Multiple sequence alignment - TraesCS7A01G053400

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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 TraesCS7A01G053400 chr7A 100.000 5471 0 0 1 5471 25927098 25921628 0.000000e+00 10104.0
1 TraesCS7A01G053400 chr7A 75.830 542 72 26 71 578 25935499 25934983 2.570000e-53 220.0
2 TraesCS7A01G053400 chr7D 93.321 5285 255 39 4 5233 25041676 25036435 0.000000e+00 7714.0
3 TraesCS7A01G053400 chr7D 77.924 607 90 23 1 578 25048624 25048033 6.790000e-89 339.0
4 TraesCS7A01G053400 chr7D 90.688 247 21 1 5226 5470 25036262 25036016 1.470000e-85 327.0
5 TraesCS7A01G053400 chr4A 92.432 4070 272 18 828 4876 708566487 708570541 0.000000e+00 5777.0
6 TraesCS7A01G053400 chr4A 88.408 578 36 8 1 550 708563413 708563987 0.000000e+00 667.0
7 TraesCS7A01G053400 chr4A 87.992 483 48 7 4971 5443 708571345 708571827 3.700000e-156 562.0
8 TraesCS7A01G053400 chr4A 79.741 617 78 18 1 578 708556615 708557223 2.370000e-108 403.0
9 TraesCS7A01G053400 chr4A 90.272 257 15 3 547 793 708566226 708566482 1.470000e-85 327.0
10 TraesCS7A01G053400 chr1A 79.078 3427 633 62 1037 4425 5871451 5874831 0.000000e+00 2279.0
11 TraesCS7A01G053400 chr2D 73.958 384 88 11 2803 3180 12906167 12906544 1.590000e-30 145.0
12 TraesCS7A01G053400 chr2B 73.698 384 89 11 2803 3180 23651087 23651464 7.390000e-29 139.0
13 TraesCS7A01G053400 chr2A 70.425 683 170 28 2513 3179 764310586 764311252 4.480000e-21 113.0
14 TraesCS7A01G053400 chr5B 78.195 133 21 7 5065 5191 382358924 382359054 1.630000e-10 78.7
15 TraesCS7A01G053400 chr5D 84.127 63 9 1 5129 5191 329257469 329257530 5.920000e-05 60.2
16 TraesCS7A01G053400 chr5A 82.540 63 10 1 5129 5191 427372200 427372139 3.000000e-03 54.7


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 TraesCS7A01G053400 chr7A 25921628 25927098 5470 True 10104.00 10104 100.0000 1 5471 1 chr7A.!!$R1 5470
1 TraesCS7A01G053400 chr7A 25934983 25935499 516 True 220.00 220 75.8300 71 578 1 chr7A.!!$R2 507
2 TraesCS7A01G053400 chr7D 25036016 25041676 5660 True 4020.50 7714 92.0045 4 5470 2 chr7D.!!$R2 5466
3 TraesCS7A01G053400 chr7D 25048033 25048624 591 True 339.00 339 77.9240 1 578 1 chr7D.!!$R1 577
4 TraesCS7A01G053400 chr4A 708563413 708571827 8414 False 1833.25 5777 89.7760 1 5443 4 chr4A.!!$F2 5442
5 TraesCS7A01G053400 chr4A 708556615 708557223 608 False 403.00 403 79.7410 1 578 1 chr4A.!!$F1 577
6 TraesCS7A01G053400 chr1A 5871451 5874831 3380 False 2279.00 2279 79.0780 1037 4425 1 chr1A.!!$F1 3388

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
636 2949 0.240945 GTTCGTTGCCCCTTGATGTG 59.759 55.0 0.00 0.0 0.00 3.21 F
1991 4319 0.034198 TTTTCGGGCATCGTCTCACA 59.966 50.0 0.00 0.0 40.32 3.58 F
2928 5256 0.033228 TGGAGGCAAATTTGTTGCGG 59.967 50.0 19.03 0.0 45.78 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2063 4391 2.027192 GGAAGAGTGTAGCCAATGTCCA 60.027 50.0 0.0 0.0 0.0 4.02 R
3496 5824 2.474359 CACACTCAGCGAAGAAACTCTG 59.526 50.0 0.0 0.0 0.0 3.35 R
4667 7015 0.468226 AGGAGCGGTTGTGAGAACAA 59.532 50.0 0.0 0.0 0.0 2.83 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
59 60 0.525029 TTGACACGCAACGTACGTCA 60.525 50.000 23.05 10.52 42.96 4.35
105 107 3.148279 GCTGAGGTCGACGGGGAT 61.148 66.667 9.92 0.00 0.00 3.85
127 129 1.001487 CTGTTGCTCGAAAATGCCACA 60.001 47.619 2.10 2.10 34.45 4.17
146 148 0.823356 AAGCAAAGTCCACGCCATGT 60.823 50.000 0.00 0.00 0.00 3.21
277 297 4.930963 CATGTGTGCTACTTTTCCAAACA 58.069 39.130 0.00 0.00 31.83 2.83
280 300 6.067263 TGTGTGCTACTTTTCCAAACATAC 57.933 37.500 0.00 0.00 0.00 2.39
286 306 3.917300 ACTTTTCCAAACATACCCACCA 58.083 40.909 0.00 0.00 0.00 4.17
373 413 1.078001 CCGACTTACCCGGCCAAAT 60.078 57.895 2.24 0.00 40.54 2.32
380 425 3.445805 ACTTACCCGGCCAAATGTATTTG 59.554 43.478 2.24 9.76 45.04 2.32
431 496 7.913297 CGGTGAAAGATTACAAACTTCAGAAAA 59.087 33.333 0.00 0.00 0.00 2.29
470 535 5.127682 GCATTCATGGAGAGGTTAAACCAAT 59.872 40.000 0.00 0.00 41.95 3.16
480 545 2.038426 GGTTAAACCAATTGGGCTTGCT 59.962 45.455 27.89 3.12 42.05 3.91
620 2933 1.882623 CCTGCAAAGGTCCTCTTGTTC 59.117 52.381 12.51 2.30 35.55 3.18
636 2949 0.240945 GTTCGTTGCCCCTTGATGTG 59.759 55.000 0.00 0.00 0.00 3.21
928 3251 6.722328 TCTCACTCCTCTTCAGTACATCTAA 58.278 40.000 0.00 0.00 0.00 2.10
957 3280 6.296432 GGCATGGTCCCTCTATATATGAACAA 60.296 42.308 0.00 0.00 0.00 2.83
1132 3460 1.203112 TCAAGTCCCAGCTCTCTGACT 60.203 52.381 0.00 0.00 42.95 3.41
1576 3904 1.613437 CATCCAGGTTCGGTTTGCTTT 59.387 47.619 0.00 0.00 0.00 3.51
1588 3916 3.316868 CGGTTTGCTTTCCAACCTTTCTA 59.683 43.478 0.00 0.00 31.97 2.10
1648 3976 2.224769 CCAGAGTTTTTGGGGAGTAGCA 60.225 50.000 0.00 0.00 31.87 3.49
1665 3993 1.268352 AGCAGTTCTCTCACGTCAGTC 59.732 52.381 0.00 0.00 0.00 3.51
1792 4120 3.073946 CCCACCTTTCCTTCAAACCTCTA 59.926 47.826 0.00 0.00 0.00 2.43
1795 4123 5.316987 CACCTTTCCTTCAAACCTCTACAT 58.683 41.667 0.00 0.00 0.00 2.29
1947 4275 6.623767 GCTTAGGTAAGATTTCAGGTTTGCAG 60.624 42.308 0.71 0.00 35.33 4.41
1987 4315 2.159382 ACAATTTTTCGGGCATCGTCT 58.841 42.857 0.00 0.00 40.32 4.18
1991 4319 0.034198 TTTTCGGGCATCGTCTCACA 59.966 50.000 0.00 0.00 40.32 3.58
2063 4391 4.827284 CCAACTTGTTGGTAGAATTCCTGT 59.173 41.667 20.87 0.00 37.32 4.00
2230 4558 1.068055 CATTGGGACACTTGAGCAAGC 60.068 52.381 9.99 0.00 41.99 4.01
2250 4578 2.096013 GCTGAAAATTCTAGACGTGGGC 59.904 50.000 0.00 0.00 0.00 5.36
2278 4606 4.891756 ACATGCTTAAATCTGGAGATTGGG 59.108 41.667 2.62 0.00 43.41 4.12
2497 4825 5.324409 TGCAAATTAATTCACTCTCAGGGT 58.676 37.500 0.10 0.00 0.00 4.34
2571 4899 2.884639 CCACAACAAACTTTCCGGAGAT 59.115 45.455 3.34 0.00 0.00 2.75
2677 5005 7.315247 AGTTTGGAAGGTTGTAAAAATTTGC 57.685 32.000 0.00 0.00 0.00 3.68
2680 5008 4.813697 TGGAAGGTTGTAAAAATTTGCTGC 59.186 37.500 0.00 0.00 0.00 5.25
2700 5028 2.362077 GCTGCTGAACCTTTCTTCCAAA 59.638 45.455 0.00 0.00 0.00 3.28
2801 5129 3.021695 TCAGTGGGAACATACCTACTCG 58.978 50.000 0.00 0.00 46.17 4.18
2872 5200 6.359804 CAATTATCAGGTGAGATTCCTTCCA 58.640 40.000 0.00 0.00 32.37 3.53
2928 5256 0.033228 TGGAGGCAAATTTGTTGCGG 59.967 50.000 19.03 0.00 45.78 5.69
2974 5302 7.872138 TGGGACTTTAAGAGGAATCAATATGT 58.128 34.615 0.00 0.00 0.00 2.29
3041 5369 8.950007 TTTTTGGAGTCATTTACCTCCTTATT 57.050 30.769 7.18 0.00 36.95 1.40
3121 5449 2.653890 CCAATTCAAGTGCAGTGTTCG 58.346 47.619 0.00 0.00 0.00 3.95
3194 5522 0.036732 TGCACCACCTTAGCTTCCAG 59.963 55.000 0.00 0.00 0.00 3.86
3216 5544 2.498167 AGGAAGAACACTGCACATGTC 58.502 47.619 0.00 0.00 0.00 3.06
3226 5554 5.100259 ACACTGCACATGTCGTAACTATAC 58.900 41.667 0.00 0.00 0.00 1.47
3259 5587 8.395633 CACTTACTACTATTGTTGTAATTGCCC 58.604 37.037 12.73 0.00 41.12 5.36
3318 5646 1.142262 ACTAAAACTGAGGGGCACGTT 59.858 47.619 0.00 0.00 0.00 3.99
3400 5728 4.009675 TGGTTTCTGTGCATCCAGTATTC 58.990 43.478 4.42 0.00 34.02 1.75
3436 5764 4.331968 CTTTGGAGTGGTATACAAAGGCA 58.668 43.478 5.01 0.00 43.56 4.75
3496 5824 1.896220 TGACCAACTTGGAGCATCAC 58.104 50.000 15.14 0.00 40.96 3.06
3513 5841 3.018598 TCACAGAGTTTCTTCGCTGAG 57.981 47.619 0.00 0.00 38.32 3.35
3555 5883 2.093394 TCGCCACCGGAATTTGATTAGA 60.093 45.455 9.46 0.00 34.56 2.10
3651 5979 4.717279 TGGTAACCTAGAAAGTTGGCTT 57.283 40.909 0.00 0.00 36.30 4.35
3654 5982 5.999600 TGGTAACCTAGAAAGTTGGCTTTAC 59.000 40.000 0.00 0.00 44.25 2.01
3658 5986 4.010349 CCTAGAAAGTTGGCTTTACCCAG 58.990 47.826 0.00 0.00 44.25 4.45
3683 6011 5.260424 AGAAAACAAAGCCAACCCAAAAAT 58.740 33.333 0.00 0.00 0.00 1.82
3768 6096 4.736473 TCCATAATCGATGTAGTCCTCCA 58.264 43.478 0.00 0.00 33.19 3.86
3807 6135 1.981256 AACCACGCAATGTCCTTCTT 58.019 45.000 0.00 0.00 0.00 2.52
3879 6207 0.905357 ATGGAGACTCTTCAACGGGG 59.095 55.000 1.74 0.00 0.00 5.73
3940 6268 6.846988 TCAATTGGATATATTGCACCTGGTA 58.153 36.000 5.42 0.00 33.91 3.25
3961 6289 7.819644 TGGTAAGCACATGCATCATTTATATC 58.180 34.615 6.64 0.00 45.16 1.63
4009 6337 8.023128 ACATGCAAAGTTAGTGACATGTAAATC 58.977 33.333 0.00 0.00 39.61 2.17
4014 6342 9.764870 CAAAGTTAGTGACATGTAAATCATCTG 57.235 33.333 0.00 0.00 34.09 2.90
4030 6358 7.771927 AATCATCTGGAATGTTTATCATCCC 57.228 36.000 0.00 0.00 35.48 3.85
4031 6359 6.520021 TCATCTGGAATGTTTATCATCCCT 57.480 37.500 0.00 0.00 31.84 4.20
4094 6437 1.779700 TGCAGAATATGGCATGGGGTA 59.220 47.619 10.98 0.00 34.58 3.69
4119 6462 6.841229 ACAAGATCTCAACAGAGGGTGATATA 59.159 38.462 0.00 0.00 29.82 0.86
4216 6559 2.993937 ACCTTCACAACTTCGTGGAAA 58.006 42.857 0.00 0.00 37.50 3.13
4219 6562 3.127895 CCTTCACAACTTCGTGGAAACAA 59.872 43.478 0.00 0.00 46.06 2.83
4318 6661 3.451141 TGGCTGAAACAAAATGGTGTC 57.549 42.857 0.00 0.00 0.00 3.67
4362 6705 3.257127 GCCTAAAGTGCTCCGAGATATCT 59.743 47.826 4.47 4.47 0.00 1.98
4365 6708 0.965439 AGTGCTCCGAGATATCTGCC 59.035 55.000 10.74 2.12 0.00 4.85
4425 6768 9.968743 GAAATCATCAGCATCAAAGAAAATTTC 57.031 29.630 0.00 0.00 0.00 2.17
4427 6770 7.878477 TCATCAGCATCAAAGAAAATTTCAC 57.122 32.000 8.55 0.00 0.00 3.18
4429 6772 7.597369 TCATCAGCATCAAAGAAAATTTCACAG 59.403 33.333 8.55 0.00 0.00 3.66
4438 6781 4.952460 AGAAAATTTCACAGCATTGCAGT 58.048 34.783 11.91 6.09 0.00 4.40
4641 6986 8.046107 TGTGATTCAATAATAGTGTGACATGGA 58.954 33.333 0.00 0.00 0.00 3.41
4655 7000 7.231722 AGTGTGACATGGATCTACCTTATCTAC 59.768 40.741 0.00 0.00 39.86 2.59
4656 7001 6.493802 TGTGACATGGATCTACCTTATCTACC 59.506 42.308 0.00 0.00 39.86 3.18
4659 7004 6.787170 ACATGGATCTACCTTATCTACCGTA 58.213 40.000 0.00 0.00 39.86 4.02
4661 7007 8.554870 ACATGGATCTACCTTATCTACCGTATA 58.445 37.037 0.00 0.00 39.86 1.47
4682 7030 2.869897 TGTTTTTGTTCTCACAACCGC 58.130 42.857 0.00 0.00 42.87 5.68
4687 7035 0.468226 TGTTCTCACAACCGCTCCTT 59.532 50.000 0.00 0.00 0.00 3.36
4805 7161 3.237268 TCCAGGTAATGTTTGGCACTT 57.763 42.857 0.00 0.00 31.94 3.16
4806 7162 4.374689 TCCAGGTAATGTTTGGCACTTA 57.625 40.909 0.00 0.00 31.94 2.24
4808 7164 3.119495 CCAGGTAATGTTTGGCACTTAGC 60.119 47.826 0.00 0.00 44.65 3.09
4831 7196 2.540515 GCTAAATGCAGTAGCGACAGA 58.459 47.619 14.46 0.00 46.23 3.41
4869 7278 1.209019 CATGACTCTGTGGAGGGGAAG 59.791 57.143 0.00 0.00 43.46 3.46
4893 7302 0.530870 GTCCTGCTAGATCAACGCCC 60.531 60.000 0.00 0.00 0.00 6.13
4894 7303 0.975556 TCCTGCTAGATCAACGCCCA 60.976 55.000 0.00 0.00 0.00 5.36
4912 7321 4.095185 CGCCCATTTCGTTTGTCCTATTAA 59.905 41.667 0.00 0.00 0.00 1.40
4927 7336 4.282703 TCCTATTAACGGCCAATCTCTACC 59.717 45.833 2.24 0.00 0.00 3.18
4962 7389 3.418047 ACAAAGTTCCCTATTTCACCCG 58.582 45.455 0.00 0.00 0.00 5.28
4997 8078 5.249393 ACCCTCACACATACATTCTCTTCTT 59.751 40.000 0.00 0.00 0.00 2.52
5000 8082 6.534436 CCTCACACATACATTCTCTTCTTCTG 59.466 42.308 0.00 0.00 0.00 3.02
5063 8151 3.917329 TTTCGTTGAAAACCACACACA 57.083 38.095 0.00 0.00 46.28 3.72
5112 8200 6.599244 TCATGGCTTCTTTGGTAAGTCAATAG 59.401 38.462 0.00 0.00 41.53 1.73
5123 8212 7.016153 TGGTAAGTCAATAGGTGTTGATCTT 57.984 36.000 0.00 2.38 39.99 2.40
5127 8216 4.009675 GTCAATAGGTGTTGATCTTGGCA 58.990 43.478 0.00 0.00 39.99 4.92
5150 8239 2.874014 TCAATTGGCATCAAGTGTCCA 58.126 42.857 5.42 0.00 45.73 4.02
5184 8274 2.087501 ATCACGGTGATTGCGTACAA 57.912 45.000 17.62 0.00 40.87 2.41
5240 8510 9.626045 CCAATTAGCTTGTTTTACCTAAAGAAG 57.374 33.333 0.00 0.00 45.27 2.85
5258 8528 5.104259 AGAAGTCAATAGTGATTGGACCC 57.896 43.478 0.00 0.00 42.45 4.46
5269 8541 3.005791 GTGATTGGACCCTTTTTCCAGTG 59.994 47.826 0.00 0.00 44.13 3.66
5279 8551 7.396339 GGACCCTTTTTCCAGTGATTAAATACT 59.604 37.037 0.00 0.00 32.82 2.12
5280 8552 9.457436 GACCCTTTTTCCAGTGATTAAATACTA 57.543 33.333 0.00 0.00 0.00 1.82
5324 8596 7.164230 ACTCAAATGTTTTGAACACAAGGTA 57.836 32.000 4.43 0.00 45.50 3.08
5355 8627 2.799126 ATTCAACATTACAGGGCCGA 57.201 45.000 0.00 0.00 0.00 5.54
5357 8629 0.981183 TCAACATTACAGGGCCGAGT 59.019 50.000 9.56 9.56 0.00 4.18
5462 8734 0.806868 TAGTGCGACGACCCAACTAG 59.193 55.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.278170 CACTAACTTGGACTTTGATGGCAA 59.722 41.667 0.00 0.00 0.00 4.52
78 80 1.739562 GACCTCAGCCGCACAGAAG 60.740 63.158 0.00 0.00 0.00 2.85
105 107 2.225491 GTGGCATTTTCGAGCAACAGTA 59.775 45.455 0.00 0.00 34.79 2.74
127 129 0.823356 ACATGGCGTGGACTTTGCTT 60.823 50.000 12.05 0.00 0.00 3.91
146 148 3.058293 ACGATCGCTCTTTGAAAATTGCA 60.058 39.130 16.60 0.00 0.00 4.08
238 255 5.868801 CACACATGCCCAAGGTTTTATTTAG 59.131 40.000 0.00 0.00 0.00 1.85
240 257 4.640364 CACACATGCCCAAGGTTTTATTT 58.360 39.130 0.00 0.00 0.00 1.40
277 297 4.479158 ACACTGTTTCATTTGGTGGGTAT 58.521 39.130 0.00 0.00 32.88 2.73
280 300 3.118811 ACAACACTGTTTCATTTGGTGGG 60.119 43.478 0.00 0.00 30.50 4.61
286 306 4.082300 TCACTGCACAACACTGTTTCATTT 60.082 37.500 0.00 0.00 31.64 2.32
373 413 5.565509 TCCATTGTACTTGCTCCAAATACA 58.434 37.500 0.00 0.00 34.90 2.29
380 425 5.841957 ATCAATTCCATTGTACTTGCTCC 57.158 39.130 0.00 0.00 41.02 4.70
434 499 5.914033 CTCCATGAATGCATTTGGAGATTT 58.086 37.500 36.35 8.49 46.97 2.17
435 500 5.531122 CTCCATGAATGCATTTGGAGATT 57.469 39.130 36.35 9.18 46.97 2.40
470 535 4.081198 TCAAAAGAAAAAGAGCAAGCCCAA 60.081 37.500 0.00 0.00 0.00 4.12
480 545 7.186804 GTCGATTCTGTGTCAAAAGAAAAAGA 58.813 34.615 3.92 2.44 36.09 2.52
517 588 5.534207 TTGACAATCCAGAAGTTTGCAAT 57.466 34.783 0.00 0.00 0.00 3.56
620 2933 3.277133 CCACATCAAGGGGCAACG 58.723 61.111 0.00 0.00 30.89 4.10
636 2949 2.743928 CCGACACAGCTCTTGGCC 60.744 66.667 0.00 0.00 43.05 5.36
866 3189 2.092968 AGGACATGTGGTGCGTATGATT 60.093 45.455 1.15 0.00 43.57 2.57
928 3251 4.701333 ATATAGAGGGACCATGCCTAGT 57.299 45.455 0.00 0.00 38.79 2.57
957 3280 3.508845 AACACTTGGTTCATGGTAGCT 57.491 42.857 0.00 0.00 33.35 3.32
1364 3692 3.118592 GCTAAGGTTGAGGTATGTGAGCT 60.119 47.826 0.00 0.00 39.10 4.09
1576 3904 5.116084 AGCAATAGCATAGAAAGGTTGGA 57.884 39.130 0.00 0.00 45.49 3.53
1623 3951 5.572885 GCTACTCCCCAAAAACTCTGGAATA 60.573 44.000 0.00 0.00 35.85 1.75
1648 3976 3.823873 AGATTGACTGACGTGAGAGAACT 59.176 43.478 9.65 0.00 0.00 3.01
1665 3993 7.253422 CACCAAGGCTGTTATTTCTTAGATTG 58.747 38.462 0.00 0.00 0.00 2.67
1773 4101 5.073144 TGATGTAGAGGTTTGAAGGAAAGGT 59.927 40.000 0.00 0.00 0.00 3.50
1792 4120 3.517100 AGTGAGAGGTATTGCAGTGATGT 59.483 43.478 0.00 0.00 0.00 3.06
1795 4123 4.772624 AGTTAGTGAGAGGTATTGCAGTGA 59.227 41.667 0.00 0.00 0.00 3.41
1987 4315 3.794028 GTGTTTGCGTAAATTGCTTGTGA 59.206 39.130 0.99 0.00 0.00 3.58
1991 4319 4.048504 GGAAGTGTTTGCGTAAATTGCTT 58.951 39.130 0.99 7.08 0.00 3.91
2063 4391 2.027192 GGAAGAGTGTAGCCAATGTCCA 60.027 50.000 0.00 0.00 0.00 4.02
2230 4558 3.125316 GTGCCCACGTCTAGAATTTTCAG 59.875 47.826 0.00 0.00 0.00 3.02
2250 4578 6.258230 TCTCCAGATTTAAGCATGTTTGTG 57.742 37.500 4.89 0.00 0.00 3.33
2278 4606 8.131731 ACAATTTGTTAGAGAAGACAAGAAAGC 58.868 33.333 0.00 0.00 37.12 3.51
2350 4678 4.724399 TCACCAAAAGAAGTAGGCATTGA 58.276 39.130 0.00 0.00 0.00 2.57
2497 4825 2.204463 TCCAAGGGTATCAGGAATGCA 58.796 47.619 0.00 0.00 0.00 3.96
2677 5005 1.538950 GGAAGAAAGGTTCAGCAGCAG 59.461 52.381 0.00 0.00 0.00 4.24
2680 5008 4.654091 TTTTGGAAGAAAGGTTCAGCAG 57.346 40.909 0.00 0.00 0.00 4.24
2700 5028 5.774690 TGACAGGATGCTTCCAAATAACTTT 59.225 36.000 19.98 0.00 45.30 2.66
2718 5046 5.532406 TGAAATGGAAAAGAGTTCTGACAGG 59.468 40.000 1.81 0.00 0.00 4.00
2720 5048 6.376864 TGTTGAAATGGAAAAGAGTTCTGACA 59.623 34.615 0.00 0.00 0.00 3.58
2974 5302 7.939039 AGACAAGTTGTTTTGAGATAGATCCAA 59.061 33.333 10.45 0.00 0.00 3.53
3194 5522 2.880890 ACATGTGCAGTGTTCTTCCTTC 59.119 45.455 0.00 0.00 0.00 3.46
3216 5544 7.093322 AGTAAGTGGAACCAGTATAGTTACG 57.907 40.000 1.37 0.00 37.80 3.18
3226 5554 7.159372 ACAACAATAGTAGTAAGTGGAACCAG 58.841 38.462 0.00 0.00 37.80 4.00
3259 5587 3.635373 AGAATGAATACAAGGCATGCCAG 59.365 43.478 37.18 29.52 38.92 4.85
3326 5654 8.262601 TGAGTATCTATTATGCTCCCTGAAAA 57.737 34.615 0.00 0.00 34.92 2.29
3327 5655 7.855784 TGAGTATCTATTATGCTCCCTGAAA 57.144 36.000 0.00 0.00 34.92 2.69
3388 5716 3.629398 CCTGAACCAAGAATACTGGATGC 59.371 47.826 0.00 0.00 0.00 3.91
3400 5728 2.555757 CTCCAAAGCTTCCTGAACCAAG 59.444 50.000 0.00 0.00 0.00 3.61
3436 5764 6.713276 TGGCAATGGATTGAAATTCTGAATT 58.287 32.000 9.76 9.76 40.14 2.17
3496 5824 2.474359 CACACTCAGCGAAGAAACTCTG 59.526 50.000 0.00 0.00 0.00 3.35
3555 5883 5.423610 AGTGGTTGAGCATAGACTAATCACT 59.576 40.000 0.00 0.00 0.00 3.41
3597 5925 7.861630 TGTACTCAAGAATAAGTGCTTTGAAC 58.138 34.615 0.00 0.00 0.00 3.18
3651 5979 4.282496 TGGCTTTGTTTTCTTCTGGGTAA 58.718 39.130 0.00 0.00 0.00 2.85
3654 5982 3.457234 GTTGGCTTTGTTTTCTTCTGGG 58.543 45.455 0.00 0.00 0.00 4.45
3658 5986 3.535280 TGGGTTGGCTTTGTTTTCTTC 57.465 42.857 0.00 0.00 0.00 2.87
3759 6087 4.288366 TCACAATGAACCAATGGAGGACTA 59.712 41.667 6.16 0.00 0.00 2.59
3768 6096 6.482973 GTGGTTTCAAATCACAATGAACCAAT 59.517 34.615 8.76 0.00 37.89 3.16
3807 6135 2.964464 ACATGCAACCATTTCTTCACCA 59.036 40.909 0.00 0.00 0.00 4.17
3940 6268 8.581578 TCAATGATATAAATGATGCATGTGCTT 58.418 29.630 2.46 0.00 42.66 3.91
3987 6315 8.454106 AGATGATTTACATGTCACTAACTTTGC 58.546 33.333 0.00 0.00 39.56 3.68
4065 6408 7.309928 CCCATGCCATATTCTGCAATATTACAA 60.310 37.037 0.00 0.00 41.50 2.41
4094 6437 3.242867 TCACCCTCTGTTGAGATCTTGT 58.757 45.455 0.00 0.00 42.73 3.16
4216 6559 4.040445 CAATTTCCCGTGAAAGTGTTGT 57.960 40.909 11.82 0.00 46.27 3.32
4318 6661 3.430218 CCAAGTTTTGCTAGTCGAGTGAG 59.570 47.826 2.10 0.00 0.00 3.51
4365 6708 1.284982 CTGTTGTCGGCCGACTCTTG 61.285 60.000 46.72 32.78 44.80 3.02
4386 6729 5.278169 GCTGATGATTTCCGCATAAACATCT 60.278 40.000 0.00 0.00 34.92 2.90
4398 6741 8.488651 AATTTTCTTTGATGCTGATGATTTCC 57.511 30.769 0.00 0.00 0.00 3.13
4425 6768 5.550232 TTTGTCTATACTGCAATGCTGTG 57.450 39.130 24.65 10.65 40.67 3.66
4427 6770 9.740239 ATTTATTTTGTCTATACTGCAATGCTG 57.260 29.630 10.59 10.59 0.00 4.41
4429 6772 9.734620 TGATTTATTTTGTCTATACTGCAATGC 57.265 29.630 0.00 0.00 0.00 3.56
4463 6806 7.396339 TGAAATAGCTAGAGGTGAGTTACAAGA 59.604 37.037 0.00 0.00 0.00 3.02
4464 6807 7.548097 TGAAATAGCTAGAGGTGAGTTACAAG 58.452 38.462 0.00 0.00 0.00 3.16
4552 6897 9.990360 TTTGTAATTCCTTATGCTCATCGTATA 57.010 29.630 0.00 0.00 0.00 1.47
4553 6898 8.902540 TTTGTAATTCCTTATGCTCATCGTAT 57.097 30.769 0.00 0.00 0.00 3.06
4554 6899 8.201464 TCTTTGTAATTCCTTATGCTCATCGTA 58.799 33.333 0.00 0.00 0.00 3.43
4555 6900 7.047891 TCTTTGTAATTCCTTATGCTCATCGT 58.952 34.615 0.00 0.00 0.00 3.73
4556 6901 7.439356 TCTCTTTGTAATTCCTTATGCTCATCG 59.561 37.037 0.00 0.00 0.00 3.84
4621 6966 8.367911 GGTAGATCCATGTCACACTATTATTGA 58.632 37.037 0.00 0.00 35.97 2.57
4625 6970 7.914427 AAGGTAGATCCATGTCACACTATTA 57.086 36.000 0.00 0.00 39.02 0.98
4628 6973 7.298374 AGATAAGGTAGATCCATGTCACACTA 58.702 38.462 0.00 0.00 39.02 2.74
4655 7000 6.799925 GGTTGTGAGAACAAAAACATATACGG 59.200 38.462 0.00 0.00 31.72 4.02
4656 7001 6.518395 CGGTTGTGAGAACAAAAACATATACG 59.482 38.462 0.00 0.00 30.88 3.06
4659 7004 5.009610 AGCGGTTGTGAGAACAAAAACATAT 59.990 36.000 0.00 0.00 30.88 1.78
4661 7007 3.130340 AGCGGTTGTGAGAACAAAAACAT 59.870 39.130 0.00 0.00 30.88 2.71
4667 7015 0.468226 AGGAGCGGTTGTGAGAACAA 59.532 50.000 0.00 0.00 0.00 2.83
4687 7035 5.882557 GGCATCTTAGTTCTCTTTGATCCAA 59.117 40.000 0.00 0.00 0.00 3.53
4697 7045 4.965200 ATAGGGTGGCATCTTAGTTCTC 57.035 45.455 0.00 0.00 0.00 2.87
4699 7047 4.816925 GTGAATAGGGTGGCATCTTAGTTC 59.183 45.833 0.00 2.02 0.00 3.01
4700 7048 4.385310 GGTGAATAGGGTGGCATCTTAGTT 60.385 45.833 0.00 0.00 0.00 2.24
4702 7050 3.136443 TGGTGAATAGGGTGGCATCTTAG 59.864 47.826 0.00 0.00 0.00 2.18
4703 7051 3.119319 TGGTGAATAGGGTGGCATCTTA 58.881 45.455 0.00 0.00 0.00 2.10
4704 7052 1.922447 TGGTGAATAGGGTGGCATCTT 59.078 47.619 0.00 0.00 0.00 2.40
4765 7121 9.566432 ACCTGGAATAGCTATTAAGAAATGAAG 57.434 33.333 18.87 7.74 0.00 3.02
4780 7136 3.699038 TGCCAAACATTACCTGGAATAGC 59.301 43.478 0.00 0.00 31.38 2.97
4781 7137 4.949856 AGTGCCAAACATTACCTGGAATAG 59.050 41.667 0.00 0.00 31.38 1.73
4786 7142 3.119495 GCTAAGTGCCAAACATTACCTGG 60.119 47.826 0.00 0.00 35.15 4.45
4826 7191 3.679389 ACAAATGTGTGATCCCTCTGTC 58.321 45.455 0.00 0.00 36.31 3.51
4850 7215 1.079490 TCTTCCCCTCCACAGAGTCAT 59.921 52.381 0.00 0.00 38.58 3.06
4869 7278 0.747255 TTGATCTAGCAGGACCGCTC 59.253 55.000 13.05 2.31 42.62 5.03
4893 7302 5.025826 GCCGTTAATAGGACAAACGAAATG 58.974 41.667 8.27 0.00 46.66 2.32
4894 7303 4.095334 GGCCGTTAATAGGACAAACGAAAT 59.905 41.667 8.27 0.00 46.66 2.17
4912 7321 1.794714 AGATGGTAGAGATTGGCCGT 58.205 50.000 0.00 0.00 0.00 5.68
4957 7366 2.359975 GTTGGAAGGAGGCGGGTG 60.360 66.667 0.00 0.00 0.00 4.61
4962 7389 1.002011 GTGAGGGTTGGAAGGAGGC 60.002 63.158 0.00 0.00 0.00 4.70
4997 8078 7.093552 TGTGGAAGGAAAAAGAAATCAAACAGA 60.094 33.333 0.00 0.00 0.00 3.41
5000 8082 7.495606 ACATGTGGAAGGAAAAAGAAATCAAAC 59.504 33.333 0.00 0.00 0.00 2.93
5092 8180 5.705905 ACACCTATTGACTTACCAAAGAAGC 59.294 40.000 0.00 0.00 36.50 3.86
5112 8200 3.940209 TGAATTGCCAAGATCAACACC 57.060 42.857 0.00 0.00 0.00 4.16
5123 8212 3.008157 ACTTGATGCCAATTGAATTGCCA 59.992 39.130 12.26 8.21 38.92 4.92
5127 8216 4.283978 TGGACACTTGATGCCAATTGAATT 59.716 37.500 7.12 0.00 36.70 2.17
5162 8252 3.183754 TGTACGCAATCACCGTGATTAG 58.816 45.455 23.24 21.00 44.60 1.73
5184 8274 9.474920 CACGTTGCAATGGGAATATAAATATTT 57.525 29.630 22.20 5.89 33.37 1.40
5196 8286 2.593148 ACGCACGTTGCAATGGGA 60.593 55.556 25.09 0.00 45.36 4.37
5200 8290 0.313672 AATTGGACGCACGTTGCAAT 59.686 45.000 0.59 5.41 45.36 3.56
5208 8298 2.989422 AACAAGCTAATTGGACGCAC 57.011 45.000 0.00 0.00 43.68 5.34
5240 8510 6.350194 GGAAAAAGGGTCCAATCACTATTGAC 60.350 42.308 0.00 0.00 44.50 3.18
5252 8522 3.611025 AATCACTGGAAAAAGGGTCCA 57.389 42.857 0.00 0.00 43.03 4.02
5269 8541 9.209175 CACCAGAGCCTATGTTAGTATTTAATC 57.791 37.037 0.00 0.00 0.00 1.75
5279 8551 4.716784 AGTTCATCACCAGAGCCTATGTTA 59.283 41.667 0.00 0.00 0.00 2.41
5280 8552 3.521126 AGTTCATCACCAGAGCCTATGTT 59.479 43.478 0.00 0.00 0.00 2.71
5324 8596 7.148018 CCTGTAATGTTGAATTTCAGCCTATGT 60.148 37.037 10.28 0.00 0.00 2.29
5393 8665 2.875933 CAACACCTTACACACGGAACAT 59.124 45.455 0.00 0.00 0.00 2.71
5400 8672 2.286772 CGCTTTCCAACACCTTACACAC 60.287 50.000 0.00 0.00 0.00 3.82
5450 8722 1.764134 TGAAACCACTAGTTGGGTCGT 59.236 47.619 5.41 0.00 45.22 4.34


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

AutoCloner maintained by Alex Coulton.