Multiple sequence alignment - TraesCS2D01G193100
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 | TraesCS2D01G193100 | chr2D | 100.000 | 4382 | 0 | 0 | 1 | 4382 | 137593688 | 137589307 | 0.000000e+00 | 8093.0 |
| 1 | TraesCS2D01G193100 | chr2A | 96.762 | 3150 | 80 | 10 | 1233 | 4382 | 164266604 | 164269731 | 0.000000e+00 | 5232.0 |
| 2 | TraesCS2D01G193100 | chr2A | 90.176 | 682 | 39 | 13 | 3 | 671 | 164264473 | 164265139 | 0.000000e+00 | 863.0 |
| 3 | TraesCS2D01G193100 | chr2A | 88.110 | 471 | 33 | 11 | 694 | 1143 | 164265865 | 164266333 | 4.990000e-149 | 538.0 |
| 4 | TraesCS2D01G193100 | chr2B | 97.854 | 2377 | 51 | 0 | 1104 | 3480 | 195693598 | 195691222 | 0.000000e+00 | 4108.0 |
| 5 | TraesCS2D01G193100 | chr2B | 95.217 | 920 | 26 | 4 | 3479 | 4382 | 195691098 | 195690181 | 0.000000e+00 | 1439.0 |
| 6 | TraesCS2D01G193100 | chr2B | 93.789 | 322 | 12 | 3 | 801 | 1115 | 195694121 | 195693801 | 1.100000e-130 | 477.0 |
| 7 | TraesCS2D01G193100 | chrUn | 99.007 | 403 | 4 | 0 | 3006 | 3408 | 478410716 | 478410314 | 0.000000e+00 | 723.0 |
| 8 | TraesCS2D01G193100 | chr3D | 86.957 | 69 | 9 | 0 | 316 | 384 | 182659048 | 182659116 | 1.310000e-10 | 78.7 |
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 | TraesCS2D01G193100 | chr2D | 137589307 | 137593688 | 4381 | True | 8093 | 8093 | 100.000000 | 1 | 4382 | 1 | chr2D.!!$R1 | 4381 |
| 1 | TraesCS2D01G193100 | chr2A | 164264473 | 164269731 | 5258 | False | 2211 | 5232 | 91.682667 | 3 | 4382 | 3 | chr2A.!!$F1 | 4379 |
| 2 | TraesCS2D01G193100 | chr2B | 195690181 | 195694121 | 3940 | True | 2008 | 4108 | 95.620000 | 801 | 4382 | 3 | chr2B.!!$R1 | 3581 |
AutoCloner calculated primer pairsThese primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible. |
|---|
| Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
|---|---|---|---|---|---|---|---|---|---|---|
| 279 | 281 | 0.539051 | CGGTGAGAGCCAAAGAGGAT | 59.461 | 55.0 | 0.0 | 0.0 | 41.22 | 3.24 | F |
| 682 | 694 | 0.763035 | ACAAAACCTACCAGCGACCT | 59.237 | 50.0 | 0.0 | 0.0 | 0.00 | 3.85 | F |
| 1805 | 2951 | 0.107945 | GCACTCTACAAGGAGGCAGG | 60.108 | 60.0 | 0.0 | 0.0 | 37.63 | 4.85 | F |
| Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
|---|---|---|---|---|---|---|---|---|---|---|
| 1794 | 2940 | 1.001641 | CACCTTCCCTGCCTCCTTG | 60.002 | 63.158 | 0.00 | 0.0 | 0.00 | 3.61 | R |
| 1947 | 3093 | 2.369532 | GTTGTAGGTTACCACACTGGGA | 59.630 | 50.000 | 3.51 | 0.0 | 43.37 | 4.37 | R |
| 3765 | 5036 | 6.496743 | TCAAGGGAGCTTAGTAACTTAGGTA | 58.503 | 40.000 | 0.00 | 0.0 | 0.00 | 3.08 | R |
All possible primersListed 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. |
|---|
| Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
|---|---|---|---|---|---|---|---|---|---|
| 36 | 37 | 2.544486 | GCTTTGAAGGCAAGTTCAGTGG | 60.544 | 50.000 | 0.00 | 0.00 | 37.72 | 4.00 |
| 45 | 46 | 3.550842 | GGCAAGTTCAGTGGTTGATTGAC | 60.551 | 47.826 | 5.33 | 0.00 | 35.27 | 3.18 |
| 47 | 48 | 4.790766 | GCAAGTTCAGTGGTTGATTGACAG | 60.791 | 45.833 | 5.33 | 0.00 | 35.27 | 3.51 |
| 53 | 54 | 6.358974 | TCAGTGGTTGATTGACAGAAGATA | 57.641 | 37.500 | 0.00 | 0.00 | 0.00 | 1.98 |
| 80 | 81 | 2.933495 | CCGTCGAGGTTAGATCACAA | 57.067 | 50.000 | 4.18 | 0.00 | 34.51 | 3.33 |
| 92 | 93 | 8.862325 | AGGTTAGATCACAATGTTCAATACAA | 57.138 | 30.769 | 0.00 | 0.00 | 40.89 | 2.41 |
| 99 | 100 | 9.447040 | GATCACAATGTTCAATACAATGATCAG | 57.553 | 33.333 | 16.77 | 0.00 | 44.34 | 2.90 |
| 106 | 107 | 6.313658 | TGTTCAATACAATGATCAGACGAAGG | 59.686 | 38.462 | 0.09 | 0.00 | 32.64 | 3.46 |
| 107 | 108 | 6.220726 | TCAATACAATGATCAGACGAAGGA | 57.779 | 37.500 | 0.09 | 0.00 | 0.00 | 3.36 |
| 108 | 109 | 6.042777 | TCAATACAATGATCAGACGAAGGAC | 58.957 | 40.000 | 0.09 | 0.00 | 0.00 | 3.85 |
| 109 | 110 | 3.961480 | ACAATGATCAGACGAAGGACA | 57.039 | 42.857 | 0.09 | 0.00 | 0.00 | 4.02 |
| 110 | 111 | 4.271696 | ACAATGATCAGACGAAGGACAA | 57.728 | 40.909 | 0.09 | 0.00 | 0.00 | 3.18 |
| 131 | 133 | 7.248743 | ACAAAAGGAAATCATCATCAATGGT | 57.751 | 32.000 | 0.00 | 0.00 | 35.94 | 3.55 |
| 159 | 161 | 7.522901 | TTCATTTGTTGTGTGAGTGAAATTG | 57.477 | 32.000 | 0.00 | 0.00 | 0.00 | 2.32 |
| 163 | 165 | 5.247507 | TGTTGTGTGAGTGAAATTGAAGG | 57.752 | 39.130 | 0.00 | 0.00 | 0.00 | 3.46 |
| 179 | 181 | 7.457380 | AATTGAAGGAGATGAATAGGAAGGA | 57.543 | 36.000 | 0.00 | 0.00 | 0.00 | 3.36 |
| 182 | 184 | 5.726308 | TGAAGGAGATGAATAGGAAGGACAA | 59.274 | 40.000 | 0.00 | 0.00 | 0.00 | 3.18 |
| 207 | 209 | 2.007608 | GAAAGAGATGGCGTACAACCC | 58.992 | 52.381 | 0.00 | 0.00 | 0.00 | 4.11 |
| 209 | 211 | 0.981183 | AGAGATGGCGTACAACCCAA | 59.019 | 50.000 | 1.56 | 0.00 | 34.25 | 4.12 |
| 210 | 212 | 1.066143 | AGAGATGGCGTACAACCCAAG | 60.066 | 52.381 | 1.56 | 0.00 | 34.25 | 3.61 |
| 213 | 215 | 2.281900 | GGCGTACAACCCAAGCCA | 60.282 | 61.111 | 0.00 | 0.00 | 46.48 | 4.75 |
| 214 | 216 | 2.622962 | GGCGTACAACCCAAGCCAC | 61.623 | 63.158 | 0.00 | 0.00 | 46.48 | 5.01 |
| 227 | 229 | 4.102996 | ACCCAAGCCACAAGAAATTGAATT | 59.897 | 37.500 | 0.00 | 0.00 | 0.00 | 2.17 |
| 234 | 236 | 6.269769 | AGCCACAAGAAATTGAATTAAAGGGA | 59.730 | 34.615 | 0.00 | 0.00 | 0.00 | 4.20 |
| 246 | 248 | 4.657814 | ATTAAAGGGAAGGCAGAGACAA | 57.342 | 40.909 | 0.00 | 0.00 | 0.00 | 3.18 |
| 279 | 281 | 0.539051 | CGGTGAGAGCCAAAGAGGAT | 59.461 | 55.000 | 0.00 | 0.00 | 41.22 | 3.24 |
| 288 | 290 | 2.512896 | AGCCAAAGAGGATGATGTGGAT | 59.487 | 45.455 | 0.00 | 0.00 | 41.22 | 3.41 |
| 317 | 325 | 3.857157 | AAGGAACCTGTAGCACAAGAA | 57.143 | 42.857 | 0.00 | 0.00 | 0.00 | 2.52 |
| 331 | 339 | 2.503356 | CACAAGAAGAGGTGGATAGGCT | 59.497 | 50.000 | 0.00 | 0.00 | 0.00 | 4.58 |
| 336 | 344 | 1.516110 | AGAGGTGGATAGGCTGCATT | 58.484 | 50.000 | 0.50 | 0.00 | 0.00 | 3.56 |
| 358 | 366 | 9.120538 | GCATTTCAAGATAAATAGGTTAGTGGA | 57.879 | 33.333 | 0.00 | 0.00 | 0.00 | 4.02 |
| 382 | 390 | 8.337739 | GGAGGTCAATCTCTTAGGTATATAGGA | 58.662 | 40.741 | 0.00 | 0.00 | 34.39 | 2.94 |
| 531 | 539 | 8.766000 | TGAAAAACAAAAGGAGTAGGAAAAAC | 57.234 | 30.769 | 0.00 | 0.00 | 0.00 | 2.43 |
| 539 | 547 | 8.846211 | CAAAAGGAGTAGGAAAAACTAACATCA | 58.154 | 33.333 | 0.00 | 0.00 | 0.00 | 3.07 |
| 540 | 548 | 8.990163 | AAAGGAGTAGGAAAAACTAACATCAA | 57.010 | 30.769 | 0.00 | 0.00 | 0.00 | 2.57 |
| 541 | 549 | 8.990163 | AAGGAGTAGGAAAAACTAACATCAAA | 57.010 | 30.769 | 0.00 | 0.00 | 0.00 | 2.69 |
| 542 | 550 | 8.990163 | AGGAGTAGGAAAAACTAACATCAAAA | 57.010 | 30.769 | 0.00 | 0.00 | 0.00 | 2.44 |
| 543 | 551 | 9.416284 | AGGAGTAGGAAAAACTAACATCAAAAA | 57.584 | 29.630 | 0.00 | 0.00 | 0.00 | 1.94 |
| 641 | 653 | 9.116054 | CAAAACAAAAAGAAGAAAAACATGGTG | 57.884 | 29.630 | 0.00 | 0.00 | 0.00 | 4.17 |
| 652 | 664 | 5.535030 | AGAAAAACATGGTGTAGGAAGGTTC | 59.465 | 40.000 | 0.00 | 0.00 | 0.00 | 3.62 |
| 673 | 685 | 9.668497 | AGGTTCTATAATCTTCACAAAACCTAC | 57.332 | 33.333 | 0.00 | 0.00 | 41.50 | 3.18 |
| 674 | 686 | 8.890718 | GGTTCTATAATCTTCACAAAACCTACC | 58.109 | 37.037 | 0.00 | 0.00 | 32.74 | 3.18 |
| 677 | 689 | 6.759497 | ATAATCTTCACAAAACCTACCAGC | 57.241 | 37.500 | 0.00 | 0.00 | 0.00 | 4.85 |
| 678 | 690 | 2.489971 | TCTTCACAAAACCTACCAGCG | 58.510 | 47.619 | 0.00 | 0.00 | 0.00 | 5.18 |
| 679 | 691 | 2.103432 | TCTTCACAAAACCTACCAGCGA | 59.897 | 45.455 | 0.00 | 0.00 | 0.00 | 4.93 |
| 681 | 693 | 0.872388 | CACAAAACCTACCAGCGACC | 59.128 | 55.000 | 0.00 | 0.00 | 0.00 | 4.79 |
| 682 | 694 | 0.763035 | ACAAAACCTACCAGCGACCT | 59.237 | 50.000 | 0.00 | 0.00 | 0.00 | 3.85 |
| 683 | 695 | 1.972795 | ACAAAACCTACCAGCGACCTA | 59.027 | 47.619 | 0.00 | 0.00 | 0.00 | 3.08 |
| 684 | 696 | 2.369532 | ACAAAACCTACCAGCGACCTAA | 59.630 | 45.455 | 0.00 | 0.00 | 0.00 | 2.69 |
| 685 | 697 | 3.008704 | ACAAAACCTACCAGCGACCTAAT | 59.991 | 43.478 | 0.00 | 0.00 | 0.00 | 1.73 |
| 687 | 699 | 5.180271 | CAAAACCTACCAGCGACCTAATAA | 58.820 | 41.667 | 0.00 | 0.00 | 0.00 | 1.40 |
| 688 | 700 | 5.425196 | AAACCTACCAGCGACCTAATAAA | 57.575 | 39.130 | 0.00 | 0.00 | 0.00 | 1.40 |
| 689 | 701 | 5.625568 | AACCTACCAGCGACCTAATAAAT | 57.374 | 39.130 | 0.00 | 0.00 | 0.00 | 1.40 |
| 691 | 703 | 6.342338 | ACCTACCAGCGACCTAATAAATAG | 57.658 | 41.667 | 0.00 | 0.00 | 0.00 | 1.73 |
| 692 | 704 | 6.073314 | ACCTACCAGCGACCTAATAAATAGA | 58.927 | 40.000 | 0.00 | 0.00 | 33.04 | 1.98 |
| 768 | 1483 | 9.426837 | CTGTGAACATTTTTATTGAATCCATGT | 57.573 | 29.630 | 0.00 | 0.00 | 0.00 | 3.21 |
| 773 | 1488 | 9.921637 | AACATTTTTATTGAATCCATGTACGTT | 57.078 | 25.926 | 0.00 | 0.00 | 0.00 | 3.99 |
| 895 | 1639 | 1.213013 | CGCCGAATAGGAGATCCCG | 59.787 | 63.158 | 0.00 | 0.00 | 43.02 | 5.14 |
| 981 | 1726 | 1.564483 | TAACCCCTAAACCCCAGCCG | 61.564 | 60.000 | 0.00 | 0.00 | 0.00 | 5.52 |
| 1067 | 1818 | 2.370445 | CGCCTCCCACCTCCAAGAT | 61.370 | 63.158 | 0.00 | 0.00 | 0.00 | 2.40 |
| 1143 | 2108 | 1.687493 | CCTCTCCTCCTCACACCCC | 60.687 | 68.421 | 0.00 | 0.00 | 0.00 | 4.95 |
| 1339 | 2485 | 4.821589 | CAACCTCCGAGCTCGCCC | 62.822 | 72.222 | 30.49 | 0.00 | 38.18 | 6.13 |
| 1805 | 2951 | 0.107945 | GCACTCTACAAGGAGGCAGG | 60.108 | 60.000 | 0.00 | 0.00 | 37.63 | 4.85 |
| 1947 | 3093 | 3.334054 | GAGCTTGGGGGCTGTCCT | 61.334 | 66.667 | 0.00 | 0.00 | 43.20 | 3.85 |
| 1983 | 3129 | 1.060713 | ACAACTCGCTCATTTCGTCG | 58.939 | 50.000 | 0.00 | 0.00 | 0.00 | 5.12 |
| 2038 | 3184 | 2.765699 | GAGCTCAAAGAGGAGATGGAGT | 59.234 | 50.000 | 9.40 | 0.00 | 37.05 | 3.85 |
| 2997 | 4143 | 1.009675 | CAAGTCAAGTGGTGCACGC | 60.010 | 57.895 | 11.45 | 6.34 | 39.64 | 5.34 |
| 3214 | 4360 | 0.896923 | TCATGGTTGCAAGCCCAATC | 59.103 | 50.000 | 24.81 | 0.00 | 33.66 | 2.67 |
| 3383 | 4529 | 7.102346 | CACACTTCAAGAGATAGAGGTTGAAT | 58.898 | 38.462 | 0.00 | 0.00 | 38.04 | 2.57 |
| 3400 | 4546 | 7.791029 | AGGTTGAATATCAAACCTTGTTTGTT | 58.209 | 30.769 | 16.65 | 12.20 | 44.86 | 2.83 |
| 3402 | 4548 | 8.547894 | GGTTGAATATCAAACCTTGTTTGTTTC | 58.452 | 33.333 | 16.65 | 16.55 | 38.10 | 2.78 |
| 3412 | 4558 | 4.274950 | ACCTTGTTTGTTTCTGTGATACGG | 59.725 | 41.667 | 0.00 | 0.00 | 0.00 | 4.02 |
| 3649 | 4920 | 3.517901 | TCATCTGTTTCCTAATCCGGTGT | 59.482 | 43.478 | 0.00 | 0.00 | 0.00 | 4.16 |
| 3811 | 5082 | 1.919816 | TGAGGCTCCTGGTGCATCA | 60.920 | 57.895 | 27.85 | 27.85 | 46.65 | 3.07 |
| 3919 | 5196 | 1.503818 | GGTTCGTGCGAGCCTTTTGA | 61.504 | 55.000 | 17.96 | 0.00 | 41.46 | 2.69 |
| 4044 | 5331 | 1.261619 | GCTGTTCTCTGTGTTCGGTTG | 59.738 | 52.381 | 0.00 | 0.00 | 0.00 | 3.77 |
| 4063 | 5350 | 3.379650 | CACCTGTTGTGTTCTCGGT | 57.620 | 52.632 | 0.00 | 0.00 | 40.26 | 4.69 |
| 4138 | 5425 | 1.995626 | TCTTCTAGGTGGGCAGGGC | 60.996 | 63.158 | 0.00 | 0.00 | 0.00 | 5.19 |
| 4240 | 5527 | 7.014230 | TGTTCCTCTCCATTTTTGTTTCCTTAG | 59.986 | 37.037 | 0.00 | 0.00 | 0.00 | 2.18 |
| 4246 | 5533 | 7.230712 | TCTCCATTTTTGTTTCCTTAGGTCTTC | 59.769 | 37.037 | 0.00 | 0.00 | 0.00 | 2.87 |
| 4254 | 5541 | 6.126409 | TGTTTCCTTAGGTCTTCATTGTTGT | 58.874 | 36.000 | 0.00 | 0.00 | 0.00 | 3.32 |
| 4270 | 5557 | 7.487484 | TCATTGTTGTGTTGATTGTGTAATGT | 58.513 | 30.769 | 0.00 | 0.00 | 0.00 | 2.71 |
| 4294 | 5581 | 3.414700 | CGTGCTGTCCTTGGTCGC | 61.415 | 66.667 | 0.00 | 0.00 | 0.00 | 5.19 |
| Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
|---|---|---|---|---|---|---|---|---|---|
| 0 | 1 | 6.259829 | GCCTTCAAAGCCTTCAAATTAAAACA | 59.740 | 34.615 | 0.00 | 0.00 | 0.00 | 2.83 |
| 1 | 2 | 6.259829 | TGCCTTCAAAGCCTTCAAATTAAAAC | 59.740 | 34.615 | 0.00 | 0.00 | 0.00 | 2.43 |
| 8 | 9 | 2.765699 | ACTTGCCTTCAAAGCCTTCAAA | 59.234 | 40.909 | 0.00 | 0.00 | 0.00 | 2.69 |
| 19 | 20 | 2.023673 | CAACCACTGAACTTGCCTTCA | 58.976 | 47.619 | 0.00 | 0.00 | 0.00 | 3.02 |
| 36 | 37 | 7.362142 | GGTTCCCTTTATCTTCTGTCAATCAAC | 60.362 | 40.741 | 0.00 | 0.00 | 0.00 | 3.18 |
| 45 | 46 | 3.119245 | TCGACGGTTCCCTTTATCTTCTG | 60.119 | 47.826 | 0.00 | 0.00 | 0.00 | 3.02 |
| 47 | 48 | 3.445857 | CTCGACGGTTCCCTTTATCTTC | 58.554 | 50.000 | 0.00 | 0.00 | 0.00 | 2.87 |
| 53 | 54 | 3.881334 | ACCTCGACGGTTCCCTTT | 58.119 | 55.556 | 0.00 | 0.00 | 46.37 | 3.11 |
| 67 | 68 | 8.862325 | TTGTATTGAACATTGTGATCTAACCT | 57.138 | 30.769 | 0.00 | 0.00 | 38.10 | 3.50 |
| 80 | 81 | 7.011763 | CCTTCGTCTGATCATTGTATTGAACAT | 59.988 | 37.037 | 0.00 | 0.00 | 38.10 | 2.71 |
| 92 | 93 | 4.020218 | TCCTTTTGTCCTTCGTCTGATCAT | 60.020 | 41.667 | 0.00 | 0.00 | 0.00 | 2.45 |
| 99 | 100 | 5.181245 | TGATGATTTCCTTTTGTCCTTCGTC | 59.819 | 40.000 | 0.00 | 0.00 | 0.00 | 4.20 |
| 106 | 107 | 7.325694 | ACCATTGATGATGATTTCCTTTTGTC | 58.674 | 34.615 | 0.00 | 0.00 | 38.03 | 3.18 |
| 107 | 108 | 7.248743 | ACCATTGATGATGATTTCCTTTTGT | 57.751 | 32.000 | 0.00 | 0.00 | 38.03 | 2.83 |
| 108 | 109 | 8.556213 | AAACCATTGATGATGATTTCCTTTTG | 57.444 | 30.769 | 0.00 | 0.00 | 38.03 | 2.44 |
| 109 | 110 | 9.577222 | AAAAACCATTGATGATGATTTCCTTTT | 57.423 | 25.926 | 0.00 | 0.00 | 29.85 | 2.27 |
| 136 | 138 | 6.861144 | TCAATTTCACTCACACAACAAATGA | 58.139 | 32.000 | 0.00 | 0.00 | 0.00 | 2.57 |
| 137 | 139 | 7.254185 | CCTTCAATTTCACTCACACAACAAATG | 60.254 | 37.037 | 0.00 | 0.00 | 0.00 | 2.32 |
| 154 | 156 | 7.777440 | GTCCTTCCTATTCATCTCCTTCAATTT | 59.223 | 37.037 | 0.00 | 0.00 | 0.00 | 1.82 |
| 159 | 161 | 5.878406 | TGTCCTTCCTATTCATCTCCTTC | 57.122 | 43.478 | 0.00 | 0.00 | 0.00 | 3.46 |
| 163 | 165 | 9.784531 | TTCATTATTGTCCTTCCTATTCATCTC | 57.215 | 33.333 | 0.00 | 0.00 | 0.00 | 2.75 |
| 179 | 181 | 6.112734 | TGTACGCCATCTCTTTCATTATTGT | 58.887 | 36.000 | 0.00 | 0.00 | 0.00 | 2.71 |
| 182 | 184 | 5.527582 | GGTTGTACGCCATCTCTTTCATTAT | 59.472 | 40.000 | 1.86 | 0.00 | 0.00 | 1.28 |
| 207 | 209 | 7.095102 | CCCTTTAATTCAATTTCTTGTGGCTTG | 60.095 | 37.037 | 0.00 | 0.00 | 33.87 | 4.01 |
| 209 | 211 | 6.269769 | TCCCTTTAATTCAATTTCTTGTGGCT | 59.730 | 34.615 | 0.00 | 0.00 | 33.87 | 4.75 |
| 210 | 212 | 6.463360 | TCCCTTTAATTCAATTTCTTGTGGC | 58.537 | 36.000 | 0.00 | 0.00 | 33.87 | 5.01 |
| 212 | 214 | 7.118245 | GCCTTCCCTTTAATTCAATTTCTTGTG | 59.882 | 37.037 | 0.00 | 0.00 | 33.87 | 3.33 |
| 213 | 215 | 7.161404 | GCCTTCCCTTTAATTCAATTTCTTGT | 58.839 | 34.615 | 0.00 | 0.00 | 33.87 | 3.16 |
| 214 | 216 | 7.160726 | TGCCTTCCCTTTAATTCAATTTCTTG | 58.839 | 34.615 | 0.00 | 0.00 | 0.00 | 3.02 |
| 227 | 229 | 4.289672 | AGATTTGTCTCTGCCTTCCCTTTA | 59.710 | 41.667 | 0.00 | 0.00 | 0.00 | 1.85 |
| 234 | 236 | 3.997021 | CGTGTTAGATTTGTCTCTGCCTT | 59.003 | 43.478 | 0.00 | 0.00 | 0.00 | 4.35 |
| 246 | 248 | 3.079578 | TCTCACCGTCTCGTGTTAGATT | 58.920 | 45.455 | 0.00 | 0.00 | 35.18 | 2.40 |
| 279 | 281 | 5.051409 | TCCTTTATCATGCATCCACATCA | 57.949 | 39.130 | 0.00 | 0.00 | 0.00 | 3.07 |
| 288 | 290 | 4.199310 | GCTACAGGTTCCTTTATCATGCA | 58.801 | 43.478 | 0.00 | 0.00 | 0.00 | 3.96 |
| 317 | 325 | 1.516110 | AATGCAGCCTATCCACCTCT | 58.484 | 50.000 | 0.00 | 0.00 | 0.00 | 3.69 |
| 331 | 339 | 8.902806 | CCACTAACCTATTTATCTTGAAATGCA | 58.097 | 33.333 | 0.00 | 0.00 | 31.51 | 3.96 |
| 336 | 344 | 8.388656 | ACCTCCACTAACCTATTTATCTTGAA | 57.611 | 34.615 | 0.00 | 0.00 | 0.00 | 2.69 |
| 500 | 508 | 8.977412 | TCCTACTCCTTTTGTTTTTCATTTTCT | 58.023 | 29.630 | 0.00 | 0.00 | 0.00 | 2.52 |
| 501 | 509 | 9.594478 | TTCCTACTCCTTTTGTTTTTCATTTTC | 57.406 | 29.630 | 0.00 | 0.00 | 0.00 | 2.29 |
| 636 | 648 | 8.568617 | AAGATTATAGAACCTTCCTACACCAT | 57.431 | 34.615 | 0.00 | 0.00 | 0.00 | 3.55 |
| 641 | 653 | 9.886132 | TTTGTGAAGATTATAGAACCTTCCTAC | 57.114 | 33.333 | 1.73 | 0.00 | 35.42 | 3.18 |
| 652 | 664 | 7.254455 | CGCTGGTAGGTTTTGTGAAGATTATAG | 60.254 | 40.741 | 0.00 | 0.00 | 0.00 | 1.31 |
| 671 | 683 | 8.867097 | AGAATTCTATTTATTAGGTCGCTGGTA | 58.133 | 33.333 | 6.06 | 0.00 | 0.00 | 3.25 |
| 672 | 684 | 7.736893 | AGAATTCTATTTATTAGGTCGCTGGT | 58.263 | 34.615 | 6.06 | 0.00 | 0.00 | 4.00 |
| 673 | 685 | 8.608844 | AAGAATTCTATTTATTAGGTCGCTGG | 57.391 | 34.615 | 8.75 | 0.00 | 0.00 | 4.85 |
| 728 | 1443 | 8.545229 | AAATGTTCACAGAATTCAAAACAACA | 57.455 | 26.923 | 8.44 | 9.75 | 31.19 | 3.33 |
| 796 | 1511 | 2.961768 | GGCACATGTGGGGTTTCG | 59.038 | 61.111 | 26.55 | 0.00 | 0.00 | 3.46 |
| 895 | 1639 | 1.273886 | GAGAAGAGGACCGGATATGGC | 59.726 | 57.143 | 9.46 | 0.00 | 0.00 | 4.40 |
| 1143 | 2108 | 2.689034 | GAGGAGGAGGTGGGGGTG | 60.689 | 72.222 | 0.00 | 0.00 | 0.00 | 4.61 |
| 1215 | 2180 | 4.431131 | AGGTTCCATGGCTGCCCG | 62.431 | 66.667 | 17.53 | 7.25 | 0.00 | 6.13 |
| 1794 | 2940 | 1.001641 | CACCTTCCCTGCCTCCTTG | 60.002 | 63.158 | 0.00 | 0.00 | 0.00 | 3.61 |
| 1805 | 2951 | 2.409975 | TCATTTCGTCGAACACCTTCC | 58.590 | 47.619 | 7.29 | 0.00 | 0.00 | 3.46 |
| 1947 | 3093 | 2.369532 | GTTGTAGGTTACCACACTGGGA | 59.630 | 50.000 | 3.51 | 0.00 | 43.37 | 4.37 |
| 1983 | 3129 | 6.827586 | TTCAACAACCCATCCTTTACATAC | 57.172 | 37.500 | 0.00 | 0.00 | 0.00 | 2.39 |
| 2038 | 3184 | 3.287222 | CATCCGGCTGAATTCCCTTAAA | 58.713 | 45.455 | 0.00 | 0.00 | 0.00 | 1.52 |
| 2123 | 3269 | 6.849588 | TCCTCAACATTTCATCATATGTCG | 57.150 | 37.500 | 1.90 | 0.00 | 34.04 | 4.35 |
| 2997 | 4143 | 6.627243 | TGTGTTATAAGAATATCGATCCGGG | 58.373 | 40.000 | 0.00 | 0.00 | 0.00 | 5.73 |
| 3214 | 4360 | 8.032952 | TGCAGTATTGAATTGTAAGTTCTCTG | 57.967 | 34.615 | 0.00 | 0.00 | 0.00 | 3.35 |
| 3383 | 4529 | 7.397892 | TCACAGAAACAAACAAGGTTTGATA | 57.602 | 32.000 | 23.97 | 0.00 | 38.50 | 2.15 |
| 3400 | 4546 | 6.650427 | ATATCTACTTGCCGTATCACAGAA | 57.350 | 37.500 | 0.00 | 0.00 | 0.00 | 3.02 |
| 3402 | 4548 | 7.539022 | CAGTTATATCTACTTGCCGTATCACAG | 59.461 | 40.741 | 0.00 | 0.00 | 0.00 | 3.66 |
| 3512 | 4783 | 7.362056 | GCAGAGAAAACTAAATGCATCTTACCA | 60.362 | 37.037 | 0.00 | 0.00 | 33.92 | 3.25 |
| 3513 | 4784 | 6.969473 | GCAGAGAAAACTAAATGCATCTTACC | 59.031 | 38.462 | 0.00 | 0.00 | 33.92 | 2.85 |
| 3765 | 5036 | 6.496743 | TCAAGGGAGCTTAGTAACTTAGGTA | 58.503 | 40.000 | 0.00 | 0.00 | 0.00 | 3.08 |
| 3811 | 5082 | 4.383770 | CCCACAACCGACTCTAAATACCAT | 60.384 | 45.833 | 0.00 | 0.00 | 0.00 | 3.55 |
| 4063 | 5350 | 1.993653 | CAGAACCAGCTCCCCATGA | 59.006 | 57.895 | 0.00 | 0.00 | 0.00 | 3.07 |
| 4240 | 5527 | 5.459762 | CACAATCAACACAACAATGAAGACC | 59.540 | 40.000 | 0.00 | 0.00 | 0.00 | 3.85 |
| 4246 | 5533 | 7.697352 | ACATTACACAATCAACACAACAATG | 57.303 | 32.000 | 0.00 | 0.00 | 0.00 | 2.82 |
| 4254 | 5541 | 6.428465 | ACGGATACAACATTACACAATCAACA | 59.572 | 34.615 | 0.00 | 0.00 | 0.00 | 3.33 |
| 4270 | 5557 | 1.338674 | CCAAGGACAGCACGGATACAA | 60.339 | 52.381 | 0.00 | 0.00 | 0.00 | 2.41 |
| 4294 | 5581 | 0.660300 | GAAACAAAGAAGCACGCCCG | 60.660 | 55.000 | 0.00 | 0.00 | 0.00 | 6.13 |
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.