Multiple sequence alignment - TraesCS3D01G011300

Loading Multiple Alignment...

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 TraesCS3D01G011300 chr3D 100.000 5102 0 0 1 5102 4076626 4071525 0.000000e+00 9422
1 TraesCS3D01G011300 chr3D 86.486 2146 203 35 1 2075 4168598 4170727 0.000000e+00 2276
2 TraesCS3D01G011300 chr3D 91.580 1544 90 19 2821 4357 4171282 4172792 0.000000e+00 2095
3 TraesCS3D01G011300 chr3D 93.697 238 11 4 2146 2382 4170726 4170960 2.260000e-93 353
4 TraesCS3D01G011300 chrUn 91.189 2372 143 21 2757 5102 246337679 246335348 0.000000e+00 3162
5 TraesCS3D01G011300 chrUn 89.495 1228 79 25 911 2092 246339296 246338073 0.000000e+00 1507
6 TraesCS3D01G011300 chrUn 93.989 915 33 2 1 915 246340247 246339355 0.000000e+00 1365
7 TraesCS3D01G011300 chrUn 79.423 1074 204 17 3010 4075 214316711 214317775 0.000000e+00 743
8 TraesCS3D01G011300 chrUn 93.227 251 15 2 1637 1886 469290953 469290704 8.070000e-98 368
9 TraesCS3D01G011300 chrUn 96.241 133 4 1 2251 2382 246337909 246337777 3.090000e-52 217
10 TraesCS3D01G011300 chrUn 93.651 126 8 0 2092 2217 246338038 246337913 6.740000e-44 189
11 TraesCS3D01G011300 chr3B 91.189 2372 143 21 2757 5102 6391779 6389448 0.000000e+00 3162
12 TraesCS3D01G011300 chr3B 89.495 1228 79 25 911 2092 6393396 6392173 0.000000e+00 1507
13 TraesCS3D01G011300 chr3B 89.111 1203 74 26 2241 3438 13940280 13941430 0.000000e+00 1443
14 TraesCS3D01G011300 chr3B 93.989 915 33 2 1 915 6394347 6393455 0.000000e+00 1365
15 TraesCS3D01G011300 chr3B 88.444 900 76 8 3440 4320 13947142 13948032 0.000000e+00 1061
16 TraesCS3D01G011300 chr3B 86.092 568 43 21 1554 2092 13939561 13940121 3.420000e-161 579
17 TraesCS3D01G011300 chr3B 81.733 531 87 5 1 522 6667141 6667670 7.850000e-118 435
18 TraesCS3D01G011300 chr3B 87.607 234 29 0 447 680 13939283 13939516 6.510000e-69 272
19 TraesCS3D01G011300 chr3B 96.241 133 4 1 2251 2382 6392009 6391877 3.090000e-52 217
20 TraesCS3D01G011300 chr3B 93.651 126 8 0 2092 2217 6392138 6392013 6.740000e-44 189
21 TraesCS3D01G011300 chr3B 93.443 122 7 1 2097 2217 13940162 13940283 4.060000e-41 180
22 TraesCS3D01G011300 chr6A 91.935 1711 113 15 2656 4357 609884965 609883271 0.000000e+00 2372
23 TraesCS3D01G011300 chr6A 88.854 960 86 14 961 1902 609886566 609885610 0.000000e+00 1160
24 TraesCS3D01G011300 chr6A 91.576 368 17 7 2241 2607 609885329 609884975 3.550000e-136 496
25 TraesCS3D01G011300 chr6A 93.050 259 18 0 1959 2217 609885584 609885326 3.730000e-101 379
26 TraesCS3D01G011300 chr3A 86.809 2115 184 42 1 2040 9613913 9611819 0.000000e+00 2272
27 TraesCS3D01G011300 chr3A 93.763 1459 78 7 2821 4272 9611809 9610357 0.000000e+00 2178
28 TraesCS3D01G011300 chr3A 91.596 1523 96 13 2821 4327 9781793 9783299 0.000000e+00 2074
29 TraesCS3D01G011300 chr3A 90.999 911 53 12 1154 2040 9780878 9781783 0.000000e+00 1201
30 TraesCS3D01G011300 chr3A 86.218 907 112 9 1 903 9779361 9780258 0.000000e+00 970
31 TraesCS3D01G011300 chr3A 87.629 776 27 16 4337 5102 9610340 9609624 0.000000e+00 837
32 TraesCS3D01G011300 chr3A 85.512 283 18 13 4611 4877 9783574 9783849 1.810000e-69 274


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 TraesCS3D01G011300 chr3D 4071525 4076626 5101 True 9422.000000 9422 100.000000 1 5102 1 chr3D.!!$R1 5101
1 TraesCS3D01G011300 chr3D 4168598 4172792 4194 False 1574.666667 2276 90.587667 1 4357 3 chr3D.!!$F1 4356
2 TraesCS3D01G011300 chrUn 246335348 246340247 4899 True 1288.000000 3162 92.913000 1 5102 5 chrUn.!!$R2 5101
3 TraesCS3D01G011300 chrUn 214316711 214317775 1064 False 743.000000 743 79.423000 3010 4075 1 chrUn.!!$F1 1065
4 TraesCS3D01G011300 chr3B 6389448 6394347 4899 True 1288.000000 3162 92.913000 1 5102 5 chr3B.!!$R1 5101
5 TraesCS3D01G011300 chr3B 13947142 13948032 890 False 1061.000000 1061 88.444000 3440 4320 1 chr3B.!!$F2 880
6 TraesCS3D01G011300 chr3B 13939283 13941430 2147 False 618.500000 1443 89.063250 447 3438 4 chr3B.!!$F3 2991
7 TraesCS3D01G011300 chr3B 6667141 6667670 529 False 435.000000 435 81.733000 1 522 1 chr3B.!!$F1 521
8 TraesCS3D01G011300 chr6A 609883271 609886566 3295 True 1101.750000 2372 91.353750 961 4357 4 chr6A.!!$R1 3396
9 TraesCS3D01G011300 chr3A 9609624 9613913 4289 True 1762.333333 2272 89.400333 1 5102 3 chr3A.!!$R1 5101
10 TraesCS3D01G011300 chr3A 9779361 9783849 4488 False 1129.750000 2074 88.581250 1 4877 4 chr3A.!!$F1 4876

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
821 830 0.035056 ATAGTCAAGCCTGGTGTGCC 60.035 55.0 0.0 0.0 0.00 5.01 F
1489 1978 0.178967 TGTTGGCCCAATCTCTTGCA 60.179 50.0 0.0 0.0 0.00 4.08 F
3273 4008 0.034089 AGCTGGCAAATGGAGTACCC 60.034 55.0 0.0 0.0 34.81 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2682 3249 0.038890 TTCAATTCATGCGGGTGGGA 59.961 50.0 0.00 0.0 0.00 4.37 R
3330 4065 0.035820 TCCTACCAATGGTCGCAACC 60.036 55.0 8.82 0.0 46.66 3.77 R
4269 5026 0.112995 ACCACCACATTGCAGACCAT 59.887 50.0 0.00 0.0 0.00 3.55 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
105 109 1.134401 AGTCATGGGCAAGTATCCACG 60.134 52.381 0.00 0.00 35.67 4.94
120 124 0.518636 CCACGTGAAGGCTCAACATG 59.481 55.000 19.30 0.00 31.88 3.21
495 504 2.670148 AACCAGGCGGATCACCTCC 61.670 63.158 3.60 0.00 41.06 4.30
513 522 3.610911 CTCCTAAACGGAAAGGATGCTT 58.389 45.455 0.00 0.00 42.53 3.91
529 538 3.708403 TGCTTGATGTCTTGGAGATGT 57.292 42.857 0.00 0.00 0.00 3.06
591 600 1.644509 TCTGCTCCAGTCTTGGCTAA 58.355 50.000 0.00 0.00 44.63 3.09
624 633 6.875972 AAGTGTGGAGGAGATTACTAATGT 57.124 37.500 0.00 0.00 0.00 2.71
738 747 6.852858 AAGAAGAAGGCTAATTATCGAAGC 57.147 37.500 0.00 0.00 35.47 3.86
760 769 3.618594 CCTGGTCTTGAATGACATACGTG 59.381 47.826 0.00 0.00 38.61 4.49
814 823 4.751767 AGAGGAAGAATAGTCAAGCCTG 57.248 45.455 3.70 0.00 0.00 4.85
815 824 3.454082 AGAGGAAGAATAGTCAAGCCTGG 59.546 47.826 3.70 0.00 0.00 4.45
816 825 3.185455 AGGAAGAATAGTCAAGCCTGGT 58.815 45.455 0.00 0.00 0.00 4.00
817 826 3.054802 AGGAAGAATAGTCAAGCCTGGTG 60.055 47.826 0.00 0.00 0.00 4.17
818 827 3.307762 GGAAGAATAGTCAAGCCTGGTGT 60.308 47.826 0.00 0.00 0.00 4.16
819 828 3.340814 AGAATAGTCAAGCCTGGTGTG 57.659 47.619 0.00 0.00 0.00 3.82
820 829 1.740025 GAATAGTCAAGCCTGGTGTGC 59.260 52.381 0.00 0.00 0.00 4.57
821 830 0.035056 ATAGTCAAGCCTGGTGTGCC 60.035 55.000 0.00 0.00 0.00 5.01
822 831 1.414866 TAGTCAAGCCTGGTGTGCCA 61.415 55.000 0.00 0.00 43.73 4.92
823 832 2.203337 TCAAGCCTGGTGTGCCAC 60.203 61.111 0.00 0.00 40.46 5.01
894 915 2.887152 GACTTGTCAAAGGCAACATCCT 59.113 45.455 0.00 0.00 41.57 3.24
982 1084 4.819088 GGCTTCATCTCATTTCCTCCTTAC 59.181 45.833 0.00 0.00 0.00 2.34
990 1092 6.653989 TCTCATTTCCTCCTTACCTTCATTC 58.346 40.000 0.00 0.00 0.00 2.67
1070 1179 0.675633 ATCAACAGGGCAACAGCAAC 59.324 50.000 0.00 0.00 39.74 4.17
1074 1183 0.890996 ACAGGGCAACAGCAACTAGC 60.891 55.000 0.00 0.00 46.19 3.42
1086 1195 2.633488 GCAACTAGCGAGGGAGATTTT 58.367 47.619 0.00 0.00 0.00 1.82
1279 1768 3.932710 TGCAATCGACTACAGATTTGGTC 59.067 43.478 0.00 0.00 36.30 4.02
1323 1812 0.846693 AATCATGGACTAGGTGCCCC 59.153 55.000 0.00 0.00 0.00 5.80
1360 1849 5.023533 TGCCACCAATCTATCAACTAGTC 57.976 43.478 0.00 0.00 0.00 2.59
1381 1870 9.557061 CTAGTCTATACATACCTGACAGTTACA 57.443 37.037 0.93 0.00 0.00 2.41
1426 1915 4.489810 ACGCTGTTCAAGAGAGTTGATAG 58.510 43.478 0.00 0.00 0.00 2.08
1448 1937 1.276622 ACAGAGAAGGCCGGTACAAT 58.723 50.000 1.90 0.00 0.00 2.71
1489 1978 0.178967 TGTTGGCCCAATCTCTTGCA 60.179 50.000 0.00 0.00 0.00 4.08
1582 2071 4.533222 CACAGTGGTTTCAAACGGTATTC 58.467 43.478 0.00 0.00 0.00 1.75
1583 2072 4.035792 CACAGTGGTTTCAAACGGTATTCA 59.964 41.667 0.00 0.00 0.00 2.57
1613 2102 5.582269 CGCGGGATTATGATATCAAATCTGT 59.418 40.000 24.22 9.00 31.66 3.41
1615 2104 7.361201 CGCGGGATTATGATATCAAATCTGTTT 60.361 37.037 24.22 7.93 31.66 2.83
1616 2105 7.752239 GCGGGATTATGATATCAAATCTGTTTG 59.248 37.037 24.22 16.52 44.81 2.93
1637 2126 3.078837 GGTTATTCACCGAAAGAGCCAA 58.921 45.455 0.00 0.00 35.12 4.52
1641 2130 2.631160 TCACCGAAAGAGCCAAAAGA 57.369 45.000 0.00 0.00 0.00 2.52
1677 2166 2.135933 GAGACAACCTTGACTTGGTCG 58.864 52.381 0.00 0.00 36.69 4.79
1693 2182 2.905085 TGGTCGGTTCCTAACATAACCA 59.095 45.455 5.21 6.24 44.49 3.67
1703 2192 7.255660 GGTTCCTAACATAACCAACATTTGTCA 60.256 37.037 0.00 0.00 43.84 3.58
1714 2203 3.111853 ACATTTGTCAAGACTGCGAGA 57.888 42.857 1.53 0.00 0.00 4.04
1779 2268 2.113860 TCTGCAAGCACCAAGGTATC 57.886 50.000 0.00 0.00 0.00 2.24
1803 2292 8.644318 TCGTTTCTAGTAATTCTTAAGCATCC 57.356 34.615 0.00 0.00 0.00 3.51
1822 2311 6.837568 AGCATCCAAGGATTTGTTCTGAATAT 59.162 34.615 0.00 0.00 31.62 1.28
1831 2321 6.291955 GGATTTGTTCTGAATATTTGCATGCG 60.292 38.462 14.09 0.00 0.00 4.73
1937 2441 7.614192 TGTCTCTGTTTACCACATATCTGAGTA 59.386 37.037 0.00 0.00 33.76 2.59
2062 2584 4.457834 AACAGCGACTATGTTTAGCTCT 57.542 40.909 0.00 0.00 37.61 4.09
2063 2585 3.775202 ACAGCGACTATGTTTAGCTCTG 58.225 45.455 0.00 0.00 35.82 3.35
2220 2779 2.113860 GCTGACAAGCCAATGAGGTA 57.886 50.000 0.00 0.00 44.22 3.08
2221 2780 2.012673 GCTGACAAGCCAATGAGGTAG 58.987 52.381 0.00 0.00 44.22 3.18
2423 2983 4.245660 CATGCTCTTCAGTAGTTCGGAAA 58.754 43.478 0.00 0.00 30.69 3.13
2424 2984 4.330944 TGCTCTTCAGTAGTTCGGAAAA 57.669 40.909 0.00 0.00 30.69 2.29
2455 3021 9.773328 ATGTCAATACGATAATTGTGTTCTTTG 57.227 29.630 0.00 0.00 37.94 2.77
2469 3035 5.009210 TGTGTTCTTTGGTAAACCTACATGC 59.991 40.000 0.02 0.00 36.82 4.06
2547 3113 7.062749 AGTCGGATTTATGGTGCTTATCTTA 57.937 36.000 0.00 0.00 0.00 2.10
2607 3173 7.567458 AGAATTGTAGCAATGCCCAATTTAAT 58.433 30.769 24.49 15.65 39.20 1.40
2609 3175 8.578448 AATTGTAGCAATGCCCAATTTAATTT 57.422 26.923 20.63 5.94 37.33 1.82
2611 3177 7.992754 TGTAGCAATGCCCAATTTAATTTTT 57.007 28.000 0.00 0.00 0.00 1.94
2682 3249 5.118990 GTCATGTGGACACTGCTATAATGT 58.881 41.667 3.91 0.00 46.19 2.71
2690 3257 1.416401 ACTGCTATAATGTCCCACCCG 59.584 52.381 0.00 0.00 0.00 5.28
2724 3291 8.084073 TGAATCTCTTTTCAATTCCATCAACAC 58.916 33.333 0.00 0.00 32.82 3.32
2756 3324 5.106317 ACATGAGTTGGTGCCTTATTTAACG 60.106 40.000 0.00 0.00 0.00 3.18
2815 3388 8.315220 AGAAATTGAAATTGCCTGGATTCTAT 57.685 30.769 0.00 0.00 0.00 1.98
2846 3577 7.832503 ATTTTCCAAGCAAAATCTAAATCGG 57.167 32.000 0.00 0.00 31.53 4.18
2968 3702 4.820284 AAGACGAAAGGAAAGAAAGCAG 57.180 40.909 0.00 0.00 0.00 4.24
2974 3708 5.157067 CGAAAGGAAAGAAAGCAGGATTTC 58.843 41.667 1.96 1.96 39.09 2.17
3048 3782 3.066291 TCATCGGTAGCCACATTTGTT 57.934 42.857 0.00 0.00 0.00 2.83
3182 3917 2.800544 CAACAAGGTACACGTTCTCTGG 59.199 50.000 0.00 0.00 0.00 3.86
3273 4008 0.034089 AGCTGGCAAATGGAGTACCC 60.034 55.000 0.00 0.00 34.81 3.69
3330 4065 3.201290 CGGGGAAGAGTTCATGAATGAG 58.799 50.000 12.12 0.00 38.19 2.90
3414 4149 1.398390 GGAACAAGGCGTGCTCTTATG 59.602 52.381 0.00 0.00 0.00 1.90
3681 4416 1.270826 AGGGATCATAGCATCGTCACG 59.729 52.381 0.00 0.00 0.00 4.35
3704 4439 0.601311 ACTGCAGCGAGAGGAACAAC 60.601 55.000 15.27 0.00 0.00 3.32
3753 4488 4.714802 TCTCGGAACTTTGGGAGAATATCA 59.285 41.667 0.00 0.00 32.92 2.15
4101 4836 0.033601 ACCCCATGCCGCAAATCTAA 60.034 50.000 0.00 0.00 0.00 2.10
4159 4894 7.556275 TCTTTTGGACACTGAGACTTAATTTGT 59.444 33.333 0.00 0.00 0.00 2.83
4251 5008 0.647410 CGGCATCTCGTCATGTGAAC 59.353 55.000 0.00 0.00 0.00 3.18
4265 5022 3.503827 TGTGAACTATCGCAATCGTCT 57.496 42.857 0.00 0.00 42.85 4.18
4266 5023 3.179048 TGTGAACTATCGCAATCGTCTG 58.821 45.455 0.00 0.00 42.85 3.51
4267 5024 2.034507 GTGAACTATCGCAATCGTCTGC 60.035 50.000 1.99 1.99 39.04 4.26
4268 5025 2.193447 GAACTATCGCAATCGTCTGCA 58.807 47.619 11.11 0.00 42.77 4.41
4269 5026 2.293677 ACTATCGCAATCGTCTGCAA 57.706 45.000 11.11 0.00 42.77 4.08
4270 5027 2.826428 ACTATCGCAATCGTCTGCAAT 58.174 42.857 11.11 2.08 42.77 3.56
4271 5028 2.541346 ACTATCGCAATCGTCTGCAATG 59.459 45.455 11.11 2.38 42.77 2.82
4357 5118 3.380954 TGTGTTTCAGAAATTGCTGCTCA 59.619 39.130 8.76 4.96 35.86 4.26
4400 5165 5.103000 GCTACTGTCACCATGTAGTGTAAG 58.897 45.833 2.58 4.44 38.91 2.34
4401 5166 5.336531 GCTACTGTCACCATGTAGTGTAAGT 60.337 44.000 12.87 12.87 38.91 2.24
4402 5167 6.127814 GCTACTGTCACCATGTAGTGTAAGTA 60.128 42.308 13.41 13.41 38.91 2.24
4403 5168 6.022163 ACTGTCACCATGTAGTGTAAGTAC 57.978 41.667 9.13 0.00 43.11 2.73
4405 5170 4.082625 TGTCACCATGTAGTGTAAGTACGG 60.083 45.833 2.58 0.00 45.77 4.02
4411 5184 1.550072 GTAGTGTAAGTACGGGGGCAA 59.450 52.381 0.00 0.00 32.31 4.52
4444 5220 0.740737 ACAACAGACTGCAAACTGGC 59.259 50.000 19.28 0.00 38.30 4.85
4471 5247 4.216411 AGCCATGGTAAATAGTTGTCGT 57.784 40.909 14.67 0.00 0.00 4.34
4554 5349 1.672881 GTACCAGCAGCAATCCATGTC 59.327 52.381 0.00 0.00 0.00 3.06
4592 5387 2.185387 TCCTACTCAGGCCAAGGTAAC 58.815 52.381 5.01 0.00 42.30 2.50
4631 5443 3.734463 TGGTAATGCACACGAGAGAAAA 58.266 40.909 0.00 0.00 0.00 2.29
4897 5725 2.988684 TGTGAAATGTGGGGCGGC 60.989 61.111 0.00 0.00 0.00 6.53
4898 5726 3.758931 GTGAAATGTGGGGCGGCC 61.759 66.667 22.00 22.00 0.00 6.13
4938 5766 2.034812 GTGTAGATCCAAGTAGGCCTCG 59.965 54.545 9.68 0.00 37.29 4.63
5089 5920 6.735510 CACGTCGTACATATAGTATACAGTGC 59.264 42.308 5.50 5.46 34.67 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 97 0.727398 GCCTTCACGTGGATACTTGC 59.273 55.000 17.00 5.61 37.61 4.01
105 109 4.083271 GGTCTAAACATGTTGAGCCTTCAC 60.083 45.833 17.14 9.97 31.71 3.18
120 124 5.180680 ACCGTGCTTTCTTATTGGTCTAAAC 59.819 40.000 0.00 0.00 0.00 2.01
495 504 4.396166 ACATCAAGCATCCTTTCCGTTTAG 59.604 41.667 0.00 0.00 0.00 1.85
496 505 4.331968 ACATCAAGCATCCTTTCCGTTTA 58.668 39.130 0.00 0.00 0.00 2.01
529 538 1.201429 GCCCCTCTTTCTCCTGTGGA 61.201 60.000 0.00 0.00 0.00 4.02
561 570 3.951037 GACTGGAGCAGAAGATACTCTCA 59.049 47.826 0.00 0.00 35.18 3.27
562 571 4.207165 AGACTGGAGCAGAAGATACTCTC 58.793 47.826 0.00 0.00 35.18 3.20
591 600 4.164221 TCTCCTCCACACTTTCAGTTCTTT 59.836 41.667 0.00 0.00 0.00 2.52
617 626 8.044908 ACGTTCCATTATACTCCAAACATTAGT 58.955 33.333 0.00 0.00 0.00 2.24
624 633 5.423704 TCCACGTTCCATTATACTCCAAA 57.576 39.130 0.00 0.00 0.00 3.28
636 645 0.309302 CGTTGCATTTCCACGTTCCA 59.691 50.000 0.00 0.00 0.00 3.53
637 646 0.386731 CCGTTGCATTTCCACGTTCC 60.387 55.000 7.07 0.00 0.00 3.62
702 711 4.425520 CCTTCTTCTTAACTCTAGCACCG 58.574 47.826 0.00 0.00 0.00 4.94
738 747 3.618594 CACGTATGTCATTCAAGACCAGG 59.381 47.826 0.00 0.00 37.73 4.45
760 769 4.009675 TCAGTCCATATGCACCAGAAAAC 58.990 43.478 0.00 0.00 0.00 2.43
816 825 4.084265 CAGCAATCAGGTGGCACA 57.916 55.556 20.82 0.00 41.98 4.57
821 830 4.520492 ACTAAGAAAACCAGCAATCAGGTG 59.480 41.667 0.00 0.00 45.23 4.00
822 831 4.729868 ACTAAGAAAACCAGCAATCAGGT 58.270 39.130 0.00 0.00 40.61 4.00
823 832 4.761739 TGACTAAGAAAACCAGCAATCAGG 59.238 41.667 0.00 0.00 0.00 3.86
824 833 5.947228 TGACTAAGAAAACCAGCAATCAG 57.053 39.130 0.00 0.00 0.00 2.90
825 834 6.321181 AGTTTGACTAAGAAAACCAGCAATCA 59.679 34.615 0.00 0.00 37.04 2.57
894 915 5.104485 GGCTACCTTTCTTCCTTATCTTCCA 60.104 44.000 0.00 0.00 0.00 3.53
953 1037 3.379688 GGAAATGAGATGAAGCCACCTTC 59.620 47.826 0.00 0.00 46.15 3.46
955 1039 2.579860 AGGAAATGAGATGAAGCCACCT 59.420 45.455 0.00 0.00 0.00 4.00
956 1040 2.948315 GAGGAAATGAGATGAAGCCACC 59.052 50.000 0.00 0.00 0.00 4.61
957 1041 2.948315 GGAGGAAATGAGATGAAGCCAC 59.052 50.000 0.00 0.00 0.00 5.01
958 1042 2.848694 AGGAGGAAATGAGATGAAGCCA 59.151 45.455 0.00 0.00 0.00 4.75
959 1043 3.574354 AGGAGGAAATGAGATGAAGCC 57.426 47.619 0.00 0.00 0.00 4.35
982 1084 7.428020 TCAAACATTTCTGTGAAGAATGAAGG 58.572 34.615 2.66 0.00 35.22 3.46
990 1092 6.019318 CCAAAGCTTCAAACATTTCTGTGAAG 60.019 38.462 0.00 7.69 37.96 3.02
1086 1195 3.096092 GGATGGTGGGCAGTTATTGAAA 58.904 45.455 0.00 0.00 0.00 2.69
1090 1199 1.063717 CCTGGATGGTGGGCAGTTATT 60.064 52.381 0.00 0.00 0.00 1.40
1115 1233 0.456221 GATCTCTGTTCCGCCTTCGA 59.544 55.000 0.00 0.00 38.10 3.71
1279 1768 0.467384 AGCGGGATGACATTCAGGAG 59.533 55.000 0.00 0.00 0.00 3.69
1381 1870 0.779997 AGGATTGCAGTTTCACCCCT 59.220 50.000 0.00 0.00 0.00 4.79
1426 1915 1.019805 GTACCGGCCTTCTCTGTTGC 61.020 60.000 0.00 0.00 0.00 4.17
1448 1937 1.000739 CTGTCCCCCGTACCTGGTA 59.999 63.158 1.49 1.49 0.00 3.25
1457 1946 1.029947 GCCAACAATACTGTCCCCCG 61.030 60.000 0.00 0.00 33.45 5.73
1489 1978 1.610522 GAACTGGCTTGTGTTGCTCAT 59.389 47.619 0.00 0.00 0.00 2.90
1582 2071 1.010125 CATAATCCCGCGGCGTTTG 60.010 57.895 22.85 5.67 0.00 2.93
1583 2072 0.534203 ATCATAATCCCGCGGCGTTT 60.534 50.000 22.85 16.19 0.00 3.60
1616 2105 2.706890 TGGCTCTTTCGGTGAATAACC 58.293 47.619 0.00 0.00 46.60 2.85
1637 2126 4.828939 TCTCACCAAATGCAATGACTCTTT 59.171 37.500 4.54 0.00 0.00 2.52
1641 2130 3.489355 TGTCTCACCAAATGCAATGACT 58.511 40.909 4.54 0.00 0.00 3.41
1677 2166 6.988522 ACAAATGTTGGTTATGTTAGGAACC 58.011 36.000 0.00 0.00 44.60 3.62
1693 2182 3.466836 TCTCGCAGTCTTGACAAATGTT 58.533 40.909 3.49 0.00 0.00 2.71
1703 2192 1.226746 CCCGTTTTTCTCGCAGTCTT 58.773 50.000 0.00 0.00 0.00 3.01
1769 2258 8.075761 AGAATTACTAGAAACGATACCTTGGT 57.924 34.615 0.00 0.00 0.00 3.67
1779 2268 8.420374 TGGATGCTTAAGAATTACTAGAAACG 57.580 34.615 6.67 0.00 0.00 3.60
1803 2292 8.600625 CATGCAAATATTCAGAACAAATCCTTG 58.399 33.333 0.00 0.00 38.61 3.61
1822 2311 8.551205 TGTCAAAAATAATTTAACGCATGCAAA 58.449 25.926 19.57 11.27 0.00 3.68
1956 2460 9.715119 ATCTTGTATATGCTATCTGTATGGGTA 57.285 33.333 0.00 0.00 0.00 3.69
2047 2569 9.155975 TCAGAAATTTCAGAGCTAAACATAGTC 57.844 33.333 19.99 0.00 0.00 2.59
2062 2584 5.774690 ACCAGCCTGTTTATCAGAAATTTCA 59.225 36.000 19.99 0.68 46.27 2.69
2063 2585 6.272822 ACCAGCCTGTTTATCAGAAATTTC 57.727 37.500 10.33 10.33 46.27 2.17
2188 2747 5.496133 GCTTGTCAGCATAATCATGAAGT 57.504 39.130 0.00 0.00 46.49 3.01
2203 2762 4.019411 TGAATCTACCTCATTGGCTTGTCA 60.019 41.667 0.00 0.00 40.22 3.58
2337 2897 9.551734 CATATATCTGAACTTTCTTGGACATCA 57.448 33.333 0.00 0.00 0.00 3.07
2338 2898 8.502387 GCATATATCTGAACTTTCTTGGACATC 58.498 37.037 0.00 0.00 0.00 3.06
2339 2899 7.994911 TGCATATATCTGAACTTTCTTGGACAT 59.005 33.333 0.00 0.00 0.00 3.06
2340 2900 7.337938 TGCATATATCTGAACTTTCTTGGACA 58.662 34.615 0.00 0.00 0.00 4.02
2341 2901 7.792374 TGCATATATCTGAACTTTCTTGGAC 57.208 36.000 0.00 0.00 0.00 4.02
2342 2902 8.806429 TTTGCATATATCTGAACTTTCTTGGA 57.194 30.769 0.00 0.00 0.00 3.53
2391 2951 3.199508 ACTGAAGAGCATGCTAGGTTCAT 59.800 43.478 27.28 18.96 0.00 2.57
2455 3021 0.377203 GCAGCGCATGTAGGTTTACC 59.623 55.000 11.47 0.00 0.00 2.85
2469 3035 7.383572 ACAGATATATTTGAACTAAGAGCAGCG 59.616 37.037 10.08 0.00 0.00 5.18
2547 3113 9.569122 TGAGAAAACCTAACAGCTTAAGTTAAT 57.431 29.630 4.02 0.00 31.66 1.40
2565 3131 9.226345 CTACAATTCTTGAACAAGTGAGAAAAC 57.774 33.333 13.15 0.00 39.38 2.43
2643 3210 7.551262 GTCCACATGACAGTATGGTAATTTGTA 59.449 37.037 0.00 0.00 43.85 2.41
2682 3249 0.038890 TTCAATTCATGCGGGTGGGA 59.961 50.000 0.00 0.00 0.00 4.37
2724 3291 3.366679 GGCACCAACTCATGTCAATTCTG 60.367 47.826 0.00 0.00 0.00 3.02
2732 3299 5.106317 CGTTAAATAAGGCACCAACTCATGT 60.106 40.000 0.00 0.00 0.00 3.21
2788 3361 7.101700 AGAATCCAGGCAATTTCAATTTCTTC 58.898 34.615 0.00 0.00 0.00 2.87
2830 3561 8.293699 AGGAAATAACCGATTTAGATTTTGCT 57.706 30.769 0.00 0.00 37.90 3.91
2846 3577 5.447279 CGTGAACCTGCATGTAGGAAATAAC 60.447 44.000 33.50 20.07 40.42 1.89
2951 3685 4.773323 AATCCTGCTTTCTTTCCTTTCG 57.227 40.909 0.00 0.00 0.00 3.46
3048 3782 1.581934 CTGCCGTCAACAAGAGAACA 58.418 50.000 0.00 0.00 0.00 3.18
3174 3909 7.797038 TGTTACCTTTTTAACTCCAGAGAAC 57.203 36.000 0.70 0.00 33.73 3.01
3182 3917 8.553696 TGAATCGTCTTGTTACCTTTTTAACTC 58.446 33.333 0.00 0.00 33.73 3.01
3273 4008 0.729116 CCAGCATCTTTACTGCCACG 59.271 55.000 0.00 0.00 40.56 4.94
3330 4065 0.035820 TCCTACCAATGGTCGCAACC 60.036 55.000 8.82 0.00 46.66 3.77
3414 4149 5.700832 TGATCCGTTAGGCATGAATTCATAC 59.299 40.000 20.32 14.89 37.47 2.39
3704 4439 1.302383 TTCTGGCGCAATGTAACCCG 61.302 55.000 10.83 0.00 0.00 5.28
3753 4488 6.963083 AAGCTATAGACATCGGACTTACTT 57.037 37.500 3.21 0.00 0.00 2.24
4101 4836 4.024556 CAGAGTCGCAGTGAAACAAATCTT 60.025 41.667 0.00 0.00 41.43 2.40
4251 5008 2.096565 CCATTGCAGACGATTGCGATAG 60.097 50.000 15.01 7.44 44.45 2.08
4266 5023 0.604578 ACCACATTGCAGACCATTGC 59.395 50.000 0.00 0.00 44.33 3.56
4267 5024 1.067425 CCACCACATTGCAGACCATTG 60.067 52.381 0.00 0.00 0.00 2.82
4268 5025 1.259609 CCACCACATTGCAGACCATT 58.740 50.000 0.00 0.00 0.00 3.16
4269 5026 0.112995 ACCACCACATTGCAGACCAT 59.887 50.000 0.00 0.00 0.00 3.55
4270 5027 0.537143 GACCACCACATTGCAGACCA 60.537 55.000 0.00 0.00 0.00 4.02
4271 5028 1.577328 CGACCACCACATTGCAGACC 61.577 60.000 0.00 0.00 0.00 3.85
4400 5165 1.153229 GGATGTCTTGCCCCCGTAC 60.153 63.158 0.00 0.00 0.00 3.67
4401 5166 2.727392 CGGATGTCTTGCCCCCGTA 61.727 63.158 0.00 0.00 35.83 4.02
4402 5167 4.096003 CGGATGTCTTGCCCCCGT 62.096 66.667 0.00 0.00 35.83 5.28
4403 5168 2.608970 AATCGGATGTCTTGCCCCCG 62.609 60.000 0.00 0.00 41.36 5.73
4405 5170 0.819666 GGAATCGGATGTCTTGCCCC 60.820 60.000 0.00 0.00 0.00 5.80
4411 5184 2.567169 TCTGTTGTGGAATCGGATGTCT 59.433 45.455 0.00 0.00 0.00 3.41
4444 5220 5.353123 ACAACTATTTACCATGGCTTGTACG 59.647 40.000 13.04 0.00 0.00 3.67
4471 5247 3.368248 ACTCCGGCTAGTACATGGTAAA 58.632 45.455 0.00 0.00 0.00 2.01
4554 5349 1.373570 GATTCCTTCCGAGCACTTGG 58.626 55.000 0.00 0.00 35.37 3.61
4592 5387 2.427453 ACCATCTCGTGTGCCTACTTAG 59.573 50.000 0.00 0.00 0.00 2.18
4631 5443 0.547954 GGTGAACCTCCTCCTTCCCT 60.548 60.000 0.00 0.00 0.00 4.20
4904 5732 2.681064 TACACCCGTCCCCTTCCG 60.681 66.667 0.00 0.00 0.00 4.30
4905 5733 0.690077 ATCTACACCCGTCCCCTTCC 60.690 60.000 0.00 0.00 0.00 3.46
4906 5734 0.751452 GATCTACACCCGTCCCCTTC 59.249 60.000 0.00 0.00 0.00 3.46
5048 5879 6.586868 ACGACGTGTACAAAAACATTAGAA 57.413 33.333 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.