Multiple sequence alignment - TraesCS3B01G340200

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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 TraesCS3B01G340200 chr3B 100.000 3514 0 0 1 3514 546184812 546181299 0.000000e+00 6490
1 TraesCS3B01G340200 chr3B 87.065 1438 131 28 4 1404 545815081 545813662 0.000000e+00 1574
2 TraesCS3B01G340200 chr3B 83.308 1312 111 50 1589 2844 545813477 545812218 0.000000e+00 1110
3 TraesCS3B01G340200 chr3B 86.380 558 54 14 1042 1582 545813451 545812899 1.090000e-164 590
4 TraesCS3B01G340200 chr3B 89.720 428 28 6 2962 3377 545811974 545811551 1.860000e-147 532
5 TraesCS3B01G340200 chr3B 87.597 387 33 5 1211 1582 546183035 546182649 5.390000e-118 435
6 TraesCS3B01G340200 chr3B 87.597 387 33 5 1778 2164 546183602 546183231 5.390000e-118 435
7 TraesCS3B01G340200 chr3B 88.293 205 21 1 1778 1982 545813855 545813654 3.500000e-60 243
8 TraesCS3B01G340200 chr3B 93.789 161 9 1 1431 1590 545813669 545813509 1.260000e-59 241
9 TraesCS3B01G340200 chr3B 89.542 153 15 1 2013 2164 545813669 545813517 3.580000e-45 193
10 TraesCS3B01G340200 chr3D 95.502 1934 76 8 1586 3514 419560837 419562764 0.000000e+00 3079
11 TraesCS3B01G340200 chr3D 97.053 509 15 0 1082 1590 419560300 419560808 0.000000e+00 857
12 TraesCS3B01G340200 chr3D 89.033 538 34 7 504 1027 419559752 419560278 0.000000e+00 643
13 TraesCS3B01G340200 chr3D 87.597 387 33 8 1778 2164 419560429 419560800 5.390000e-118 435
14 TraesCS3B01G340200 chr3D 83.061 490 51 19 1124 1582 419560927 419561415 1.950000e-112 416
15 TraesCS3B01G340200 chr3D 80.463 389 57 12 3 379 419520264 419520645 2.670000e-71 279
16 TraesCS3B01G340200 chr3A 89.935 1848 103 24 1589 3377 531667767 531665944 0.000000e+00 2305
17 TraesCS3B01G340200 chr3A 94.607 853 38 5 739 1590 531668644 531667799 0.000000e+00 1314
18 TraesCS3B01G340200 chr3A 82.781 755 86 26 6 735 531669710 531668975 4.950000e-178 634
19 TraesCS3B01G340200 chr3A 88.889 387 28 5 1778 2164 531668178 531667807 2.470000e-126 462
20 TraesCS3B01G340200 chr3A 84.100 478 46 17 1135 1582 531667660 531667183 5.390000e-118 435


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 TraesCS3B01G340200 chr3B 546181299 546184812 3513 True 2453.333333 6490 91.731333 1 3514 3 chr3B.!!$R2 3513
1 TraesCS3B01G340200 chr3B 545811551 545815081 3530 True 640.428571 1574 88.299571 4 3377 7 chr3B.!!$R1 3373
2 TraesCS3B01G340200 chr3D 419559752 419562764 3012 False 1086.000000 3079 90.449200 504 3514 5 chr3D.!!$F2 3010
3 TraesCS3B01G340200 chr3A 531665944 531669710 3766 True 1030.000000 2305 88.062400 6 3377 5 chr3A.!!$R1 3371

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
675 695 0.255604 ATGGATTCATCGCACCCACA 59.744 50.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2643 3102 0.108662 GGGCAAGGCATAACAAGCAC 60.109 55.0 0.0 0.0 0.0 4.4 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
27 28 6.522855 GCACAAAACATTTGTCAAAGTTTTCC 59.477 34.615 22.23 15.29 40.89 3.13
30 31 6.735678 AAACATTTGTCAAAGTTTTCCACC 57.264 33.333 14.74 0.00 30.64 4.61
35 36 7.392953 ACATTTGTCAAAGTTTTCCACCAAAAT 59.607 29.630 4.03 0.00 36.35 1.82
36 37 8.887717 CATTTGTCAAAGTTTTCCACCAAAATA 58.112 29.630 4.03 0.00 36.35 1.40
85 86 8.717821 TCCTATTTGTTCTGATTTTACTGTTCG 58.282 33.333 0.00 0.00 0.00 3.95
86 87 7.962918 CCTATTTGTTCTGATTTTACTGTTCGG 59.037 37.037 0.00 0.00 0.00 4.30
88 89 5.917541 TGTTCTGATTTTACTGTTCGGTC 57.082 39.130 0.00 0.00 0.00 4.79
102 103 0.690192 TCGGTCAGGGAGCATTTGAA 59.310 50.000 0.00 0.00 0.00 2.69
103 104 1.073125 TCGGTCAGGGAGCATTTGAAA 59.927 47.619 0.00 0.00 0.00 2.69
113 114 2.164219 GAGCATTTGAAATCGGGAGCAA 59.836 45.455 1.00 0.00 0.00 3.91
118 119 4.712122 TTTGAAATCGGGAGCAAATACC 57.288 40.909 0.00 0.00 0.00 2.73
119 120 3.358111 TGAAATCGGGAGCAAATACCA 57.642 42.857 0.00 0.00 0.00 3.25
134 139 1.282382 TACCACCCTAAGCCCTCAAC 58.718 55.000 0.00 0.00 0.00 3.18
135 140 0.770557 ACCACCCTAAGCCCTCAACA 60.771 55.000 0.00 0.00 0.00 3.33
170 178 3.426615 TCAACACAACCCTTGTCACTTT 58.573 40.909 0.00 0.00 43.23 2.66
179 187 2.958355 CCCTTGTCACTTTTCCACACAT 59.042 45.455 0.00 0.00 0.00 3.21
181 189 3.374745 CTTGTCACTTTTCCACACATGC 58.625 45.455 0.00 0.00 0.00 4.06
184 192 2.030805 GTCACTTTTCCACACATGCCTC 60.031 50.000 0.00 0.00 0.00 4.70
186 194 2.030540 CACTTTTCCACACATGCCTCAG 60.031 50.000 0.00 0.00 0.00 3.35
190 198 0.986527 TCCACACATGCCTCAGTGAT 59.013 50.000 0.00 0.00 39.03 3.06
195 203 1.471287 CACATGCCTCAGTGATGTTGG 59.529 52.381 0.00 0.00 37.97 3.77
201 209 3.318839 TGCCTCAGTGATGTTGGAAAAAG 59.681 43.478 0.00 0.00 0.00 2.27
202 210 3.319122 GCCTCAGTGATGTTGGAAAAAGT 59.681 43.478 0.00 0.00 0.00 2.66
204 212 5.009610 GCCTCAGTGATGTTGGAAAAAGTAA 59.990 40.000 0.00 0.00 0.00 2.24
207 215 5.827797 TCAGTGATGTTGGAAAAAGTAAGCT 59.172 36.000 0.00 0.00 0.00 3.74
213 221 8.349983 TGATGTTGGAAAAAGTAAGCTAGAAAC 58.650 33.333 0.00 0.00 0.00 2.78
219 227 6.127703 GGAAAAAGTAAGCTAGAAACCCATCC 60.128 42.308 0.00 0.00 0.00 3.51
239 247 1.305201 GGTCCAGACGCTTTTGTCAA 58.695 50.000 0.00 0.00 41.41 3.18
261 269 8.119226 GTCAAGTACATCTAAAATGAGTGCATC 58.881 37.037 0.00 0.00 32.35 3.91
264 273 8.206325 AGTACATCTAAAATGAGTGCATCTTG 57.794 34.615 0.00 0.00 32.35 3.02
273 282 2.027745 TGAGTGCATCTTGACCTCTTCC 60.028 50.000 0.00 0.00 0.00 3.46
343 352 1.344438 TCGTGGTGCACAAGAGAGAAT 59.656 47.619 20.43 0.00 32.51 2.40
344 353 1.462283 CGTGGTGCACAAGAGAGAATG 59.538 52.381 20.43 0.00 33.40 2.67
345 354 1.198637 GTGGTGCACAAGAGAGAATGC 59.801 52.381 20.43 0.00 38.59 3.56
356 365 0.399454 AGAGAATGCCATCCATCCCG 59.601 55.000 0.00 0.00 31.43 5.14
367 376 1.559368 TCCATCCCGAACGTTTCCTA 58.441 50.000 0.46 0.00 0.00 2.94
372 381 3.508744 TCCCGAACGTTTCCTATGTAC 57.491 47.619 0.46 0.00 0.00 2.90
373 382 3.091545 TCCCGAACGTTTCCTATGTACT 58.908 45.455 0.46 0.00 0.00 2.73
439 448 2.186076 GAGCTTCCTCACATTACGACG 58.814 52.381 0.00 0.00 38.03 5.12
444 453 1.138047 CCTCACATTACGACGCGGAC 61.138 60.000 12.47 2.84 0.00 4.79
471 480 6.404293 GCGTTTGAGGCCTTTCAATTCTATTA 60.404 38.462 6.77 0.00 36.97 0.98
472 481 7.682021 GCGTTTGAGGCCTTTCAATTCTATTAT 60.682 37.037 6.77 0.00 36.97 1.28
473 482 8.190784 CGTTTGAGGCCTTTCAATTCTATTATT 58.809 33.333 6.77 0.00 36.97 1.40
538 553 5.809001 AGTGTTGCTATCTCCTTCATGAAA 58.191 37.500 9.88 0.00 0.00 2.69
541 556 5.645067 TGTTGCTATCTCCTTCATGAAACAG 59.355 40.000 9.88 8.14 0.00 3.16
582 602 7.524367 GCTCAAGCATAATATTACAAATGGGCT 60.524 37.037 13.64 6.12 41.59 5.19
585 605 7.838079 AGCATAATATTACAAATGGGCTCAA 57.162 32.000 0.00 0.00 0.00 3.02
619 639 2.695147 CCCAAAACTCCAGCTTGTTTCT 59.305 45.455 8.95 0.42 35.63 2.52
672 692 2.301346 AGAAATGGATTCATCGCACCC 58.699 47.619 0.00 0.00 40.72 4.61
674 694 1.392589 AATGGATTCATCGCACCCAC 58.607 50.000 0.00 0.00 32.24 4.61
675 695 0.255604 ATGGATTCATCGCACCCACA 59.744 50.000 0.00 0.00 0.00 4.17
676 696 0.255604 TGGATTCATCGCACCCACAT 59.744 50.000 0.00 0.00 0.00 3.21
677 697 0.947244 GGATTCATCGCACCCACATC 59.053 55.000 0.00 0.00 0.00 3.06
679 699 1.439353 ATTCATCGCACCCACATCGC 61.439 55.000 0.00 0.00 0.00 4.58
680 700 2.794820 TTCATCGCACCCACATCGCA 62.795 55.000 0.00 0.00 0.00 5.10
683 703 2.874648 ATCGCACCCACATCGCACAT 62.875 55.000 0.00 0.00 0.00 3.21
728 756 0.917333 TCCCCACCTAACCCACATCC 60.917 60.000 0.00 0.00 0.00 3.51
765 1111 2.503356 GAGGAGAAGCAAGAGATGGGAA 59.497 50.000 0.00 0.00 0.00 3.97
792 1144 3.532155 CGCCGGGAGAGAAGGGAG 61.532 72.222 2.18 0.00 0.00 4.30
897 1249 1.596895 GACGGCGGAGAAGGAAGAGT 61.597 60.000 13.24 0.00 0.00 3.24
944 1311 2.612251 GGGGAGGAGGAGGAGGAG 59.388 72.222 0.00 0.00 0.00 3.69
945 1312 2.015726 GGGGAGGAGGAGGAGGAGA 61.016 68.421 0.00 0.00 0.00 3.71
946 1313 1.541672 GGGAGGAGGAGGAGGAGAG 59.458 68.421 0.00 0.00 0.00 3.20
947 1314 1.152546 GGAGGAGGAGGAGGAGAGC 60.153 68.421 0.00 0.00 0.00 4.09
948 1315 1.528309 GAGGAGGAGGAGGAGAGCG 60.528 68.421 0.00 0.00 0.00 5.03
949 1316 3.223589 GGAGGAGGAGGAGAGCGC 61.224 72.222 0.00 0.00 0.00 5.92
950 1317 3.223589 GAGGAGGAGGAGAGCGCC 61.224 72.222 2.29 0.00 0.00 6.53
951 1318 4.067512 AGGAGGAGGAGAGCGCCA 62.068 66.667 2.29 0.00 0.00 5.69
952 1319 3.844090 GGAGGAGGAGAGCGCCAC 61.844 72.222 2.29 0.00 0.00 5.01
1036 1403 1.281925 GCAGGGGAGATGGAAGGGAA 61.282 60.000 0.00 0.00 0.00 3.97
1040 1407 2.047296 AGGGGAGATGGAAGGGAAGTTA 59.953 50.000 0.00 0.00 0.00 2.24
1076 1443 6.425735 TGAAATTGCATTATCTGAGAAGGGA 58.574 36.000 0.00 0.00 0.00 4.20
1078 1445 7.562454 TGAAATTGCATTATCTGAGAAGGGAAT 59.438 33.333 9.97 9.97 31.24 3.01
1080 1447 5.378230 TGCATTATCTGAGAAGGGAATGT 57.622 39.130 0.00 0.00 0.00 2.71
1122 1489 0.179258 GGAGCGACAACGTTTTAGCG 60.179 55.000 12.79 8.70 41.98 4.26
1170 1537 1.617947 GGGAGCGATGGAAGAGGTGT 61.618 60.000 0.00 0.00 0.00 4.16
1332 1699 1.302033 GGCATCATCCAGCTACCCG 60.302 63.158 0.00 0.00 0.00 5.28
1608 2008 2.882137 GACCAGATAGAGGAGGAAGACG 59.118 54.545 0.00 0.00 0.00 4.18
1616 2016 1.115930 AGGAGGAAGACGTGTGCACT 61.116 55.000 19.41 0.00 0.00 4.40
1706 2127 4.162690 CGGCCGGAGAAGAAGGGG 62.163 72.222 20.10 0.00 0.00 4.79
1714 2135 2.193248 GAAGAAGGGGGCGATGGG 59.807 66.667 0.00 0.00 0.00 4.00
1722 2143 3.237741 GGGCGATGGGAGAGGAGG 61.238 72.222 0.00 0.00 0.00 4.30
1761 2182 4.372640 GCGAAAACGACACATTTTTCTTCG 60.373 41.667 0.00 0.00 38.86 3.79
1826 2247 1.671379 GTTCAAGGTGTCGGAGGCC 60.671 63.158 0.00 0.00 0.00 5.19
2109 2530 0.752658 CTACGACCTCATCATGGCCA 59.247 55.000 8.56 8.56 0.00 5.36
2321 2761 5.127194 GGTAACATCTCACTGTATCTGGTGA 59.873 44.000 0.00 0.00 39.71 4.02
2360 2800 7.200434 TCTGCCTCCTTTATCACTAATTTCT 57.800 36.000 0.00 0.00 0.00 2.52
2423 2874 1.057636 TCGTCTTTCGCGTGCTTAAG 58.942 50.000 5.77 0.00 39.67 1.85
2469 2920 6.257849 CGAAGAAGATTGGGATCGAATTTGTA 59.742 38.462 0.00 0.00 37.37 2.41
2511 2963 5.164620 TGCTTCAAGTGGATGAATGAGTA 57.835 39.130 0.00 0.00 38.55 2.59
2627 3086 3.442625 TCTTGATCTGCTTGGCTGAATTG 59.557 43.478 3.49 0.00 39.70 2.32
2635 3094 2.353109 GCTTGGCTGAATTGGGAAGTTC 60.353 50.000 0.00 0.00 0.00 3.01
2647 3106 2.278332 GGAAGTTCCCTCAAAGTGCT 57.722 50.000 11.17 0.00 0.00 4.40
2679 3138 0.248289 CCCATTTTCTTGCAGCTGGG 59.752 55.000 17.12 4.30 37.57 4.45
2684 3143 4.100498 CCATTTTCTTGCAGCTGGGAATAT 59.900 41.667 17.12 0.00 0.00 1.28
2694 3153 4.267536 CAGCTGGGAATATCATACCATGG 58.732 47.826 11.19 11.19 31.62 3.66
2811 3279 7.876582 TGATTAGAGATACCATGAATTGCTCTG 59.123 37.037 0.00 0.00 33.69 3.35
2893 3416 5.808540 CCATGCAATTGGTGAGTTTCTTATG 59.191 40.000 7.72 0.00 31.74 1.90
3068 3709 5.696724 CACCATGTAACGGATAAGGATCTTC 59.303 44.000 0.00 0.00 32.15 2.87
3245 3888 2.739379 TCATTTGCGATGCGTAAACTCA 59.261 40.909 5.30 0.00 43.10 3.41
3290 3933 4.033709 ACTATACAGTCAGGGAACATGCT 58.966 43.478 0.00 0.00 0.00 3.79
3305 3948 4.226427 ACATGCTTCATACTGGTGATGT 57.774 40.909 0.00 0.00 0.00 3.06
3365 4008 3.005791 TCTGTTTCTCGCTCTTGATGTCA 59.994 43.478 0.00 0.00 0.00 3.58
3406 4049 3.585990 AGCGCGCTTTGCTGTGTT 61.586 55.556 31.32 0.91 42.14 3.32
3422 4065 4.261994 GCTGTGTTGTTGGTGTTATTGGAT 60.262 41.667 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.838665 ACTTTGACAAATGTTTTGTGCG 57.161 36.364 10.13 0.00 31.96 5.34
2 3 6.522855 GGAAAACTTTGACAAATGTTTTGTGC 59.477 34.615 27.28 19.30 45.91 4.57
10 11 6.734104 TTTGGTGGAAAACTTTGACAAATG 57.266 33.333 0.05 0.00 0.00 2.32
60 61 7.962918 CCGAACAGTAAAATCAGAACAAATAGG 59.037 37.037 0.00 0.00 0.00 2.57
70 71 3.684788 CCCTGACCGAACAGTAAAATCAG 59.315 47.826 7.73 0.00 36.30 2.90
85 86 2.098117 CGATTTCAAATGCTCCCTGACC 59.902 50.000 0.00 0.00 0.00 4.02
86 87 2.098117 CCGATTTCAAATGCTCCCTGAC 59.902 50.000 0.00 0.00 0.00 3.51
88 89 1.406539 CCCGATTTCAAATGCTCCCTG 59.593 52.381 0.00 0.00 0.00 4.45
102 103 1.409661 GGGTGGTATTTGCTCCCGATT 60.410 52.381 0.00 0.00 0.00 3.34
103 104 0.182775 GGGTGGTATTTGCTCCCGAT 59.817 55.000 0.00 0.00 0.00 4.18
113 114 2.241430 GTTGAGGGCTTAGGGTGGTATT 59.759 50.000 0.00 0.00 0.00 1.89
118 119 0.322546 GGTGTTGAGGGCTTAGGGTG 60.323 60.000 0.00 0.00 0.00 4.61
119 120 0.770557 TGGTGTTGAGGGCTTAGGGT 60.771 55.000 0.00 0.00 0.00 4.34
134 139 8.716909 GGGTTGTGTTGAATATTTTAAATGGTG 58.283 33.333 0.00 0.00 0.00 4.17
135 140 8.655901 AGGGTTGTGTTGAATATTTTAAATGGT 58.344 29.630 0.00 0.00 0.00 3.55
170 178 0.764271 TCACTGAGGCATGTGTGGAA 59.236 50.000 0.00 0.00 35.82 3.53
179 187 2.655090 TTTCCAACATCACTGAGGCA 57.345 45.000 0.00 0.00 0.00 4.75
181 189 6.633500 TTACTTTTTCCAACATCACTGAGG 57.367 37.500 0.00 0.00 0.00 3.86
184 192 6.076981 AGCTTACTTTTTCCAACATCACTG 57.923 37.500 0.00 0.00 0.00 3.66
186 194 7.435068 TCTAGCTTACTTTTTCCAACATCAC 57.565 36.000 0.00 0.00 0.00 3.06
190 198 6.040054 GGGTTTCTAGCTTACTTTTTCCAACA 59.960 38.462 0.00 0.00 0.00 3.33
195 203 6.403309 CGGATGGGTTTCTAGCTTACTTTTTC 60.403 42.308 0.00 0.00 0.00 2.29
201 209 2.835027 CCGGATGGGTTTCTAGCTTAC 58.165 52.381 0.00 0.00 0.00 2.34
213 221 4.530857 GCGTCTGGACCGGATGGG 62.531 72.222 21.75 9.14 40.75 4.00
219 227 0.878523 TGACAAAAGCGTCTGGACCG 60.879 55.000 0.00 0.00 36.82 4.79
227 235 6.854496 TTTAGATGTACTTGACAAAAGCGT 57.146 33.333 0.00 0.00 42.78 5.07
228 236 8.015087 TCATTTTAGATGTACTTGACAAAAGCG 58.985 33.333 0.00 0.00 42.78 4.68
239 247 8.043113 TCAAGATGCACTCATTTTAGATGTACT 58.957 33.333 0.00 0.00 31.96 2.73
261 269 5.050490 CCATATACAACGGAAGAGGTCAAG 58.950 45.833 0.00 0.00 0.00 3.02
264 273 4.796618 GCTCCATATACAACGGAAGAGGTC 60.797 50.000 0.00 0.00 0.00 3.85
273 282 2.502213 TGGACGCTCCATATACAACG 57.498 50.000 3.02 0.00 42.67 4.10
312 321 1.331138 TGCACCACGAAAACTAAACGG 59.669 47.619 0.00 0.00 0.00 4.44
315 324 3.690139 TCTTGTGCACCACGAAAACTAAA 59.310 39.130 15.69 0.00 37.14 1.85
343 352 2.189257 CGTTCGGGATGGATGGCA 59.811 61.111 0.00 0.00 0.00 4.92
344 353 1.029947 AAACGTTCGGGATGGATGGC 61.030 55.000 0.00 0.00 0.00 4.40
345 354 1.014352 GAAACGTTCGGGATGGATGG 58.986 55.000 0.00 0.00 0.00 3.51
356 365 9.230932 GAACTATACAGTACATAGGAAACGTTC 57.769 37.037 0.00 0.00 33.48 3.95
390 399 6.374333 AGTTGCACAATCATACGGTAGAATTT 59.626 34.615 0.00 0.00 0.00 1.82
397 406 2.778299 ACAGTTGCACAATCATACGGT 58.222 42.857 0.00 0.00 0.00 4.83
401 410 4.074259 AGCTCAACAGTTGCACAATCATA 58.926 39.130 8.58 0.00 0.00 2.15
471 480 6.260936 CCACACGCAGAAGGAAGAATAATAAT 59.739 38.462 0.00 0.00 0.00 1.28
472 481 5.584649 CCACACGCAGAAGGAAGAATAATAA 59.415 40.000 0.00 0.00 0.00 1.40
473 482 5.116180 CCACACGCAGAAGGAAGAATAATA 58.884 41.667 0.00 0.00 0.00 0.98
474 483 3.941483 CCACACGCAGAAGGAAGAATAAT 59.059 43.478 0.00 0.00 0.00 1.28
475 484 3.334691 CCACACGCAGAAGGAAGAATAA 58.665 45.455 0.00 0.00 0.00 1.40
476 485 2.935238 GCCACACGCAGAAGGAAGAATA 60.935 50.000 0.00 0.00 37.47 1.75
477 486 1.813513 CCACACGCAGAAGGAAGAAT 58.186 50.000 0.00 0.00 0.00 2.40
520 529 4.194640 GCTGTTTCATGAAGGAGATAGCA 58.805 43.478 17.00 0.98 36.54 3.49
582 602 5.951747 AGTTTTGGGCTGCTAGATTTATTGA 59.048 36.000 0.00 0.00 0.00 2.57
585 605 4.889995 GGAGTTTTGGGCTGCTAGATTTAT 59.110 41.667 0.00 0.00 0.00 1.40
619 639 1.980052 CCTACTTCTGGGCCGAACA 59.020 57.895 0.00 0.00 0.00 3.18
679 699 3.490759 GGCCGAGTGTGCGATGTG 61.491 66.667 0.00 0.00 0.00 3.21
680 700 2.803155 AATGGCCGAGTGTGCGATGT 62.803 55.000 0.00 0.00 0.00 3.06
683 703 2.031919 AAATGGCCGAGTGTGCGA 59.968 55.556 0.00 0.00 0.00 5.10
948 1315 4.404654 CTTTTGCTCCGCCGTGGC 62.405 66.667 0.00 0.00 37.80 5.01
949 1316 3.737172 CCTTTTGCTCCGCCGTGG 61.737 66.667 0.00 0.00 40.09 4.94
950 1317 3.737172 CCCTTTTGCTCCGCCGTG 61.737 66.667 0.00 0.00 0.00 4.94
951 1318 1.906105 TATCCCTTTTGCTCCGCCGT 61.906 55.000 0.00 0.00 0.00 5.68
952 1319 0.746563 TTATCCCTTTTGCTCCGCCG 60.747 55.000 0.00 0.00 0.00 6.46
994 1361 1.075659 GCCTTCTTCTTGTGCCCCT 59.924 57.895 0.00 0.00 0.00 4.79
1036 1403 6.265196 TGCAATTTCAGAGAACCATGTTAACT 59.735 34.615 7.22 0.00 0.00 2.24
1040 1407 5.733620 ATGCAATTTCAGAGAACCATGTT 57.266 34.783 0.00 0.00 0.00 2.71
1076 1443 4.514577 CTCTCCGCCGCCGACATT 62.515 66.667 0.00 0.00 36.29 2.71
1122 1489 2.322830 GCCGTTGTCCCTTCGTTCC 61.323 63.158 0.00 0.00 0.00 3.62
1608 2008 0.947244 CCAGAGAACCAAGTGCACAC 59.053 55.000 21.04 3.05 0.00 3.82
1706 2127 3.934962 GCCTCCTCTCCCATCGCC 61.935 72.222 0.00 0.00 0.00 5.54
1714 2135 3.535962 CCTGCTCCGCCTCCTCTC 61.536 72.222 0.00 0.00 0.00 3.20
1761 2182 1.329913 ATGATTTTTCCGCTGGCCCC 61.330 55.000 0.00 0.00 0.00 5.80
2009 2430 0.907486 ATGCCTCAGAGTTGCAGCTA 59.093 50.000 1.86 0.00 38.58 3.32
2021 2442 3.785859 GCCTCACCGGATGCCTCA 61.786 66.667 9.46 0.00 33.16 3.86
2109 2530 2.224867 CCTTGATGTGGAGGAAGTTGGT 60.225 50.000 0.00 0.00 34.91 3.67
2321 2761 2.706190 AGGCAGAACAGAACCACTAAGT 59.294 45.455 0.00 0.00 0.00 2.24
2386 2837 5.855045 AGACGAATCAAGTTGACCTTACTT 58.145 37.500 7.96 0.00 36.31 2.24
2423 2874 5.460646 TCGACAGAATGAAATGAAAAAGGC 58.539 37.500 0.00 0.00 39.69 4.35
2469 2920 5.544650 AGCATGCAGTTCAAAGCTTTAAAT 58.455 33.333 21.98 3.71 36.96 1.40
2511 2963 7.004086 TGAGAAATGTCAGGTAATTCAGGTTT 58.996 34.615 0.00 0.00 0.00 3.27
2635 3094 2.094545 GGCATAACAAGCACTTTGAGGG 60.095 50.000 0.00 0.00 39.21 4.30
2643 3102 0.108662 GGGCAAGGCATAACAAGCAC 60.109 55.000 0.00 0.00 0.00 4.40
2647 3106 3.582208 AGAAAATGGGCAAGGCATAACAA 59.418 39.130 0.00 0.00 0.00 2.83
2679 3138 6.000219 ACTGAGCAACCATGGTATGATATTC 59.000 40.000 20.12 9.73 37.41 1.75
2684 3143 2.840038 AGACTGAGCAACCATGGTATGA 59.160 45.455 20.12 0.37 37.41 2.15
2694 3153 1.530293 CAACTGCAGAGACTGAGCAAC 59.470 52.381 23.35 0.00 37.89 4.17
2743 3202 1.938016 GCCATTCACTGCAAGCCTTTG 60.938 52.381 0.00 0.00 37.60 2.77
2811 3279 4.965119 AAGAAAAGTCCAACACAGACAC 57.035 40.909 0.00 0.00 36.68 3.67
3178 3821 4.586001 AGAAGATGCAAGCTCAAAGGAAAA 59.414 37.500 0.00 0.00 0.00 2.29
3290 3933 7.616542 TGGTAGTACTAACATCACCAGTATGAA 59.383 37.037 16.81 0.00 39.69 2.57
3305 3948 9.275572 ACCAGGAAGAAATAATGGTAGTACTAA 57.724 33.333 3.61 0.00 42.37 2.24
3457 4100 7.276438 GGCTTTTCCAAAACTAATGCATCTAAG 59.724 37.037 0.00 0.53 34.01 2.18


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

AutoCloner maintained by Alex Coulton.