Multiple sequence alignment - TraesCS6B01G024400

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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 TraesCS6B01G024400 chr6B 100.000 3050 0 0 1 3050 14630619 14627570 0.000000e+00 5633.0
1 TraesCS6B01G024400 chr6B 82.545 613 101 5 1438 2047 14333982 14334591 4.480000e-148 534.0
2 TraesCS6B01G024400 chr6B 81.600 625 107 6 1438 2058 14544837 14544217 7.540000e-141 510.0
3 TraesCS6B01G024400 chr6B 87.441 422 49 2 981 1401 15751021 15750603 1.640000e-132 483.0
4 TraesCS6B01G024400 chr6B 86.437 435 54 3 966 1399 52568277 52567847 3.560000e-129 472.0
5 TraesCS6B01G024400 chr6B 80.160 625 115 7 1437 2055 17500183 17499562 2.770000e-125 459.0
6 TraesCS6B01G024400 chr6B 79.002 581 73 21 2478 3050 65173440 65172901 4.840000e-93 351.0
7 TraesCS6B01G024400 chr6B 78.201 578 83 19 2479 3050 52572322 52571782 2.270000e-86 329.0
8 TraesCS6B01G024400 chr6B 77.990 577 87 19 2479 3050 15224050 15223509 2.930000e-85 326.0
9 TraesCS6B01G024400 chr6B 84.513 226 27 7 2478 2701 39328210 39328429 1.840000e-52 217.0
10 TraesCS6B01G024400 chr6B 80.476 210 31 8 2265 2468 15218307 15218102 5.270000e-33 152.0
11 TraesCS6B01G024400 chr6A 94.932 1618 47 3 1437 3050 8211992 8210406 0.000000e+00 2501.0
12 TraesCS6B01G024400 chr6A 86.787 999 94 14 2080 3050 8394845 8393857 0.000000e+00 1079.0
13 TraesCS6B01G024400 chr6A 90.032 632 63 0 1448 2079 8393049 8392418 0.000000e+00 819.0
14 TraesCS6B01G024400 chr6A 93.737 479 30 0 965 1443 8212572 8212094 0.000000e+00 719.0
15 TraesCS6B01G024400 chr6A 90.494 547 41 4 2080 2615 8392381 8391835 0.000000e+00 712.0
16 TraesCS6B01G024400 chr6A 85.841 678 68 15 791 1443 8398890 8398216 0.000000e+00 695.0
17 TraesCS6B01G024400 chr6A 89.844 512 52 0 1568 2079 8395393 8394882 0.000000e+00 658.0
18 TraesCS6B01G024400 chr6A 84.420 629 93 4 1437 2063 8401578 8400953 5.590000e-172 614.0
19 TraesCS6B01G024400 chr6A 85.542 498 70 2 1557 2053 8197804 8197308 1.250000e-143 520.0
20 TraesCS6B01G024400 chr6A 80.417 623 114 7 1437 2055 7991840 7992458 4.600000e-128 468.0
21 TraesCS6B01G024400 chr6A 78.840 586 72 21 2478 3050 35579906 35579360 6.260000e-92 348.0
22 TraesCS6B01G024400 chr6A 89.394 264 20 2 2716 2971 8391500 8391237 2.930000e-85 326.0
23 TraesCS6B01G024400 chr6A 89.313 262 22 3 2069 2324 8448780 8448519 1.050000e-84 324.0
24 TraesCS6B01G024400 chr6A 86.667 240 18 5 2377 2605 8447611 8447375 1.400000e-63 254.0
25 TraesCS6B01G024400 chr6A 82.870 216 25 9 2265 2472 35567908 35567697 1.870000e-42 183.0
26 TraesCS6B01G024400 chr6D 98.312 770 13 0 1437 2206 7998516 7997747 0.000000e+00 1351.0
27 TraesCS6B01G024400 chr6D 94.882 723 13 2 2328 3050 7997747 7997049 0.000000e+00 1109.0
28 TraesCS6B01G024400 chr6D 88.718 585 55 9 864 1443 7999196 7998618 0.000000e+00 704.0
29 TraesCS6B01G024400 chr6D 84.842 475 64 7 970 1440 8552828 8552358 3.560000e-129 472.0
30 TraesCS6B01G024400 chr6D 80.320 625 114 7 1437 2055 9547669 9547048 5.960000e-127 464.0
31 TraesCS6B01G024400 chr6D 80.285 421 60 13 81 500 468555656 468555258 2.300000e-76 296.0
32 TraesCS6B01G024400 chr6D 85.333 225 26 4 2478 2701 7654668 7654886 3.060000e-55 226.0
33 TraesCS6B01G024400 chr6D 83.628 226 30 6 2478 2701 24254510 24254730 3.990000e-49 206.0
34 TraesCS6B01G024400 chr6D 77.011 261 46 9 2207 2460 8816974 8817227 1.470000e-28 137.0
35 TraesCS6B01G024400 chr6D 78.065 155 29 4 2297 2447 8970473 8970626 3.240000e-15 93.5
36 TraesCS6B01G024400 chr5D 86.853 502 59 4 80 581 551606374 551606868 3.440000e-154 555.0
37 TraesCS6B01G024400 chr5D 79.335 421 63 17 81 500 162874647 162875044 1.080000e-69 274.0
38 TraesCS6B01G024400 chr3B 86.992 492 57 2 81 572 629661432 629661916 5.750000e-152 547.0
39 TraesCS6B01G024400 chr2D 87.045 494 52 7 80 572 300440037 300440519 5.750000e-152 547.0
40 TraesCS6B01G024400 chr2D 81.676 513 66 15 80 573 560315580 560316083 4.740000e-108 401.0
41 TraesCS6B01G024400 chr2D 90.909 55 5 0 25 79 300438921 300438975 1.170000e-09 75.0
42 TraesCS6B01G024400 chr2B 84.211 475 67 7 970 1440 709426202 709425732 3.580000e-124 455.0
43 TraesCS6B01G024400 chr2B 82.093 430 60 11 81 500 401800119 401799697 4.840000e-93 351.0
44 TraesCS6B01G024400 chr2B 77.959 245 44 6 2207 2447 709423317 709423079 8.810000e-31 145.0
45 TraesCS6B01G024400 chr3A 84.701 451 62 6 953 1399 45938021 45937574 7.760000e-121 444.0
46 TraesCS6B01G024400 chr3D 84.106 453 64 6 953 1399 33330543 33330093 6.040000e-117 431.0
47 TraesCS6B01G024400 chr2A 86.528 386 44 5 81 465 370494939 370495317 4.700000e-113 418.0
48 TraesCS6B01G024400 chr1B 78.425 584 83 27 2475 3047 630646423 630646974 1.050000e-89 340.0
49 TraesCS6B01G024400 chr1A 81.481 432 55 16 81 500 77473115 77473533 6.300000e-87 331.0
50 TraesCS6B01G024400 chr4B 80.896 424 57 15 80 488 51820197 51819783 2.280000e-81 313.0
51 TraesCS6B01G024400 chr7D 80.285 421 59 13 81 500 575769178 575769575 2.300000e-76 296.0
52 TraesCS6B01G024400 chr1D 79.196 423 62 17 81 500 386418657 386418258 1.390000e-68 270.0


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 TraesCS6B01G024400 chr6B 14627570 14630619 3049 True 5633.000000 5633 100.000000 1 3050 1 chr6B.!!$R2 3049
1 TraesCS6B01G024400 chr6B 14333982 14334591 609 False 534.000000 534 82.545000 1438 2047 1 chr6B.!!$F1 609
2 TraesCS6B01G024400 chr6B 14544217 14544837 620 True 510.000000 510 81.600000 1438 2058 1 chr6B.!!$R1 620
3 TraesCS6B01G024400 chr6B 17499562 17500183 621 True 459.000000 459 80.160000 1437 2055 1 chr6B.!!$R6 618
4 TraesCS6B01G024400 chr6B 52567847 52572322 4475 True 400.500000 472 82.319000 966 3050 2 chr6B.!!$R8 2084
5 TraesCS6B01G024400 chr6B 65172901 65173440 539 True 351.000000 351 79.002000 2478 3050 1 chr6B.!!$R7 572
6 TraesCS6B01G024400 chr6B 15223509 15224050 541 True 326.000000 326 77.990000 2479 3050 1 chr6B.!!$R4 571
7 TraesCS6B01G024400 chr6A 8210406 8212572 2166 True 1610.000000 2501 94.334500 965 3050 2 chr6A.!!$R4 2085
8 TraesCS6B01G024400 chr6A 8391237 8401578 10341 True 700.428571 1079 88.116000 791 3050 7 chr6A.!!$R5 2259
9 TraesCS6B01G024400 chr6A 7991840 7992458 618 False 468.000000 468 80.417000 1437 2055 1 chr6A.!!$F1 618
10 TraesCS6B01G024400 chr6A 35579360 35579906 546 True 348.000000 348 78.840000 2478 3050 1 chr6A.!!$R3 572
11 TraesCS6B01G024400 chr6A 8447375 8448780 1405 True 289.000000 324 87.990000 2069 2605 2 chr6A.!!$R6 536
12 TraesCS6B01G024400 chr6D 7997049 7999196 2147 True 1054.666667 1351 93.970667 864 3050 3 chr6D.!!$R4 2186
13 TraesCS6B01G024400 chr6D 9547048 9547669 621 True 464.000000 464 80.320000 1437 2055 1 chr6D.!!$R2 618
14 TraesCS6B01G024400 chr2D 560315580 560316083 503 False 401.000000 401 81.676000 80 573 1 chr2D.!!$F1 493
15 TraesCS6B01G024400 chr2D 300438921 300440519 1598 False 311.000000 547 88.977000 25 572 2 chr2D.!!$F2 547
16 TraesCS6B01G024400 chr2B 709423079 709426202 3123 True 300.000000 455 81.085000 970 2447 2 chr2B.!!$R2 1477
17 TraesCS6B01G024400 chr1B 630646423 630646974 551 False 340.000000 340 78.425000 2475 3047 1 chr1B.!!$F1 572

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
112 1174 0.182061 AGCGATGTCAGGCCAATCAT 59.818 50.0 5.01 5.84 0.0 2.45 F
897 2796 0.393673 CCCGTTGACATATGCCACCA 60.394 55.0 1.58 0.00 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1315 4399 1.374758 CCAGTGTTCTCTCCACGCC 60.375 63.158 0.00 0.00 37.88 5.68 R
2228 9736 1.303309 GACAAGTTCACTGCAGTGCT 58.697 50.000 36.76 27.06 45.25 4.40 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
18 19 1.949257 CGTGCCAAGTTGGAGTTCC 59.051 57.895 26.52 7.79 40.96 3.62
19 20 1.515521 CGTGCCAAGTTGGAGTTCCC 61.516 60.000 26.52 7.04 40.96 3.97
112 1174 0.182061 AGCGATGTCAGGCCAATCAT 59.818 50.000 5.01 5.84 0.00 2.45
119 1181 3.499338 TGTCAGGCCAATCATCAAAACT 58.501 40.909 5.01 0.00 0.00 2.66
203 1266 6.389091 CAAATATGGAGCTAGCACAAAAACA 58.611 36.000 18.83 3.98 0.00 2.83
204 1267 6.588719 AATATGGAGCTAGCACAAAAACAA 57.411 33.333 18.83 0.07 0.00 2.83
205 1268 4.935352 ATGGAGCTAGCACAAAAACAAA 57.065 36.364 18.83 0.00 0.00 2.83
206 1269 4.727507 TGGAGCTAGCACAAAAACAAAA 57.272 36.364 18.83 0.00 0.00 2.44
234 1297 5.554822 AAAAGTGTGCACGAGAAAGTTAA 57.445 34.783 13.13 0.00 36.20 2.01
306 1369 2.225491 TGCAGCTAACCGTGAATTGAAC 59.775 45.455 0.00 0.00 0.00 3.18
322 1386 2.069465 GAACCGCAACACACCATGCA 62.069 55.000 0.00 0.00 42.68 3.96
343 1407 6.392354 TGCAAAAGAATCAATTGAGATGGAC 58.608 36.000 14.54 1.98 0.00 4.02
365 1429 4.458989 ACAACCCTACATATGTTGCAACAG 59.541 41.667 33.44 23.46 43.04 3.16
368 1432 5.509498 ACCCTACATATGTTGCAACAGAAT 58.491 37.500 33.44 25.84 43.04 2.40
377 1441 8.892723 CATATGTTGCAACAGAATAGGAAGTTA 58.107 33.333 33.44 18.33 43.04 2.24
380 1444 6.204688 TGTTGCAACAGAATAGGAAGTTAGTG 59.795 38.462 27.96 0.00 34.30 2.74
574 1654 3.181468 GCACGGGCTTATTTCCTAGTACT 60.181 47.826 0.00 0.00 36.96 2.73
575 1655 4.038402 GCACGGGCTTATTTCCTAGTACTA 59.962 45.833 0.00 1.89 36.96 1.82
576 1656 5.527033 CACGGGCTTATTTCCTAGTACTAC 58.473 45.833 0.00 0.00 0.00 2.73
578 1658 5.837438 ACGGGCTTATTTCCTAGTACTACAT 59.163 40.000 0.00 0.00 0.00 2.29
579 1659 7.006509 ACGGGCTTATTTCCTAGTACTACATA 58.993 38.462 0.00 0.00 0.00 2.29
580 1660 7.506938 ACGGGCTTATTTCCTAGTACTACATAA 59.493 37.037 0.00 0.00 0.00 1.90
581 1661 7.811713 CGGGCTTATTTCCTAGTACTACATAAC 59.188 40.741 0.00 0.00 0.00 1.89
582 1662 8.868103 GGGCTTATTTCCTAGTACTACATAACT 58.132 37.037 0.00 0.00 0.00 2.24
597 1677 8.779354 ACTACATAACTTTGGTCTCATTCTTC 57.221 34.615 0.00 0.00 0.00 2.87
598 1678 8.598041 ACTACATAACTTTGGTCTCATTCTTCT 58.402 33.333 0.00 0.00 0.00 2.85
607 1687 6.471233 TGGTCTCATTCTTCTATCGTCATT 57.529 37.500 0.00 0.00 0.00 2.57
608 1688 6.276091 TGGTCTCATTCTTCTATCGTCATTG 58.724 40.000 0.00 0.00 0.00 2.82
611 1691 6.640499 GTCTCATTCTTCTATCGTCATTGAGG 59.360 42.308 0.00 0.00 31.33 3.86
615 1695 2.767644 TCTATCGTCATTGAGGGGGA 57.232 50.000 6.52 1.02 0.00 4.81
618 1698 0.541863 ATCGTCATTGAGGGGGACAC 59.458 55.000 6.52 0.00 0.00 3.67
619 1699 1.078426 CGTCATTGAGGGGGACACC 60.078 63.158 0.00 0.00 39.11 4.16
635 1715 4.017126 GGACACCCTTTTATCTTCTTGGG 58.983 47.826 0.00 0.00 40.37 4.12
636 1716 3.431415 ACACCCTTTTATCTTCTTGGGC 58.569 45.455 0.00 0.00 38.23 5.36
638 1718 3.696548 CACCCTTTTATCTTCTTGGGCTC 59.303 47.826 0.00 0.00 38.23 4.70
641 1721 5.193728 ACCCTTTTATCTTCTTGGGCTCATA 59.806 40.000 0.00 0.00 38.23 2.15
642 1722 5.767168 CCCTTTTATCTTCTTGGGCTCATAG 59.233 44.000 0.00 0.00 0.00 2.23
643 1723 6.409695 CCCTTTTATCTTCTTGGGCTCATAGA 60.410 42.308 0.00 0.00 0.00 1.98
649 1729 6.126863 TCTTCTTGGGCTCATAGAGAAAAA 57.873 37.500 1.05 0.00 0.00 1.94
651 1731 4.848357 TCTTGGGCTCATAGAGAAAAAGG 58.152 43.478 0.00 0.00 0.00 3.11
654 1734 4.104086 TGGGCTCATAGAGAAAAAGGAGA 58.896 43.478 0.00 0.00 0.00 3.71
655 1735 4.536090 TGGGCTCATAGAGAAAAAGGAGAA 59.464 41.667 0.00 0.00 0.00 2.87
656 1736 4.878971 GGGCTCATAGAGAAAAAGGAGAAC 59.121 45.833 0.00 0.00 0.00 3.01
659 1739 5.940470 GCTCATAGAGAAAAAGGAGAACCAA 59.060 40.000 0.00 0.00 38.94 3.67
660 1740 6.093357 GCTCATAGAGAAAAAGGAGAACCAAG 59.907 42.308 0.00 0.00 38.94 3.61
661 1741 7.316393 TCATAGAGAAAAAGGAGAACCAAGA 57.684 36.000 0.00 0.00 38.94 3.02
665 1745 7.340122 AGAGAAAAAGGAGAACCAAGAAAAG 57.660 36.000 0.00 0.00 38.94 2.27
666 1746 5.907207 AGAAAAAGGAGAACCAAGAAAAGC 58.093 37.500 0.00 0.00 38.94 3.51
668 1748 5.939764 AAAAGGAGAACCAAGAAAAGCTT 57.060 34.783 0.00 0.00 38.94 3.74
670 1750 7.603180 AAAAGGAGAACCAAGAAAAGCTTAT 57.397 32.000 0.00 0.00 38.94 1.73
671 1751 6.825944 AAGGAGAACCAAGAAAAGCTTATC 57.174 37.500 0.00 0.00 38.94 1.75
672 1752 6.133253 AGGAGAACCAAGAAAAGCTTATCT 57.867 37.500 0.00 0.00 38.94 1.98
673 1753 6.547402 AGGAGAACCAAGAAAAGCTTATCTT 58.453 36.000 0.00 0.00 38.94 2.40
674 1754 7.007116 AGGAGAACCAAGAAAAGCTTATCTTT 58.993 34.615 0.00 0.00 41.68 2.52
675 1755 7.507277 AGGAGAACCAAGAAAAGCTTATCTTTT 59.493 33.333 0.00 2.67 46.12 2.27
676 1756 8.144478 GGAGAACCAAGAAAAGCTTATCTTTTT 58.856 33.333 0.00 0.00 43.55 1.94
740 1820 6.773976 TTTTACATGCCTCCCTCTATTTTG 57.226 37.500 0.00 0.00 0.00 2.44
742 1822 4.322057 ACATGCCTCCCTCTATTTTGTT 57.678 40.909 0.00 0.00 0.00 2.83
743 1823 4.677182 ACATGCCTCCCTCTATTTTGTTT 58.323 39.130 0.00 0.00 0.00 2.83
744 1824 4.706962 ACATGCCTCCCTCTATTTTGTTTC 59.293 41.667 0.00 0.00 0.00 2.78
745 1825 4.380843 TGCCTCCCTCTATTTTGTTTCA 57.619 40.909 0.00 0.00 0.00 2.69
746 1826 4.934356 TGCCTCCCTCTATTTTGTTTCAT 58.066 39.130 0.00 0.00 0.00 2.57
747 1827 5.332743 TGCCTCCCTCTATTTTGTTTCATT 58.667 37.500 0.00 0.00 0.00 2.57
749 1829 5.185828 GCCTCCCTCTATTTTGTTTCATTGT 59.814 40.000 0.00 0.00 0.00 2.71
751 1831 7.093945 GCCTCCCTCTATTTTGTTTCATTGTAA 60.094 37.037 0.00 0.00 0.00 2.41
752 1832 8.802267 CCTCCCTCTATTTTGTTTCATTGTAAA 58.198 33.333 0.00 0.00 0.00 2.01
753 1833 9.626045 CTCCCTCTATTTTGTTTCATTGTAAAC 57.374 33.333 0.00 0.00 39.35 2.01
754 1834 8.581578 TCCCTCTATTTTGTTTCATTGTAAACC 58.418 33.333 0.00 0.00 38.35 3.27
756 1836 9.981114 CCTCTATTTTGTTTCATTGTAAACCTT 57.019 29.630 0.00 0.00 38.35 3.50
764 1844 9.658799 TTGTTTCATTGTAAACCTTTCAAATCA 57.341 25.926 0.00 0.00 38.35 2.57
766 1846 9.528018 GTTTCATTGTAAACCTTTCAAATCAGA 57.472 29.630 0.00 0.00 34.02 3.27
856 2755 0.593128 AACACATTCGTCTGCAAGCC 59.407 50.000 0.00 0.00 0.00 4.35
857 2756 1.237285 ACACATTCGTCTGCAAGCCC 61.237 55.000 0.00 0.00 0.00 5.19
859 2758 0.957395 ACATTCGTCTGCAAGCCCAG 60.957 55.000 0.00 0.00 0.00 4.45
860 2759 2.042831 ATTCGTCTGCAAGCCCAGC 61.043 57.895 0.00 0.00 32.87 4.85
896 2795 1.724582 GCCCGTTGACATATGCCACC 61.725 60.000 1.58 0.00 0.00 4.61
897 2796 0.393673 CCCGTTGACATATGCCACCA 60.394 55.000 1.58 0.00 0.00 4.17
908 2838 2.032681 GCCACCAGGACCAGACAC 59.967 66.667 0.00 0.00 36.89 3.67
948 2882 2.614057 CACCACTCTCAAACAACAGACC 59.386 50.000 0.00 0.00 0.00 3.85
953 2887 1.202604 TCTCAAACAACAGACCGGACC 60.203 52.381 9.46 0.00 0.00 4.46
1222 4306 1.750399 CTCAAGTCCCCCGCCAATG 60.750 63.158 0.00 0.00 0.00 2.82
1380 4464 1.800315 CGGCGTACCACGTTCTGAG 60.800 63.158 0.00 0.00 44.73 3.35
1403 4487 2.180017 GCGCCTCGTCTCGGTTAA 59.820 61.111 0.00 0.00 0.00 2.01
1404 4488 1.444895 GCGCCTCGTCTCGGTTAAA 60.445 57.895 0.00 0.00 0.00 1.52
1649 7545 0.249405 GAGAAGATCGCTGCCAGAGG 60.249 60.000 0.00 0.00 0.00 3.69
1974 9271 3.118112 AGTTCATATGCCCTCACAAGGAG 60.118 47.826 0.00 0.00 46.67 3.69
2075 9476 2.811317 CGGGCTGTGAGAAGCGAC 60.811 66.667 0.00 0.00 44.52 5.19
2752 11151 3.304057 GCTGTTGCTGTTCTGAAAGTACC 60.304 47.826 0.00 0.00 32.71 3.34
2954 11367 0.320421 TGCCACACGAGTTAAGCTCC 60.320 55.000 0.00 0.00 41.10 4.70
2967 11380 0.530650 AAGCTCCATGTATCCGCACG 60.531 55.000 0.00 0.00 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.920828 TGGGAACTCCAACTTGGC 57.079 55.556 2.52 0.00 43.84 4.52
11 12 3.440127 TCCAATCCAATTTGGGAACTCC 58.560 45.455 15.37 0.00 45.21 3.85
13 14 5.807909 CAAATCCAATCCAATTTGGGAACT 58.192 37.500 15.37 0.00 45.21 3.01
19 20 8.564509 AACAATACCAAATCCAATCCAATTTG 57.435 30.769 0.00 0.00 40.78 2.32
23 24 6.933521 CACAAACAATACCAAATCCAATCCAA 59.066 34.615 0.00 0.00 0.00 3.53
60 61 7.279090 GCTTTTCCAAAGACTCTAATACCTCTC 59.721 40.741 0.25 0.00 0.00 3.20
62 63 7.065204 CAGCTTTTCCAAAGACTCTAATACCTC 59.935 40.741 0.25 0.00 0.00 3.85
64 65 6.879458 TCAGCTTTTCCAAAGACTCTAATACC 59.121 38.462 0.25 0.00 0.00 2.73
156 1218 5.183713 TGCATATTTCTTCCTCCTGTGTTTG 59.816 40.000 0.00 0.00 0.00 2.93
157 1219 5.324409 TGCATATTTCTTCCTCCTGTGTTT 58.676 37.500 0.00 0.00 0.00 2.83
161 1223 7.232127 CCATATTTGCATATTTCTTCCTCCTGT 59.768 37.037 0.00 0.00 0.00 4.00
162 1224 7.449395 TCCATATTTGCATATTTCTTCCTCCTG 59.551 37.037 0.00 0.00 0.00 3.86
216 1279 6.908284 TGTATTTTTAACTTTCTCGTGCACAC 59.092 34.615 18.64 1.32 0.00 3.82
231 1294 8.526978 TCTGGCTGCATATTTGTGTATTTTTAA 58.473 29.630 0.50 0.00 0.00 1.52
234 1297 6.528537 TCTGGCTGCATATTTGTGTATTTT 57.471 33.333 0.50 0.00 0.00 1.82
306 1369 0.529337 TTTTGCATGGTGTGTTGCGG 60.529 50.000 0.00 0.00 41.80 5.69
322 1386 7.381323 GGTTGTCCATCTCAATTGATTCTTTT 58.619 34.615 8.96 0.00 0.00 2.27
343 1407 4.699735 TCTGTTGCAACATATGTAGGGTTG 59.300 41.667 31.17 15.43 43.53 3.77
368 1432 8.706322 TGTCATATAGATGCACTAACTTCCTA 57.294 34.615 0.00 0.00 34.56 2.94
470 1546 6.597672 TGAGTGACAACAAACACATAAGAGTT 59.402 34.615 0.00 0.00 39.18 3.01
549 1629 0.743345 AGGAAATAAGCCCGTGCGTC 60.743 55.000 0.00 0.00 44.33 5.19
575 1655 9.606631 GATAGAAGAATGAGACCAAAGTTATGT 57.393 33.333 0.00 0.00 0.00 2.29
576 1656 8.759641 CGATAGAAGAATGAGACCAAAGTTATG 58.240 37.037 0.00 0.00 39.76 1.90
578 1658 7.837863 ACGATAGAAGAATGAGACCAAAGTTA 58.162 34.615 0.00 0.00 41.38 2.24
579 1659 6.702329 ACGATAGAAGAATGAGACCAAAGTT 58.298 36.000 0.00 0.00 41.38 2.66
580 1660 6.071334 TGACGATAGAAGAATGAGACCAAAGT 60.071 38.462 0.00 0.00 41.38 2.66
581 1661 6.333416 TGACGATAGAAGAATGAGACCAAAG 58.667 40.000 0.00 0.00 41.38 2.77
582 1662 6.280855 TGACGATAGAAGAATGAGACCAAA 57.719 37.500 0.00 0.00 41.38 3.28
583 1663 5.914898 TGACGATAGAAGAATGAGACCAA 57.085 39.130 0.00 0.00 41.38 3.67
584 1664 6.096846 TCAATGACGATAGAAGAATGAGACCA 59.903 38.462 0.00 0.00 41.38 4.02
585 1665 6.507900 TCAATGACGATAGAAGAATGAGACC 58.492 40.000 0.00 0.00 41.38 3.85
588 1668 5.925397 CCCTCAATGACGATAGAAGAATGAG 59.075 44.000 0.00 0.00 41.38 2.90
597 1677 2.039418 TGTCCCCCTCAATGACGATAG 58.961 52.381 0.00 0.00 46.19 2.08
598 1678 1.760613 GTGTCCCCCTCAATGACGATA 59.239 52.381 0.00 0.00 0.00 2.92
615 1695 3.076032 AGCCCAAGAAGATAAAAGGGTGT 59.924 43.478 0.00 0.00 38.56 4.16
618 1698 3.968265 TGAGCCCAAGAAGATAAAAGGG 58.032 45.455 0.00 0.00 39.33 3.95
619 1699 6.595682 TCTATGAGCCCAAGAAGATAAAAGG 58.404 40.000 0.00 0.00 0.00 3.11
620 1700 7.504403 TCTCTATGAGCCCAAGAAGATAAAAG 58.496 38.462 0.00 0.00 0.00 2.27
622 1702 7.437713 TTCTCTATGAGCCCAAGAAGATAAA 57.562 36.000 0.00 0.00 0.00 1.40
627 1707 5.356470 CCTTTTTCTCTATGAGCCCAAGAAG 59.644 44.000 0.00 0.00 0.00 2.85
628 1708 5.014123 TCCTTTTTCTCTATGAGCCCAAGAA 59.986 40.000 0.00 0.00 0.00 2.52
629 1709 4.536090 TCCTTTTTCTCTATGAGCCCAAGA 59.464 41.667 0.00 0.00 0.00 3.02
630 1710 4.848357 TCCTTTTTCTCTATGAGCCCAAG 58.152 43.478 0.00 0.00 0.00 3.61
632 1712 4.104086 TCTCCTTTTTCTCTATGAGCCCA 58.896 43.478 0.00 0.00 0.00 5.36
633 1713 4.762289 TCTCCTTTTTCTCTATGAGCCC 57.238 45.455 0.00 0.00 0.00 5.19
635 1715 5.491982 TGGTTCTCCTTTTTCTCTATGAGC 58.508 41.667 0.00 0.00 34.23 4.26
636 1716 7.390027 TCTTGGTTCTCCTTTTTCTCTATGAG 58.610 38.462 0.00 0.00 34.23 2.90
638 1718 7.986085 TTCTTGGTTCTCCTTTTTCTCTATG 57.014 36.000 0.00 0.00 34.23 2.23
641 1721 6.183360 GCTTTTCTTGGTTCTCCTTTTTCTCT 60.183 38.462 0.00 0.00 34.23 3.10
642 1722 5.980116 GCTTTTCTTGGTTCTCCTTTTTCTC 59.020 40.000 0.00 0.00 34.23 2.87
643 1723 5.658634 AGCTTTTCTTGGTTCTCCTTTTTCT 59.341 36.000 0.00 0.00 34.23 2.52
649 1729 6.133253 AGATAAGCTTTTCTTGGTTCTCCT 57.867 37.500 13.03 0.00 36.25 3.69
718 1798 5.826643 ACAAAATAGAGGGAGGCATGTAAA 58.173 37.500 0.00 0.00 0.00 2.01
719 1799 5.450818 ACAAAATAGAGGGAGGCATGTAA 57.549 39.130 0.00 0.00 0.00 2.41
720 1800 5.450818 AACAAAATAGAGGGAGGCATGTA 57.549 39.130 0.00 0.00 0.00 2.29
721 1801 4.322057 AACAAAATAGAGGGAGGCATGT 57.678 40.909 0.00 0.00 0.00 3.21
722 1802 4.706476 TGAAACAAAATAGAGGGAGGCATG 59.294 41.667 0.00 0.00 0.00 4.06
723 1803 4.934356 TGAAACAAAATAGAGGGAGGCAT 58.066 39.130 0.00 0.00 0.00 4.40
725 1805 5.185828 ACAATGAAACAAAATAGAGGGAGGC 59.814 40.000 0.00 0.00 0.00 4.70
726 1806 6.840780 ACAATGAAACAAAATAGAGGGAGG 57.159 37.500 0.00 0.00 0.00 4.30
727 1807 9.626045 GTTTACAATGAAACAAAATAGAGGGAG 57.374 33.333 0.00 0.00 38.84 4.30
729 1809 8.585018 AGGTTTACAATGAAACAAAATAGAGGG 58.415 33.333 9.33 0.00 40.43 4.30
730 1810 9.981114 AAGGTTTACAATGAAACAAAATAGAGG 57.019 29.630 9.33 0.00 40.43 3.69
738 1818 9.658799 TGATTTGAAAGGTTTACAATGAAACAA 57.341 25.926 9.33 0.00 40.43 2.83
740 1820 9.528018 TCTGATTTGAAAGGTTTACAATGAAAC 57.472 29.630 0.00 0.00 38.38 2.78
789 1869 9.185192 GGTGTTCTAACAAAATCTGATTTGAAG 57.815 33.333 15.80 11.37 41.73 3.02
790 1870 8.912988 AGGTGTTCTAACAAAATCTGATTTGAA 58.087 29.630 15.80 11.37 41.73 2.69
791 1871 8.463930 AGGTGTTCTAACAAAATCTGATTTGA 57.536 30.769 15.80 6.25 41.73 2.69
834 2733 3.115554 GCTTGCAGACGAATGTGTTTTT 58.884 40.909 0.00 0.00 0.00 1.94
835 2734 2.543653 GGCTTGCAGACGAATGTGTTTT 60.544 45.455 0.00 0.00 0.00 2.43
896 2795 1.071471 GGTGTGGTGTCTGGTCCTG 59.929 63.158 0.00 0.00 0.00 3.86
897 2796 0.986019 TTGGTGTGGTGTCTGGTCCT 60.986 55.000 0.00 0.00 0.00 3.85
908 2838 2.070654 GAGGGTTTGCGTTGGTGTGG 62.071 60.000 0.00 0.00 0.00 4.17
1312 4396 2.915659 TGTTCTCTCCACGCCGGT 60.916 61.111 1.90 0.00 35.57 5.28
1315 4399 1.374758 CCAGTGTTCTCTCCACGCC 60.375 63.158 0.00 0.00 37.88 5.68
1366 4450 1.546834 GCGATCTCAGAACGTGGTAC 58.453 55.000 6.18 0.00 30.73 3.34
1369 4453 2.508891 GCGCGATCTCAGAACGTGG 61.509 63.158 18.26 6.60 38.43 4.94
1649 7545 5.794894 TGAATGTCTTCTTCAAGTAGTCCC 58.205 41.667 0.00 0.00 32.29 4.46
1974 9271 3.982241 GCAAGGTGTGGTGCAGCC 61.982 66.667 14.36 5.89 46.08 4.85
2075 9476 6.750501 CACTGAATCAGAAATTACCAGCATTG 59.249 38.462 18.20 0.00 35.18 2.82
2212 9720 6.800543 TGCAGTGCTATACTTTCTTCTCTAG 58.199 40.000 17.60 0.00 37.60 2.43
2228 9736 1.303309 GACAAGTTCACTGCAGTGCT 58.697 50.000 36.76 27.06 45.25 4.40
2651 11050 6.153680 CCTAGAATAAGTATCAGCCAGTAGGG 59.846 46.154 0.00 0.00 40.85 3.53
2752 11151 5.183713 TCTGAAATAACCATGAAACTGCCAG 59.816 40.000 0.00 0.00 0.00 4.85
2967 11380 3.721035 ACAGTCCAAGTTTACACCGTAC 58.279 45.455 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.