Multiple sequence alignment - TraesCS4D01G105800

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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 TraesCS4D01G105800 chr4D 100.000 3657 0 0 1 3657 84300931 84304587 0.000000e+00 6754
1 TraesCS4D01G105800 chr4D 97.222 72 2 0 1509 1580 84302369 84302440 4.960000e-24 122
2 TraesCS4D01G105800 chr4D 97.222 72 2 0 1439 1510 84302439 84302510 4.960000e-24 122
3 TraesCS4D01G105800 chr4B 93.238 3372 178 21 1 3360 119351873 119355206 0.000000e+00 4918
4 TraesCS4D01G105800 chr4B 95.833 72 3 0 1509 1580 119353299 119353370 2.310000e-22 117
5 TraesCS4D01G105800 chr4B 93.056 72 1 1 1439 1510 119353369 119353436 6.460000e-18 102
6 TraesCS4D01G105800 chr4A 90.466 1909 114 25 1509 3402 497075826 497077681 0.000000e+00 2455
7 TraesCS4D01G105800 chr4A 92.947 1517 92 12 1 1510 497074389 497075897 0.000000e+00 2194
8 TraesCS4D01G105800 chr7D 84.672 274 13 14 3405 3651 418626268 418625997 2.820000e-61 246
9 TraesCS4D01G105800 chr7D 95.575 113 5 0 3405 3517 417937377 417937265 8.070000e-42 182
10 TraesCS4D01G105800 chr7D 95.575 113 5 0 3405 3517 418074566 418074454 8.070000e-42 182
11 TraesCS4D01G105800 chr7D 84.181 177 22 5 2936 3110 388908465 388908637 2.260000e-37 167
12 TraesCS4D01G105800 chr1D 83.929 280 18 9 3405 3657 180954204 180954483 3.650000e-60 243
13 TraesCS4D01G105800 chr1D 84.015 269 22 13 3408 3657 94449074 94449340 4.720000e-59 239
14 TraesCS4D01G105800 chr1D 78.502 414 49 25 2935 3318 313794437 313794034 6.110000e-58 235
15 TraesCS4D01G105800 chr1D 86.503 163 22 0 2933 3095 108102532 108102370 2.900000e-41 180
16 TraesCS4D01G105800 chr2A 83.273 275 16 12 3405 3651 600415205 600414933 3.670000e-55 226
17 TraesCS4D01G105800 chr2A 83.137 255 16 12 3404 3631 600412056 600411802 1.330000e-49 207
18 TraesCS4D01G105800 chr2A 81.624 234 14 12 3405 3611 600409105 600408874 2.260000e-37 167
19 TraesCS4D01G105800 chr2A 91.743 109 9 0 3405 3513 523457459 523457567 6.320000e-33 152
20 TraesCS4D01G105800 chr2D 84.615 182 28 0 2930 3111 65684092 65684273 8.070000e-42 182
21 TraesCS4D01G105800 chr2D 85.393 178 21 5 2932 3106 420565487 420565312 2.900000e-41 180
22 TraesCS4D01G105800 chr3D 76.271 413 55 19 2932 3311 302295408 302295810 2.900000e-41 180
23 TraesCS4D01G105800 chr5A 83.333 180 25 5 2933 3112 593504627 593504801 1.050000e-35 161


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 TraesCS4D01G105800 chr4D 84300931 84304587 3656 False 2332.666667 6754 98.148000 1 3657 3 chr4D.!!$F1 3656
1 TraesCS4D01G105800 chr4B 119351873 119355206 3333 False 1712.333333 4918 94.042333 1 3360 3 chr4B.!!$F1 3359
2 TraesCS4D01G105800 chr4A 497074389 497077681 3292 False 2324.500000 2455 91.706500 1 3402 2 chr4A.!!$F1 3401

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
24 25 2.497675 AGAGTGATGCCGTATGTCAACT 59.502 45.455 0.00 0.0 0.00 3.16 F
598 604 3.283751 CGGCCACACCCTTATATTTTCA 58.716 45.455 2.24 0.0 33.26 2.69 F
2541 2562 0.032678 GATGGAGCCGATGACGATGT 59.967 55.000 0.00 0.0 42.66 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1405 1415 0.515564 GGAAACGTGGTCAATGGTCG 59.484 55.0 0.00 0.0 0.00 4.79 R
2550 2571 0.824109 ATCTCCATCTTCGCCGACAA 59.176 50.0 0.00 0.0 0.00 3.18 R
3478 3505 0.097674 GTGCGCTTCTGGCTACAATG 59.902 55.0 9.73 0.0 39.13 2.82 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
23 24 2.860735 GAGAGTGATGCCGTATGTCAAC 59.139 50.000 0.00 0.00 0.00 3.18
24 25 2.497675 AGAGTGATGCCGTATGTCAACT 59.502 45.455 0.00 0.00 0.00 3.16
30 31 6.374333 AGTGATGCCGTATGTCAACTTTTTAT 59.626 34.615 0.00 0.00 0.00 1.40
33 35 5.933790 TGCCGTATGTCAACTTTTTATGTC 58.066 37.500 0.00 0.00 0.00 3.06
66 68 5.617609 TGACGCTTGAAATTCGTTGATTAG 58.382 37.500 0.00 0.00 36.50 1.73
67 69 5.178623 TGACGCTTGAAATTCGTTGATTAGT 59.821 36.000 0.00 0.00 36.50 2.24
71 73 6.031417 CGCTTGAAATTCGTTGATTAGTTGAC 59.969 38.462 0.00 0.00 0.00 3.18
124 128 3.761752 TCATGTCGTCCAACAGATGTCTA 59.238 43.478 0.00 0.00 32.85 2.59
144 148 5.698545 GTCTAGTGGTAGCCATGAATGATTC 59.301 44.000 0.00 0.00 35.28 2.52
154 158 7.506361 AGCCATGAATGATTCTGGAGATATA 57.494 36.000 20.47 0.00 32.90 0.86
283 287 7.433131 GGATTGTGTGCATTGTAGTATGAAATG 59.567 37.037 0.00 0.00 34.98 2.32
390 396 6.947733 ACAACCTGACATGAGAATATCCAAAA 59.052 34.615 0.00 0.00 0.00 2.44
391 397 7.121759 ACAACCTGACATGAGAATATCCAAAAG 59.878 37.037 0.00 0.00 0.00 2.27
392 398 6.962182 ACCTGACATGAGAATATCCAAAAGA 58.038 36.000 0.00 0.00 0.00 2.52
393 399 7.580910 ACCTGACATGAGAATATCCAAAAGAT 58.419 34.615 0.00 0.00 39.15 2.40
394 400 8.057623 ACCTGACATGAGAATATCCAAAAGATT 58.942 33.333 0.00 0.00 36.33 2.40
486 492 7.487509 CCATCAATGCAACATATACGAAAACAA 59.512 33.333 0.00 0.00 0.00 2.83
568 574 6.682423 TGCACAAAAGATGTATATGACTGG 57.318 37.500 0.00 0.00 41.46 4.00
598 604 3.283751 CGGCCACACCCTTATATTTTCA 58.716 45.455 2.24 0.00 33.26 2.69
645 651 5.945784 CCATTTCCATCTTGTCCTTAAGTGA 59.054 40.000 0.97 0.00 0.00 3.41
689 695 6.540914 TCAACGTCTTAGGAAATTTTGAGTGT 59.459 34.615 0.00 0.00 0.00 3.55
877 886 4.834534 ACGTATGTAACAATAGGGTGCAA 58.165 39.130 0.00 0.00 0.00 4.08
960 969 8.314021 TCACTAGCTTGTTGAATTGAGAGATTA 58.686 33.333 0.00 0.00 0.00 1.75
991 1000 3.644335 ACTAACCAGAGACCATAGGACC 58.356 50.000 0.00 0.00 0.00 4.46
994 1003 3.315880 ACCAGAGACCATAGGACCTAC 57.684 52.381 2.46 0.00 0.00 3.18
1071 1080 3.616821 GGTTTGTGAAGGTTTTCTTGCAC 59.383 43.478 0.00 0.00 35.50 4.57
1125 1134 6.379988 TGGCTACTCACAATAGTTATGACTCA 59.620 38.462 0.00 0.00 37.33 3.41
1155 1164 3.711704 TCACTCTGAAAAGACTGGGAAGT 59.288 43.478 0.00 0.00 0.00 3.01
1161 1170 6.756221 TCTGAAAAGACTGGGAAGTAACTAC 58.244 40.000 0.00 0.00 0.00 2.73
1337 1347 3.671008 CATAATCATGCATGGTTGGGG 57.329 47.619 31.03 17.71 32.49 4.96
1381 1391 3.576550 GTGGAGCCCAAGGAAATTTTACA 59.423 43.478 0.00 0.00 34.18 2.41
1389 1399 9.283768 AGCCCAAGGAAATTTTACAAAATAAAG 57.716 29.630 0.56 0.00 37.62 1.85
1393 1403 9.877137 CAAGGAAATTTTACAAAATAAAGCACC 57.123 29.630 0.56 0.00 37.62 5.01
1405 1415 9.423061 ACAAAATAAAGCACCACAATTAAGATC 57.577 29.630 0.00 0.00 0.00 2.75
1408 1418 4.946784 AAGCACCACAATTAAGATCGAC 57.053 40.909 0.00 0.00 0.00 4.20
1498 1508 4.823989 ACTACTTGTACGTCTTGGTGTAGT 59.176 41.667 0.00 2.31 35.84 2.73
1540 1550 9.435688 AGGCCATGTTCTTAATTATTTCAAAAC 57.564 29.630 5.01 0.00 0.00 2.43
1541 1551 9.213799 GGCCATGTTCTTAATTATTTCAAAACA 57.786 29.630 0.00 0.00 0.00 2.83
1632 1643 2.097954 CGCAAATTGCAAGGCTAGATCA 59.902 45.455 18.65 0.00 45.36 2.92
1652 1663 6.602406 AGATCACCGCTTTCTAGTACTCTTTA 59.398 38.462 0.00 0.00 0.00 1.85
1690 1701 3.968649 TGCAAGAGAATGTTTCAACTGC 58.031 40.909 0.00 0.00 0.00 4.40
1750 1761 8.428186 TTGATCCTTACCGTTATAATTGTGTC 57.572 34.615 0.00 0.00 0.00 3.67
1778 1789 2.635915 ACCTAACGAACAAGTGGGATCA 59.364 45.455 0.00 0.00 0.00 2.92
1802 1814 6.603940 TTCCTTTTTCTGGTCAAATATGGG 57.396 37.500 0.00 0.00 0.00 4.00
1909 1921 3.668447 GATGAGTGAAGAAGAAGGTGCA 58.332 45.455 0.00 0.00 0.00 4.57
1918 1930 7.550906 AGTGAAGAAGAAGGTGCAATAGATAAC 59.449 37.037 0.00 0.00 0.00 1.89
1966 1978 5.121768 CGTGGATGGTTATCGTTTCTTTCTT 59.878 40.000 0.00 0.00 33.98 2.52
1983 1995 0.405585 CTTGGTGAAGTCCCATGGGT 59.594 55.000 30.28 11.86 36.47 4.51
1994 2006 1.351017 TCCCATGGGTGTGAGTTCTTC 59.649 52.381 30.28 0.00 36.47 2.87
2046 2062 9.562583 GCCTCTTATGTAGAATTCTATAGTTCG 57.437 37.037 17.95 6.41 30.91 3.95
2092 2109 8.472007 AACAACTAAATGTTACAGGGATTTCA 57.528 30.769 0.00 0.00 41.56 2.69
2093 2110 8.650143 ACAACTAAATGTTACAGGGATTTCAT 57.350 30.769 0.00 0.00 37.07 2.57
2269 2290 2.270275 TTTCAGTGGTTTGTTGCACG 57.730 45.000 0.00 0.00 0.00 5.34
2318 2339 9.463443 GCATCACAAGTTTTTCTACTACAAAAT 57.537 29.630 0.00 0.00 0.00 1.82
2407 2428 5.936372 GCATGCAGACAATGAGGAATATCTA 59.064 40.000 14.21 0.00 0.00 1.98
2429 2450 4.293494 AGAAGAGGGAGATGCAGATAACA 58.707 43.478 0.00 0.00 0.00 2.41
2509 2530 2.639286 CTGGACGCTGTTGTTGCC 59.361 61.111 0.00 0.00 0.00 4.52
2541 2562 0.032678 GATGGAGCCGATGACGATGT 59.967 55.000 0.00 0.00 42.66 3.06
2550 2571 2.554462 CCGATGACGATGTAGATGGAGT 59.446 50.000 0.00 0.00 42.66 3.85
2715 2736 3.081061 CAAGCCTGGTTGCAGTTACATA 58.919 45.455 0.00 0.00 0.00 2.29
2923 2946 0.455633 GCCTGCATGTTGCTTCTTCG 60.456 55.000 0.75 0.00 45.31 3.79
2953 2976 2.068519 GAAAATTGCTTTTGGAGGCCG 58.931 47.619 0.00 0.00 34.73 6.13
3052 3075 9.696572 ACAGATATACGTGGAGGTATAATGTAT 57.303 33.333 0.00 0.00 38.47 2.29
3082 3106 9.176181 TGTGTAAATTTTCAAGACGAAATAAGC 57.824 29.630 0.00 0.00 43.12 3.09
3139 3163 9.918630 CATCCTCAAAGTCTATGAATTTGTTTT 57.081 29.630 16.37 2.97 44.49 2.43
3197 3222 9.038072 TCTTGGACTTTTACACACATATACCTA 57.962 33.333 0.00 0.00 0.00 3.08
3282 3307 4.918810 TTTTTCAGAAGTTTCAGGCTCC 57.081 40.909 0.00 0.00 0.00 4.70
3283 3308 3.576078 TTTCAGAAGTTTCAGGCTCCA 57.424 42.857 0.00 0.00 0.00 3.86
3386 3413 5.687828 CAAAAGTTTCTCTCTGATGTGCTC 58.312 41.667 0.00 0.00 0.00 4.26
3389 3416 2.643933 TTCTCTCTGATGTGCTCGTG 57.356 50.000 0.00 0.00 0.00 4.35
3402 3429 2.476997 GTGCTCGTGAAAGGTTTCTCTC 59.523 50.000 4.19 0.00 38.02 3.20
3403 3430 2.070028 GCTCGTGAAAGGTTTCTCTCC 58.930 52.381 4.19 0.00 38.02 3.71
3404 3431 2.329379 CTCGTGAAAGGTTTCTCTCCG 58.671 52.381 4.19 2.29 38.02 4.63
3405 3432 1.000506 TCGTGAAAGGTTTCTCTCCGG 59.999 52.381 0.00 0.00 38.02 5.14
3406 3433 1.000506 CGTGAAAGGTTTCTCTCCGGA 59.999 52.381 2.93 2.93 38.02 5.14
3407 3434 2.689646 GTGAAAGGTTTCTCTCCGGAG 58.310 52.381 26.32 26.32 40.73 4.63
3408 3435 1.623811 TGAAAGGTTTCTCTCCGGAGG 59.376 52.381 30.80 20.79 43.39 4.30
3409 3436 1.624312 GAAAGGTTTCTCTCCGGAGGT 59.376 52.381 30.80 4.34 40.74 3.85
3410 3437 2.353903 GAAAGGTTTCTCTCCGGAGGTC 60.354 54.545 30.80 15.67 40.74 3.85
3411 3438 5.491507 GAAAGGTTTCTCTCCGGAGGTCC 62.492 56.522 30.80 22.55 40.74 4.46
3428 3455 1.953559 TCCTATTGGACGCATTCTGC 58.046 50.000 0.00 0.00 37.46 4.26
3438 3465 3.885777 GCATTCTGCGTCAACTAGC 57.114 52.632 0.00 0.00 31.71 3.42
3439 3466 0.025513 GCATTCTGCGTCAACTAGCG 59.974 55.000 0.00 0.00 31.71 4.26
3440 3467 1.629013 CATTCTGCGTCAACTAGCGA 58.371 50.000 0.00 0.00 35.87 4.93
3441 3468 1.321743 CATTCTGCGTCAACTAGCGAC 59.678 52.381 3.34 3.34 35.87 5.19
3442 3469 0.388134 TTCTGCGTCAACTAGCGACC 60.388 55.000 7.19 2.32 35.87 4.79
3443 3470 1.805945 CTGCGTCAACTAGCGACCC 60.806 63.158 7.19 0.19 35.87 4.46
3444 3471 2.508663 GCGTCAACTAGCGACCCC 60.509 66.667 7.19 0.00 0.00 4.95
3445 3472 2.202570 CGTCAACTAGCGACCCCG 60.203 66.667 7.19 0.00 39.16 5.73
3446 3473 2.693762 CGTCAACTAGCGACCCCGA 61.694 63.158 7.19 0.00 38.22 5.14
3447 3474 1.153881 GTCAACTAGCGACCCCGAC 60.154 63.158 2.15 0.00 38.22 4.79
3448 3475 2.202570 CAACTAGCGACCCCGACG 60.203 66.667 0.00 0.00 38.22 5.12
3493 3520 2.110296 GCCCATTGTAGCCAGAAGC 58.890 57.895 0.00 0.00 44.25 3.86
3526 3553 2.177531 CGTACCGCGCACTGTAGT 59.822 61.111 8.75 0.00 0.00 2.73
3539 3566 3.769739 ACTGTAGTGATCCAGTTTGCA 57.230 42.857 0.00 0.00 38.76 4.08
3540 3567 3.668447 ACTGTAGTGATCCAGTTTGCAG 58.332 45.455 0.00 0.00 38.76 4.41
3541 3568 3.071602 ACTGTAGTGATCCAGTTTGCAGT 59.928 43.478 0.00 0.00 38.76 4.40
3542 3569 4.283467 ACTGTAGTGATCCAGTTTGCAGTA 59.717 41.667 0.00 0.00 38.76 2.74
3543 3570 4.820897 TGTAGTGATCCAGTTTGCAGTAG 58.179 43.478 0.00 0.00 0.00 2.57
3544 3571 2.704572 AGTGATCCAGTTTGCAGTAGC 58.295 47.619 0.00 0.00 42.57 3.58
3545 3572 1.394917 GTGATCCAGTTTGCAGTAGCG 59.605 52.381 0.00 0.00 46.23 4.26
3546 3573 1.275010 TGATCCAGTTTGCAGTAGCGA 59.725 47.619 0.00 0.00 46.23 4.93
3547 3574 2.289382 TGATCCAGTTTGCAGTAGCGAA 60.289 45.455 0.00 0.00 46.23 4.70
3548 3575 2.472695 TCCAGTTTGCAGTAGCGAAT 57.527 45.000 0.00 0.00 45.47 3.34
3549 3576 2.346803 TCCAGTTTGCAGTAGCGAATC 58.653 47.619 0.00 0.00 45.47 2.52
3550 3577 1.061131 CCAGTTTGCAGTAGCGAATCG 59.939 52.381 0.00 0.00 45.47 3.34
3551 3578 1.061131 CAGTTTGCAGTAGCGAATCGG 59.939 52.381 4.35 0.00 45.47 4.18
3552 3579 1.076332 GTTTGCAGTAGCGAATCGGT 58.924 50.000 13.06 13.06 45.47 4.69
3553 3580 1.463444 GTTTGCAGTAGCGAATCGGTT 59.537 47.619 13.83 0.00 45.47 4.44
3554 3581 1.803334 TTGCAGTAGCGAATCGGTTT 58.197 45.000 13.83 0.00 46.23 3.27
3555 3582 1.803334 TGCAGTAGCGAATCGGTTTT 58.197 45.000 13.83 0.00 46.23 2.43
3556 3583 2.147958 TGCAGTAGCGAATCGGTTTTT 58.852 42.857 13.83 0.00 46.23 1.94
3575 3602 5.736486 TTTTTGGCCCGTGTTTTTATTTC 57.264 34.783 0.00 0.00 0.00 2.17
3576 3603 2.708386 TGGCCCGTGTTTTTATTTCG 57.292 45.000 0.00 0.00 0.00 3.46
3577 3604 2.228059 TGGCCCGTGTTTTTATTTCGA 58.772 42.857 0.00 0.00 0.00 3.71
3578 3605 2.621998 TGGCCCGTGTTTTTATTTCGAA 59.378 40.909 0.00 0.00 0.00 3.71
3579 3606 2.981805 GGCCCGTGTTTTTATTTCGAAC 59.018 45.455 0.00 0.00 0.00 3.95
3580 3607 3.550436 GGCCCGTGTTTTTATTTCGAACA 60.550 43.478 0.00 0.00 0.00 3.18
3581 3608 4.231439 GCCCGTGTTTTTATTTCGAACAT 58.769 39.130 0.00 0.00 35.91 2.71
3582 3609 4.682401 GCCCGTGTTTTTATTTCGAACATT 59.318 37.500 0.00 0.00 35.91 2.71
3583 3610 5.176039 GCCCGTGTTTTTATTTCGAACATTT 59.824 36.000 0.00 0.00 35.91 2.32
3584 3611 6.292435 GCCCGTGTTTTTATTTCGAACATTTT 60.292 34.615 0.00 0.00 35.91 1.82
3585 3612 7.622880 CCCGTGTTTTTATTTCGAACATTTTT 58.377 30.769 0.00 0.00 35.91 1.94
3586 3613 7.790216 CCCGTGTTTTTATTTCGAACATTTTTC 59.210 33.333 0.00 0.00 35.91 2.29
3587 3614 7.790216 CCGTGTTTTTATTTCGAACATTTTTCC 59.210 33.333 0.00 0.00 35.91 3.13
3588 3615 8.321716 CGTGTTTTTATTTCGAACATTTTTCCA 58.678 29.630 0.00 0.00 35.91 3.53
3589 3616 9.631639 GTGTTTTTATTTCGAACATTTTTCCAG 57.368 29.630 0.00 0.00 35.91 3.86
3590 3617 9.587772 TGTTTTTATTTCGAACATTTTTCCAGA 57.412 25.926 0.00 0.00 0.00 3.86
3594 3621 9.810545 TTTATTTCGAACATTTTTCCAGAAAGT 57.189 25.926 0.00 0.00 31.08 2.66
3597 3624 9.810545 ATTTCGAACATTTTTCCAGAAAGTAAA 57.189 25.926 0.00 0.00 31.08 2.01
3598 3625 9.810545 TTTCGAACATTTTTCCAGAAAGTAAAT 57.189 25.926 0.00 0.00 0.00 1.40
3651 3678 9.547753 TGAAATTCCGACAAATTTAAAATTGGA 57.452 25.926 17.93 8.42 38.59 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 6.150307 ACATAAAAAGTTGACATACGGCATCA 59.850 34.615 0.00 0.00 0.00 3.07
23 24 6.291060 GCGTCAAACTGTTGTGACATAAAAAG 60.291 38.462 23.00 13.11 43.57 2.27
24 25 5.513495 GCGTCAAACTGTTGTGACATAAAAA 59.487 36.000 23.00 0.00 43.57 1.94
30 31 1.732941 AGCGTCAAACTGTTGTGACA 58.267 45.000 23.00 0.00 43.57 3.58
33 35 2.823196 TCAAGCGTCAAACTGTTGTG 57.177 45.000 0.00 0.00 36.07 3.33
66 68 2.095853 CGCCACACTATCCAATGTCAAC 59.904 50.000 0.00 0.00 0.00 3.18
67 69 2.355197 CGCCACACTATCCAATGTCAA 58.645 47.619 0.00 0.00 0.00 3.18
71 73 1.299541 GTCCGCCACACTATCCAATG 58.700 55.000 0.00 0.00 0.00 2.82
107 110 2.492088 CCACTAGACATCTGTTGGACGA 59.508 50.000 0.00 0.00 33.42 4.20
124 128 4.458397 CAGAATCATTCATGGCTACCACT 58.542 43.478 0.00 0.00 35.80 4.00
220 224 9.065871 GCGTGCATTTATTATAGAAATCCATTC 57.934 33.333 0.00 0.00 38.39 2.67
283 287 7.957002 TCCATGTTCCATAGAAGATTACTCTC 58.043 38.462 0.00 0.00 33.90 3.20
435 441 5.587388 AAAGATACCATTTGACCTGCATG 57.413 39.130 0.00 0.00 0.00 4.06
568 574 4.776647 GTGTGGCCGGAAATGCGC 62.777 66.667 5.05 0.00 0.00 6.09
669 675 9.399403 GAAATGACACTCAAAATTTCCTAAGAC 57.601 33.333 0.00 0.00 34.43 3.01
713 719 4.037923 CCTTGTTTTTCAGCTTCAGCCTTA 59.962 41.667 0.00 0.00 43.38 2.69
991 1000 1.967066 AGAAGCATCCATCGGAGGTAG 59.033 52.381 0.00 0.00 35.75 3.18
994 1003 1.047002 AGAGAAGCATCCATCGGAGG 58.953 55.000 0.00 0.00 36.49 4.30
999 1008 3.471680 GGGTACAAGAGAAGCATCCATC 58.528 50.000 0.00 0.00 0.00 3.51
1125 1134 5.934781 AGTCTTTTCAGAGTGAAGGACAAT 58.065 37.500 18.34 0.00 40.21 2.71
1180 1189 7.665690 ACAAATTGTAACATATTGTTGCCTGA 58.334 30.769 0.00 0.00 41.35 3.86
1181 1190 7.887996 ACAAATTGTAACATATTGTTGCCTG 57.112 32.000 0.00 1.00 41.35 4.85
1290 1299 3.561310 GCTAGATTCGGATGTTGCATTCA 59.439 43.478 2.38 0.00 29.87 2.57
1337 1347 6.127897 CCACCTCCATGTTAAGATCTTTTGAC 60.128 42.308 14.36 10.73 0.00 3.18
1381 1391 8.519526 TCGATCTTAATTGTGGTGCTTTATTTT 58.480 29.630 0.00 0.00 0.00 1.82
1389 1399 3.006940 TGGTCGATCTTAATTGTGGTGC 58.993 45.455 0.00 0.00 0.00 5.01
1393 1403 5.353956 TGGTCAATGGTCGATCTTAATTGTG 59.646 40.000 0.00 0.00 31.63 3.33
1405 1415 0.515564 GGAAACGTGGTCAATGGTCG 59.484 55.000 0.00 0.00 0.00 4.79
1408 1418 3.658757 AAATGGAAACGTGGTCAATGG 57.341 42.857 0.00 0.00 0.00 3.16
1498 1508 2.450886 TGGCCTAGGTGATCTAGATCCA 59.549 50.000 26.33 14.33 46.48 3.41
1538 1548 6.183360 ACCAAGACGTACAAGTAGTAACTGTT 60.183 38.462 0.00 0.00 35.62 3.16
1539 1549 5.300286 ACCAAGACGTACAAGTAGTAACTGT 59.700 40.000 0.00 0.00 35.62 3.55
1540 1550 5.628193 CACCAAGACGTACAAGTAGTAACTG 59.372 44.000 0.00 0.00 35.62 3.16
1541 1551 5.300286 ACACCAAGACGTACAAGTAGTAACT 59.700 40.000 0.00 0.00 37.65 2.24
1632 1643 6.433716 ACTTCTAAAGAGTACTAGAAAGCGGT 59.566 38.462 0.00 0.00 0.00 5.68
1652 1663 8.123639 TCTCTTGCATAAACACTAGTACTTCT 57.876 34.615 0.00 0.00 0.00 2.85
1750 1761 2.069273 CTTGTTCGTTAGGTGGCTCAG 58.931 52.381 0.00 0.00 0.00 3.35
1773 1784 5.982890 TTGACCAGAAAAAGGAATGATCC 57.017 39.130 0.00 0.00 46.98 3.36
1778 1789 6.352137 GCCCATATTTGACCAGAAAAAGGAAT 60.352 38.462 0.00 0.00 0.00 3.01
1840 1852 8.474025 TGTGAAACTGAACAATACAAAGGAAAT 58.526 29.630 0.00 0.00 38.04 2.17
1918 1930 6.457359 CGTTATCGTACAAAAACATGAAGTCG 59.543 38.462 0.00 0.00 0.00 4.18
1966 1978 1.065410 ACACCCATGGGACTTCACCA 61.065 55.000 38.07 0.00 43.22 4.17
2092 2109 9.512588 AATGTAGATCTTCTTGACTGAAACAAT 57.487 29.630 0.00 0.00 0.00 2.71
2093 2110 8.908786 AATGTAGATCTTCTTGACTGAAACAA 57.091 30.769 0.00 0.00 0.00 2.83
2269 2290 1.798813 CGAGCCTACACCACTTTGTTC 59.201 52.381 0.00 0.00 0.00 3.18
2407 2428 4.293494 TGTTATCTGCATCTCCCTCTTCT 58.707 43.478 0.00 0.00 0.00 2.85
2429 2450 1.601419 GCACCAGCATTGCCATCACT 61.601 55.000 4.70 0.00 41.58 3.41
2509 2530 1.255882 CTCCATCTCCCTCATCCTCG 58.744 60.000 0.00 0.00 0.00 4.63
2541 2562 1.134367 CTTCGCCGACAACTCCATCTA 59.866 52.381 0.00 0.00 0.00 1.98
2550 2571 0.824109 ATCTCCATCTTCGCCGACAA 59.176 50.000 0.00 0.00 0.00 3.18
2660 2681 5.063204 TCCTGGATGCCACTAAATATTTCG 58.937 41.667 3.39 0.63 0.00 3.46
2715 2736 3.810310 AGCTAGCGAGAATTAAGCAGT 57.190 42.857 9.55 0.00 35.63 4.40
2781 2802 7.065324 TCTCAAACATATGTGGGATAAACGTTC 59.935 37.037 9.63 0.00 0.00 3.95
2830 2853 6.073276 TCGGATATTCAAAAGCGATTGTATGG 60.073 38.462 0.00 0.00 0.00 2.74
2835 2858 8.017373 ACATATTCGGATATTCAAAAGCGATTG 58.983 33.333 0.00 0.00 0.00 2.67
2877 2900 1.901464 GTGTGGGGCGGTTCACAAT 60.901 57.895 0.00 0.00 44.19 2.71
2923 2946 1.173913 AGCAATTTTCGCACTACCCC 58.826 50.000 0.00 0.00 0.00 4.95
2953 2976 2.828145 GAGGCCTCCATGGAGCTC 59.172 66.667 32.97 28.38 40.69 4.09
3080 3104 0.822164 GCCATGCCTTCATTTCAGCT 59.178 50.000 0.00 0.00 0.00 4.24
3082 3106 3.322211 TTTGCCATGCCTTCATTTCAG 57.678 42.857 0.00 0.00 0.00 3.02
3139 3163 7.731054 ACCTTGAAATGCAACCTATACAAAAA 58.269 30.769 0.00 0.00 31.96 1.94
3140 3164 7.296628 ACCTTGAAATGCAACCTATACAAAA 57.703 32.000 0.00 0.00 31.96 2.44
3271 3296 1.457346 CATGGAGTGGAGCCTGAAAC 58.543 55.000 0.00 0.00 0.00 2.78
3282 3307 1.222936 GAGTGGCCTCCATGGAGTG 59.777 63.158 34.49 26.84 40.44 3.51
3283 3308 1.229625 TGAGTGGCCTCCATGGAGT 60.230 57.895 34.49 19.68 40.44 3.85
3294 3319 2.335011 GGCGTTTTGGTGAGTGGC 59.665 61.111 0.00 0.00 0.00 5.01
3326 3351 9.719355 TCACGGATAAACTTTATATATGCACAT 57.281 29.630 0.00 0.00 0.00 3.21
3386 3413 1.000506 TCCGGAGAGAAACCTTTCACG 59.999 52.381 0.00 0.48 39.61 4.35
3389 3416 1.624312 ACCTCCGGAGAGAAACCTTTC 59.376 52.381 33.39 0.00 43.39 2.62
3421 3448 1.321743 GTCGCTAGTTGACGCAGAATG 59.678 52.381 2.20 0.00 40.87 2.67
3422 3449 1.630148 GTCGCTAGTTGACGCAGAAT 58.370 50.000 2.20 0.00 0.00 2.40
3423 3450 0.388134 GGTCGCTAGTTGACGCAGAA 60.388 55.000 10.02 0.00 37.22 3.02
3424 3451 1.211969 GGTCGCTAGTTGACGCAGA 59.788 57.895 10.02 0.00 37.22 4.26
3425 3452 1.805945 GGGTCGCTAGTTGACGCAG 60.806 63.158 21.19 0.00 45.52 5.18
3426 3453 2.260434 GGGTCGCTAGTTGACGCA 59.740 61.111 21.19 0.00 45.52 5.24
3427 3454 2.508663 GGGGTCGCTAGTTGACGC 60.509 66.667 19.23 19.23 45.48 5.19
3428 3455 2.202570 CGGGGTCGCTAGTTGACG 60.203 66.667 10.02 0.00 37.22 4.35
3429 3456 1.153881 GTCGGGGTCGCTAGTTGAC 60.154 63.158 8.29 8.29 36.13 3.18
3430 3457 2.693762 CGTCGGGGTCGCTAGTTGA 61.694 63.158 0.00 0.00 36.13 3.18
3431 3458 2.202570 CGTCGGGGTCGCTAGTTG 60.203 66.667 0.00 0.00 36.13 3.16
3475 3502 1.718757 CGCTTCTGGCTACAATGGGC 61.719 60.000 0.00 0.00 39.13 5.36
3476 3503 1.718757 GCGCTTCTGGCTACAATGGG 61.719 60.000 0.00 0.00 39.13 4.00
3477 3504 1.026182 TGCGCTTCTGGCTACAATGG 61.026 55.000 9.73 0.00 39.13 3.16
3478 3505 0.097674 GTGCGCTTCTGGCTACAATG 59.902 55.000 9.73 0.00 39.13 2.82
3479 3506 1.361668 CGTGCGCTTCTGGCTACAAT 61.362 55.000 9.73 0.00 39.13 2.71
3480 3507 2.027073 CGTGCGCTTCTGGCTACAA 61.027 57.895 9.73 0.00 39.13 2.41
3481 3508 2.432456 CGTGCGCTTCTGGCTACA 60.432 61.111 9.73 0.00 39.13 2.74
3482 3509 3.854459 GCGTGCGCTTCTGGCTAC 61.854 66.667 9.73 0.00 39.13 3.58
3483 3510 4.371590 TGCGTGCGCTTCTGGCTA 62.372 61.111 17.49 0.00 42.51 3.93
3510 3537 0.179145 ATCACTACAGTGCGCGGTAC 60.179 55.000 8.83 0.00 45.25 3.34
3511 3538 0.099968 GATCACTACAGTGCGCGGTA 59.900 55.000 8.83 9.88 45.25 4.02
3512 3539 1.153823 GATCACTACAGTGCGCGGT 60.154 57.895 8.83 8.40 45.25 5.68
3513 3540 1.878522 GGATCACTACAGTGCGCGG 60.879 63.158 8.83 0.00 45.25 6.46
3514 3541 1.142185 CTGGATCACTACAGTGCGCG 61.142 60.000 0.00 0.00 45.25 6.86
3515 3542 0.108615 ACTGGATCACTACAGTGCGC 60.109 55.000 0.00 0.00 45.54 6.09
3516 3543 2.370281 AACTGGATCACTACAGTGCG 57.630 50.000 4.43 0.00 46.49 5.34
3517 3544 2.160417 GCAAACTGGATCACTACAGTGC 59.840 50.000 4.43 1.17 46.49 4.40
3518 3545 3.402110 TGCAAACTGGATCACTACAGTG 58.598 45.455 2.84 2.84 46.49 3.66
3519 3546 8.949612 GCTACTGCAAACTGGATCACTACAGT 62.950 46.154 0.00 0.00 43.28 3.55
3520 3547 3.668447 ACTGCAAACTGGATCACTACAG 58.332 45.455 0.00 0.00 40.48 2.74
3521 3548 3.769739 ACTGCAAACTGGATCACTACA 57.230 42.857 0.00 0.00 0.00 2.74
3522 3549 3.619038 GCTACTGCAAACTGGATCACTAC 59.381 47.826 0.00 0.00 39.41 2.73
3523 3550 3.676049 CGCTACTGCAAACTGGATCACTA 60.676 47.826 0.00 0.00 39.64 2.74
3524 3551 2.704572 GCTACTGCAAACTGGATCACT 58.295 47.619 0.00 0.00 39.41 3.41
3525 3552 1.394917 CGCTACTGCAAACTGGATCAC 59.605 52.381 0.00 0.00 39.64 3.06
3526 3553 1.275010 TCGCTACTGCAAACTGGATCA 59.725 47.619 0.00 0.00 39.64 2.92
3527 3554 2.010145 TCGCTACTGCAAACTGGATC 57.990 50.000 0.00 0.00 39.64 3.36
3528 3555 2.472695 TTCGCTACTGCAAACTGGAT 57.527 45.000 0.00 0.00 39.64 3.41
3529 3556 2.346803 GATTCGCTACTGCAAACTGGA 58.653 47.619 0.00 0.00 39.64 3.86
3530 3557 1.061131 CGATTCGCTACTGCAAACTGG 59.939 52.381 0.00 0.00 39.64 4.00
3531 3558 1.061131 CCGATTCGCTACTGCAAACTG 59.939 52.381 0.00 0.00 39.64 3.16
3532 3559 1.337823 ACCGATTCGCTACTGCAAACT 60.338 47.619 0.00 0.00 39.64 2.66
3533 3560 1.076332 ACCGATTCGCTACTGCAAAC 58.924 50.000 0.00 0.00 39.64 2.93
3534 3561 1.803334 AACCGATTCGCTACTGCAAA 58.197 45.000 0.00 0.00 39.64 3.68
3535 3562 1.803334 AAACCGATTCGCTACTGCAA 58.197 45.000 0.00 0.00 39.64 4.08
3536 3563 1.803334 AAAACCGATTCGCTACTGCA 58.197 45.000 0.00 0.00 39.64 4.41
3537 3564 2.894307 AAAAACCGATTCGCTACTGC 57.106 45.000 0.00 0.00 0.00 4.40
3553 3580 4.270325 CGAAATAAAAACACGGGCCAAAAA 59.730 37.500 4.39 0.00 0.00 1.94
3554 3581 3.802685 CGAAATAAAAACACGGGCCAAAA 59.197 39.130 4.39 0.00 0.00 2.44
3555 3582 3.067742 TCGAAATAAAAACACGGGCCAAA 59.932 39.130 4.39 0.00 0.00 3.28
3556 3583 2.621998 TCGAAATAAAAACACGGGCCAA 59.378 40.909 4.39 0.00 0.00 4.52
3557 3584 2.228059 TCGAAATAAAAACACGGGCCA 58.772 42.857 4.39 0.00 0.00 5.36
3558 3585 2.981805 GTTCGAAATAAAAACACGGGCC 59.018 45.455 0.00 0.00 0.00 5.80
3559 3586 3.630101 TGTTCGAAATAAAAACACGGGC 58.370 40.909 0.00 0.00 0.00 6.13
3560 3587 6.757026 AAATGTTCGAAATAAAAACACGGG 57.243 33.333 0.00 0.00 35.87 5.28
3561 3588 7.790216 GGAAAAATGTTCGAAATAAAAACACGG 59.210 33.333 0.00 0.00 35.87 4.94
3562 3589 8.321716 TGGAAAAATGTTCGAAATAAAAACACG 58.678 29.630 0.00 0.00 35.87 4.49
3563 3590 9.631639 CTGGAAAAATGTTCGAAATAAAAACAC 57.368 29.630 0.00 0.00 35.87 3.32
3564 3591 9.587772 TCTGGAAAAATGTTCGAAATAAAAACA 57.412 25.926 0.00 0.00 37.32 2.83
3568 3595 9.810545 ACTTTCTGGAAAAATGTTCGAAATAAA 57.189 25.926 0.00 0.00 0.00 1.40
3571 3598 9.810545 TTTACTTTCTGGAAAAATGTTCGAAAT 57.189 25.926 0.00 0.00 0.00 2.17
3572 3599 9.810545 ATTTACTTTCTGGAAAAATGTTCGAAA 57.189 25.926 0.00 0.00 0.00 3.46
3625 3652 9.547753 TCCAATTTTAAATTTGTCGGAATTTCA 57.452 25.926 17.23 0.00 39.32 2.69


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

AutoCloner maintained by Alex Coulton.