Multiple sequence alignment - TraesCS2A01G202100

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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 TraesCS2A01G202100 chr2A 100.000 2576 0 0 1 2576 176654466 176657041 0.000000e+00 4758.0
1 TraesCS2A01G202100 chr2A 82.119 151 26 1 341 490 27631845 27631695 7.480000e-26 128.0
2 TraesCS2A01G202100 chr2D 89.648 1362 53 33 477 1801 163023342 163022032 0.000000e+00 1653.0
3 TraesCS2A01G202100 chr2D 93.182 88 6 0 1872 1959 163022010 163021923 2.080000e-26 130.0
4 TraesCS2A01G202100 chr2D 76.836 177 39 2 315 490 117184738 117184913 5.870000e-17 99.0
5 TraesCS2A01G202100 chr2B 87.725 1442 61 41 491 1856 224645395 224646796 0.000000e+00 1576.0
6 TraesCS2A01G202100 chr2B 91.765 170 7 5 4 169 224645045 224645211 1.990000e-56 230.0
7 TraesCS2A01G202100 chr2B 86.792 212 7 5 122 316 224645194 224645401 1.550000e-52 217.0
8 TraesCS2A01G202100 chr2B 95.349 86 4 0 1872 1957 224646783 224646868 1.240000e-28 137.0
9 TraesCS2A01G202100 chr2B 81.481 81 12 3 407 485 223735136 223735215 2.140000e-06 63.9
10 TraesCS2A01G202100 chr5B 98.534 614 8 1 1963 2576 689861092 689861704 0.000000e+00 1083.0
11 TraesCS2A01G202100 chr5B 97.809 502 11 0 2075 2576 412262940 412263441 0.000000e+00 867.0
12 TraesCS2A01G202100 chr5B 92.784 97 5 2 1958 2054 412262858 412262952 3.460000e-29 139.0
13 TraesCS2A01G202100 chr5B 86.179 123 11 4 334 450 61147955 61148077 7.480000e-26 128.0
14 TraesCS2A01G202100 chr3A 97.419 620 16 0 1957 2576 99250926 99251545 0.000000e+00 1057.0
15 TraesCS2A01G202100 chr3A 96.658 389 10 2 1952 2339 692489798 692490184 0.000000e+00 643.0
16 TraesCS2A01G202100 chr3A 98.558 208 3 0 2369 2576 692490181 692490388 4.050000e-98 368.0
17 TraesCS2A01G202100 chr7D 88.320 625 55 8 1958 2576 579745429 579746041 0.000000e+00 734.0
18 TraesCS2A01G202100 chr7D 85.484 124 15 3 310 430 220025370 220025247 2.690000e-25 126.0
19 TraesCS2A01G202100 chr4D 86.581 544 57 8 1953 2493 234843233 234842703 1.030000e-163 586.0
20 TraesCS2A01G202100 chr1D 90.249 441 30 6 1082 1514 1836842 1836407 4.810000e-157 564.0
21 TraesCS2A01G202100 chr1D 80.117 171 31 3 322 490 263194890 263194721 9.680000e-25 124.0
22 TraesCS2A01G202100 chr6D 79.418 894 81 62 888 1731 400077991 400077151 1.050000e-148 536.0
23 TraesCS2A01G202100 chr4A 97.232 289 8 0 2288 2576 709886410 709886122 8.280000e-135 490.0
24 TraesCS2A01G202100 chr6B 78.194 908 90 74 888 1740 599073076 599072222 4.990000e-132 481.0
25 TraesCS2A01G202100 chr6B 83.878 490 39 28 957 1428 604597814 604598281 5.090000e-117 431.0
26 TraesCS2A01G202100 chr6B 82.222 135 20 4 1957 2090 658802175 658802306 2.090000e-21 113.0
27 TraesCS2A01G202100 chr6A 81.919 542 49 36 888 1408 545830493 545829980 1.840000e-111 412.0
28 TraesCS2A01G202100 chr5D 82.778 180 23 6 319 490 462454618 462454797 1.230000e-33 154.0
29 TraesCS2A01G202100 chr7A 83.432 169 17 7 324 490 682176878 682176719 2.070000e-31 147.0
30 TraesCS2A01G202100 chr1B 84.783 138 18 3 1954 2090 647927245 647927110 4.470000e-28 135.0
31 TraesCS2A01G202100 chr1B 81.529 157 22 5 317 468 569514620 569514466 3.480000e-24 122.0
32 TraesCS2A01G202100 chr1B 82.609 138 21 3 1955 2090 186795430 186795294 4.500000e-23 119.0
33 TraesCS2A01G202100 chr5A 78.286 175 29 7 321 490 51793030 51793200 1.260000e-18 104.0


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 TraesCS2A01G202100 chr2A 176654466 176657041 2575 False 4758.0 4758 100.00000 1 2576 1 chr2A.!!$F1 2575
1 TraesCS2A01G202100 chr2D 163021923 163023342 1419 True 891.5 1653 91.41500 477 1959 2 chr2D.!!$R1 1482
2 TraesCS2A01G202100 chr2B 224645045 224646868 1823 False 540.0 1576 90.40775 4 1957 4 chr2B.!!$F2 1953
3 TraesCS2A01G202100 chr5B 689861092 689861704 612 False 1083.0 1083 98.53400 1963 2576 1 chr5B.!!$F2 613
4 TraesCS2A01G202100 chr5B 412262858 412263441 583 False 503.0 867 95.29650 1958 2576 2 chr5B.!!$F3 618
5 TraesCS2A01G202100 chr3A 99250926 99251545 619 False 1057.0 1057 97.41900 1957 2576 1 chr3A.!!$F1 619
6 TraesCS2A01G202100 chr3A 692489798 692490388 590 False 505.5 643 97.60800 1952 2576 2 chr3A.!!$F2 624
7 TraesCS2A01G202100 chr7D 579745429 579746041 612 False 734.0 734 88.32000 1958 2576 1 chr7D.!!$F1 618
8 TraesCS2A01G202100 chr4D 234842703 234843233 530 True 586.0 586 86.58100 1953 2493 1 chr4D.!!$R1 540
9 TraesCS2A01G202100 chr6D 400077151 400077991 840 True 536.0 536 79.41800 888 1731 1 chr6D.!!$R1 843
10 TraesCS2A01G202100 chr6B 599072222 599073076 854 True 481.0 481 78.19400 888 1740 1 chr6B.!!$R1 852
11 TraesCS2A01G202100 chr6A 545829980 545830493 513 True 412.0 412 81.91900 888 1408 1 chr6A.!!$R1 520

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
694 751 0.683504 CACGCAGGGTCCCTACTACT 60.684 60.0 11.12 0.0 29.64 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1824 2029 0.108424 AGCTCTCGGCAGCAAGTAAG 60.108 55.0 8.91 0.0 42.4 2.34 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
37 38 1.538512 CCGTCATGAATGCATCCATCC 59.461 52.381 0.00 0.00 30.68 3.51
39 40 2.817844 CGTCATGAATGCATCCATCCAT 59.182 45.455 0.00 0.00 30.68 3.41
40 41 3.119955 CGTCATGAATGCATCCATCCATC 60.120 47.826 0.00 0.00 30.68 3.51
41 42 3.078837 TCATGAATGCATCCATCCATCG 58.921 45.455 0.00 0.00 30.68 3.84
42 43 2.934886 TGAATGCATCCATCCATCGA 57.065 45.000 0.00 0.00 0.00 3.59
76 79 2.811873 GCACCCAGCTTGAAAGAGAAGA 60.812 50.000 0.00 0.00 41.15 2.87
91 94 8.265055 TGAAAGAGAAGAGTAAAGGTTTCTCAA 58.735 33.333 13.59 0.00 44.94 3.02
101 104 5.984695 AAAGGTTTCTCAAGAATAAGGGC 57.015 39.130 0.00 0.00 33.54 5.19
127 130 8.019669 CCGAATATGATTTGTCATTCAAGATCC 58.980 37.037 0.00 0.00 37.35 3.36
145 148 2.248248 TCCAAGTCGCATATCCCCTAG 58.752 52.381 0.00 0.00 0.00 3.02
211 254 5.539582 TCGTGTGTAATTTAAGGTGATGC 57.460 39.130 0.00 0.00 0.00 3.91
221 268 3.414272 GGTGATGCGCATCTCCAC 58.586 61.111 44.05 35.08 45.82 4.02
240 287 3.189287 CCACACCTAAAGTTGCAGATGAC 59.811 47.826 0.00 0.00 0.00 3.06
242 289 4.516698 CACACCTAAAGTTGCAGATGACTT 59.483 41.667 0.00 0.00 37.69 3.01
250 297 1.250328 TGCAGATGACTTTTGCTGGG 58.750 50.000 5.60 0.00 38.60 4.45
251 298 1.251251 GCAGATGACTTTTGCTGGGT 58.749 50.000 0.00 0.00 35.05 4.51
252 299 2.224744 TGCAGATGACTTTTGCTGGGTA 60.225 45.455 5.60 0.00 38.60 3.69
275 322 7.822822 GGTAGTAATTAAGAACTCAAGGCTGAA 59.177 37.037 0.00 0.00 0.00 3.02
293 341 1.393883 GAAAACTTGAGATCGCCGACC 59.606 52.381 0.00 0.00 0.00 4.79
342 390 8.154649 ACATTCTTGTTAAATTTCAGTCGACT 57.845 30.769 13.58 13.58 29.55 4.18
343 391 8.070171 ACATTCTTGTTAAATTTCAGTCGACTG 58.930 33.333 34.76 34.76 37.86 3.51
368 416 4.724303 ACTTCGTTAAGTCTCAGTCGATG 58.276 43.478 0.00 0.00 42.42 3.84
369 417 4.215827 ACTTCGTTAAGTCTCAGTCGATGT 59.784 41.667 0.00 0.00 42.42 3.06
370 418 4.761235 TCGTTAAGTCTCAGTCGATGTT 57.239 40.909 0.00 0.00 0.00 2.71
371 419 5.868043 TCGTTAAGTCTCAGTCGATGTTA 57.132 39.130 0.00 0.00 0.00 2.41
372 420 6.432607 TCGTTAAGTCTCAGTCGATGTTAT 57.567 37.500 0.00 0.00 0.00 1.89
373 421 7.543947 TCGTTAAGTCTCAGTCGATGTTATA 57.456 36.000 0.00 0.00 0.00 0.98
374 422 8.151141 TCGTTAAGTCTCAGTCGATGTTATAT 57.849 34.615 0.00 0.00 0.00 0.86
375 423 8.281194 TCGTTAAGTCTCAGTCGATGTTATATC 58.719 37.037 0.00 0.00 0.00 1.63
376 424 7.534578 CGTTAAGTCTCAGTCGATGTTATATCC 59.465 40.741 0.00 0.00 0.00 2.59
377 425 6.961360 AAGTCTCAGTCGATGTTATATCCA 57.039 37.500 0.00 0.00 0.00 3.41
378 426 7.531857 AAGTCTCAGTCGATGTTATATCCAT 57.468 36.000 0.00 0.00 0.00 3.41
379 427 8.637196 AAGTCTCAGTCGATGTTATATCCATA 57.363 34.615 0.00 0.00 0.00 2.74
380 428 8.275015 AGTCTCAGTCGATGTTATATCCATAG 57.725 38.462 0.00 0.00 0.00 2.23
381 429 7.338196 AGTCTCAGTCGATGTTATATCCATAGG 59.662 40.741 0.00 0.00 0.00 2.57
382 430 7.337184 GTCTCAGTCGATGTTATATCCATAGGA 59.663 40.741 0.00 0.00 35.55 2.94
383 431 8.055790 TCTCAGTCGATGTTATATCCATAGGAT 58.944 37.037 3.74 3.74 45.40 3.24
384 432 8.226819 TCAGTCGATGTTATATCCATAGGATC 57.773 38.462 1.05 0.00 42.11 3.36
385 433 8.055790 TCAGTCGATGTTATATCCATAGGATCT 58.944 37.037 1.05 0.00 42.11 2.75
386 434 8.690884 CAGTCGATGTTATATCCATAGGATCTT 58.309 37.037 1.05 0.00 42.11 2.40
387 435 9.922477 AGTCGATGTTATATCCATAGGATCTTA 57.078 33.333 1.05 0.00 42.11 2.10
388 436 9.953697 GTCGATGTTATATCCATAGGATCTTAC 57.046 37.037 1.05 0.00 42.11 2.34
389 437 9.695155 TCGATGTTATATCCATAGGATCTTACA 57.305 33.333 1.05 4.05 42.11 2.41
418 466 9.947433 AAGATCCATGCAAATTTTTATTTCAGA 57.053 25.926 0.00 0.00 0.00 3.27
450 498 8.547967 TTTCTAGATTGTTATGTCACTTGACC 57.452 34.615 6.91 0.00 44.15 4.02
451 499 7.239763 TCTAGATTGTTATGTCACTTGACCA 57.760 36.000 6.91 0.00 44.15 4.02
452 500 7.676004 TCTAGATTGTTATGTCACTTGACCAA 58.324 34.615 6.91 4.44 44.15 3.67
453 501 6.808008 AGATTGTTATGTCACTTGACCAAG 57.192 37.500 6.91 8.11 44.15 3.61
454 502 6.533730 AGATTGTTATGTCACTTGACCAAGA 58.466 36.000 15.84 0.00 44.15 3.02
455 503 7.170965 AGATTGTTATGTCACTTGACCAAGAT 58.829 34.615 15.84 2.54 44.15 2.40
456 504 7.667219 AGATTGTTATGTCACTTGACCAAGATT 59.333 33.333 15.84 0.00 44.15 2.40
457 505 7.581213 TTGTTATGTCACTTGACCAAGATTT 57.419 32.000 15.84 0.00 44.15 2.17
458 506 6.969366 TGTTATGTCACTTGACCAAGATTTG 58.031 36.000 15.84 4.93 44.15 2.32
473 521 7.061752 CCAAGATTTGGTTAAGTCTTAGTCG 57.938 40.000 0.00 0.00 45.93 4.18
474 522 6.872020 CCAAGATTTGGTTAAGTCTTAGTCGA 59.128 38.462 0.00 0.00 45.93 4.20
475 523 7.148623 CCAAGATTTGGTTAAGTCTTAGTCGAC 60.149 40.741 7.70 7.70 45.93 4.20
476 524 7.229581 AGATTTGGTTAAGTCTTAGTCGACT 57.770 36.000 23.66 23.66 45.73 4.18
477 525 7.091443 AGATTTGGTTAAGTCTTAGTCGACTG 58.909 38.462 28.12 12.46 43.14 3.51
478 526 6.395426 TTTGGTTAAGTCTTAGTCGACTGA 57.605 37.500 28.12 19.13 43.14 3.41
479 527 5.624344 TGGTTAAGTCTTAGTCGACTGAG 57.376 43.478 26.80 26.80 43.14 3.35
480 528 5.068636 TGGTTAAGTCTTAGTCGACTGAGT 58.931 41.667 29.82 19.11 43.14 3.41
481 529 5.180868 TGGTTAAGTCTTAGTCGACTGAGTC 59.819 44.000 29.82 25.53 43.14 3.36
484 532 4.822685 AGTCTTAGTCGACTGAGTCCTA 57.177 45.455 29.82 13.41 42.39 2.94
487 535 2.328819 TAGTCGACTGAGTCCTAGCC 57.671 55.000 28.12 0.00 0.00 3.93
495 543 4.762765 CGACTGAGTCCTAGCCACTATAAT 59.237 45.833 7.07 0.00 0.00 1.28
496 544 5.938710 CGACTGAGTCCTAGCCACTATAATA 59.061 44.000 7.07 0.00 0.00 0.98
497 545 6.600032 CGACTGAGTCCTAGCCACTATAATAT 59.400 42.308 7.07 0.00 0.00 1.28
498 546 7.769507 CGACTGAGTCCTAGCCACTATAATATA 59.230 40.741 7.07 0.00 0.00 0.86
499 547 9.635404 GACTGAGTCCTAGCCACTATAATATAT 57.365 37.037 0.00 0.00 0.00 0.86
500 548 9.415008 ACTGAGTCCTAGCCACTATAATATATG 57.585 37.037 0.00 0.00 0.00 1.78
501 549 9.415008 CTGAGTCCTAGCCACTATAATATATGT 57.585 37.037 0.00 0.00 0.00 2.29
502 550 9.409918 TGAGTCCTAGCCACTATAATATATGTC 57.590 37.037 0.00 0.00 0.00 3.06
503 551 9.409918 GAGTCCTAGCCACTATAATATATGTCA 57.590 37.037 0.00 0.00 0.00 3.58
538 586 8.871629 ATAGACACTTCCTACTATCGAATGAT 57.128 34.615 0.00 0.00 38.67 2.45
580 631 1.730772 GCGCCTGCAGAGAGATATACG 60.731 57.143 17.39 5.60 42.15 3.06
610 661 2.778270 AGAAATAAGTAGCCTCCCCCAC 59.222 50.000 0.00 0.00 0.00 4.61
694 751 0.683504 CACGCAGGGTCCCTACTACT 60.684 60.000 11.12 0.00 29.64 2.57
696 753 1.316651 CGCAGGGTCCCTACTACTAC 58.683 60.000 11.12 0.00 29.64 2.73
697 754 1.133853 CGCAGGGTCCCTACTACTACT 60.134 57.143 11.12 0.00 29.64 2.57
698 755 2.105477 CGCAGGGTCCCTACTACTACTA 59.895 54.545 11.12 0.00 29.64 1.82
699 756 3.485394 GCAGGGTCCCTACTACTACTAC 58.515 54.545 11.12 0.00 29.64 2.73
700 757 3.750276 GCAGGGTCCCTACTACTACTACC 60.750 56.522 11.12 0.00 29.64 3.18
952 1025 2.123251 ACGCCTCCGATCATCCCT 60.123 61.111 0.00 0.00 38.29 4.20
1052 1152 2.029110 AGACAGCAAGAGAAGCTCACTC 60.029 50.000 11.42 11.42 41.14 3.51
1053 1153 1.690893 ACAGCAAGAGAAGCTCACTCA 59.309 47.619 18.61 0.00 41.14 3.41
1290 1420 2.595655 GGCACCCACTACATCCCC 59.404 66.667 0.00 0.00 0.00 4.81
1669 1841 4.521639 TGTAGTCGTGTATGGGATATGGAC 59.478 45.833 0.00 0.00 0.00 4.02
1788 1993 4.801147 TGCATGATCGATTAAGCTTGAC 57.199 40.909 16.76 0.00 0.00 3.18
1801 2006 0.855349 GCTTGACATCGCCATCGTAG 59.145 55.000 0.00 0.00 36.96 3.51
1813 2018 2.417379 GCCATCGTAGAGTGTCATGTGT 60.417 50.000 0.00 0.00 43.63 3.72
1824 2029 5.303078 AGAGTGTCATGTGTCCATATACTCC 59.697 44.000 0.00 0.00 36.32 3.85
1828 2033 6.924060 GTGTCATGTGTCCATATACTCCTTAC 59.076 42.308 0.00 0.00 0.00 2.34
1858 2063 2.933260 GAGAGCTCGAACCAAAATCTCC 59.067 50.000 8.37 0.00 0.00 3.71
1859 2064 2.010497 GAGCTCGAACCAAAATCTCCC 58.990 52.381 0.00 0.00 0.00 4.30
1860 2065 0.727398 GCTCGAACCAAAATCTCCCG 59.273 55.000 0.00 0.00 0.00 5.14
1861 2066 1.369625 CTCGAACCAAAATCTCCCGG 58.630 55.000 0.00 0.00 0.00 5.73
1862 2067 0.978151 TCGAACCAAAATCTCCCGGA 59.022 50.000 0.73 0.00 0.00 5.14
1863 2068 1.348366 TCGAACCAAAATCTCCCGGAA 59.652 47.619 0.73 0.00 0.00 4.30
1864 2069 2.156098 CGAACCAAAATCTCCCGGAAA 58.844 47.619 0.73 0.00 0.00 3.13
1865 2070 2.554893 CGAACCAAAATCTCCCGGAAAA 59.445 45.455 0.73 0.00 0.00 2.29
1866 2071 3.004944 CGAACCAAAATCTCCCGGAAAAA 59.995 43.478 0.73 0.00 0.00 1.94
1890 2095 1.818674 ACTCGAACCAAAATCATGGGC 59.181 47.619 0.00 0.00 45.18 5.36
1891 2096 1.818060 CTCGAACCAAAATCATGGGCA 59.182 47.619 0.00 0.00 45.18 5.36
2019 2224 2.036604 GGGGCGTGGAAAATTTTCTCAA 59.963 45.455 25.86 12.47 37.35 3.02
2405 2625 3.777925 CGACGAACTGCCGGCAAG 61.778 66.667 32.09 25.07 37.43 4.01
2406 2626 3.423154 GACGAACTGCCGGCAAGG 61.423 66.667 32.09 22.42 44.97 3.61
2407 2627 4.250305 ACGAACTGCCGGCAAGGT 62.250 61.111 32.09 23.17 43.70 3.50
2408 2628 3.726517 CGAACTGCCGGCAAGGTG 61.727 66.667 32.09 21.22 43.70 4.00
2409 2629 3.365265 GAACTGCCGGCAAGGTGG 61.365 66.667 32.09 20.81 43.70 4.61
2495 2715 0.675633 GCAAGGCAGCAAGAGGAAAA 59.324 50.000 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.607939 TGACGGTCAAATGTAGATACCAT 57.392 39.130 8.68 0.00 0.00 3.55
1 2 5.128008 TCATGACGGTCAAATGTAGATACCA 59.872 40.000 15.72 0.00 0.00 3.25
2 3 5.597806 TCATGACGGTCAAATGTAGATACC 58.402 41.667 15.72 0.00 0.00 2.73
8 9 4.006319 TGCATTCATGACGGTCAAATGTA 58.994 39.130 25.11 21.27 30.94 2.29
37 38 2.051614 GGCGCATGCATGTCGATG 60.052 61.111 32.83 18.66 45.35 3.84
60 63 5.994668 ACCTTTACTCTTCTCTTTCAAGCTG 59.005 40.000 0.00 0.00 0.00 4.24
66 69 8.664211 TTGAGAAACCTTTACTCTTCTCTTTC 57.336 34.615 10.92 0.00 42.74 2.62
76 79 6.659668 GCCCTTATTCTTGAGAAACCTTTACT 59.340 38.462 0.00 0.00 37.61 2.24
91 94 6.306987 ACAAATCATATTCGGCCCTTATTCT 58.693 36.000 0.00 0.00 0.00 2.40
101 104 8.019669 GGATCTTGAATGACAAATCATATTCGG 58.980 37.037 0.00 0.00 45.26 4.30
127 130 4.336889 TTTCTAGGGGATATGCGACTTG 57.663 45.455 0.00 0.00 0.00 3.16
203 246 1.153289 GTGGAGATGCGCATCACCT 60.153 57.895 44.75 31.01 45.22 4.00
211 254 2.386661 ACTTTAGGTGTGGAGATGCG 57.613 50.000 0.00 0.00 0.00 4.73
221 268 5.695851 AAAGTCATCTGCAACTTTAGGTG 57.304 39.130 11.60 0.00 42.37 4.00
240 287 8.336801 AGTTCTTAATTACTACCCAGCAAAAG 57.663 34.615 0.00 0.00 0.00 2.27
242 289 7.455058 TGAGTTCTTAATTACTACCCAGCAAA 58.545 34.615 0.00 0.00 0.00 3.68
250 297 8.773404 TTCAGCCTTGAGTTCTTAATTACTAC 57.227 34.615 0.00 0.00 34.15 2.73
251 298 9.787435 TTTTCAGCCTTGAGTTCTTAATTACTA 57.213 29.630 0.00 0.00 34.15 1.82
252 299 8.568794 GTTTTCAGCCTTGAGTTCTTAATTACT 58.431 33.333 0.00 0.00 34.15 2.24
275 322 0.608640 AGGTCGGCGATCTCAAGTTT 59.391 50.000 18.56 0.00 0.00 2.66
316 364 9.268268 AGTCGACTGAAATTTAACAAGAATGTA 57.732 29.630 19.30 0.00 39.40 2.29
317 365 8.070171 CAGTCGACTGAAATTTAACAAGAATGT 58.930 33.333 36.73 0.00 46.59 2.71
318 366 8.427181 CAGTCGACTGAAATTTAACAAGAATG 57.573 34.615 36.73 7.03 46.59 2.67
333 381 1.880271 ACGAAGTCTCAGTCGACTGA 58.120 50.000 38.24 38.24 44.92 3.41
334 382 2.690173 AACGAAGTCTCAGTCGACTG 57.310 50.000 34.76 34.76 45.00 3.51
335 383 3.814283 ACTTAACGAAGTCTCAGTCGACT 59.186 43.478 13.58 13.58 45.00 4.18
336 384 4.144534 ACTTAACGAAGTCTCAGTCGAC 57.855 45.455 7.70 7.70 45.00 4.20
347 395 4.724303 ACATCGACTGAGACTTAACGAAG 58.276 43.478 0.00 0.00 38.76 3.79
348 396 4.761235 ACATCGACTGAGACTTAACGAA 57.239 40.909 0.00 0.00 33.77 3.85
349 397 4.761235 AACATCGACTGAGACTTAACGA 57.239 40.909 0.00 0.00 0.00 3.85
350 398 7.534578 GGATATAACATCGACTGAGACTTAACG 59.465 40.741 0.00 0.00 0.00 3.18
351 399 8.350722 TGGATATAACATCGACTGAGACTTAAC 58.649 37.037 0.00 0.00 0.00 2.01
352 400 8.459911 TGGATATAACATCGACTGAGACTTAA 57.540 34.615 0.00 0.00 0.00 1.85
353 401 8.637196 ATGGATATAACATCGACTGAGACTTA 57.363 34.615 0.00 0.00 0.00 2.24
354 402 6.961360 TGGATATAACATCGACTGAGACTT 57.039 37.500 0.00 0.00 0.00 3.01
355 403 7.338196 CCTATGGATATAACATCGACTGAGACT 59.662 40.741 0.00 0.00 0.00 3.24
356 404 7.337184 TCCTATGGATATAACATCGACTGAGAC 59.663 40.741 0.00 0.00 0.00 3.36
357 405 7.402862 TCCTATGGATATAACATCGACTGAGA 58.597 38.462 0.00 0.00 0.00 3.27
358 406 7.631717 TCCTATGGATATAACATCGACTGAG 57.368 40.000 0.00 0.00 0.00 3.35
359 407 8.055790 AGATCCTATGGATATAACATCGACTGA 58.944 37.037 0.00 0.00 43.27 3.41
360 408 8.231692 AGATCCTATGGATATAACATCGACTG 57.768 38.462 0.00 0.00 43.27 3.51
361 409 8.830915 AAGATCCTATGGATATAACATCGACT 57.169 34.615 0.00 0.00 43.27 4.18
362 410 9.953697 GTAAGATCCTATGGATATAACATCGAC 57.046 37.037 0.00 0.00 43.27 4.20
363 411 9.695155 TGTAAGATCCTATGGATATAACATCGA 57.305 33.333 0.00 0.00 43.27 3.59
392 440 9.947433 TCTGAAATAAAAATTTGCATGGATCTT 57.053 25.926 0.00 0.00 0.00 2.40
424 472 8.999431 GGTCAAGTGACATAACAATCTAGAAAA 58.001 33.333 13.21 0.00 46.47 2.29
425 473 8.154203 TGGTCAAGTGACATAACAATCTAGAAA 58.846 33.333 13.21 0.00 46.47 2.52
426 474 7.676004 TGGTCAAGTGACATAACAATCTAGAA 58.324 34.615 13.21 0.00 46.47 2.10
427 475 7.239763 TGGTCAAGTGACATAACAATCTAGA 57.760 36.000 13.21 0.00 46.47 2.43
428 476 7.819415 TCTTGGTCAAGTGACATAACAATCTAG 59.181 37.037 13.21 0.86 46.47 2.43
429 477 7.676004 TCTTGGTCAAGTGACATAACAATCTA 58.324 34.615 13.21 0.00 46.47 1.98
430 478 6.533730 TCTTGGTCAAGTGACATAACAATCT 58.466 36.000 13.21 0.00 46.47 2.40
431 479 6.801539 TCTTGGTCAAGTGACATAACAATC 57.198 37.500 13.21 0.00 46.47 2.67
432 480 7.765695 AATCTTGGTCAAGTGACATAACAAT 57.234 32.000 13.21 1.23 46.47 2.71
433 481 7.424803 CAAATCTTGGTCAAGTGACATAACAA 58.575 34.615 13.21 7.11 46.47 2.83
434 482 6.016360 CCAAATCTTGGTCAAGTGACATAACA 60.016 38.462 13.21 0.00 46.47 2.41
435 483 6.381801 CCAAATCTTGGTCAAGTGACATAAC 58.618 40.000 13.21 0.00 46.47 1.89
436 484 6.573664 CCAAATCTTGGTCAAGTGACATAA 57.426 37.500 13.21 6.92 46.47 1.90
449 497 7.148623 GTCGACTAAGACTTAACCAAATCTTGG 60.149 40.741 8.70 3.84 45.49 3.61
450 498 7.730778 GTCGACTAAGACTTAACCAAATCTTG 58.269 38.462 8.70 0.00 38.09 3.02
451 499 7.886405 GTCGACTAAGACTTAACCAAATCTT 57.114 36.000 8.70 0.00 38.09 2.40
464 512 3.310501 GCTAGGACTCAGTCGACTAAGAC 59.689 52.174 22.79 15.82 41.23 3.01
465 513 3.533547 GCTAGGACTCAGTCGACTAAGA 58.466 50.000 22.79 13.60 32.65 2.10
466 514 2.614983 GGCTAGGACTCAGTCGACTAAG 59.385 54.545 19.57 16.88 32.65 2.18
467 515 2.026542 TGGCTAGGACTCAGTCGACTAA 60.027 50.000 19.57 1.94 32.65 2.24
468 516 1.558294 TGGCTAGGACTCAGTCGACTA 59.442 52.381 19.57 6.17 32.65 2.59
469 517 0.328592 TGGCTAGGACTCAGTCGACT 59.671 55.000 13.58 13.58 32.65 4.18
470 518 0.452585 GTGGCTAGGACTCAGTCGAC 59.547 60.000 7.70 7.70 32.65 4.20
471 519 0.328592 AGTGGCTAGGACTCAGTCGA 59.671 55.000 0.00 0.00 32.65 4.20
472 520 2.039818 TAGTGGCTAGGACTCAGTCG 57.960 55.000 0.00 0.00 32.65 4.18
473 521 7.948034 ATATTATAGTGGCTAGGACTCAGTC 57.052 40.000 0.00 0.00 0.00 3.51
474 522 9.415008 CATATATTATAGTGGCTAGGACTCAGT 57.585 37.037 0.00 0.00 0.00 3.41
475 523 9.415008 ACATATATTATAGTGGCTAGGACTCAG 57.585 37.037 0.00 0.00 0.00 3.35
476 524 9.409918 GACATATATTATAGTGGCTAGGACTCA 57.590 37.037 0.00 0.00 0.00 3.41
477 525 9.409918 TGACATATATTATAGTGGCTAGGACTC 57.590 37.037 0.00 0.00 0.00 3.36
478 526 9.415008 CTGACATATATTATAGTGGCTAGGACT 57.585 37.037 0.00 0.00 0.00 3.85
479 527 9.409918 TCTGACATATATTATAGTGGCTAGGAC 57.590 37.037 0.00 0.00 0.00 3.85
498 546 9.606631 GGAAGTGTCTATTCTTAAATCTGACAT 57.393 33.333 0.00 0.00 39.00 3.06
499 547 8.816894 AGGAAGTGTCTATTCTTAAATCTGACA 58.183 33.333 0.00 0.00 36.75 3.58
510 558 8.788806 CATTCGATAGTAGGAAGTGTCTATTCT 58.211 37.037 0.00 0.00 37.40 2.40
538 586 1.578897 TGCACAATGGGGAGTAGCTA 58.421 50.000 0.00 0.00 0.00 3.32
580 631 3.553302 GGCTACTTATTTCTCCTCTCGCC 60.553 52.174 0.00 0.00 0.00 5.54
694 751 5.221702 GGTTGAGTTGGTTACTTGGGTAGTA 60.222 44.000 0.00 0.00 37.17 1.82
696 753 4.070009 GGTTGAGTTGGTTACTTGGGTAG 58.930 47.826 0.00 0.00 37.17 3.18
697 754 3.494749 CGGTTGAGTTGGTTACTTGGGTA 60.495 47.826 0.00 0.00 37.17 3.69
698 755 2.747135 CGGTTGAGTTGGTTACTTGGGT 60.747 50.000 0.00 0.00 37.17 4.51
699 756 1.877443 CGGTTGAGTTGGTTACTTGGG 59.123 52.381 0.00 0.00 37.17 4.12
700 757 1.265905 GCGGTTGAGTTGGTTACTTGG 59.734 52.381 0.00 0.00 37.17 3.61
793 850 1.135803 GCTATTTTTGCCTTGCGTCGA 60.136 47.619 0.00 0.00 0.00 4.20
833 900 4.015382 TTGTTACCAACGCCGCGC 62.015 61.111 13.88 0.00 0.00 6.86
834 901 2.127534 GTTGTTACCAACGCCGCG 60.128 61.111 12.14 12.14 41.41 6.46
841 908 2.415625 GGCACACGTTTGTTGTTACCAA 60.416 45.455 3.29 0.00 31.66 3.67
842 909 1.132643 GGCACACGTTTGTTGTTACCA 59.867 47.619 3.29 0.00 31.66 3.25
843 910 1.830086 GGCACACGTTTGTTGTTACC 58.170 50.000 3.29 0.00 31.66 2.85
844 911 1.458746 CGGCACACGTTTGTTGTTAC 58.541 50.000 3.29 0.00 37.93 2.50
845 912 3.899836 CGGCACACGTTTGTTGTTA 57.100 47.368 3.29 0.00 37.93 2.41
846 913 4.775746 CGGCACACGTTTGTTGTT 57.224 50.000 3.29 0.00 37.93 2.83
935 1008 2.123251 AGGGATGATCGGAGGCGT 60.123 61.111 0.00 0.00 0.00 5.68
1052 1152 0.108424 GACTGGTGGTAGCTGAGCTG 60.108 60.000 18.79 0.00 40.10 4.24
1053 1153 1.261238 GGACTGGTGGTAGCTGAGCT 61.261 60.000 13.25 13.25 43.41 4.09
1205 1335 4.015406 TGTCCGGCCGCTTCACAT 62.015 61.111 22.85 0.00 0.00 3.21
1206 1336 4.980805 GTGTCCGGCCGCTTCACA 62.981 66.667 27.66 20.75 0.00 3.58
1332 1462 2.966732 GCCGGGGATGAACTGTCCA 61.967 63.158 2.18 0.00 37.49 4.02
1335 1465 4.778143 GCGCCGGGGATGAACTGT 62.778 66.667 24.68 0.00 0.00 3.55
1481 1621 2.668212 ATGGACGGGTGCAACGTG 60.668 61.111 20.56 6.75 45.68 4.49
1483 1623 1.082117 GTAGATGGACGGGTGCAACG 61.082 60.000 10.16 10.16 38.12 4.10
1493 1633 4.022676 GCTAGCTCTACCAAGTAGATGGAC 60.023 50.000 7.70 0.00 43.08 4.02
1669 1841 4.758692 ATGCTTCCTACGCATCCG 57.241 55.556 0.00 0.00 44.24 4.18
1788 1993 1.065551 TGACACTCTACGATGGCGATG 59.934 52.381 0.00 0.00 41.64 3.84
1801 2006 5.303078 AGGAGTATATGGACACATGACACTC 59.697 44.000 0.00 0.00 38.45 3.51
1813 2018 4.040461 GGCAGCAAGTAAGGAGTATATGGA 59.960 45.833 0.00 0.00 0.00 3.41
1824 2029 0.108424 AGCTCTCGGCAGCAAGTAAG 60.108 55.000 8.91 0.00 42.40 2.34
1866 2071 5.296748 CCCATGATTTTGGTTCGAGTTTTT 58.703 37.500 0.00 0.00 34.77 1.94
1867 2072 4.799255 GCCCATGATTTTGGTTCGAGTTTT 60.799 41.667 0.00 0.00 34.77 2.43
1868 2073 3.306019 GCCCATGATTTTGGTTCGAGTTT 60.306 43.478 0.00 0.00 34.77 2.66
1869 2074 2.231235 GCCCATGATTTTGGTTCGAGTT 59.769 45.455 0.00 0.00 34.77 3.01
1870 2075 1.818674 GCCCATGATTTTGGTTCGAGT 59.181 47.619 0.00 0.00 34.77 4.18
1871 2076 1.818060 TGCCCATGATTTTGGTTCGAG 59.182 47.619 0.00 0.00 34.77 4.04
1872 2077 1.818060 CTGCCCATGATTTTGGTTCGA 59.182 47.619 0.00 0.00 34.77 3.71
1873 2078 1.545582 ACTGCCCATGATTTTGGTTCG 59.454 47.619 0.00 0.00 34.77 3.95
1874 2079 3.427503 CGTACTGCCCATGATTTTGGTTC 60.428 47.826 0.00 0.00 34.77 3.62
1875 2080 2.491693 CGTACTGCCCATGATTTTGGTT 59.508 45.455 0.00 0.00 34.77 3.67
1876 2081 2.091541 CGTACTGCCCATGATTTTGGT 58.908 47.619 0.00 0.00 34.77 3.67
1877 2082 1.405105 CCGTACTGCCCATGATTTTGG 59.595 52.381 0.00 0.00 36.46 3.28
1878 2083 2.364632 TCCGTACTGCCCATGATTTTG 58.635 47.619 0.00 0.00 0.00 2.44
1879 2084 2.752903 GTTCCGTACTGCCCATGATTTT 59.247 45.455 0.00 0.00 0.00 1.82
1880 2085 2.290641 TGTTCCGTACTGCCCATGATTT 60.291 45.455 0.00 0.00 0.00 2.17
1881 2086 1.280710 TGTTCCGTACTGCCCATGATT 59.719 47.619 0.00 0.00 0.00 2.57
1882 2087 0.908910 TGTTCCGTACTGCCCATGAT 59.091 50.000 0.00 0.00 0.00 2.45
1890 2095 3.827625 CTCTTCTGTCTGTTCCGTACTG 58.172 50.000 0.00 0.00 0.00 2.74
1891 2096 2.229302 GCTCTTCTGTCTGTTCCGTACT 59.771 50.000 0.00 0.00 0.00 2.73
2495 2715 2.961526 AGAGATACGACCATTTGCGT 57.038 45.000 0.00 0.00 43.86 5.24


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

AutoCloner maintained by Alex Coulton.