 0.00 0.00 0.00 1.40
2176 2273 8.689251 TCTTAGAATGAACTCTGACAATTACG 57.311 34.615 0.00 0.00 0.00 3.18
2231 2328 5.491982 GAAGGAGCAAATGAGTTCTTCCTA 58.508 41.667 0.00 0.00 0.00 2.94
2344 2441 1.598130 GCAACAGCGAGACCAACCT 60.598 57.895 0.00 0.00 0.00 3.50
2381 2481 0.810031 GCAGCGATACCGTCACCATT 60.810 55.000 0.00 0.00 38.24 3.16
2385 2485 1.405461 CGATACCGTCACCATTAGCG 58.595 55.000 0.00 0.00 0.00 4.26
2399 2499 1.481901 TTAGCGGCAGTAACCCCACA 61.482 55.000 1.45 0.00 0.00 4.17
2400 2500 1.481901 TAGCGGCAGTAACCCCACAA 61.482 55.000 1.45 0.00 0.00 3.33
2412 2512 1.674764 CCCCACAAACAACAGCAGCA 61.675 55.000 0.00 0.00 0.00 4.41
2432 2532 0.531532 GCGATACCATCAGCAGCAGT 60.532 55.000 0.00 0.00 0.00 4.40
2441 2541 1.073025 CAGCAGCAGTAACCCCACA 59.927 57.895 0.00 0.00 0.00 4.17
2452 2552 2.200373 AACCCCACAGATAACAGCAC 57.800 50.000 0.00 0.00 0.00 4.40
2453 2553 1.362224 ACCCCACAGATAACAGCACT 58.638 50.000 0.00 0.00 0.00 4.40
2477 2577 1.003116 GATAGCAGCAACATCCGCAAG 60.003 52.381 0.00 0.00 0.00 4.01
2543 2643 4.498009 CCAAACCACAGTTGTTAGCTGAAG 60.498 45.833 0.00 0.00 35.97 3.02
2551 2651 6.854892 CACAGTTGTTAGCTGAAGAAAGATTG 59.145 38.462 0.00 0.00 37.40 2.67
2560 2660 5.591877 AGCTGAAGAAAGATTGTTTGACAGT 59.408 36.000 0.00 0.00 0.00 3.55
2597 2697 8.163408 TCCTTTCTTGGTTCTTCATCTTAATCA 58.837 33.333 0.00 0.00 0.00 2.57
2698 2799 1.145803 GGTGTAACACGCCTGAAGTC 58.854 55.000 3.72 0.00 45.06 3.01
3018 3119 6.849588 ATTGAAGGTTCATGCAAAAAGAAC 57.150 33.333 13.17 13.17 40.58 3.01
3019 3120 5.596836 TGAAGGTTCATGCAAAAAGAACT 57.403 34.783 18.03 5.78 40.97 3.01
3021 3122 5.811613 TGAAGGTTCATGCAAAAAGAACTTG 59.188 36.000 18.03 0.00 40.97 3.16
3022 3123 5.596836 AGGTTCATGCAAAAAGAACTTGA 57.403 34.783 18.03 1.68 40.97 3.02
3023 3124 6.165700 AGGTTCATGCAAAAAGAACTTGAT 57.834 33.333 18.03 5.95 40.97 2.57
3024 3125 5.987347 AGGTTCATGCAAAAAGAACTTGATG 59.013 36.000 18.03 0.00 40.97 3.07
3025 3126 5.984926 GGTTCATGCAAAAAGAACTTGATGA 59.015 36.000 18.03 0.43 40.97 2.92
3026 3127 6.145048 GGTTCATGCAAAAAGAACTTGATGAG 59.855 38.462 18.03 0.00 40.97 2.90
3027 3128 5.775686 TCATGCAAAAAGAACTTGATGAGG 58.224 37.500 0.00 0.00 0.00 3.86
3028 3129 5.535783 TCATGCAAAAAGAACTTGATGAGGA 59.464 36.000 0.00 0.00 0.00 3.71
3029 3130 5.443185 TGCAAAAAGAACTTGATGAGGAG 57.557 39.130 0.00 0.00 0.00 3.69
3037 3138 9.793259 AAAAGAACTTGATGAGGAGTAATAACA 57.207 29.630 0.00 0.00 0.00 2.41
3106 3207 3.728385 AAGGATAATGAGCTATGCCCC 57.272 47.619 0.00 0.00 0.00 5.80
3267 3368 6.210385 ACACAAATAATATGGCAACCTCACAA 59.790 34.615 0.00 0.00 0.00 3.33
3346 3447 6.601613 GTGGTCAGGATGGTAAAATGTATCAA 59.398 38.462 0.00 0.00 36.16 2.57
3347 3448 7.285401 GTGGTCAGGATGGTAAAATGTATCAAT 59.715 37.037 0.00 0.00 36.16 2.57
3348 3449 7.285172 TGGTCAGGATGGTAAAATGTATCAATG 59.715 37.037 0.00 0.00 36.16 2.82
3506 3612 4.148128 AGGAAATAGTGACATCCAGCAG 57.852 45.455 0.00 0.00 34.30 4.24
3543 3649 6.903883 AAAGGTTACATAGTTCACATAGCG 57.096 37.500 0.00 0.00 0.00 4.26
3564 3670 1.013596 CTTGCAATATCGTTCCCGCA 58.986 50.000 0.00 0.00 0.00 5.69
3611 3717 6.265196 AGCAAGACTGGAAAAATAACATCACA 59.735 34.615 0.00 0.00 0.00 3.58
3633 3739 6.000219 ACAGTTCTAGCATGAAACACTTGAT 59.000 36.000 0.00 0.00 0.00 2.57
3667 3773 6.935240 ATGGGGAAAATAGATAGTGATCGA 57.065 37.500 0.00 0.00 37.15 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 9.726232 GTCCACCGTTAGATTTTTAATATTTCC 57.274 33.333 0.00 0.00 0.00 3.13
25 26 4.391155 ACATGCTTAAAAGTCCACCGTTA 58.609 39.130 0.00 0.00 0.00 3.18
26 27 3.219281 ACATGCTTAAAAGTCCACCGTT 58.781 40.909 0.00 0.00 0.00 4.44
29 30 4.846779 TTGACATGCTTAAAAGTCCACC 57.153 40.909 0.00 0.00 0.00 4.61
30 31 8.243426 TCATATTTGACATGCTTAAAAGTCCAC 58.757 33.333 0.00 0.00 0.00 4.02
33 34 8.749499 GCATCATATTTGACATGCTTAAAAGTC 58.251 33.333 4.95 0.00 35.77 3.01
35 36 8.867112 AGCATCATATTTGACATGCTTAAAAG 57.133 30.769 8.05 0.00 42.71 2.27
44 45 5.999600 TCATTCCGAGCATCATATTTGACAT 59.000 36.000 0.00 0.00 33.85 3.06
84 85 4.278919 TGCTGAAGAAAATTGTCATGCTCA 59.721 37.500 0.00 0.00 0.00 4.26
132 133 4.265073 ACAAATCCCTGATGTGCTTAGTC 58.735 43.478 0.00 0.00 30.88 2.59
134 135 4.264253 TGACAAATCCCTGATGTGCTTAG 58.736 43.478 0.00 0.00 30.88 2.18
135 136 4.299586 TGACAAATCCCTGATGTGCTTA 57.700 40.909 0.00 0.00 30.88 3.09
136 137 3.159213 TGACAAATCCCTGATGTGCTT 57.841 42.857 0.00 0.00 30.88 3.91
137 138 2.885135 TGACAAATCCCTGATGTGCT 57.115 45.000 0.00 0.00 30.88 4.40
138 139 2.480759 GCATGACAAATCCCTGATGTGC 60.481 50.000 0.00 0.00 30.88 4.57
139 140 3.021695 AGCATGACAAATCCCTGATGTG 58.978 45.455 0.00 0.00 33.77 3.21
141 142 4.711399 TCTAGCATGACAAATCCCTGATG 58.289 43.478 0.00 0.00 0.00 3.07
142 143 5.378230 TTCTAGCATGACAAATCCCTGAT 57.622 39.130 0.00 0.00 0.00 2.90
143 144 4.842531 TTCTAGCATGACAAATCCCTGA 57.157 40.909 0.00 0.00 0.00 3.86
146 148 5.506317 CGGATTTTCTAGCATGACAAATCCC 60.506 44.000 21.71 13.73 45.47 3.85
154 156 3.119280 TGACGTCGGATTTTCTAGCATGA 60.119 43.478 11.62 0.00 0.00 3.07
205 207 4.039973 TCGGTAGATTGTGTCTTGAAAGGT 59.960 41.667 0.00 0.00 38.42 3.50
216 218 4.438744 GGCAATTTCCTTCGGTAGATTGTG 60.439 45.833 0.00 0.00 0.00 3.33
224 226 3.279434 GAGTATGGCAATTTCCTTCGGT 58.721 45.455 0.00 0.00 0.00 4.69
226 228 2.286418 GCGAGTATGGCAATTTCCTTCG 60.286 50.000 0.00 1.88 40.68 3.79
252 254 4.141287 CGGCTTGGGGTATCAATTTATGA 58.859 43.478 0.00 0.00 43.67 2.15
263 265 0.988832 AAATCTGACGGCTTGGGGTA 59.011 50.000 0.00 0.00 0.00 3.69
265 267 1.937546 GCAAATCTGACGGCTTGGGG 61.938 60.000 0.00 0.00 0.00 4.96
269 271 2.991250 ACATAGCAAATCTGACGGCTT 58.009 42.857 5.11 0.00 37.79 4.35
270 272 2.698855 ACATAGCAAATCTGACGGCT 57.301 45.000 0.00 5.15 40.26 5.52
271 273 3.119849 ACAAACATAGCAAATCTGACGGC 60.120 43.478 0.00 0.00 0.00 5.68
354 356 0.808125 GTATGCGGTGTTGCCAATCA 59.192 50.000 0.00 0.00 36.97 2.57
359 361 3.813166 ACATAATAGTATGCGGTGTTGCC 59.187 43.478 10.02 0.00 40.83 4.52
484 511 1.081481 TTCCCCTTCCTTTCCCTTCC 58.919 55.000 0.00 0.00 0.00 3.46
485 512 2.992847 TTTCCCCTTCCTTTCCCTTC 57.007 50.000 0.00 0.00 0.00 3.46
486 513 3.717507 TTTTTCCCCTTCCTTTCCCTT 57.282 42.857 0.00 0.00 0.00 3.95
503 530 4.216257 CGTCCATCTCATCTGTTGGTTTTT 59.784 41.667 0.00 0.00 0.00 1.94
504 531 3.753272 CGTCCATCTCATCTGTTGGTTTT 59.247 43.478 0.00 0.00 0.00 2.43
505 532 3.338249 CGTCCATCTCATCTGTTGGTTT 58.662 45.455 0.00 0.00 0.00 3.27
506 533 2.936993 GCGTCCATCTCATCTGTTGGTT 60.937 50.000 0.00 0.00 0.00 3.67
507 534 1.406069 GCGTCCATCTCATCTGTTGGT 60.406 52.381 0.00 0.00 0.00 3.67
508 535 1.293924 GCGTCCATCTCATCTGTTGG 58.706 55.000 0.00 0.00 0.00 3.77
509 536 0.926155 CGCGTCCATCTCATCTGTTG 59.074 55.000 0.00 0.00 0.00 3.33
510 537 0.807667 GCGCGTCCATCTCATCTGTT 60.808 55.000 8.43 0.00 0.00 3.16
511 538 1.227089 GCGCGTCCATCTCATCTGT 60.227 57.895 8.43 0.00 0.00 3.41
512 539 0.599466 ATGCGCGTCCATCTCATCTG 60.599 55.000 8.43 0.00 0.00 2.90
513 540 0.319383 GATGCGCGTCCATCTCATCT 60.319 55.000 19.11 0.00 38.80 2.90
514 541 0.598419 TGATGCGCGTCCATCTCATC 60.598 55.000 26.06 17.12 41.65 2.92
517 544 0.026803 GTTTGATGCGCGTCCATCTC 59.973 55.000 26.06 8.99 41.65 2.75
525 552 2.871080 CTTGCGGTTTGATGCGCG 60.871 61.111 0.00 0.00 0.00 6.86
598 625 1.472878 GAAAGGAAGATTTGGGGTCGC 59.527 52.381 0.00 0.00 0.00 5.19
650 677 3.502595 CCTTCCCTTTCTTTCTCGTTTCC 59.497 47.826 0.00 0.00 0.00 3.13
669 697 3.897505 CCACCATTTTCTCTTGTTCCCTT 59.102 43.478 0.00 0.00 0.00 3.95
737 765 1.838112 TGCCATGAATTGACTCCACC 58.162 50.000 0.00 0.00 0.00 4.61
886 914 3.050619 GGAGTCGAGTTTATATGCACCG 58.949 50.000 0.00 0.00 0.00 4.94
931 959 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
932 960 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
933 961 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
934 962 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
935 963 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
936 964 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
937 965 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
938 966 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
939 967 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
940 968 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
941 969 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
942 970 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
943 971 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
944 972 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
945 973 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
946 974 4.892345 TGAGAGAGAGAGAGAGAGAGAGAG 59.108 50.000 0.00 0.00 0.00 3.20
947 975 4.871822 TGAGAGAGAGAGAGAGAGAGAGA 58.128 47.826 0.00 0.00 0.00 3.10
948 976 5.539979 CATGAGAGAGAGAGAGAGAGAGAG 58.460 50.000 0.00 0.00 0.00 3.20
949 977 4.202295 GCATGAGAGAGAGAGAGAGAGAGA 60.202 50.000 0.00 0.00 0.00 3.10
950 978 4.063689 GCATGAGAGAGAGAGAGAGAGAG 58.936 52.174 0.00 0.00 0.00 3.20
951 979 3.181451 GGCATGAGAGAGAGAGAGAGAGA 60.181 52.174 0.00 0.00 0.00 3.10
952 980 3.144506 GGCATGAGAGAGAGAGAGAGAG 58.855 54.545 0.00 0.00 0.00 3.20
953 981 2.509131 TGGCATGAGAGAGAGAGAGAGA 59.491 50.000 0.00 0.00 0.00 3.10
954 982 2.934887 TGGCATGAGAGAGAGAGAGAG 58.065 52.381 0.00 0.00 0.00 3.20
955 983 3.289836 CTTGGCATGAGAGAGAGAGAGA 58.710 50.000 0.00 0.00 0.00 3.10
996 1024 4.323868 GGAGAAAGCAAGGATGGTAGAGTT 60.324 45.833 0.00 0.00 35.91 3.01
997 1025 3.198853 GGAGAAAGCAAGGATGGTAGAGT 59.801 47.826 0.00 0.00 35.91 3.24
1007 1035 3.272574 TGCTATGAGGAGAAAGCAAGG 57.727 47.619 0.00 0.00 41.74 3.61
1016 1044 2.178580 GGAGGAGGATGCTATGAGGAG 58.821 57.143 0.00 0.00 36.27 3.69
1205 1237 2.159653 GCATAGCAGGAACACAACTTCG 60.160 50.000 0.00 0.00 0.00 3.79
1349 1383 4.810191 GACCATCTGTCTTCTTACCAGT 57.190 45.455 0.00 0.00 41.03 4.00
1362 1396 1.797046 GCGCACATGATAGACCATCTG 59.203 52.381 0.30 0.00 34.46 2.90
1370 1404 1.091197 TGTGGCTGCGCACATGATAG 61.091 55.000 5.66 0.00 0.00 2.08
1407 1441 9.492973 AACCCAAAATTAATCAATCAGAAACAG 57.507 29.630 0.00 0.00 0.00 3.16
1427 1461 1.203001 CCTGCTTAGGACCAAACCCAA 60.203 52.381 0.00 0.00 0.00 4.12
1548 1582 6.707440 TTGAGCAGACCAAATCAAACTAAA 57.293 33.333 0.00 0.00 0.00 1.85
1748 1812 6.899393 AAGTTTCTAAATCAGCACCATCAA 57.101 33.333 0.00 0.00 0.00 2.57
1754 1818 8.883731 TCAGCTATAAAGTTTCTAAATCAGCAC 58.116 33.333 0.00 0.00 0.00 4.40
1981 2045 6.423905 CGACAACCGTATCATTCCATATCTTT 59.576 38.462 0.00 0.00 0.00 2.52
1990 2054 5.964070 GAAAGATCGACAACCGTATCATTC 58.036 41.667 0.00 0.00 39.75 2.67
2048 2112 0.533755 GCACTGGTGAGTTGTCTGCT 60.534 55.000 4.79 0.00 0.00 4.24
2064 2128 4.508124 CCGATAGAAATAGACAAGTGGCAC 59.492 45.833 10.29 10.29 39.76 5.01
2086 2150 2.034179 GGGTTTTTACTCCATATGCGCC 59.966 50.000 4.18 0.00 0.00 6.53
2145 2210 8.001881 TGTCAGAGTTCATTCTAAGATCCTAC 57.998 38.462 0.00 0.00 0.00 3.18
2146 2211 8.595362 TTGTCAGAGTTCATTCTAAGATCCTA 57.405 34.615 0.00 0.00 0.00 2.94
2174 2271 5.124776 TCTGATTCAGAACAAACAAAACCGT 59.875 36.000 13.96 0.00 37.57 4.83
2176 2273 6.074142 GCATCTGATTCAGAACAAACAAAACC 60.074 38.462 19.73 0.00 44.04 3.27
2231 2328 3.259876 TGTCTGATAGCCGTACTGGTTTT 59.740 43.478 0.00 0.00 41.21 2.43
2344 2441 0.101040 GCTGCTGCTGTTGTTTGTGA 59.899 50.000 8.53 0.00 36.03 3.58
2373 2473 1.664151 GTTACTGCCGCTAATGGTGAC 59.336 52.381 0.00 0.00 0.00 3.67
2375 2475 1.014352 GGTTACTGCCGCTAATGGTG 58.986 55.000 0.00 0.00 0.00 4.17
2381 2481 1.481901 TTGTGGGGTTACTGCCGCTA 61.482 55.000 0.00 0.00 41.45 4.26
2385 2485 1.067974 GTTGTTTGTGGGGTTACTGCC 59.932 52.381 0.00 0.00 0.00 4.85
2399 2499 1.197721 GTATCGCTGCTGCTGTTGTTT 59.802 47.619 14.03 0.00 36.97 2.83
2400 2500 0.798776 GTATCGCTGCTGCTGTTGTT 59.201 50.000 14.03 0.00 36.97 2.83
2412 2512 0.249784 CTGCTGCTGATGGTATCGCT 60.250 55.000 0.00 0.00 32.64 4.93
2432 2532 2.910319 AGTGCTGTTATCTGTGGGGTTA 59.090 45.455 0.00 0.00 0.00 2.85
2441 2541 3.452264 TGCTATCACCAGTGCTGTTATCT 59.548 43.478 0.00 0.00 0.00 1.98
2452 2552 1.945394 GGATGTTGCTGCTATCACCAG 59.055 52.381 0.00 0.00 0.00 4.00
2453 2553 1.743431 CGGATGTTGCTGCTATCACCA 60.743 52.381 0.00 0.00 0.00 4.17
2477 2577 1.424493 CGTCATCTGCCGCCTTTCTC 61.424 60.000 0.00 0.00 0.00 2.87
2505 2605 1.338020 GTTTGGTCTGCTTGTCTTGGG 59.662 52.381 0.00 0.00 0.00 4.12
2597 2697 7.170965 ACATACAAATCAGATGTCAGAAACCT 58.829 34.615 0.00 0.00 32.27 3.50
2654 2754 0.036388 TGGTCGACTGGATTCAAGCC 60.036 55.000 16.46 0.00 0.00 4.35
2698 2799 2.230130 TTGGCCTGAAGGTATTTGGG 57.770 50.000 3.32 0.00 37.57 4.12
2744 2845 3.815809 AGGTGTAGCAAGCTGTTTGTAA 58.184 40.909 4.53 0.00 39.08 2.41
3018 3119 7.988737 TGCATTTGTTATTACTCCTCATCAAG 58.011 34.615 0.00 0.00 0.00 3.02
3019 3120 7.611467 ACTGCATTTGTTATTACTCCTCATCAA 59.389 33.333 0.00 0.00 0.00 2.57
3021 3122 7.559590 ACTGCATTTGTTATTACTCCTCATC 57.440 36.000 0.00 0.00 0.00 2.92
3022 3123 7.944729 AACTGCATTTGTTATTACTCCTCAT 57.055 32.000 0.00 0.00 0.00 2.90
3023 3124 7.309133 CCAAACTGCATTTGTTATTACTCCTCA 60.309 37.037 15.67 0.00 45.45 3.86
3024 3125 7.029563 CCAAACTGCATTTGTTATTACTCCTC 58.970 38.462 15.67 0.00 45.45 3.71
3025 3126 6.572314 GCCAAACTGCATTTGTTATTACTCCT 60.572 38.462 15.67 0.00 45.45 3.69
3026 3127 5.576774 GCCAAACTGCATTTGTTATTACTCC 59.423 40.000 15.67 0.00 45.45 3.85
3027 3128 6.155827 TGCCAAACTGCATTTGTTATTACTC 58.844 36.000 15.67 0.00 45.45 2.59
3028 3129 6.095432 TGCCAAACTGCATTTGTTATTACT 57.905 33.333 15.67 0.00 45.45 2.24
3106 3207 9.464714 AAGTATATTAATGTCTTAGTCGCTGTG 57.535 33.333 0.00 0.00 0.00 3.66
3157 3258 3.138304 TCCACACACTAACTGATTGTGC 58.862 45.455 0.92 0.00 43.72 4.57
3273 3374 8.476447 TGCTGATAATTTTCTGATTTGCCATAA 58.524 29.630 6.91 0.00 0.00 1.90
3275 3376 6.880484 TGCTGATAATTTTCTGATTTGCCAT 58.120 32.000 6.91 0.00 0.00 4.40
3304 3405 2.497675 ACCACTTGCGTCTCATAGACAT 59.502 45.455 7.75 0.00 45.30 3.06
3305 3406 1.893137 ACCACTTGCGTCTCATAGACA 59.107 47.619 7.75 0.00 45.30 3.41
3364 3465 0.037975 CCCTTGTTGTGCTTGGATGC 60.038 55.000 0.00 0.00 0.00 3.91
3477 3583 6.070021 TGGATGTCACTATTTCCTTCACAGAT 60.070 38.462 0.00 0.00 0.00 2.90
3523 3629 5.589192 AGTCGCTATGTGAACTATGTAACC 58.411 41.667 0.00 0.00 0.00 2.85
3525 3631 5.518847 GCAAGTCGCTATGTGAACTATGTAA 59.481 40.000 0.00 0.00 37.77 2.41
3586 3692 6.265196 TGTGATGTTATTTTTCCAGTCTTGCT 59.735 34.615 0.00 0.00 0.00 3.91
3596 3702 9.282247 CATGCTAGAACTGTGATGTTATTTTTC 57.718 33.333 0.00 0.00 0.00 2.29
3611 3717 5.645497 GGATCAAGTGTTTCATGCTAGAACT 59.355 40.000 0.00 0.00 0.00 3.01
3659 3765 2.315925 ACGGCAAATCATCGATCACT 57.684 45.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.