Multiple sequence alignment - TraesCS5D01G430300

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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 TraesCS5D01G430300 chr5D 100.000 3562 0 0 1 3562 487600882 487597321 0.000000e+00 6578.0
1 TraesCS5D01G430300 chr5D 92.364 1100 75 4 907 1997 487836890 487835791 0.000000e+00 1557.0
2 TraesCS5D01G430300 chr5D 87.173 382 38 3 3 373 394597596 394597977 1.180000e-114 424.0
3 TraesCS5D01G430300 chr5D 81.734 542 57 12 3046 3562 564448130 564447606 7.110000e-112 414.0
4 TraesCS5D01G430300 chr5D 86.494 385 40 4 1 374 368324002 368324385 2.560000e-111 412.0
5 TraesCS5D01G430300 chr5D 79.952 419 48 18 3178 3562 376942966 376943382 3.500000e-70 276.0
6 TraesCS5D01G430300 chr5D 94.118 136 8 0 2314 2449 487834352 487834217 1.300000e-49 207.0
7 TraesCS5D01G430300 chr5D 79.668 241 21 17 2024 2260 487835794 487835578 7.970000e-32 148.0
8 TraesCS5D01G430300 chr5A 93.821 2282 107 15 590 2848 608362163 608359893 0.000000e+00 3402.0
9 TraesCS5D01G430300 chr5A 92.463 1088 70 7 920 1997 608447785 608446700 0.000000e+00 1544.0
10 TraesCS5D01G430300 chr5A 87.583 604 56 10 1 591 608362800 608362203 0.000000e+00 682.0
11 TraesCS5D01G430300 chr5A 88.127 379 41 3 1 375 515496733 515496355 7.010000e-122 448.0
12 TraesCS5D01G430300 chr5A 82.322 379 41 14 3108 3461 480178566 480178189 4.470000e-79 305.0
13 TraesCS5D01G430300 chr5A 78.151 357 50 21 1639 1984 42259926 42260265 6.030000e-48 202.0
14 TraesCS5D01G430300 chr5A 78.486 251 23 17 2013 2260 608446717 608446495 6.200000e-28 135.0
15 TraesCS5D01G430300 chr5B 92.102 2393 107 45 590 2912 600135590 600133210 0.000000e+00 3297.0
16 TraesCS5D01G430300 chr5B 92.029 1104 73 9 907 1997 600338639 600337538 0.000000e+00 1537.0
17 TraesCS5D01G430300 chr5B 88.980 608 50 4 1 591 600136240 600135633 0.000000e+00 736.0
18 TraesCS5D01G430300 chr5B 84.543 427 49 12 3044 3461 692745520 692745938 1.190000e-109 407.0
19 TraesCS5D01G430300 chr5B 86.100 259 15 1 2191 2449 600337357 600337120 3.530000e-65 259.0
20 TraesCS5D01G430300 chr5B 77.060 449 66 19 3149 3562 354503154 354502708 1.290000e-54 224.0
21 TraesCS5D01G430300 chr5B 90.541 74 4 1 2013 2083 600337555 600337482 1.050000e-15 95.3
22 TraesCS5D01G430300 chr7A 86.279 430 50 7 3042 3464 136538007 136537580 3.240000e-125 459.0
23 TraesCS5D01G430300 chr4B 87.500 384 37 3 1 373 639085949 639086332 1.960000e-117 433.0
24 TraesCS5D01G430300 chr4B 83.295 431 60 5 3046 3464 44080102 44079672 1.550000e-103 387.0
25 TraesCS5D01G430300 chr4B 78.557 485 66 21 3105 3562 640021818 640022291 5.820000e-73 285.0
26 TraesCS5D01G430300 chr4B 80.328 122 22 2 2319 2439 464953857 464953737 1.360000e-14 91.6
27 TraesCS5D01G430300 chr4D 85.142 424 49 9 3044 3461 374784883 374784468 4.250000e-114 422.0
28 TraesCS5D01G430300 chr4D 80.800 125 22 2 2316 2439 378449413 378449290 2.930000e-16 97.1
29 TraesCS5D01G430300 chr6D 84.706 425 57 5 3044 3464 311807070 311806650 5.500000e-113 418.0
30 TraesCS5D01G430300 chr6D 90.385 52 2 3 636 687 58046110 58046158 8.250000e-07 65.8
31 TraesCS5D01G430300 chr1D 86.269 386 42 3 1 375 46490764 46491149 3.310000e-110 409.0
32 TraesCS5D01G430300 chr1D 84.400 250 27 4 141 378 491756946 491756697 5.950000e-58 235.0
33 TraesCS5D01G430300 chr1D 92.157 51 3 1 712 761 394271113 394271163 1.770000e-08 71.3
34 TraesCS5D01G430300 chr1A 86.234 385 42 8 1 374 46312339 46312723 1.190000e-109 407.0
35 TraesCS5D01G430300 chr1A 79.144 561 73 10 3043 3562 574508125 574507568 7.320000e-92 348.0
36 TraesCS5D01G430300 chr2B 85.901 383 42 4 1 372 639247398 639247779 7.170000e-107 398.0
37 TraesCS5D01G430300 chr2B 88.024 334 35 3 3135 3464 198274947 198274615 1.200000e-104 390.0
38 TraesCS5D01G430300 chr2B 82.160 426 60 9 3041 3461 423823592 423824006 5.660000e-93 351.0
39 TraesCS5D01G430300 chr2B 78.858 473 65 9 3112 3552 759544408 759544877 1.620000e-73 287.0
40 TraesCS5D01G430300 chrUn 85.523 373 41 4 12 373 82327434 82327804 9.330000e-101 377.0
41 TraesCS5D01G430300 chrUn 85.523 373 41 4 12 373 82333658 82334028 9.330000e-101 377.0
42 TraesCS5D01G430300 chrUn 85.637 369 42 3 19 376 234380386 234380018 9.330000e-101 377.0
43 TraesCS5D01G430300 chrUn 85.637 369 42 3 19 376 327347213 327346845 9.330000e-101 377.0
44 TraesCS5D01G430300 chr4A 84.051 395 56 6 3076 3464 515882072 515881679 1.210000e-99 374.0
45 TraesCS5D01G430300 chr4A 80.672 119 21 2 2313 2430 86991425 86991542 1.360000e-14 91.6
46 TraesCS5D01G430300 chr3A 82.974 417 59 7 3048 3460 69061778 69062186 2.020000e-97 366.0
47 TraesCS5D01G430300 chr3A 81.681 464 60 15 3113 3553 505527816 505528277 2.610000e-96 363.0
48 TraesCS5D01G430300 chr2D 88.489 278 31 1 1 277 20375439 20375716 5.700000e-88 335.0
49 TraesCS5D01G430300 chr2D 78.664 539 65 14 3046 3552 63917216 63917736 2.670000e-81 313.0


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 TraesCS5D01G430300 chr5D 487597321 487600882 3561 True 6578.000000 6578 100.000000 1 3562 1 chr5D.!!$R1 3561
1 TraesCS5D01G430300 chr5D 487834217 487836890 2673 True 637.333333 1557 88.716667 907 2449 3 chr5D.!!$R3 1542
2 TraesCS5D01G430300 chr5D 564447606 564448130 524 True 414.000000 414 81.734000 3046 3562 1 chr5D.!!$R2 516
3 TraesCS5D01G430300 chr5A 608359893 608362800 2907 True 2042.000000 3402 90.702000 1 2848 2 chr5A.!!$R3 2847
4 TraesCS5D01G430300 chr5A 608446495 608447785 1290 True 839.500000 1544 85.474500 920 2260 2 chr5A.!!$R4 1340
5 TraesCS5D01G430300 chr5B 600133210 600136240 3030 True 2016.500000 3297 90.541000 1 2912 2 chr5B.!!$R2 2911
6 TraesCS5D01G430300 chr5B 600337120 600338639 1519 True 630.433333 1537 89.556667 907 2449 3 chr5B.!!$R3 1542
7 TraesCS5D01G430300 chr1A 574507568 574508125 557 True 348.000000 348 79.144000 3043 3562 1 chr1A.!!$R1 519
8 TraesCS5D01G430300 chr2D 63917216 63917736 520 False 313.000000 313 78.664000 3046 3552 1 chr2D.!!$F2 506

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
264 266 0.331616 ACCCTTGCTTGTATGGGACC 59.668 55.000 14.64 0.0 42.11 4.46 F
295 307 1.192428 GAGGCTTCGAAACTCCCCTA 58.808 55.000 15.21 0.0 0.00 3.53 F
513 531 1.343465 GCCGGTATATAGTGTGGCAGT 59.657 52.381 1.90 0.0 42.03 4.40 F
2378 3715 0.104304 TATTCCGCGGGAAGAAGCTC 59.896 55.000 27.83 0.0 45.48 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2103 2203 2.893637 TGCAAGCGAAGGTAGAGAATC 58.106 47.619 0.00 0.00 37.06 2.52 R
2360 3697 1.153349 GAGCTTCTTCCCGCGGAAT 60.153 57.895 30.73 3.33 41.23 3.01 R
2426 3763 2.651361 CGGTCGTGCTCCTTGACT 59.349 61.111 0.00 0.00 33.21 3.41 R
3500 4921 1.001641 GGTGGAGCAGCAGGAACAT 60.002 57.895 0.00 0.00 0.00 2.71 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
33 34 2.223829 CCTATGGAAGCGAAGATGACGT 60.224 50.000 0.00 0.00 0.00 4.34
42 43 1.135112 CGAAGATGACGTCCATGGACA 60.135 52.381 37.42 23.07 44.77 4.02
71 72 0.601311 GACTTGCGCTTCACTGGTCT 60.601 55.000 9.73 0.00 0.00 3.85
79 80 2.772287 GCTTCACTGGTCTAACTTGCT 58.228 47.619 0.00 0.00 0.00 3.91
94 95 3.290710 ACTTGCTGTTGGTTGTGAAGAT 58.709 40.909 0.00 0.00 0.00 2.40
176 178 4.708177 CGAACCAGGTCAATGGATTAGAT 58.292 43.478 0.00 0.00 43.57 1.98
189 191 5.651387 TGGATTAGATGGATTCTAGCTCG 57.349 43.478 0.00 0.00 38.19 5.03
264 266 0.331616 ACCCTTGCTTGTATGGGACC 59.668 55.000 14.64 0.00 42.11 4.46
293 305 4.619852 GAGGCTTCGAAACTCCCC 57.380 61.111 15.21 4.82 0.00 4.81
295 307 1.192428 GAGGCTTCGAAACTCCCCTA 58.808 55.000 15.21 0.00 0.00 3.53
322 334 6.127869 GGAAATAGCTAGCATCGTCATCTCTA 60.128 42.308 18.83 0.00 0.00 2.43
356 368 5.012354 ACCATGGCTGATGAATGAAAAGTTT 59.988 36.000 13.04 0.00 33.31 2.66
451 469 5.118357 TGCGCAACATCACAAACATAAATTC 59.882 36.000 8.16 0.00 0.00 2.17
452 470 5.118357 GCGCAACATCACAAACATAAATTCA 59.882 36.000 0.30 0.00 0.00 2.57
483 501 2.103771 ACATCTTGATGAGGGTCGATGG 59.896 50.000 16.43 0.00 34.20 3.51
513 531 1.343465 GCCGGTATATAGTGTGGCAGT 59.657 52.381 1.90 0.00 42.03 4.40
612 674 7.567622 ACTCAGAGCTTTACAGGGGTATTATTA 59.432 37.037 0.00 0.00 0.00 0.98
672 734 4.072131 GGCTATCAGTTGGAAAAGTGACA 58.928 43.478 0.00 0.00 35.19 3.58
676 738 1.681264 CAGTTGGAAAAGTGACACCCC 59.319 52.381 0.84 0.00 0.00 4.95
722 784 5.015391 AGGAGAGAAGTTTAGTACTCCCTCA 59.985 44.000 0.00 0.00 43.12 3.86
831 897 4.580167 CACAATCCTCCTCACACTTTTTCA 59.420 41.667 0.00 0.00 0.00 2.69
885 951 3.191581 AGTCACGATCCTTGTCACACTAG 59.808 47.826 0.00 0.00 0.00 2.57
893 959 5.196341 TCCTTGTCACACTAGTTACTGTG 57.804 43.478 11.40 11.40 39.38 3.66
898 964 3.184581 GTCACACTAGTTACTGTGCAAGC 59.815 47.826 12.42 0.00 38.14 4.01
899 965 3.130633 CACACTAGTTACTGTGCAAGCA 58.869 45.455 12.42 0.00 37.68 3.91
902 968 3.187227 CACTAGTTACTGTGCAAGCAAGG 59.813 47.826 0.00 0.00 0.00 3.61
909 995 6.884295 AGTTACTGTGCAAGCAAGGATAAATA 59.116 34.615 0.00 0.00 0.00 1.40
2103 2203 1.924524 CGACAATACCAACGCACTAGG 59.075 52.381 0.00 0.00 0.00 3.02
2360 3697 0.892358 AGAACGTGGAGTCGGTGCTA 60.892 55.000 0.00 0.00 34.94 3.49
2378 3715 0.104304 TATTCCGCGGGAAGAAGCTC 59.896 55.000 27.83 0.00 45.48 4.09
2563 3903 2.290260 TGTTCACCAGCATCTTGTAGGG 60.290 50.000 0.00 0.00 0.00 3.53
2711 4078 6.126863 TGAGGATGAGGATTAACAAAGTGT 57.873 37.500 0.00 0.00 0.00 3.55
2714 4081 7.038302 TGAGGATGAGGATTAACAAAGTGTACT 60.038 37.037 0.00 0.00 0.00 2.73
2715 4082 8.375493 AGGATGAGGATTAACAAAGTGTACTA 57.625 34.615 0.00 0.00 0.00 1.82
2716 4083 8.258708 AGGATGAGGATTAACAAAGTGTACTAC 58.741 37.037 0.00 0.00 0.00 2.73
2824 4202 5.174035 GGTGATCGATCGAGTTGACTAAATG 59.826 44.000 23.84 0.00 0.00 2.32
2857 4235 3.004752 AGAATATGTTCCACCAGCACC 57.995 47.619 0.00 0.00 34.81 5.01
2858 4236 2.308570 AGAATATGTTCCACCAGCACCA 59.691 45.455 0.00 0.00 34.81 4.17
2863 4241 0.955919 GTTCCACCAGCACCACTAGC 60.956 60.000 0.00 0.00 0.00 3.42
2864 4242 1.127567 TTCCACCAGCACCACTAGCT 61.128 55.000 0.00 0.00 44.62 3.32
2877 4255 2.622436 CACTAGCTGGTTTAGTGGAGC 58.378 52.381 0.00 0.00 42.63 4.70
2881 4259 1.352352 AGCTGGTTTAGTGGAGCACAT 59.648 47.619 0.00 0.00 36.74 3.21
2884 4264 3.411446 CTGGTTTAGTGGAGCACATGAA 58.589 45.455 0.00 0.00 36.74 2.57
2889 4269 5.183904 GGTTTAGTGGAGCACATGAAAGATT 59.816 40.000 0.00 0.00 36.74 2.40
2904 4284 8.746530 ACATGAAAGATTGAAACAGCATAATCT 58.253 29.630 0.00 0.00 40.53 2.40
2912 4292 8.894768 ATTGAAACAGCATAATCTAGTACTCC 57.105 34.615 0.00 0.00 0.00 3.85
2913 4293 7.661536 TGAAACAGCATAATCTAGTACTCCT 57.338 36.000 0.00 0.00 0.00 3.69
2914 4294 8.762481 TGAAACAGCATAATCTAGTACTCCTA 57.238 34.615 0.00 0.00 0.00 2.94
2915 4295 8.630917 TGAAACAGCATAATCTAGTACTCCTAC 58.369 37.037 0.00 0.00 0.00 3.18
2916 4296 8.770010 AAACAGCATAATCTAGTACTCCTACT 57.230 34.615 0.00 0.00 37.04 2.57
2917 4297 8.770010 AACAGCATAATCTAGTACTCCTACTT 57.230 34.615 0.00 0.00 34.79 2.24
2918 4298 9.863650 AACAGCATAATCTAGTACTCCTACTTA 57.136 33.333 0.00 0.00 34.79 2.24
2919 4299 9.863650 ACAGCATAATCTAGTACTCCTACTTAA 57.136 33.333 0.00 0.00 34.79 1.85
2926 4306 9.765295 AATCTAGTACTCCTACTTAAACTGGAA 57.235 33.333 0.00 0.00 34.79 3.53
2927 4307 9.939424 ATCTAGTACTCCTACTTAAACTGGAAT 57.061 33.333 0.00 0.00 34.79 3.01
2928 4308 9.765295 TCTAGTACTCCTACTTAAACTGGAATT 57.235 33.333 0.00 0.00 34.79 2.17
2984 4364 8.750515 TGCTAAAAATGATGGACATCTATTCA 57.249 30.769 12.97 0.00 38.38 2.57
2985 4365 9.187996 TGCTAAAAATGATGGACATCTATTCAA 57.812 29.630 12.97 0.00 38.38 2.69
2986 4366 9.455847 GCTAAAAATGATGGACATCTATTCAAC 57.544 33.333 12.97 0.00 38.38 3.18
2989 4369 8.585471 AAAATGATGGACATCTATTCAACAGT 57.415 30.769 12.97 0.00 38.38 3.55
2990 4370 8.585471 AAATGATGGACATCTATTCAACAGTT 57.415 30.769 12.97 0.00 38.38 3.16
2991 4371 6.990341 TGATGGACATCTATTCAACAGTTG 57.010 37.500 6.99 6.99 38.60 3.16
2992 4372 6.475504 TGATGGACATCTATTCAACAGTTGT 58.524 36.000 13.14 0.00 38.60 3.32
2993 4373 6.942005 TGATGGACATCTATTCAACAGTTGTT 59.058 34.615 13.14 5.14 38.60 2.83
2994 4374 7.448161 TGATGGACATCTATTCAACAGTTGTTT 59.552 33.333 13.14 4.81 38.60 2.83
2995 4375 6.969366 TGGACATCTATTCAACAGTTGTTTG 58.031 36.000 13.14 4.13 35.83 2.93
2996 4376 5.858581 GGACATCTATTCAACAGTTGTTTGC 59.141 40.000 13.14 0.00 35.83 3.68
2997 4377 6.389830 ACATCTATTCAACAGTTGTTTGCA 57.610 33.333 13.14 0.00 35.83 4.08
2998 4378 6.804677 ACATCTATTCAACAGTTGTTTGCAA 58.195 32.000 13.14 0.00 35.83 4.08
2999 4379 7.436118 ACATCTATTCAACAGTTGTTTGCAAT 58.564 30.769 13.14 7.62 35.83 3.56
3000 4380 7.927629 ACATCTATTCAACAGTTGTTTGCAATT 59.072 29.630 13.14 0.00 35.83 2.32
3001 4381 8.767085 CATCTATTCAACAGTTGTTTGCAATTT 58.233 29.630 13.14 0.00 35.83 1.82
3002 4382 8.715191 TCTATTCAACAGTTGTTTGCAATTTT 57.285 26.923 13.14 0.00 35.83 1.82
3003 4383 9.160496 TCTATTCAACAGTTGTTTGCAATTTTT 57.840 25.926 13.14 0.00 35.83 1.94
3020 4400 2.977772 TTTTTGGAAAGGTGTGGCTG 57.022 45.000 0.00 0.00 0.00 4.85
3021 4401 0.463620 TTTTGGAAAGGTGTGGCTGC 59.536 50.000 0.00 0.00 0.00 5.25
3022 4402 0.396974 TTTGGAAAGGTGTGGCTGCT 60.397 50.000 0.00 0.00 0.00 4.24
3023 4403 0.823356 TTGGAAAGGTGTGGCTGCTC 60.823 55.000 0.00 0.00 0.00 4.26
3024 4404 1.973812 GGAAAGGTGTGGCTGCTCC 60.974 63.158 0.00 0.00 0.00 4.70
3025 4405 1.973812 GAAAGGTGTGGCTGCTCCC 60.974 63.158 0.00 0.00 0.00 4.30
3026 4406 3.850098 AAAGGTGTGGCTGCTCCCG 62.850 63.158 0.00 0.00 0.00 5.14
3033 4413 4.468689 GGCTGCTCCCGGGTGTAC 62.469 72.222 22.86 11.94 0.00 2.90
3034 4414 3.702048 GCTGCTCCCGGGTGTACA 61.702 66.667 22.86 13.44 0.00 2.90
3035 4415 2.264794 CTGCTCCCGGGTGTACAC 59.735 66.667 22.86 18.01 0.00 2.90
3036 4416 2.524640 TGCTCCCGGGTGTACACA 60.525 61.111 26.51 8.50 0.00 3.72
3037 4417 2.047560 GCTCCCGGGTGTACACAC 60.048 66.667 26.51 22.86 45.72 3.82
3086 4473 3.784178 TGTCAAATATGGCCCCTCAAAA 58.216 40.909 0.00 0.00 0.00 2.44
3145 4532 2.157668 CCGGACACGTCTCAAATTTCAG 59.842 50.000 0.00 0.00 38.78 3.02
3157 4544 6.003326 TCTCAAATTTCAGTAGTTGCATCCA 58.997 36.000 0.00 0.00 0.00 3.41
3204 4592 4.133820 TCCATACAAGGATATGCAAACGG 58.866 43.478 0.00 0.00 32.12 4.44
3328 4725 2.352805 CTTTGCTCCGGCCTCCTT 59.647 61.111 0.00 0.00 37.74 3.36
3341 4738 1.821666 GCCTCCTTCGCCTCTATCTCT 60.822 57.143 0.00 0.00 0.00 3.10
3355 4752 1.306642 ATCTCTGCGTCGAGTTCGGT 61.307 55.000 0.00 0.00 40.29 4.69
3358 4755 1.797933 CTGCGTCGAGTTCGGTGAG 60.798 63.158 0.00 0.00 40.29 3.51
3383 4783 2.989253 TCGGACGCCTGCTTCTGA 60.989 61.111 3.28 3.28 0.00 3.27
3414 4814 1.622607 CCGGTTGCCCTCCACATAGA 61.623 60.000 0.00 0.00 0.00 1.98
3451 4851 0.984961 TCTAGGATGGCCTGCTGCTT 60.985 55.000 3.32 0.00 46.45 3.91
3492 4913 0.609957 CTGCTCCATGTTGAAGCCCA 60.610 55.000 0.00 0.00 0.00 5.36
3500 4921 1.601759 GTTGAAGCCCAGCAGCTCA 60.602 57.895 0.00 0.00 44.11 4.26
3503 4924 1.378250 GAAGCCCAGCAGCTCATGT 60.378 57.895 0.00 0.00 44.11 3.21
3507 4928 1.302285 CCCAGCAGCTCATGTTCCT 59.698 57.895 0.00 0.00 0.00 3.36
3508 4929 1.030488 CCCAGCAGCTCATGTTCCTG 61.030 60.000 0.00 0.00 0.00 3.86
3553 4974 0.793617 TCCTGTTCCTCCTCTTCCCT 59.206 55.000 0.00 0.00 0.00 4.20
3554 4975 0.908198 CCTGTTCCTCCTCTTCCCTG 59.092 60.000 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.471676 GGACGTCATCTTCGCTTCCAT 60.472 52.381 18.91 0.00 0.00 3.41
33 34 1.631405 CAAAGCCCTTTGTCCATGGA 58.369 50.000 11.44 11.44 43.52 3.41
42 43 1.109323 AGCGCAAGTCAAAGCCCTTT 61.109 50.000 11.47 0.00 41.68 3.11
71 72 4.265893 TCTTCACAACCAACAGCAAGTTA 58.734 39.130 0.00 0.00 38.74 2.24
79 80 3.213506 CAGTCCATCTTCACAACCAACA 58.786 45.455 0.00 0.00 0.00 3.33
94 95 1.146041 AACAACTCAGCGCAGTCCA 59.854 52.632 11.47 0.00 0.00 4.02
176 178 3.096852 TCCTTTCACGAGCTAGAATCCA 58.903 45.455 0.00 0.00 0.00 3.41
219 221 2.566833 TGCTACATTTGCCTGTCTGT 57.433 45.000 0.00 0.00 0.00 3.41
226 228 2.351738 GGTGTGACTTGCTACATTTGCC 60.352 50.000 0.00 0.00 0.00 4.52
277 279 1.486726 CATAGGGGAGTTTCGAAGCCT 59.513 52.381 8.51 3.75 0.00 4.58
293 305 5.714047 TGACGATGCTAGCTATTTCCATAG 58.286 41.667 17.23 2.04 36.20 2.23
295 307 4.607293 TGACGATGCTAGCTATTTCCAT 57.393 40.909 17.23 0.00 0.00 3.41
322 334 5.202765 TCATCAGCCATGGTGATTACATTT 58.797 37.500 20.58 3.82 46.65 2.32
451 469 6.374613 CCCTCATCAAGATGTTCATGGATATG 59.625 42.308 9.66 0.00 39.72 1.78
452 470 6.045224 ACCCTCATCAAGATGTTCATGGATAT 59.955 38.462 9.66 0.00 39.72 1.63
483 501 3.518303 ACTATATACCGGCCTCCATTTCC 59.482 47.826 0.00 0.00 0.00 3.13
513 531 1.595929 GTTTCGAACGGGTCCAGCA 60.596 57.895 0.00 0.00 0.00 4.41
552 570 3.009723 GTCCAATGTGACGTGGAATGAT 58.990 45.455 9.12 0.00 45.42 2.45
555 573 2.559698 TGTCCAATGTGACGTGGAAT 57.440 45.000 9.12 0.00 45.42 3.01
612 674 2.653726 TGCACTGTTTCATGGTCAACT 58.346 42.857 0.00 0.00 0.00 3.16
684 746 4.862641 TCTCTCCTGAATTTTAAGGGGG 57.137 45.455 3.55 0.00 34.51 5.40
685 747 5.821097 ACTTCTCTCCTGAATTTTAAGGGG 58.179 41.667 3.69 0.81 35.13 4.79
686 748 7.767250 AAACTTCTCTCCTGAATTTTAAGGG 57.233 36.000 3.69 0.00 34.08 3.95
687 749 9.508642 ACTAAACTTCTCTCCTGAATTTTAAGG 57.491 33.333 0.00 0.00 33.69 2.69
741 804 4.738740 CGGCCTACTTTAGTGATCTAAACG 59.261 45.833 0.00 0.00 40.05 3.60
831 897 5.796424 AGTGTGAGGATTTGCTCAAAAAT 57.204 34.783 3.17 0.00 33.56 1.82
885 951 5.371115 TTTATCCTTGCTTGCACAGTAAC 57.629 39.130 0.00 0.00 0.00 2.50
893 959 5.358160 ACTCCAGTTATTTATCCTTGCTTGC 59.642 40.000 0.00 0.00 0.00 4.01
898 964 5.057149 CCGGACTCCAGTTATTTATCCTTG 58.943 45.833 0.00 0.00 0.00 3.61
899 965 4.720273 ACCGGACTCCAGTTATTTATCCTT 59.280 41.667 9.46 0.00 0.00 3.36
902 968 5.068723 TGAGACCGGACTCCAGTTATTTATC 59.931 44.000 27.36 3.13 36.22 1.75
909 995 1.536943 GCTGAGACCGGACTCCAGTT 61.537 60.000 27.36 0.00 36.22 3.16
1633 1730 2.970324 GTCGCCGAACACCTTGCA 60.970 61.111 0.00 0.00 0.00 4.08
2103 2203 2.893637 TGCAAGCGAAGGTAGAGAATC 58.106 47.619 0.00 0.00 37.06 2.52
2360 3697 1.153349 GAGCTTCTTCCCGCGGAAT 60.153 57.895 30.73 3.33 41.23 3.01
2426 3763 2.651361 CGGTCGTGCTCCTTGACT 59.349 61.111 0.00 0.00 33.21 3.41
2634 3987 1.610522 CAACAGCAAACAGAAGAGGGG 59.389 52.381 0.00 0.00 0.00 4.79
2671 4038 4.079253 TCCTCATTTACAAAACCCAGCTC 58.921 43.478 0.00 0.00 0.00 4.09
2711 4078 1.219664 GGCACGCACCATGGTAGTA 59.780 57.895 19.28 0.00 0.00 1.82
2857 4235 2.028112 TGCTCCACTAAACCAGCTAGTG 60.028 50.000 6.60 6.60 43.91 2.74
2858 4236 2.028020 GTGCTCCACTAAACCAGCTAGT 60.028 50.000 0.00 0.00 32.76 2.57
2863 4241 3.057969 TCATGTGCTCCACTAAACCAG 57.942 47.619 0.00 0.00 35.11 4.00
2864 4242 3.500448 TTCATGTGCTCCACTAAACCA 57.500 42.857 0.00 0.00 35.11 3.67
2877 4255 8.697846 ATTATGCTGTTTCAATCTTTCATGTG 57.302 30.769 0.00 0.00 0.00 3.21
2881 4259 9.453572 ACTAGATTATGCTGTTTCAATCTTTCA 57.546 29.630 0.00 0.00 38.40 2.69
2889 4269 7.661536 AGGAGTACTAGATTATGCTGTTTCA 57.338 36.000 0.00 0.00 0.00 2.69
2958 4338 9.187996 TGAATAGATGTCCATCATTTTTAGCAA 57.812 29.630 9.76 0.00 40.22 3.91
2959 4339 8.750515 TGAATAGATGTCCATCATTTTTAGCA 57.249 30.769 9.76 0.74 40.22 3.49
2960 4340 9.455847 GTTGAATAGATGTCCATCATTTTTAGC 57.544 33.333 9.76 0.00 40.22 3.09
2963 4343 9.028284 ACTGTTGAATAGATGTCCATCATTTTT 57.972 29.630 9.76 0.00 40.22 1.94
2964 4344 8.585471 ACTGTTGAATAGATGTCCATCATTTT 57.415 30.769 9.76 0.67 40.22 1.82
2965 4345 8.464404 CAACTGTTGAATAGATGTCCATCATTT 58.536 33.333 15.26 2.90 40.22 2.32
2966 4346 7.613022 ACAACTGTTGAATAGATGTCCATCATT 59.387 33.333 26.00 7.18 40.22 2.57
2967 4347 7.114754 ACAACTGTTGAATAGATGTCCATCAT 58.885 34.615 26.00 0.00 40.22 2.45
2968 4348 6.475504 ACAACTGTTGAATAGATGTCCATCA 58.524 36.000 26.00 0.00 40.22 3.07
2969 4349 6.992063 ACAACTGTTGAATAGATGTCCATC 57.008 37.500 26.00 0.00 38.09 3.51
2970 4350 7.596494 CAAACAACTGTTGAATAGATGTCCAT 58.404 34.615 26.00 0.00 38.44 3.41
2971 4351 6.514870 GCAAACAACTGTTGAATAGATGTCCA 60.515 38.462 26.00 0.00 38.44 4.02
2972 4352 5.858581 GCAAACAACTGTTGAATAGATGTCC 59.141 40.000 26.00 1.01 38.44 4.02
2973 4353 6.437928 TGCAAACAACTGTTGAATAGATGTC 58.562 36.000 26.00 11.13 38.44 3.06
2974 4354 6.389830 TGCAAACAACTGTTGAATAGATGT 57.610 33.333 26.00 0.00 38.44 3.06
2975 4355 7.878477 ATTGCAAACAACTGTTGAATAGATG 57.122 32.000 26.00 14.66 38.99 2.90
2976 4356 8.891671 AAATTGCAAACAACTGTTGAATAGAT 57.108 26.923 26.00 10.00 38.99 1.98
2977 4357 8.715191 AAAATTGCAAACAACTGTTGAATAGA 57.285 26.923 26.00 8.28 38.99 1.98
3001 4381 1.134551 GCAGCCACACCTTTCCAAAAA 60.135 47.619 0.00 0.00 0.00 1.94
3002 4382 0.463620 GCAGCCACACCTTTCCAAAA 59.536 50.000 0.00 0.00 0.00 2.44
3003 4383 0.396974 AGCAGCCACACCTTTCCAAA 60.397 50.000 0.00 0.00 0.00 3.28
3004 4384 0.823356 GAGCAGCCACACCTTTCCAA 60.823 55.000 0.00 0.00 0.00 3.53
3005 4385 1.228245 GAGCAGCCACACCTTTCCA 60.228 57.895 0.00 0.00 0.00 3.53
3006 4386 1.973812 GGAGCAGCCACACCTTTCC 60.974 63.158 0.00 0.00 36.34 3.13
3007 4387 1.973812 GGGAGCAGCCACACCTTTC 60.974 63.158 0.00 0.00 38.95 2.62
3008 4388 2.116125 GGGAGCAGCCACACCTTT 59.884 61.111 0.00 0.00 38.95 3.11
3009 4389 4.335647 CGGGAGCAGCCACACCTT 62.336 66.667 0.00 0.00 38.95 3.50
3016 4396 4.468689 GTACACCCGGGAGCAGCC 62.469 72.222 32.02 5.63 0.00 4.85
3017 4397 3.702048 TGTACACCCGGGAGCAGC 61.702 66.667 32.02 13.66 0.00 5.25
3018 4398 2.264794 GTGTACACCCGGGAGCAG 59.735 66.667 32.02 16.32 0.00 4.24
3019 4399 2.524640 TGTGTACACCCGGGAGCA 60.525 61.111 32.02 16.84 0.00 4.26
3020 4400 2.047560 GTGTGTACACCCGGGAGC 60.048 66.667 32.02 14.25 40.85 4.70
3021 4401 3.462169 TGTGTGTACACCCGGGAG 58.538 61.111 32.02 24.28 45.88 4.30
3029 4409 1.621814 GCTCTAAGGGGTGTGTGTACA 59.378 52.381 0.00 0.00 0.00 2.90
3030 4410 1.621814 TGCTCTAAGGGGTGTGTGTAC 59.378 52.381 0.00 0.00 0.00 2.90
3031 4411 2.018355 TGCTCTAAGGGGTGTGTGTA 57.982 50.000 0.00 0.00 0.00 2.90
3032 4412 1.279271 GATGCTCTAAGGGGTGTGTGT 59.721 52.381 0.00 0.00 0.00 3.72
3033 4413 1.556911 AGATGCTCTAAGGGGTGTGTG 59.443 52.381 0.00 0.00 0.00 3.82
3034 4414 1.958288 AGATGCTCTAAGGGGTGTGT 58.042 50.000 0.00 0.00 0.00 3.72
3035 4415 2.766263 TGTAGATGCTCTAAGGGGTGTG 59.234 50.000 0.00 0.00 29.58 3.82
3036 4416 3.034635 CTGTAGATGCTCTAAGGGGTGT 58.965 50.000 0.00 0.00 29.58 4.16
3037 4417 2.224161 GCTGTAGATGCTCTAAGGGGTG 60.224 54.545 0.00 0.00 29.58 4.61
3038 4418 2.043227 GCTGTAGATGCTCTAAGGGGT 58.957 52.381 0.00 0.00 29.58 4.95
3039 4419 1.346068 GGCTGTAGATGCTCTAAGGGG 59.654 57.143 0.00 0.00 29.58 4.79
3040 4420 1.000283 CGGCTGTAGATGCTCTAAGGG 60.000 57.143 0.00 0.00 29.58 3.95
3041 4421 1.957177 TCGGCTGTAGATGCTCTAAGG 59.043 52.381 0.00 0.00 29.58 2.69
3061 4448 5.337956 TGAGGGGCCATATTTGACATATT 57.662 39.130 4.39 0.00 0.00 1.28
3107 4494 2.742372 GACATTGCCTGCGGACGT 60.742 61.111 0.00 0.00 0.00 4.34
3115 4502 2.047274 CGTGTCCGGACATTGCCT 60.047 61.111 38.11 0.00 43.97 4.75
3120 4507 0.677288 TTTGAGACGTGTCCGGACAT 59.323 50.000 38.11 24.95 43.97 3.06
3123 4510 2.224090 TGAAATTTGAGACGTGTCCGGA 60.224 45.455 10.56 0.00 38.78 5.14
3145 4532 7.437748 AGTATAAGATGTCTGGATGCAACTAC 58.562 38.462 0.00 0.00 0.00 2.73
3194 4581 5.177326 ACGTAGGTTTATTCCGTTTGCATA 58.823 37.500 0.00 0.00 0.00 3.14
3310 4698 3.927481 AAGGAGGCCGGAGCAAAGC 62.927 63.158 5.05 0.00 42.56 3.51
3313 4701 4.082523 CGAAGGAGGCCGGAGCAA 62.083 66.667 5.05 0.00 42.56 3.91
3341 4738 2.254350 CTCACCGAACTCGACGCA 59.746 61.111 0.00 0.00 43.02 5.24
3402 4802 1.974236 GGATGAGGTCTATGTGGAGGG 59.026 57.143 0.00 0.00 0.00 4.30
3434 4834 1.528824 GAAGCAGCAGGCCATCCTA 59.471 57.895 5.01 0.00 46.50 2.94
3451 4851 4.841617 AGGCGGAGGAGATGGCGA 62.842 66.667 0.00 0.00 0.00 5.54
3492 4913 1.684035 AGCAGGAACATGAGCTGCT 59.316 52.632 0.00 0.00 45.20 4.24
3500 4921 1.001641 GGTGGAGCAGCAGGAACAT 60.002 57.895 0.00 0.00 0.00 2.71
3503 4924 2.596851 GGAGGTGGAGCAGCAGGAA 61.597 63.158 0.00 0.00 33.95 3.36
3507 4928 2.993008 GATGGAGGTGGAGCAGCA 59.007 61.111 0.00 0.00 33.95 4.41
3508 4929 2.202987 CGATGGAGGTGGAGCAGC 60.203 66.667 0.00 0.00 0.00 5.25
3511 4932 2.818132 CTCCGATGGAGGTGGAGC 59.182 66.667 4.89 0.00 45.43 4.70
3538 4959 1.916206 GCCCAGGGAAGAGGAGGAAC 61.916 65.000 10.89 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.