Multiple sequence alignment - TraesCS7B01G058000

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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 TraesCS7B01G058000 chr7B 100.000 2703 0 0 1 2703 60371550 60374252 0.000000e+00 4992.0
1 TraesCS7B01G058000 chr7B 95.365 863 27 3 804 1663 59923138 59923990 0.000000e+00 1360.0
2 TraesCS7B01G058000 chr7B 98.206 223 4 0 1 223 706745421 706745199 9.070000e-105 390.0
3 TraesCS7B01G058000 chr7B 84.911 338 27 14 1654 1979 59925481 59925806 1.210000e-83 320.0
4 TraesCS7B01G058000 chr7B 83.260 227 29 8 584 805 619070000 619070222 1.640000e-47 200.0
5 TraesCS7B01G058000 chr7B 92.373 118 8 1 243 359 680675449 680675566 1.660000e-37 167.0
6 TraesCS7B01G058000 chr7B 90.141 71 7 0 368 438 450683246 450683316 2.870000e-15 93.5
7 TraesCS7B01G058000 chr7A 87.395 1190 99 24 809 1979 709824886 709826043 0.000000e+00 1319.0
8 TraesCS7B01G058000 chr7A 91.566 581 32 9 1294 1871 106954563 106955129 0.000000e+00 785.0
9 TraesCS7B01G058000 chr4B 99.455 550 1 2 1 548 59868723 59868174 0.000000e+00 998.0
10 TraesCS7B01G058000 chr4B 96.864 287 7 2 520 805 59868119 59867834 1.880000e-131 479.0
11 TraesCS7B01G058000 chr4B 90.179 112 6 5 259 365 180200094 180199983 1.010000e-29 141.0
12 TraesCS7B01G058000 chrUn 100.000 535 0 0 1 535 395473793 395474327 0.000000e+00 989.0
13 TraesCS7B01G058000 chrUn 87.736 106 11 2 702 806 358531453 358531349 3.650000e-24 122.0
14 TraesCS7B01G058000 chrUn 86.792 106 12 2 702 806 357719699 357719595 1.700000e-22 117.0
15 TraesCS7B01G058000 chr3D 84.317 644 75 8 2081 2703 591724936 591724298 8.280000e-170 606.0
16 TraesCS7B01G058000 chr3D 95.349 215 10 0 1 215 582263248 582263462 2.580000e-90 342.0
17 TraesCS7B01G058000 chr3B 83.307 641 81 9 2083 2703 792878285 792878919 3.910000e-158 568.0
18 TraesCS7B01G058000 chr3B 82.484 628 70 16 2090 2699 727053728 727054333 5.160000e-142 514.0
19 TraesCS7B01G058000 chr3B 98.206 223 4 0 1 223 16047210 16047432 9.070000e-105 390.0
20 TraesCS7B01G058000 chr5D 80.739 758 82 32 1990 2703 113748965 113748228 1.420000e-147 532.0
21 TraesCS7B01G058000 chr1A 82.222 630 78 18 2092 2703 427507002 427506389 1.860000e-141 512.0
22 TraesCS7B01G058000 chr2B 81.763 658 68 23 2081 2701 737227379 737228021 1.120000e-138 503.0
23 TraesCS7B01G058000 chr2B 80.851 658 73 21 2081 2701 737246434 737247075 4.070000e-128 468.0
24 TraesCS7B01G058000 chr2B 94.581 203 7 4 584 784 798302892 798302692 7.270000e-81 311.0
25 TraesCS7B01G058000 chr2B 82.328 232 32 8 584 810 774828240 774828013 2.750000e-45 193.0
26 TraesCS7B01G058000 chr2B 86.916 107 14 0 253 359 791146586 791146692 1.310000e-23 121.0
27 TraesCS7B01G058000 chr1B 81.832 644 75 20 2083 2703 368077841 368077217 1.120000e-138 503.0
28 TraesCS7B01G058000 chr1B 82.051 234 35 6 584 813 2329189 2328959 2.750000e-45 193.0
29 TraesCS7B01G058000 chr1B 80.745 161 25 6 648 805 374015817 374015974 1.310000e-23 121.0
30 TraesCS7B01G058000 chr1B 85.882 85 9 3 153 236 623879623 623879705 1.330000e-13 87.9
31 TraesCS7B01G058000 chr1B 89.552 67 7 0 287 353 374015125 374015191 4.800000e-13 86.1
32 TraesCS7B01G058000 chr6D 80.685 642 79 20 2084 2703 429975342 429975960 8.820000e-125 457.0
33 TraesCS7B01G058000 chr4A 98.148 216 2 2 335 548 740889707 740889922 2.540000e-100 375.0
34 TraesCS7B01G058000 chr4A 78.667 150 25 7 643 789 45520257 45520112 2.870000e-15 93.5
35 TraesCS7B01G058000 chr4A 100.000 35 0 0 243 277 740889662 740889696 6.250000e-07 65.8
36 TraesCS7B01G058000 chr3A 83.582 402 52 8 2090 2488 722290579 722290969 5.500000e-97 364.0
37 TraesCS7B01G058000 chr2D 87.879 231 21 5 2126 2353 497335210 497335436 5.740000e-67 265.0
38 TraesCS7B01G058000 chr2D 92.373 118 8 1 243 359 542306540 542306657 1.660000e-37 167.0
39 TraesCS7B01G058000 chr2D 91.525 118 9 1 243 359 38529431 38529548 7.740000e-36 161.0
40 TraesCS7B01G058000 chr2D 87.826 115 12 2 253 365 542525357 542525243 1.690000e-27 134.0
41 TraesCS7B01G058000 chr6B 94.681 94 5 0 130 223 134277034 134276941 2.170000e-31 147.0
42 TraesCS7B01G058000 chr6B 80.982 163 23 8 648 806 72316817 72316975 3.650000e-24 122.0
43 TraesCS7B01G058000 chr6B 87.736 106 11 2 702 806 72319664 72319768 3.650000e-24 122.0
44 TraesCS7B01G058000 chr6B 86.792 106 12 2 702 806 72322464 72322568 1.700000e-22 117.0
45 TraesCS7B01G058000 chr6B 86.792 106 12 2 702 806 72325258 72325362 1.700000e-22 117.0
46 TraesCS7B01G058000 chr5A 78.000 150 26 7 643 789 534026821 534026966 1.330000e-13 87.9
47 TraesCS7B01G058000 chr2A 96.000 50 2 0 174 223 610181646 610181597 6.200000e-12 82.4


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 TraesCS7B01G058000 chr7B 60371550 60374252 2702 False 4992.0 4992 100.0000 1 2703 1 chr7B.!!$F1 2702
1 TraesCS7B01G058000 chr7B 59923138 59925806 2668 False 840.0 1360 90.1380 804 1979 2 chr7B.!!$F5 1175
2 TraesCS7B01G058000 chr7A 709824886 709826043 1157 False 1319.0 1319 87.3950 809 1979 1 chr7A.!!$F2 1170
3 TraesCS7B01G058000 chr7A 106954563 106955129 566 False 785.0 785 91.5660 1294 1871 1 chr7A.!!$F1 577
4 TraesCS7B01G058000 chr4B 59867834 59868723 889 True 738.5 998 98.1595 1 805 2 chr4B.!!$R2 804
5 TraesCS7B01G058000 chrUn 395473793 395474327 534 False 989.0 989 100.0000 1 535 1 chrUn.!!$F1 534
6 TraesCS7B01G058000 chr3D 591724298 591724936 638 True 606.0 606 84.3170 2081 2703 1 chr3D.!!$R1 622
7 TraesCS7B01G058000 chr3B 792878285 792878919 634 False 568.0 568 83.3070 2083 2703 1 chr3B.!!$F3 620
8 TraesCS7B01G058000 chr3B 727053728 727054333 605 False 514.0 514 82.4840 2090 2699 1 chr3B.!!$F2 609
9 TraesCS7B01G058000 chr5D 113748228 113748965 737 True 532.0 532 80.7390 1990 2703 1 chr5D.!!$R1 713
10 TraesCS7B01G058000 chr1A 427506389 427507002 613 True 512.0 512 82.2220 2092 2703 1 chr1A.!!$R1 611
11 TraesCS7B01G058000 chr2B 737227379 737228021 642 False 503.0 503 81.7630 2081 2701 1 chr2B.!!$F1 620
12 TraesCS7B01G058000 chr2B 737246434 737247075 641 False 468.0 468 80.8510 2081 2701 1 chr2B.!!$F2 620
13 TraesCS7B01G058000 chr1B 368077217 368077841 624 True 503.0 503 81.8320 2083 2703 1 chr1B.!!$R2 620
14 TraesCS7B01G058000 chr6D 429975342 429975960 618 False 457.0 457 80.6850 2084 2703 1 chr6D.!!$F1 619

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
776 862 0.81321 CAAATCGCTGAGGAGCCTCC 60.813 60.0 13.69 1.26 42.91 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2330 3988 0.107897 GGTGTCACATCCGCATGGTA 60.108 55.0 5.12 0.0 33.82 3.25 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
643 729 5.697473 TTTACAGTCCGATGCAATTGAAA 57.303 34.783 10.34 0.00 0.00 2.69
653 739 7.277539 GTCCGATGCAATTGAAATTTTATCCAA 59.722 33.333 10.34 0.00 0.00 3.53
657 743 8.866970 ATGCAATTGAAATTTTATCCAAAGGT 57.133 26.923 10.34 0.00 0.00 3.50
758 844 4.116328 CGACGGCCGAGAAGCTCA 62.116 66.667 35.90 0.00 41.76 4.26
769 855 1.932511 GAGAAGCTCAAATCGCTGAGG 59.067 52.381 9.95 0.00 42.68 3.86
770 856 1.552337 AGAAGCTCAAATCGCTGAGGA 59.448 47.619 9.95 0.00 42.68 3.71
771 857 1.932511 GAAGCTCAAATCGCTGAGGAG 59.067 52.381 9.95 0.00 42.68 3.69
772 858 2.013021 GCTCAAATCGCTGAGGAGC 58.987 57.895 9.95 0.00 42.68 4.70
776 862 0.813210 CAAATCGCTGAGGAGCCTCC 60.813 60.000 13.69 1.26 42.91 4.30
792 878 1.202330 CTCCTGCATCCACTCCTCTT 58.798 55.000 0.00 0.00 0.00 2.85
847 938 5.542616 CAGCCATGCATAGCTTATACTTC 57.457 43.478 17.42 0.00 37.18 3.01
908 999 2.386661 ACAACAAGATGGAGGCTACG 57.613 50.000 0.00 0.00 0.00 3.51
932 1023 7.174946 ACGCTTTCAGATTGAATTAGGAAGAAA 59.825 33.333 3.83 0.00 36.11 2.52
1005 1096 1.095600 GGAGGAAGAAAACGATGGCC 58.904 55.000 0.00 0.00 0.00 5.36
1171 1265 2.037871 CACAAAAAGGTCCCGGTGG 58.962 57.895 0.00 0.00 0.00 4.61
1172 1266 1.830847 ACAAAAAGGTCCCGGTGGC 60.831 57.895 0.00 0.00 0.00 5.01
1173 1267 2.203582 AAAAAGGTCCCGGTGGCC 60.204 61.111 0.00 2.51 0.00 5.36
1234 1328 1.921243 CCATCATGCAGTACGTCGAA 58.079 50.000 0.00 0.00 0.00 3.71
1318 1418 2.842462 TGGGCCGCCTATGTCGAT 60.842 61.111 9.86 0.00 0.00 3.59
1352 1452 2.750657 GCCTGGCTAGCCATCCTGT 61.751 63.158 35.93 0.00 46.15 4.00
1395 1495 4.120331 GCAAAAGCTCGCCGCCAT 62.120 61.111 0.00 0.00 40.39 4.40
1432 1532 0.693767 CCATGGAGGAGGCCTTCTCT 60.694 60.000 35.27 18.14 42.10 3.10
1583 1686 4.752879 GCTTAGCCGCGTGGACCA 62.753 66.667 21.76 0.00 37.49 4.02
1726 3329 0.891373 CTCGGTGGAGCTTCTTGAGA 59.109 55.000 0.00 0.00 32.61 3.27
1736 3339 1.135373 GCTTCTTGAGATCGACCGACA 60.135 52.381 0.00 0.00 0.00 4.35
1742 3346 1.816224 TGAGATCGACCGACATGTGAA 59.184 47.619 1.15 0.00 0.00 3.18
1743 3347 2.159379 TGAGATCGACCGACATGTGAAG 60.159 50.000 1.15 0.00 0.00 3.02
1746 3350 3.442625 AGATCGACCGACATGTGAAGTAA 59.557 43.478 1.15 0.00 0.00 2.24
1747 3351 3.861276 TCGACCGACATGTGAAGTAAT 57.139 42.857 1.15 0.00 0.00 1.89
1749 3353 2.603110 CGACCGACATGTGAAGTAATGG 59.397 50.000 1.15 0.00 0.00 3.16
1751 3355 2.027192 ACCGACATGTGAAGTAATGGCT 60.027 45.455 1.15 0.00 28.94 4.75
1753 3357 4.188462 CCGACATGTGAAGTAATGGCTAA 58.812 43.478 1.15 0.00 28.94 3.09
1754 3358 4.816385 CCGACATGTGAAGTAATGGCTAAT 59.184 41.667 1.15 0.00 28.94 1.73
1759 3364 6.437162 ACATGTGAAGTAATGGCTAATGGTTT 59.563 34.615 0.00 0.00 0.00 3.27
1762 3367 7.151308 TGTGAAGTAATGGCTAATGGTTTTTG 58.849 34.615 0.00 0.00 0.00 2.44
1793 3398 0.506932 AATCGCGTGTCGTCACTTTG 59.493 50.000 5.77 1.12 41.89 2.77
1836 3442 4.303086 TCGTCTTTCGTCAGTCTTCTTT 57.697 40.909 0.00 0.00 40.80 2.52
1871 3486 1.831106 TCATCACGCCTGTCCAGTATT 59.169 47.619 0.00 0.00 0.00 1.89
1872 3487 3.028130 TCATCACGCCTGTCCAGTATTA 58.972 45.455 0.00 0.00 0.00 0.98
1873 3488 3.641436 TCATCACGCCTGTCCAGTATTAT 59.359 43.478 0.00 0.00 0.00 1.28
1885 3500 6.980593 TGTCCAGTATTATGCAATAAATGGC 58.019 36.000 0.00 0.00 42.96 4.40
1900 3515 7.308830 GCAATAAATGGCCATTTGTTTTGGTAA 60.309 33.333 41.35 25.03 39.17 2.85
1906 3521 3.498018 GCCATTTGTTTTGGTAAAGCTGG 59.502 43.478 0.00 0.00 36.57 4.85
1908 3523 4.990426 CCATTTGTTTTGGTAAAGCTGGAG 59.010 41.667 0.00 0.00 0.00 3.86
1909 3524 5.453198 CCATTTGTTTTGGTAAAGCTGGAGT 60.453 40.000 0.00 0.00 0.00 3.85
1910 3525 4.647424 TTGTTTTGGTAAAGCTGGAGTG 57.353 40.909 0.00 0.00 0.00 3.51
1913 3528 4.707448 TGTTTTGGTAAAGCTGGAGTGAAA 59.293 37.500 0.00 0.00 0.00 2.69
1915 3530 5.923733 TTTGGTAAAGCTGGAGTGAAAAA 57.076 34.783 0.00 0.00 0.00 1.94
1979 3594 7.544217 GCGACTATTCCAACCAAAATATGTTTT 59.456 33.333 0.00 0.00 38.03 2.43
1980 3595 9.418045 CGACTATTCCAACCAAAATATGTTTTT 57.582 29.630 0.00 0.00 35.41 1.94
2004 3619 8.537049 TTTCTTATGGAAAAGTTTACGATCGA 57.463 30.769 24.34 2.23 40.51 3.59
2023 3638 4.690719 ACGCCGGCCGAATGTTCA 62.691 61.111 30.73 0.00 41.02 3.18
2052 3667 2.268022 CGCTACGCCTAGGATCCAT 58.732 57.895 14.75 1.47 0.00 3.41
2053 3668 1.460504 CGCTACGCCTAGGATCCATA 58.539 55.000 14.75 2.68 0.00 2.74
2054 3669 2.025155 CGCTACGCCTAGGATCCATAT 58.975 52.381 14.75 0.00 0.00 1.78
2055 3670 2.223595 CGCTACGCCTAGGATCCATATG 60.224 54.545 14.75 1.89 0.00 1.78
2056 3671 2.101582 GCTACGCCTAGGATCCATATGG 59.898 54.545 16.25 16.25 0.00 2.74
2068 3683 2.959516 TCCATATGGATCGAACGCATC 58.040 47.619 20.98 0.00 39.78 3.91
2069 3684 2.298729 TCCATATGGATCGAACGCATCA 59.701 45.455 20.98 0.00 39.78 3.07
2070 3685 3.055891 TCCATATGGATCGAACGCATCAT 60.056 43.478 20.98 0.00 39.78 2.45
2071 3686 4.159506 TCCATATGGATCGAACGCATCATA 59.840 41.667 20.98 0.00 39.78 2.15
2072 3687 5.052481 CCATATGGATCGAACGCATCATAT 58.948 41.667 17.49 0.00 37.39 1.78
2073 3688 5.050567 CCATATGGATCGAACGCATCATATG 60.051 44.000 17.49 21.01 37.39 1.78
2074 3689 3.658757 TGGATCGAACGCATCATATGA 57.341 42.857 8.10 8.10 0.00 2.15
2075 3690 3.317150 TGGATCGAACGCATCATATGAC 58.683 45.455 7.78 0.00 0.00 3.06
2077 3692 2.148916 TCGAACGCATCATATGACCC 57.851 50.000 7.78 0.91 0.00 4.46
2078 3693 1.410882 TCGAACGCATCATATGACCCA 59.589 47.619 7.78 0.00 0.00 4.51
2079 3694 1.526887 CGAACGCATCATATGACCCAC 59.473 52.381 7.78 0.00 0.00 4.61
2080 3695 2.560504 GAACGCATCATATGACCCACA 58.439 47.619 7.78 0.00 0.00 4.17
2081 3696 1.953559 ACGCATCATATGACCCACAC 58.046 50.000 7.78 0.00 0.00 3.82
2082 3697 1.209261 ACGCATCATATGACCCACACA 59.791 47.619 7.78 0.00 0.00 3.72
2083 3698 2.158769 ACGCATCATATGACCCACACAT 60.159 45.455 7.78 0.00 0.00 3.21
2084 3699 2.481568 CGCATCATATGACCCACACATC 59.518 50.000 7.78 0.00 0.00 3.06
2085 3700 3.748083 GCATCATATGACCCACACATCT 58.252 45.455 7.78 0.00 0.00 2.90
2086 3701 4.139786 GCATCATATGACCCACACATCTT 58.860 43.478 7.78 0.00 0.00 2.40
2087 3702 4.214971 GCATCATATGACCCACACATCTTC 59.785 45.833 7.78 0.00 0.00 2.87
2088 3703 5.618236 CATCATATGACCCACACATCTTCT 58.382 41.667 7.78 0.00 0.00 2.85
2097 3728 3.054875 CCCACACATCTTCTCTCCATTCA 60.055 47.826 0.00 0.00 0.00 2.57
2109 3740 7.946776 TCTTCTCTCCATTCATTTTCTTTCCTT 59.053 33.333 0.00 0.00 0.00 3.36
2142 3781 0.764369 CTCCTCCAATCGATCCCCCA 60.764 60.000 0.00 0.00 0.00 4.96
2169 3808 2.514592 CCTCGCCATGAACGCCAT 60.515 61.111 0.00 0.00 35.44 4.40
2231 3873 1.690845 CCACTCTACCTCCCTGCTGAT 60.691 57.143 0.00 0.00 0.00 2.90
2237 3879 3.200593 CTCCCTGCTGATGCGTGC 61.201 66.667 0.00 0.00 43.34 5.34
2241 3883 2.749044 CTGCTGATGCGTGCCCTT 60.749 61.111 0.00 0.00 43.34 3.95
2242 3884 3.047718 CTGCTGATGCGTGCCCTTG 62.048 63.158 0.00 0.00 43.34 3.61
2243 3885 3.058160 GCTGATGCGTGCCCTTGT 61.058 61.111 0.00 0.00 0.00 3.16
2252 3901 3.636231 TGCCCTTGTCACCTCCCG 61.636 66.667 0.00 0.00 0.00 5.14
2254 3903 3.636231 CCCTTGTCACCTCCCGCA 61.636 66.667 0.00 0.00 0.00 5.69
2353 4012 1.064505 CATGCGGATGTGACACCATTC 59.935 52.381 9.01 0.00 0.00 2.67
2395 4056 4.519540 TCCTGCTATGGCTTTGTTTTTC 57.480 40.909 1.68 0.00 39.59 2.29
2404 4065 8.229811 GCTATGGCTTTGTTTTTCATTTTTAGG 58.770 33.333 0.00 0.00 35.22 2.69
2412 4073 5.292101 TGTTTTTCATTTTTAGGTGGTTGCG 59.708 36.000 0.00 0.00 0.00 4.85
2415 4076 0.242555 ATTTTTAGGTGGTTGCGGCG 59.757 50.000 0.51 0.51 0.00 6.46
2428 4089 3.238441 GTTGCGGCGTTTTGATTTATCA 58.762 40.909 9.37 0.00 34.44 2.15
2458 4120 6.363357 CAGCTTTTTATTTCACCAGTTGTAGC 59.637 38.462 0.00 0.00 0.00 3.58
2520 4198 2.666619 CGGTAGTAGCTTTTCACGTCGT 60.667 50.000 0.00 0.00 0.00 4.34
2535 4213 2.096335 ACGTCGTTGGTTCCAACTTTTC 59.904 45.455 25.59 14.78 42.75 2.29
2542 4220 4.993029 TGGTTCCAACTTTTCATTTCGT 57.007 36.364 0.00 0.00 0.00 3.85
2576 4256 2.378547 TCCCCCTTTTTGACAGTAGCAT 59.621 45.455 0.00 0.00 0.00 3.79
2615 4295 5.061684 GGTTGTAGCATTTTATTTTGTCGGC 59.938 40.000 0.00 0.00 0.00 5.54
2616 4296 4.407818 TGTAGCATTTTATTTTGTCGGCG 58.592 39.130 0.00 0.00 0.00 6.46
2684 4368 0.400594 AACCACCTACCACAGAAGCC 59.599 55.000 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
643 729 7.414098 CGATCGTTCTCAACCTTTGGATAAAAT 60.414 37.037 7.03 0.00 0.00 1.82
653 739 0.391263 GGCCGATCGTTCTCAACCTT 60.391 55.000 15.09 0.00 0.00 3.50
657 743 0.391130 CTTGGGCCGATCGTTCTCAA 60.391 55.000 15.09 15.61 0.00 3.02
758 844 0.980231 AGGAGGCTCCTCAGCGATTT 60.980 55.000 30.46 5.18 45.66 2.17
769 855 1.145819 GAGTGGATGCAGGAGGCTC 59.854 63.158 5.78 5.78 45.15 4.70
770 856 2.373707 GGAGTGGATGCAGGAGGCT 61.374 63.158 0.00 0.00 45.15 4.58
771 857 2.191641 GGAGTGGATGCAGGAGGC 59.808 66.667 0.00 0.00 45.13 4.70
772 858 0.690411 AGAGGAGTGGATGCAGGAGG 60.690 60.000 0.00 0.00 0.00 4.30
776 862 5.884792 AGAAATAAAAGAGGAGTGGATGCAG 59.115 40.000 0.00 0.00 0.00 4.41
777 863 5.649395 CAGAAATAAAAGAGGAGTGGATGCA 59.351 40.000 0.00 0.00 0.00 3.96
830 916 7.552050 AAGAGGAGAAGTATAAGCTATGCAT 57.448 36.000 3.79 3.79 0.00 3.96
834 920 8.982723 TGTTGAAAGAGGAGAAGTATAAGCTAT 58.017 33.333 0.00 0.00 0.00 2.97
842 933 5.057149 GCAGTTGTTGAAAGAGGAGAAGTA 58.943 41.667 0.00 0.00 0.00 2.24
843 934 3.879892 GCAGTTGTTGAAAGAGGAGAAGT 59.120 43.478 0.00 0.00 0.00 3.01
844 935 4.133078 AGCAGTTGTTGAAAGAGGAGAAG 58.867 43.478 0.00 0.00 0.00 2.85
845 936 4.130118 GAGCAGTTGTTGAAAGAGGAGAA 58.870 43.478 0.00 0.00 0.00 2.87
846 937 3.134623 TGAGCAGTTGTTGAAAGAGGAGA 59.865 43.478 0.00 0.00 0.00 3.71
847 938 3.470709 TGAGCAGTTGTTGAAAGAGGAG 58.529 45.455 0.00 0.00 0.00 3.69
908 999 9.133627 GTTTTCTTCCTAATTCAATCTGAAAGC 57.866 33.333 0.00 0.00 40.12 3.51
980 1071 4.563580 CCATCGTTTTCTTCCTCCTCTTCA 60.564 45.833 0.00 0.00 0.00 3.02
1005 1096 1.066422 TAGCTGCAGATCTTCGCCG 59.934 57.895 20.43 0.00 0.00 6.46
1077 1171 2.211250 ACTCGTAGCTCACACCCTTA 57.789 50.000 0.00 0.00 0.00 2.69
1175 1269 2.845752 TTACCGGCGTGGATGAGCAC 62.846 60.000 6.01 0.00 42.00 4.40
1176 1270 2.572095 CTTACCGGCGTGGATGAGCA 62.572 60.000 6.01 0.00 42.00 4.26
1177 1271 1.883084 CTTACCGGCGTGGATGAGC 60.883 63.158 6.01 0.00 42.00 4.26
1220 1314 1.132643 GACCTCTTCGACGTACTGCAT 59.867 52.381 0.00 0.00 0.00 3.96
1318 1418 1.228245 GGCAGGGAACAGCTTGTCA 60.228 57.895 0.00 0.00 43.36 3.58
1583 1686 0.114560 TCCGTCTCCAGGAACCTCTT 59.885 55.000 0.00 0.00 34.33 2.85
1726 3329 3.861276 TTACTTCACATGTCGGTCGAT 57.139 42.857 0.00 0.00 0.00 3.59
1736 3339 7.480760 AAAACCATTAGCCATTACTTCACAT 57.519 32.000 0.00 0.00 0.00 3.21
1742 3346 9.705290 CTTAAACAAAAACCATTAGCCATTACT 57.295 29.630 0.00 0.00 0.00 2.24
1743 3347 8.931775 CCTTAAACAAAAACCATTAGCCATTAC 58.068 33.333 0.00 0.00 0.00 1.89
1746 3350 7.073457 ACCTTAAACAAAAACCATTAGCCAT 57.927 32.000 0.00 0.00 0.00 4.40
1747 3351 6.487299 ACCTTAAACAAAAACCATTAGCCA 57.513 33.333 0.00 0.00 0.00 4.75
1749 3353 6.258947 TGCAACCTTAAACAAAAACCATTAGC 59.741 34.615 0.00 0.00 0.00 3.09
1751 3355 8.738645 ATTGCAACCTTAAACAAAAACCATTA 57.261 26.923 0.00 0.00 0.00 1.90
1753 3357 6.018343 CGATTGCAACCTTAAACAAAAACCAT 60.018 34.615 0.00 0.00 0.00 3.55
1754 3358 5.292101 CGATTGCAACCTTAAACAAAAACCA 59.708 36.000 0.00 0.00 0.00 3.67
1759 3364 3.046390 CGCGATTGCAACCTTAAACAAA 58.954 40.909 0.00 0.00 42.97 2.83
1762 3367 1.976045 CACGCGATTGCAACCTTAAAC 59.024 47.619 15.93 0.00 42.97 2.01
1793 3398 8.293114 ACGATGATGTTGGAAAACAAATAAAC 57.707 30.769 0.00 0.00 41.58 2.01
1836 3442 3.003171 CGTGATGAAATGGTCACACAACA 59.997 43.478 6.35 0.00 43.74 3.33
1871 3486 7.148120 CCAAAACAAATGGCCATTTATTGCATA 60.148 33.333 36.92 0.00 38.84 3.14
1872 3487 6.350277 CCAAAACAAATGGCCATTTATTGCAT 60.350 34.615 36.92 21.79 38.84 3.96
1873 3488 5.048224 CCAAAACAAATGGCCATTTATTGCA 60.048 36.000 36.92 0.00 38.84 4.08
1885 3500 4.954875 TCCAGCTTTACCAAAACAAATGG 58.045 39.130 0.00 0.00 43.84 3.16
1928 3543 1.511305 CACCGCATCTACCGACTGT 59.489 57.895 0.00 0.00 0.00 3.55
1932 3547 3.845259 GCCCACCGCATCTACCGA 61.845 66.667 0.00 0.00 37.47 4.69
1933 3548 4.910585 GGCCCACCGCATCTACCG 62.911 72.222 0.00 0.00 40.31 4.02
1934 3549 3.338275 TTGGCCCACCGCATCTACC 62.338 63.158 0.00 0.00 40.31 3.18
1935 3550 1.819632 CTTGGCCCACCGCATCTAC 60.820 63.158 0.00 0.00 40.31 2.59
1936 3551 2.589540 CTTGGCCCACCGCATCTA 59.410 61.111 0.00 0.00 40.31 1.98
1979 3594 8.437742 GTCGATCGTAAACTTTTCCATAAGAAA 58.562 33.333 15.94 0.00 42.82 2.52
1980 3595 7.599621 TGTCGATCGTAAACTTTTCCATAAGAA 59.400 33.333 15.94 0.00 0.00 2.52
1981 3596 7.062605 GTGTCGATCGTAAACTTTTCCATAAGA 59.937 37.037 15.94 0.00 0.00 2.10
1982 3597 7.171434 GTGTCGATCGTAAACTTTTCCATAAG 58.829 38.462 15.94 0.00 0.00 1.73
1983 3598 6.183360 CGTGTCGATCGTAAACTTTTCCATAA 60.183 38.462 15.94 0.00 0.00 1.90
1984 3599 5.286797 CGTGTCGATCGTAAACTTTTCCATA 59.713 40.000 15.94 0.00 0.00 2.74
1985 3600 4.090930 CGTGTCGATCGTAAACTTTTCCAT 59.909 41.667 15.94 0.00 0.00 3.41
1986 3601 3.426191 CGTGTCGATCGTAAACTTTTCCA 59.574 43.478 15.94 0.00 0.00 3.53
1987 3602 3.720051 GCGTGTCGATCGTAAACTTTTCC 60.720 47.826 15.94 0.00 0.00 3.13
1988 3603 3.393022 GCGTGTCGATCGTAAACTTTTC 58.607 45.455 15.94 0.00 0.00 2.29
1989 3604 2.156310 GGCGTGTCGATCGTAAACTTTT 59.844 45.455 15.94 0.00 0.00 2.27
1990 3605 1.723003 GGCGTGTCGATCGTAAACTTT 59.277 47.619 15.94 0.00 0.00 2.66
1991 3606 1.343506 GGCGTGTCGATCGTAAACTT 58.656 50.000 15.94 0.00 0.00 2.66
1992 3607 0.795735 CGGCGTGTCGATCGTAAACT 60.796 55.000 15.94 0.00 0.00 2.66
1993 3608 1.622269 CGGCGTGTCGATCGTAAAC 59.378 57.895 15.94 6.75 0.00 2.01
1994 3609 1.514657 CCGGCGTGTCGATCGTAAA 60.515 57.895 15.94 0.00 0.00 2.01
1995 3610 2.100797 CCGGCGTGTCGATCGTAA 59.899 61.111 15.94 1.36 0.00 3.18
1996 3611 4.541482 GCCGGCGTGTCGATCGTA 62.541 66.667 12.58 2.69 0.00 3.43
2050 3665 5.750067 TCATATGATGCGTTCGATCCATATG 59.250 40.000 20.62 20.62 34.75 1.78
2052 3667 5.102313 GTCATATGATGCGTTCGATCCATA 58.898 41.667 9.02 0.00 0.00 2.74
2053 3668 3.928992 GTCATATGATGCGTTCGATCCAT 59.071 43.478 9.02 0.00 0.00 3.41
2054 3669 3.317150 GTCATATGATGCGTTCGATCCA 58.683 45.455 9.02 0.00 0.00 3.41
2055 3670 2.668457 GGTCATATGATGCGTTCGATCC 59.332 50.000 9.02 0.00 0.00 3.36
2056 3671 2.668457 GGGTCATATGATGCGTTCGATC 59.332 50.000 9.02 0.00 0.00 3.69
2057 3672 2.037121 TGGGTCATATGATGCGTTCGAT 59.963 45.455 9.02 0.00 0.00 3.59
2058 3673 1.410882 TGGGTCATATGATGCGTTCGA 59.589 47.619 9.02 0.00 0.00 3.71
2059 3674 1.526887 GTGGGTCATATGATGCGTTCG 59.473 52.381 9.02 0.00 0.00 3.95
2062 3677 1.209261 TGTGTGGGTCATATGATGCGT 59.791 47.619 9.02 0.00 0.00 5.24
2063 3678 1.952193 TGTGTGGGTCATATGATGCG 58.048 50.000 9.02 0.00 0.00 4.73
2066 3681 5.605908 AGAGAAGATGTGTGGGTCATATGAT 59.394 40.000 9.02 0.00 0.00 2.45
2067 3682 4.964897 AGAGAAGATGTGTGGGTCATATGA 59.035 41.667 0.00 0.00 0.00 2.15
2068 3683 5.287674 AGAGAAGATGTGTGGGTCATATG 57.712 43.478 0.00 0.00 0.00 1.78
2069 3684 4.346418 GGAGAGAAGATGTGTGGGTCATAT 59.654 45.833 0.00 0.00 0.00 1.78
2070 3685 3.706594 GGAGAGAAGATGTGTGGGTCATA 59.293 47.826 0.00 0.00 0.00 2.15
2071 3686 2.503356 GGAGAGAAGATGTGTGGGTCAT 59.497 50.000 0.00 0.00 0.00 3.06
2072 3687 1.902508 GGAGAGAAGATGTGTGGGTCA 59.097 52.381 0.00 0.00 0.00 4.02
2073 3688 1.902508 TGGAGAGAAGATGTGTGGGTC 59.097 52.381 0.00 0.00 0.00 4.46
2074 3689 2.030027 TGGAGAGAAGATGTGTGGGT 57.970 50.000 0.00 0.00 0.00 4.51
2075 3690 3.054875 TGAATGGAGAGAAGATGTGTGGG 60.055 47.826 0.00 0.00 0.00 4.61
2077 3692 6.754702 AAATGAATGGAGAGAAGATGTGTG 57.245 37.500 0.00 0.00 0.00 3.82
2078 3693 7.173722 AGAAAATGAATGGAGAGAAGATGTGT 58.826 34.615 0.00 0.00 0.00 3.72
2079 3694 7.627298 AGAAAATGAATGGAGAGAAGATGTG 57.373 36.000 0.00 0.00 0.00 3.21
2080 3695 8.647256 AAAGAAAATGAATGGAGAGAAGATGT 57.353 30.769 0.00 0.00 0.00 3.06
2081 3696 8.189460 GGAAAGAAAATGAATGGAGAGAAGATG 58.811 37.037 0.00 0.00 0.00 2.90
2082 3697 8.114743 AGGAAAGAAAATGAATGGAGAGAAGAT 58.885 33.333 0.00 0.00 0.00 2.40
2083 3698 7.465116 AGGAAAGAAAATGAATGGAGAGAAGA 58.535 34.615 0.00 0.00 0.00 2.87
2084 3699 7.700022 AGGAAAGAAAATGAATGGAGAGAAG 57.300 36.000 0.00 0.00 0.00 2.85
2085 3700 8.482852 AAAGGAAAGAAAATGAATGGAGAGAA 57.517 30.769 0.00 0.00 0.00 2.87
2086 3701 7.946776 AGAAAGGAAAGAAAATGAATGGAGAGA 59.053 33.333 0.00 0.00 0.00 3.10
2087 3702 8.120140 AGAAAGGAAAGAAAATGAATGGAGAG 57.880 34.615 0.00 0.00 0.00 3.20
2088 3703 7.946776 AGAGAAAGGAAAGAAAATGAATGGAGA 59.053 33.333 0.00 0.00 0.00 3.71
2097 3728 9.290988 GAACTAAGGAGAGAAAGGAAAGAAAAT 57.709 33.333 0.00 0.00 0.00 1.82
2109 3740 4.676799 TGGAGGAGAACTAAGGAGAGAA 57.323 45.455 0.00 0.00 0.00 2.87
2142 3781 1.839994 TCATGGCGAGGGAAGAGAAAT 59.160 47.619 0.00 0.00 0.00 2.17
2169 3808 2.191908 GCCGCATCCATGGTGGTA 59.808 61.111 12.58 0.00 39.03 3.25
2205 3847 1.591280 GGGAGGTAGAGTGGGGAGGA 61.591 65.000 0.00 0.00 0.00 3.71
2213 3855 1.786937 CATCAGCAGGGAGGTAGAGT 58.213 55.000 0.00 0.00 0.00 3.24
2231 3873 3.825160 GAGGTGACAAGGGCACGCA 62.825 63.158 0.00 0.00 37.13 5.24
2237 3879 2.690653 TTTGCGGGAGGTGACAAGGG 62.691 60.000 0.00 0.00 0.00 3.95
2241 3883 1.896660 GCTTTTGCGGGAGGTGACA 60.897 57.895 0.00 0.00 34.86 3.58
2242 3884 2.954611 GCTTTTGCGGGAGGTGAC 59.045 61.111 0.00 0.00 34.86 3.67
2252 3901 4.233408 CTGAACGCAGGCTTTTGC 57.767 55.556 0.00 0.00 46.64 3.68
2267 3918 2.277373 GTAGCTCGTCGTCGCCTG 60.277 66.667 0.00 0.00 36.96 4.85
2330 3988 0.107897 GGTGTCACATCCGCATGGTA 60.108 55.000 5.12 0.00 33.82 3.25
2353 4012 1.112459 GCACGACGTCTTGCAAAAAG 58.888 50.000 34.15 10.49 40.37 2.27
2395 4056 1.708822 GCCGCAACCACCTAAAAATG 58.291 50.000 0.00 0.00 0.00 2.32
2404 4065 0.596341 AATCAAAACGCCGCAACCAC 60.596 50.000 0.00 0.00 0.00 4.16
2412 4073 5.054390 TGGAACTGATAAATCAAAACGCC 57.946 39.130 0.00 0.00 36.18 5.68
2415 4076 8.593492 AAAAGCTGGAACTGATAAATCAAAAC 57.407 30.769 0.00 0.00 36.18 2.43
2428 4089 5.598417 ACTGGTGAAATAAAAAGCTGGAACT 59.402 36.000 0.00 0.00 0.00 3.01
2447 4108 4.218417 GTGGATGAAATTGCTACAACTGGT 59.782 41.667 0.00 0.00 0.00 4.00
2458 4120 1.811965 TGGTGCTCGTGGATGAAATTG 59.188 47.619 0.00 0.00 0.00 2.32
2520 4198 5.331876 ACGAAATGAAAAGTTGGAACCAA 57.668 34.783 1.83 1.83 0.00 3.67
2535 4213 3.479006 GATTGTTGTGACCGACGAAATG 58.521 45.455 0.00 0.00 0.00 2.32
2542 4220 1.131303 AGGGGGATTGTTGTGACCGA 61.131 55.000 0.00 0.00 0.00 4.69
2576 4256 5.592282 TGCTACAACCTGTGAATCAAAAAGA 59.408 36.000 0.00 0.00 0.00 2.52
2671 4354 1.347707 TGGTTGAGGCTTCTGTGGTAG 59.652 52.381 0.00 0.00 0.00 3.18
2684 4368 3.327600 TCTGGCACACATGGTTGAG 57.672 52.632 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.