Multiple sequence alignment - TraesCS5D01G167700

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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 TraesCS5D01G167700 chr5D 100.000 6627 0 0 1 6627 261985773 261992399 0.000000e+00 12238.0
1 TraesCS5D01G167700 chr5D 90.000 180 12 5 6453 6627 195652959 195652781 1.860000e-55 228.0
2 TraesCS5D01G167700 chr5A 96.518 6003 114 34 667 6627 347452877 347458826 0.000000e+00 9840.0
3 TraesCS5D01G167700 chr5A 90.909 264 7 6 390 645 347452245 347452499 8.230000e-89 339.0
4 TraesCS5D01G167700 chr5A 87.097 217 15 8 1 210 347411734 347411944 4.000000e-57 233.0
5 TraesCS5D01G167700 chr5A 89.444 180 12 6 6453 6627 232836610 232836433 3.110000e-53 220.0
6 TraesCS5D01G167700 chr5A 89.714 175 15 3 6456 6627 608443149 608443323 3.110000e-53 220.0
7 TraesCS5D01G167700 chr5A 88.991 109 12 0 211 319 347451548 347451656 1.160000e-27 135.0
8 TraesCS5D01G167700 chr5A 97.561 41 1 0 6414 6454 456058414 456058374 3.320000e-08 71.3
9 TraesCS5D01G167700 chr5B 97.459 5668 113 14 360 6006 295106102 295111759 0.000000e+00 9640.0
10 TraesCS5D01G167700 chr5B 90.848 448 18 11 6012 6442 295111736 295112177 4.460000e-161 579.0
11 TraesCS5D01G167700 chr5B 89.049 347 31 6 1 342 295105652 295105996 2.210000e-114 424.0
12 TraesCS5D01G167700 chr5B 86.857 175 17 5 6458 6627 190122522 190122349 2.440000e-44 191.0
13 TraesCS5D01G167700 chr3A 83.824 408 41 10 1 384 431960898 431960492 1.360000e-96 364.0
14 TraesCS5D01G167700 chr3A 88.701 177 16 4 6455 6627 481877450 481877274 5.210000e-51 213.0
15 TraesCS5D01G167700 chr3D 88.439 173 15 4 6459 6626 595107613 595107785 3.130000e-48 204.0
16 TraesCS5D01G167700 chr3D 97.297 37 1 0 6418 6454 332628248 332628212 5.550000e-06 63.9
17 TraesCS5D01G167700 chr2A 88.000 175 16 4 6458 6627 775768545 775768371 1.130000e-47 202.0
18 TraesCS5D01G167700 chr7A 79.672 305 40 13 105 388 380284507 380284810 4.050000e-47 200.0
19 TraesCS5D01G167700 chr7A 97.297 37 0 1 6418 6454 734101366 734101401 2.000000e-05 62.1
20 TraesCS5D01G167700 chr2D 87.151 179 17 6 6454 6627 573914224 573914401 1.460000e-46 198.0
21 TraesCS5D01G167700 chr6A 82.379 227 26 6 105 318 307990361 307990586 1.130000e-42 185.0
22 TraesCS5D01G167700 chr7D 77.850 307 41 15 105 386 623701393 623701089 1.480000e-36 165.0
23 TraesCS5D01G167700 chr2B 95.000 40 2 0 6415 6454 58845164 58845125 5.550000e-06 63.9
24 TraesCS5D01G167700 chr3B 100.000 33 0 0 6422 6454 149467872 149467840 2.000000e-05 62.1
25 TraesCS5D01G167700 chr4A 94.872 39 1 1 6418 6456 666105437 666105400 7.180000e-05 60.2


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 TraesCS5D01G167700 chr5D 261985773 261992399 6626 False 12238.000000 12238 100.000000 1 6627 1 chr5D.!!$F1 6626
1 TraesCS5D01G167700 chr5A 347451548 347458826 7278 False 3438.000000 9840 92.139333 211 6627 3 chr5A.!!$F3 6416
2 TraesCS5D01G167700 chr5B 295105652 295112177 6525 False 3547.666667 9640 92.452000 1 6442 3 chr5B.!!$F1 6441

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
377 618 0.093535 CTGCAACACACGAGCGTATG 59.906 55.000 0.00 0.00 0.00 2.39 F
1038 2014 0.108138 GTACTGCTGTTCCGCCATCT 60.108 55.000 0.09 0.00 0.00 2.90 F
1161 2139 1.267806 CTTGCTGTACCTTGCCTTGTG 59.732 52.381 0.00 0.00 0.00 3.33 F
1848 2830 1.202394 CGGAGTCTCCTGAGAATGCAG 60.202 57.143 17.00 5.58 42.66 4.41 F
2726 3729 1.277557 AGTCATGGTTCTCTGACCTGC 59.722 52.381 0.00 0.00 42.18 4.85 F
3949 4960 0.538584 AGATGGACGAGAAGCATGCA 59.461 50.000 21.98 0.00 0.00 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1730 2712 0.107459 GAAAGCTCCTGAAGGCCGAT 60.107 55.000 0.00 0.0 34.44 4.18 R
1848 2830 0.396060 TCATTTTTGCCAGGGTTGCC 59.604 50.000 0.00 0.0 0.00 4.52 R
3136 4141 0.179073 ATCGGTGAAATGAGGGCTCG 60.179 55.000 0.00 0.0 0.00 5.03 R
3694 4705 6.489675 GTTGTGCACTGTGAATATAAGGATG 58.510 40.000 19.41 0.0 0.00 3.51 R
4453 5464 1.340248 CACAACTGTACTCCCGACTGT 59.660 52.381 0.00 0.0 0.00 3.55 R
5627 6650 2.615986 TCCAGGTACAAGCTACTCCA 57.384 50.000 0.00 0.0 0.00 3.86 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
101 102 5.864628 GTGAAACGCTCTCTATCCTTTTT 57.135 39.130 0.00 0.00 0.00 1.94
102 103 5.859557 GTGAAACGCTCTCTATCCTTTTTC 58.140 41.667 0.00 0.00 0.00 2.29
103 104 5.639931 GTGAAACGCTCTCTATCCTTTTTCT 59.360 40.000 0.00 0.00 0.00 2.52
104 105 6.812160 GTGAAACGCTCTCTATCCTTTTTCTA 59.188 38.462 0.00 0.00 0.00 2.10
105 106 7.492994 GTGAAACGCTCTCTATCCTTTTTCTAT 59.507 37.037 0.00 0.00 0.00 1.98
128 134 9.250624 CTATCTTTAGTGCTATTGGACTGTAAC 57.749 37.037 11.35 0.00 44.61 2.50
130 136 7.446769 TCTTTAGTGCTATTGGACTGTAACAA 58.553 34.615 11.35 0.71 44.61 2.83
139 145 7.254795 GCTATTGGACTGTAACAATGGACATAC 60.255 40.741 18.57 3.95 37.65 2.39
140 146 5.755409 TGGACTGTAACAATGGACATACT 57.245 39.130 0.00 0.00 0.00 2.12
143 149 7.497595 TGGACTGTAACAATGGACATACTATC 58.502 38.462 0.00 0.00 0.00 2.08
152 158 2.703536 TGGACATACTATCCACGCCAAT 59.296 45.455 0.00 0.00 41.47 3.16
194 200 3.123621 ACAAGACGCTAATGCTCTTTTCG 59.876 43.478 0.00 0.00 35.82 3.46
204 210 7.409697 GCTAATGCTCTTTTCGTGATTAATGA 58.590 34.615 0.00 0.00 36.03 2.57
208 214 6.554419 TGCTCTTTTCGTGATTAATGATTGG 58.446 36.000 0.00 0.00 0.00 3.16
273 279 0.242825 CTTGACGGGACAACTAGCGA 59.757 55.000 0.00 0.00 0.00 4.93
274 280 0.675083 TTGACGGGACAACTAGCGAA 59.325 50.000 0.00 0.00 0.00 4.70
280 286 3.194116 ACGGGACAACTAGCGAATTCTTA 59.806 43.478 3.52 0.00 0.00 2.10
373 614 3.568907 CTGCTGCAACACACGAGCG 62.569 63.158 3.02 0.00 33.97 5.03
377 618 0.093535 CTGCAACACACGAGCGTATG 59.906 55.000 0.00 0.00 0.00 2.39
378 619 0.598942 TGCAACACACGAGCGTATGT 60.599 50.000 0.53 0.53 37.35 2.29
413 1025 3.771577 AAAGTACTCAAGGGTCCACTG 57.228 47.619 0.00 0.00 0.00 3.66
528 1148 7.357777 CCGTAAACAAAAAGACGAAAAATAGCC 60.358 37.037 0.00 0.00 37.50 3.93
529 1149 7.377662 CGTAAACAAAAAGACGAAAAATAGCCT 59.622 33.333 0.00 0.00 37.50 4.58
997 1973 6.990341 TGGTACTGATGTTCAATTGATGAG 57.010 37.500 9.40 0.56 39.77 2.90
1038 2014 0.108138 GTACTGCTGTTCCGCCATCT 60.108 55.000 0.09 0.00 0.00 2.90
1084 2060 3.021451 AAGGTGAACTTCCCTTGCG 57.979 52.632 9.54 0.00 39.59 4.85
1123 2101 4.893424 TTTCACACTAGGTTGCTTGTTC 57.107 40.909 0.00 0.00 0.00 3.18
1161 2139 1.267806 CTTGCTGTACCTTGCCTTGTG 59.732 52.381 0.00 0.00 0.00 3.33
1188 2167 4.935352 TGGTGTATTTTCTTGCTTTGCT 57.065 36.364 0.00 0.00 0.00 3.91
1235 2214 8.447833 TGTGAATTGTTTATTATGTCCGAGTTC 58.552 33.333 0.00 0.00 0.00 3.01
1625 2607 5.449041 CGAGTATATTTTGTGGCAGTTGCAT 60.449 40.000 6.43 0.00 44.36 3.96
1671 2653 2.485426 CACCACATTAGTTCTGCAGGTG 59.515 50.000 15.13 11.64 37.02 4.00
1724 2706 4.130118 CCAACCCTGATCGAATTAAGAGG 58.870 47.826 0.00 0.00 0.00 3.69
1730 2712 7.802117 ACCCTGATCGAATTAAGAGGATTAAA 58.198 34.615 0.00 0.00 0.00 1.52
1848 2830 1.202394 CGGAGTCTCCTGAGAATGCAG 60.202 57.143 17.00 5.58 42.66 4.41
2337 3320 6.627395 TCTGTTTCCACATTATTTGTCGTT 57.373 33.333 0.00 0.00 36.00 3.85
2360 3343 7.321153 GTTCAGTGTAGAATCTGTTAGCCTTA 58.679 38.462 0.00 0.00 33.89 2.69
2529 3532 6.844097 TTTTTGTTGTGAGGGTTAACTTCT 57.156 33.333 5.42 3.74 0.00 2.85
2530 3533 6.844097 TTTTGTTGTGAGGGTTAACTTCTT 57.156 33.333 5.42 0.00 0.00 2.52
2531 3534 6.844097 TTTGTTGTGAGGGTTAACTTCTTT 57.156 33.333 5.42 0.00 0.00 2.52
2532 3535 6.844097 TTGTTGTGAGGGTTAACTTCTTTT 57.156 33.333 5.42 0.00 0.00 2.27
2533 3536 6.202516 TGTTGTGAGGGTTAACTTCTTTTG 57.797 37.500 5.42 0.00 0.00 2.44
2534 3537 5.946972 TGTTGTGAGGGTTAACTTCTTTTGA 59.053 36.000 5.42 0.00 0.00 2.69
2535 3538 6.605594 TGTTGTGAGGGTTAACTTCTTTTGAT 59.394 34.615 5.42 0.00 0.00 2.57
2536 3539 7.776030 TGTTGTGAGGGTTAACTTCTTTTGATA 59.224 33.333 5.42 0.00 0.00 2.15
2537 3540 7.739498 TGTGAGGGTTAACTTCTTTTGATAC 57.261 36.000 5.42 0.00 0.00 2.24
2538 3541 7.514721 TGTGAGGGTTAACTTCTTTTGATACT 58.485 34.615 5.42 0.00 0.00 2.12
2539 3542 8.653191 TGTGAGGGTTAACTTCTTTTGATACTA 58.347 33.333 5.42 0.00 0.00 1.82
2540 3543 9.152595 GTGAGGGTTAACTTCTTTTGATACTAG 57.847 37.037 5.42 0.00 0.00 2.57
2541 3544 7.822822 TGAGGGTTAACTTCTTTTGATACTAGC 59.177 37.037 5.42 0.00 0.00 3.42
2542 3545 7.919151 AGGGTTAACTTCTTTTGATACTAGCT 58.081 34.615 5.42 0.00 0.00 3.32
2543 3546 9.043548 AGGGTTAACTTCTTTTGATACTAGCTA 57.956 33.333 5.42 0.00 0.00 3.32
2544 3547 9.662947 GGGTTAACTTCTTTTGATACTAGCTAA 57.337 33.333 5.42 0.00 0.00 3.09
2595 3598 5.524971 ACCAATCATGTTAAGCCATCATG 57.475 39.130 0.00 0.00 39.87 3.07
2651 3654 2.105006 TGAGCTCATCCAAGTTCTGC 57.895 50.000 13.74 0.00 0.00 4.26
2726 3729 1.277557 AGTCATGGTTCTCTGACCTGC 59.722 52.381 0.00 0.00 42.18 4.85
2817 3821 8.780846 TTTCGCAATATTACTGGTCTTAAGAA 57.219 30.769 6.78 0.00 0.00 2.52
2818 3822 7.766219 TCGCAATATTACTGGTCTTAAGAAC 57.234 36.000 13.89 13.89 0.00 3.01
2907 3912 2.012673 GTGCTGCTATGTTCTCCCTTG 58.987 52.381 0.00 0.00 0.00 3.61
3045 4050 5.301045 GCTTTGTTTTGGGTTAGGTTCTAGT 59.699 40.000 0.00 0.00 0.00 2.57
3094 4099 1.714794 AGATTCAACAAGACGCTCGG 58.285 50.000 0.00 0.00 0.00 4.63
3136 4141 4.434713 AAATGCGTTACAATCTTGTCCC 57.565 40.909 0.00 0.00 42.35 4.46
3694 4705 4.483476 AGTTATTGTTCGACTTGTTGCC 57.517 40.909 0.00 0.00 0.00 4.52
3949 4960 0.538584 AGATGGACGAGAAGCATGCA 59.461 50.000 21.98 0.00 0.00 3.96
4453 5464 4.640201 GTGGCAACTAATCTTGGAGCAATA 59.360 41.667 0.00 0.00 37.61 1.90
4522 5533 2.614983 TGTTTTCAAACCTACAGCGTCC 59.385 45.455 0.00 0.00 38.11 4.79
4671 5682 6.012858 TCAGGTCCTGGAAACTGTAATGTTAT 60.013 38.462 19.11 0.00 32.92 1.89
4714 5725 1.047801 GTGGTTGGGCTTTCAATGGT 58.952 50.000 0.00 0.00 0.00 3.55
4953 5964 9.455847 CCTTGAACAAGAAAAACTCTTAATGAG 57.544 33.333 14.99 0.00 42.84 2.90
5060 6080 5.448225 CCACATGTATCTGTTGAATCTGTGC 60.448 44.000 0.00 0.00 32.26 4.57
5627 6650 2.236146 TCTGGCCGTTATCTTGTGTGAT 59.764 45.455 0.00 0.00 0.00 3.06
6004 7029 3.102204 CTCCCATTCCAGCATTTTTCCT 58.898 45.455 0.00 0.00 0.00 3.36
6005 7030 3.516700 CTCCCATTCCAGCATTTTTCCTT 59.483 43.478 0.00 0.00 0.00 3.36
6006 7031 3.261390 TCCCATTCCAGCATTTTTCCTTG 59.739 43.478 0.00 0.00 0.00 3.61
6007 7032 3.008266 CCCATTCCAGCATTTTTCCTTGT 59.992 43.478 0.00 0.00 0.00 3.16
6008 7033 4.505390 CCCATTCCAGCATTTTTCCTTGTT 60.505 41.667 0.00 0.00 0.00 2.83
6009 7034 5.279910 CCCATTCCAGCATTTTTCCTTGTTA 60.280 40.000 0.00 0.00 0.00 2.41
6010 7035 6.408869 CCATTCCAGCATTTTTCCTTGTTAT 58.591 36.000 0.00 0.00 0.00 1.89
6011 7036 7.364585 CCCATTCCAGCATTTTTCCTTGTTATA 60.365 37.037 0.00 0.00 0.00 0.98
6012 7037 7.492344 CCATTCCAGCATTTTTCCTTGTTATAC 59.508 37.037 0.00 0.00 0.00 1.47
6013 7038 7.775053 TTCCAGCATTTTTCCTTGTTATACT 57.225 32.000 0.00 0.00 0.00 2.12
6014 7039 7.391148 TCCAGCATTTTTCCTTGTTATACTC 57.609 36.000 0.00 0.00 0.00 2.59
6015 7040 6.377146 TCCAGCATTTTTCCTTGTTATACTCC 59.623 38.462 0.00 0.00 0.00 3.85
6016 7041 6.405842 CCAGCATTTTTCCTTGTTATACTCCC 60.406 42.308 0.00 0.00 0.00 4.30
6017 7042 6.152661 CAGCATTTTTCCTTGTTATACTCCCA 59.847 38.462 0.00 0.00 0.00 4.37
6018 7043 6.897413 AGCATTTTTCCTTGTTATACTCCCAT 59.103 34.615 0.00 0.00 0.00 4.00
6019 7044 7.400052 AGCATTTTTCCTTGTTATACTCCCATT 59.600 33.333 0.00 0.00 0.00 3.16
6020 7045 7.706607 GCATTTTTCCTTGTTATACTCCCATTC 59.293 37.037 0.00 0.00 0.00 2.67
6021 7046 7.712204 TTTTTCCTTGTTATACTCCCATTCC 57.288 36.000 0.00 0.00 0.00 3.01
6022 7047 6.395780 TTTCCTTGTTATACTCCCATTCCA 57.604 37.500 0.00 0.00 0.00 3.53
6023 7048 5.630415 TCCTTGTTATACTCCCATTCCAG 57.370 43.478 0.00 0.00 0.00 3.86
6024 7049 4.137543 CCTTGTTATACTCCCATTCCAGC 58.862 47.826 0.00 0.00 0.00 4.85
6025 7050 4.385199 CCTTGTTATACTCCCATTCCAGCA 60.385 45.833 0.00 0.00 0.00 4.41
6026 7051 5.380043 CTTGTTATACTCCCATTCCAGCAT 58.620 41.667 0.00 0.00 0.00 3.79
6027 7052 5.387113 TGTTATACTCCCATTCCAGCATT 57.613 39.130 0.00 0.00 0.00 3.56
6028 7053 5.765510 TGTTATACTCCCATTCCAGCATTT 58.234 37.500 0.00 0.00 0.00 2.32
6029 7054 6.194235 TGTTATACTCCCATTCCAGCATTTT 58.806 36.000 0.00 0.00 0.00 1.82
6030 7055 6.667414 TGTTATACTCCCATTCCAGCATTTTT 59.333 34.615 0.00 0.00 0.00 1.94
6031 7056 5.859205 ATACTCCCATTCCAGCATTTTTC 57.141 39.130 0.00 0.00 0.00 2.29
6032 7057 2.833943 ACTCCCATTCCAGCATTTTTCC 59.166 45.455 0.00 0.00 0.00 3.13
6033 7058 3.102204 CTCCCATTCCAGCATTTTTCCT 58.898 45.455 0.00 0.00 0.00 3.36
6034 7059 3.516700 CTCCCATTCCAGCATTTTTCCTT 59.483 43.478 0.00 0.00 0.00 3.36
6035 7060 3.261390 TCCCATTCCAGCATTTTTCCTTG 59.739 43.478 0.00 0.00 0.00 3.61
6345 7399 7.907214 ACTGTTTGGTGATCATTTCTACTAC 57.093 36.000 0.00 0.00 0.00 2.73
6503 7558 7.094420 CGGTGCACAAATCCCAATATGAATATA 60.094 37.037 20.43 0.00 0.00 0.86
6568 7624 1.182667 GTTATGAAACCTGGGTGCCC 58.817 55.000 0.00 0.00 0.00 5.36
6580 7636 2.600475 GGTGCCCGTTGTACACACG 61.600 63.158 17.90 17.90 36.00 4.49
6584 7640 1.430707 GCCCGTTGTACACACGTGTT 61.431 55.000 20.79 13.10 41.83 3.32
6585 7641 0.578211 CCCGTTGTACACACGTGTTC 59.422 55.000 20.79 12.93 41.83 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 7.354751 AGATAGAAAAAGGATAGAGAGCGTT 57.645 36.000 0.00 0.00 0.00 4.84
97 98 9.959721 AGTCCAATAGCACTAAAGATAGAAAAA 57.040 29.630 0.00 0.00 33.15 1.94
101 102 7.661536 ACAGTCCAATAGCACTAAAGATAGA 57.338 36.000 0.00 0.00 33.15 1.98
102 103 9.250624 GTTACAGTCCAATAGCACTAAAGATAG 57.749 37.037 0.00 0.00 35.14 2.08
103 104 8.755028 TGTTACAGTCCAATAGCACTAAAGATA 58.245 33.333 0.00 0.00 0.00 1.98
104 105 7.620880 TGTTACAGTCCAATAGCACTAAAGAT 58.379 34.615 0.00 0.00 0.00 2.40
105 106 6.999950 TGTTACAGTCCAATAGCACTAAAGA 58.000 36.000 0.00 0.00 0.00 2.52
128 134 3.067106 GGCGTGGATAGTATGTCCATTG 58.933 50.000 0.00 0.00 46.68 2.82
130 136 2.325484 TGGCGTGGATAGTATGTCCAT 58.675 47.619 0.00 0.00 46.68 3.41
180 186 9.941664 AATCATTAATCACGAAAAGAGCATTAG 57.058 29.630 0.00 0.00 0.00 1.73
194 200 6.704493 AGAAATGCATGCCAATCATTAATCAC 59.296 34.615 16.68 0.00 31.79 3.06
204 210 6.290294 AGTCTAAAAGAAATGCATGCCAAT 57.710 33.333 16.68 0.00 0.00 3.16
351 592 0.179086 TCGTGTGTTGCAGCAGAAGA 60.179 50.000 11.67 11.67 0.00 2.87
352 593 0.234106 CTCGTGTGTTGCAGCAGAAG 59.766 55.000 2.40 5.26 0.00 2.85
353 594 1.775039 GCTCGTGTGTTGCAGCAGAA 61.775 55.000 2.40 0.00 0.00 3.02
354 595 2.246739 GCTCGTGTGTTGCAGCAGA 61.247 57.895 2.40 0.00 0.00 4.26
356 597 2.962697 TACGCTCGTGTGTTGCAGCA 62.963 55.000 9.16 0.00 38.05 4.41
357 598 1.626654 ATACGCTCGTGTGTTGCAGC 61.627 55.000 9.16 0.00 38.05 5.25
358 599 0.093535 CATACGCTCGTGTGTTGCAG 59.906 55.000 9.16 0.00 38.05 4.41
364 605 1.191944 CTAGCACATACGCTCGTGTG 58.808 55.000 15.72 15.72 46.42 3.82
365 606 0.100682 CCTAGCACATACGCTCGTGT 59.899 55.000 5.05 0.00 42.62 4.49
401 1013 2.034687 CTGCCCAGTGGACCCTTG 59.965 66.667 11.95 0.00 0.00 3.61
528 1148 0.829990 GAGAGGAAGGAAGGGCAGAG 59.170 60.000 0.00 0.00 0.00 3.35
529 1149 0.415429 AGAGAGGAAGGAAGGGCAGA 59.585 55.000 0.00 0.00 0.00 4.26
997 1973 2.672961 TCCATCGGAACAGTCATCAC 57.327 50.000 0.00 0.00 0.00 3.06
1077 2053 1.819632 GATGCCAGGTACGCAAGGG 60.820 63.158 0.00 0.00 40.22 3.95
1084 2060 4.991687 GTGAAATAGCTAGATGCCAGGTAC 59.008 45.833 0.00 0.00 44.23 3.34
1161 2139 5.376854 AGCAAGAAAATACACCATCACAC 57.623 39.130 0.00 0.00 0.00 3.82
1229 2208 2.288030 ACGGTTAGTGGTTGAGAACTCG 60.288 50.000 0.00 0.00 0.00 4.18
1416 2398 6.710295 TCATCATTTATATCCAAAGGTCACGG 59.290 38.462 0.00 0.00 0.00 4.94
1625 2607 5.932303 CCTGAACTCCTCGATTCTTTTGTAA 59.068 40.000 0.00 0.00 0.00 2.41
1671 2653 0.455633 CCGTTTTGAGATGCAGCTGC 60.456 55.000 31.89 31.89 42.50 5.25
1685 2667 1.698506 TGGCATTGTTCTTCCCGTTT 58.301 45.000 0.00 0.00 0.00 3.60
1688 2670 0.243636 GGTTGGCATTGTTCTTCCCG 59.756 55.000 0.00 0.00 0.00 5.14
1724 2706 2.550180 GCTCCTGAAGGCCGATTTAATC 59.450 50.000 0.00 0.00 34.44 1.75
1730 2712 0.107459 GAAAGCTCCTGAAGGCCGAT 60.107 55.000 0.00 0.00 34.44 4.18
1848 2830 0.396060 TCATTTTTGCCAGGGTTGCC 59.604 50.000 0.00 0.00 0.00 4.52
2009 2991 3.272574 CAGATTGAAGCTGCCTCCTTA 57.727 47.619 0.00 0.00 0.00 2.69
2314 3297 6.261158 TGAACGACAAATAATGTGGAAACAGA 59.739 34.615 0.00 0.00 44.12 3.41
2337 3320 7.178628 ACTTAAGGCTAACAGATTCTACACTGA 59.821 37.037 7.53 0.00 37.54 3.41
2360 3343 8.192774 CCATGCAAAATTATACAGATGTGACTT 58.807 33.333 0.00 0.00 0.00 3.01
2528 3531 9.869844 GCACATGTATTTAGCTAGTATCAAAAG 57.130 33.333 0.00 0.00 0.00 2.27
2529 3532 9.613428 AGCACATGTATTTAGCTAGTATCAAAA 57.387 29.630 5.87 0.00 33.06 2.44
2530 3533 9.613428 AAGCACATGTATTTAGCTAGTATCAAA 57.387 29.630 7.93 0.00 34.66 2.69
2531 3534 9.613428 AAAGCACATGTATTTAGCTAGTATCAA 57.387 29.630 7.93 0.00 34.66 2.57
2532 3535 9.045223 CAAAGCACATGTATTTAGCTAGTATCA 57.955 33.333 7.93 0.00 34.66 2.15
2533 3536 8.012241 GCAAAGCACATGTATTTAGCTAGTATC 58.988 37.037 7.93 0.00 34.66 2.24
2534 3537 7.716998 AGCAAAGCACATGTATTTAGCTAGTAT 59.283 33.333 19.37 0.00 34.66 2.12
2535 3538 7.047891 AGCAAAGCACATGTATTTAGCTAGTA 58.952 34.615 19.37 0.00 34.66 1.82
2536 3539 5.882557 AGCAAAGCACATGTATTTAGCTAGT 59.117 36.000 19.37 7.58 34.66 2.57
2537 3540 6.369059 AGCAAAGCACATGTATTTAGCTAG 57.631 37.500 19.37 12.79 34.66 3.42
2538 3541 6.483307 CCTAGCAAAGCACATGTATTTAGCTA 59.517 38.462 21.72 21.72 34.66 3.32
2539 3542 5.297776 CCTAGCAAAGCACATGTATTTAGCT 59.702 40.000 21.77 21.77 37.08 3.32
2540 3543 5.506317 CCCTAGCAAAGCACATGTATTTAGC 60.506 44.000 0.00 9.34 0.00 3.09
2541 3544 5.009010 CCCCTAGCAAAGCACATGTATTTAG 59.991 44.000 0.00 0.00 0.00 1.85
2542 3545 4.887071 CCCCTAGCAAAGCACATGTATTTA 59.113 41.667 0.00 0.00 0.00 1.40
2543 3546 3.701040 CCCCTAGCAAAGCACATGTATTT 59.299 43.478 0.00 0.00 0.00 1.40
2544 3547 3.053693 TCCCCTAGCAAAGCACATGTATT 60.054 43.478 0.00 0.00 0.00 1.89
2545 3548 2.509548 TCCCCTAGCAAAGCACATGTAT 59.490 45.455 0.00 0.00 0.00 2.29
2546 3549 1.912731 TCCCCTAGCAAAGCACATGTA 59.087 47.619 0.00 0.00 0.00 2.29
2550 3553 1.960689 GTTTTCCCCTAGCAAAGCACA 59.039 47.619 0.00 0.00 0.00 4.57
2595 3598 6.578023 AGATGTAGATAAGGCTGAGTTGTTC 58.422 40.000 0.00 0.00 0.00 3.18
2651 3654 7.994425 AGACTGAGTATGATGTCTGTATAGG 57.006 40.000 0.00 0.00 38.22 2.57
2726 3729 8.572855 TGATCATCTGATATACTGAGGTACAG 57.427 38.462 0.00 0.00 42.45 2.74
2817 3821 2.537633 ATGGCTTGGGACATTCATGT 57.462 45.000 0.00 0.00 38.13 3.21
2818 3822 3.559069 ACTATGGCTTGGGACATTCATG 58.441 45.455 0.00 0.00 38.13 3.07
2907 3912 6.560251 CGAAACTGCAAACATAAAGAACTTGC 60.560 38.462 0.00 0.00 42.12 4.01
3045 4050 2.033141 GCTCAGGCTCCAGTTGCA 59.967 61.111 0.00 0.00 35.22 4.08
3094 4099 7.634522 CATTTAGCAAAACCAGTAGAGCTATC 58.365 38.462 0.00 0.00 34.89 2.08
3136 4141 0.179073 ATCGGTGAAATGAGGGCTCG 60.179 55.000 0.00 0.00 0.00 5.03
3598 4609 7.329499 CAGAAGAGAGGAGAATTTTCAGATCA 58.671 38.462 0.00 0.00 0.00 2.92
3694 4705 6.489675 GTTGTGCACTGTGAATATAAGGATG 58.510 40.000 19.41 0.00 0.00 3.51
3949 4960 4.836825 TCCAGAAGAAAGATCGAGCATTT 58.163 39.130 2.38 0.33 0.00 2.32
4453 5464 1.340248 CACAACTGTACTCCCGACTGT 59.660 52.381 0.00 0.00 0.00 3.55
4522 5533 3.320673 AGTACTTTTGGGAGCTTCTCG 57.679 47.619 0.00 0.00 0.00 4.04
4671 5682 3.648067 AGAAGACATGGGAAGTGACTCAA 59.352 43.478 0.00 0.00 0.00 3.02
4714 5725 3.967326 TGCTAGAAATAGCCTCTTGCCTA 59.033 43.478 4.90 0.00 42.17 3.93
4953 5964 7.442062 CAGCCAAATGAACATTATTTAATCCCC 59.558 37.037 0.37 0.00 0.00 4.81
5060 6080 4.551056 GCATCAAACTTGTATTGTTGCG 57.449 40.909 6.57 0.00 41.12 4.85
5497 6520 3.640967 CAGGGTCAAAAAGGTGGAAATCA 59.359 43.478 0.00 0.00 0.00 2.57
5627 6650 2.615986 TCCAGGTACAAGCTACTCCA 57.384 50.000 0.00 0.00 0.00 3.86
6004 7029 4.853468 TGCTGGAATGGGAGTATAACAA 57.147 40.909 0.00 0.00 0.00 2.83
6005 7030 5.387113 AATGCTGGAATGGGAGTATAACA 57.613 39.130 0.00 0.00 0.00 2.41
6006 7031 6.715347 AAAATGCTGGAATGGGAGTATAAC 57.285 37.500 0.00 0.00 0.00 1.89
6007 7032 6.323739 GGAAAAATGCTGGAATGGGAGTATAA 59.676 38.462 0.00 0.00 0.00 0.98
6008 7033 5.833131 GGAAAAATGCTGGAATGGGAGTATA 59.167 40.000 0.00 0.00 0.00 1.47
6009 7034 4.651045 GGAAAAATGCTGGAATGGGAGTAT 59.349 41.667 0.00 0.00 0.00 2.12
6010 7035 4.023291 GGAAAAATGCTGGAATGGGAGTA 58.977 43.478 0.00 0.00 0.00 2.59
6011 7036 2.833943 GGAAAAATGCTGGAATGGGAGT 59.166 45.455 0.00 0.00 0.00 3.85
6012 7037 3.102204 AGGAAAAATGCTGGAATGGGAG 58.898 45.455 0.00 0.00 0.00 4.30
6013 7038 3.188880 AGGAAAAATGCTGGAATGGGA 57.811 42.857 0.00 0.00 0.00 4.37
6014 7039 3.008266 ACAAGGAAAAATGCTGGAATGGG 59.992 43.478 0.00 0.00 0.00 4.00
6015 7040 4.276058 ACAAGGAAAAATGCTGGAATGG 57.724 40.909 0.00 0.00 0.00 3.16
6016 7041 7.820872 AGAATAACAAGGAAAAATGCTGGAATG 59.179 33.333 0.00 0.00 0.00 2.67
6017 7042 7.910584 AGAATAACAAGGAAAAATGCTGGAAT 58.089 30.769 0.00 0.00 0.00 3.01
6018 7043 7.301868 AGAATAACAAGGAAAAATGCTGGAA 57.698 32.000 0.00 0.00 0.00 3.53
6019 7044 6.916360 AGAATAACAAGGAAAAATGCTGGA 57.084 33.333 0.00 0.00 0.00 3.86
6020 7045 7.967890 AAAGAATAACAAGGAAAAATGCTGG 57.032 32.000 0.00 0.00 0.00 4.85
6294 7341 6.096141 TCAAACCAAATGAGAAACTGCACTAA 59.904 34.615 0.00 0.00 0.00 2.24
6359 7413 9.371136 CAACATAACATCTAGTACAGTCAACAT 57.629 33.333 0.00 0.00 0.00 2.71
6393 7447 4.437239 CAGCTCAGGATTGAAACTACGAT 58.563 43.478 0.00 0.00 31.69 3.73
6457 7511 0.915364 AGAGCCACAAATCCTCTCCC 59.085 55.000 0.00 0.00 30.46 4.30
6568 7624 1.921887 ACTGAACACGTGTGTACAACG 59.078 47.619 24.16 21.14 44.13 4.10
6580 7636 1.892209 ATCCCCACGAAACTGAACAC 58.108 50.000 0.00 0.00 0.00 3.32
6584 7640 0.037590 CCCAATCCCCACGAAACTGA 59.962 55.000 0.00 0.00 0.00 3.41
6585 7641 0.251165 ACCCAATCCCCACGAAACTG 60.251 55.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.