Multiple sequence alignment - TraesCS3A01G154700

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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 TraesCS3A01G154700 chr3A 100.000 3790 0 0 1 3790 146558171 146561960 0.000000e+00 6999
1 TraesCS3A01G154700 chr3A 96.774 930 25 2 2861 3790 705259401 705258477 0.000000e+00 1546
2 TraesCS3A01G154700 chr3A 100.000 75 0 0 2861 2935 726235331 726235405 5.100000e-29 139
3 TraesCS3A01G154700 chr3B 90.990 2020 104 26 861 2850 189383897 189385868 0.000000e+00 2651
4 TraesCS3A01G154700 chr3D 90.556 1726 109 27 2 1700 132902570 132904268 0.000000e+00 2235
5 TraesCS3A01G154700 chr3D 88.809 697 49 10 1685 2370 132904286 132904964 0.000000e+00 828
6 TraesCS3A01G154700 chr3D 95.918 392 14 2 2457 2847 132905119 132905509 5.340000e-178 634
7 TraesCS3A01G154700 chr2A 97.754 935 16 2 2857 3790 775767408 775766478 0.000000e+00 1605
8 TraesCS3A01G154700 chr2A 96.989 930 23 2 2861 3790 496561821 496560897 0.000000e+00 1557
9 TraesCS3A01G154700 chr4A 96.989 930 23 2 2861 3790 620868371 620867447 0.000000e+00 1557
10 TraesCS3A01G154700 chr7B 96.989 930 20 2 2861 3790 562174581 562173660 0.000000e+00 1555
11 TraesCS3A01G154700 chr7B 76.842 285 37 14 3269 3536 139528892 139529164 2.380000e-27 134
12 TraesCS3A01G154700 chr2B 96.371 937 25 3 2854 3790 759455201 759456128 0.000000e+00 1533
13 TraesCS3A01G154700 chr5B 96.941 523 8 2 2861 3383 430665006 430665520 0.000000e+00 870
14 TraesCS3A01G154700 chr5B 97.356 416 11 0 3375 3790 430666747 430667162 0.000000e+00 708
15 TraesCS3A01G154700 chr5D 80.000 550 95 13 190 734 344989083 344989622 3.550000e-105 392
16 TraesCS3A01G154700 chr5D 79.464 560 99 12 190 740 62529901 62530453 2.140000e-102 383
17 TraesCS3A01G154700 chr5D 78.508 563 105 12 211 763 6689133 6688577 4.660000e-94 355
18 TraesCS3A01G154700 chr5D 78.626 262 41 9 3275 3531 365087557 365087306 3.920000e-35 159
19 TraesCS3A01G154700 chr6A 79.570 558 101 13 190 740 608085816 608085265 1.650000e-103 387
20 TraesCS3A01G154700 chr6A 79.661 531 87 18 211 729 11128037 11128558 2.780000e-96 363
21 TraesCS3A01G154700 chr2D 79.070 559 103 12 190 740 429043045 429043597 4.620000e-99 372
22 TraesCS3A01G154700 chrUn 78.689 549 103 13 190 729 315895589 315895046 1.670000e-93 353
23 TraesCS3A01G154700 chrUn 78.689 549 103 13 190 729 315906416 315905873 1.670000e-93 353
24 TraesCS3A01G154700 chr7A 78.906 256 39 11 3269 3519 176280010 176280255 3.920000e-35 159


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 TraesCS3A01G154700 chr3A 146558171 146561960 3789 False 6999.000000 6999 100.0000 1 3790 1 chr3A.!!$F1 3789
1 TraesCS3A01G154700 chr3A 705258477 705259401 924 True 1546.000000 1546 96.7740 2861 3790 1 chr3A.!!$R1 929
2 TraesCS3A01G154700 chr3B 189383897 189385868 1971 False 2651.000000 2651 90.9900 861 2850 1 chr3B.!!$F1 1989
3 TraesCS3A01G154700 chr3D 132902570 132905509 2939 False 1232.333333 2235 91.7610 2 2847 3 chr3D.!!$F1 2845
4 TraesCS3A01G154700 chr2A 775766478 775767408 930 True 1605.000000 1605 97.7540 2857 3790 1 chr2A.!!$R2 933
5 TraesCS3A01G154700 chr2A 496560897 496561821 924 True 1557.000000 1557 96.9890 2861 3790 1 chr2A.!!$R1 929
6 TraesCS3A01G154700 chr4A 620867447 620868371 924 True 1557.000000 1557 96.9890 2861 3790 1 chr4A.!!$R1 929
7 TraesCS3A01G154700 chr7B 562173660 562174581 921 True 1555.000000 1555 96.9890 2861 3790 1 chr7B.!!$R1 929
8 TraesCS3A01G154700 chr2B 759455201 759456128 927 False 1533.000000 1533 96.3710 2854 3790 1 chr2B.!!$F1 936
9 TraesCS3A01G154700 chr5B 430665006 430667162 2156 False 789.000000 870 97.1485 2861 3790 2 chr5B.!!$F1 929
10 TraesCS3A01G154700 chr5D 344989083 344989622 539 False 392.000000 392 80.0000 190 734 1 chr5D.!!$F2 544
11 TraesCS3A01G154700 chr5D 62529901 62530453 552 False 383.000000 383 79.4640 190 740 1 chr5D.!!$F1 550
12 TraesCS3A01G154700 chr5D 6688577 6689133 556 True 355.000000 355 78.5080 211 763 1 chr5D.!!$R1 552
13 TraesCS3A01G154700 chr6A 608085265 608085816 551 True 387.000000 387 79.5700 190 740 1 chr6A.!!$R1 550
14 TraesCS3A01G154700 chr6A 11128037 11128558 521 False 363.000000 363 79.6610 211 729 1 chr6A.!!$F1 518
15 TraesCS3A01G154700 chr2D 429043045 429043597 552 False 372.000000 372 79.0700 190 740 1 chr2D.!!$F1 550
16 TraesCS3A01G154700 chrUn 315895046 315895589 543 True 353.000000 353 78.6890 190 729 1 chrUn.!!$R1 539
17 TraesCS3A01G154700 chrUn 315905873 315906416 543 True 353.000000 353 78.6890 190 729 1 chrUn.!!$R2 539

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
727 739 0.666577 AAAAACGGAGACCTCTCGCG 60.667 55.0 0.0 0.0 43.76 5.87 F
2093 2191 0.598065 GAGCACCATCACCAAACACC 59.402 55.0 0.0 0.0 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2372 2470 0.398664 AGAGCCATAACCGCTACCCT 60.399 55.000 0.0 0.0 36.48 4.34 R
2980 3178 3.130869 TCACATATACCGCTTACGTTGGT 59.869 43.478 0.0 0.0 39.80 3.67 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
99 100 3.609853 TCGTTCAAAATATGAGCAGCCT 58.390 40.909 0.00 0.00 39.06 4.58
108 109 6.901081 AAATATGAGCAGCCTAATAAACCC 57.099 37.500 0.00 0.00 0.00 4.11
118 119 3.806157 GCCTAATAAACCCCATCGGAGTC 60.806 52.174 0.00 0.00 34.64 3.36
122 123 2.521958 AAACCCCATCGGAGTCGCTG 62.522 60.000 0.00 0.00 36.13 5.18
134 135 2.070028 GAGTCGCTGGAACCTCTTTTC 58.930 52.381 0.00 0.00 0.00 2.29
160 161 6.656693 CCCTCAAAGAGACTGAAATGTACATT 59.343 38.462 15.47 15.47 0.00 2.71
299 303 2.941064 CCACCTATCGACGACTACAAGA 59.059 50.000 0.00 0.00 0.00 3.02
335 339 2.033911 TGCCCTGCTTTCATCGCA 59.966 55.556 0.00 0.00 35.80 5.10
336 340 1.378911 TGCCCTGCTTTCATCGCAT 60.379 52.632 0.00 0.00 36.70 4.73
340 344 1.747355 CCCTGCTTTCATCGCATCTTT 59.253 47.619 0.00 0.00 36.70 2.52
375 379 5.763204 CCGGGCAAACATTATTGTAGTAGAT 59.237 40.000 0.00 0.00 34.06 1.98
400 404 1.336609 GGAAAGTCGTCGTGCTAAGGT 60.337 52.381 0.00 0.00 0.00 3.50
407 412 3.011818 TCGTCGTGCTAAGGTCTCATAA 58.988 45.455 0.00 0.00 0.00 1.90
410 415 4.624024 CGTCGTGCTAAGGTCTCATAAAAA 59.376 41.667 0.00 0.00 0.00 1.94
427 432 0.814457 AAACAGCGCACCAAAACAGA 59.186 45.000 11.47 0.00 0.00 3.41
503 508 2.728922 GAACACAGACGAACGAAGACT 58.271 47.619 0.14 0.00 0.00 3.24
578 584 3.309388 CTCGAGACAAATCTTCACACGT 58.691 45.455 6.58 0.00 34.34 4.49
586 592 3.584406 AATCTTCACACGTCCTCTGAG 57.416 47.619 0.00 0.00 0.00 3.35
626 635 0.824182 CGGGGCTAGACGAGAAGGAT 60.824 60.000 0.00 0.00 0.00 3.24
634 643 6.463190 GGGCTAGACGAGAAGGATCTTATTTT 60.463 42.308 0.00 0.00 35.54 1.82
665 675 2.202623 GTCGTCGCCTCGCATCTT 60.203 61.111 0.00 0.00 0.00 2.40
677 687 3.941483 CCTCGCATCTTTAAACAGGACAT 59.059 43.478 0.00 0.00 0.00 3.06
727 739 0.666577 AAAAACGGAGACCTCTCGCG 60.667 55.000 0.00 0.00 43.76 5.87
729 741 3.914579 AACGGAGACCTCTCGCGGA 62.915 63.158 6.13 1.01 43.76 5.54
736 754 2.272918 GACCTCTCGCGGACAAGGAG 62.273 65.000 19.10 11.48 32.99 3.69
766 784 1.597027 CCGTGGTCCCAAGACACAC 60.597 63.158 0.49 0.00 45.48 3.82
767 785 1.145156 CGTGGTCCCAAGACACACA 59.855 57.895 12.24 0.00 45.48 3.72
769 787 1.148273 TGGTCCCAAGACACACAGC 59.852 57.895 0.00 0.00 45.48 4.40
770 788 1.600916 GGTCCCAAGACACACAGCC 60.601 63.158 0.00 0.00 45.48 4.85
771 789 1.148273 GTCCCAAGACACACAGCCA 59.852 57.895 0.00 0.00 42.99 4.75
772 790 1.148273 TCCCAAGACACACAGCCAC 59.852 57.895 0.00 0.00 0.00 5.01
773 791 1.152984 CCCAAGACACACAGCCACA 60.153 57.895 0.00 0.00 0.00 4.17
774 792 1.168407 CCCAAGACACACAGCCACAG 61.168 60.000 0.00 0.00 0.00 3.66
775 793 1.650912 CAAGACACACAGCCACAGC 59.349 57.895 0.00 0.00 40.32 4.40
776 794 1.526917 AAGACACACAGCCACAGCC 60.527 57.895 0.00 0.00 41.25 4.85
811 829 2.869801 TCGTTTGAAGCGTTGAACTGAT 59.130 40.909 0.64 0.00 0.00 2.90
892 910 1.691976 CAGACACACCCCTGTCAAGTA 59.308 52.381 2.38 0.00 42.74 2.24
893 911 1.971357 AGACACACCCCTGTCAAGTAG 59.029 52.381 2.38 0.00 42.74 2.57
894 912 1.968493 GACACACCCCTGTCAAGTAGA 59.032 52.381 0.00 0.00 40.40 2.59
895 913 1.971357 ACACACCCCTGTCAAGTAGAG 59.029 52.381 0.00 0.00 0.00 2.43
896 914 1.971357 CACACCCCTGTCAAGTAGAGT 59.029 52.381 0.00 0.00 0.00 3.24
1254 1279 2.041115 GCGAGGTTGGCTTCTTCCC 61.041 63.158 0.00 0.00 0.00 3.97
1281 1306 4.513198 TGGTTTCCGATTCCAATTTGTC 57.487 40.909 0.00 0.00 0.00 3.18
1479 1504 5.013391 ACCCTACCTACTATACTCTCTGCTC 59.987 48.000 0.00 0.00 0.00 4.26
1480 1505 5.249852 CCCTACCTACTATACTCTCTGCTCT 59.750 48.000 0.00 0.00 0.00 4.09
1481 1506 6.170506 CCTACCTACTATACTCTCTGCTCTG 58.829 48.000 0.00 0.00 0.00 3.35
1482 1507 4.394729 ACCTACTATACTCTCTGCTCTGC 58.605 47.826 0.00 0.00 0.00 4.26
1483 1508 4.104102 ACCTACTATACTCTCTGCTCTGCT 59.896 45.833 0.00 0.00 0.00 4.24
1525 1550 4.616181 ATGCCAGCATAAACTCGTTTAC 57.384 40.909 2.61 0.00 37.80 2.01
1550 1578 7.093771 ACTGGGTGAAATGGAAATTAATCTCAC 60.094 37.037 0.00 0.00 32.94 3.51
1595 1623 2.905959 TGCTTGATCAGTTGCAATCG 57.094 45.000 14.75 0.00 32.12 3.34
1603 1631 3.063670 TCAGTTGCAATCGTTGTGTTG 57.936 42.857 0.59 0.00 0.00 3.33
1604 1632 2.118683 CAGTTGCAATCGTTGTGTTGG 58.881 47.619 0.59 0.00 0.00 3.77
1620 1648 1.956477 GTTGGTTGATCAGTTGCTGGT 59.044 47.619 0.00 0.00 31.51 4.00
1649 1691 2.815211 GATGTTCTGCAGCCGCGA 60.815 61.111 8.23 0.00 42.97 5.87
1681 1723 6.493449 TTTCATGTTGTATTTCTCGCATGA 57.507 33.333 0.00 0.00 40.28 3.07
1687 1729 8.929746 CATGTTGTATTTCTCGCATGAGTATAT 58.070 33.333 0.00 0.00 43.09 0.86
1730 1812 8.050930 GGATAATCTTGGTTGGTAAAGGACTAA 58.949 37.037 0.00 0.00 0.00 2.24
1796 1878 3.812156 TGACGACCTCAAGTCAAAAGA 57.188 42.857 0.00 0.00 46.69 2.52
1797 1879 4.131649 TGACGACCTCAAGTCAAAAGAA 57.868 40.909 0.00 0.00 46.69 2.52
1798 1880 4.509616 TGACGACCTCAAGTCAAAAGAAA 58.490 39.130 0.00 0.00 46.69 2.52
1799 1881 4.938832 TGACGACCTCAAGTCAAAAGAAAA 59.061 37.500 0.00 0.00 46.69 2.29
1800 1882 5.413213 TGACGACCTCAAGTCAAAAGAAAAA 59.587 36.000 0.00 0.00 46.69 1.94
1901 1993 6.825721 GGTTTATGAGAATCTGGGGCATATAG 59.174 42.308 0.00 0.00 34.92 1.31
1961 2056 0.947244 AAGGCAAAAGCTGTGTCGAG 59.053 50.000 0.00 0.00 0.00 4.04
1966 2061 2.600792 GCAAAAGCTGTGTCGAGTTCAG 60.601 50.000 0.00 6.96 0.00 3.02
2019 2114 4.338400 GTGGCTTGGTTTATATGAGAACCC 59.662 45.833 12.28 2.05 43.69 4.11
2022 2120 3.916359 TGGTTTATATGAGAACCCGCA 57.084 42.857 12.28 0.00 43.69 5.69
2044 2142 6.426327 GCAAAAACCACGCAAAATAAGAAAT 58.574 32.000 0.00 0.00 0.00 2.17
2069 2167 2.812011 AGAAAAACCCGACTTGATTCCG 59.188 45.455 0.00 0.00 0.00 4.30
2093 2191 0.598065 GAGCACCATCACCAAACACC 59.402 55.000 0.00 0.00 0.00 4.16
2131 2229 5.581126 TGCAGAGGTAAATTAATGCCTTG 57.419 39.130 7.60 8.61 32.77 3.61
2138 2236 7.553044 AGAGGTAAATTAATGCCTTGACACTAC 59.447 37.037 7.60 0.00 0.00 2.73
2151 2249 1.141881 CACTACTGAGGCGGCGATT 59.858 57.895 12.98 0.00 0.00 3.34
2152 2250 0.872021 CACTACTGAGGCGGCGATTC 60.872 60.000 12.98 7.69 0.00 2.52
2271 2369 5.411669 GGTTGATTATTCCTTCTGAACGTGT 59.588 40.000 0.00 0.00 35.31 4.49
2331 2429 7.254218 GCAAAACTCTTCAACCATTTCTTCTTG 60.254 37.037 0.00 0.00 0.00 3.02
2352 2450 5.871396 TGGAGTAGTTATAAGGCAAGAGG 57.129 43.478 0.00 0.00 0.00 3.69
2372 2470 1.470890 GCGCCAAGGCTACACATTAAA 59.529 47.619 9.73 0.00 39.32 1.52
2376 2474 3.697166 CCAAGGCTACACATTAAAGGGT 58.303 45.455 0.00 0.00 0.00 4.34
2413 2511 0.109597 CATTTTCGGCCTCAGCACAC 60.110 55.000 0.00 0.00 42.56 3.82
2453 2551 6.438425 ACATTCTTATCTTTGCCCAGACAAAT 59.562 34.615 0.00 0.00 38.76 2.32
2466 2660 4.941263 CCCAGACAAATCACTAATTTCCGA 59.059 41.667 0.00 0.00 35.32 4.55
2499 2696 4.168760 CCATTTCAGACGCTTTCCATTTC 58.831 43.478 0.00 0.00 0.00 2.17
2510 2707 4.615682 CGCTTTCCATTTCATTGCACAGTA 60.616 41.667 0.00 0.00 0.00 2.74
2590 2787 2.310577 GCGTGCAAGTTTCATCAAGAC 58.689 47.619 0.59 0.00 0.00 3.01
2610 2807 7.174946 TCAAGACCAAGGCTGAAGTAAAATAAG 59.825 37.037 0.00 0.00 0.00 1.73
2690 2887 3.718210 GAGGATGACGGCGGTGACC 62.718 68.421 13.24 9.56 0.00 4.02
2719 2916 2.509561 GAAGAAGGAGTCCGGCGC 60.510 66.667 0.00 0.00 0.00 6.53
2777 2974 3.435601 CCAGACCAAAGGGATATCAAGGG 60.436 52.174 4.83 1.23 38.05 3.95
2805 3002 4.279420 AGCTATGATACAGCAACGATGAGA 59.721 41.667 0.00 0.00 41.66 3.27
2852 3050 9.979578 TTGATTAACTGACAATGTTAAATGCTT 57.020 25.926 4.65 0.00 41.34 3.91
2858 3056 9.979578 AACTGACAATGTTAAATGCTTATTTGA 57.020 25.926 0.00 0.00 0.00 2.69
2859 3057 9.630098 ACTGACAATGTTAAATGCTTATTTGAG 57.370 29.630 0.00 0.00 0.00 3.02
2979 3177 0.605083 AAGACTGCACTGCTCGATCA 59.395 50.000 1.98 0.00 0.00 2.92
2980 3178 0.605083 AGACTGCACTGCTCGATCAA 59.395 50.000 1.98 0.00 0.00 2.57
2981 3179 0.718343 GACTGCACTGCTCGATCAAC 59.282 55.000 1.98 0.00 0.00 3.18
2982 3180 0.671781 ACTGCACTGCTCGATCAACC 60.672 55.000 1.98 0.00 0.00 3.77
3152 3350 4.457496 CATGGCGCAGGTCTCGGT 62.457 66.667 10.83 0.00 0.00 4.69
3306 3505 3.844211 ACCTTTGTAGAGAGTTGGCCATA 59.156 43.478 6.09 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 5.484173 TTAGGCTGCTCATATTTTGAACG 57.516 39.130 0.00 0.00 32.78 3.95
99 100 2.224113 GCGACTCCGATGGGGTTTATTA 60.224 50.000 0.00 0.00 38.22 0.98
122 123 2.971901 TTGAGGGGAAAAGAGGTTCC 57.028 50.000 0.00 0.00 45.54 3.62
134 135 4.026356 ACATTTCAGTCTCTTTGAGGGG 57.974 45.455 0.00 0.00 0.00 4.79
299 303 2.262915 CTTCGGCTCGCTCCAGTT 59.737 61.111 0.00 0.00 0.00 3.16
318 322 2.033911 TGCGATGAAAGCAGGGCA 59.966 55.556 0.00 0.00 40.01 5.36
335 339 2.648059 CCCGGCTTCAATGAGAAAGAT 58.352 47.619 0.00 0.00 35.40 2.40
336 340 1.950484 GCCCGGCTTCAATGAGAAAGA 60.950 52.381 0.71 0.00 35.40 2.52
340 344 0.251121 TTTGCCCGGCTTCAATGAGA 60.251 50.000 11.61 0.00 0.00 3.27
375 379 1.338973 AGCACGACGACTTTCCAACTA 59.661 47.619 0.00 0.00 0.00 2.24
400 404 2.499197 TGGTGCGCTGTTTTTATGAGA 58.501 42.857 9.73 0.00 0.00 3.27
407 412 1.203523 TCTGTTTTGGTGCGCTGTTTT 59.796 42.857 9.73 0.00 0.00 2.43
410 415 0.814457 TTTCTGTTTTGGTGCGCTGT 59.186 45.000 9.73 0.00 0.00 4.40
578 584 5.280011 GGTGGTGTTTCTAATTCTCAGAGGA 60.280 44.000 0.00 0.00 0.00 3.71
586 592 4.460505 CGTTTCGGTGGTGTTTCTAATTC 58.539 43.478 0.00 0.00 0.00 2.17
766 784 2.981909 CCTGTGTGGCTGTGGCTG 60.982 66.667 0.00 0.00 38.73 4.85
767 785 3.170672 TCCTGTGTGGCTGTGGCT 61.171 61.111 0.00 0.00 38.73 4.75
769 787 1.302033 GTCTCCTGTGTGGCTGTGG 60.302 63.158 0.00 0.00 35.26 4.17
770 788 1.665916 CGTCTCCTGTGTGGCTGTG 60.666 63.158 0.00 0.00 35.26 3.66
771 789 1.188219 ATCGTCTCCTGTGTGGCTGT 61.188 55.000 0.00 0.00 35.26 4.40
772 790 0.459237 GATCGTCTCCTGTGTGGCTG 60.459 60.000 0.00 0.00 35.26 4.85
773 791 1.893786 GATCGTCTCCTGTGTGGCT 59.106 57.895 0.00 0.00 35.26 4.75
774 792 1.517257 CGATCGTCTCCTGTGTGGC 60.517 63.158 7.03 0.00 35.26 5.01
775 793 0.243907 AACGATCGTCTCCTGTGTGG 59.756 55.000 22.98 0.00 37.10 4.17
776 794 1.721389 CAAACGATCGTCTCCTGTGTG 59.279 52.381 22.98 6.06 0.00 3.82
892 910 6.796648 ACTCCTACTCTTCTTTTCCTACTCT 58.203 40.000 0.00 0.00 0.00 3.24
893 911 7.283807 CCTACTCCTACTCTTCTTTTCCTACTC 59.716 44.444 0.00 0.00 0.00 2.59
894 912 7.120716 CCTACTCCTACTCTTCTTTTCCTACT 58.879 42.308 0.00 0.00 0.00 2.57
895 913 6.891361 ACCTACTCCTACTCTTCTTTTCCTAC 59.109 42.308 0.00 0.00 0.00 3.18
896 914 7.036717 AGACCTACTCCTACTCTTCTTTTCCTA 60.037 40.741 0.00 0.00 0.00 2.94
1214 1239 3.129300 CGCCAGGGCTCGAGATAA 58.871 61.111 18.75 0.00 39.32 1.75
1235 1260 2.391389 GGAAGAAGCCAACCTCGCG 61.391 63.158 0.00 0.00 0.00 5.87
1254 1279 2.080693 TGGAATCGGAAACCAATCACG 58.919 47.619 4.46 0.00 0.00 4.35
1479 1504 0.108233 GGAGGAACAGAGCAGAGCAG 60.108 60.000 0.00 0.00 0.00 4.24
1480 1505 0.543883 AGGAGGAACAGAGCAGAGCA 60.544 55.000 0.00 0.00 0.00 4.26
1481 1506 0.175531 GAGGAGGAACAGAGCAGAGC 59.824 60.000 0.00 0.00 0.00 4.09
1482 1507 0.823460 GGAGGAGGAACAGAGCAGAG 59.177 60.000 0.00 0.00 0.00 3.35
1483 1508 0.115152 TGGAGGAGGAACAGAGCAGA 59.885 55.000 0.00 0.00 0.00 4.26
1525 1550 7.123247 AGTGAGATTAATTTCCATTTCACCCAG 59.877 37.037 3.70 0.00 35.50 4.45
1595 1623 3.115554 GCAACTGATCAACCAACACAAC 58.884 45.455 0.00 0.00 0.00 3.32
1603 1631 4.846779 TTTAACCAGCAACTGATCAACC 57.153 40.909 0.00 0.00 32.44 3.77
1630 1672 2.679934 CGCGGCTGCAGAACATCAA 61.680 57.895 20.43 0.00 42.97 2.57
1641 1683 2.351418 TGAAATTCAGTATTCGCGGCTG 59.649 45.455 6.13 10.22 0.00 4.85
1700 1782 9.455144 TCCTTTACCAACCAAGATTATCCTATA 57.545 33.333 0.00 0.00 0.00 1.31
1743 1825 2.688507 ACGCATAAAGACTCCACACAG 58.311 47.619 0.00 0.00 0.00 3.66
1836 1918 9.859427 TGTGCTTTTTCCTATCTTATTGAAATG 57.141 29.630 0.00 0.00 0.00 2.32
1982 2077 2.283145 AGCCACTCTGCATTCTTGTT 57.717 45.000 0.00 0.00 0.00 2.83
2019 2114 3.487574 TCTTATTTTGCGTGGTTTTTGCG 59.512 39.130 0.00 0.00 0.00 4.85
2022 2120 9.535878 TCTTATTTCTTATTTTGCGTGGTTTTT 57.464 25.926 0.00 0.00 0.00 1.94
2044 2142 5.704053 GGAATCAAGTCGGGTTTTTCTCTTA 59.296 40.000 0.00 0.00 0.00 2.10
2055 2153 1.134521 TCCATTCGGAATCAAGTCGGG 60.135 52.381 0.00 0.00 38.83 5.14
2093 2191 5.824624 ACCTCTGCATATTTTACTCATGGTG 59.175 40.000 0.00 0.00 0.00 4.17
2131 2229 2.005960 ATCGCCGCCTCAGTAGTGTC 62.006 60.000 0.00 0.00 0.00 3.67
2151 2249 2.696409 TACCGAACAAAGCACGCCGA 62.696 55.000 0.00 0.00 0.00 5.54
2152 2250 2.222953 CTACCGAACAAAGCACGCCG 62.223 60.000 0.00 0.00 0.00 6.46
2159 2257 8.818057 CCTTTATAATCTGTCTACCGAACAAAG 58.182 37.037 0.00 0.00 0.00 2.77
2271 2369 8.911918 TCCAACTTTATTTACTCTACAAAGCA 57.088 30.769 0.00 0.00 30.97 3.91
2331 2429 4.633175 GCCTCTTGCCTTATAACTACTCC 58.367 47.826 0.00 0.00 0.00 3.85
2352 2450 1.091537 TTAATGTGTAGCCTTGGCGC 58.908 50.000 0.00 0.00 0.00 6.53
2363 2461 3.428413 AACCGCTACCCTTTAATGTGT 57.572 42.857 0.00 0.00 0.00 3.72
2372 2470 0.398664 AGAGCCATAACCGCTACCCT 60.399 55.000 0.00 0.00 36.48 4.34
2435 2533 4.922206 AGTGATTTGTCTGGGCAAAGATA 58.078 39.130 6.52 0.00 41.00 1.98
2441 2539 4.462483 GGAAATTAGTGATTTGTCTGGGCA 59.538 41.667 0.00 0.00 38.06 5.36
2453 2551 4.982295 CGTATGCTGATCGGAAATTAGTGA 59.018 41.667 5.48 0.00 0.00 3.41
2466 2660 2.874701 GTCTGAAATGGCGTATGCTGAT 59.125 45.455 6.92 0.00 42.25 2.90
2499 2696 5.778161 TGACGACTTAATACTGTGCAATG 57.222 39.130 0.00 0.00 0.00 2.82
2510 2707 6.146184 CAGACAATGTGACTTGACGACTTAAT 59.854 38.462 0.00 0.00 0.00 1.40
2590 2787 7.308435 CAGAACTTATTTTACTTCAGCCTTGG 58.692 38.462 0.00 0.00 0.00 3.61
2610 2807 5.186996 TCCTGAAAACATTTCAGCAGAAC 57.813 39.130 21.65 0.00 43.33 3.01
2777 2974 3.060003 CGTTGCTGTATCATAGCTTGCTC 60.060 47.826 0.00 0.00 41.66 4.26
2805 3002 8.585471 ATCAATGAATTTGGACAGATAGTGTT 57.415 30.769 0.00 0.00 35.06 3.32
2850 3048 5.875359 ACCGTAAAAGAGCTCCTCAAATAAG 59.125 40.000 10.93 0.00 32.06 1.73
2851 3049 5.801380 ACCGTAAAAGAGCTCCTCAAATAA 58.199 37.500 10.93 0.00 32.06 1.40
2852 3050 5.416271 ACCGTAAAAGAGCTCCTCAAATA 57.584 39.130 10.93 0.00 32.06 1.40
2853 3051 4.287766 ACCGTAAAAGAGCTCCTCAAAT 57.712 40.909 10.93 0.00 32.06 2.32
2854 3052 3.764237 ACCGTAAAAGAGCTCCTCAAA 57.236 42.857 10.93 0.00 32.06 2.69
2855 3053 3.056322 GGTACCGTAAAAGAGCTCCTCAA 60.056 47.826 10.93 0.00 32.06 3.02
2856 3054 2.494870 GGTACCGTAAAAGAGCTCCTCA 59.505 50.000 10.93 0.00 32.06 3.86
2857 3055 2.479219 CGGTACCGTAAAAGAGCTCCTC 60.479 54.545 26.39 0.00 34.35 3.71
2858 3056 1.475682 CGGTACCGTAAAAGAGCTCCT 59.524 52.381 26.39 0.00 34.35 3.69
2859 3057 1.470458 CCGGTACCGTAAAAGAGCTCC 60.470 57.143 31.24 0.00 37.81 4.70
2979 3177 3.866910 CACATATACCGCTTACGTTGGTT 59.133 43.478 0.00 0.00 37.20 3.67
2980 3178 3.130869 TCACATATACCGCTTACGTTGGT 59.869 43.478 0.00 0.00 39.80 3.67
2981 3179 3.708890 TCACATATACCGCTTACGTTGG 58.291 45.455 0.00 0.00 37.70 3.77
2982 3180 5.900339 AATCACATATACCGCTTACGTTG 57.100 39.130 0.00 0.00 37.70 4.10
3306 3505 6.372381 GCTTAAAACCTGAATTTGCATTGGAT 59.628 34.615 0.00 0.00 0.00 3.41
3404 4838 7.610865 AGTGATGTCAAAAACTTTCTTCCAAA 58.389 30.769 0.00 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.