Multiple sequence alignment - TraesCS3D01G220700

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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 TraesCS3D01G220700 chr3D 100.000 3470 0 0 1 3470 301412280 301415749 0.000000e+00 6408.0
1 TraesCS3D01G220700 chr3B 90.252 3457 219 67 1 3382 419967872 419964459 0.000000e+00 4409.0
2 TraesCS3D01G220700 chr3B 84.000 75 9 3 1927 2001 303333778 303333707 6.210000e-08 69.4
3 TraesCS3D01G220700 chr3A 91.920 2364 102 36 645 2941 434070550 434068209 0.000000e+00 3225.0
4 TraesCS3D01G220700 chr3A 90.341 528 46 5 2939 3466 434067184 434066662 0.000000e+00 688.0
5 TraesCS3D01G220700 chr1B 88.889 243 25 1 1889 2129 665061681 665061923 7.280000e-77 298.0
6 TraesCS3D01G220700 chr1D 88.066 243 27 1 1889 2129 477480536 477480778 1.580000e-73 287.0
7 TraesCS3D01G220700 chr1A 91.038 212 19 0 1903 2114 573921813 573922024 1.580000e-73 287.0
8 TraesCS3D01G220700 chr4A 79.295 227 38 8 1893 2116 143252299 143252519 2.160000e-32 150.0
9 TraesCS3D01G220700 chr4B 78.814 236 39 10 1897 2128 407056972 407056744 7.760000e-32 148.0
10 TraesCS3D01G220700 chr4D 78.378 222 39 8 1896 2114 327719429 327719214 6.040000e-28 135.0


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 TraesCS3D01G220700 chr3D 301412280 301415749 3469 False 6408.0 6408 100.0000 1 3470 1 chr3D.!!$F1 3469
1 TraesCS3D01G220700 chr3B 419964459 419967872 3413 True 4409.0 4409 90.2520 1 3382 1 chr3B.!!$R2 3381
2 TraesCS3D01G220700 chr3A 434066662 434070550 3888 True 1956.5 3225 91.1305 645 3466 2 chr3A.!!$R1 2821

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
444 452 0.03779 GCAATGCCGCCTTAAACCAA 60.038 50.0 0.0 0.0 0.0 3.67 F
1691 1754 0.03601 ACCTCAAGATGAACCAGGCG 60.036 55.0 0.0 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2203 2277 1.200483 CGTGTATGCGTAGGCTTGAG 58.80 55.0 9.11 0.0 40.82 3.02 R
2507 2617 0.249868 TGTCACCTCAACTTCGCAGG 60.25 55.0 0.00 0.0 0.00 4.85 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
29 30 6.612247 TGTAAGTTTGACCAAGTGTGTATG 57.388 37.500 0.00 0.00 0.00 2.39
45 46 9.884636 AAGTGTGTATGCAAAACTATGTAGATA 57.115 29.630 0.00 0.00 0.00 1.98
121 122 4.927267 ATTCAGTCAATACAGGGTTGGA 57.073 40.909 0.00 0.00 0.00 3.53
130 131 2.683211 ACAGGGTTGGAAGAGCAATT 57.317 45.000 0.00 0.00 0.00 2.32
176 177 4.457496 CAGCGGCCGGACAGTCAT 62.457 66.667 29.38 0.00 0.00 3.06
177 178 3.706373 AGCGGCCGGACAGTCATT 61.706 61.111 29.38 0.00 0.00 2.57
189 190 3.076621 GACAGTCATTGATGCAGACCAA 58.923 45.455 0.00 0.00 32.82 3.67
191 192 2.089980 AGTCATTGATGCAGACCAAGC 58.910 47.619 0.00 0.00 32.82 4.01
194 195 1.674441 CATTGATGCAGACCAAGCGAT 59.326 47.619 0.00 0.00 33.85 4.58
195 196 2.689553 TTGATGCAGACCAAGCGATA 57.310 45.000 0.00 0.00 33.85 2.92
233 237 1.555075 AGCAAATCGCCTTACCAGAGA 59.445 47.619 0.00 0.00 44.04 3.10
235 239 2.945668 GCAAATCGCCTTACCAGAGAAT 59.054 45.455 0.00 0.00 32.94 2.40
239 243 6.487103 CAAATCGCCTTACCAGAGAATAAAC 58.513 40.000 0.00 0.00 0.00 2.01
240 244 3.777478 TCGCCTTACCAGAGAATAAACG 58.223 45.455 0.00 0.00 0.00 3.60
241 245 3.194116 TCGCCTTACCAGAGAATAAACGT 59.806 43.478 0.00 0.00 0.00 3.99
242 246 3.550678 CGCCTTACCAGAGAATAAACGTC 59.449 47.826 0.00 0.00 0.00 4.34
260 266 4.012374 ACGTCGATAAGGACCTGTAGAAA 58.988 43.478 0.00 0.00 33.30 2.52
262 268 4.680702 GTCGATAAGGACCTGTAGAAACC 58.319 47.826 0.00 0.00 0.00 3.27
263 269 4.159135 GTCGATAAGGACCTGTAGAAACCA 59.841 45.833 0.00 0.00 0.00 3.67
270 276 3.306849 GGACCTGTAGAAACCAGAAGACC 60.307 52.174 0.00 0.00 31.38 3.85
278 285 1.692411 AACCAGAAGACCACAAAGCC 58.308 50.000 0.00 0.00 0.00 4.35
282 289 2.597510 AAGACCACAAAGCCGGCC 60.598 61.111 26.15 4.59 0.00 6.13
292 299 2.478335 AAAGCCGGCCGAATCCAGAA 62.478 55.000 30.73 0.00 0.00 3.02
306 313 1.982226 TCCAGAAGGATCCACCGAAAA 59.018 47.619 15.82 0.00 44.74 2.29
312 319 3.629142 AGGATCCACCGAAAACCTAAG 57.371 47.619 15.82 0.00 44.74 2.18
315 322 0.320946 TCCACCGAAAACCTAAGCCG 60.321 55.000 0.00 0.00 0.00 5.52
324 331 1.410004 AACCTAAGCCGATCGGATCA 58.590 50.000 37.64 18.18 37.50 2.92
326 333 0.387367 CCTAAGCCGATCGGATCACG 60.387 60.000 37.64 21.22 46.11 4.35
351 358 0.734253 CCTTCGAAGACACAGCTCCG 60.734 60.000 26.61 1.53 34.32 4.63
352 359 1.347817 CTTCGAAGACACAGCTCCGC 61.348 60.000 20.74 0.00 34.32 5.54
364 371 4.200283 CTCCGCACGCTCTCCTCC 62.200 72.222 0.00 0.00 0.00 4.30
368 375 4.803426 GCACGCTCTCCTCCGGTG 62.803 72.222 0.00 0.00 0.00 4.94
375 382 1.542547 GCTCTCCTCCGGTGAAAAACA 60.543 52.381 4.76 0.00 0.00 2.83
389 396 5.336150 TGAAAAACACACCAACATGATGT 57.664 34.783 0.00 0.00 0.00 3.06
391 398 4.998671 AAAACACACCAACATGATGTGA 57.001 36.364 21.99 0.00 44.69 3.58
398 405 4.637534 ACACCAACATGATGTGAATAGAGC 59.362 41.667 16.78 0.00 34.18 4.09
399 406 4.637091 CACCAACATGATGTGAATAGAGCA 59.363 41.667 0.00 0.00 31.66 4.26
402 410 5.121105 CAACATGATGTGAATAGAGCAGGA 58.879 41.667 0.00 0.00 0.00 3.86
407 415 5.423015 TGATGTGAATAGAGCAGGAAGAAC 58.577 41.667 0.00 0.00 0.00 3.01
426 434 5.685728 AGAACATTATTCCTACCTCAAGGC 58.314 41.667 0.00 0.00 39.32 4.35
444 452 0.037790 GCAATGCCGCCTTAAACCAA 60.038 50.000 0.00 0.00 0.00 3.67
458 466 6.571731 GCCTTAAACCAAACATAAAGACTCCC 60.572 42.308 0.00 0.00 0.00 4.30
459 467 6.719829 CCTTAAACCAAACATAAAGACTCCCT 59.280 38.462 0.00 0.00 0.00 4.20
460 468 7.886446 CCTTAAACCAAACATAAAGACTCCCTA 59.114 37.037 0.00 0.00 0.00 3.53
462 470 7.761038 AAACCAAACATAAAGACTCCCTAAG 57.239 36.000 0.00 0.00 0.00 2.18
463 471 6.697641 ACCAAACATAAAGACTCCCTAAGA 57.302 37.500 0.00 0.00 0.00 2.10
464 472 7.086685 ACCAAACATAAAGACTCCCTAAGAA 57.913 36.000 0.00 0.00 0.00 2.52
467 475 8.297426 CCAAACATAAAGACTCCCTAAGAAAAC 58.703 37.037 0.00 0.00 0.00 2.43
468 476 7.997773 AACATAAAGACTCCCTAAGAAAACC 57.002 36.000 0.00 0.00 0.00 3.27
469 477 7.331089 ACATAAAGACTCCCTAAGAAAACCT 57.669 36.000 0.00 0.00 0.00 3.50
470 478 7.168905 ACATAAAGACTCCCTAAGAAAACCTG 58.831 38.462 0.00 0.00 0.00 4.00
471 479 5.906772 AAAGACTCCCTAAGAAAACCTGA 57.093 39.130 0.00 0.00 0.00 3.86
476 486 5.386060 ACTCCCTAAGAAAACCTGAAAAGG 58.614 41.667 0.00 0.00 0.00 3.11
485 495 6.170506 AGAAAACCTGAAAAGGAAAAACACC 58.829 36.000 0.00 0.00 0.00 4.16
496 506 1.686052 GAAAAACACCCATGCCACTGA 59.314 47.619 0.00 0.00 0.00 3.41
507 517 2.738521 CCACTGAACGACTGGCCG 60.739 66.667 0.00 0.00 0.00 6.13
510 520 4.003788 CTGAACGACTGGCCGGGT 62.004 66.667 18.00 8.92 0.00 5.28
526 536 0.958822 GGGTTTTCAGAACCGTGCAT 59.041 50.000 0.00 0.00 41.18 3.96
528 538 2.393764 GGTTTTCAGAACCGTGCATTG 58.606 47.619 0.00 0.00 0.00 2.82
531 541 1.960417 TTCAGAACCGTGCATTGACA 58.040 45.000 0.00 0.00 0.00 3.58
534 544 0.108585 AGAACCGTGCATTGACACCT 59.891 50.000 0.00 0.00 37.25 4.00
541 551 2.158449 CGTGCATTGACACCTTCTTCTC 59.842 50.000 0.00 0.00 37.25 2.87
545 555 1.814429 TTGACACCTTCTTCTCCCCA 58.186 50.000 0.00 0.00 0.00 4.96
548 558 2.716424 TGACACCTTCTTCTCCCCAATT 59.284 45.455 0.00 0.00 0.00 2.32
553 563 6.322931 ACACCTTCTTCTCCCCAATTATTTT 58.677 36.000 0.00 0.00 0.00 1.82
599 609 9.690434 CTTAGAAAACTATGTGAATTTAGACGC 57.310 33.333 0.00 0.00 0.00 5.19
622 632 2.658285 TCAATCCTTGCATAGGCCAAG 58.342 47.619 5.01 0.00 44.37 3.61
630 640 0.463833 GCATAGGCCAAGGTTACGCT 60.464 55.000 5.01 0.00 0.00 5.07
634 644 0.400594 AGGCCAAGGTTACGCTCTTT 59.599 50.000 5.01 0.00 0.00 2.52
636 646 1.068541 GGCCAAGGTTACGCTCTTTTG 60.069 52.381 0.00 0.00 0.00 2.44
698 711 4.124970 GGCCTAGGTGAAACGGTAAATAG 58.875 47.826 11.31 0.00 38.12 1.73
738 751 0.664166 GAGCCACAATGCAACAACCG 60.664 55.000 0.00 0.00 0.00 4.44
739 752 2.309501 GCCACAATGCAACAACCGC 61.310 57.895 0.00 0.00 0.00 5.68
740 753 2.015627 CCACAATGCAACAACCGCG 61.016 57.895 0.00 0.00 0.00 6.46
741 754 2.015627 CACAATGCAACAACCGCGG 61.016 57.895 26.86 26.86 0.00 6.46
743 756 1.729131 CAATGCAACAACCGCGGAC 60.729 57.895 35.90 13.75 0.00 4.79
744 757 2.190170 AATGCAACAACCGCGGACA 61.190 52.632 35.90 18.98 0.00 4.02
745 758 2.400896 AATGCAACAACCGCGGACAC 62.401 55.000 35.90 14.88 0.00 3.67
746 759 4.659874 GCAACAACCGCGGACACG 62.660 66.667 35.90 18.67 44.63 4.49
866 892 4.552365 ACACACGCTGCCTGCACT 62.552 61.111 0.00 0.00 43.06 4.40
867 893 2.357396 CACACGCTGCCTGCACTA 60.357 61.111 0.00 0.00 43.06 2.74
868 894 2.357517 ACACGCTGCCTGCACTAC 60.358 61.111 0.00 0.00 43.06 2.73
869 895 2.357396 CACGCTGCCTGCACTACA 60.357 61.111 0.00 0.00 43.06 2.74
870 896 2.357517 ACGCTGCCTGCACTACAC 60.358 61.111 0.00 0.00 43.06 2.90
881 907 1.213537 CACTACACCCGTGTACCCG 59.786 63.158 3.57 0.00 44.42 5.28
947 1004 4.637534 CCAAGAGGTATCACCAACATTCTG 59.362 45.833 0.00 0.00 41.95 3.02
952 1009 4.086457 GGTATCACCAACATTCTGGGTTT 58.914 43.478 0.00 0.00 41.16 3.27
953 1010 4.157840 GGTATCACCAACATTCTGGGTTTC 59.842 45.833 0.00 0.00 41.16 2.78
954 1011 3.593442 TCACCAACATTCTGGGTTTCT 57.407 42.857 0.00 0.00 41.16 2.52
965 1022 6.986231 ACATTCTGGGTTTCTTTTTCAACATC 59.014 34.615 0.00 0.00 0.00 3.06
967 1024 4.343814 TCTGGGTTTCTTTTTCAACATCCC 59.656 41.667 0.00 0.00 0.00 3.85
1174 1237 4.154347 GGACCAGCGCCTCTCCTG 62.154 72.222 2.29 0.00 0.00 3.86
1691 1754 0.036010 ACCTCAAGATGAACCAGGCG 60.036 55.000 0.00 0.00 0.00 5.52
1692 1755 0.250234 CCTCAAGATGAACCAGGCGA 59.750 55.000 0.00 0.00 0.00 5.54
1694 1757 0.684535 TCAAGATGAACCAGGCGACA 59.315 50.000 0.00 0.00 0.00 4.35
2186 2260 2.743718 CGCCACAGTCTGAACCCT 59.256 61.111 6.91 0.00 0.00 4.34
2188 2262 0.951040 CGCCACAGTCTGAACCCTTC 60.951 60.000 6.91 0.00 0.00 3.46
2199 2273 3.072211 CTGAACCCTTCTTTTACCGTCC 58.928 50.000 0.00 0.00 0.00 4.79
2203 2277 2.156917 CCCTTCTTTTACCGTCCCAAC 58.843 52.381 0.00 0.00 0.00 3.77
2553 2663 8.331022 CGGATGTCTTCTTGTTTGTATTCTATG 58.669 37.037 0.00 0.00 0.00 2.23
2554 2664 9.383519 GGATGTCTTCTTGTTTGTATTCTATGA 57.616 33.333 0.00 0.00 0.00 2.15
2557 2667 9.942850 TGTCTTCTTGTTTGTATTCTATGATGA 57.057 29.630 0.00 0.00 0.00 2.92
2679 2791 6.749923 ATTAAGTTGGCATCTTTCTCAGTC 57.250 37.500 15.42 0.00 0.00 3.51
2686 2798 3.149196 GCATCTTTCTCAGTCCCAACAA 58.851 45.455 0.00 0.00 0.00 2.83
2771 2884 2.628657 ACTCTTTACTCCGCTGTGTCTT 59.371 45.455 0.00 0.00 0.00 3.01
2781 2894 2.029828 CCGCTGTGTCTTACTGTCTCTT 60.030 50.000 0.00 0.00 0.00 2.85
2852 2973 1.804748 GGTAAAGAACCTCAACCTGCG 59.195 52.381 0.00 0.00 45.75 5.18
2928 3049 7.486802 AAGCTACTTAACTCGCTTGTAAAAA 57.513 32.000 0.00 0.00 40.83 1.94
2929 3050 6.885247 AGCTACTTAACTCGCTTGTAAAAAC 58.115 36.000 0.00 0.00 0.00 2.43
2956 4104 1.832883 TGTAAAATGCACGCCCTGAT 58.167 45.000 0.00 0.00 0.00 2.90
3038 4186 6.299578 CGTTTAAACAACGGCAATCTTATG 57.700 37.500 18.07 0.00 39.73 1.90
3081 4229 2.743664 GCAGGGCATTTCCAATGTTTTC 59.256 45.455 0.00 0.00 36.21 2.29
3105 4253 4.763279 TCTGTCAGTGTTAGTTGTATCGGA 59.237 41.667 0.00 0.00 0.00 4.55
3132 4280 7.173218 GGTGACAGTTTCTTCAGAATAACATGA 59.827 37.037 0.00 0.00 33.54 3.07
3164 4314 7.338800 TGGAAGGATGATAATTTTGAGCTTC 57.661 36.000 0.00 0.00 0.00 3.86
3217 4367 2.586635 TGCCACGACACGACCAAC 60.587 61.111 0.00 0.00 0.00 3.77
3293 4443 8.594550 GTCAGCCATATAAGAGGTCCTTAAATA 58.405 37.037 0.00 0.00 40.45 1.40
3294 4444 9.166222 TCAGCCATATAAGAGGTCCTTAAATAA 57.834 33.333 0.00 0.00 40.45 1.40
3397 4547 9.744468 TTCTTTCAAAGATTAACCAAAACTAGC 57.256 29.630 0.00 0.00 37.38 3.42
3398 4548 8.908903 TCTTTCAAAGATTAACCAAAACTAGCA 58.091 29.630 0.00 0.00 31.20 3.49
3410 4560 4.162320 CCAAAACTAGCAGATCCTAGTCCA 59.838 45.833 10.87 0.00 45.40 4.02
3412 4562 2.952116 ACTAGCAGATCCTAGTCCACC 58.048 52.381 5.98 0.00 43.33 4.61
3428 4578 2.436646 CCCCTACCGCTGCAGTTG 60.437 66.667 16.64 9.31 0.00 3.16
3441 4591 4.433283 CGCTGCAGTTGACAAATAAAATGC 60.433 41.667 16.64 1.26 45.07 3.56
3443 4593 5.613142 GCTGCAGTTGACAAATAAAATGCAC 60.613 40.000 16.64 1.85 46.68 4.57
3445 4595 5.990386 TGCAGTTGACAAATAAAATGCACAT 59.010 32.000 6.44 0.00 46.68 3.21
3469 4619 3.006728 CCCCTCCACCTACCGCAA 61.007 66.667 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 6.012658 ACATAGTTTTGCATACACACTTGG 57.987 37.500 0.00 0.00 0.00 3.61
103 104 4.256920 CTCTTCCAACCCTGTATTGACTG 58.743 47.826 0.00 0.00 0.00 3.51
105 106 3.010420 GCTCTTCCAACCCTGTATTGAC 58.990 50.000 0.00 0.00 0.00 3.18
107 108 3.071874 TGCTCTTCCAACCCTGTATTG 57.928 47.619 0.00 0.00 0.00 1.90
130 131 4.748102 ACGAGCTTCTATGTGTTCGAAAAA 59.252 37.500 0.00 0.00 32.81 1.94
135 136 4.274421 TCTACGAGCTTCTATGTGTTCG 57.726 45.455 0.00 0.00 0.00 3.95
136 137 4.602995 CCTCTACGAGCTTCTATGTGTTC 58.397 47.826 0.00 0.00 0.00 3.18
137 138 3.181485 GCCTCTACGAGCTTCTATGTGTT 60.181 47.826 0.00 0.00 0.00 3.32
139 140 2.359214 TGCCTCTACGAGCTTCTATGTG 59.641 50.000 0.00 0.00 0.00 3.21
146 147 2.492090 CGCTGCCTCTACGAGCTT 59.508 61.111 0.00 0.00 0.00 3.74
161 162 3.499737 CAATGACTGTCCGGCCGC 61.500 66.667 22.85 7.92 0.00 6.53
163 164 1.718757 GCATCAATGACTGTCCGGCC 61.719 60.000 5.17 0.00 0.00 6.13
165 166 1.012086 CTGCATCAATGACTGTCCGG 58.988 55.000 5.17 0.00 0.00 5.14
166 167 1.662629 GTCTGCATCAATGACTGTCCG 59.337 52.381 5.17 0.00 0.00 4.79
167 168 2.012673 GGTCTGCATCAATGACTGTCC 58.987 52.381 5.17 0.00 0.00 4.02
168 169 2.703416 TGGTCTGCATCAATGACTGTC 58.297 47.619 0.00 0.00 0.00 3.51
170 171 2.159421 GCTTGGTCTGCATCAATGACTG 60.159 50.000 3.40 0.00 0.00 3.51
176 177 2.279741 GTATCGCTTGGTCTGCATCAA 58.720 47.619 0.00 0.00 0.00 2.57
177 178 1.473257 GGTATCGCTTGGTCTGCATCA 60.473 52.381 0.00 0.00 0.00 3.07
189 190 4.247612 GCGGTCGTCGGTATCGCT 62.248 66.667 4.49 0.00 42.62 4.93
191 192 2.352001 CTGCGGTCGTCGGTATCG 60.352 66.667 0.00 0.00 39.69 2.92
209 210 1.067915 TGGTAAGGCGATTTGCTTTGC 60.068 47.619 3.61 2.21 43.56 3.68
211 212 2.749621 CTCTGGTAAGGCGATTTGCTTT 59.250 45.455 0.00 0.00 45.86 3.51
233 237 5.334724 ACAGGTCCTTATCGACGTTTATT 57.665 39.130 0.00 0.00 33.30 1.40
235 239 5.185454 TCTACAGGTCCTTATCGACGTTTA 58.815 41.667 0.00 0.00 33.30 2.01
239 243 4.349501 GTTTCTACAGGTCCTTATCGACG 58.650 47.826 0.00 0.00 33.30 5.12
240 244 4.159135 TGGTTTCTACAGGTCCTTATCGAC 59.841 45.833 0.00 0.00 0.00 4.20
241 245 4.346730 TGGTTTCTACAGGTCCTTATCGA 58.653 43.478 0.00 0.00 0.00 3.59
242 246 4.401519 TCTGGTTTCTACAGGTCCTTATCG 59.598 45.833 0.00 0.00 36.62 2.92
260 266 0.535102 CGGCTTTGTGGTCTTCTGGT 60.535 55.000 0.00 0.00 0.00 4.00
262 268 1.856265 GCCGGCTTTGTGGTCTTCTG 61.856 60.000 22.15 0.00 0.00 3.02
263 269 1.600916 GCCGGCTTTGTGGTCTTCT 60.601 57.895 22.15 0.00 0.00 2.85
270 276 2.485122 GATTCGGCCGGCTTTGTG 59.515 61.111 28.56 11.45 0.00 3.33
278 285 2.900273 TCCTTCTGGATTCGGCCG 59.100 61.111 22.12 22.12 37.46 6.13
292 299 2.355818 GCTTAGGTTTTCGGTGGATCCT 60.356 50.000 14.23 0.00 0.00 3.24
303 310 2.169769 TGATCCGATCGGCTTAGGTTTT 59.830 45.455 29.62 4.85 34.68 2.43
306 313 0.674534 GTGATCCGATCGGCTTAGGT 59.325 55.000 29.62 10.17 34.68 3.08
312 319 1.215655 CCTTTCGTGATCCGATCGGC 61.216 60.000 29.62 16.76 46.75 5.54
315 322 0.105039 AGGCCTTTCGTGATCCGATC 59.895 55.000 0.00 1.01 46.75 3.69
326 333 1.801178 CTGTGTCTTCGAAGGCCTTTC 59.199 52.381 25.99 11.90 0.00 2.62
366 373 5.108517 ACATCATGTTGGTGTGTTTTTCAC 58.891 37.500 8.58 0.00 40.78 3.18
375 382 4.637534 GCTCTATTCACATCATGTTGGTGT 59.362 41.667 8.58 0.21 43.61 4.16
383 390 5.883685 TCTTCCTGCTCTATTCACATCAT 57.116 39.130 0.00 0.00 0.00 2.45
384 391 5.046376 TGTTCTTCCTGCTCTATTCACATCA 60.046 40.000 0.00 0.00 0.00 3.07
385 392 5.423015 TGTTCTTCCTGCTCTATTCACATC 58.577 41.667 0.00 0.00 0.00 3.06
389 396 7.716998 GGAATAATGTTCTTCCTGCTCTATTCA 59.283 37.037 3.43 0.00 38.31 2.57
402 410 6.122964 GCCTTGAGGTAGGAATAATGTTCTT 58.877 40.000 0.00 0.00 37.50 2.52
407 415 5.278660 GCATTGCCTTGAGGTAGGAATAATG 60.279 44.000 0.00 0.00 37.50 1.90
426 434 2.065512 GTTTGGTTTAAGGCGGCATTG 58.934 47.619 13.08 0.00 0.00 2.82
444 452 7.665974 CAGGTTTTCTTAGGGAGTCTTTATGTT 59.334 37.037 0.00 0.00 0.00 2.71
458 466 8.869897 GTGTTTTTCCTTTTCAGGTTTTCTTAG 58.130 33.333 0.00 0.00 41.69 2.18
459 467 7.820386 GGTGTTTTTCCTTTTCAGGTTTTCTTA 59.180 33.333 0.00 0.00 41.69 2.10
460 468 6.653320 GGTGTTTTTCCTTTTCAGGTTTTCTT 59.347 34.615 0.00 0.00 41.69 2.52
462 470 5.353123 GGGTGTTTTTCCTTTTCAGGTTTTC 59.647 40.000 0.00 0.00 41.69 2.29
463 471 5.221945 TGGGTGTTTTTCCTTTTCAGGTTTT 60.222 36.000 0.00 0.00 41.69 2.43
464 472 4.287326 TGGGTGTTTTTCCTTTTCAGGTTT 59.713 37.500 0.00 0.00 41.69 3.27
467 475 4.379652 CATGGGTGTTTTTCCTTTTCAGG 58.620 43.478 0.00 0.00 42.50 3.86
468 476 3.809279 GCATGGGTGTTTTTCCTTTTCAG 59.191 43.478 0.00 0.00 0.00 3.02
469 477 3.432890 GGCATGGGTGTTTTTCCTTTTCA 60.433 43.478 0.00 0.00 0.00 2.69
470 478 3.138304 GGCATGGGTGTTTTTCCTTTTC 58.862 45.455 0.00 0.00 0.00 2.29
471 479 2.507471 TGGCATGGGTGTTTTTCCTTTT 59.493 40.909 0.00 0.00 0.00 2.27
476 486 1.686052 TCAGTGGCATGGGTGTTTTTC 59.314 47.619 0.00 0.00 0.00 2.29
485 495 1.300971 CCAGTCGTTCAGTGGCATGG 61.301 60.000 0.00 0.00 38.87 3.66
496 506 1.895231 GAAAACCCGGCCAGTCGTT 60.895 57.895 2.24 0.00 0.00 3.85
507 517 0.958822 ATGCACGGTTCTGAAAACCC 59.041 50.000 0.00 0.00 36.99 4.11
510 520 2.685388 TGTCAATGCACGGTTCTGAAAA 59.315 40.909 0.00 0.00 0.00 2.29
526 536 1.814429 TGGGGAGAAGAAGGTGTCAA 58.186 50.000 0.00 0.00 0.00 3.18
528 538 3.441500 AATTGGGGAGAAGAAGGTGTC 57.558 47.619 0.00 0.00 0.00 3.67
575 585 7.820386 TGGCGTCTAAATTCACATAGTTTTCTA 59.180 33.333 0.00 0.00 36.78 2.10
581 591 5.670485 TGATGGCGTCTAAATTCACATAGT 58.330 37.500 8.40 0.00 0.00 2.12
622 632 2.563297 CCCCCAAAAGAGCGTAACC 58.437 57.895 0.00 0.00 0.00 2.85
721 734 2.309501 GCGGTTGTTGCATTGTGGC 61.310 57.895 0.00 0.00 0.00 5.01
738 751 0.456995 CTCCTTCTTCTCGTGTCCGC 60.457 60.000 0.00 0.00 0.00 5.54
739 752 0.456995 GCTCCTTCTTCTCGTGTCCG 60.457 60.000 0.00 0.00 0.00 4.79
740 753 0.892063 AGCTCCTTCTTCTCGTGTCC 59.108 55.000 0.00 0.00 0.00 4.02
741 754 1.135228 GGAGCTCCTTCTTCTCGTGTC 60.135 57.143 26.25 0.00 0.00 3.67
743 756 0.179150 CGGAGCTCCTTCTTCTCGTG 60.179 60.000 29.73 6.88 0.00 4.35
744 757 1.316706 CCGGAGCTCCTTCTTCTCGT 61.317 60.000 29.73 0.00 0.00 4.18
745 758 1.316706 ACCGGAGCTCCTTCTTCTCG 61.317 60.000 29.73 13.83 0.00 4.04
746 759 0.174617 CACCGGAGCTCCTTCTTCTC 59.825 60.000 29.73 1.58 0.00 2.87
806 832 1.986757 GCCAGGAGCAGAGGAGACA 60.987 63.158 0.00 0.00 42.97 3.41
866 892 3.381136 GGCGGGTACACGGGTGTA 61.381 66.667 20.88 7.55 44.42 2.90
868 894 4.446413 GAGGCGGGTACACGGGTG 62.446 72.222 20.88 0.00 0.00 4.61
947 1004 3.319689 TCGGGATGTTGAAAAAGAAACCC 59.680 43.478 0.00 0.00 0.00 4.11
952 1009 4.829064 CAACTCGGGATGTTGAAAAAGA 57.171 40.909 0.00 0.00 45.27 2.52
965 1022 2.351738 GCAGTGGAAAATTCAACTCGGG 60.352 50.000 0.07 0.00 39.42 5.14
967 1024 3.624326 TGCAGTGGAAAATTCAACTCG 57.376 42.857 0.07 0.00 39.42 4.18
1004 1061 9.165035 ACAAACAGATCAAAATGTCACAATTTT 57.835 25.926 0.00 0.00 39.71 1.82
1007 1066 7.439056 GGAACAAACAGATCAAAATGTCACAAT 59.561 33.333 0.00 0.00 0.00 2.71
1019 1078 4.705110 TTCTCTGGGAACAAACAGATCA 57.295 40.909 0.00 0.00 42.33 2.92
1460 1523 4.207281 TTCTCGCGGCGGAGGATG 62.207 66.667 23.46 6.34 34.74 3.51
1661 1724 5.250235 TCATCTTGAGGTAGTCATTCGAC 57.750 43.478 0.00 0.00 42.95 4.20
1715 1778 2.100216 GGCTTGCGGTTGTATGCG 59.900 61.111 0.00 0.00 32.71 4.73
1718 1781 2.106683 GCTCGGCTTGCGGTTGTAT 61.107 57.895 0.39 0.00 0.00 2.29
1979 2053 4.600576 TGCGCGAACTGGCACTGA 62.601 61.111 12.10 0.00 33.52 3.41
2186 2260 3.842007 TGAGTTGGGACGGTAAAAGAA 57.158 42.857 0.00 0.00 0.00 2.52
2188 2262 2.225727 GCTTGAGTTGGGACGGTAAAAG 59.774 50.000 0.00 0.00 0.00 2.27
2199 2273 1.933853 GTATGCGTAGGCTTGAGTTGG 59.066 52.381 9.11 0.00 40.82 3.77
2203 2277 1.200483 CGTGTATGCGTAGGCTTGAG 58.800 55.000 9.11 0.00 40.82 3.02
2507 2617 0.249868 TGTCACCTCAACTTCGCAGG 60.250 55.000 0.00 0.00 0.00 4.85
2553 2663 7.754924 GCTATACAAGATCTACTGCTTCTCATC 59.245 40.741 0.00 0.00 0.00 2.92
2554 2664 7.232330 TGCTATACAAGATCTACTGCTTCTCAT 59.768 37.037 0.00 0.00 0.00 2.90
2555 2665 6.547510 TGCTATACAAGATCTACTGCTTCTCA 59.452 38.462 0.00 0.00 0.00 3.27
2556 2666 6.976088 TGCTATACAAGATCTACTGCTTCTC 58.024 40.000 0.00 0.00 0.00 2.87
2557 2667 6.516527 GCTGCTATACAAGATCTACTGCTTCT 60.517 42.308 0.00 0.00 0.00 2.85
2679 2791 3.181470 ACAAATCGGGAACTTTTGTTGGG 60.181 43.478 0.00 0.00 43.66 4.12
2686 2798 1.146152 TGGGGACAAATCGGGAACTTT 59.854 47.619 0.00 0.00 37.44 2.66
2753 2866 3.921021 CAGTAAGACACAGCGGAGTAAAG 59.079 47.826 0.00 0.00 0.00 1.85
2771 2884 6.866770 CCGAAAAGTCATACAAAGAGACAGTA 59.133 38.462 0.00 0.00 34.80 2.74
2781 2894 6.931838 AGAGTACATCCGAAAAGTCATACAA 58.068 36.000 0.00 0.00 0.00 2.41
2852 2973 4.032900 CAGTACCGATCATGCACAAGTTAC 59.967 45.833 0.00 0.00 0.00 2.50
2928 3049 4.926832 GGCGTGCATTTTACATTTTTAGGT 59.073 37.500 0.00 0.00 0.00 3.08
2929 3050 4.328712 GGGCGTGCATTTTACATTTTTAGG 59.671 41.667 0.00 0.00 0.00 2.69
2956 4104 1.471327 GCTTTGTTGTTGCCTTGCAGA 60.471 47.619 0.00 0.00 40.61 4.26
3025 4173 3.262420 GTCAGTCACATAAGATTGCCGT 58.738 45.455 0.00 0.00 0.00 5.68
3038 4186 2.128035 CTTCCAGTGAACGTCAGTCAC 58.872 52.381 10.26 10.26 34.84 3.67
3081 4229 5.096169 CCGATACAACTAACACTGACAGAG 58.904 45.833 10.08 3.49 0.00 3.35
3105 4253 6.591935 TGTTATTCTGAAGAAACTGTCACCT 58.408 36.000 15.29 0.00 37.61 4.00
3142 4290 7.579761 AGGAAGCTCAAAATTATCATCCTTC 57.420 36.000 0.00 0.00 30.86 3.46
3143 4291 7.968014 AAGGAAGCTCAAAATTATCATCCTT 57.032 32.000 2.73 2.73 39.33 3.36
3195 4345 1.433837 GGTCGTGTCGTGGCAGTTTT 61.434 55.000 0.00 0.00 0.00 2.43
3206 4356 3.866910 TGACAGTTTTAGTTGGTCGTGTC 59.133 43.478 0.00 0.00 34.86 3.67
3217 4367 6.636447 TGCGAACATTTTGATGACAGTTTTAG 59.364 34.615 0.00 0.00 0.00 1.85
3395 4545 0.399233 GGGGTGGACTAGGATCTGCT 60.399 60.000 0.00 0.00 0.00 4.24
3397 4547 2.599677 GTAGGGGTGGACTAGGATCTG 58.400 57.143 0.00 0.00 0.00 2.90
3398 4548 1.504221 GGTAGGGGTGGACTAGGATCT 59.496 57.143 0.00 0.00 0.00 2.75
3410 4560 2.928396 AACTGCAGCGGTAGGGGT 60.928 61.111 15.27 0.00 0.00 4.95
3412 4562 1.741770 GTCAACTGCAGCGGTAGGG 60.742 63.158 15.27 0.59 0.00 3.53
3428 4578 5.351458 GGGAGGATGTGCATTTTATTTGTC 58.649 41.667 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.