Multiple sequence alignment - TraesCS1D01G198600

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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 TraesCS1D01G198600 chr1D 100.000 4405 0 0 1 4405 280225255 280220851 0.000000e+00 8135
1 TraesCS1D01G198600 chr1A 93.698 1698 56 21 1011 2670 352140065 352138381 0.000000e+00 2495
2 TraesCS1D01G198600 chr1A 86.077 1652 128 49 2816 4405 352137902 352136291 0.000000e+00 1683
3 TraesCS1D01G198600 chr1A 92.880 618 24 6 334 941 352141065 352140458 0.000000e+00 880
4 TraesCS1D01G198600 chr1A 92.000 350 8 6 1 342 352173029 352172692 1.430000e-129 473
5 TraesCS1D01G198600 chr1A 90.909 154 9 3 2669 2819 352138145 352137994 7.470000e-48 202
6 TraesCS1D01G198600 chr1B 93.950 1653 50 23 1241 2852 380885900 380884257 0.000000e+00 2453
7 TraesCS1D01G198600 chr1B 93.360 1235 39 17 1 1215 380887109 380885898 0.000000e+00 1786
8 TraesCS1D01G198600 chr1B 96.176 863 27 5 2851 3712 380884176 380883319 0.000000e+00 1406
9 TraesCS1D01G198600 chr1B 78.715 498 53 31 3919 4404 380883236 380882780 2.590000e-72 283


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 TraesCS1D01G198600 chr1D 280220851 280225255 4404 True 8135 8135 100.00000 1 4405 1 chr1D.!!$R1 4404
1 TraesCS1D01G198600 chr1A 352136291 352141065 4774 True 1315 2495 90.89100 334 4405 4 chr1A.!!$R2 4071
2 TraesCS1D01G198600 chr1B 380882780 380887109 4329 True 1482 2453 90.55025 1 4404 4 chr1B.!!$R1 4403

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
424 438 0.893727 GTGACCTTTGCCCGTCCAAT 60.894 55.0 0.00 0.00 0.00 3.16 F
1112 1466 0.686224 CCAAGAAATGGCCCTGCAAA 59.314 50.0 0.00 0.00 43.80 3.68 F
1386 1754 0.242017 GCACTTTACTTGCCTGCAGG 59.758 55.0 29.34 29.34 33.58 4.85 F
2592 2986 1.148310 CGTTCAGCGTGGAATCTGTT 58.852 50.0 0.00 0.00 35.54 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1386 1754 0.669077 AGTCGATACCTGGCGTGATC 59.331 55.000 0.00 0.0 0.00 2.92 R
2932 3745 1.399440 GCATGTATGTGAGGTGCAGTG 59.601 52.381 0.00 0.0 35.93 3.66 R
3212 4025 0.035056 CGGACCCAGCTGATTTCCTT 60.035 55.000 17.39 0.0 0.00 3.36 R
3844 4701 0.950555 GTGCCAGTGATCAGCGTGAA 60.951 55.000 0.00 0.0 0.00 3.18 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
49 51 2.293677 ACGGCGACAGTAGGAAGATATG 59.706 50.000 16.62 0.00 0.00 1.78
56 58 6.071840 GCGACAGTAGGAAGATATGAATAGGT 60.072 42.308 0.00 0.00 0.00 3.08
62 64 7.789831 AGTAGGAAGATATGAATAGGTGTGGAA 59.210 37.037 0.00 0.00 0.00 3.53
70 72 9.566432 GATATGAATAGGTGTGGAAGAAAGATT 57.434 33.333 0.00 0.00 0.00 2.40
73 75 9.927081 ATGAATAGGTGTGGAAGAAAGATTATT 57.073 29.630 0.00 0.00 0.00 1.40
74 76 9.753674 TGAATAGGTGTGGAAGAAAGATTATTT 57.246 29.630 0.00 0.00 0.00 1.40
76 78 9.533831 AATAGGTGTGGAAGAAAGATTATTTGT 57.466 29.630 0.00 0.00 0.00 2.83
79 81 8.960591 AGGTGTGGAAGAAAGATTATTTGTATG 58.039 33.333 0.00 0.00 0.00 2.39
80 82 7.702348 GGTGTGGAAGAAAGATTATTTGTATGC 59.298 37.037 0.00 0.00 0.00 3.14
143 150 1.078567 CAGGCAGGGCTCTGAAGAC 60.079 63.158 20.53 3.65 43.49 3.01
147 154 3.764466 AGGGCTCTGAAGACGCGG 61.764 66.667 12.47 0.00 0.00 6.46
160 167 4.688419 CGCGGCAAGCCAACACAG 62.688 66.667 12.19 0.00 44.76 3.66
256 266 3.922171 AAGCTCGATTTCCTTCCTCAT 57.078 42.857 0.00 0.00 0.00 2.90
286 296 4.318332 TGGCTGATCTTACAGTTGAGTTG 58.682 43.478 0.00 0.00 39.73 3.16
292 306 6.166279 TGATCTTACAGTTGAGTTGGATCAC 58.834 40.000 0.00 0.00 35.48 3.06
306 320 2.101415 TGGATCACCTGATGACACGATC 59.899 50.000 0.00 0.00 41.24 3.69
317 331 3.520290 TGACACGATCACCAGGATTAC 57.480 47.619 0.00 0.00 36.00 1.89
367 381 6.260714 TGAAGGATAATCAAATGATGACCACG 59.739 38.462 0.00 0.00 41.93 4.94
424 438 0.893727 GTGACCTTTGCCCGTCCAAT 60.894 55.000 0.00 0.00 0.00 3.16
483 497 5.758784 CGAAAAGTAGAAGAGGGAAAACAGT 59.241 40.000 0.00 0.00 0.00 3.55
762 781 1.089481 CGCTTCGGGCTGCTGATTTA 61.089 55.000 0.00 0.00 39.13 1.40
894 925 6.463483 TCGTATGTATACTGCTCGTCTAAG 57.537 41.667 4.17 0.00 0.00 2.18
908 939 1.060698 GTCTAAGCGCGATCAAACCAC 59.939 52.381 12.10 0.00 0.00 4.16
980 1011 5.190132 TCCCTTCCCTTGTAAATCAATCGTA 59.810 40.000 0.00 0.00 35.35 3.43
981 1012 5.296035 CCCTTCCCTTGTAAATCAATCGTAC 59.704 44.000 0.00 0.00 35.35 3.67
982 1013 5.878116 CCTTCCCTTGTAAATCAATCGTACA 59.122 40.000 0.00 0.00 35.35 2.90
983 1014 6.542370 CCTTCCCTTGTAAATCAATCGTACAT 59.458 38.462 0.00 0.00 35.35 2.29
984 1015 7.713507 CCTTCCCTTGTAAATCAATCGTACATA 59.286 37.037 0.00 0.00 35.35 2.29
985 1016 8.428186 TTCCCTTGTAAATCAATCGTACATAC 57.572 34.615 0.00 0.00 35.35 2.39
1112 1466 0.686224 CCAAGAAATGGCCCTGCAAA 59.314 50.000 0.00 0.00 43.80 3.68
1182 1536 1.625315 AGCTGTAGCATCACAAGGACA 59.375 47.619 6.65 0.00 45.16 4.02
1215 1569 4.676546 TCTGTCAGATATGCTCAAGAACG 58.323 43.478 0.00 0.00 0.00 3.95
1334 1688 4.075963 AGTGAATTGCAATTTTGGTGCT 57.924 36.364 24.81 13.51 42.69 4.40
1346 1706 5.712152 ATTTTGGTGCTCGATTTCTTCTT 57.288 34.783 0.00 0.00 0.00 2.52
1349 1709 2.226437 TGGTGCTCGATTTCTTCTTTGC 59.774 45.455 0.00 0.00 0.00 3.68
1361 1721 6.808008 TTTCTTCTTTGCTATCTTGTCCTG 57.192 37.500 0.00 0.00 0.00 3.86
1362 1722 5.745312 TCTTCTTTGCTATCTTGTCCTGA 57.255 39.130 0.00 0.00 0.00 3.86
1386 1754 0.242017 GCACTTTACTTGCCTGCAGG 59.758 55.000 29.34 29.34 33.58 4.85
1551 1919 6.622462 GCATGAGTTTCAAGATGAAGGAGTTC 60.622 42.308 0.00 0.00 37.70 3.01
1842 2210 2.614057 GGTGAAGCTTATTGATGACCCG 59.386 50.000 0.00 0.00 0.00 5.28
1941 2309 3.071892 ACCTTCCCGTGTATGAAGAAACA 59.928 43.478 0.00 0.00 40.30 2.83
2003 2371 6.372937 GCTCTCTGGTTAAACTAGCTGATTTT 59.627 38.462 0.00 0.00 0.00 1.82
2204 2574 3.784338 ACAATGTTGTGCCTGAAACTTG 58.216 40.909 0.00 0.00 40.49 3.16
2212 2582 6.488344 TGTTGTGCCTGAAACTTGTATCATTA 59.512 34.615 0.00 0.00 0.00 1.90
2213 2583 6.741992 TGTGCCTGAAACTTGTATCATTAG 57.258 37.500 0.00 0.00 0.00 1.73
2214 2584 6.472016 TGTGCCTGAAACTTGTATCATTAGA 58.528 36.000 0.00 0.00 0.00 2.10
2215 2585 6.371548 TGTGCCTGAAACTTGTATCATTAGAC 59.628 38.462 0.00 0.00 0.00 2.59
2216 2586 6.595716 GTGCCTGAAACTTGTATCATTAGACT 59.404 38.462 0.00 0.00 0.00 3.24
2217 2587 6.595326 TGCCTGAAACTTGTATCATTAGACTG 59.405 38.462 0.00 0.00 0.00 3.51
2218 2588 6.457528 GCCTGAAACTTGTATCATTAGACTGC 60.458 42.308 0.00 0.00 0.00 4.40
2219 2589 6.037610 CCTGAAACTTGTATCATTAGACTGCC 59.962 42.308 0.00 0.00 0.00 4.85
2221 2591 6.595326 TGAAACTTGTATCATTAGACTGCCTG 59.405 38.462 0.00 0.00 0.00 4.85
2224 2594 6.711277 ACTTGTATCATTAGACTGCCTGAAA 58.289 36.000 0.00 0.00 0.00 2.69
2225 2595 6.595716 ACTTGTATCATTAGACTGCCTGAAAC 59.404 38.462 0.00 0.00 0.00 2.78
2226 2596 6.299805 TGTATCATTAGACTGCCTGAAACT 57.700 37.500 0.00 0.00 0.00 2.66
2227 2597 6.711277 TGTATCATTAGACTGCCTGAAACTT 58.289 36.000 0.00 0.00 0.00 2.66
2228 2598 7.847096 TGTATCATTAGACTGCCTGAAACTTA 58.153 34.615 0.00 0.00 0.00 2.24
2229 2599 8.486210 TGTATCATTAGACTGCCTGAAACTTAT 58.514 33.333 0.00 0.00 0.00 1.73
2230 2600 9.982651 GTATCATTAGACTGCCTGAAACTTATA 57.017 33.333 0.00 0.00 0.00 0.98
2367 2761 2.502142 ATTCTGATGCAGCACAGGAA 57.498 45.000 18.97 3.78 35.20 3.36
2406 2800 4.320788 CCAGATGAAAGTTTTGCTCCAGTC 60.321 45.833 0.00 0.00 0.00 3.51
2454 2848 2.563427 GCTTTTGAGGTGGCTCGC 59.437 61.111 0.00 0.00 0.00 5.03
2534 2928 5.445964 AGAGGTTAGTCTTTTCTTTTGCCA 58.554 37.500 0.00 0.00 0.00 4.92
2565 2959 4.838986 AGAAACTCCAGCTTAGGTGAGTAA 59.161 41.667 13.44 0.00 32.22 2.24
2592 2986 1.148310 CGTTCAGCGTGGAATCTGTT 58.852 50.000 0.00 0.00 35.54 3.16
2847 3575 7.865706 ACTGACAGTTTGTTAAGAACTTCAT 57.134 32.000 1.07 0.00 35.26 2.57
2929 3742 3.588842 TCATCAACTCCCTGTCCTGATTT 59.411 43.478 0.00 0.00 27.09 2.17
2932 3745 3.084786 CAACTCCCTGTCCTGATTTTCC 58.915 50.000 0.00 0.00 0.00 3.13
3212 4025 4.966787 GGCAAAGACACCCCCGCA 62.967 66.667 0.00 0.00 0.00 5.69
3245 4058 2.045131 GTCCGGTGGTCGCTCTAGT 61.045 63.158 0.00 0.00 37.59 2.57
3380 4193 5.488341 GGCTTGTGATCAACGGGTATATAT 58.512 41.667 0.00 0.00 0.00 0.86
3381 4194 5.351465 GGCTTGTGATCAACGGGTATATATG 59.649 44.000 0.00 0.00 0.00 1.78
3449 4262 5.973565 GTGCATTTCCAAACTATGATACAGC 59.026 40.000 0.00 0.00 0.00 4.40
3535 4348 2.221169 GTGGCAGTGAGTTTCATGTGA 58.779 47.619 0.00 0.00 0.00 3.58
3538 4351 2.816087 GGCAGTGAGTTTCATGTGACAT 59.184 45.455 0.00 0.00 0.00 3.06
3596 4409 2.044650 GAATGCTGGGGCTGCTCA 60.045 61.111 0.21 0.00 39.59 4.26
3635 4448 9.586435 GGGTAAGTATATAAGTTTGTACAACGT 57.414 33.333 8.07 5.01 0.00 3.99
3731 4575 2.430921 AGCGACGAACGAAGGCAG 60.431 61.111 0.00 0.00 45.77 4.85
3732 4576 2.430244 GCGACGAACGAAGGCAGA 60.430 61.111 0.00 0.00 45.77 4.26
3734 4578 1.773496 CGACGAACGAAGGCAGAAC 59.227 57.895 0.14 0.00 45.77 3.01
3735 4579 0.663568 CGACGAACGAAGGCAGAACT 60.664 55.000 0.14 0.00 45.77 3.01
3736 4580 1.400629 CGACGAACGAAGGCAGAACTA 60.401 52.381 0.14 0.00 45.77 2.24
3737 4581 2.731341 CGACGAACGAAGGCAGAACTAT 60.731 50.000 0.14 0.00 45.77 2.12
3739 4583 1.324736 CGAACGAAGGCAGAACTATGC 59.675 52.381 0.00 0.00 45.74 3.14
3740 4584 2.622436 GAACGAAGGCAGAACTATGCT 58.378 47.619 0.00 0.00 45.75 3.79
3751 4599 5.007528 GGCAGAACTATGCTTCTCTTCATTC 59.992 44.000 0.00 0.00 45.75 2.67
3759 4607 5.874895 TGCTTCTCTTCATTCATGTTCAG 57.125 39.130 0.00 0.00 0.00 3.02
3770 4618 2.621338 TCATGTTCAGAATCGACAGGC 58.379 47.619 0.00 0.00 0.00 4.85
3812 4660 1.871080 CTTACAGGCCAGGAATAGCG 58.129 55.000 5.01 0.00 0.00 4.26
3813 4661 0.179056 TTACAGGCCAGGAATAGCGC 60.179 55.000 5.01 0.00 0.00 5.92
3857 4714 2.109126 GGGCCTTCACGCTGATCAC 61.109 63.158 0.84 0.00 0.00 3.06
3862 4719 0.671472 CTTCACGCTGATCACTGGCA 60.671 55.000 6.28 0.00 0.00 4.92
3864 4721 2.046892 ACGCTGATCACTGGCACC 60.047 61.111 6.28 0.00 0.00 5.01
3883 4740 1.550976 CCGGCCCATAGAGATTAGGTC 59.449 57.143 0.00 0.00 0.00 3.85
3907 4764 0.108281 GGGAACGACTAACTGGAGGC 60.108 60.000 0.00 0.00 0.00 4.70
3913 4770 1.405821 CGACTAACTGGAGGCTACCTG 59.594 57.143 0.00 1.41 31.76 4.00
3916 4773 3.248888 ACTAACTGGAGGCTACCTGTTT 58.751 45.455 22.85 11.12 45.20 2.83
3917 4774 2.861147 AACTGGAGGCTACCTGTTTC 57.139 50.000 16.63 0.00 45.20 2.78
3918 4775 0.984995 ACTGGAGGCTACCTGTTTCC 59.015 55.000 0.00 0.00 38.60 3.13
3919 4776 0.253327 CTGGAGGCTACCTGTTTCCC 59.747 60.000 0.00 0.00 31.76 3.97
3920 4777 0.474854 TGGAGGCTACCTGTTTCCCA 60.475 55.000 0.00 0.00 31.76 4.37
3921 4778 0.035343 GGAGGCTACCTGTTTCCCAC 60.035 60.000 0.00 0.00 31.76 4.61
4117 4975 9.498307 TTTCACGTGTTTTAGAATTTCTTCTTC 57.502 29.630 16.51 0.00 41.91 2.87
4118 4976 8.203937 TCACGTGTTTTAGAATTTCTTCTTCA 57.796 30.769 16.51 0.00 41.91 3.02
4180 5056 1.882912 TTTCTCGCATGAAGCACACT 58.117 45.000 0.00 0.00 46.13 3.55
4181 5057 1.150827 TTCTCGCATGAAGCACACTG 58.849 50.000 0.00 0.00 46.13 3.66
4182 5058 1.134075 CTCGCATGAAGCACACTGC 59.866 57.895 0.00 0.00 46.13 4.40
4198 5074 3.059868 ACACTGCGTGAAAAACATAGACG 60.060 43.478 14.18 0.00 36.96 4.18
4206 5082 5.614668 CGTGAAAAACATAGACGTGCTTCAT 60.615 40.000 0.00 0.00 0.00 2.57
4223 5099 3.902261 TCATGATGAAGCACAACACAC 57.098 42.857 0.00 0.00 34.32 3.82
4248 5124 4.095782 TGTGTTCTACAGAAAAGCACAACC 59.904 41.667 9.99 0.00 36.37 3.77
4259 5135 4.707988 CACAACCGTGCTTTGGTG 57.292 55.556 0.00 0.00 40.35 4.17
4262 5138 0.678366 ACAACCGTGCTTTGGTGTGA 60.678 50.000 0.00 0.00 40.35 3.58
4263 5139 0.453793 CAACCGTGCTTTGGTGTGAA 59.546 50.000 0.00 0.00 40.35 3.18
4264 5140 0.738389 AACCGTGCTTTGGTGTGAAG 59.262 50.000 0.00 0.00 40.35 3.02
4317 5193 5.217978 TGGAAAGTGAAGTACGGTTGTAT 57.782 39.130 0.00 0.00 32.11 2.29
4332 5208 5.238650 ACGGTTGTATTTCTCAAAAGTGGAG 59.761 40.000 0.00 0.00 0.00 3.86
4344 5220 7.453393 TCTCAAAAGTGGAGAATACAGTTCAT 58.547 34.615 0.00 0.00 38.40 2.57
4345 5221 8.593679 TCTCAAAAGTGGAGAATACAGTTCATA 58.406 33.333 0.00 0.00 38.40 2.15
4368 5244 2.051345 GAACAACGGTGCTTGGCG 60.051 61.111 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 58 7.120579 ACGCATACAAATAATCTTTCTTCCACA 59.879 33.333 0.00 0.00 0.00 4.17
62 64 6.510157 CGCTCACGCATACAAATAATCTTTCT 60.510 38.462 0.00 0.00 35.30 2.52
80 82 2.220315 TAAAATTCAACGCGCTCACG 57.780 45.000 5.73 0.00 44.07 4.35
95 97 2.737359 CGCGTGCTCTGGACCTATAAAA 60.737 50.000 0.00 0.00 0.00 1.52
143 150 4.688419 CTGTGTTGGCTTGCCGCG 62.688 66.667 0.00 0.00 40.44 6.46
147 154 2.138656 CTCCAGCTGTGTTGGCTTGC 62.139 60.000 13.81 0.00 38.03 4.01
256 266 4.225942 ACTGTAAGATCAGCCAGAATTCCA 59.774 41.667 0.65 0.00 38.84 3.53
286 296 2.101415 TGATCGTGTCATCAGGTGATCC 59.899 50.000 0.00 0.00 39.48 3.36
306 320 5.515797 TGATAGTCTTCGTAATCCTGGTG 57.484 43.478 0.00 0.00 0.00 4.17
393 407 0.961019 AAGGTCACGTACGCTAACCA 59.039 50.000 26.41 1.72 32.25 3.67
424 438 1.691434 GAAGGAATGGTGCAAACCCAA 59.309 47.619 0.00 0.00 35.14 4.12
504 518 6.563163 TCTCCTTTTTCCCTCTTCTACTACT 58.437 40.000 0.00 0.00 0.00 2.57
687 706 1.632589 GGCTCACCTTGTTCCCAATT 58.367 50.000 0.00 0.00 0.00 2.32
717 736 4.778415 CGACGGCGGTGACAGAGG 62.778 72.222 13.24 0.00 0.00 3.69
762 781 1.919600 GCAGGCTGAGAAGGGTGGAT 61.920 60.000 20.86 0.00 0.00 3.41
894 925 2.175811 GTGGTGGTTTGATCGCGC 59.824 61.111 0.00 0.00 0.00 6.86
908 939 2.124860 GAAATCGGGGGACGGTGG 60.125 66.667 0.00 0.00 44.45 4.61
1009 1040 4.523173 TGACAGGACAGGTAGTACTCTTTG 59.477 45.833 0.00 0.00 40.32 2.77
1182 1536 6.382570 AGCATATCTGACAGAAACTAGAACCT 59.617 38.462 9.70 0.00 0.00 3.50
1215 1569 3.597255 GGAAGCTGAACAACCTACCTAC 58.403 50.000 0.00 0.00 0.00 3.18
1334 1688 6.313905 GGACAAGATAGCAAAGAAGAAATCGA 59.686 38.462 0.00 0.00 0.00 3.59
1346 1706 4.162131 TGCTACATCAGGACAAGATAGCAA 59.838 41.667 0.00 0.00 35.36 3.91
1361 1721 3.181506 GCAGGCAAGTAAAGTGCTACATC 60.182 47.826 0.00 0.00 41.88 3.06
1362 1722 2.749621 GCAGGCAAGTAAAGTGCTACAT 59.250 45.455 0.00 0.00 41.88 2.29
1386 1754 0.669077 AGTCGATACCTGGCGTGATC 59.331 55.000 0.00 0.00 0.00 2.92
1551 1919 1.180029 CCATGTTCTGGCCTTGGAAG 58.820 55.000 3.32 0.00 38.47 3.46
1842 2210 6.423905 TGTTTCTGTTGTTGACTATAGTCTGC 59.576 38.462 28.53 21.47 44.99 4.26
1893 2261 2.015081 CTCCTCTCCTGACTCCCCT 58.985 63.158 0.00 0.00 0.00 4.79
1896 2264 2.807247 GAGCTCCTCTCCTGACTCC 58.193 63.158 0.87 0.00 35.77 3.85
1965 2333 2.159043 CCAGAGAGCATTCCGTGTATGT 60.159 50.000 0.00 0.00 0.00 2.29
2003 2371 2.366266 AGTAAAGCACTGTGTTCCGGTA 59.634 45.455 9.86 0.00 35.62 4.02
2204 2574 8.894768 ATAAGTTTCAGGCAGTCTAATGATAC 57.105 34.615 0.00 0.00 0.00 2.24
2212 2582 7.284034 CCAAATGATATAAGTTTCAGGCAGTCT 59.716 37.037 0.00 0.00 0.00 3.24
2213 2583 7.067494 ACCAAATGATATAAGTTTCAGGCAGTC 59.933 37.037 0.00 0.00 0.00 3.51
2214 2584 6.891908 ACCAAATGATATAAGTTTCAGGCAGT 59.108 34.615 0.00 0.00 0.00 4.40
2215 2585 7.338800 ACCAAATGATATAAGTTTCAGGCAG 57.661 36.000 0.00 0.00 0.00 4.85
2216 2586 7.716799 AACCAAATGATATAAGTTTCAGGCA 57.283 32.000 0.00 0.00 0.00 4.75
2217 2587 9.087424 GAAAACCAAATGATATAAGTTTCAGGC 57.913 33.333 0.00 0.00 0.00 4.85
2218 2588 9.289303 CGAAAACCAAATGATATAAGTTTCAGG 57.711 33.333 0.00 0.00 0.00 3.86
2219 2589 9.840427 ACGAAAACCAAATGATATAAGTTTCAG 57.160 29.630 0.00 0.00 0.00 3.02
2224 2594 7.598278 TGCAACGAAAACCAAATGATATAAGT 58.402 30.769 0.00 0.00 0.00 2.24
2225 2595 7.967854 TCTGCAACGAAAACCAAATGATATAAG 59.032 33.333 0.00 0.00 0.00 1.73
2226 2596 7.821652 TCTGCAACGAAAACCAAATGATATAA 58.178 30.769 0.00 0.00 0.00 0.98
2227 2597 7.384439 TCTGCAACGAAAACCAAATGATATA 57.616 32.000 0.00 0.00 0.00 0.86
2228 2598 6.266168 TCTGCAACGAAAACCAAATGATAT 57.734 33.333 0.00 0.00 0.00 1.63
2229 2599 5.697473 TCTGCAACGAAAACCAAATGATA 57.303 34.783 0.00 0.00 0.00 2.15
2230 2600 4.549458 CTCTGCAACGAAAACCAAATGAT 58.451 39.130 0.00 0.00 0.00 2.45
2367 2761 6.581388 TCATCTGGAATTTCTTGATACCCT 57.419 37.500 0.00 0.00 0.00 4.34
2406 2800 2.954684 TACAGAAGGGGCAGCACGG 61.955 63.158 0.00 0.00 0.00 4.94
2454 2848 3.745975 TGGACAGAAGTTCAACGCTATTG 59.254 43.478 5.50 0.00 27.66 1.90
2472 2866 4.305769 GAGATGATGATAGCACTGTGGAC 58.694 47.826 10.21 0.00 0.00 4.02
2534 2928 6.013293 ACCTAAGCTGGAGTTTCTAATTGACT 60.013 38.462 0.00 0.00 0.00 3.41
2592 2986 5.070313 TCACAGACTGCACATTGCCTATATA 59.930 40.000 1.25 0.00 44.23 0.86
2719 3350 9.450807 GCCATTGTTGCTGTATTTACTATTAAG 57.549 33.333 0.00 0.00 0.00 1.85
2721 3352 7.013846 GGGCCATTGTTGCTGTATTTACTATTA 59.986 37.037 4.39 0.00 0.00 0.98
2722 3353 6.183360 GGGCCATTGTTGCTGTATTTACTATT 60.183 38.462 4.39 0.00 0.00 1.73
2723 3354 5.301805 GGGCCATTGTTGCTGTATTTACTAT 59.698 40.000 4.39 0.00 0.00 2.12
2725 3356 3.447229 GGGCCATTGTTGCTGTATTTACT 59.553 43.478 4.39 0.00 0.00 2.24
2726 3357 3.447229 AGGGCCATTGTTGCTGTATTTAC 59.553 43.478 6.18 0.00 0.00 2.01
2729 3360 1.826720 CAGGGCCATTGTTGCTGTATT 59.173 47.619 6.18 0.00 0.00 1.89
2734 3366 2.999063 GCCAGGGCCATTGTTGCT 60.999 61.111 6.18 0.00 34.56 3.91
2918 3731 2.227388 GTGCAGTGGAAAATCAGGACAG 59.773 50.000 0.00 0.00 0.00 3.51
2929 3742 1.696884 TGTATGTGAGGTGCAGTGGAA 59.303 47.619 0.00 0.00 0.00 3.53
2932 3745 1.399440 GCATGTATGTGAGGTGCAGTG 59.601 52.381 0.00 0.00 35.93 3.66
3212 4025 0.035056 CGGACCCAGCTGATTTCCTT 60.035 55.000 17.39 0.00 0.00 3.36
3245 4058 2.819984 GAAGCAAGTCATCCCCGCCA 62.820 60.000 0.00 0.00 0.00 5.69
3362 4175 8.467598 ACAGATACATATATACCCGTTGATCAC 58.532 37.037 0.00 0.00 0.00 3.06
3380 4193 1.899814 AGTTTCAGCCGGACAGATACA 59.100 47.619 5.05 0.00 0.00 2.29
3381 4194 2.673368 CAAGTTTCAGCCGGACAGATAC 59.327 50.000 5.05 4.65 0.00 2.24
3535 4348 7.352079 ACAATCACAGAAAGAAAAGGAATGT 57.648 32.000 0.00 0.00 0.00 2.71
3538 4351 7.867403 GCATAACAATCACAGAAAGAAAAGGAA 59.133 33.333 0.00 0.00 0.00 3.36
3632 4445 2.800629 CGTCTTTGTACCACTGGAACGT 60.801 50.000 0.71 0.00 0.00 3.99
3635 4448 1.071071 CCCGTCTTTGTACCACTGGAA 59.929 52.381 0.71 0.00 0.00 3.53
3731 4575 7.551035 ACATGAATGAAGAGAAGCATAGTTC 57.449 36.000 0.00 0.00 0.00 3.01
3732 4576 7.609146 TGAACATGAATGAAGAGAAGCATAGTT 59.391 33.333 0.00 0.00 0.00 2.24
3734 4578 7.494952 TCTGAACATGAATGAAGAGAAGCATAG 59.505 37.037 0.00 0.00 0.00 2.23
3735 4579 7.333323 TCTGAACATGAATGAAGAGAAGCATA 58.667 34.615 0.00 0.00 0.00 3.14
3736 4580 6.178324 TCTGAACATGAATGAAGAGAAGCAT 58.822 36.000 0.00 0.00 0.00 3.79
3737 4581 5.554070 TCTGAACATGAATGAAGAGAAGCA 58.446 37.500 0.00 0.00 0.00 3.91
3739 4583 7.277319 TCGATTCTGAACATGAATGAAGAGAAG 59.723 37.037 0.00 0.00 34.67 2.85
3740 4584 7.063898 GTCGATTCTGAACATGAATGAAGAGAA 59.936 37.037 0.00 2.11 34.67 2.87
3751 4599 2.625737 AGCCTGTCGATTCTGAACATG 58.374 47.619 0.00 0.00 0.00 3.21
3759 4607 4.383052 CGTCATGTTATAGCCTGTCGATTC 59.617 45.833 5.86 0.00 0.00 2.52
3770 4618 3.908978 CGAGCTACTGCGTCATGTTATAG 59.091 47.826 0.00 0.00 45.42 1.31
3787 4635 2.581354 CTGGCCTGTAAGCGAGCT 59.419 61.111 3.32 0.00 31.64 4.09
3813 4661 2.780094 TTGTTGTGCGTGCCAAGGG 61.780 57.895 0.00 0.00 0.00 3.95
3842 4699 1.364626 GCCAGTGATCAGCGTGAAGG 61.365 60.000 0.00 0.00 0.00 3.46
3844 4701 0.950555 GTGCCAGTGATCAGCGTGAA 60.951 55.000 0.00 0.00 0.00 3.18
3862 4719 1.132817 ACCTAATCTCTATGGGCCGGT 60.133 52.381 1.90 0.00 0.00 5.28
3864 4721 1.202582 CGACCTAATCTCTATGGGCCG 59.797 57.143 0.00 0.00 0.00 6.13
3883 4740 1.402456 CCAGTTAGTCGTTCCCTGACG 60.402 57.143 0.00 0.00 44.06 4.35
3907 4764 2.668144 TTTGGGTGGGAAACAGGTAG 57.332 50.000 0.00 0.00 0.00 3.18
4020 4877 1.300080 GCACCACCACATGTTGCAC 60.300 57.895 13.31 0.00 0.00 4.57
4024 4881 1.896660 GGACGCACCACCACATGTT 60.897 57.895 0.00 0.00 38.79 2.71
4046 4903 2.977456 GTGTGACACATGGCGGCA 60.977 61.111 16.34 16.34 34.08 5.69
4064 4921 1.557099 TCTCTATGGGTGCGTTCAGT 58.443 50.000 0.00 0.00 0.00 3.41
4094 4951 9.450807 AATGAAGAAGAAATTCTAAAACACGTG 57.549 29.630 15.48 15.48 0.00 4.49
4123 4981 4.749099 CCATGCAAAATCGAAAAACTCCAA 59.251 37.500 0.00 0.00 0.00 3.53
4125 4983 4.306600 ACCATGCAAAATCGAAAAACTCC 58.693 39.130 0.00 0.00 0.00 3.85
4167 5043 2.949106 ACGCAGTGTGCTTCATGC 59.051 55.556 2.91 0.00 42.51 4.06
4180 5056 2.349060 GCACGTCTATGTTTTTCACGCA 60.349 45.455 0.00 0.00 0.00 5.24
4181 5057 2.096417 AGCACGTCTATGTTTTTCACGC 60.096 45.455 0.00 0.00 0.00 5.34
4182 5058 3.788434 AGCACGTCTATGTTTTTCACG 57.212 42.857 0.00 0.00 0.00 4.35
4206 5082 3.016031 ACAAGTGTGTTGTGCTTCATCA 58.984 40.909 0.00 0.00 32.58 3.07
4223 5099 5.484173 TGTGCTTTTCTGTAGAACACAAG 57.516 39.130 11.71 6.98 36.37 3.16
4231 5107 3.253371 CACGGTTGTGCTTTTCTGTAG 57.747 47.619 0.00 0.00 39.67 2.74
4248 5124 4.614673 GCTTCACACCAAAGCACG 57.385 55.556 3.12 0.00 46.63 5.34
4290 5166 4.773013 ACCGTACTTCACTTTCCAAAAGA 58.227 39.130 6.44 0.00 0.00 2.52
4291 5167 5.163693 ACAACCGTACTTCACTTTCCAAAAG 60.164 40.000 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.