Multiple sequence alignment - TraesCS7B01G263300

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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 TraesCS7B01G263300 chr7B 100.000 2288 0 0 1 2288 483869589 483867302 0.000000e+00 4226
1 TraesCS7B01G263300 chr7B 94.275 1572 79 8 122 1688 639856077 639857642 0.000000e+00 2394
2 TraesCS7B01G263300 chr7B 90.419 501 39 3 1774 2268 483891119 483890622 0.000000e+00 651
3 TraesCS7B01G263300 chr7B 96.899 129 2 2 2 130 425684116 425684242 4.950000e-52 215
4 TraesCS7B01G263300 chr7B 96.183 131 3 2 1 130 129590835 129590706 1.780000e-51 213
5 TraesCS7B01G263300 chr6B 95.238 1575 68 5 122 1691 643872130 643870558 0.000000e+00 2486
6 TraesCS7B01G263300 chr6B 94.423 1578 75 6 122 1688 711404708 711406283 0.000000e+00 2414
7 TraesCS7B01G263300 chr1D 94.930 1578 70 7 124 1695 209755995 209757568 0.000000e+00 2462
8 TraesCS7B01G263300 chr1D 91.892 148 10 2 8 153 96087310 96087163 2.980000e-49 206
9 TraesCS7B01G263300 chr1D 87.591 137 17 0 2056 2192 478992224 478992088 2.350000e-35 159
10 TraesCS7B01G263300 chr1B 94.734 1576 73 8 122 1691 311135820 311134249 0.000000e+00 2442
11 TraesCS7B01G263300 chr1B 95.003 1541 74 3 122 1661 566609887 566611425 0.000000e+00 2416
12 TraesCS7B01G263300 chr1B 86.957 138 18 0 2055 2192 667058756 667058619 3.040000e-34 156
13 TraesCS7B01G263300 chr1B 85.612 139 20 0 2054 2192 667136272 667136134 1.830000e-31 147
14 TraesCS7B01G263300 chr3B 94.084 1572 84 7 122 1688 745588963 745590530 0.000000e+00 2379
15 TraesCS7B01G263300 chr5B 94.024 1573 87 4 124 1691 693957642 693956072 0.000000e+00 2377
16 TraesCS7B01G263300 chr5B 94.017 1571 81 9 125 1688 369339716 369338152 0.000000e+00 2368
17 TraesCS7B01G263300 chr7D 93.233 532 27 2 1763 2288 461400966 461400438 0.000000e+00 774
18 TraesCS7B01G263300 chr7D 91.946 149 6 5 8 153 6193438 6193293 1.070000e-48 204
19 TraesCS7B01G263300 chr7D 89.091 165 11 6 8 167 119358958 119358796 4.990000e-47 198
20 TraesCS7B01G263300 chr7A 89.366 536 39 7 1720 2251 538711148 538711669 0.000000e+00 658
21 TraesCS7B01G263300 chr5A 96.850 127 2 2 8 133 670055674 670055549 6.400000e-51 211
22 TraesCS7B01G263300 chr5A 89.313 131 14 0 2060 2190 77791589 77791459 5.060000e-37 165
23 TraesCS7B01G263300 chr4D 94.815 135 5 1 2 134 51363606 51363740 2.300000e-50 209
24 TraesCS7B01G263300 chr4D 94.161 137 6 2 2 137 481566355 481566490 8.280000e-50 207
25 TraesCS7B01G263300 chr4B 93.056 144 7 3 2 143 74522802 74522944 8.280000e-50 207
26 TraesCS7B01G263300 chr1A 78.481 237 44 5 2054 2288 575227601 575227370 5.090000e-32 148
27 TraesCS7B01G263300 chr1A 78.481 237 44 5 2054 2288 575246072 575245841 5.090000e-32 148


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 TraesCS7B01G263300 chr7B 483867302 483869589 2287 True 4226 4226 100.000 1 2288 1 chr7B.!!$R2 2287
1 TraesCS7B01G263300 chr7B 639856077 639857642 1565 False 2394 2394 94.275 122 1688 1 chr7B.!!$F2 1566
2 TraesCS7B01G263300 chr6B 643870558 643872130 1572 True 2486 2486 95.238 122 1691 1 chr6B.!!$R1 1569
3 TraesCS7B01G263300 chr6B 711404708 711406283 1575 False 2414 2414 94.423 122 1688 1 chr6B.!!$F1 1566
4 TraesCS7B01G263300 chr1D 209755995 209757568 1573 False 2462 2462 94.930 124 1695 1 chr1D.!!$F1 1571
5 TraesCS7B01G263300 chr1B 311134249 311135820 1571 True 2442 2442 94.734 122 1691 1 chr1B.!!$R1 1569
6 TraesCS7B01G263300 chr1B 566609887 566611425 1538 False 2416 2416 95.003 122 1661 1 chr1B.!!$F1 1539
7 TraesCS7B01G263300 chr3B 745588963 745590530 1567 False 2379 2379 94.084 122 1688 1 chr3B.!!$F1 1566
8 TraesCS7B01G263300 chr5B 693956072 693957642 1570 True 2377 2377 94.024 124 1691 1 chr5B.!!$R2 1567
9 TraesCS7B01G263300 chr5B 369338152 369339716 1564 True 2368 2368 94.017 125 1688 1 chr5B.!!$R1 1563
10 TraesCS7B01G263300 chr7D 461400438 461400966 528 True 774 774 93.233 1763 2288 1 chr7D.!!$R3 525
11 TraesCS7B01G263300 chr7A 538711148 538711669 521 False 658 658 89.366 1720 2251 1 chr7A.!!$F1 531

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
822 825 0.032813 CCCTTCACCCAATGCCTGAT 60.033 55.0 0.0 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1767 1784 0.110486 GGGTTTGAGGCTTGTCAGGA 59.89 55.0 0.0 0.0 0.0 3.86 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
36 37 2.101700 GGTCTACGAGGGTACGTGG 58.898 63.158 0.00 0.00 46.02 4.94
38 39 3.159298 TCTACGAGGGTACGTGGAC 57.841 57.895 0.00 0.00 45.53 4.02
39 40 0.324614 TCTACGAGGGTACGTGGACA 59.675 55.000 0.00 0.00 45.53 4.02
40 41 1.167851 CTACGAGGGTACGTGGACAA 58.832 55.000 0.00 0.00 44.98 3.18
41 42 0.881118 TACGAGGGTACGTGGACAAC 59.119 55.000 0.00 0.00 46.02 3.32
42 43 1.108727 ACGAGGGTACGTGGACAACA 61.109 55.000 0.00 0.00 44.84 3.33
43 44 0.665369 CGAGGGTACGTGGACAACAC 60.665 60.000 0.00 0.00 46.78 3.32
51 52 2.453242 GTGGACAACACTCTCCCCT 58.547 57.895 0.00 0.00 46.72 4.79
52 53 0.321996 GTGGACAACACTCTCCCCTC 59.678 60.000 0.00 0.00 46.72 4.30
53 54 0.191064 TGGACAACACTCTCCCCTCT 59.809 55.000 0.00 0.00 0.00 3.69
54 55 0.899019 GGACAACACTCTCCCCTCTC 59.101 60.000 0.00 0.00 0.00 3.20
55 56 0.528470 GACAACACTCTCCCCTCTCG 59.472 60.000 0.00 0.00 0.00 4.04
56 57 0.178958 ACAACACTCTCCCCTCTCGT 60.179 55.000 0.00 0.00 0.00 4.18
57 58 0.969894 CAACACTCTCCCCTCTCGTT 59.030 55.000 0.00 0.00 0.00 3.85
58 59 0.969894 AACACTCTCCCCTCTCGTTG 59.030 55.000 0.00 0.00 0.00 4.10
59 60 1.216710 CACTCTCCCCTCTCGTTGC 59.783 63.158 0.00 0.00 0.00 4.17
60 61 1.077625 ACTCTCCCCTCTCGTTGCT 59.922 57.895 0.00 0.00 0.00 3.91
61 62 0.331954 ACTCTCCCCTCTCGTTGCTA 59.668 55.000 0.00 0.00 0.00 3.49
62 63 1.063567 ACTCTCCCCTCTCGTTGCTAT 60.064 52.381 0.00 0.00 0.00 2.97
63 64 1.339610 CTCTCCCCTCTCGTTGCTATG 59.660 57.143 0.00 0.00 0.00 2.23
64 65 0.249657 CTCCCCTCTCGTTGCTATGC 60.250 60.000 0.00 0.00 0.00 3.14
65 66 0.975556 TCCCCTCTCGTTGCTATGCA 60.976 55.000 0.00 0.00 36.47 3.96
66 67 0.107456 CCCCTCTCGTTGCTATGCAT 59.893 55.000 3.79 3.79 38.76 3.96
67 68 1.506493 CCCTCTCGTTGCTATGCATC 58.494 55.000 0.19 0.00 38.76 3.91
68 69 1.202568 CCCTCTCGTTGCTATGCATCA 60.203 52.381 0.19 0.00 38.76 3.07
69 70 1.863454 CCTCTCGTTGCTATGCATCAC 59.137 52.381 0.19 0.00 38.76 3.06
70 71 1.863454 CTCTCGTTGCTATGCATCACC 59.137 52.381 0.19 0.00 38.76 4.02
71 72 1.206849 TCTCGTTGCTATGCATCACCA 59.793 47.619 0.19 0.00 38.76 4.17
72 73 2.158914 TCTCGTTGCTATGCATCACCAT 60.159 45.455 0.19 0.00 38.76 3.55
73 74 1.941975 TCGTTGCTATGCATCACCATG 59.058 47.619 0.19 0.00 38.76 3.66
74 75 1.941975 CGTTGCTATGCATCACCATGA 59.058 47.619 0.19 0.00 38.76 3.07
75 76 2.551032 CGTTGCTATGCATCACCATGAT 59.449 45.455 0.19 0.00 38.76 2.45
76 77 3.364664 CGTTGCTATGCATCACCATGATC 60.365 47.826 0.19 0.00 38.76 2.92
77 78 3.782656 TGCTATGCATCACCATGATCT 57.217 42.857 0.19 0.00 34.28 2.75
78 79 4.094830 TGCTATGCATCACCATGATCTT 57.905 40.909 0.19 0.00 34.28 2.40
79 80 3.818773 TGCTATGCATCACCATGATCTTG 59.181 43.478 0.19 1.60 34.28 3.02
80 81 3.366070 GCTATGCATCACCATGATCTTGC 60.366 47.826 0.19 0.00 34.28 4.01
81 82 1.018910 TGCATCACCATGATCTTGCG 58.981 50.000 3.07 0.30 34.28 4.85
82 83 1.019673 GCATCACCATGATCTTGCGT 58.980 50.000 3.07 0.87 34.28 5.24
83 84 1.268386 GCATCACCATGATCTTGCGTG 60.268 52.381 17.02 17.02 34.28 5.34
84 85 2.011947 CATCACCATGATCTTGCGTGT 58.988 47.619 19.89 6.63 34.28 4.49
85 86 1.441738 TCACCATGATCTTGCGTGTG 58.558 50.000 19.89 14.96 0.00 3.82
86 87 0.179181 CACCATGATCTTGCGTGTGC 60.179 55.000 15.81 0.00 43.20 4.57
94 95 1.405526 ATCTTGCGTGTGCGTAGGATT 60.406 47.619 0.00 0.00 44.18 3.01
95 96 2.935238 ATCTTGCGTGTGCGTAGGATTT 60.935 45.455 0.00 0.00 44.18 2.17
96 97 4.419949 ATCTTGCGTGTGCGTAGGATTTT 61.420 43.478 0.00 0.00 44.18 1.82
97 98 5.865159 ATCTTGCGTGTGCGTAGGATTTTT 61.865 41.667 0.00 0.00 44.18 1.94
130 131 1.208535 CGTTCCCTAACACCTGGCATA 59.791 52.381 0.00 0.00 35.16 3.14
162 163 2.166907 TCTTCCTCCTCCTTAGGCTG 57.833 55.000 0.00 0.00 43.31 4.85
166 167 1.690633 CTCCTCCTTAGGCTGCCCA 60.691 63.158 16.57 0.00 43.31 5.36
252 253 3.813166 GCAAAGTAGGTCTTGTACTTGCA 59.187 43.478 0.00 0.00 39.34 4.08
280 281 2.599408 TCCTCTGTTTAGGGTCGTCT 57.401 50.000 0.00 0.00 37.24 4.18
351 352 0.690192 TTCGCTGGGTCAGGAATCAA 59.310 50.000 0.00 0.00 31.21 2.57
389 390 1.375908 GTGGCCTTCATGAGCACGA 60.376 57.895 3.32 0.00 0.00 4.35
421 422 2.442458 TGCATTGCCGGCATGGAT 60.442 55.556 33.25 19.05 42.00 3.41
441 442 0.600255 CCGAAGTTCGAGCACACCTT 60.600 55.000 26.37 0.00 43.74 3.50
527 528 2.445155 CCCAAGGGAAGGGGTTGG 59.555 66.667 0.00 0.00 42.90 3.77
542 543 0.610232 GTTGGCATTGGAGCTGGAGT 60.610 55.000 0.00 0.00 34.17 3.85
793 796 2.664851 CGGCCGTTGACAGCAAGA 60.665 61.111 19.50 0.00 34.01 3.02
822 825 0.032813 CCCTTCACCCAATGCCTGAT 60.033 55.000 0.00 0.00 0.00 2.90
832 835 2.619849 CCAATGCCTGATGAGGTTGAGT 60.620 50.000 0.00 0.00 42.15 3.41
865 868 1.202770 CCAAGGAAGACCCAAAGACGT 60.203 52.381 0.00 0.00 37.41 4.34
866 869 1.873591 CAAGGAAGACCCAAAGACGTG 59.126 52.381 0.00 0.00 37.41 4.49
885 888 3.823330 GAGGGTGGCGACGACGAT 61.823 66.667 12.29 0.00 42.66 3.73
1195 1201 0.687354 GTTCAAGCTCCTCACTCCCA 59.313 55.000 0.00 0.00 0.00 4.37
1296 1302 4.020878 AAGGAGTAGGGCCGGGGT 62.021 66.667 2.18 0.00 0.00 4.95
1313 1319 3.969466 GGGTCTCCCTAAGTACTACCT 57.031 52.381 8.30 0.00 41.34 3.08
1315 1321 5.597430 GGGTCTCCCTAAGTACTACCTAT 57.403 47.826 8.30 0.00 41.34 2.57
1358 1364 5.467705 AGAACTGTTATGAACTGTCGTACC 58.532 41.667 0.00 0.00 41.84 3.34
1360 1366 3.254166 ACTGTTATGAACTGTCGTACCGT 59.746 43.478 0.00 0.00 38.97 4.83
1376 1382 9.401873 TGTCGTACCGTTTATATCTGAATTATG 57.598 33.333 0.00 0.00 0.00 1.90
1432 1438 0.819259 ATGTGTGCTGCCGAAGTGTT 60.819 50.000 0.00 0.00 0.00 3.32
1445 1451 3.399330 CGAAGTGTTGTGGTAACCTCAT 58.601 45.455 0.00 0.00 0.00 2.90
1523 1536 3.895041 CCTTGGGTTTGTGGACTAACATT 59.105 43.478 6.47 0.00 34.16 2.71
1544 1557 2.027460 GCAACCAAACACCAGGCG 59.973 61.111 0.00 0.00 0.00 5.52
1545 1558 2.027460 CAACCAAACACCAGGCGC 59.973 61.111 0.00 0.00 0.00 6.53
1590 1603 1.297364 GGCATGCAGGCAACCAAAT 59.703 52.632 26.25 0.00 43.51 2.32
1593 1606 2.420408 GGCATGCAGGCAACCAAATAAT 60.420 45.455 26.25 0.00 43.51 1.28
1695 1712 1.202830 ACCAAACACGCCCATAGTGAA 60.203 47.619 3.20 0.00 41.83 3.18
1696 1713 1.199097 CCAAACACGCCCATAGTGAAC 59.801 52.381 3.20 0.00 41.83 3.18
1697 1714 2.151202 CAAACACGCCCATAGTGAACT 58.849 47.619 3.20 0.00 41.83 3.01
1698 1715 2.552315 CAAACACGCCCATAGTGAACTT 59.448 45.455 3.20 0.00 41.83 2.66
1699 1716 2.094762 ACACGCCCATAGTGAACTTC 57.905 50.000 3.20 0.00 41.83 3.01
1700 1717 0.999406 CACGCCCATAGTGAACTTCG 59.001 55.000 0.00 0.00 41.83 3.79
1701 1718 0.108329 ACGCCCATAGTGAACTTCGG 60.108 55.000 0.00 0.00 0.00 4.30
1702 1719 0.174845 CGCCCATAGTGAACTTCGGA 59.825 55.000 0.00 0.00 0.00 4.55
1703 1720 1.404986 CGCCCATAGTGAACTTCGGAA 60.405 52.381 0.00 0.00 0.00 4.30
1704 1721 2.706890 GCCCATAGTGAACTTCGGAAA 58.293 47.619 0.00 0.00 0.00 3.13
1705 1722 3.078837 GCCCATAGTGAACTTCGGAAAA 58.921 45.455 0.00 0.00 0.00 2.29
1706 1723 3.127030 GCCCATAGTGAACTTCGGAAAAG 59.873 47.826 0.00 0.00 0.00 2.27
1707 1724 4.575885 CCCATAGTGAACTTCGGAAAAGA 58.424 43.478 0.00 0.00 0.00 2.52
1708 1725 5.001232 CCCATAGTGAACTTCGGAAAAGAA 58.999 41.667 0.00 0.00 0.00 2.52
1709 1726 5.472137 CCCATAGTGAACTTCGGAAAAGAAA 59.528 40.000 0.00 0.00 0.00 2.52
1710 1727 6.016610 CCCATAGTGAACTTCGGAAAAGAAAA 60.017 38.462 0.00 0.00 0.00 2.29
1711 1728 7.422399 CCATAGTGAACTTCGGAAAAGAAAAA 58.578 34.615 0.00 0.00 0.00 1.94
1733 1750 4.354893 AAATGCAATCCCTTCAAAGCAA 57.645 36.364 0.00 0.00 35.45 3.91
1742 1759 6.866010 ATCCCTTCAAAGCAAAAATGAAAC 57.134 33.333 0.00 0.00 33.08 2.78
1750 1767 8.994429 TCAAAGCAAAAATGAAACAAACTAGA 57.006 26.923 0.00 0.00 0.00 2.43
1753 1770 9.651913 AAAGCAAAAATGAAACAAACTAGAAGA 57.348 25.926 0.00 0.00 0.00 2.87
1754 1771 9.651913 AAGCAAAAATGAAACAAACTAGAAGAA 57.348 25.926 0.00 0.00 0.00 2.52
1755 1772 9.305925 AGCAAAAATGAAACAAACTAGAAGAAG 57.694 29.630 0.00 0.00 0.00 2.85
1756 1773 9.301153 GCAAAAATGAAACAAACTAGAAGAAGA 57.699 29.630 0.00 0.00 0.00 2.87
1761 1778 9.468532 AATGAAACAAACTAGAAGAAGATTTGC 57.531 29.630 0.00 0.00 34.34 3.68
1767 1784 5.262455 ACTAGAAGAAGATTTGCCCCTTT 57.738 39.130 0.00 0.00 0.00 3.11
1771 1788 2.812658 AGAAGATTTGCCCCTTTCCTG 58.187 47.619 0.00 0.00 0.00 3.86
1931 1955 4.891992 TCCAAGAAGAGAAAATCGGAGT 57.108 40.909 0.00 0.00 0.00 3.85
1976 2000 3.206150 GAAATCTTAAGCCATGAGCCGA 58.794 45.455 0.00 0.00 45.47 5.54
2012 2036 2.661866 CGCCCGAATCCGACATCC 60.662 66.667 0.00 0.00 38.22 3.51
2020 2047 1.136305 GAATCCGACATCCGAGAACCA 59.864 52.381 0.00 0.00 41.76 3.67
2021 2048 0.460311 ATCCGACATCCGAGAACCAC 59.540 55.000 0.00 0.00 41.76 4.16
2025 2052 2.227089 GACATCCGAGAACCACCGCT 62.227 60.000 0.00 0.00 0.00 5.52
2104 2131 0.970937 TCGGCGACTTCATCTCCCTT 60.971 55.000 4.99 0.00 0.00 3.95
2224 2251 2.427232 CCGAAGGTGACAACGTTCTA 57.573 50.000 0.00 0.00 45.03 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.226603 CCCTCGTAGACCGAAAGCG 60.227 63.158 0.00 0.00 46.75 4.68
12 13 1.098050 TACCCTCGTAGACCGAAAGC 58.902 55.000 0.00 0.00 46.75 3.51
13 14 1.063174 CGTACCCTCGTAGACCGAAAG 59.937 57.143 0.00 0.00 46.75 2.62
14 15 1.086696 CGTACCCTCGTAGACCGAAA 58.913 55.000 0.00 0.00 46.75 3.46
15 16 0.036388 ACGTACCCTCGTAGACCGAA 60.036 55.000 0.00 0.00 46.75 4.30
16 17 0.740868 CACGTACCCTCGTAGACCGA 60.741 60.000 0.00 0.00 45.00 4.69
17 18 1.709147 CCACGTACCCTCGTAGACCG 61.709 65.000 0.00 0.00 42.27 4.79
18 19 0.392998 TCCACGTACCCTCGTAGACC 60.393 60.000 0.00 0.00 42.27 3.85
19 20 0.729690 GTCCACGTACCCTCGTAGAC 59.270 60.000 0.00 2.79 42.50 2.59
20 21 0.324614 TGTCCACGTACCCTCGTAGA 59.675 55.000 0.00 0.00 42.27 2.59
21 22 1.135575 GTTGTCCACGTACCCTCGTAG 60.136 57.143 0.00 0.00 42.27 3.51
22 23 0.881118 GTTGTCCACGTACCCTCGTA 59.119 55.000 0.00 0.00 42.27 3.43
23 24 1.108727 TGTTGTCCACGTACCCTCGT 61.109 55.000 0.00 0.00 45.10 4.18
24 25 0.665369 GTGTTGTCCACGTACCCTCG 60.665 60.000 0.00 0.00 33.61 4.63
25 26 3.206090 GTGTTGTCCACGTACCCTC 57.794 57.895 0.00 0.00 33.61 4.30
30 31 4.748514 AGGGGAGAGTGTTGTCCACGTA 62.749 54.545 0.00 0.00 44.77 3.57
32 33 1.472662 AGGGGAGAGTGTTGTCCACG 61.473 60.000 0.00 0.00 44.77 4.94
33 34 0.321996 GAGGGGAGAGTGTTGTCCAC 59.678 60.000 0.00 0.00 40.47 4.02
34 35 0.191064 AGAGGGGAGAGTGTTGTCCA 59.809 55.000 0.00 0.00 38.50 4.02
35 36 0.899019 GAGAGGGGAGAGTGTTGTCC 59.101 60.000 0.00 0.00 36.03 4.02
36 37 0.528470 CGAGAGGGGAGAGTGTTGTC 59.472 60.000 0.00 0.00 0.00 3.18
37 38 0.178958 ACGAGAGGGGAGAGTGTTGT 60.179 55.000 0.00 0.00 0.00 3.32
38 39 0.969894 AACGAGAGGGGAGAGTGTTG 59.030 55.000 0.00 0.00 0.00 3.33
39 40 0.969894 CAACGAGAGGGGAGAGTGTT 59.030 55.000 0.00 0.00 0.00 3.32
40 41 1.536943 GCAACGAGAGGGGAGAGTGT 61.537 60.000 0.00 0.00 0.00 3.55
41 42 1.216710 GCAACGAGAGGGGAGAGTG 59.783 63.158 0.00 0.00 0.00 3.51
42 43 0.331954 TAGCAACGAGAGGGGAGAGT 59.668 55.000 0.00 0.00 0.00 3.24
43 44 1.339610 CATAGCAACGAGAGGGGAGAG 59.660 57.143 0.00 0.00 0.00 3.20
44 45 1.403814 CATAGCAACGAGAGGGGAGA 58.596 55.000 0.00 0.00 0.00 3.71
45 46 0.249657 GCATAGCAACGAGAGGGGAG 60.250 60.000 0.00 0.00 0.00 4.30
46 47 0.975556 TGCATAGCAACGAGAGGGGA 60.976 55.000 0.00 0.00 34.76 4.81
47 48 0.107456 ATGCATAGCAACGAGAGGGG 59.893 55.000 0.00 0.00 43.62 4.79
48 49 1.202568 TGATGCATAGCAACGAGAGGG 60.203 52.381 0.00 0.00 43.62 4.30
49 50 1.863454 GTGATGCATAGCAACGAGAGG 59.137 52.381 0.00 0.00 43.62 3.69
50 51 1.863454 GGTGATGCATAGCAACGAGAG 59.137 52.381 0.00 0.00 43.62 3.20
51 52 1.206849 TGGTGATGCATAGCAACGAGA 59.793 47.619 0.00 0.00 43.62 4.04
52 53 1.655484 TGGTGATGCATAGCAACGAG 58.345 50.000 0.00 0.00 43.62 4.18
53 54 1.941975 CATGGTGATGCATAGCAACGA 59.058 47.619 0.00 0.00 43.62 3.85
54 55 1.941975 TCATGGTGATGCATAGCAACG 59.058 47.619 0.00 1.35 43.62 4.10
55 56 3.819337 AGATCATGGTGATGCATAGCAAC 59.181 43.478 0.00 0.00 43.62 4.17
56 57 4.094830 AGATCATGGTGATGCATAGCAA 57.905 40.909 0.00 0.00 43.62 3.91
57 58 3.782656 AGATCATGGTGATGCATAGCA 57.217 42.857 0.00 4.86 44.86 3.49
58 59 3.366070 GCAAGATCATGGTGATGCATAGC 60.366 47.826 0.00 0.00 37.20 2.97
59 60 3.120304 CGCAAGATCATGGTGATGCATAG 60.120 47.826 0.00 0.00 37.20 2.23
60 61 2.809696 CGCAAGATCATGGTGATGCATA 59.190 45.455 0.00 0.00 37.20 3.14
61 62 1.607148 CGCAAGATCATGGTGATGCAT 59.393 47.619 0.00 0.00 37.20 3.96
62 63 1.018910 CGCAAGATCATGGTGATGCA 58.981 50.000 11.83 0.00 37.20 3.96
63 64 1.019673 ACGCAAGATCATGGTGATGC 58.980 50.000 0.00 3.06 37.20 3.91
64 65 2.011947 ACACGCAAGATCATGGTGATG 58.988 47.619 19.56 8.58 37.20 3.07
65 66 2.011947 CACACGCAAGATCATGGTGAT 58.988 47.619 19.56 0.00 40.34 3.06
66 67 1.441738 CACACGCAAGATCATGGTGA 58.558 50.000 19.56 0.00 43.62 4.02
67 68 0.179181 GCACACGCAAGATCATGGTG 60.179 55.000 14.17 14.17 43.62 4.17
68 69 1.638388 CGCACACGCAAGATCATGGT 61.638 55.000 0.00 0.00 43.62 3.55
69 70 1.061411 CGCACACGCAAGATCATGG 59.939 57.895 0.00 0.00 43.62 3.66
70 71 0.998669 TACGCACACGCAAGATCATG 59.001 50.000 0.00 0.00 45.53 3.07
71 72 1.280982 CTACGCACACGCAAGATCAT 58.719 50.000 0.00 0.00 45.53 2.45
72 73 0.735978 CCTACGCACACGCAAGATCA 60.736 55.000 0.00 0.00 45.53 2.92
73 74 0.457853 TCCTACGCACACGCAAGATC 60.458 55.000 0.00 0.00 45.53 2.75
74 75 0.175760 ATCCTACGCACACGCAAGAT 59.824 50.000 0.00 0.00 45.53 2.40
75 76 0.037697 AATCCTACGCACACGCAAGA 60.038 50.000 0.00 0.00 45.53 3.02
76 77 0.796312 AAATCCTACGCACACGCAAG 59.204 50.000 0.00 0.00 45.53 4.01
77 78 1.231221 AAAATCCTACGCACACGCAA 58.769 45.000 0.00 0.00 45.53 4.85
78 79 1.231221 AAAAATCCTACGCACACGCA 58.769 45.000 0.00 0.00 45.53 5.24
95 96 9.118300 TGTTAGGGAACGTAGTAATTTCAAAAA 57.882 29.630 0.00 0.00 45.00 1.94
96 97 8.558700 GTGTTAGGGAACGTAGTAATTTCAAAA 58.441 33.333 0.00 0.00 45.00 2.44
97 98 7.173047 GGTGTTAGGGAACGTAGTAATTTCAAA 59.827 37.037 0.00 0.00 45.00 2.69
98 99 6.650390 GGTGTTAGGGAACGTAGTAATTTCAA 59.350 38.462 0.00 0.00 45.00 2.69
99 100 6.014327 AGGTGTTAGGGAACGTAGTAATTTCA 60.014 38.462 0.00 0.00 45.00 2.69
100 101 6.312180 CAGGTGTTAGGGAACGTAGTAATTTC 59.688 42.308 0.00 0.00 45.00 2.17
101 102 6.168389 CAGGTGTTAGGGAACGTAGTAATTT 58.832 40.000 0.00 0.00 45.00 1.82
102 103 5.337813 CCAGGTGTTAGGGAACGTAGTAATT 60.338 44.000 0.00 0.00 45.00 1.40
103 104 4.161001 CCAGGTGTTAGGGAACGTAGTAAT 59.839 45.833 0.00 0.00 45.00 1.89
104 105 3.511146 CCAGGTGTTAGGGAACGTAGTAA 59.489 47.826 0.00 0.00 45.00 2.24
105 106 3.091545 CCAGGTGTTAGGGAACGTAGTA 58.908 50.000 0.00 0.00 45.00 1.82
107 108 1.405121 GCCAGGTGTTAGGGAACGTAG 60.405 57.143 0.00 0.00 38.51 3.51
108 109 0.609662 GCCAGGTGTTAGGGAACGTA 59.390 55.000 0.00 0.00 38.51 3.57
109 110 1.373812 GCCAGGTGTTAGGGAACGT 59.626 57.895 0.00 0.00 38.51 3.99
110 111 0.035439 ATGCCAGGTGTTAGGGAACG 60.035 55.000 0.00 0.00 38.51 3.95
111 112 3.214328 CATATGCCAGGTGTTAGGGAAC 58.786 50.000 0.00 0.00 36.00 3.62
112 113 2.422803 GCATATGCCAGGTGTTAGGGAA 60.423 50.000 17.26 0.00 34.31 3.97
113 114 1.142870 GCATATGCCAGGTGTTAGGGA 59.857 52.381 17.26 0.00 34.31 4.20
114 115 1.133823 TGCATATGCCAGGTGTTAGGG 60.134 52.381 24.54 0.00 41.18 3.53
115 116 1.949525 GTGCATATGCCAGGTGTTAGG 59.050 52.381 24.54 0.00 41.18 2.69
116 117 1.949525 GGTGCATATGCCAGGTGTTAG 59.050 52.381 24.54 0.00 41.18 2.34
117 118 1.745484 CGGTGCATATGCCAGGTGTTA 60.745 52.381 24.54 0.28 41.18 2.41
118 119 1.031571 CGGTGCATATGCCAGGTGTT 61.032 55.000 24.54 0.00 41.18 3.32
119 120 1.451927 CGGTGCATATGCCAGGTGT 60.452 57.895 24.54 0.00 41.18 4.16
120 121 2.837883 GCGGTGCATATGCCAGGTG 61.838 63.158 24.54 11.00 41.18 4.00
130 131 1.078143 GGAAGAAGAGGCGGTGCAT 60.078 57.895 0.00 0.00 0.00 3.96
252 253 3.328050 CCCTAAACAGAGGAAGAAGTGGT 59.672 47.826 0.00 0.00 39.15 4.16
280 281 0.178767 CCATGAATCAGGCCGTCTCA 59.821 55.000 0.00 0.00 0.00 3.27
351 352 3.229276 CTCAAGATGAGCTGAAGACGT 57.771 47.619 0.00 0.00 37.72 4.34
389 390 3.674138 GCAATGCAGAACGAATCCAATGT 60.674 43.478 0.00 0.00 0.00 2.71
421 422 1.006571 GGTGTGCTCGAACTTCGGA 60.007 57.895 11.21 0.00 40.88 4.55
441 442 2.104111 ACCAAGTTCGAGAACACCATGA 59.896 45.455 17.00 0.00 43.47 3.07
527 528 2.559440 CTCTAACTCCAGCTCCAATGC 58.441 52.381 0.00 0.00 0.00 3.56
542 543 0.394192 CCCATCGCCATGAGCTCTAA 59.606 55.000 16.19 0.00 40.39 2.10
638 641 2.584965 TCACTCTTCTCCTCCTCTCCAT 59.415 50.000 0.00 0.00 0.00 3.41
793 796 1.685820 GGTGAAGGGGCTACTTGCT 59.314 57.895 0.00 0.00 42.39 3.91
822 825 2.281484 GGCGGCAACTCAACCTCA 60.281 61.111 3.07 0.00 0.00 3.86
847 850 1.489230 ACACGTCTTTGGGTCTTCCTT 59.511 47.619 0.00 0.00 36.20 3.36
865 868 3.986006 GTCGTCGCCACCCTCACA 61.986 66.667 0.00 0.00 0.00 3.58
1296 1302 6.102910 AGCAGAATAGGTAGTACTTAGGGAGA 59.897 42.308 0.00 0.00 0.00 3.71
1311 1317 4.997395 ACGCATAAACCATAGCAGAATAGG 59.003 41.667 0.00 0.00 0.00 2.57
1313 1319 6.988522 TCTACGCATAAACCATAGCAGAATA 58.011 36.000 0.00 0.00 0.00 1.75
1315 1321 5.270893 TCTACGCATAAACCATAGCAGAA 57.729 39.130 0.00 0.00 0.00 3.02
1376 1382 7.976734 ACAGAGTATAAACAGAGCATCAACTAC 59.023 37.037 0.00 0.00 37.82 2.73
1432 1438 3.055385 GGCTAGTTGATGAGGTTACCACA 60.055 47.826 3.66 3.66 0.00 4.17
1445 1451 3.649023 TGGTAACCTCTTTGGCTAGTTGA 59.351 43.478 0.00 0.00 40.22 3.18
1523 1536 0.754957 CCTGGTGTTTGGTTGCCTGA 60.755 55.000 0.00 0.00 0.00 3.86
1545 1558 1.592400 CTGCATGGGCTGAACCACAG 61.592 60.000 0.00 0.00 44.72 3.66
1629 1642 0.764890 CACTTCTCCACCCAACCTGA 59.235 55.000 0.00 0.00 0.00 3.86
1710 1727 4.716794 TGCTTTGAAGGGATTGCATTTTT 58.283 34.783 0.00 0.00 0.00 1.94
1711 1728 4.354893 TGCTTTGAAGGGATTGCATTTT 57.645 36.364 0.00 0.00 0.00 1.82
1712 1729 4.354893 TTGCTTTGAAGGGATTGCATTT 57.645 36.364 0.00 0.00 0.00 2.32
1713 1730 4.354893 TTTGCTTTGAAGGGATTGCATT 57.645 36.364 0.00 0.00 0.00 3.56
1714 1731 4.354893 TTTTGCTTTGAAGGGATTGCAT 57.645 36.364 0.00 0.00 0.00 3.96
1715 1732 3.834489 TTTTGCTTTGAAGGGATTGCA 57.166 38.095 0.00 0.00 0.00 4.08
1716 1733 4.756135 TCATTTTTGCTTTGAAGGGATTGC 59.244 37.500 0.00 0.00 0.00 3.56
1717 1734 6.864360 TTCATTTTTGCTTTGAAGGGATTG 57.136 33.333 0.00 0.00 0.00 2.67
1718 1735 6.827762 TGTTTCATTTTTGCTTTGAAGGGATT 59.172 30.769 0.00 0.00 31.54 3.01
1724 1741 9.429359 TCTAGTTTGTTTCATTTTTGCTTTGAA 57.571 25.926 0.00 0.00 0.00 2.69
1742 1759 5.012893 AGGGGCAAATCTTCTTCTAGTTTG 58.987 41.667 0.00 0.00 33.98 2.93
1750 1767 3.168292 CAGGAAAGGGGCAAATCTTCTT 58.832 45.455 0.00 0.00 0.00 2.52
1753 1770 2.158325 TGTCAGGAAAGGGGCAAATCTT 60.158 45.455 0.00 0.00 0.00 2.40
1754 1771 1.428912 TGTCAGGAAAGGGGCAAATCT 59.571 47.619 0.00 0.00 0.00 2.40
1755 1772 1.923356 TGTCAGGAAAGGGGCAAATC 58.077 50.000 0.00 0.00 0.00 2.17
1756 1773 2.250924 CTTGTCAGGAAAGGGGCAAAT 58.749 47.619 0.00 0.00 0.00 2.32
1757 1774 1.703411 CTTGTCAGGAAAGGGGCAAA 58.297 50.000 0.00 0.00 0.00 3.68
1758 1775 0.827507 GCTTGTCAGGAAAGGGGCAA 60.828 55.000 0.00 0.00 0.00 4.52
1759 1776 1.228552 GCTTGTCAGGAAAGGGGCA 60.229 57.895 0.00 0.00 0.00 5.36
1760 1777 1.979155 GGCTTGTCAGGAAAGGGGC 60.979 63.158 0.00 0.00 0.00 5.80
1761 1778 0.322906 GAGGCTTGTCAGGAAAGGGG 60.323 60.000 0.00 0.00 0.00 4.79
1767 1784 0.110486 GGGTTTGAGGCTTGTCAGGA 59.890 55.000 0.00 0.00 0.00 3.86
1771 1788 1.239347 GTGAGGGTTTGAGGCTTGTC 58.761 55.000 0.00 0.00 0.00 3.18
1873 1897 1.077501 CATCTCCATGGCCGGTTGT 60.078 57.895 6.96 0.00 0.00 3.32
1875 1899 2.597340 CCATCTCCATGGCCGGTT 59.403 61.111 6.96 0.00 43.55 4.44
1910 1934 4.891992 ACTCCGATTTTCTCTTCTTGGA 57.108 40.909 0.00 0.00 0.00 3.53
1962 1986 2.499205 CCGTCGGCTCATGGCTTA 59.501 61.111 0.00 0.00 41.46 3.09
2093 2120 1.584724 GTGGGGAGAAGGGAGATGAA 58.415 55.000 0.00 0.00 0.00 2.57
2214 2241 3.581024 TGAGGCGTATTAGAACGTTGT 57.419 42.857 5.00 3.64 44.64 3.32
2215 2242 5.464965 AAATGAGGCGTATTAGAACGTTG 57.535 39.130 5.00 0.00 44.64 4.10
2216 2243 4.569564 GGAAATGAGGCGTATTAGAACGTT 59.430 41.667 0.00 0.00 44.64 3.99
2224 2251 3.496870 GGATCTGGGAAATGAGGCGTATT 60.497 47.826 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.