Multiple sequence alignment - TraesCS7D01G396000

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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 TraesCS7D01G396000 chr7D 100.000 5489 0 0 1 5489 510610665 510616153 0.000000e+00 10137.0
1 TraesCS7D01G396000 chr7D 95.556 45 2 0 5311 5355 205240067 205240111 7.630000e-09 73.1
2 TraesCS7D01G396000 chr7B 95.361 4247 140 31 643 4875 539216167 539220370 0.000000e+00 6698.0
3 TraesCS7D01G396000 chr7B 85.023 661 42 21 6 637 539215493 539216125 2.170000e-173 619.0
4 TraesCS7D01G396000 chr7B 90.625 448 23 10 4867 5301 539220398 539220839 1.330000e-160 577.0
5 TraesCS7D01G396000 chr7B 96.581 117 3 1 5374 5489 539222140 539222256 5.610000e-45 193.0
6 TraesCS7D01G396000 chr7B 97.619 42 1 0 5309 5350 226902893 226902852 7.630000e-09 73.1
7 TraesCS7D01G396000 chr7B 95.455 44 2 0 2822 2865 86226692 86226649 2.740000e-08 71.3
8 TraesCS7D01G396000 chr7B 90.385 52 4 1 5298 5348 604782722 604782671 3.550000e-07 67.6
9 TraesCS7D01G396000 chr7A 94.553 4333 154 24 1 4299 581371481 581375765 0.000000e+00 6619.0
10 TraesCS7D01G396000 chr7A 95.238 546 16 8 4337 4875 581375752 581376294 0.000000e+00 856.0
11 TraesCS7D01G396000 chr7A 93.261 371 20 4 4867 5236 581376322 581376688 4.840000e-150 542.0
12 TraesCS7D01G396000 chr7A 93.701 127 8 0 5363 5489 581378078 581378204 2.020000e-44 191.0
13 TraesCS7D01G396000 chr1D 89.865 296 16 8 493 785 418606552 418606268 8.690000e-98 368.0
14 TraesCS7D01G396000 chr1A 89.116 294 20 6 493 785 439488133 439487851 6.760000e-94 355.0
15 TraesCS7D01G396000 chr1A 88.095 294 23 6 493 785 31697780 31697498 6.810000e-89 339.0
16 TraesCS7D01G396000 chr1A 86.411 287 27 6 497 782 534010893 534010618 2.480000e-78 303.0
17 TraesCS7D01G396000 chr1A 100.000 28 0 0 375 402 31697892 31697865 1.000000e-02 52.8
18 TraesCS7D01G396000 chr3B 88.660 291 21 6 493 782 685090031 685090310 1.460000e-90 344.0
19 TraesCS7D01G396000 chr3B 87.415 294 25 6 493 785 615703933 615704215 1.470000e-85 327.0
20 TraesCS7D01G396000 chr3B 85.789 190 20 5 493 679 231188975 231189160 1.560000e-45 195.0
21 TraesCS7D01G396000 chr3B 92.000 50 3 1 5310 5359 694025495 694025447 9.870000e-08 69.4
22 TraesCS7D01G396000 chr3B 100.000 28 0 0 375 402 615703821 615703848 1.000000e-02 52.8
23 TraesCS7D01G396000 chr2B 87.285 291 25 6 493 782 632573728 632574007 6.860000e-84 322.0
24 TraesCS7D01G396000 chr2B 85.859 99 12 1 2766 2864 206114821 206114725 2.700000e-18 104.0
25 TraesCS7D01G396000 chr6B 86.735 294 27 6 493 785 304065666 304065384 3.190000e-82 316.0
26 TraesCS7D01G396000 chr6B 97.674 43 1 0 5315 5357 675442974 675443016 2.120000e-09 75.0
27 TraesCS7D01G396000 chr3D 86.552 290 15 6 499 785 139731702 139731434 1.160000e-76 298.0
28 TraesCS7D01G396000 chr2D 92.391 92 6 1 326 417 645284908 645284998 4.460000e-26 130.0
29 TraesCS7D01G396000 chr3A 86.869 99 13 0 2765 2863 589797300 589797202 1.620000e-20 111.0
30 TraesCS7D01G396000 chr6D 85.000 100 13 2 2766 2864 41640809 41640907 3.500000e-17 100.0
31 TraesCS7D01G396000 chr6D 93.878 49 1 1 5315 5361 57469923 57469971 7.630000e-09 73.1
32 TraesCS7D01G396000 chr4D 81.633 98 14 4 2769 2864 455290525 455290430 1.640000e-10 78.7
33 TraesCS7D01G396000 chr4D 81.053 95 14 2 2783 2874 499394253 499394160 7.630000e-09 73.1
34 TraesCS7D01G396000 chr4B 92.308 52 3 1 2820 2871 12236108 12236158 7.630000e-09 73.1
35 TraesCS7D01G396000 chr4B 93.617 47 2 1 5314 5359 20318435 20318389 9.870000e-08 69.4
36 TraesCS7D01G396000 chr4A 97.619 42 1 0 5309 5350 697899829 697899870 7.630000e-09 73.1
37 TraesCS7D01G396000 chr1B 90.566 53 5 0 5298 5350 322104648 322104596 2.740000e-08 71.3


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 TraesCS7D01G396000 chr7D 510610665 510616153 5488 False 10137.00 10137 100.00000 1 5489 1 chr7D.!!$F2 5488
1 TraesCS7D01G396000 chr7B 539215493 539222256 6763 False 2021.75 6698 91.89750 6 5489 4 chr7B.!!$F1 5483
2 TraesCS7D01G396000 chr7A 581371481 581378204 6723 False 2052.00 6619 94.18825 1 5489 4 chr7A.!!$F1 5488

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
152 153 0.247185 ATTTTGGCACCAATCTGCGG 59.753 50.0 2.31 0.00 38.12 5.69 F
619 651 0.674895 GGCGCCATTTCTCACTGACT 60.675 55.0 24.80 0.00 0.00 3.41 F
1344 1443 0.735471 CAGGTCTTCGATCGAGCAGA 59.265 55.0 18.54 16.08 0.00 4.26 F
2785 2888 0.905357 ACTCCCTCTGACCCGAATTG 59.095 55.0 0.00 0.00 0.00 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1344 1443 0.839946 CGACCAAGGATCCCCAATCT 59.160 55.000 8.55 0.0 34.56 2.40 R
2531 2633 1.136252 CGCGCATTCCCATAAGAATCG 60.136 52.381 8.75 0.0 34.19 3.34 R
3300 3403 0.038159 GACGCTACAGTGCCAACTCT 60.038 55.000 0.00 0.0 32.98 3.24 R
4624 4728 1.280710 TGAATCACCCGTGGCTAATGT 59.719 47.619 0.00 0.0 0.00 2.71 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
17 18 2.931386 GTAGCAAGGCATAGCGCG 59.069 61.111 0.00 0.00 43.84 6.86
142 143 3.375782 AACAGCTCTGAATTTTGGCAC 57.624 42.857 3.60 0.00 0.00 5.01
145 146 2.036217 CAGCTCTGAATTTTGGCACCAA 59.964 45.455 0.00 0.00 0.00 3.67
146 147 2.901839 AGCTCTGAATTTTGGCACCAAT 59.098 40.909 2.31 0.00 35.70 3.16
149 150 4.491676 CTCTGAATTTTGGCACCAATCTG 58.508 43.478 2.31 2.94 35.70 2.90
152 153 0.247185 ATTTTGGCACCAATCTGCGG 59.753 50.000 2.31 0.00 38.12 5.69
160 161 3.550842 GGCACCAATCTGCGGAATTTATC 60.551 47.826 0.00 0.00 38.12 1.75
166 167 5.283294 CAATCTGCGGAATTTATCATGCAA 58.717 37.500 0.00 0.00 39.51 4.08
174 175 7.086376 GCGGAATTTATCATGCAATTCATACT 58.914 34.615 18.69 0.00 40.00 2.12
177 178 9.846248 GGAATTTATCATGCAATTCATACTACC 57.154 33.333 18.69 4.94 40.00 3.18
216 218 4.351874 TCAAATAGGCATGGTAGCTACC 57.648 45.455 32.37 32.37 46.62 3.18
264 269 4.475135 GAGCCGGAGCAAGGGGAC 62.475 72.222 5.05 0.00 43.56 4.46
270 275 1.682684 GGAGCAAGGGGACGAGAGA 60.683 63.158 0.00 0.00 0.00 3.10
463 495 2.481795 GCAAATCGCGGTAGGTAGGTTA 60.482 50.000 6.13 0.00 0.00 2.85
619 651 0.674895 GGCGCCATTTCTCACTGACT 60.675 55.000 24.80 0.00 0.00 3.41
825 897 4.802051 CCGGCCCATGGACCTGTG 62.802 72.222 15.91 0.00 0.00 3.66
827 899 4.052518 GGCCCATGGACCTGTGCT 62.053 66.667 15.22 0.00 0.00 4.40
908 985 4.115279 CTGGACGCCAGCACATAG 57.885 61.111 12.01 0.00 45.13 2.23
1085 1184 1.203313 GTTACACGTGGACGCTTGC 59.797 57.895 21.57 0.00 44.43 4.01
1086 1185 1.957186 TTACACGTGGACGCTTGCC 60.957 57.895 21.57 0.00 44.43 4.52
1087 1186 2.372040 TTACACGTGGACGCTTGCCT 62.372 55.000 21.57 0.00 44.43 4.75
1093 1192 1.908299 TGGACGCTTGCCTCTCTCA 60.908 57.895 0.00 0.00 0.00 3.27
1102 1201 2.015456 TGCCTCTCTCACTTTCTCCA 57.985 50.000 0.00 0.00 0.00 3.86
1104 1203 1.403514 GCCTCTCTCACTTTCTCCACG 60.404 57.143 0.00 0.00 0.00 4.94
1344 1443 0.735471 CAGGTCTTCGATCGAGCAGA 59.265 55.000 18.54 16.08 0.00 4.26
1503 1604 2.485479 GCACTCCTGGAGTTCACTTTGA 60.485 50.000 26.37 0.00 41.37 2.69
1508 1609 6.017192 ACTCCTGGAGTTCACTTTGATAGTA 58.983 40.000 23.49 0.00 40.28 1.82
1509 1610 6.153680 ACTCCTGGAGTTCACTTTGATAGTAG 59.846 42.308 23.49 0.00 40.28 2.57
1510 1611 6.017192 TCCTGGAGTTCACTTTGATAGTAGT 58.983 40.000 0.00 0.00 34.56 2.73
1511 1612 6.497259 TCCTGGAGTTCACTTTGATAGTAGTT 59.503 38.462 0.00 0.00 34.56 2.24
1560 1661 6.909550 TTATGCTATTTGTTTGGAGTGGTT 57.090 33.333 0.00 0.00 0.00 3.67
1577 1678 6.043243 GGAGTGGTTTATGATCATTAGAGGGA 59.957 42.308 14.65 0.00 0.00 4.20
1659 1760 6.815089 TGATTGCCTGATTAGTTTTGTGTTT 58.185 32.000 0.00 0.00 0.00 2.83
1674 1776 5.766150 TTGTGTTTGTGTCCCTGATAAAG 57.234 39.130 0.00 0.00 0.00 1.85
1740 1842 6.013725 TCACTCACTTTGCCTTAATTCCTAGA 60.014 38.462 0.00 0.00 0.00 2.43
1757 1859 9.771534 AATTCCTAGAGTGATTAAAGCATAGTC 57.228 33.333 0.00 0.00 0.00 2.59
1974 2076 6.549364 ACTCATGTATTTTCCCAACTCACAAA 59.451 34.615 0.00 0.00 0.00 2.83
2077 2179 1.815003 GGAGGGTTCAAACAGATGCTG 59.185 52.381 0.00 0.00 37.52 4.41
2126 2228 3.703001 TTGATGTTGGTCTCTTCTCCC 57.297 47.619 0.00 0.00 0.00 4.30
2147 2249 4.522789 CCCGTATTTCCCCCTCAAAATATG 59.477 45.833 0.00 0.00 35.52 1.78
2400 2502 2.103263 GCCCCACAGGTAGTCTATTCTG 59.897 54.545 10.05 10.05 38.26 3.02
2449 2551 3.763057 GGTACTCCCATCCACTTTGTTT 58.237 45.455 0.00 0.00 0.00 2.83
2531 2633 3.199946 TCCTTGGGATCAACACTATGACC 59.800 47.826 0.00 0.00 30.82 4.02
2774 2877 8.043710 CAGACTAACATTTCATTTACTCCCTCT 58.956 37.037 0.00 0.00 0.00 3.69
2777 2880 7.824779 ACTAACATTTCATTTACTCCCTCTGAC 59.175 37.037 0.00 0.00 0.00 3.51
2785 2888 0.905357 ACTCCCTCTGACCCGAATTG 59.095 55.000 0.00 0.00 0.00 2.32
2809 2912 1.795286 GACGCAGCCTCTATACAATGC 59.205 52.381 0.00 0.00 0.00 3.56
2813 2916 3.303593 CGCAGCCTCTATACAATGCAAAG 60.304 47.826 0.00 0.00 33.33 2.77
2822 2925 4.846779 ATACAATGCAAAGTGGACGTTT 57.153 36.364 0.00 0.00 0.00 3.60
2834 2937 3.118738 AGTGGACGTTTTATAGAGGCTGG 60.119 47.826 0.00 0.00 0.00 4.85
3118 3221 5.048224 CGAGGAAAGTTACTGGAGACTTACA 60.048 44.000 0.00 0.00 35.17 2.41
3198 3301 7.230849 TCCCATCCATTTCATTATGTATTGC 57.769 36.000 0.00 0.00 0.00 3.56
3242 3345 5.459536 TGTAGCTACATATTCAGCCTCTG 57.540 43.478 22.67 0.00 38.61 3.35
3300 3403 6.306643 TGTTAATCTATGGACACATGGACA 57.693 37.500 0.00 0.00 45.64 4.02
3317 3420 0.319900 ACAGAGTTGGCACTGTAGCG 60.320 55.000 7.40 0.00 43.07 4.26
3320 3423 1.344942 GAGTTGGCACTGTAGCGTCG 61.345 60.000 0.00 0.00 31.22 5.12
3400 3503 9.480053 CAAAGACCAATTACTGTTGAATTCATT 57.520 29.630 9.40 0.00 0.00 2.57
3526 3629 7.751732 TGATCTTCAAAATTTCCATACGTGAG 58.248 34.615 0.00 0.00 0.00 3.51
3747 3850 1.135972 CACGTTTGCCCAAGATTCGAG 60.136 52.381 0.00 0.00 0.00 4.04
3865 3968 5.698741 TCCATCATGAACACCTCTAACAT 57.301 39.130 0.00 0.00 0.00 2.71
3878 3981 6.549364 ACACCTCTAACATGGACAAAAATGAA 59.451 34.615 0.00 0.00 0.00 2.57
3928 4031 2.027837 GGGCCTTTTGTTCTCATGCATT 60.028 45.455 0.84 0.00 0.00 3.56
4008 4111 3.188667 GCAAGTACTTGTGCCTCTTTACC 59.811 47.826 30.90 10.69 42.31 2.85
4324 4428 8.481492 ACCTTCATGAATGAAATAATGGCATA 57.519 30.769 16.48 0.00 45.26 3.14
4491 4595 1.270839 TGGTCAAGGCACTCTTAGCAC 60.271 52.381 0.00 0.00 38.49 4.40
4510 4614 3.754965 CACCATCCTTTTCCTGTCTTGA 58.245 45.455 0.00 0.00 0.00 3.02
4624 4728 6.925718 CGCCTTTCATCTTCAGTTATCTCATA 59.074 38.462 0.00 0.00 0.00 2.15
4678 4782 5.220605 GGTTCTTCCGTAAATGTATGCTGAC 60.221 44.000 0.00 0.00 0.00 3.51
4706 4810 4.631377 CGGTCTGAAGTTGATGCATTAAGA 59.369 41.667 3.81 0.00 0.00 2.10
4707 4811 5.220548 CGGTCTGAAGTTGATGCATTAAGAG 60.221 44.000 3.81 0.00 0.00 2.85
4708 4812 5.645497 GGTCTGAAGTTGATGCATTAAGAGT 59.355 40.000 3.81 0.00 0.00 3.24
4709 4813 6.818644 GGTCTGAAGTTGATGCATTAAGAGTA 59.181 38.462 3.81 0.00 0.00 2.59
4710 4814 7.497249 GGTCTGAAGTTGATGCATTAAGAGTAT 59.503 37.037 3.81 0.00 0.00 2.12
4741 4845 5.238432 TGTGTTGTGTGGTAGATTCATTGTC 59.762 40.000 0.00 0.00 0.00 3.18
4825 4929 1.227527 TGGTCAGAGGCGTTGTGTG 60.228 57.895 0.00 0.00 0.00 3.82
4838 4942 1.064003 TTGTGTGCACTAGGATGGGT 58.936 50.000 19.41 0.00 0.00 4.51
4859 4965 4.466827 GTGGGTGATATTATTCGGGGTTT 58.533 43.478 0.00 0.00 0.00 3.27
4860 4966 4.277423 GTGGGTGATATTATTCGGGGTTTG 59.723 45.833 0.00 0.00 0.00 2.93
4861 4967 3.254903 GGGTGATATTATTCGGGGTTTGC 59.745 47.826 0.00 0.00 0.00 3.68
4862 4968 3.886505 GGTGATATTATTCGGGGTTTGCA 59.113 43.478 0.00 0.00 0.00 4.08
4863 4969 4.339814 GGTGATATTATTCGGGGTTTGCAA 59.660 41.667 0.00 0.00 0.00 4.08
4864 4970 5.010617 GGTGATATTATTCGGGGTTTGCAAT 59.989 40.000 0.00 0.00 0.00 3.56
4865 4971 5.920273 GTGATATTATTCGGGGTTTGCAATG 59.080 40.000 0.00 0.00 0.00 2.82
4946 5091 8.454106 CCCACTAAACAGATTCTAACATCTTTG 58.546 37.037 0.00 0.00 30.50 2.77
5027 5172 5.982890 ATTTGGACACTACTTGGAAATGG 57.017 39.130 0.00 0.00 0.00 3.16
5074 5219 5.050091 CGGTATGATTTGAATGGTGCTAGTC 60.050 44.000 0.00 0.00 0.00 2.59
5075 5220 5.050091 GGTATGATTTGAATGGTGCTAGTCG 60.050 44.000 0.00 0.00 0.00 4.18
5079 5224 1.523938 GAATGGTGCTAGTCGCCCC 60.524 63.158 12.35 0.00 44.80 5.80
5100 5245 3.054361 CCCCTGTCTTGTACTAGGCAAAT 60.054 47.826 12.58 0.00 0.00 2.32
5107 5252 9.612620 CTGTCTTGTACTAGGCAAATTTTAAAG 57.387 33.333 12.58 0.00 0.00 1.85
5220 5365 2.875087 TGTGTATTACATCCGTCCCG 57.125 50.000 0.00 0.00 33.42 5.14
5329 7209 0.115745 AAAGTACTCCCTCCGTCCCA 59.884 55.000 0.00 0.00 0.00 4.37
5331 7211 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
5334 7214 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
5339 7219 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
5342 7222 2.132762 CCGTCCCATAATGTAAGACGC 58.867 52.381 5.39 0.00 46.66 5.19
5344 7224 3.454375 CGTCCCATAATGTAAGACGCTT 58.546 45.455 0.00 0.00 43.07 4.68
5345 7225 3.869246 CGTCCCATAATGTAAGACGCTTT 59.131 43.478 0.00 0.00 43.07 3.51
5346 7226 4.331717 CGTCCCATAATGTAAGACGCTTTT 59.668 41.667 0.00 0.00 43.07 2.27
5347 7227 5.163794 CGTCCCATAATGTAAGACGCTTTTT 60.164 40.000 0.00 0.00 43.07 1.94
5348 7228 6.027749 GTCCCATAATGTAAGACGCTTTTTG 58.972 40.000 0.00 0.00 0.00 2.44
5349 7229 5.941058 TCCCATAATGTAAGACGCTTTTTGA 59.059 36.000 0.00 0.00 0.00 2.69
5350 7230 6.093495 TCCCATAATGTAAGACGCTTTTTGAG 59.907 38.462 0.00 0.00 0.00 3.02
5351 7231 6.258160 CCATAATGTAAGACGCTTTTTGAGG 58.742 40.000 0.00 0.00 0.00 3.86
5352 7232 4.766404 AATGTAAGACGCTTTTTGAGGG 57.234 40.909 0.00 0.00 43.55 4.30
5353 7233 3.478857 TGTAAGACGCTTTTTGAGGGA 57.521 42.857 0.00 0.00 40.59 4.20
5354 7234 3.399330 TGTAAGACGCTTTTTGAGGGAG 58.601 45.455 0.00 0.00 40.59 4.30
5360 7961 6.726490 AGACGCTTTTTGAGGGAGTATATA 57.274 37.500 0.00 0.00 40.59 0.86
5361 7962 6.750148 AGACGCTTTTTGAGGGAGTATATAG 58.250 40.000 0.00 0.00 40.59 1.31
5365 7966 7.711339 ACGCTTTTTGAGGGAGTATATAGAAAG 59.289 37.037 0.00 0.00 40.59 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.993736 AGCCGAAAACCAAATGTAAATGC 59.006 39.130 0.00 0.00 0.00 3.56
142 143 4.232221 GCATGATAAATTCCGCAGATTGG 58.768 43.478 0.00 0.00 0.00 3.16
145 146 5.717078 ATTGCATGATAAATTCCGCAGAT 57.283 34.783 0.00 0.00 34.40 2.90
146 147 5.067544 TGAATTGCATGATAAATTCCGCAGA 59.932 36.000 18.53 5.04 40.51 4.26
149 150 7.086376 AGTATGAATTGCATGATAAATTCCGC 58.914 34.615 18.53 12.12 40.51 5.54
160 161 8.158169 ACTTGTATGGTAGTATGAATTGCATG 57.842 34.615 0.00 0.00 37.87 4.06
166 167 9.982651 GATGTGTACTTGTATGGTAGTATGAAT 57.017 33.333 0.00 0.00 0.00 2.57
178 179 9.712305 GCCTATTTGATAGATGTGTACTTGTAT 57.288 33.333 0.00 0.00 34.77 2.29
179 180 8.700973 TGCCTATTTGATAGATGTGTACTTGTA 58.299 33.333 0.00 0.00 34.77 2.41
216 218 4.201832 CGAGCTGTTAGGTGAGTACTACTG 60.202 50.000 0.00 0.00 0.00 2.74
260 265 2.094649 ACTCGTGATTTTCTCTCGTCCC 60.095 50.000 0.00 0.00 40.73 4.46
264 269 2.177977 CGGACTCGTGATTTTCTCTCG 58.822 52.381 0.00 0.00 41.14 4.04
270 275 1.156736 CTTGCCGGACTCGTGATTTT 58.843 50.000 5.05 0.00 33.95 1.82
313 325 3.385384 CAGCTGCAGGACGAGGGA 61.385 66.667 17.12 0.00 0.00 4.20
364 376 2.678934 AGGCTGCGGAGGTACGAA 60.679 61.111 5.93 0.00 35.47 3.85
463 495 3.688159 CGTTTCCGTCCCCCGTCT 61.688 66.667 0.00 0.00 33.66 4.18
487 519 2.172483 CTCCTACAAGGCACGCTGGT 62.172 60.000 0.00 0.00 34.61 4.00
488 520 1.448540 CTCCTACAAGGCACGCTGG 60.449 63.158 0.00 0.00 34.61 4.85
490 522 1.889530 GACCTCCTACAAGGCACGCT 61.890 60.000 0.00 0.00 40.34 5.07
821 893 2.194388 ATCCTGGTCCAGCAGCACAG 62.194 60.000 13.99 0.00 0.00 3.66
825 897 2.191641 GGATCCTGGTCCAGCAGC 59.808 66.667 13.99 0.30 38.20 5.25
826 898 2.503061 CGGATCCTGGTCCAGCAG 59.497 66.667 13.99 0.79 38.21 4.24
827 899 3.785859 GCGGATCCTGGTCCAGCA 61.786 66.667 13.99 0.00 38.21 4.41
1085 1184 1.889829 ACGTGGAGAAAGTGAGAGAGG 59.110 52.381 0.00 0.00 0.00 3.69
1086 1185 3.243569 ACAACGTGGAGAAAGTGAGAGAG 60.244 47.826 0.00 0.00 0.00 3.20
1087 1186 2.693591 ACAACGTGGAGAAAGTGAGAGA 59.306 45.455 0.00 0.00 0.00 3.10
1093 1192 1.567504 CGTCACAACGTGGAGAAAGT 58.432 50.000 0.00 0.00 43.94 2.66
1344 1443 0.839946 CGACCAAGGATCCCCAATCT 59.160 55.000 8.55 0.00 34.56 2.40
1536 1637 7.480760 AACCACTCCAAACAAATAGCATAAT 57.519 32.000 0.00 0.00 0.00 1.28
1541 1642 6.919721 TCATAAACCACTCCAAACAAATAGC 58.080 36.000 0.00 0.00 0.00 2.97
1555 1656 9.965902 AATATCCCTCTAATGATCATAAACCAC 57.034 33.333 9.04 0.00 0.00 4.16
1577 1678 8.481492 TGGCATTCAGAATAACAATCCAATAT 57.519 30.769 0.00 0.00 0.00 1.28
1659 1760 1.702401 TGCCACTTTATCAGGGACACA 59.298 47.619 0.00 0.00 0.00 3.72
1674 1776 1.885887 TGTGCTTTAACAGGATGCCAC 59.114 47.619 0.00 0.00 42.53 5.01
1757 1859 5.348724 ACACTATTTGAACAGTCTACGCATG 59.651 40.000 0.00 0.00 0.00 4.06
1768 1870 6.951062 TTCACCAATCACACTATTTGAACA 57.049 33.333 0.00 0.00 0.00 3.18
1894 1996 3.232213 TCAGATAAAACGCTCGCTTCT 57.768 42.857 0.00 0.00 0.00 2.85
1974 2076 5.359009 AGATCGGATGAATCAGCAAATGTTT 59.641 36.000 0.00 0.00 0.00 2.83
2077 2179 3.306166 CGTCGTCATCACCAAGTAATTCC 59.694 47.826 0.00 0.00 0.00 3.01
2126 2228 4.582656 TGCATATTTTGAGGGGGAAATACG 59.417 41.667 0.00 0.00 32.37 3.06
2147 2249 2.755103 AGGGTGCTTAACTGCTTATTGC 59.245 45.455 0.00 0.00 43.25 3.56
2350 2452 8.995027 TTATGGTAATTAGATGCTTCCACATT 57.005 30.769 0.00 0.00 0.00 2.71
2354 2456 7.094805 GCGAATTATGGTAATTAGATGCTTCCA 60.095 37.037 6.70 0.00 0.00 3.53
2400 2502 3.272031 GCTGTGCTTTCCTCCAGC 58.728 61.111 0.00 0.00 42.94 4.85
2449 2551 4.006780 TGCAGCACTTCAACTATCTTGA 57.993 40.909 0.00 0.00 0.00 3.02
2531 2633 1.136252 CGCGCATTCCCATAAGAATCG 60.136 52.381 8.75 0.00 34.19 3.34
2774 2877 1.083489 GCGTCAATCAATTCGGGTCA 58.917 50.000 0.00 0.00 0.00 4.02
2777 2880 0.248215 GCTGCGTCAATCAATTCGGG 60.248 55.000 0.00 0.00 0.00 5.14
2785 2888 3.371102 TGTATAGAGGCTGCGTCAATC 57.629 47.619 22.55 11.10 0.00 2.67
2809 2912 4.935808 AGCCTCTATAAAACGTCCACTTTG 59.064 41.667 0.00 0.00 0.00 2.77
2813 2916 3.195661 CCAGCCTCTATAAAACGTCCAC 58.804 50.000 0.00 0.00 0.00 4.02
2822 2925 6.934645 CGAATTAATTGACCCAGCCTCTATAA 59.065 38.462 5.17 0.00 0.00 0.98
2834 2937 3.746492 CCTCCGATCCGAATTAATTGACC 59.254 47.826 5.17 0.00 0.00 4.02
2887 2990 7.633193 ATTTAAATAACTGTTACATGCGGGA 57.367 32.000 1.73 0.00 0.00 5.14
3118 3221 3.818210 TGGAAAATATCAGCGTGTGTGTT 59.182 39.130 0.00 0.00 0.00 3.32
3242 3345 8.828688 AACAGAAGGTCAATAGTTAAGTACAC 57.171 34.615 0.00 0.00 0.00 2.90
3300 3403 0.038159 GACGCTACAGTGCCAACTCT 60.038 55.000 0.00 0.00 32.98 3.24
3400 3503 6.730507 TCAATGGGCTCATGGAGATATACTAA 59.269 38.462 0.00 0.00 33.18 2.24
3412 3515 3.581755 CAAAACACTCAATGGGCTCATG 58.418 45.455 0.00 0.00 33.18 3.07
3526 3629 6.713450 TCACTTCTTTCCAATTGGTAGTTACC 59.287 38.462 23.76 1.25 46.62 2.85
3747 3850 5.865085 TGGGTGTTAGAATATGATAGTGGC 58.135 41.667 0.00 0.00 0.00 5.01
3865 3968 8.485392 AGAAGGAAGAAAATTCATTTTTGTCCA 58.515 29.630 19.86 0.00 41.08 4.02
3928 4031 8.817100 CGAACTATCATGCAAGATGTAGTTTAA 58.183 33.333 16.94 0.00 30.74 1.52
4008 4111 5.924825 ACGGAACAGTTAGTTAACTAGCAAG 59.075 40.000 25.52 20.14 44.19 4.01
4132 4236 2.267324 GCTGGAGAGGTGGAGCAC 59.733 66.667 0.00 0.00 0.00 4.40
4491 4595 3.754965 TGTCAAGACAGGAAAAGGATGG 58.245 45.455 0.00 0.00 36.21 3.51
4510 4614 3.614092 CTTGTAGAGCACCAATGGATGT 58.386 45.455 6.16 0.00 0.00 3.06
4624 4728 1.280710 TGAATCACCCGTGGCTAATGT 59.719 47.619 0.00 0.00 0.00 2.71
4678 4782 2.350772 GCATCAACTTCAGACCGGTTTG 60.351 50.000 18.80 18.80 0.00 2.93
4706 4810 3.380004 CCACACAACACACAAACCATACT 59.620 43.478 0.00 0.00 0.00 2.12
4707 4811 3.129638 ACCACACAACACACAAACCATAC 59.870 43.478 0.00 0.00 0.00 2.39
4708 4812 3.357203 ACCACACAACACACAAACCATA 58.643 40.909 0.00 0.00 0.00 2.74
4709 4813 2.175202 ACCACACAACACACAAACCAT 58.825 42.857 0.00 0.00 0.00 3.55
4710 4814 1.621992 ACCACACAACACACAAACCA 58.378 45.000 0.00 0.00 0.00 3.67
4825 4929 1.224592 CACCCACCCATCCTAGTGC 59.775 63.158 0.00 0.00 32.48 4.40
4838 4942 4.465886 CAAACCCCGAATAATATCACCCA 58.534 43.478 0.00 0.00 0.00 4.51
4859 4965 0.587768 CGAGCAGAACACACATTGCA 59.412 50.000 0.00 0.00 38.97 4.08
4860 4966 0.867746 TCGAGCAGAACACACATTGC 59.132 50.000 0.00 0.00 36.83 3.56
4861 4967 3.248363 TCTTTCGAGCAGAACACACATTG 59.752 43.478 0.00 0.00 38.83 2.82
4862 4968 3.466836 TCTTTCGAGCAGAACACACATT 58.533 40.909 0.00 0.00 38.83 2.71
4863 4969 3.111853 TCTTTCGAGCAGAACACACAT 57.888 42.857 0.00 0.00 38.83 3.21
4864 4970 2.595124 TCTTTCGAGCAGAACACACA 57.405 45.000 0.00 0.00 38.83 3.72
4865 4971 3.494626 TGAATCTTTCGAGCAGAACACAC 59.505 43.478 0.87 0.00 38.83 3.82
5027 5172 3.124636 CACACGCTAGTAAATGGACAACC 59.875 47.826 0.00 0.00 0.00 3.77
5079 5224 3.695830 TTTGCCTAGTACAAGACAGGG 57.304 47.619 0.00 0.00 30.92 4.45
5082 5227 8.079809 GCTTTAAAATTTGCCTAGTACAAGACA 58.920 33.333 0.00 0.00 0.00 3.41
5095 5240 6.384258 TGGGGAAAAAGCTTTAAAATTTGC 57.616 33.333 13.10 7.78 0.00 3.68
5211 5356 9.037058 TGTCTAGACAAATAATTCGGGACGGAT 62.037 40.741 23.24 0.00 46.25 4.18
5311 5923 0.338814 ATGGGACGGAGGGAGTACTT 59.661 55.000 0.00 0.00 0.00 2.24
5324 7204 5.813080 AAAAGCGTCTTACATTATGGGAC 57.187 39.130 0.00 1.75 0.00 4.46
5326 7206 6.189677 TCAAAAAGCGTCTTACATTATGGG 57.810 37.500 0.00 0.00 0.00 4.00
5329 7209 6.177610 TCCCTCAAAAAGCGTCTTACATTAT 58.822 36.000 0.00 0.00 0.00 1.28
5331 7211 4.394729 TCCCTCAAAAAGCGTCTTACATT 58.605 39.130 0.00 0.00 0.00 2.71
5334 7214 3.400255 ACTCCCTCAAAAAGCGTCTTAC 58.600 45.455 0.00 0.00 0.00 2.34
5339 7219 6.726490 TCTATATACTCCCTCAAAAAGCGT 57.274 37.500 0.00 0.00 0.00 5.07
5341 7221 8.966069 ACTTTCTATATACTCCCTCAAAAAGC 57.034 34.615 0.00 0.00 0.00 3.51
5344 7224 8.925338 GGAGACTTTCTATATACTCCCTCAAAA 58.075 37.037 0.00 0.00 38.23 2.44
5345 7225 8.290277 AGGAGACTTTCTATATACTCCCTCAAA 58.710 37.037 0.00 0.00 43.12 2.69
5346 7226 7.827787 AGGAGACTTTCTATATACTCCCTCAA 58.172 38.462 0.00 0.00 43.12 3.02
5347 7227 7.409408 AGGAGACTTTCTATATACTCCCTCA 57.591 40.000 0.00 0.00 43.12 3.86


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

AutoCloner maintained by Alex Coulton.