Multiple sequence alignment - TraesCS3A01G113600

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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 TraesCS3A01G113600 chr3A 100.000 4134 0 0 1 4134 80690669 80686536 0.000000e+00 7635.0
1 TraesCS3A01G113600 chr3A 95.288 191 7 2 1370 1559 77542424 77542613 6.720000e-78 302.0
2 TraesCS3A01G113600 chr3D 94.895 3565 144 19 585 4134 69501385 69497844 0.000000e+00 5541.0
3 TraesCS3A01G113600 chr3D 91.331 496 34 3 1 487 69502203 69501708 0.000000e+00 669.0
4 TraesCS3A01G113600 chr3B 93.504 2617 116 35 1555 4134 115397975 115395376 0.000000e+00 3842.0
5 TraesCS3A01G113600 chr3B 94.823 792 35 4 584 1375 115398742 115397957 0.000000e+00 1230.0
6 TraesCS3A01G113600 chr3B 94.444 486 25 2 1 485 115399264 115398780 0.000000e+00 747.0
7 TraesCS3A01G113600 chr3B 96.277 188 6 1 1370 1556 368605653 368605466 1.440000e-79 307.0
8 TraesCS3A01G113600 chr3B 95.767 189 6 1 1363 1551 766145376 766145190 1.870000e-78 303.0
9 TraesCS3A01G113600 chr3B 92.771 83 6 0 1469 1551 29868844 29868762 2.020000e-23 121.0
10 TraesCS3A01G113600 chr1D 96.277 188 6 1 1370 1556 211684749 211684936 1.440000e-79 307.0
11 TraesCS3A01G113600 chr1B 96.277 188 6 1 1374 1561 70318388 70318574 1.440000e-79 307.0
12 TraesCS3A01G113600 chr1B 95.238 105 4 1 488 592 549902440 549902337 9.190000e-37 165.0
13 TraesCS3A01G113600 chr1B 88.043 92 5 6 1249 1337 493871965 493871877 2.030000e-18 104.0
14 TraesCS3A01G113600 chr1B 86.000 100 6 6 1245 1342 493871877 493871970 2.630000e-17 100.0
15 TraesCS3A01G113600 chr6D 96.216 185 7 0 1374 1558 95293872 95293688 1.870000e-78 303.0
16 TraesCS3A01G113600 chr7B 95.263 190 9 0 1374 1563 55865145 55864956 6.720000e-78 302.0
17 TraesCS3A01G113600 chr5B 94.792 192 8 2 1374 1565 573807748 573807559 8.690000e-77 298.0
18 TraesCS3A01G113600 chr5D 96.296 108 0 2 485 592 281848127 281848230 1.530000e-39 174.0
19 TraesCS3A01G113600 chr7D 89.157 83 8 1 1249 1330 119897077 119896995 7.310000e-18 102.0
20 TraesCS3A01G113600 chr7D 88.235 85 5 5 1249 1330 419793198 419793116 3.400000e-16 97.1
21 TraesCS3A01G113600 chr2D 89.286 84 5 4 1249 1330 459300641 459300560 7.310000e-18 102.0
22 TraesCS3A01G113600 chr2A 85.870 92 7 6 1249 1337 743987846 743987934 4.400000e-15 93.5
23 TraesCS3A01G113600 chr5A 83.495 103 9 8 1248 1345 444560941 444560842 5.690000e-14 89.8


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 TraesCS3A01G113600 chr3A 80686536 80690669 4133 True 7635.000000 7635 100.000 1 4134 1 chr3A.!!$R1 4133
1 TraesCS3A01G113600 chr3D 69497844 69502203 4359 True 3105.000000 5541 93.113 1 4134 2 chr3D.!!$R1 4133
2 TraesCS3A01G113600 chr3B 115395376 115399264 3888 True 1939.666667 3842 94.257 1 4134 3 chr3B.!!$R4 4133


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
37 38 0.387565 GCGATTTTGTTGGTGGGTGT 59.612 50.0 0.00 0.00 0.00 4.16 F
517 528 0.400213 CTGGTGTAGGGCTTGTCCAA 59.600 55.0 0.00 0.00 36.21 3.53 F
1411 1649 0.523519 GTGGTAAAGCTGCTGCCTTC 59.476 55.0 12.44 0.95 40.80 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1459 1697 0.107654 ACGCAGCCTTTCCCTACATC 60.108 55.000 0.00 0.00 0.00 3.06 R
1519 1757 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85 R
3136 3374 0.027455 TTTCAGCTTCGCACACGTTG 59.973 50.000 0.00 0.00 41.18 4.10 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
35 36 1.801309 CGGCGATTTTGTTGGTGGGT 61.801 55.000 0.00 0.00 0.00 4.51
37 38 0.387565 GCGATTTTGTTGGTGGGTGT 59.612 50.000 0.00 0.00 0.00 4.16
112 115 5.689383 TTAATCGGATTTGCTATTGCTCC 57.311 39.130 8.76 0.00 40.48 4.70
134 137 7.042119 GCTCCTCTAGATGAGAATTAACAAAGC 60.042 40.741 24.37 5.70 45.39 3.51
135 138 8.083828 TCCTCTAGATGAGAATTAACAAAGCT 57.916 34.615 0.00 0.00 45.39 3.74
145 148 9.162764 TGAGAATTAACAAAGCTACATCTAACC 57.837 33.333 0.00 0.00 0.00 2.85
163 166 9.224267 CATCTAACCCCTACATCATTTGATTAG 57.776 37.037 0.00 0.00 31.21 1.73
237 241 5.817816 CCAAATGGTGTAGGAGTTAGATGTC 59.182 44.000 0.00 0.00 0.00 3.06
331 335 6.978343 TCGTTTGGTATGTAAGAAGGATTG 57.022 37.500 0.00 0.00 0.00 2.67
457 468 0.610232 ATCAAAGGAGCAGTGTGCCC 60.610 55.000 0.00 0.00 46.52 5.36
501 512 9.559732 TTCCATCTTATCATGTAATTGTACTGG 57.440 33.333 0.00 0.00 0.00 4.00
502 513 8.713971 TCCATCTTATCATGTAATTGTACTGGT 58.286 33.333 0.00 0.00 0.00 4.00
503 514 8.777413 CCATCTTATCATGTAATTGTACTGGTG 58.223 37.037 0.00 0.00 0.00 4.17
508 519 5.984725 TCATGTAATTGTACTGGTGTAGGG 58.015 41.667 0.00 0.00 0.00 3.53
509 520 4.210724 TGTAATTGTACTGGTGTAGGGC 57.789 45.455 0.00 0.00 0.00 5.19
512 523 2.851263 TTGTACTGGTGTAGGGCTTG 57.149 50.000 0.00 0.00 0.00 4.01
513 524 1.724545 TGTACTGGTGTAGGGCTTGT 58.275 50.000 0.00 0.00 0.00 3.16
514 525 1.621814 TGTACTGGTGTAGGGCTTGTC 59.378 52.381 0.00 0.00 0.00 3.18
515 526 1.066358 GTACTGGTGTAGGGCTTGTCC 60.066 57.143 0.00 0.00 0.00 4.02
516 527 0.766674 ACTGGTGTAGGGCTTGTCCA 60.767 55.000 0.00 0.00 36.21 4.02
517 528 0.400213 CTGGTGTAGGGCTTGTCCAA 59.600 55.000 0.00 0.00 36.21 3.53
520 531 1.463674 GTGTAGGGCTTGTCCAATGG 58.536 55.000 0.00 0.00 36.21 3.16
521 532 1.072266 TGTAGGGCTTGTCCAATGGT 58.928 50.000 0.00 0.00 36.21 3.55
522 533 2.026636 GTGTAGGGCTTGTCCAATGGTA 60.027 50.000 0.00 0.00 36.21 3.25
523 534 2.026636 TGTAGGGCTTGTCCAATGGTAC 60.027 50.000 0.00 0.00 36.21 3.34
524 535 1.072266 AGGGCTTGTCCAATGGTACA 58.928 50.000 0.00 0.00 39.17 2.90
525 536 1.640670 AGGGCTTGTCCAATGGTACAT 59.359 47.619 0.00 0.00 39.36 2.29
526 537 1.750778 GGGCTTGTCCAATGGTACATG 59.249 52.381 0.00 6.33 39.36 3.21
527 538 2.446435 GGCTTGTCCAATGGTACATGT 58.554 47.619 2.69 2.69 37.85 3.21
528 539 2.164219 GGCTTGTCCAATGGTACATGTG 59.836 50.000 9.11 0.00 37.85 3.21
529 540 4.373055 GGCTTGTCCAATGGTACATGTGT 61.373 47.826 9.11 0.00 37.85 3.72
530 541 5.825660 GGCTTGTCCAATGGTACATGTGTT 61.826 45.833 9.11 0.00 37.85 3.32
539 550 4.691326 TGGTACATGTGTTGGACTTGTA 57.309 40.909 9.11 0.00 41.78 2.41
544 555 4.072131 ACATGTGTTGGACTTGTACATCC 58.928 43.478 8.35 8.35 40.30 3.51
545 556 3.134574 TGTGTTGGACTTGTACATCCC 57.865 47.619 12.07 7.26 33.69 3.85
546 557 2.708861 TGTGTTGGACTTGTACATCCCT 59.291 45.455 12.07 0.00 33.69 4.20
547 558 3.137544 TGTGTTGGACTTGTACATCCCTT 59.862 43.478 12.07 0.00 33.69 3.95
548 559 3.502211 GTGTTGGACTTGTACATCCCTTG 59.498 47.826 12.07 0.00 33.69 3.61
549 560 3.137544 TGTTGGACTTGTACATCCCTTGT 59.862 43.478 12.07 0.00 42.62 3.16
551 562 5.163184 TGTTGGACTTGTACATCCCTTGTAA 60.163 40.000 12.07 0.00 42.37 2.41
552 563 4.901868 TGGACTTGTACATCCCTTGTAAC 58.098 43.478 12.07 0.00 42.37 2.50
553 564 4.348461 TGGACTTGTACATCCCTTGTAACA 59.652 41.667 12.07 0.00 42.37 2.41
555 566 5.766174 GGACTTGTACATCCCTTGTAACAAA 59.234 40.000 4.38 0.00 42.37 2.83
556 567 6.293790 GGACTTGTACATCCCTTGTAACAAAC 60.294 42.308 4.38 0.00 42.37 2.93
558 569 6.485648 ACTTGTACATCCCTTGTAACAAACTC 59.514 38.462 0.00 0.00 42.37 3.01
559 570 5.310451 TGTACATCCCTTGTAACAAACTCC 58.690 41.667 0.00 0.00 42.37 3.85
560 571 4.724279 ACATCCCTTGTAACAAACTCCT 57.276 40.909 0.00 0.00 36.57 3.69
561 572 4.652822 ACATCCCTTGTAACAAACTCCTC 58.347 43.478 0.00 0.00 36.57 3.71
562 573 4.351111 ACATCCCTTGTAACAAACTCCTCT 59.649 41.667 0.00 0.00 36.57 3.69
563 574 5.546499 ACATCCCTTGTAACAAACTCCTCTA 59.454 40.000 0.00 0.00 36.57 2.43
564 575 6.043938 ACATCCCTTGTAACAAACTCCTCTAA 59.956 38.462 0.00 0.00 36.57 2.10
566 577 6.293698 TCCCTTGTAACAAACTCCTCTAAAC 58.706 40.000 0.00 0.00 0.00 2.01
567 578 5.472478 CCCTTGTAACAAACTCCTCTAAACC 59.528 44.000 0.00 0.00 0.00 3.27
568 579 5.472478 CCTTGTAACAAACTCCTCTAAACCC 59.528 44.000 0.00 0.00 0.00 4.11
569 580 4.976864 TGTAACAAACTCCTCTAAACCCC 58.023 43.478 0.00 0.00 0.00 4.95
570 581 3.520691 AACAAACTCCTCTAAACCCCC 57.479 47.619 0.00 0.00 0.00 5.40
669 907 9.020813 GTCGTACTTGCATATATGTACATATGG 57.979 37.037 30.35 23.72 38.69 2.74
693 931 9.790344 TGGATTTGTTTCAATTGTAATTTCCAT 57.210 25.926 5.13 0.00 0.00 3.41
748 986 1.661112 GATCTGAGTTTACGTGCTGCC 59.339 52.381 0.00 0.00 0.00 4.85
857 1095 3.963374 TGACTCCCTCCTGTCTATTCATG 59.037 47.826 0.00 0.00 34.57 3.07
883 1121 7.520119 TGTATCTTATGTCTTAACTTGTGCG 57.480 36.000 0.00 0.00 0.00 5.34
887 1125 5.404366 TCTTATGTCTTAACTTGTGCGACAC 59.596 40.000 3.44 3.44 37.43 3.67
970 1208 2.227388 CACTGCAGTTGAGTTTGGATCC 59.773 50.000 18.94 4.20 0.00 3.36
1213 1451 5.769662 TCAGTGGTGTTTAATCTGCTTGATT 59.230 36.000 9.68 9.68 46.22 2.57
1257 1495 6.999272 CAGTGTACATAGTACATACTCCCTCT 59.001 42.308 12.53 1.24 37.73 3.69
1268 1506 9.004231 AGTACATACTCCCTCTATCCAAAAATT 57.996 33.333 0.00 0.00 0.00 1.82
1322 1560 4.028993 ACCACGACACTTATTTTGGGAT 57.971 40.909 0.00 0.00 0.00 3.85
1326 1564 4.457603 CACGACACTTATTTTGGGATGGAA 59.542 41.667 0.00 0.00 0.00 3.53
1361 1599 7.398024 ACTATTGTTTTCTCCTGTGCTTCTAT 58.602 34.615 0.00 0.00 0.00 1.98
1411 1649 0.523519 GTGGTAAAGCTGCTGCCTTC 59.476 55.000 12.44 0.95 40.80 3.46
1459 1697 3.685139 TGGAAACAGCCTCTTACAGAG 57.315 47.619 0.00 0.00 37.73 3.35
1508 1746 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
1509 1747 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
1510 1748 3.714001 GTGGTCGGACCCTTCCCC 61.714 72.222 23.81 0.00 38.99 4.81
1517 1755 4.735599 GACCCTTCCCCGGACCCT 62.736 72.222 0.73 0.00 0.00 4.34
1570 1808 4.464947 CCCCCTTTCTATTCACAGATTCC 58.535 47.826 0.00 0.00 0.00 3.01
1713 1951 5.501413 CGTCACTGCTATTTCATGTTAGCTG 60.501 44.000 19.69 19.69 42.62 4.24
1855 2093 8.909423 TTTACTCCCCTTTCCATTTATCAAAT 57.091 30.769 0.00 0.00 0.00 2.32
2044 2282 8.877808 TCATGATTCATGAAGTACACTGATAC 57.122 34.615 23.72 0.00 46.17 2.24
2045 2283 8.477256 TCATGATTCATGAAGTACACTGATACA 58.523 33.333 23.72 0.00 46.17 2.29
2046 2284 8.762426 CATGATTCATGAAGTACACTGATACAG 58.238 37.037 19.84 0.00 43.81 2.74
2258 2496 1.318158 GCTGATGCTCCCCACAAAGG 61.318 60.000 0.00 0.00 36.03 3.11
2266 2504 2.199652 CCCCACAAAGGCGCTTGAA 61.200 57.895 15.47 0.00 35.39 2.69
2374 2612 1.666209 CGGTTGGTTCATCCCATGGC 61.666 60.000 6.09 0.00 33.60 4.40
2466 2704 1.204146 CTCCCCTCAATCGGAAGGAA 58.796 55.000 0.00 0.00 29.94 3.36
2569 2807 1.670811 CAAGTGACACGCAAAGGAAGT 59.329 47.619 0.00 0.00 0.00 3.01
2624 2862 1.168714 GGTGGATGTCTTCAAGCACC 58.831 55.000 0.00 0.00 30.29 5.01
2656 2894 7.510549 ACTTTACACCATTGATGTATATGGC 57.489 36.000 0.00 0.00 44.17 4.40
2662 2900 3.436704 CCATTGATGTATATGGCACGGTC 59.563 47.826 0.00 0.00 35.31 4.79
2764 3002 4.035208 CACTACCAACACCAGAAGTTCAAC 59.965 45.833 5.50 0.00 0.00 3.18
2791 3029 3.756727 GAGACCCCGTCCGGACAC 61.757 72.222 32.80 17.58 37.50 3.67
3007 3245 1.282570 CATGTGCGCGTTCAACCTT 59.717 52.632 8.43 0.00 0.00 3.50
3013 3251 1.868997 CGCGTTCAACCTTGAGCAT 59.131 52.632 0.00 0.00 38.17 3.79
3136 3374 6.540551 GGTTAATCCCTTCTCTGAAGTGATTC 59.459 42.308 16.84 7.85 0.00 2.52
3178 3416 4.042560 ACTGGCGTGTACCTATATCCTAGA 59.957 45.833 0.00 0.00 0.00 2.43
3195 3433 3.119209 CCTAGAAACCGGTACTCTGAACC 60.119 52.174 23.20 1.44 0.00 3.62
3196 3434 2.322658 AGAAACCGGTACTCTGAACCA 58.677 47.619 8.00 0.00 36.78 3.67
3198 3436 1.713297 AACCGGTACTCTGAACCACT 58.287 50.000 8.00 0.00 36.78 4.00
3201 3439 2.560105 ACCGGTACTCTGAACCACTTAC 59.440 50.000 4.49 0.00 36.78 2.34
3202 3440 2.415090 CCGGTACTCTGAACCACTTACG 60.415 54.545 0.00 0.00 36.78 3.18
3205 3443 4.095483 CGGTACTCTGAACCACTTACGTAT 59.905 45.833 0.00 0.00 36.78 3.06
3206 3444 5.294306 CGGTACTCTGAACCACTTACGTATA 59.706 44.000 0.00 0.00 36.78 1.47
3209 3447 6.830873 ACTCTGAACCACTTACGTATAACT 57.169 37.500 0.00 0.00 0.00 2.24
3210 3448 7.928307 ACTCTGAACCACTTACGTATAACTA 57.072 36.000 0.00 0.00 0.00 2.24
3211 3449 7.983307 ACTCTGAACCACTTACGTATAACTAG 58.017 38.462 0.00 0.00 0.00 2.57
3303 3544 1.608822 GTCGTTGCGTGTGTTTGTTT 58.391 45.000 0.00 0.00 0.00 2.83
3305 3546 1.979469 TCGTTGCGTGTGTTTGTTTTG 59.021 42.857 0.00 0.00 0.00 2.44
3356 3600 8.524487 TGTGTTTTTGGACAAAGTTGTATTACT 58.476 29.630 0.00 0.00 42.43 2.24
3370 3614 5.687166 TGTATTACTAGTCCTGGGTTTGG 57.313 43.478 0.00 0.00 0.00 3.28
3416 3662 3.003068 GCCAGTGACACATGCAGAATATC 59.997 47.826 8.59 0.00 0.00 1.63
3460 3709 1.814394 GACATGAGCAGTGCATTTCCA 59.186 47.619 19.20 7.22 0.00 3.53
3514 3763 3.976169 TGGTTTCTTGCGAATTTGGAAG 58.024 40.909 18.38 18.38 38.51 3.46
3544 3793 2.275318 CTCGGTCAGGAATTCAGAAGC 58.725 52.381 7.93 0.44 0.00 3.86
3554 3803 2.568623 ATTCAGAAGCCGGAAGTGTT 57.431 45.000 5.05 0.00 30.42 3.32
3556 3805 0.884704 TCAGAAGCCGGAAGTGTTGC 60.885 55.000 5.05 0.00 0.00 4.17
3561 3810 2.280524 CCGGAAGTGTTGCCGTGA 60.281 61.111 0.00 0.00 45.85 4.35
3562 3811 2.317609 CCGGAAGTGTTGCCGTGAG 61.318 63.158 0.00 0.00 45.85 3.51
3597 3850 1.814248 GCCGATTATCCCCGCTTCTTT 60.814 52.381 0.00 0.00 0.00 2.52
3598 3851 2.143925 CCGATTATCCCCGCTTCTTTC 58.856 52.381 0.00 0.00 0.00 2.62
3599 3852 2.143925 CGATTATCCCCGCTTCTTTCC 58.856 52.381 0.00 0.00 0.00 3.13
3684 3943 0.669318 GAGATCAACCCAACGCGTCA 60.669 55.000 14.44 0.00 0.00 4.35
3719 3978 0.332972 ATTCCCCACTTTCTCAGGCC 59.667 55.000 0.00 0.00 0.00 5.19
3747 4008 2.279120 CACCAGCTCGATCTCGCC 60.279 66.667 0.00 0.00 39.60 5.54
3976 4261 4.253257 GGAGCCTCGCCTACGTCG 62.253 72.222 0.00 0.00 41.18 5.12
4032 4317 2.186384 CTCGGGAAGCTGAGCCTG 59.814 66.667 0.00 0.00 0.00 4.85
4125 4410 3.115892 TTCGCCAACGTCATCGCC 61.116 61.111 0.00 0.00 41.18 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 0.386731 CCACCAACAAAATCGCCGAC 60.387 55.000 0.00 0.00 0.00 4.79
35 36 1.228003 AAATCAACGCGTCCCCACA 60.228 52.632 14.44 0.00 0.00 4.17
37 38 1.969064 CCAAATCAACGCGTCCCCA 60.969 57.895 14.44 0.00 0.00 4.96
106 109 7.423844 TGTTAATTCTCATCTAGAGGAGCAA 57.576 36.000 25.97 20.42 44.81 3.91
112 115 9.809096 TGTAGCTTTGTTAATTCTCATCTAGAG 57.191 33.333 0.00 0.00 46.14 2.43
134 137 7.735917 TCAAATGATGTAGGGGTTAGATGTAG 58.264 38.462 0.00 0.00 0.00 2.74
135 138 7.684317 TCAAATGATGTAGGGGTTAGATGTA 57.316 36.000 0.00 0.00 0.00 2.29
191 195 4.258543 GTTTTACACGGAGATTCATGGGA 58.741 43.478 0.00 0.00 0.00 4.37
196 200 5.048364 CCATTTGGTTTTACACGGAGATTCA 60.048 40.000 0.00 0.00 0.00 2.57
276 280 1.175983 GGCCACGGAATCACACCAAA 61.176 55.000 0.00 0.00 0.00 3.28
306 310 6.980051 ATCCTTCTTACATACCAAACGAAC 57.020 37.500 0.00 0.00 0.00 3.95
323 327 9.522804 TTAAACAACACAAATACACAATCCTTC 57.477 29.630 0.00 0.00 0.00 3.46
487 498 4.473559 AGCCCTACACCAGTACAATTACAT 59.526 41.667 0.00 0.00 0.00 2.29
488 499 3.841845 AGCCCTACACCAGTACAATTACA 59.158 43.478 0.00 0.00 0.00 2.41
491 502 3.073946 ACAAGCCCTACACCAGTACAATT 59.926 43.478 0.00 0.00 0.00 2.32
493 504 2.038033 GACAAGCCCTACACCAGTACAA 59.962 50.000 0.00 0.00 0.00 2.41
494 505 1.621814 GACAAGCCCTACACCAGTACA 59.378 52.381 0.00 0.00 0.00 2.90
495 506 1.066358 GGACAAGCCCTACACCAGTAC 60.066 57.143 0.00 0.00 0.00 2.73
496 507 1.272807 GGACAAGCCCTACACCAGTA 58.727 55.000 0.00 0.00 0.00 2.74
497 508 0.766674 TGGACAAGCCCTACACCAGT 60.767 55.000 0.00 0.00 34.97 4.00
498 509 0.400213 TTGGACAAGCCCTACACCAG 59.600 55.000 0.00 0.00 34.97 4.00
500 511 1.463674 CATTGGACAAGCCCTACACC 58.536 55.000 0.00 0.00 34.97 4.16
501 512 1.271926 ACCATTGGACAAGCCCTACAC 60.272 52.381 10.37 0.00 34.97 2.90
502 513 1.072266 ACCATTGGACAAGCCCTACA 58.928 50.000 10.37 0.00 34.97 2.74
503 514 2.026636 TGTACCATTGGACAAGCCCTAC 60.027 50.000 10.37 0.00 34.97 3.18
505 516 1.072266 TGTACCATTGGACAAGCCCT 58.928 50.000 10.37 0.00 34.97 5.19
508 519 2.819608 ACACATGTACCATTGGACAAGC 59.180 45.455 10.37 0.00 0.00 4.01
509 520 4.321156 CCAACACATGTACCATTGGACAAG 60.321 45.833 18.70 8.94 42.04 3.16
512 523 3.417101 TCCAACACATGTACCATTGGAC 58.583 45.455 20.72 4.12 42.99 4.02
513 524 3.073798 AGTCCAACACATGTACCATTGGA 59.926 43.478 20.72 20.72 45.07 3.53
514 525 3.420893 AGTCCAACACATGTACCATTGG 58.579 45.455 17.91 17.91 41.04 3.16
515 526 4.278170 ACAAGTCCAACACATGTACCATTG 59.722 41.667 0.00 1.27 35.12 2.82
516 527 4.469657 ACAAGTCCAACACATGTACCATT 58.530 39.130 0.00 0.00 35.12 3.16
517 528 4.098914 ACAAGTCCAACACATGTACCAT 57.901 40.909 0.00 0.00 35.12 3.55
521 532 5.242434 GGATGTACAAGTCCAACACATGTA 58.758 41.667 10.14 0.00 38.00 2.29
522 533 4.072131 GGATGTACAAGTCCAACACATGT 58.928 43.478 10.14 0.00 40.13 3.21
523 534 3.440173 GGGATGTACAAGTCCAACACATG 59.560 47.826 15.72 0.00 36.19 3.21
524 535 3.330701 AGGGATGTACAAGTCCAACACAT 59.669 43.478 15.72 0.00 36.19 3.21
525 536 2.708861 AGGGATGTACAAGTCCAACACA 59.291 45.455 15.72 0.00 36.19 3.72
526 537 3.418684 AGGGATGTACAAGTCCAACAC 57.581 47.619 15.72 0.80 36.19 3.32
527 538 3.137544 ACAAGGGATGTACAAGTCCAACA 59.862 43.478 15.72 0.00 41.63 3.33
528 539 3.751518 ACAAGGGATGTACAAGTCCAAC 58.248 45.455 15.72 1.73 41.63 3.77
529 540 5.163184 TGTTACAAGGGATGTACAAGTCCAA 60.163 40.000 15.72 0.68 44.11 3.53
530 541 4.348461 TGTTACAAGGGATGTACAAGTCCA 59.652 41.667 15.72 0.00 44.11 4.02
532 543 6.485648 AGTTTGTTACAAGGGATGTACAAGTC 59.514 38.462 0.00 0.00 44.11 3.01
533 544 6.362248 AGTTTGTTACAAGGGATGTACAAGT 58.638 36.000 0.00 0.00 44.11 3.16
534 545 6.072673 GGAGTTTGTTACAAGGGATGTACAAG 60.073 42.308 0.00 0.00 44.11 3.16
535 546 5.766174 GGAGTTTGTTACAAGGGATGTACAA 59.234 40.000 0.00 0.00 44.11 2.41
536 547 5.072600 AGGAGTTTGTTACAAGGGATGTACA 59.927 40.000 0.00 0.00 44.11 2.90
537 548 5.557866 AGGAGTTTGTTACAAGGGATGTAC 58.442 41.667 0.00 0.00 44.11 2.90
539 550 4.351111 AGAGGAGTTTGTTACAAGGGATGT 59.649 41.667 0.00 0.00 46.36 3.06
540 551 4.911390 AGAGGAGTTTGTTACAAGGGATG 58.089 43.478 0.00 0.00 0.00 3.51
544 555 5.472478 GGGTTTAGAGGAGTTTGTTACAAGG 59.528 44.000 0.00 0.00 0.00 3.61
545 556 5.472478 GGGGTTTAGAGGAGTTTGTTACAAG 59.528 44.000 0.00 0.00 0.00 3.16
546 557 5.379187 GGGGTTTAGAGGAGTTTGTTACAA 58.621 41.667 0.00 0.00 0.00 2.41
547 558 4.202493 GGGGGTTTAGAGGAGTTTGTTACA 60.202 45.833 0.00 0.00 0.00 2.41
548 559 4.330250 GGGGGTTTAGAGGAGTTTGTTAC 58.670 47.826 0.00 0.00 0.00 2.50
549 560 4.645863 GGGGGTTTAGAGGAGTTTGTTA 57.354 45.455 0.00 0.00 0.00 2.41
567 578 5.761234 CAGCATTTTCATTGATATTTGGGGG 59.239 40.000 0.00 0.00 0.00 5.40
568 579 5.761234 CCAGCATTTTCATTGATATTTGGGG 59.239 40.000 0.00 0.00 0.00 4.96
569 580 6.584488 TCCAGCATTTTCATTGATATTTGGG 58.416 36.000 0.00 0.00 0.00 4.12
570 581 7.494211 TCTCCAGCATTTTCATTGATATTTGG 58.506 34.615 0.00 0.00 0.00 3.28
571 582 9.193133 GATCTCCAGCATTTTCATTGATATTTG 57.807 33.333 0.00 0.00 0.00 2.32
573 584 8.577296 CAGATCTCCAGCATTTTCATTGATATT 58.423 33.333 0.00 0.00 0.00 1.28
574 585 7.176865 CCAGATCTCCAGCATTTTCATTGATAT 59.823 37.037 0.00 0.00 0.00 1.63
576 587 5.302059 CCAGATCTCCAGCATTTTCATTGAT 59.698 40.000 0.00 0.00 0.00 2.57
577 588 4.643334 CCAGATCTCCAGCATTTTCATTGA 59.357 41.667 0.00 0.00 0.00 2.57
579 590 4.607239 ACCAGATCTCCAGCATTTTCATT 58.393 39.130 0.00 0.00 0.00 2.57
580 591 4.246712 ACCAGATCTCCAGCATTTTCAT 57.753 40.909 0.00 0.00 0.00 2.57
582 593 5.065731 CAGTTACCAGATCTCCAGCATTTTC 59.934 44.000 0.00 0.00 0.00 2.29
583 594 4.946157 CAGTTACCAGATCTCCAGCATTTT 59.054 41.667 0.00 0.00 0.00 1.82
642 880 9.788960 CATATGTACATATATGCAAGTACGACT 57.211 33.333 24.50 0.00 39.63 4.18
693 931 8.197439 CAGATGACCTACATGTACTACATTTCA 58.803 37.037 0.08 0.00 36.53 2.69
748 986 0.787787 TAAACTTACGCTGCTGCACG 59.212 50.000 16.29 18.29 39.64 5.34
857 1095 7.898309 CGCACAAGTTAAGACATAAGATACAAC 59.102 37.037 0.00 0.00 0.00 3.32
874 1112 4.217035 TGCAGTGTCGCACAAGTT 57.783 50.000 11.58 0.00 36.86 2.66
883 1121 2.679837 CAACATATCCTGGTGCAGTGTC 59.320 50.000 0.00 0.00 35.33 3.67
970 1208 8.194104 ACTACAATAACTTCAGCTGATGTAGAG 58.806 37.037 36.49 26.10 40.72 2.43
1213 1451 9.587772 GTACACTGCTTTAAGATCTTCATTCTA 57.412 33.333 12.24 0.00 0.00 2.10
1257 1495 4.255301 ACGGCGACACTAATTTTTGGATA 58.745 39.130 16.62 0.00 0.00 2.59
1268 1506 3.367992 TTGAACTAAACGGCGACACTA 57.632 42.857 16.62 0.00 0.00 2.74
1322 1560 3.705051 ACAATAGTACTCCGTCCTTCCA 58.295 45.455 0.00 0.00 0.00 3.53
1326 1564 5.105432 GGAGAAAACAATAGTACTCCGTCCT 60.105 44.000 0.00 0.00 35.06 3.85
1361 1599 2.026822 GCTCCCCTTCAGAATCTGTGAA 60.027 50.000 10.36 0.00 32.61 3.18
1391 1629 0.895559 AAGGCAGCAGCTTTACCACC 60.896 55.000 0.00 0.00 38.40 4.61
1427 1665 2.749800 GCTGTTTCCAGGACTTGAACCT 60.750 50.000 0.00 0.00 39.22 3.50
1429 1667 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
1457 1695 1.808133 CGCAGCCTTTCCCTACATCTC 60.808 57.143 0.00 0.00 0.00 2.75
1459 1697 0.107654 ACGCAGCCTTTCCCTACATC 60.108 55.000 0.00 0.00 0.00 3.06
1516 1754 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
1519 1757 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
1570 1808 4.875536 TCATGGATAAACATGGTCAAGTCG 59.124 41.667 0.00 0.00 46.33 4.18
1648 1886 5.745227 AGAATGTTGGTAAGGATCGAATGT 58.255 37.500 0.00 0.00 0.00 2.71
1713 1951 2.746362 CAAAGACCATTCACCAGAGAGC 59.254 50.000 0.00 0.00 0.00 4.09
1821 2059 7.770366 TGGAAAGGGGAGTAAATAAGAAAAC 57.230 36.000 0.00 0.00 0.00 2.43
1855 2093 8.820831 TCCATTTAAGCTCATTTAATTTTGGGA 58.179 29.630 0.00 0.00 0.00 4.37
2258 2496 2.636768 AATTTAGCACCTTCAAGCGC 57.363 45.000 0.00 0.00 35.48 5.92
2301 2539 3.181454 ACTCGGGATATGGATGGTTTGAC 60.181 47.826 0.00 0.00 0.00 3.18
2466 2704 2.541907 ATGGCCTTGGACAGGTGCT 61.542 57.895 3.32 0.00 46.07 4.40
2569 2807 2.823984 TCGACAAACGACCAGCTTTTA 58.176 42.857 0.00 0.00 46.45 1.52
2624 2862 3.252215 TCAATGGTGTAAAGTTGCCTTCG 59.748 43.478 0.00 0.00 0.00 3.79
2662 2900 4.767255 GGCTCTGCCCACACCTCG 62.767 72.222 0.00 0.00 44.06 4.63
2788 3026 1.066143 CGCTTGACCCTTATGAGGTGT 60.066 52.381 2.39 0.17 41.85 4.16
2789 3027 1.656652 CGCTTGACCCTTATGAGGTG 58.343 55.000 2.39 0.00 41.85 4.00
2791 3029 0.815615 GGCGCTTGACCCTTATGAGG 60.816 60.000 7.64 0.00 43.15 3.86
3007 3245 1.993653 CTCCTTGGTCCCATGCTCA 59.006 57.895 0.00 0.00 0.00 4.26
3013 3251 0.970937 CTACGAGCTCCTTGGTCCCA 60.971 60.000 8.47 0.00 39.84 4.37
3136 3374 0.027455 TTTCAGCTTCGCACACGTTG 59.973 50.000 0.00 0.00 41.18 4.10
3178 3416 2.044758 AGTGGTTCAGAGTACCGGTTT 58.955 47.619 15.04 0.32 38.55 3.27
3314 3555 5.920193 AAACACAAGCCAGTTGCATATAT 57.080 34.783 0.00 0.00 44.83 0.86
3315 3556 5.720371 AAAACACAAGCCAGTTGCATATA 57.280 34.783 0.00 0.00 44.83 0.86
3356 3600 1.992557 AGAATGCCAAACCCAGGACTA 59.007 47.619 0.00 0.00 0.00 2.59
3357 3601 0.779997 AGAATGCCAAACCCAGGACT 59.220 50.000 0.00 0.00 0.00 3.85
3360 3604 2.583472 GGAGAATGCCAAACCCAGG 58.417 57.895 0.00 0.00 0.00 4.45
3370 3614 0.106967 GGGACAAGGAGGGAGAATGC 60.107 60.000 0.00 0.00 0.00 3.56
3416 3662 1.575244 CCACACAGATATGCGACCAG 58.425 55.000 0.00 0.00 0.00 4.00
3514 3763 1.891150 TCCTGACCGAGTGGAAGTTAC 59.109 52.381 0.00 0.00 39.21 2.50
3599 3852 3.788766 CTGCTCGGAAAACGCGGG 61.789 66.667 12.47 0.00 43.86 6.13
3625 3878 3.565902 GGTTGGCTTATATTGGACAGAGC 59.434 47.826 0.00 0.00 0.00 4.09
3684 3943 2.438385 GAATGGCGACGCACGTGTTT 62.438 55.000 23.09 3.83 44.60 2.83
3696 3955 0.322456 TGAGAAAGTGGGGAATGGCG 60.322 55.000 0.00 0.00 0.00 5.69
3728 3989 2.279120 CGAGATCGAGCTGGTGCC 60.279 66.667 8.50 0.00 43.02 5.01
3976 4261 2.801679 CGAGGAGATAGTAGGTGACGAC 59.198 54.545 0.00 0.00 36.03 4.34
3990 4275 2.113433 GTAGAGCACGGCGAGGAGA 61.113 63.158 16.62 0.00 0.00 3.71



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

AutoCloner maintained by Alex Coulton.