Multiple sequence alignment - TraesCS1D01G366500

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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 TraesCS1D01G366500 chr1D 100.000 2513 0 0 1 2513 446475101 446477613 0.000000e+00 4641.0
1 TraesCS1D01G366500 chr1D 91.972 710 50 6 682 1388 355827694 355828399 0.000000e+00 989.0
2 TraesCS1D01G366500 chr1D 92.544 684 43 6 809 1488 445367079 445366400 0.000000e+00 974.0
3 TraesCS1D01G366500 chr1D 82.115 766 90 23 1635 2365 355828646 355829399 1.650000e-171 612.0
4 TraesCS1D01G366500 chr1D 84.202 595 47 19 1480 2045 445366370 445365794 3.680000e-148 534.0
5 TraesCS1D01G366500 chr1D 97.059 34 1 0 2385 2418 446477395 446477428 9.710000e-05 58.4
6 TraesCS1D01G366500 chr1D 97.059 34 1 0 2295 2328 446477485 446477518 9.710000e-05 58.4
7 TraesCS1D01G366500 chr1A 89.507 1601 104 42 807 2380 541343556 541345119 0.000000e+00 1967.0
8 TraesCS1D01G366500 chr1A 90.671 686 37 13 807 1488 541461051 541460389 0.000000e+00 887.0
9 TraesCS1D01G366500 chr1A 94.192 551 25 4 844 1392 543928135 543928680 0.000000e+00 833.0
10 TraesCS1D01G366500 chr1A 88.337 403 33 5 1987 2377 541459884 541459484 2.930000e-129 472.0
11 TraesCS1D01G366500 chr1A 95.918 49 2 0 2444 2492 541459436 541459388 2.070000e-11 80.5
12 TraesCS1D01G366500 chr1B 94.787 1055 22 6 1488 2513 610893709 610894759 0.000000e+00 1613.0
13 TraesCS1D01G366500 chr1B 91.515 990 74 6 495 1478 610892682 610893667 0.000000e+00 1354.0
14 TraesCS1D01G366500 chr1B 85.319 1301 116 45 495 1756 608336211 608334947 0.000000e+00 1275.0
15 TraesCS1D01G366500 chr1B 89.882 1018 64 17 495 1499 607317343 607316352 0.000000e+00 1273.0
16 TraesCS1D01G366500 chr1B 89.332 1003 67 18 511 1499 607138195 607137219 0.000000e+00 1223.0
17 TraesCS1D01G366500 chr1B 91.535 697 47 6 800 1488 608043033 608042341 0.000000e+00 950.0
18 TraesCS1D01G366500 chr1B 89.753 283 27 2 495 776 608043536 608043255 6.610000e-96 361.0
19 TraesCS1D01G366500 chr1B 83.908 87 8 3 2221 2301 608041726 608041640 7.450000e-11 78.7
20 TraesCS1D01G366500 chr1B 97.059 34 1 0 2385 2418 610894531 610894564 9.710000e-05 58.4
21 TraesCS1D01G366500 chr1B 97.059 34 1 0 2295 2328 610894621 610894654 9.710000e-05 58.4
22 TraesCS1D01G366500 chr3D 89.898 683 55 6 806 1478 114880995 114880317 0.000000e+00 867.0
23 TraesCS1D01G366500 chr3D 82.456 342 36 14 2176 2513 114879630 114879309 6.850000e-71 278.0
24 TraesCS1D01G366500 chr5D 81.490 416 70 7 34 445 239591144 239591556 4.010000e-88 335.0
25 TraesCS1D01G366500 chr5D 80.529 416 73 8 34 445 239589800 239590211 1.880000e-81 313.0
26 TraesCS1D01G366500 chr2A 80.407 393 72 5 56 445 277616168 277616558 6.800000e-76 294.0
27 TraesCS1D01G366500 chr2A 77.556 450 94 6 1 445 5106728 5106281 5.330000e-67 265.0
28 TraesCS1D01G366500 chr4B 78.241 432 87 6 8 435 513055503 513055931 1.150000e-68 270.0
29 TraesCS1D01G366500 chr2B 82.530 166 21 3 1 163 10594034 10594194 3.370000e-29 139.0
30 TraesCS1D01G366500 chr3B 78.659 164 30 5 4 163 25372514 25372352 1.230000e-18 104.0
31 TraesCS1D01G366500 chr7D 81.739 115 18 3 1 112 17256163 17256049 2.660000e-15 93.5
32 TraesCS1D01G366500 chr7A 80.392 102 16 3 8 105 16648348 16648247 9.640000e-10 75.0


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 TraesCS1D01G366500 chr1D 446475101 446477613 2512 False 1585.933333 4641 98.039333 1 2513 3 chr1D.!!$F2 2512
1 TraesCS1D01G366500 chr1D 355827694 355829399 1705 False 800.500000 989 87.043500 682 2365 2 chr1D.!!$F1 1683
2 TraesCS1D01G366500 chr1D 445365794 445367079 1285 True 754.000000 974 88.373000 809 2045 2 chr1D.!!$R1 1236
3 TraesCS1D01G366500 chr1A 541343556 541345119 1563 False 1967.000000 1967 89.507000 807 2380 1 chr1A.!!$F1 1573
4 TraesCS1D01G366500 chr1A 543928135 543928680 545 False 833.000000 833 94.192000 844 1392 1 chr1A.!!$F2 548
5 TraesCS1D01G366500 chr1A 541459388 541461051 1663 True 479.833333 887 91.642000 807 2492 3 chr1A.!!$R1 1685
6 TraesCS1D01G366500 chr1B 608334947 608336211 1264 True 1275.000000 1275 85.319000 495 1756 1 chr1B.!!$R3 1261
7 TraesCS1D01G366500 chr1B 607316352 607317343 991 True 1273.000000 1273 89.882000 495 1499 1 chr1B.!!$R2 1004
8 TraesCS1D01G366500 chr1B 607137219 607138195 976 True 1223.000000 1223 89.332000 511 1499 1 chr1B.!!$R1 988
9 TraesCS1D01G366500 chr1B 610892682 610894759 2077 False 770.950000 1613 95.105000 495 2513 4 chr1B.!!$F1 2018
10 TraesCS1D01G366500 chr1B 608041640 608043536 1896 True 463.233333 950 88.398667 495 2301 3 chr1B.!!$R4 1806
11 TraesCS1D01G366500 chr3D 114879309 114880995 1686 True 572.500000 867 86.177000 806 2513 2 chr3D.!!$R1 1707
12 TraesCS1D01G366500 chr5D 239589800 239591556 1756 False 324.000000 335 81.009500 34 445 2 chr5D.!!$F1 411

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
395 399 0.034896 AGGGCAACGACGACTCAAAT 59.965 50.0 0.0 0.0 37.6 2.32 F
471 475 0.333993 TACTAGCGGGTCCTTGGAGT 59.666 55.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1417 2083 0.893447 GCTTTTGGAATCTGCAGGCT 59.107 50.000 15.13 0.21 0.0 4.58 R
2428 3253 2.159448 TGAAGTTGGTTGTGACAAAGCG 60.159 45.455 0.00 0.00 0.0 4.68 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
42 43 3.540367 TTCCGTCCAAGGCCGAACC 62.540 63.158 0.00 0.00 39.61 3.62
49 50 0.608035 CCAAGGCCGAACCAAGCTTA 60.608 55.000 0.00 0.00 43.14 3.09
51 52 0.400594 AAGGCCGAACCAAGCTTACT 59.599 50.000 0.00 0.00 43.14 2.24
64 67 2.933769 AGCTTACTTGCAAATTCGTGC 58.066 42.857 0.00 0.77 45.15 5.34
71 74 1.141665 GCAAATTCGTGCCCATCCC 59.858 57.895 0.00 0.00 38.66 3.85
72 75 1.433064 CAAATTCGTGCCCATCCCG 59.567 57.895 0.00 0.00 0.00 5.14
74 77 2.493273 AAATTCGTGCCCATCCCGGT 62.493 55.000 0.00 0.00 0.00 5.28
97 101 0.684805 ACCACCAGATCGACCTCCTC 60.685 60.000 0.00 0.00 0.00 3.71
105 109 0.183971 ATCGACCTCCTCCGTCATCT 59.816 55.000 0.00 0.00 0.00 2.90
107 111 1.211212 TCGACCTCCTCCGTCATCTAA 59.789 52.381 0.00 0.00 0.00 2.10
117 121 0.930310 CGTCATCTAACACGCCCATG 59.070 55.000 0.00 0.00 0.00 3.66
121 125 1.140052 CATCTAACACGCCCATGGGTA 59.860 52.381 31.58 14.73 35.62 3.69
163 167 4.008933 GACCGGAGCTGCACCACT 62.009 66.667 9.46 0.00 0.00 4.00
165 169 4.320456 CCGGAGCTGCACCACTGT 62.320 66.667 16.29 0.00 0.00 3.55
168 172 2.427320 GAGCTGCACCACTGTCCA 59.573 61.111 1.02 0.00 0.00 4.02
174 178 0.323816 TGCACCACTGTCCAAAACCA 60.324 50.000 0.00 0.00 0.00 3.67
175 179 0.102300 GCACCACTGTCCAAAACCAC 59.898 55.000 0.00 0.00 0.00 4.16
176 180 0.744281 CACCACTGTCCAAAACCACC 59.256 55.000 0.00 0.00 0.00 4.61
177 181 0.333312 ACCACTGTCCAAAACCACCA 59.667 50.000 0.00 0.00 0.00 4.17
180 184 0.333312 ACTGTCCAAAACCACCACCA 59.667 50.000 0.00 0.00 0.00 4.17
202 206 2.678580 TGGGTGAGCCATCGACGA 60.679 61.111 0.00 0.00 36.17 4.20
204 208 2.202756 GGTGAGCCATCGACGACC 60.203 66.667 0.00 0.00 34.09 4.79
251 255 2.436646 CCTGGGGACGCACATGTC 60.437 66.667 0.00 0.00 38.17 3.06
262 266 1.577328 GCACATGTCCAAGACACCCG 61.577 60.000 0.00 0.00 45.65 5.28
298 302 4.100084 CCACATCCTGGAGCCGCA 62.100 66.667 1.52 0.00 43.95 5.69
300 304 4.479993 ACATCCTGGAGCCGCAGC 62.480 66.667 1.52 0.00 40.32 5.25
330 334 2.591753 CGCCACCACCATCATCCT 59.408 61.111 0.00 0.00 0.00 3.24
333 337 1.925285 GCCACCACCATCATCCTCCA 61.925 60.000 0.00 0.00 0.00 3.86
334 338 0.107017 CCACCACCATCATCCTCCAC 60.107 60.000 0.00 0.00 0.00 4.02
377 381 2.182030 GGCGACGGTGAGGAGAAG 59.818 66.667 0.00 0.00 0.00 2.85
379 383 2.885861 CGACGGTGAGGAGAAGGG 59.114 66.667 0.00 0.00 0.00 3.95
381 385 2.203788 ACGGTGAGGAGAAGGGCA 60.204 61.111 0.00 0.00 0.00 5.36
383 387 1.376037 CGGTGAGGAGAAGGGCAAC 60.376 63.158 0.00 0.00 0.00 4.17
385 389 1.671742 GTGAGGAGAAGGGCAACGA 59.328 57.895 0.00 0.00 37.60 3.85
387 391 1.446272 GAGGAGAAGGGCAACGACG 60.446 63.158 0.00 0.00 37.60 5.12
388 392 1.874345 GAGGAGAAGGGCAACGACGA 61.874 60.000 0.00 0.00 37.60 4.20
391 395 0.733223 GAGAAGGGCAACGACGACTC 60.733 60.000 0.00 0.00 37.60 3.36
392 396 1.006571 GAAGGGCAACGACGACTCA 60.007 57.895 0.00 0.00 37.60 3.41
395 399 0.034896 AGGGCAACGACGACTCAAAT 59.965 50.000 0.00 0.00 37.60 2.32
405 409 3.315470 CGACGACTCAAATCCCTAGATCA 59.685 47.826 0.00 0.00 0.00 2.92
410 414 5.242615 CGACTCAAATCCCTAGATCAGATCA 59.757 44.000 13.14 0.00 0.00 2.92
411 415 6.239148 CGACTCAAATCCCTAGATCAGATCAA 60.239 42.308 13.14 0.00 0.00 2.57
424 428 2.021639 TCAGATCAAGAGGGAGGGGATT 60.022 50.000 0.00 0.00 0.00 3.01
425 429 3.209843 TCAGATCAAGAGGGAGGGGATTA 59.790 47.826 0.00 0.00 0.00 1.75
427 431 2.496679 TCAAGAGGGAGGGGATTAGG 57.503 55.000 0.00 0.00 0.00 2.69
445 449 1.539665 GAGGGAGGAGATCGGGAGT 59.460 63.158 0.00 0.00 0.00 3.85
446 450 0.538746 GAGGGAGGAGATCGGGAGTC 60.539 65.000 0.00 0.00 0.00 3.36
447 451 1.532078 GGGAGGAGATCGGGAGTCC 60.532 68.421 0.00 0.00 0.00 3.85
448 452 1.532078 GGAGGAGATCGGGAGTCCC 60.532 68.421 19.37 19.37 41.09 4.46
461 465 1.616456 GGAGTCCCCTATACTAGCGGG 60.616 61.905 0.00 0.00 37.52 6.13
462 466 1.075212 GAGTCCCCTATACTAGCGGGT 59.925 57.143 6.34 0.00 37.48 5.28
463 467 1.075212 AGTCCCCTATACTAGCGGGTC 59.925 57.143 6.34 0.00 37.48 4.46
464 468 0.407139 TCCCCTATACTAGCGGGTCC 59.593 60.000 6.34 0.00 37.48 4.46
465 469 0.408700 CCCCTATACTAGCGGGTCCT 59.591 60.000 6.34 0.00 36.18 3.85
466 470 1.203149 CCCCTATACTAGCGGGTCCTT 60.203 57.143 6.34 0.00 36.18 3.36
467 471 1.893801 CCCTATACTAGCGGGTCCTTG 59.106 57.143 0.00 0.00 33.16 3.61
471 475 0.333993 TACTAGCGGGTCCTTGGAGT 59.666 55.000 0.00 0.00 0.00 3.85
472 476 0.971447 ACTAGCGGGTCCTTGGAGTC 60.971 60.000 0.00 0.00 0.00 3.36
473 477 0.970937 CTAGCGGGTCCTTGGAGTCA 60.971 60.000 0.00 0.00 0.00 3.41
475 479 1.201429 AGCGGGTCCTTGGAGTCAAT 61.201 55.000 0.00 0.00 31.75 2.57
476 480 1.026718 GCGGGTCCTTGGAGTCAATG 61.027 60.000 0.00 0.00 31.75 2.82
478 482 0.698818 GGGTCCTTGGAGTCAATGGT 59.301 55.000 0.00 0.00 31.75 3.55
479 483 1.075536 GGGTCCTTGGAGTCAATGGTT 59.924 52.381 0.00 0.00 31.75 3.67
480 484 2.162681 GGTCCTTGGAGTCAATGGTTG 58.837 52.381 0.00 0.00 31.75 3.77
481 485 2.489073 GGTCCTTGGAGTCAATGGTTGT 60.489 50.000 0.00 0.00 31.75 3.32
482 486 2.554032 GTCCTTGGAGTCAATGGTTGTG 59.446 50.000 0.00 0.00 31.75 3.33
483 487 1.270550 CCTTGGAGTCAATGGTTGTGC 59.729 52.381 0.00 0.00 31.75 4.57
484 488 2.233271 CTTGGAGTCAATGGTTGTGCT 58.767 47.619 0.00 0.00 31.75 4.40
485 489 1.896220 TGGAGTCAATGGTTGTGCTC 58.104 50.000 0.00 7.78 35.07 4.26
486 490 1.168714 GGAGTCAATGGTTGTGCTCC 58.831 55.000 14.76 14.76 42.03 4.70
487 491 1.271597 GGAGTCAATGGTTGTGCTCCT 60.272 52.381 18.89 0.00 43.51 3.69
489 493 2.485814 GAGTCAATGGTTGTGCTCCTTC 59.514 50.000 0.00 0.00 32.20 3.46
493 497 2.206576 ATGGTTGTGCTCCTTCTTCC 57.793 50.000 0.00 0.00 0.00 3.46
502 506 2.293170 GCTCCTTCTTCCTTGGCATAC 58.707 52.381 0.00 0.00 0.00 2.39
527 531 4.021981 AGCTCTAACTTGAATTTGGTTGGC 60.022 41.667 0.00 0.00 0.00 4.52
726 792 7.994425 TTGAACATTTAAGTGCCTGAATAGA 57.006 32.000 0.00 0.00 0.00 1.98
732 798 8.680903 ACATTTAAGTGCCTGAATAGAGAATTG 58.319 33.333 0.00 0.00 0.00 2.32
876 1142 3.565214 TCCAAGCTTCCGGCCACA 61.565 61.111 2.24 0.00 43.05 4.17
907 1173 3.178611 GCATCCCTCCCCCGGATT 61.179 66.667 0.73 0.00 38.08 3.01
1006 1479 2.764314 CGCCCCTCCTTCGCAAATG 61.764 63.158 0.00 0.00 0.00 2.32
1116 1600 3.330720 AAGGGACTCGGCAAGGGG 61.331 66.667 0.00 0.00 38.49 4.79
1411 2077 1.444553 CCGACTGTCGCCTGTCTTC 60.445 63.158 23.87 0.00 38.82 2.87
1417 2083 3.666253 TCGCCTGTCTTCGTCGCA 61.666 61.111 0.00 0.00 0.00 5.10
1482 2150 4.705507 AGTTCGCTATTTCCTCTGTCTGTA 59.294 41.667 0.00 0.00 0.00 2.74
1486 2194 5.038033 CGCTATTTCCTCTGTCTGTAGTTC 58.962 45.833 0.00 0.00 0.00 3.01
1603 2312 1.985473 TTGTGATGCTTGAGTTGGCT 58.015 45.000 0.00 0.00 0.00 4.75
1758 2506 2.805671 TCATTGTTACTTCTGTGGTGCG 59.194 45.455 0.00 0.00 0.00 5.34
1777 2525 5.278512 GGTGCGATGTCTGTAATAGAGATGA 60.279 44.000 0.00 0.00 39.34 2.92
1816 2565 1.686587 TCACCGAGTTCTTGCTTGAGA 59.313 47.619 0.00 0.00 0.00 3.27
1817 2566 2.064762 CACCGAGTTCTTGCTTGAGAG 58.935 52.381 0.00 0.00 0.00 3.20
1829 2578 2.573462 TGCTTGAGAGTGGCTATCCTTT 59.427 45.455 0.00 0.00 0.00 3.11
2063 2823 1.414181 CGATACCCTCTTGGCAGTGAT 59.586 52.381 0.00 0.00 37.83 3.06
2428 3253 1.545582 TCTGCTTATTTGCTGCCAACC 59.454 47.619 0.00 0.00 32.95 3.77
2492 3327 8.982723 ACTGAACACCTGATACAAGTATTAGAT 58.017 33.333 12.10 0.00 32.71 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 3.540367 TTCGGCCTTGGACGGAACC 62.540 63.158 15.45 0.00 0.00 3.62
23 24 2.031465 TTCGGCCTTGGACGGAAC 59.969 61.111 15.45 0.00 0.00 3.62
24 25 2.031465 GTTCGGCCTTGGACGGAA 59.969 61.111 15.45 5.47 0.00 4.30
25 26 4.011517 GGTTCGGCCTTGGACGGA 62.012 66.667 15.45 2.71 0.00 4.69
26 27 3.835790 TTGGTTCGGCCTTGGACGG 62.836 63.158 15.45 0.00 38.35 4.79
27 28 2.281208 TTGGTTCGGCCTTGGACG 60.281 61.111 8.88 8.88 38.35 4.79
28 29 2.626780 GCTTGGTTCGGCCTTGGAC 61.627 63.158 0.00 0.00 38.35 4.02
29 30 2.282180 GCTTGGTTCGGCCTTGGA 60.282 61.111 0.00 0.00 38.35 3.53
30 31 0.608035 TAAGCTTGGTTCGGCCTTGG 60.608 55.000 9.86 0.00 38.35 3.61
31 32 0.521735 GTAAGCTTGGTTCGGCCTTG 59.478 55.000 9.86 0.00 38.35 3.61
32 33 0.400594 AGTAAGCTTGGTTCGGCCTT 59.599 50.000 9.86 0.00 38.35 4.35
49 50 0.968405 ATGGGCACGAATTTGCAAGT 59.032 45.000 0.00 0.00 44.94 3.16
51 52 0.246086 GGATGGGCACGAATTTGCAA 59.754 50.000 0.00 0.00 44.94 4.08
71 74 1.447838 CGATCTGGTGGTCCAACCG 60.448 63.158 3.92 0.00 42.58 4.44
72 75 0.391263 GTCGATCTGGTGGTCCAACC 60.391 60.000 3.92 4.03 43.81 3.77
74 77 0.544357 AGGTCGATCTGGTGGTCCAA 60.544 55.000 0.00 0.00 43.81 3.53
84 88 0.183971 ATGACGGAGGAGGTCGATCT 59.816 55.000 0.00 0.00 37.22 2.75
90 94 2.100989 GTGTTAGATGACGGAGGAGGT 58.899 52.381 0.00 0.00 0.00 3.85
91 95 1.065701 CGTGTTAGATGACGGAGGAGG 59.934 57.143 0.00 0.00 31.84 4.30
97 101 0.179084 ATGGGCGTGTTAGATGACGG 60.179 55.000 0.00 0.00 36.09 4.79
105 109 0.391395 CGTTACCCATGGGCGTGTTA 60.391 55.000 31.73 12.51 39.32 2.41
107 111 2.046700 CGTTACCCATGGGCGTGT 60.047 61.111 31.73 14.08 39.32 4.49
149 153 2.740055 GACAGTGGTGCAGCTCCG 60.740 66.667 18.08 8.57 0.00 4.63
154 158 0.385390 GGTTTTGGACAGTGGTGCAG 59.615 55.000 0.00 0.00 46.45 4.41
155 159 0.323816 TGGTTTTGGACAGTGGTGCA 60.324 50.000 0.00 0.00 44.17 4.57
160 164 0.744281 GGTGGTGGTTTTGGACAGTG 59.256 55.000 0.00 0.00 0.00 3.66
163 167 1.032657 CGTGGTGGTGGTTTTGGACA 61.033 55.000 0.00 0.00 0.00 4.02
165 169 2.122167 GCGTGGTGGTGGTTTTGGA 61.122 57.895 0.00 0.00 0.00 3.53
168 172 2.124693 CAGGCGTGGTGGTGGTTTT 61.125 57.895 0.00 0.00 0.00 2.43
242 246 1.577328 GGGTGTCTTGGACATGTGCG 61.577 60.000 13.03 0.00 44.63 5.34
244 248 0.250295 ACGGGTGTCTTGGACATGTG 60.250 55.000 1.15 0.00 44.63 3.21
251 255 0.673644 GATCCACACGGGTGTCTTGG 60.674 60.000 18.16 0.00 42.83 3.61
254 258 1.258445 GGAGATCCACACGGGTGTCT 61.258 60.000 18.16 14.03 42.83 3.41
269 273 1.003839 GATGTGGTTGCGGTGGAGA 60.004 57.895 0.00 0.00 0.00 3.71
310 314 4.127744 ATGATGGTGGTGGCGGGG 62.128 66.667 0.00 0.00 0.00 5.73
314 318 1.152881 GGAGGATGATGGTGGTGGC 60.153 63.158 0.00 0.00 0.00 5.01
317 321 0.253347 AGGTGGAGGATGATGGTGGT 60.253 55.000 0.00 0.00 0.00 4.16
360 364 2.182030 CTTCTCCTCACCGTCGCC 59.818 66.667 0.00 0.00 0.00 5.54
363 367 1.827399 TTGCCCTTCTCCTCACCGTC 61.827 60.000 0.00 0.00 0.00 4.79
364 368 1.841556 TTGCCCTTCTCCTCACCGT 60.842 57.895 0.00 0.00 0.00 4.83
368 372 1.671742 GTCGTTGCCCTTCTCCTCA 59.328 57.895 0.00 0.00 0.00 3.86
376 380 0.034896 ATTTGAGTCGTCGTTGCCCT 59.965 50.000 0.00 0.00 0.00 5.19
377 381 0.442699 GATTTGAGTCGTCGTTGCCC 59.557 55.000 0.00 0.00 0.00 5.36
379 383 0.442699 GGGATTTGAGTCGTCGTTGC 59.557 55.000 0.00 0.00 0.00 4.17
381 385 3.087031 TCTAGGGATTTGAGTCGTCGTT 58.913 45.455 0.00 0.00 0.00 3.85
383 387 3.315470 TGATCTAGGGATTTGAGTCGTCG 59.685 47.826 0.00 0.00 31.46 5.12
385 389 4.537751 TCTGATCTAGGGATTTGAGTCGT 58.462 43.478 0.00 0.00 31.46 4.34
387 391 6.662865 TGATCTGATCTAGGGATTTGAGTC 57.337 41.667 17.82 0.00 31.46 3.36
388 392 6.843333 TCTTGATCTGATCTAGGGATTTGAGT 59.157 38.462 22.76 0.00 33.76 3.41
391 395 6.465948 CCTCTTGATCTGATCTAGGGATTTG 58.534 44.000 24.47 8.85 35.05 2.32
392 396 5.547276 CCCTCTTGATCTGATCTAGGGATTT 59.453 44.000 29.80 0.00 42.32 2.17
395 399 3.729524 TCCCTCTTGATCTGATCTAGGGA 59.270 47.826 30.91 30.91 44.19 4.20
405 409 2.906169 AATCCCCTCCCTCTTGATCT 57.094 50.000 0.00 0.00 0.00 2.75
410 414 1.224381 CCTCCTAATCCCCTCCCTCTT 59.776 57.143 0.00 0.00 0.00 2.85
411 415 0.871024 CCTCCTAATCCCCTCCCTCT 59.129 60.000 0.00 0.00 0.00 3.69
424 428 0.403008 TCCCGATCTCCTCCCTCCTA 60.403 60.000 0.00 0.00 0.00 2.94
425 429 1.701757 TCCCGATCTCCTCCCTCCT 60.702 63.158 0.00 0.00 0.00 3.69
427 431 0.538746 GACTCCCGATCTCCTCCCTC 60.539 65.000 0.00 0.00 0.00 4.30
448 452 1.893801 CCAAGGACCCGCTAGTATAGG 59.106 57.143 0.00 0.00 39.70 2.57
449 453 2.820787 CTCCAAGGACCCGCTAGTATAG 59.179 54.545 0.00 0.00 43.09 1.31
450 454 2.176364 ACTCCAAGGACCCGCTAGTATA 59.824 50.000 0.00 0.00 0.00 1.47
451 455 1.063114 ACTCCAAGGACCCGCTAGTAT 60.063 52.381 0.00 0.00 0.00 2.12
452 456 0.333993 ACTCCAAGGACCCGCTAGTA 59.666 55.000 0.00 0.00 0.00 1.82
453 457 0.971447 GACTCCAAGGACCCGCTAGT 60.971 60.000 0.00 0.00 0.00 2.57
458 462 0.392998 CCATTGACTCCAAGGACCCG 60.393 60.000 0.00 0.00 36.26 5.28
459 463 0.698818 ACCATTGACTCCAAGGACCC 59.301 55.000 0.00 0.00 36.26 4.46
461 465 2.554032 CACAACCATTGACTCCAAGGAC 59.446 50.000 0.00 0.00 36.26 3.85
462 466 2.862541 CACAACCATTGACTCCAAGGA 58.137 47.619 0.00 0.00 36.26 3.36
463 467 1.270550 GCACAACCATTGACTCCAAGG 59.729 52.381 0.00 0.00 35.48 3.61
464 468 2.227388 GAGCACAACCATTGACTCCAAG 59.773 50.000 0.00 0.00 35.48 3.61
465 469 2.229792 GAGCACAACCATTGACTCCAA 58.770 47.619 0.00 0.00 33.99 3.53
466 470 1.545428 GGAGCACAACCATTGACTCCA 60.545 52.381 20.61 0.00 46.81 3.86
467 471 1.168714 GGAGCACAACCATTGACTCC 58.831 55.000 14.92 14.92 44.16 3.85
471 475 2.957402 AGAAGGAGCACAACCATTGA 57.043 45.000 0.00 0.00 0.00 2.57
472 476 2.229784 GGAAGAAGGAGCACAACCATTG 59.770 50.000 0.00 0.00 0.00 2.82
473 477 2.108952 AGGAAGAAGGAGCACAACCATT 59.891 45.455 0.00 0.00 0.00 3.16
475 479 1.140312 AGGAAGAAGGAGCACAACCA 58.860 50.000 0.00 0.00 0.00 3.67
476 480 1.882623 CAAGGAAGAAGGAGCACAACC 59.117 52.381 0.00 0.00 0.00 3.77
478 482 1.819305 GCCAAGGAAGAAGGAGCACAA 60.819 52.381 0.00 0.00 0.00 3.33
479 483 0.250901 GCCAAGGAAGAAGGAGCACA 60.251 55.000 0.00 0.00 0.00 4.57
480 484 0.250901 TGCCAAGGAAGAAGGAGCAC 60.251 55.000 0.00 0.00 0.00 4.40
481 485 0.700564 ATGCCAAGGAAGAAGGAGCA 59.299 50.000 0.00 0.00 0.00 4.26
482 486 2.293170 GTATGCCAAGGAAGAAGGAGC 58.707 52.381 0.00 0.00 0.00 4.70
483 487 2.239654 TGGTATGCCAAGGAAGAAGGAG 59.760 50.000 0.00 0.00 42.83 3.69
484 488 2.239654 CTGGTATGCCAAGGAAGAAGGA 59.760 50.000 3.43 0.00 45.51 3.36
485 489 2.648059 CTGGTATGCCAAGGAAGAAGG 58.352 52.381 3.43 0.00 45.51 3.46
486 490 2.019984 GCTGGTATGCCAAGGAAGAAG 58.980 52.381 3.43 0.00 45.51 2.85
487 491 1.635487 AGCTGGTATGCCAAGGAAGAA 59.365 47.619 3.43 0.00 45.51 2.52
489 493 1.211457 AGAGCTGGTATGCCAAGGAAG 59.789 52.381 3.43 0.00 45.51 3.46
493 497 3.550437 AGTTAGAGCTGGTATGCCAAG 57.450 47.619 3.43 0.00 45.51 3.61
502 506 5.464168 CAACCAAATTCAAGTTAGAGCTGG 58.536 41.667 0.00 0.00 0.00 4.85
704 770 7.849804 TCTCTATTCAGGCACTTAAATGTTC 57.150 36.000 0.00 0.00 34.60 3.18
712 778 4.853007 AGCAATTCTCTATTCAGGCACTT 58.147 39.130 0.00 0.00 34.60 3.16
776 844 5.058490 CCATAAACATGCCCCATTTTCATC 58.942 41.667 0.00 0.00 0.00 2.92
911 1177 1.313812 ATGGAGTGGACGGTCGAGAC 61.314 60.000 1.43 0.00 0.00 3.36
997 1470 0.592637 CTGGTGCTGTCATTTGCGAA 59.407 50.000 0.00 0.00 0.00 4.70
998 1471 0.534877 ACTGGTGCTGTCATTTGCGA 60.535 50.000 0.00 0.00 0.00 5.10
1006 1479 1.376037 GGTGGCTACTGGTGCTGTC 60.376 63.158 0.00 0.00 0.00 3.51
1095 1579 3.665675 CTTGCCGAGTCCCTTCCCG 62.666 68.421 0.00 0.00 0.00 5.14
1098 1582 2.269241 CCCTTGCCGAGTCCCTTC 59.731 66.667 0.00 0.00 0.00 3.46
1417 2083 0.893447 GCTTTTGGAATCTGCAGGCT 59.107 50.000 15.13 0.21 0.00 4.58
1482 2150 5.357032 AGACAAGTTTCATTTCCAACGAACT 59.643 36.000 0.00 0.00 0.00 3.01
1486 2194 5.207768 CAGAGACAAGTTTCATTTCCAACG 58.792 41.667 0.00 0.00 0.00 4.10
1603 2312 3.880047 AACAGGTTCGATTCATACGGA 57.120 42.857 0.00 0.00 0.00 4.69
1777 2525 5.128919 GGTGATGAAATGCAGACTAATCCT 58.871 41.667 0.00 0.00 0.00 3.24
1816 2565 3.725634 ACTCAGGTAAAGGATAGCCACT 58.274 45.455 0.00 0.00 36.29 4.00
1817 2566 4.489306 AACTCAGGTAAAGGATAGCCAC 57.511 45.455 0.00 0.00 36.29 5.01
1829 2578 4.774660 TTGTACACCCAAAACTCAGGTA 57.225 40.909 0.00 0.00 30.98 3.08
2063 2823 5.221722 ACTCAACTGAAGGATGAAGTTGCTA 60.222 40.000 9.37 0.00 46.66 3.49
2169 2948 4.607293 TTCTGTAGCATGTCTTGTCAGT 57.393 40.909 0.00 0.00 0.00 3.41
2174 2953 5.181811 TGGTTGAATTCTGTAGCATGTCTTG 59.818 40.000 7.05 0.00 0.00 3.02
2428 3253 2.159448 TGAAGTTGGTTGTGACAAAGCG 60.159 45.455 0.00 0.00 0.00 4.68


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

AutoCloner maintained by Alex Coulton.