Multiple sequence alignment - TraesCS2A01G333100

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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 TraesCS2A01G333100 chr2A 100.000 3093 0 0 1 3093 566082383 566085475 0.000000e+00 5712.0
1 TraesCS2A01G333100 chr2D 91.006 1779 121 19 986 2749 422826985 422825231 0.000000e+00 2362.0
2 TraesCS2A01G333100 chr2D 90.968 919 46 16 69 952 422827904 422826988 0.000000e+00 1203.0
3 TraesCS2A01G333100 chr2D 92.507 347 23 2 2748 3093 422825204 422824860 7.710000e-136 494.0
4 TraesCS2A01G333100 chr2D 78.683 638 118 15 2103 2727 6181547 6180915 2.870000e-110 409.0
5 TraesCS2A01G333100 chr2B 88.794 1990 121 43 50 1987 495494774 495492835 0.000000e+00 2346.0
6 TraesCS2A01G333100 chr2B 81.279 641 101 12 2103 2727 87168268 87168905 4.600000e-138 501.0
7 TraesCS2A01G333100 chr2B 92.366 131 7 2 1981 2108 495492429 495492299 1.890000e-42 183.0
8 TraesCS2A01G333100 chr2B 90.625 64 4 1 2991 3052 688059375 688059312 1.980000e-12 84.2
9 TraesCS2A01G333100 chr7A 82.372 624 94 7 2115 2727 700634050 700634668 2.110000e-146 529.0
10 TraesCS2A01G333100 chr7A 81.731 624 98 7 2115 2727 700651674 700652292 9.900000e-140 507.0
11 TraesCS2A01G333100 chr4A 81.591 641 100 14 2102 2727 520134885 520134248 5.910000e-142 514.0
12 TraesCS2A01G333100 chr5D 81.005 637 103 13 2101 2724 547504245 547504876 9.970000e-135 490.0
13 TraesCS2A01G333100 chr5D 83.582 134 12 8 2943 3072 216977974 216977847 1.950000e-22 117.0
14 TraesCS2A01G333100 chr1B 80.929 624 107 7 2103 2717 371470120 371470740 1.670000e-132 483.0
15 TraesCS2A01G333100 chr1B 83.030 165 24 2 2932 3092 552313645 552313809 2.490000e-31 147.0
16 TraesCS2A01G333100 chr1D 80.660 636 97 22 2100 2720 8279263 8278639 1.300000e-128 470.0
17 TraesCS2A01G333100 chr1D 79.100 622 111 14 2102 2713 468560347 468560959 7.980000e-111 411.0
18 TraesCS2A01G333100 chr1A 78.415 593 110 14 2102 2683 561381701 561382286 1.350000e-98 370.0
19 TraesCS2A01G333100 chr3B 85.443 158 21 1 2937 3092 19600724 19600881 2.470000e-36 163.0
20 TraesCS2A01G333100 chr3D 87.786 131 14 1 2945 3073 341717518 341717388 5.340000e-33 152.0
21 TraesCS2A01G333100 chr4D 82.022 178 26 3 2114 2285 421524277 421524454 2.490000e-31 147.0
22 TraesCS2A01G333100 chr4D 85.542 83 10 1 2993 3073 399192072 399191990 5.500000e-13 86.1
23 TraesCS2A01G333100 chr6A 80.682 176 28 6 2102 2275 126352132 126351961 6.960000e-27 132.0
24 TraesCS2A01G333100 chr6A 84.524 84 11 1 2988 3069 209263801 209263884 7.110000e-12 82.4
25 TraesCS2A01G333100 chr5A 84.685 111 8 8 2987 3092 574718058 574717952 5.460000e-18 102.0


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 TraesCS2A01G333100 chr2A 566082383 566085475 3092 False 5712.0 5712 100.000000 1 3093 1 chr2A.!!$F1 3092
1 TraesCS2A01G333100 chr2D 422824860 422827904 3044 True 1353.0 2362 91.493667 69 3093 3 chr2D.!!$R2 3024
2 TraesCS2A01G333100 chr2D 6180915 6181547 632 True 409.0 409 78.683000 2103 2727 1 chr2D.!!$R1 624
3 TraesCS2A01G333100 chr2B 495492299 495494774 2475 True 1264.5 2346 90.580000 50 2108 2 chr2B.!!$R2 2058
4 TraesCS2A01G333100 chr2B 87168268 87168905 637 False 501.0 501 81.279000 2103 2727 1 chr2B.!!$F1 624
5 TraesCS2A01G333100 chr7A 700634050 700634668 618 False 529.0 529 82.372000 2115 2727 1 chr7A.!!$F1 612
6 TraesCS2A01G333100 chr7A 700651674 700652292 618 False 507.0 507 81.731000 2115 2727 1 chr7A.!!$F2 612
7 TraesCS2A01G333100 chr4A 520134248 520134885 637 True 514.0 514 81.591000 2102 2727 1 chr4A.!!$R1 625
8 TraesCS2A01G333100 chr5D 547504245 547504876 631 False 490.0 490 81.005000 2101 2724 1 chr5D.!!$F1 623
9 TraesCS2A01G333100 chr1B 371470120 371470740 620 False 483.0 483 80.929000 2103 2717 1 chr1B.!!$F1 614
10 TraesCS2A01G333100 chr1D 8278639 8279263 624 True 470.0 470 80.660000 2100 2720 1 chr1D.!!$R1 620
11 TraesCS2A01G333100 chr1D 468560347 468560959 612 False 411.0 411 79.100000 2102 2713 1 chr1D.!!$F1 611
12 TraesCS2A01G333100 chr1A 561381701 561382286 585 False 370.0 370 78.415000 2102 2683 1 chr1A.!!$F1 581

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
377 406 0.035439 ACCCATCAAGTAGCCAACCG 60.035 55.0 0.0 0.0 0.00 4.44 F
438 467 0.330604 ACAGGAGCATGACAAGGCAT 59.669 50.0 0.0 0.0 34.88 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1935 2004 0.102300 GTGCCACAAGGTTGGTTCAC 59.898 55.0 0.00 0.00 39.09 3.18 R
2290 2791 0.179081 GGGGTCTTAGCACGATGACC 60.179 60.0 7.13 7.13 45.86 4.02 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
27 28 5.112129 CCTTTGGCACTAGGTAAATAGGT 57.888 43.478 6.67 0.00 0.00 3.08
28 29 5.506708 CCTTTGGCACTAGGTAAATAGGTT 58.493 41.667 6.67 0.00 0.00 3.50
29 30 5.949952 CCTTTGGCACTAGGTAAATAGGTTT 59.050 40.000 6.67 0.00 0.00 3.27
30 31 6.127730 CCTTTGGCACTAGGTAAATAGGTTTG 60.128 42.308 6.67 0.00 0.00 2.93
31 32 5.508280 TGGCACTAGGTAAATAGGTTTGT 57.492 39.130 0.00 0.00 0.00 2.83
32 33 5.883180 TGGCACTAGGTAAATAGGTTTGTT 58.117 37.500 0.00 0.00 0.00 2.83
33 34 5.708230 TGGCACTAGGTAAATAGGTTTGTTG 59.292 40.000 0.00 0.00 0.00 3.33
34 35 5.124936 GGCACTAGGTAAATAGGTTTGTTGG 59.875 44.000 0.00 0.00 0.00 3.77
35 36 5.124936 GCACTAGGTAAATAGGTTTGTTGGG 59.875 44.000 0.00 0.00 0.00 4.12
36 37 6.243148 CACTAGGTAAATAGGTTTGTTGGGT 58.757 40.000 0.00 0.00 0.00 4.51
37 38 7.396418 CACTAGGTAAATAGGTTTGTTGGGTA 58.604 38.462 0.00 0.00 0.00 3.69
38 39 7.335171 CACTAGGTAAATAGGTTTGTTGGGTAC 59.665 40.741 0.00 0.00 0.00 3.34
39 40 6.203526 AGGTAAATAGGTTTGTTGGGTACA 57.796 37.500 0.00 0.00 34.12 2.90
40 41 6.796648 AGGTAAATAGGTTTGTTGGGTACAT 58.203 36.000 0.00 0.00 36.44 2.29
41 42 6.661805 AGGTAAATAGGTTTGTTGGGTACATG 59.338 38.462 0.00 0.00 36.44 3.21
42 43 6.660094 GGTAAATAGGTTTGTTGGGTACATGA 59.340 38.462 0.00 0.00 36.44 3.07
43 44 7.340999 GGTAAATAGGTTTGTTGGGTACATGAT 59.659 37.037 0.00 0.00 36.44 2.45
44 45 6.773976 AATAGGTTTGTTGGGTACATGATG 57.226 37.500 0.00 0.00 36.44 3.07
45 46 4.380843 AGGTTTGTTGGGTACATGATGA 57.619 40.909 0.00 0.00 36.44 2.92
46 47 4.335416 AGGTTTGTTGGGTACATGATGAG 58.665 43.478 0.00 0.00 36.44 2.90
47 48 4.042809 AGGTTTGTTGGGTACATGATGAGA 59.957 41.667 0.00 0.00 36.44 3.27
48 49 4.949856 GGTTTGTTGGGTACATGATGAGAT 59.050 41.667 0.00 0.00 36.44 2.75
53 54 6.244654 TGTTGGGTACATGATGAGATTTTGA 58.755 36.000 0.00 0.00 0.00 2.69
76 77 7.156673 TGACACTAGGTAAATAGGTTTGTCAC 58.843 38.462 0.00 0.00 34.21 3.67
108 110 7.809331 TGATGAGATTTTGTACACATGCTTTTC 59.191 33.333 0.00 0.00 0.00 2.29
115 117 8.445275 TTTTGTACACATGCTTTTCTTCTCTA 57.555 30.769 0.00 0.00 0.00 2.43
247 253 5.248870 TCTTTGTTTTGCTCTCCTTCAAC 57.751 39.130 0.00 0.00 0.00 3.18
317 323 8.934697 ACTGCTTCATTAGGTAGGATAAACATA 58.065 33.333 0.00 0.00 0.00 2.29
377 406 0.035439 ACCCATCAAGTAGCCAACCG 60.035 55.000 0.00 0.00 0.00 4.44
399 428 5.221561 CCGTTTCCTTTTTCCTTTATTGGGT 60.222 40.000 0.00 0.00 0.00 4.51
406 435 6.495526 CCTTTTTCCTTTATTGGGTTCTACCA 59.504 38.462 0.00 0.00 41.02 3.25
438 467 0.330604 ACAGGAGCATGACAAGGCAT 59.669 50.000 0.00 0.00 34.88 4.40
465 494 1.672356 CAAGCAGGGGACGTCAAGG 60.672 63.158 18.91 4.66 0.00 3.61
613 650 1.389784 GGCAACGAATTTTCAATGGCG 59.610 47.619 0.00 0.00 31.70 5.69
682 722 6.016360 GGGCACATGTCTATATAATTTGCACA 60.016 38.462 0.00 0.00 31.06 4.57
885 952 1.153939 CCTCGTCAGCGACCAGAAG 60.154 63.158 5.25 0.00 42.81 2.85
906 973 4.184629 AGAACGGAGAAATTTCCATCTCG 58.815 43.478 14.61 13.25 42.40 4.04
938 1005 1.406180 TGTATATGACCGGTCACCACG 59.594 52.381 38.46 0.00 43.11 4.94
941 1008 1.925415 TATGACCGGTCACCACGACG 61.925 60.000 38.46 0.00 46.42 5.12
953 1020 3.359523 ACGACGCGTCCTAGCACA 61.360 61.111 31.84 0.00 33.69 4.57
954 1021 2.577112 CGACGCGTCCTAGCACAG 60.577 66.667 31.84 12.61 36.85 3.66
955 1022 2.881352 GACGCGTCCTAGCACAGC 60.881 66.667 28.61 0.00 36.85 4.40
956 1023 4.436998 ACGCGTCCTAGCACAGCC 62.437 66.667 5.58 0.00 36.85 4.85
957 1024 4.435436 CGCGTCCTAGCACAGCCA 62.435 66.667 0.00 0.00 36.85 4.75
958 1025 2.510238 GCGTCCTAGCACAGCCAG 60.510 66.667 0.00 0.00 37.05 4.85
959 1026 2.510238 CGTCCTAGCACAGCCAGC 60.510 66.667 0.00 0.00 0.00 4.85
960 1027 2.665000 GTCCTAGCACAGCCAGCA 59.335 61.111 0.00 0.00 0.00 4.41
961 1028 1.743252 GTCCTAGCACAGCCAGCAC 60.743 63.158 0.00 0.00 0.00 4.40
962 1029 1.915266 TCCTAGCACAGCCAGCACT 60.915 57.895 0.00 0.00 0.00 4.40
963 1030 0.614697 TCCTAGCACAGCCAGCACTA 60.615 55.000 0.00 0.00 0.00 2.74
964 1031 0.467384 CCTAGCACAGCCAGCACTAT 59.533 55.000 0.00 0.00 0.00 2.12
965 1032 1.539929 CCTAGCACAGCCAGCACTATC 60.540 57.143 0.00 0.00 0.00 2.08
966 1033 1.411977 CTAGCACAGCCAGCACTATCT 59.588 52.381 0.00 0.00 0.00 1.98
967 1034 1.489481 AGCACAGCCAGCACTATCTA 58.511 50.000 0.00 0.00 0.00 1.98
968 1035 2.045524 AGCACAGCCAGCACTATCTAT 58.954 47.619 0.00 0.00 0.00 1.98
969 1036 2.141517 GCACAGCCAGCACTATCTATG 58.858 52.381 0.00 0.00 0.00 2.23
970 1037 2.141517 CACAGCCAGCACTATCTATGC 58.858 52.381 0.00 0.00 43.74 3.14
971 1038 1.764723 ACAGCCAGCACTATCTATGCA 59.235 47.619 0.00 0.00 45.92 3.96
972 1039 2.371179 ACAGCCAGCACTATCTATGCAT 59.629 45.455 3.79 3.79 45.92 3.96
973 1040 2.742589 CAGCCAGCACTATCTATGCATG 59.257 50.000 10.16 0.00 45.92 4.06
974 1041 1.467734 GCCAGCACTATCTATGCATGC 59.532 52.381 11.82 11.82 45.92 4.06
975 1042 1.730612 CCAGCACTATCTATGCATGCG 59.269 52.381 14.09 0.00 45.92 4.73
976 1043 2.410939 CAGCACTATCTATGCATGCGT 58.589 47.619 18.07 18.07 45.92 5.24
977 1044 3.578688 CAGCACTATCTATGCATGCGTA 58.421 45.455 18.39 18.39 45.92 4.42
978 1045 3.611549 CAGCACTATCTATGCATGCGTAG 59.388 47.826 32.47 32.47 45.92 3.51
1102 1169 6.226787 ACACCATGAGAGTAAGAAGTTCTTG 58.773 40.000 25.27 8.84 37.29 3.02
1120 1187 4.651778 TCTTGGAGTCCAGTTTATGTTGG 58.348 43.478 12.67 0.00 33.81 3.77
1275 1344 3.215616 CGTCAGCGGTAAGTACGAG 57.784 57.895 0.00 0.00 35.66 4.18
1279 1348 2.105729 GCGGTAAGTACGAGCCCC 59.894 66.667 0.00 0.00 0.00 5.80
1281 1350 2.105729 GGTAAGTACGAGCCCCGC 59.894 66.667 0.00 0.00 43.32 6.13
1283 1352 3.520862 TAAGTACGAGCCCCGCGG 61.521 66.667 21.04 21.04 43.32 6.46
1293 1362 4.609018 CCCCGCGGCTGATCGATT 62.609 66.667 22.85 0.00 0.00 3.34
1294 1363 3.038417 CCCGCGGCTGATCGATTC 61.038 66.667 22.85 0.00 0.00 2.52
1295 1364 2.028190 CCGCGGCTGATCGATTCT 59.972 61.111 14.67 0.00 0.00 2.40
1296 1365 1.592669 CCGCGGCTGATCGATTCTT 60.593 57.895 14.67 0.00 0.00 2.52
1297 1366 1.552348 CCGCGGCTGATCGATTCTTC 61.552 60.000 14.67 0.00 0.00 2.87
1312 1381 0.826715 TCTTCCTTCCTCTGCATCCG 59.173 55.000 0.00 0.00 0.00 4.18
1334 1403 3.257375 GGTGAATTAAACTGGGTGGGTTC 59.743 47.826 0.00 0.00 0.00 3.62
1431 1500 2.738000 CGAGAGCCATCTGACCAAGAAG 60.738 54.545 0.00 0.00 38.79 2.85
1434 1503 2.169352 GAGCCATCTGACCAAGAAGCTA 59.831 50.000 0.00 0.00 44.46 3.32
1573 1642 1.024579 GTACCACTTGCATCCCACGG 61.025 60.000 0.00 0.00 0.00 4.94
1924 1993 3.733727 CCAATGTTTGCCGTTTCAAGTAC 59.266 43.478 0.00 0.00 0.00 2.73
1925 1994 4.499019 CCAATGTTTGCCGTTTCAAGTACT 60.499 41.667 0.00 0.00 0.00 2.73
1935 2004 6.077838 GCCGTTTCAAGTACTGTATTTCAAG 58.922 40.000 0.00 0.00 0.00 3.02
1946 2015 5.445964 ACTGTATTTCAAGTGAACCAACCT 58.554 37.500 0.00 0.00 33.13 3.50
1993 2474 4.537015 GCACTACATTGTGGTGTTCTTTC 58.463 43.478 27.36 11.38 44.82 2.62
2004 2485 3.001838 TGGTGTTCTTTCGTTCATTCGTG 59.998 43.478 0.00 0.00 0.00 4.35
2043 2524 8.850454 TTTGAATTTAGTGCACAAAGTTAGTC 57.150 30.769 21.04 7.19 0.00 2.59
2084 2565 9.543018 CTGAACGAATTTTAAGATAAAGGTGTC 57.457 33.333 0.00 0.00 0.00 3.67
2206 2695 0.244450 CCGTAAACCACCTAGCGACA 59.756 55.000 0.00 0.00 0.00 4.35
2275 2776 3.486875 GGAGTCGGACAAAACTTGTTGTG 60.487 47.826 11.27 2.41 45.52 3.33
2290 2791 4.280436 TGTTGTGGTATACAGTTGGGAG 57.720 45.455 5.01 0.00 41.10 4.30
2305 2806 1.112113 GGGAGGTCATCGTGCTAAGA 58.888 55.000 0.00 0.00 0.00 2.10
2324 2825 0.623723 ACCCCATAGAACCAACGCAT 59.376 50.000 0.00 0.00 0.00 4.73
2336 2837 4.454728 ACCAACGCATCAAATAAGCAAT 57.545 36.364 0.00 0.00 0.00 3.56
2337 2838 4.423732 ACCAACGCATCAAATAAGCAATC 58.576 39.130 0.00 0.00 0.00 2.67
2338 2839 4.158394 ACCAACGCATCAAATAAGCAATCT 59.842 37.500 0.00 0.00 0.00 2.40
2343 2844 4.036027 CGCATCAAATAAGCAATCTCCACT 59.964 41.667 0.00 0.00 0.00 4.00
2357 2864 1.942776 TCCACTGATGAAGAGGAGCA 58.057 50.000 0.00 0.00 40.39 4.26
2358 2865 2.259917 TCCACTGATGAAGAGGAGCAA 58.740 47.619 0.00 0.00 40.39 3.91
2389 2896 3.650942 AGGATCCAACCTAAAGACACACA 59.349 43.478 15.82 0.00 38.65 3.72
2477 2984 1.361271 CATGCCCATTGACGATGCC 59.639 57.895 0.00 0.00 34.25 4.40
2489 2996 0.179037 ACGATGCCAGATCCACCATG 60.179 55.000 0.00 0.00 0.00 3.66
2605 3116 4.684703 CGAAGACACATCTAAAAACGGAGT 59.315 41.667 0.00 0.00 36.98 3.85
2620 3131 1.003233 GAGTCCTCCCACTGGCAAC 60.003 63.158 0.00 0.00 0.00 4.17
2653 3164 1.027357 CATGCACCCATGGCTCTAAC 58.973 55.000 6.09 0.00 44.07 2.34
2670 3181 1.745320 AACGCCACTGAAGACGAGGT 61.745 55.000 0.00 0.00 0.00 3.85
2743 3256 1.203441 AGGTTCATGCCTGAGGAGCA 61.203 55.000 0.65 0.00 45.94 4.26
2770 3312 5.006941 CCTTGTGAAAACAAATTTGAGCCAG 59.993 40.000 24.64 8.55 0.00 4.85
2776 3318 4.861102 AACAAATTTGAGCCAGGAGAAG 57.139 40.909 24.64 0.00 0.00 2.85
2782 3324 3.458044 TTGAGCCAGGAGAAGTAGAGA 57.542 47.619 0.00 0.00 0.00 3.10
2783 3325 3.458044 TGAGCCAGGAGAAGTAGAGAA 57.542 47.619 0.00 0.00 0.00 2.87
2796 3338 5.703130 AGAAGTAGAGAAAACCAATCTGTGC 59.297 40.000 0.00 0.00 0.00 4.57
2803 3345 4.590222 AGAAAACCAATCTGTGCTTGGATT 59.410 37.500 8.55 0.51 44.95 3.01
2808 3350 5.018809 ACCAATCTGTGCTTGGATTGTTAT 58.981 37.500 8.55 0.83 44.95 1.89
2836 3378 7.164230 GATAGTGGTATCCTAGTCAATCAGG 57.836 44.000 0.00 0.00 30.28 3.86
2845 3387 4.782691 TCCTAGTCAATCAGGGATCAAACA 59.217 41.667 0.00 0.00 32.40 2.83
2849 3391 5.191426 AGTCAATCAGGGATCAAACATCAG 58.809 41.667 0.00 0.00 0.00 2.90
2864 3406 2.559668 ACATCAGGTTGCCACTTTGATG 59.440 45.455 22.38 22.38 43.36 3.07
2939 3481 1.676014 CCACTAGTGGCTAAGTGGTGC 60.676 57.143 28.48 0.00 44.73 5.01
2953 3495 2.292292 AGTGGTGCGGTGAACAAATTAC 59.708 45.455 0.00 0.00 0.00 1.89
2960 3502 3.003897 GCGGTGAACAAATTACAGTTGGA 59.996 43.478 0.00 0.00 0.00 3.53
3022 3564 9.234827 TGAGCATTCATGGTATAATTTCATAGG 57.765 33.333 0.00 0.00 38.85 2.57
3046 3588 8.654997 AGGCATTATGTCTGTGATAAGTAGATT 58.345 33.333 0.00 0.00 26.79 2.40
3079 3621 7.011950 CCAACTGCATCTATTATTAACGTTCCA 59.988 37.037 2.82 0.00 0.00 3.53
3085 3627 8.774586 GCATCTATTATTAACGTTCCACTCAAT 58.225 33.333 2.82 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.112129 ACCTATTTACCTAGTGCCAAAGG 57.888 43.478 0.00 0.00 38.93 3.11
6 7 6.433093 ACAAACCTATTTACCTAGTGCCAAAG 59.567 38.462 0.00 0.00 0.00 2.77
8 9 5.883180 ACAAACCTATTTACCTAGTGCCAA 58.117 37.500 0.00 0.00 0.00 4.52
9 10 5.508280 ACAAACCTATTTACCTAGTGCCA 57.492 39.130 0.00 0.00 0.00 4.92
10 11 5.124936 CCAACAAACCTATTTACCTAGTGCC 59.875 44.000 0.00 0.00 0.00 5.01
11 12 5.124936 CCCAACAAACCTATTTACCTAGTGC 59.875 44.000 0.00 0.00 0.00 4.40
12 13 6.243148 ACCCAACAAACCTATTTACCTAGTG 58.757 40.000 0.00 0.00 0.00 2.74
13 14 6.458630 ACCCAACAAACCTATTTACCTAGT 57.541 37.500 0.00 0.00 0.00 2.57
14 15 7.396418 TGTACCCAACAAACCTATTTACCTAG 58.604 38.462 0.00 0.00 34.29 3.02
15 16 7.327064 TGTACCCAACAAACCTATTTACCTA 57.673 36.000 0.00 0.00 34.29 3.08
16 17 6.203526 TGTACCCAACAAACCTATTTACCT 57.796 37.500 0.00 0.00 34.29 3.08
17 18 6.660094 TCATGTACCCAACAAACCTATTTACC 59.340 38.462 0.00 0.00 42.70 2.85
18 19 7.690952 TCATGTACCCAACAAACCTATTTAC 57.309 36.000 0.00 0.00 42.70 2.01
19 20 8.110271 TCATCATGTACCCAACAAACCTATTTA 58.890 33.333 0.00 0.00 42.70 1.40
20 21 6.951198 TCATCATGTACCCAACAAACCTATTT 59.049 34.615 0.00 0.00 42.70 1.40
21 22 6.489603 TCATCATGTACCCAACAAACCTATT 58.510 36.000 0.00 0.00 42.70 1.73
22 23 6.069673 TCTCATCATGTACCCAACAAACCTAT 60.070 38.462 0.00 0.00 42.70 2.57
23 24 5.249622 TCTCATCATGTACCCAACAAACCTA 59.750 40.000 0.00 0.00 42.70 3.08
24 25 4.042809 TCTCATCATGTACCCAACAAACCT 59.957 41.667 0.00 0.00 42.70 3.50
25 26 4.331968 TCTCATCATGTACCCAACAAACC 58.668 43.478 0.00 0.00 42.70 3.27
26 27 6.515272 AATCTCATCATGTACCCAACAAAC 57.485 37.500 0.00 0.00 42.70 2.93
27 28 7.232330 TCAAAATCTCATCATGTACCCAACAAA 59.768 33.333 0.00 0.00 42.70 2.83
28 29 6.718912 TCAAAATCTCATCATGTACCCAACAA 59.281 34.615 0.00 0.00 42.70 2.83
29 30 6.150976 GTCAAAATCTCATCATGTACCCAACA 59.849 38.462 0.00 0.00 43.86 3.33
30 31 6.150976 TGTCAAAATCTCATCATGTACCCAAC 59.849 38.462 0.00 0.00 0.00 3.77
31 32 6.150976 GTGTCAAAATCTCATCATGTACCCAA 59.849 38.462 0.00 0.00 0.00 4.12
32 33 5.647658 GTGTCAAAATCTCATCATGTACCCA 59.352 40.000 0.00 0.00 0.00 4.51
33 34 5.882557 AGTGTCAAAATCTCATCATGTACCC 59.117 40.000 0.00 0.00 0.00 3.69
34 35 6.992063 AGTGTCAAAATCTCATCATGTACC 57.008 37.500 0.00 0.00 0.00 3.34
35 36 7.766278 ACCTAGTGTCAAAATCTCATCATGTAC 59.234 37.037 0.00 0.00 0.00 2.90
36 37 7.851228 ACCTAGTGTCAAAATCTCATCATGTA 58.149 34.615 0.00 0.00 0.00 2.29
37 38 6.715280 ACCTAGTGTCAAAATCTCATCATGT 58.285 36.000 0.00 0.00 0.00 3.21
38 39 8.722480 TTACCTAGTGTCAAAATCTCATCATG 57.278 34.615 0.00 0.00 0.00 3.07
39 40 9.911788 ATTTACCTAGTGTCAAAATCTCATCAT 57.088 29.630 0.00 0.00 0.00 2.45
42 43 9.838339 CCTATTTACCTAGTGTCAAAATCTCAT 57.162 33.333 0.00 0.00 0.00 2.90
43 44 8.822805 ACCTATTTACCTAGTGTCAAAATCTCA 58.177 33.333 0.00 0.00 0.00 3.27
44 45 9.668497 AACCTATTTACCTAGTGTCAAAATCTC 57.332 33.333 0.00 0.00 0.00 2.75
47 48 9.582648 ACAAACCTATTTACCTAGTGTCAAAAT 57.417 29.630 0.00 0.00 0.00 1.82
48 49 8.983702 ACAAACCTATTTACCTAGTGTCAAAA 57.016 30.769 0.00 0.00 0.00 2.44
53 54 6.161381 CGTGACAAACCTATTTACCTAGTGT 58.839 40.000 0.00 0.00 0.00 3.55
76 77 7.289587 TGTGTACAAAATCTCATCATGTACG 57.710 36.000 0.00 0.00 45.74 3.67
108 110 7.329717 AGAGCTGTACGTGAAATTTTAGAGAAG 59.670 37.037 0.00 0.00 0.00 2.85
115 117 4.385825 TGGAGAGCTGTACGTGAAATTTT 58.614 39.130 0.00 0.00 0.00 1.82
247 253 0.326264 CAGAAACCACTCTGGGGAGG 59.674 60.000 0.00 0.00 43.37 4.30
326 335 4.760530 ATAATTGCAGGTCAGCTCTACA 57.239 40.909 0.00 0.00 34.99 2.74
355 364 2.359900 GTTGGCTACTTGATGGGTGAG 58.640 52.381 0.00 0.00 0.00 3.51
377 406 7.506114 AGAACCCAATAAAGGAAAAAGGAAAC 58.494 34.615 0.00 0.00 0.00 2.78
399 428 6.667848 TCCTGTCATCTTTATCACTGGTAGAA 59.332 38.462 0.00 0.00 31.55 2.10
406 435 5.129980 TCATGCTCCTGTCATCTTTATCACT 59.870 40.000 0.00 0.00 0.00 3.41
613 650 6.199937 TCTCAAGGAAAAAGCAATCATAGC 57.800 37.500 0.00 0.00 0.00 2.97
885 952 4.181578 TCGAGATGGAAATTTCTCCGTTC 58.818 43.478 17.42 8.58 38.44 3.95
906 973 6.603997 ACCGGTCATATACATCTCCTATCTTC 59.396 42.308 0.00 0.00 0.00 2.87
919 986 1.677576 TCGTGGTGACCGGTCATATAC 59.322 52.381 38.11 30.89 42.18 1.47
938 1005 2.881352 GCTGTGCTAGGACGCGTC 60.881 66.667 30.67 30.67 0.00 5.19
941 1008 2.510238 CTGGCTGTGCTAGGACGC 60.510 66.667 18.01 18.01 33.47 5.19
953 1020 2.874861 GCATGCATAGATAGTGCTGGCT 60.875 50.000 14.21 0.00 42.92 4.75
954 1021 1.467734 GCATGCATAGATAGTGCTGGC 59.532 52.381 14.21 0.00 42.92 4.85
955 1022 1.730612 CGCATGCATAGATAGTGCTGG 59.269 52.381 19.57 0.00 42.92 4.85
956 1023 2.410939 ACGCATGCATAGATAGTGCTG 58.589 47.619 19.57 0.00 42.92 4.41
957 1024 2.827800 ACGCATGCATAGATAGTGCT 57.172 45.000 19.57 0.00 42.92 4.40
958 1025 2.346847 GCTACGCATGCATAGATAGTGC 59.653 50.000 24.12 4.85 42.81 4.40
959 1026 2.595977 CGCTACGCATGCATAGATAGTG 59.404 50.000 24.12 14.80 0.00 2.74
960 1027 2.868662 CGCTACGCATGCATAGATAGT 58.131 47.619 24.12 10.88 0.00 2.12
978 1045 3.251043 GCTGTAGAGCTCGTGCGC 61.251 66.667 8.37 0.00 45.42 6.09
979 1046 2.580867 GGCTGTAGAGCTCGTGCG 60.581 66.667 12.15 0.00 45.44 5.34
980 1047 0.385751 TATGGCTGTAGAGCTCGTGC 59.614 55.000 12.15 10.94 45.44 5.34
981 1048 1.598183 CGTATGGCTGTAGAGCTCGTG 60.598 57.143 12.15 1.09 45.44 4.35
982 1049 0.663688 CGTATGGCTGTAGAGCTCGT 59.336 55.000 12.15 6.12 45.44 4.18
983 1050 0.039978 CCGTATGGCTGTAGAGCTCG 60.040 60.000 12.15 11.01 45.44 5.03
1102 1169 4.015872 TCACCAACATAAACTGGACTCC 57.984 45.455 0.00 0.00 36.49 3.85
1120 1187 4.032217 CAGATAAACAGACAGACGCATCAC 59.968 45.833 0.00 0.00 0.00 3.06
1279 1348 1.552348 GGAAGAATCGATCAGCCGCG 61.552 60.000 0.00 0.00 0.00 6.46
1281 1350 2.131183 GAAGGAAGAATCGATCAGCCG 58.869 52.381 0.00 0.00 0.00 5.52
1283 1352 3.069443 AGAGGAAGGAAGAATCGATCAGC 59.931 47.826 0.00 0.00 0.00 4.26
1284 1353 4.619973 CAGAGGAAGGAAGAATCGATCAG 58.380 47.826 0.00 0.00 0.00 2.90
1285 1354 3.181471 GCAGAGGAAGGAAGAATCGATCA 60.181 47.826 0.00 0.00 0.00 2.92
1286 1355 3.181471 TGCAGAGGAAGGAAGAATCGATC 60.181 47.826 0.00 0.00 0.00 3.69
1287 1356 2.768527 TGCAGAGGAAGGAAGAATCGAT 59.231 45.455 0.00 0.00 0.00 3.59
1289 1358 2.680312 TGCAGAGGAAGGAAGAATCG 57.320 50.000 0.00 0.00 0.00 3.34
1290 1359 3.475575 GGATGCAGAGGAAGGAAGAATC 58.524 50.000 0.00 0.00 0.00 2.52
1291 1360 2.158842 CGGATGCAGAGGAAGGAAGAAT 60.159 50.000 0.00 0.00 0.00 2.40
1293 1362 0.826715 CGGATGCAGAGGAAGGAAGA 59.173 55.000 0.00 0.00 0.00 2.87
1294 1363 0.179062 CCGGATGCAGAGGAAGGAAG 60.179 60.000 0.00 0.00 0.00 3.46
1295 1364 0.909610 ACCGGATGCAGAGGAAGGAA 60.910 55.000 9.46 0.00 0.00 3.36
1296 1365 1.306141 ACCGGATGCAGAGGAAGGA 60.306 57.895 9.46 0.00 0.00 3.36
1297 1366 1.153289 CACCGGATGCAGAGGAAGG 60.153 63.158 9.46 2.47 0.00 3.46
1312 1381 2.884320 ACCCACCCAGTTTAATTCACC 58.116 47.619 0.00 0.00 0.00 4.02
1334 1403 1.001974 TCGACACCACTCCTGAATTGG 59.998 52.381 0.00 0.00 36.39 3.16
1431 1500 0.178301 CCCCGACCTCCTTCTTTAGC 59.822 60.000 0.00 0.00 0.00 3.09
1434 1503 0.910088 CCTCCCCGACCTCCTTCTTT 60.910 60.000 0.00 0.00 0.00 2.52
1500 1569 4.564110 GTGCCCGGCAGATACCCC 62.564 72.222 13.92 0.00 40.08 4.95
1674 1743 1.007618 GGACGCGCTGGGATAGTAC 60.008 63.158 5.73 0.00 0.00 2.73
1924 1993 6.183360 ACAAGGTTGGTTCACTTGAAATACAG 60.183 38.462 10.25 0.00 43.13 2.74
1925 1994 5.654650 ACAAGGTTGGTTCACTTGAAATACA 59.345 36.000 10.25 0.00 43.13 2.29
1935 2004 0.102300 GTGCCACAAGGTTGGTTCAC 59.898 55.000 0.00 0.00 39.09 3.18
1946 2015 2.147958 GTTTCCATCGTAGTGCCACAA 58.852 47.619 0.00 0.00 0.00 3.33
1993 2474 2.069273 AGGAAGAAGCACGAATGAACG 58.931 47.619 0.00 0.00 39.31 3.95
2004 2485 8.919661 CACTAAATTCAAATTCAAGGAAGAAGC 58.080 33.333 0.00 0.00 0.00 3.86
2043 2524 0.602638 TTCAGGTGTACAAGCCGCTG 60.603 55.000 0.00 0.00 0.00 5.18
2135 2621 6.750039 GGTTTTCGTTGTACATCCATAATTGG 59.250 38.462 0.00 0.00 45.15 3.16
2206 2695 1.711206 GTCTTCGGCTCGCTTTAGTT 58.289 50.000 0.00 0.00 0.00 2.24
2275 2776 3.243771 CGATGACCTCCCAACTGTATACC 60.244 52.174 0.00 0.00 0.00 2.73
2290 2791 0.179081 GGGGTCTTAGCACGATGACC 60.179 60.000 7.13 7.13 45.86 4.02
2305 2806 0.623723 ATGCGTTGGTTCTATGGGGT 59.376 50.000 0.00 0.00 0.00 4.95
2324 2825 6.417258 TCATCAGTGGAGATTGCTTATTTGA 58.583 36.000 0.00 0.00 0.00 2.69
2338 2839 1.942776 TGCTCCTCTTCATCAGTGGA 58.057 50.000 0.00 0.00 42.01 4.02
2343 2844 6.550938 TTAGATCTTTGCTCCTCTTCATCA 57.449 37.500 0.00 0.00 0.00 3.07
2379 2886 6.092944 TCGTTTGTCTATGTTTGTGTGTCTTT 59.907 34.615 0.00 0.00 0.00 2.52
2389 2896 5.045215 TCTGTTCGTCGTTTGTCTATGTTT 58.955 37.500 0.00 0.00 0.00 2.83
2477 2984 0.182061 CTGTCCCCATGGTGGATCTG 59.818 60.000 20.81 14.90 40.96 2.90
2605 3116 3.160585 CTGTTGCCAGTGGGAGGA 58.839 61.111 12.15 0.00 35.59 3.71
2620 3131 2.203252 CATGGTGGATCCCGGCTG 60.203 66.667 9.90 0.00 34.77 4.85
2621 3132 4.195334 GCATGGTGGATCCCGGCT 62.195 66.667 9.90 0.00 33.38 5.52
2648 3159 1.199327 CTCGTCTTCAGTGGCGTTAGA 59.801 52.381 0.00 0.00 0.00 2.10
2653 3164 1.734477 CACCTCGTCTTCAGTGGCG 60.734 63.158 0.00 0.00 0.00 5.69
2743 3256 5.007921 GCTCAAATTTGTTTTCACAAGGCAT 59.992 36.000 17.47 0.00 43.92 4.40
2770 3312 6.370166 CACAGATTGGTTTTCTCTACTTCTCC 59.630 42.308 0.00 0.00 0.00 3.71
2776 3318 5.335191 CCAAGCACAGATTGGTTTTCTCTAC 60.335 44.000 5.90 0.00 43.64 2.59
2782 3324 5.396660 AACAATCCAAGCACAGATTGGTTTT 60.397 36.000 20.08 6.56 45.81 2.43
2783 3325 4.101430 AACAATCCAAGCACAGATTGGTTT 59.899 37.500 20.08 8.82 45.81 3.27
2836 3378 2.094545 GTGGCAACCTGATGTTTGATCC 60.095 50.000 0.00 0.00 34.00 3.36
2845 3387 2.821969 GACATCAAAGTGGCAACCTGAT 59.178 45.455 1.33 1.33 32.28 2.90
2849 3391 6.509418 TTATAAGACATCAAAGTGGCAACC 57.491 37.500 0.00 0.00 0.00 3.77
2864 3406 5.760743 GCCTCCCACTGAATCTTTATAAGAC 59.239 44.000 0.00 0.00 41.01 3.01
2880 3422 1.463674 ATGAAAACATCGCCTCCCAC 58.536 50.000 0.00 0.00 0.00 4.61
2939 3481 4.035792 TGTCCAACTGTAATTTGTTCACCG 59.964 41.667 0.00 0.00 0.00 4.94
2953 3495 5.953183 TGCAATTTAATAGCTGTCCAACTG 58.047 37.500 0.00 0.00 0.00 3.16
2999 3541 7.829725 TGCCTATGAAATTATACCATGAATGC 58.170 34.615 0.00 0.00 0.00 3.56
3015 3557 8.432013 ACTTATCACAGACATAATGCCTATGAA 58.568 33.333 9.30 0.00 40.02 2.57
3021 3563 8.715998 CAATCTACTTATCACAGACATAATGCC 58.284 37.037 0.00 0.00 0.00 4.40
3022 3564 9.265901 ACAATCTACTTATCACAGACATAATGC 57.734 33.333 0.00 0.00 0.00 3.56
3056 3598 7.272978 AGTGGAACGTTAATAATAGATGCAGT 58.727 34.615 0.00 0.00 45.86 4.40


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

AutoCloner maintained by Alex Coulton.