Multiple sequence alignment - TraesCS5A01G339600

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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 TraesCS5A01G339600 chr5A 100.000 3568 0 0 1 3568 546771710 546768143 0.000000e+00 6589.0
1 TraesCS5A01G339600 chr5A 88.571 70 5 3 336 405 503504483 503504549 8.210000e-12 82.4
2 TraesCS5A01G339600 chr5A 91.525 59 4 1 347 405 452934737 452934794 2.950000e-11 80.5
3 TraesCS5A01G339600 chr5D 94.931 3058 126 16 426 3479 513307573 513310605 0.000000e+00 4761.0
4 TraesCS5A01G339600 chr5D 94.713 2913 124 17 571 3479 431780586 431783472 0.000000e+00 4499.0
5 TraesCS5A01G339600 chr5D 93.855 2978 130 27 512 3485 433685235 433682307 0.000000e+00 4436.0
6 TraesCS5A01G339600 chr5D 89.944 179 14 3 1 179 431780112 431780286 9.970000e-56 228.0
7 TraesCS5A01G339600 chr5D 86.592 179 14 6 1 179 513307401 513307569 4.700000e-44 189.0
8 TraesCS5A01G339600 chr5D 92.366 131 9 1 446 575 431780299 431780429 6.080000e-43 185.0
9 TraesCS5A01G339600 chr5D 93.913 115 7 0 232 346 90311578 90311464 1.320000e-39 174.0
10 TraesCS5A01G339600 chr5D 83.799 179 13 5 1 179 433685467 433685305 4.770000e-34 156.0
11 TraesCS5A01G339600 chr5D 90.000 70 2 5 336 405 398490630 398490694 6.350000e-13 86.1
12 TraesCS5A01G339600 chr5D 97.436 39 1 0 3499 3537 431783474 431783512 2.300000e-07 67.6
13 TraesCS5A01G339600 chr5D 97.436 39 1 0 3499 3537 433682309 433682271 2.300000e-07 67.6
14 TraesCS5A01G339600 chr5D 97.436 39 1 0 3499 3537 513310607 513310645 2.300000e-07 67.6
15 TraesCS5A01G339600 chr5B 94.591 3069 126 19 426 3479 522862231 522859188 0.000000e+00 4711.0
16 TraesCS5A01G339600 chr5B 95.342 2941 97 17 505 3433 522407942 522410854 0.000000e+00 4636.0
17 TraesCS5A01G339600 chr5B 93.737 495 12 2 1 476 522407142 522407636 0.000000e+00 725.0
18 TraesCS5A01G339600 chr5B 96.476 227 7 1 511 737 522931485 522931260 1.210000e-99 374.0
19 TraesCS5A01G339600 chr5B 91.589 214 17 1 2530 2743 521276716 521276504 9.690000e-76 294.0
20 TraesCS5A01G339600 chr5B 84.916 179 9 3 1 179 522862395 522862235 7.920000e-37 165.0
21 TraesCS5A01G339600 chr5B 91.304 115 10 0 232 346 94148159 94148273 1.330000e-34 158.0
22 TraesCS5A01G339600 chr5B 91.667 60 4 1 347 405 415995374 415995315 8.210000e-12 82.4
23 TraesCS5A01G339600 chr5B 97.436 39 1 0 3499 3537 522859186 522859148 2.300000e-07 67.6
24 TraesCS5A01G339600 chr2A 84.366 1695 151 49 1030 2676 27956706 27958334 0.000000e+00 1557.0
25 TraesCS5A01G339600 chr2A 85.390 1321 125 34 1316 2590 27952723 27954021 0.000000e+00 1308.0
26 TraesCS5A01G339600 chr2A 93.827 162 10 0 1030 1191 27952462 27952623 9.890000e-61 244.0
27 TraesCS5A01G339600 chr2A 85.507 69 3 2 899 967 27952310 27952371 8.270000e-07 65.8
28 TraesCS5A01G339600 chr2D 84.382 1415 143 40 1368 2737 25339348 25340729 0.000000e+00 1317.0
29 TraesCS5A01G339600 chr2D 85.231 1124 108 33 1030 2116 25347630 25348732 0.000000e+00 1103.0
30 TraesCS5A01G339600 chr2D 88.940 217 11 7 1030 1237 25339017 25339229 4.570000e-64 255.0
31 TraesCS5A01G339600 chr2D 86.364 176 20 3 231 406 596567585 596567756 4.700000e-44 189.0
32 TraesCS5A01G339600 chr2D 81.818 220 22 15 590 805 25338448 25338653 6.130000e-38 169.0
33 TraesCS5A01G339600 chr2D 97.297 37 1 0 931 967 25338888 25338924 2.970000e-06 63.9
34 TraesCS5A01G339600 chr2D 96.970 33 1 0 1 33 25338146 25338178 4.980000e-04 56.5
35 TraesCS5A01G339600 chr2B 85.412 1323 125 31 1316 2589 41132976 41134279 0.000000e+00 1312.0
36 TraesCS5A01G339600 chr2B 94.444 162 9 0 1030 1191 41132714 41132875 2.130000e-62 250.0
37 TraesCS5A01G339600 chr2B 85.650 223 25 6 1030 1247 41141186 41141406 9.970000e-56 228.0
38 TraesCS5A01G339600 chr2B 86.127 173 21 3 234 405 573810884 573810714 2.190000e-42 183.0
39 TraesCS5A01G339600 chr2B 83.412 211 20 4 596 805 41140622 41140818 7.870000e-42 182.0
40 TraesCS5A01G339600 chr2B 76.817 289 43 19 516 796 41132058 41132330 1.340000e-29 141.0
41 TraesCS5A01G339600 chr2B 85.507 69 3 2 899 967 41132562 41132623 8.270000e-07 65.8
42 TraesCS5A01G339600 chr1A 88.435 147 14 3 225 369 98583084 98582939 1.320000e-39 174.0
43 TraesCS5A01G339600 chr7D 87.413 143 15 2 2966 3106 60437943 60437802 1.030000e-35 161.0
44 TraesCS5A01G339600 chr7A 83.505 97 15 1 234 329 649128054 649127958 4.910000e-14 89.8
45 TraesCS5A01G339600 chr3B 93.103 58 3 1 347 404 94493108 94493052 2.280000e-12 84.2
46 TraesCS5A01G339600 chr3B 89.231 65 6 1 347 411 578810956 578810893 2.950000e-11 80.5


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 TraesCS5A01G339600 chr5A 546768143 546771710 3567 True 6589.000000 6589 100.000000 1 3568 1 chr5A.!!$R1 3567
1 TraesCS5A01G339600 chr5D 513307401 513310645 3244 False 1672.533333 4761 92.986333 1 3537 3 chr5D.!!$F3 3536
2 TraesCS5A01G339600 chr5D 433682271 433685467 3196 True 1553.200000 4436 91.696667 1 3537 3 chr5D.!!$R2 3536
3 TraesCS5A01G339600 chr5D 431780112 431783512 3400 False 1244.900000 4499 93.614750 1 3537 4 chr5D.!!$F2 3536
4 TraesCS5A01G339600 chr5B 522407142 522410854 3712 False 2680.500000 4636 94.539500 1 3433 2 chr5B.!!$F2 3432
5 TraesCS5A01G339600 chr5B 522859148 522862395 3247 True 1647.866667 4711 92.314333 1 3537 3 chr5B.!!$R4 3536
6 TraesCS5A01G339600 chr2A 27952310 27958334 6024 False 793.700000 1557 87.272500 899 2676 4 chr2A.!!$F1 1777
7 TraesCS5A01G339600 chr2D 25347630 25348732 1102 False 1103.000000 1103 85.231000 1030 2116 1 chr2D.!!$F1 1086
8 TraesCS5A01G339600 chr2D 25338146 25340729 2583 False 372.280000 1317 89.881400 1 2737 5 chr2D.!!$F3 2736
9 TraesCS5A01G339600 chr2B 41132058 41134279 2221 False 442.200000 1312 85.545000 516 2589 4 chr2B.!!$F1 2073
10 TraesCS5A01G339600 chr2B 41140622 41141406 784 False 205.000000 228 84.531000 596 1247 2 chr2B.!!$F2 651

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
377 403 0.179062 ATCGCTTGATGCAGAGGTCC 60.179 55.000 0.00 0.0 43.06 4.46 F
749 1229 1.213430 TGGCATCCATCTCTTCATGCA 59.787 47.619 5.21 0.0 42.94 3.96 F
1662 6647 1.814634 GCCGATCTACTCCTCCGAAGA 60.815 57.143 0.00 0.0 0.00 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1708 6693 0.326522 TGATCCCTCTTGCTGCCCTA 60.327 55.000 0.0 0.0 0.00 3.53 R
2010 7005 1.134877 TGCGGAGAAGAGATCTTGCTG 60.135 52.381 0.0 0.0 38.96 4.41 R
3019 8065 2.161410 GCTTTGCGTGACCATGTATTGA 59.839 45.455 0.0 0.0 0.00 2.57 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
189 214 6.293462 GGGAACTGCATATAAAACGGAGAATC 60.293 42.308 0.00 0.00 0.00 2.52
330 356 9.556030 GATGTATTACTTTGTAAGGCTTTGTTC 57.444 33.333 4.45 0.00 0.00 3.18
377 403 0.179062 ATCGCTTGATGCAGAGGTCC 60.179 55.000 0.00 0.00 43.06 4.46
458 484 5.704053 ACGGAGAATTTTCGTTTCAGGTATT 59.296 36.000 0.00 0.00 32.95 1.89
459 485 6.021596 CGGAGAATTTTCGTTTCAGGTATTG 58.978 40.000 0.00 0.00 0.00 1.90
491 517 9.985730 ACATCAATATTCACTGACAACAAAAAT 57.014 25.926 0.00 0.00 0.00 1.82
537 841 8.986929 ATAAAGCTAAAGGTGCTCAATAAGAT 57.013 30.769 0.00 0.00 40.22 2.40
749 1229 1.213430 TGGCATCCATCTCTTCATGCA 59.787 47.619 5.21 0.00 42.94 3.96
904 1460 5.471257 GCTCCAGGTAGCATATAAGTACAC 58.529 45.833 0.00 0.00 42.30 2.90
1322 6291 3.837731 AGAGGCTAGGAATTAGGATGCTC 59.162 47.826 0.00 0.00 0.00 4.26
1363 6332 9.511272 GGTTTCACCCTTAATCTTTAGTTAAGA 57.489 33.333 7.09 0.00 40.10 2.10
1445 6427 5.021033 ACCATCTTCTCATCACAAGCTAG 57.979 43.478 0.00 0.00 0.00 3.42
1464 6446 5.010933 GCTAGCCTACAGTACATAGATGGA 58.989 45.833 2.29 0.00 0.00 3.41
1500 6482 4.905429 TGCTGCAAAGTCTAACTTCCATA 58.095 39.130 0.00 0.00 37.47 2.74
1662 6647 1.814634 GCCGATCTACTCCTCCGAAGA 60.815 57.143 0.00 0.00 0.00 2.87
1708 6693 3.166679 GTCCCTTGTCTTCTACAGAGGT 58.833 50.000 0.00 0.00 39.87 3.85
2010 7005 0.038166 TCCATTGCCTGGGACAACTC 59.962 55.000 0.00 0.00 45.98 3.01
2259 7272 2.942804 TCTTGCCATTCCAAACACAGA 58.057 42.857 0.00 0.00 0.00 3.41
2741 7775 2.777832 ACAGAGAGAAGAATGGGTGC 57.222 50.000 0.00 0.00 0.00 5.01
2752 7786 5.824624 AGAAGAATGGGTGCATTGTGTATAG 59.175 40.000 0.00 0.00 0.00 1.31
2753 7787 5.116084 AGAATGGGTGCATTGTGTATAGT 57.884 39.130 0.00 0.00 0.00 2.12
2864 7902 5.471556 TCACAAACTTGCAATGGATTGAT 57.528 34.783 13.36 0.00 40.14 2.57
2880 7918 9.471702 AATGGATTGATAAACTCTGAAACTGAT 57.528 29.630 0.00 0.00 0.00 2.90
2989 8027 6.795399 TCAAACACAAGCTCTTTCCTTTAAG 58.205 36.000 0.00 0.00 0.00 1.85
3004 8042 3.057174 CCTTTAAGCCGCAAATACCAACA 60.057 43.478 0.00 0.00 0.00 3.33
3005 8043 4.381505 CCTTTAAGCCGCAAATACCAACAT 60.382 41.667 0.00 0.00 0.00 2.71
3014 8052 6.149474 GCCGCAAATACCAACATAGAATATCT 59.851 38.462 0.00 0.00 0.00 1.98
3019 8065 9.060347 CAAATACCAACATAGAATATCTGCAGT 57.940 33.333 14.67 3.75 0.00 4.40
3034 8080 2.345876 TGCAGTCAATACATGGTCACG 58.654 47.619 0.00 0.00 0.00 4.35
3052 8098 4.790140 GTCACGCAAAGCAGAAAATCATAG 59.210 41.667 0.00 0.00 0.00 2.23
3093 8139 0.539051 CCGCCAAGGTCAATCTCTCT 59.461 55.000 0.00 0.00 34.51 3.10
3303 8351 1.297689 CAGCTACAGCAAGCCCAGA 59.702 57.895 3.70 0.00 43.86 3.86
3323 8371 6.333416 CCAGACAGTATTTCGAAATCAGAGA 58.667 40.000 25.89 6.43 0.00 3.10
3324 8372 6.983307 CCAGACAGTATTTCGAAATCAGAGAT 59.017 38.462 25.89 8.98 0.00 2.75
3374 8422 0.309922 CAGAACAGCTTGCACACCAG 59.690 55.000 0.00 0.00 0.00 4.00
3380 8428 1.884579 CAGCTTGCACACCAGATTCTT 59.115 47.619 0.00 0.00 0.00 2.52
3384 8432 3.120060 GCTTGCACACCAGATTCTTACAG 60.120 47.826 0.00 0.00 0.00 2.74
3446 8494 5.770162 AGTGGCATATATTTGCTTTAGGGTC 59.230 40.000 16.28 0.20 42.38 4.46
3448 8496 6.040391 GTGGCATATATTTGCTTTAGGGTCAA 59.960 38.462 16.28 0.00 42.38 3.18
3462 8510 4.051661 AGGGTCAATTTGTGGATGATGT 57.948 40.909 0.00 0.00 0.00 3.06
3479 8527 3.261643 TGATGTACTGTGCAGTGGAATCT 59.738 43.478 14.44 0.00 42.52 2.40
3480 8528 4.466015 TGATGTACTGTGCAGTGGAATCTA 59.534 41.667 14.44 4.42 42.52 1.98
3481 8529 4.456280 TGTACTGTGCAGTGGAATCTAG 57.544 45.455 14.44 0.00 42.52 2.43
3482 8530 3.832490 TGTACTGTGCAGTGGAATCTAGT 59.168 43.478 14.44 0.00 42.52 2.57
3483 8531 4.283467 TGTACTGTGCAGTGGAATCTAGTT 59.717 41.667 14.44 0.00 42.52 2.24
3484 8532 5.479027 TGTACTGTGCAGTGGAATCTAGTTA 59.521 40.000 14.44 0.00 42.52 2.24
3485 8533 5.483685 ACTGTGCAGTGGAATCTAGTTAA 57.516 39.130 3.80 0.00 40.75 2.01
3486 8534 6.054860 ACTGTGCAGTGGAATCTAGTTAAT 57.945 37.500 3.80 0.00 40.75 1.40
3487 8535 6.476378 ACTGTGCAGTGGAATCTAGTTAATT 58.524 36.000 3.80 0.00 40.75 1.40
3488 8536 6.372659 ACTGTGCAGTGGAATCTAGTTAATTG 59.627 38.462 3.80 0.00 40.75 2.32
3489 8537 5.123820 TGTGCAGTGGAATCTAGTTAATTGC 59.876 40.000 0.00 0.00 0.00 3.56
3490 8538 5.355350 GTGCAGTGGAATCTAGTTAATTGCT 59.645 40.000 0.00 0.00 0.00 3.91
3491 8539 5.945784 TGCAGTGGAATCTAGTTAATTGCTT 59.054 36.000 0.00 0.00 0.00 3.91
3492 8540 6.127925 TGCAGTGGAATCTAGTTAATTGCTTG 60.128 38.462 0.00 0.00 0.00 4.01
3493 8541 6.094048 GCAGTGGAATCTAGTTAATTGCTTGA 59.906 38.462 0.00 0.00 0.00 3.02
3494 8542 7.362056 GCAGTGGAATCTAGTTAATTGCTTGAA 60.362 37.037 0.00 0.00 0.00 2.69
3495 8543 8.680903 CAGTGGAATCTAGTTAATTGCTTGAAT 58.319 33.333 0.00 0.00 0.00 2.57
3496 8544 8.897752 AGTGGAATCTAGTTAATTGCTTGAATC 58.102 33.333 0.00 0.00 0.00 2.52
3497 8545 8.897752 GTGGAATCTAGTTAATTGCTTGAATCT 58.102 33.333 9.37 0.00 0.00 2.40
3528 8576 3.194116 CCCAGTTTGATGCTGTTATTGCT 59.806 43.478 0.00 0.00 32.41 3.91
3537 8585 3.884169 TGCTGTTATTGCTCGAACAAAC 58.116 40.909 5.19 1.04 35.24 2.93
3538 8586 3.313803 TGCTGTTATTGCTCGAACAAACA 59.686 39.130 5.19 5.70 35.24 2.83
3539 8587 4.023279 TGCTGTTATTGCTCGAACAAACAT 60.023 37.500 5.19 0.00 35.24 2.71
3540 8588 4.321745 GCTGTTATTGCTCGAACAAACATG 59.678 41.667 5.19 0.00 35.24 3.21
3541 8589 4.225984 TGTTATTGCTCGAACAAACATGC 58.774 39.130 5.19 0.00 32.74 4.06
3542 8590 4.023279 TGTTATTGCTCGAACAAACATGCT 60.023 37.500 5.19 0.00 32.74 3.79
3543 8591 3.648339 ATTGCTCGAACAAACATGCTT 57.352 38.095 5.19 0.00 32.27 3.91
3544 8592 3.435105 TTGCTCGAACAAACATGCTTT 57.565 38.095 0.00 0.00 0.00 3.51
3545 8593 3.435105 TGCTCGAACAAACATGCTTTT 57.565 38.095 0.00 0.00 0.00 2.27
3546 8594 4.560136 TGCTCGAACAAACATGCTTTTA 57.440 36.364 0.00 0.00 0.00 1.52
3547 8595 4.926244 TGCTCGAACAAACATGCTTTTAA 58.074 34.783 0.00 0.00 0.00 1.52
3548 8596 4.737765 TGCTCGAACAAACATGCTTTTAAC 59.262 37.500 0.00 0.00 0.00 2.01
3549 8597 4.976116 GCTCGAACAAACATGCTTTTAACT 59.024 37.500 0.00 0.00 0.00 2.24
3550 8598 6.140110 GCTCGAACAAACATGCTTTTAACTA 58.860 36.000 0.00 0.00 0.00 2.24
3551 8599 6.801862 GCTCGAACAAACATGCTTTTAACTAT 59.198 34.615 0.00 0.00 0.00 2.12
3552 8600 7.326063 GCTCGAACAAACATGCTTTTAACTATT 59.674 33.333 0.00 0.00 0.00 1.73
3553 8601 9.180678 CTCGAACAAACATGCTTTTAACTATTT 57.819 29.630 0.00 0.00 0.00 1.40
3554 8602 8.963130 TCGAACAAACATGCTTTTAACTATTTG 58.037 29.630 0.00 0.00 33.17 2.32
3555 8603 8.751335 CGAACAAACATGCTTTTAACTATTTGT 58.249 29.630 0.00 0.00 39.91 2.83
3556 8604 9.848172 GAACAAACATGCTTTTAACTATTTGTG 57.152 29.630 0.00 0.00 38.61 3.33
3557 8605 7.850501 ACAAACATGCTTTTAACTATTTGTGC 58.149 30.769 0.00 0.00 37.57 4.57
3558 8606 7.493971 ACAAACATGCTTTTAACTATTTGTGCA 59.506 29.630 0.00 0.00 37.57 4.57
3559 8607 8.497554 CAAACATGCTTTTAACTATTTGTGCAT 58.502 29.630 0.00 0.00 39.99 3.96
3560 8608 7.816945 ACATGCTTTTAACTATTTGTGCATC 57.183 32.000 0.00 0.00 37.74 3.91
3561 8609 6.813152 ACATGCTTTTAACTATTTGTGCATCC 59.187 34.615 0.00 0.00 37.74 3.51
3562 8610 6.588719 TGCTTTTAACTATTTGTGCATCCT 57.411 33.333 0.00 0.00 0.00 3.24
3563 8611 7.695480 TGCTTTTAACTATTTGTGCATCCTA 57.305 32.000 0.00 0.00 0.00 2.94
3564 8612 8.116651 TGCTTTTAACTATTTGTGCATCCTAA 57.883 30.769 0.00 0.00 0.00 2.69
3565 8613 8.580720 TGCTTTTAACTATTTGTGCATCCTAAA 58.419 29.630 0.00 0.00 0.00 1.85
3566 8614 9.076596 GCTTTTAACTATTTGTGCATCCTAAAG 57.923 33.333 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 138 7.255242 GGCATTACATAATGTGAGTGCTAACAT 60.255 37.037 12.12 0.00 43.72 2.71
227 253 3.609853 TGAAGGAGGTGCACATAATGAC 58.390 45.455 20.43 0.00 0.00 3.06
377 403 1.483415 TCGAAAAGGAGGATAACCCCG 59.517 52.381 0.00 0.00 36.73 5.73
458 484 8.620116 TGTCAGTGAATATTGATGTTCTTTCA 57.380 30.769 0.00 0.00 0.00 2.69
459 485 9.334693 GTTGTCAGTGAATATTGATGTTCTTTC 57.665 33.333 0.00 0.00 0.00 2.62
537 841 4.696402 ACCGACCGAAACTATAAATGCAAA 59.304 37.500 0.00 0.00 0.00 3.68
569 873 4.685169 AAAGACATGCAATTCCAGTACG 57.315 40.909 0.00 0.00 0.00 3.67
749 1229 2.943978 AACTAAGACAGGCCGCGCT 61.944 57.895 5.56 0.00 0.00 5.92
796 1276 2.653726 TCTCTGTTTGAAAGCTGCCAA 58.346 42.857 0.00 0.00 0.00 4.52
849 1380 1.679898 CCACAGGTCTGAAGGGTCC 59.320 63.158 4.84 0.00 0.00 4.46
1038 1688 0.765903 ACCCCGGCATGATGATCTCT 60.766 55.000 0.00 0.00 0.00 3.10
1363 6332 0.693049 ACGGATGAGCCCAAGACTTT 59.307 50.000 0.00 0.00 0.00 2.66
1445 6427 7.176865 TGAGTAATCCATCTATGTACTGTAGGC 59.823 40.741 0.00 0.00 0.00 3.93
1500 6482 1.205893 GCTCTGTCGTTGAGAAGGGAT 59.794 52.381 6.34 0.00 33.68 3.85
1662 6647 1.925455 AGGCCTATGCACCTGGTGT 60.925 57.895 26.48 11.61 40.13 4.16
1708 6693 0.326522 TGATCCCTCTTGCTGCCCTA 60.327 55.000 0.00 0.00 0.00 3.53
1969 6964 1.451504 CCCCAAGTGTGAGACAGCA 59.548 57.895 0.00 0.00 0.00 4.41
2010 7005 1.134877 TGCGGAGAAGAGATCTTGCTG 60.135 52.381 0.00 0.00 38.96 4.41
2695 7729 6.536582 AGCTCTGCTGTTAACAAGTGTATATG 59.463 38.462 10.03 0.00 37.57 1.78
2782 7817 4.067896 CTCTCCACACAAAGTACAGCATT 58.932 43.478 0.00 0.00 0.00 3.56
2820 7855 5.480073 TGAAGCTGCCCATATTGTAACTTTT 59.520 36.000 0.00 0.00 0.00 2.27
2824 7859 3.694072 TGTGAAGCTGCCCATATTGTAAC 59.306 43.478 0.00 0.00 0.00 2.50
2989 8027 4.568152 ATTCTATGTTGGTATTTGCGGC 57.432 40.909 0.00 0.00 0.00 6.53
3004 8042 8.600668 ACCATGTATTGACTGCAGATATTCTAT 58.399 33.333 23.35 11.99 0.00 1.98
3005 8043 7.966812 ACCATGTATTGACTGCAGATATTCTA 58.033 34.615 23.35 4.58 0.00 2.10
3014 8052 2.345876 CGTGACCATGTATTGACTGCA 58.654 47.619 0.00 0.00 0.00 4.41
3019 8065 2.161410 GCTTTGCGTGACCATGTATTGA 59.839 45.455 0.00 0.00 0.00 2.57
3034 8080 5.958955 AGTTCCTATGATTTTCTGCTTTGC 58.041 37.500 0.00 0.00 0.00 3.68
3093 8139 9.893634 AAAATCCATCTTTCATTGCATTTATCA 57.106 25.926 0.00 0.00 0.00 2.15
3303 8351 8.147058 AGCATATCTCTGATTTCGAAATACTGT 58.853 33.333 22.78 9.98 0.00 3.55
3323 8371 7.790027 ACTGAGATGTTCTTAACTGAGCATAT 58.210 34.615 0.00 0.00 37.87 1.78
3324 8372 7.175347 ACTGAGATGTTCTTAACTGAGCATA 57.825 36.000 0.00 0.00 37.87 3.14
3374 8422 9.167311 AGATGGTGTATTTGAACTGTAAGAATC 57.833 33.333 0.00 0.00 37.43 2.52
3380 8428 6.170506 GGTCAGATGGTGTATTTGAACTGTA 58.829 40.000 0.00 0.00 35.34 2.74
3384 8432 5.957842 TTGGTCAGATGGTGTATTTGAAC 57.042 39.130 0.00 0.00 37.93 3.18
3446 8494 5.097529 GCACAGTACATCATCCACAAATTG 58.902 41.667 0.00 0.00 0.00 2.32
3448 8496 4.334552 TGCACAGTACATCATCCACAAAT 58.665 39.130 0.00 0.00 0.00 2.32
3462 8510 6.599356 TTAACTAGATTCCACTGCACAGTA 57.401 37.500 2.38 0.00 40.20 2.74
3483 8531 9.693739 TGGGATTAGTAAAGATTCAAGCAATTA 57.306 29.630 0.00 0.00 0.00 1.40
3484 8532 8.593945 TGGGATTAGTAAAGATTCAAGCAATT 57.406 30.769 0.00 0.00 0.00 2.32
3485 8533 7.836183 ACTGGGATTAGTAAAGATTCAAGCAAT 59.164 33.333 0.00 0.00 0.00 3.56
3486 8534 7.175104 ACTGGGATTAGTAAAGATTCAAGCAA 58.825 34.615 0.00 0.00 0.00 3.91
3487 8535 6.721318 ACTGGGATTAGTAAAGATTCAAGCA 58.279 36.000 0.00 0.00 0.00 3.91
3488 8536 7.631717 AACTGGGATTAGTAAAGATTCAAGC 57.368 36.000 0.00 0.00 0.00 4.01
3489 8537 9.231297 TCAAACTGGGATTAGTAAAGATTCAAG 57.769 33.333 0.00 0.00 0.00 3.02
3490 8538 9.753674 ATCAAACTGGGATTAGTAAAGATTCAA 57.246 29.630 0.00 0.00 0.00 2.69
3491 8539 9.177608 CATCAAACTGGGATTAGTAAAGATTCA 57.822 33.333 0.00 0.00 0.00 2.57
3492 8540 8.131731 GCATCAAACTGGGATTAGTAAAGATTC 58.868 37.037 0.00 0.00 0.00 2.52
3493 8541 7.836183 AGCATCAAACTGGGATTAGTAAAGATT 59.164 33.333 0.00 0.00 0.00 2.40
3494 8542 7.284034 CAGCATCAAACTGGGATTAGTAAAGAT 59.716 37.037 0.00 0.00 0.00 2.40
3495 8543 6.599244 CAGCATCAAACTGGGATTAGTAAAGA 59.401 38.462 0.00 0.00 0.00 2.52
3496 8544 6.375455 ACAGCATCAAACTGGGATTAGTAAAG 59.625 38.462 0.00 0.00 39.55 1.85
3497 8545 6.245408 ACAGCATCAAACTGGGATTAGTAAA 58.755 36.000 0.00 0.00 39.55 2.01
3528 8576 8.963130 CAAATAGTTAAAAGCATGTTTGTTCGA 58.037 29.630 0.00 0.00 0.00 3.71
3537 8585 7.037438 AGGATGCACAAATAGTTAAAAGCATG 58.963 34.615 0.00 0.00 41.07 4.06
3538 8586 7.174107 AGGATGCACAAATAGTTAAAAGCAT 57.826 32.000 0.00 0.00 43.38 3.79
3539 8587 6.588719 AGGATGCACAAATAGTTAAAAGCA 57.411 33.333 0.00 0.00 35.03 3.91
3540 8588 8.980143 TTTAGGATGCACAAATAGTTAAAAGC 57.020 30.769 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.