Multiple sequence alignment - TraesCS2D01G332100

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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 TraesCS2D01G332100 chr2D 100.000 9653 0 0 1 9653 424861482 424851830 0.000000e+00 17826.0
1 TraesCS2D01G332100 chr2D 89.030 1103 68 32 8571 9653 587252559 587251490 0.000000e+00 1317.0
2 TraesCS2D01G332100 chr2D 90.885 384 20 8 7772 8143 433874745 433875125 1.450000e-137 501.0
3 TraesCS2D01G332100 chr2D 100.000 31 0 0 8173 8203 433875123 433875153 3.770000e-04 58.4
4 TraesCS2D01G332100 chr2B 97.101 8002 172 32 587 8570 500196536 500188577 0.000000e+00 13437.0
5 TraesCS2D01G332100 chr2B 90.957 376 20 6 7772 8135 512924047 512924420 2.420000e-135 494.0
6 TraesCS2D01G332100 chr2B 94.444 36 2 0 599 634 484420029 484419994 1.000000e-03 56.5
7 TraesCS2D01G332100 chr2B 100.000 30 0 0 8174 8203 512924429 512924458 1.000000e-03 56.5
8 TraesCS2D01G332100 chr2A 97.863 7253 113 16 1344 8570 563765562 563772798 0.000000e+00 12497.0
9 TraesCS2D01G332100 chr2A 90.400 750 51 8 8924 9653 695480730 695481478 0.000000e+00 966.0
10 TraesCS2D01G332100 chr2A 93.681 633 18 6 576 1195 563764525 563765148 0.000000e+00 928.0
11 TraesCS2D01G332100 chr2A 90.862 383 22 6 7772 8143 553267846 553267466 1.450000e-137 501.0
12 TraesCS2D01G332100 chr7D 92.748 1117 52 15 8565 9653 6371355 6372470 0.000000e+00 1587.0
13 TraesCS2D01G332100 chr7D 87.887 1098 40 22 8634 9653 28797928 28796846 0.000000e+00 1205.0
14 TraesCS2D01G332100 chr7D 91.058 917 40 16 8777 9653 563502655 563501741 0.000000e+00 1201.0
15 TraesCS2D01G332100 chr7D 96.747 584 17 2 1 582 407297995 407298578 0.000000e+00 972.0
16 TraesCS2D01G332100 chr7D 89.068 311 22 7 8571 8881 563502891 563502593 9.150000e-100 375.0
17 TraesCS2D01G332100 chr6B 90.571 1103 68 14 8571 9653 675448641 675447555 0.000000e+00 1428.0
18 TraesCS2D01G332100 chr4A 90.080 1119 72 19 8571 9653 200186899 200185784 0.000000e+00 1415.0
19 TraesCS2D01G332100 chr4A 87.155 1160 69 29 8571 9650 702132060 702133219 0.000000e+00 1243.0
20 TraesCS2D01G332100 chr5D 89.755 1103 81 18 8570 9653 411846850 411847939 0.000000e+00 1382.0
21 TraesCS2D01G332100 chr5D 88.958 1132 67 23 8571 9653 11211384 11212506 0.000000e+00 1345.0
22 TraesCS2D01G332100 chr5D 96.747 584 17 2 1 582 259749275 259748692 0.000000e+00 972.0
23 TraesCS2D01G332100 chr5D 96.575 584 18 2 1 582 56369176 56368593 0.000000e+00 966.0
24 TraesCS2D01G332100 chr5D 96.575 584 18 2 1 582 130387924 130388507 0.000000e+00 966.0
25 TraesCS2D01G332100 chr6D 89.157 1162 46 28 8571 9653 308898665 308897505 0.000000e+00 1375.0
26 TraesCS2D01G332100 chr6D 89.746 1102 66 22 8571 9653 421682882 421683955 0.000000e+00 1365.0
27 TraesCS2D01G332100 chr7B 86.842 1102 65 46 8571 9653 6166819 6165779 0.000000e+00 1158.0
28 TraesCS2D01G332100 chr1D 89.245 874 51 11 8823 9653 22873520 22874393 0.000000e+00 1053.0
29 TraesCS2D01G332100 chr1D 96.575 584 18 2 1 582 215939704 215940287 0.000000e+00 966.0
30 TraesCS2D01G332100 chr3D 92.552 725 33 5 8949 9653 564940389 564941112 0.000000e+00 1020.0
31 TraesCS2D01G332100 chr3D 96.747 584 17 2 1 582 282385574 282386157 0.000000e+00 972.0
32 TraesCS2D01G332100 chr3D 96.747 584 16 3 1 582 284701623 284701041 0.000000e+00 970.0
33 TraesCS2D01G332100 chr3D 92.251 271 17 2 8571 8838 32190575 32190306 1.970000e-101 381.0
34 TraesCS2D01G332100 chr3D 92.952 227 16 0 8571 8797 568225452 568225678 2.010000e-86 331.0
35 TraesCS2D01G332100 chr3D 92.511 227 17 0 8571 8797 596081244 596081470 9.350000e-85 326.0
36 TraesCS2D01G332100 chr3A 87.007 939 67 25 8571 9465 649573793 649574720 0.000000e+00 1007.0
37 TraesCS2D01G332100 chr3A 86.678 593 54 15 8571 9144 468000142 467999556 1.370000e-177 634.0
38 TraesCS2D01G332100 chr4D 96.747 584 17 2 1 582 90257177 90256594 0.000000e+00 972.0
39 TraesCS2D01G332100 chr4D 96.575 584 18 2 1 582 302450084 302450667 0.000000e+00 966.0
40 TraesCS2D01G332100 chr5B 88.038 744 74 10 8922 9652 662868842 662868101 0.000000e+00 867.0


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 TraesCS2D01G332100 chr2D 424851830 424861482 9652 True 17826.0 17826 100.000 1 9653 1 chr2D.!!$R1 9652
1 TraesCS2D01G332100 chr2D 587251490 587252559 1069 True 1317.0 1317 89.030 8571 9653 1 chr2D.!!$R2 1082
2 TraesCS2D01G332100 chr2B 500188577 500196536 7959 True 13437.0 13437 97.101 587 8570 1 chr2B.!!$R2 7983
3 TraesCS2D01G332100 chr2A 563764525 563772798 8273 False 6712.5 12497 95.772 576 8570 2 chr2A.!!$F2 7994
4 TraesCS2D01G332100 chr2A 695480730 695481478 748 False 966.0 966 90.400 8924 9653 1 chr2A.!!$F1 729
5 TraesCS2D01G332100 chr7D 6371355 6372470 1115 False 1587.0 1587 92.748 8565 9653 1 chr7D.!!$F1 1088
6 TraesCS2D01G332100 chr7D 28796846 28797928 1082 True 1205.0 1205 87.887 8634 9653 1 chr7D.!!$R1 1019
7 TraesCS2D01G332100 chr7D 407297995 407298578 583 False 972.0 972 96.747 1 582 1 chr7D.!!$F2 581
8 TraesCS2D01G332100 chr7D 563501741 563502891 1150 True 788.0 1201 90.063 8571 9653 2 chr7D.!!$R2 1082
9 TraesCS2D01G332100 chr6B 675447555 675448641 1086 True 1428.0 1428 90.571 8571 9653 1 chr6B.!!$R1 1082
10 TraesCS2D01G332100 chr4A 200185784 200186899 1115 True 1415.0 1415 90.080 8571 9653 1 chr4A.!!$R1 1082
11 TraesCS2D01G332100 chr4A 702132060 702133219 1159 False 1243.0 1243 87.155 8571 9650 1 chr4A.!!$F1 1079
12 TraesCS2D01G332100 chr5D 411846850 411847939 1089 False 1382.0 1382 89.755 8570 9653 1 chr5D.!!$F3 1083
13 TraesCS2D01G332100 chr5D 11211384 11212506 1122 False 1345.0 1345 88.958 8571 9653 1 chr5D.!!$F1 1082
14 TraesCS2D01G332100 chr5D 259748692 259749275 583 True 972.0 972 96.747 1 582 1 chr5D.!!$R2 581
15 TraesCS2D01G332100 chr5D 56368593 56369176 583 True 966.0 966 96.575 1 582 1 chr5D.!!$R1 581
16 TraesCS2D01G332100 chr5D 130387924 130388507 583 False 966.0 966 96.575 1 582 1 chr5D.!!$F2 581
17 TraesCS2D01G332100 chr6D 308897505 308898665 1160 True 1375.0 1375 89.157 8571 9653 1 chr6D.!!$R1 1082
18 TraesCS2D01G332100 chr6D 421682882 421683955 1073 False 1365.0 1365 89.746 8571 9653 1 chr6D.!!$F1 1082
19 TraesCS2D01G332100 chr7B 6165779 6166819 1040 True 1158.0 1158 86.842 8571 9653 1 chr7B.!!$R1 1082
20 TraesCS2D01G332100 chr1D 22873520 22874393 873 False 1053.0 1053 89.245 8823 9653 1 chr1D.!!$F1 830
21 TraesCS2D01G332100 chr1D 215939704 215940287 583 False 966.0 966 96.575 1 582 1 chr1D.!!$F2 581
22 TraesCS2D01G332100 chr3D 564940389 564941112 723 False 1020.0 1020 92.552 8949 9653 1 chr3D.!!$F2 704
23 TraesCS2D01G332100 chr3D 282385574 282386157 583 False 972.0 972 96.747 1 582 1 chr3D.!!$F1 581
24 TraesCS2D01G332100 chr3D 284701041 284701623 582 True 970.0 970 96.747 1 582 1 chr3D.!!$R2 581
25 TraesCS2D01G332100 chr3A 649573793 649574720 927 False 1007.0 1007 87.007 8571 9465 1 chr3A.!!$F1 894
26 TraesCS2D01G332100 chr3A 467999556 468000142 586 True 634.0 634 86.678 8571 9144 1 chr3A.!!$R1 573
27 TraesCS2D01G332100 chr4D 90256594 90257177 583 True 972.0 972 96.747 1 582 1 chr4D.!!$R1 581
28 TraesCS2D01G332100 chr4D 302450084 302450667 583 False 966.0 966 96.575 1 582 1 chr4D.!!$F1 581
29 TraesCS2D01G332100 chr5B 662868101 662868842 741 True 867.0 867 88.038 8922 9652 1 chr5B.!!$R1 730

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
728 732 0.321298 GCCCAGTCAAAGTTAGCGGA 60.321 55.000 0.00 0.00 0.00 5.54 F
1206 1223 1.165270 GCTGTGATTTGTTAGCCCGT 58.835 50.000 0.00 0.00 0.00 5.28 F
1922 2208 0.685097 TTGTCTTCCACCCCTCTTCG 59.315 55.000 0.00 0.00 0.00 3.79 F
2379 2671 1.000843 GGTTTAGCAGCTTGGGGTTTG 59.999 52.381 0.00 0.00 0.00 2.93 F
3512 3807 1.264045 GGCTCTTCTGTCAGGCTCCT 61.264 60.000 0.00 0.00 32.47 3.69 F
4679 4983 1.656441 CCAGCTGTGAACAAGGTGC 59.344 57.895 13.81 0.00 0.00 5.01 F
4807 5111 1.819632 CAAGCCTATCGGTGCACCC 60.820 63.158 29.95 14.67 0.00 4.61 F
6340 6648 3.181485 CCTCGGTCTCCAGAAATACTCAC 60.181 52.174 0.00 0.00 0.00 3.51 F
6832 7140 1.338579 CCTCCAGCAAGAGAAGGTGAC 60.339 57.143 4.67 0.00 36.64 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1922 2208 0.396556 GAGTGGAGAGGGGGAGAGAC 60.397 65.000 0.00 0.00 0.00 3.36 R
2355 2647 2.024414 CCCCAAGCTGCTAAACCATAC 58.976 52.381 0.90 0.00 0.00 2.39 R
3892 4196 1.334869 CGCTTCAAGCAAAGTTCCAGT 59.665 47.619 10.73 0.00 42.58 4.00 R
4256 4560 1.079750 GTCGAGCAACCTCTGTCCC 60.080 63.158 0.00 0.00 35.90 4.46 R
4807 5111 1.479323 CCATCATTGCCCAAGACCAAG 59.521 52.381 0.00 0.00 0.00 3.61 R
6340 6648 1.159713 TTGCACTGCAACAGTCCTCG 61.160 55.000 12.59 0.00 43.43 4.63 R
6832 7140 3.077359 CAACTTCTCCTTAGCCAACTGG 58.923 50.000 0.00 0.00 38.53 4.00 R
7364 7672 1.115326 GGAGGCCCAACAAAGTTGCT 61.115 55.000 0.00 0.00 0.00 3.91 R
8838 9187 0.836606 ATGGATCCCACGTATGTGCA 59.163 50.000 9.90 2.36 45.04 4.57 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
29 30 2.816087 GCAGAAAGAAATCAGCTGGTGA 59.184 45.455 15.13 12.41 40.38 4.02
30 31 3.254166 GCAGAAAGAAATCAGCTGGTGAA 59.746 43.478 15.13 0.00 39.19 3.18
189 190 0.478072 TGGTGCAGACATTTGGAGGT 59.522 50.000 0.00 0.00 0.00 3.85
191 192 2.107378 TGGTGCAGACATTTGGAGGTAA 59.893 45.455 0.00 0.00 0.00 2.85
272 274 7.732222 ATGGGTTAAATCCATTGAAGCTAAA 57.268 32.000 5.93 0.00 41.87 1.85
300 303 2.664402 AATGTTTCTGGGTCAGCAGT 57.336 45.000 0.00 0.00 0.00 4.40
301 304 1.901591 ATGTTTCTGGGTCAGCAGTG 58.098 50.000 0.00 0.00 0.00 3.66
429 432 5.682234 TCCTCTCTTGTTTCAGCATCATA 57.318 39.130 0.00 0.00 0.00 2.15
467 470 7.173047 GCAATCTTGGTGTAATTGGAAAATGTT 59.827 33.333 0.00 0.00 32.31 2.71
582 586 5.391950 CCTTCCGGAACAGAACACAATTATG 60.392 44.000 14.35 0.00 0.00 1.90
583 587 4.647611 TCCGGAACAGAACACAATTATGT 58.352 39.130 0.00 0.00 41.61 2.29
584 588 5.067273 TCCGGAACAGAACACAATTATGTT 58.933 37.500 0.00 0.73 45.52 2.71
585 589 6.231951 TCCGGAACAGAACACAATTATGTTA 58.768 36.000 0.00 0.00 42.89 2.41
604 608 2.779755 ATTCGCCAACAGACCACATA 57.220 45.000 0.00 0.00 0.00 2.29
615 619 2.113807 AGACCACATATCAGCTCTGCA 58.886 47.619 0.00 0.00 0.00 4.41
631 635 1.131693 CTGCATTGCGACATGTGTCAT 59.868 47.619 1.15 0.00 44.99 3.06
640 644 3.728864 GCGACATGTGTCATCATTCAACC 60.729 47.826 1.15 0.00 44.99 3.77
674 678 5.075858 CCAATTAAACAGTGGCATGTGAT 57.924 39.130 6.80 1.80 32.72 3.06
677 681 6.350027 CCAATTAAACAGTGGCATGTGATACA 60.350 38.462 6.80 0.00 32.72 2.29
681 685 2.294979 CAGTGGCATGTGATACAGCAT 58.705 47.619 0.00 0.00 0.00 3.79
728 732 0.321298 GCCCAGTCAAAGTTAGCGGA 60.321 55.000 0.00 0.00 0.00 5.54
1196 1213 6.479884 ACTTTCCTCTATCTTGCTGTGATTT 58.520 36.000 0.00 0.00 0.00 2.17
1204 1221 2.819608 TCTTGCTGTGATTTGTTAGCCC 59.180 45.455 0.00 0.00 35.36 5.19
1206 1223 1.165270 GCTGTGATTTGTTAGCCCGT 58.835 50.000 0.00 0.00 0.00 5.28
1474 1757 1.810151 GCCTTTCGTAGATTTGGTGCA 59.190 47.619 0.00 0.00 35.04 4.57
1632 1916 4.487714 TTCTCACCACATATGTTCCCTC 57.512 45.455 5.37 0.00 0.00 4.30
1669 1953 3.625853 CCTCCTCCCTTTCTCCATTTTC 58.374 50.000 0.00 0.00 0.00 2.29
1753 2038 5.239525 GCAACTGTTCATCTCTTGTTACCTT 59.760 40.000 0.00 0.00 0.00 3.50
1894 2180 4.558080 GTGGTTTCGTCTTCGACTAATCTC 59.442 45.833 0.00 0.00 46.03 2.75
1922 2208 0.685097 TTGTCTTCCACCCCTCTTCG 59.315 55.000 0.00 0.00 0.00 3.79
2202 2494 2.516888 CCCAGTCTGTGGTTCGGGT 61.517 63.158 0.00 0.00 46.37 5.28
2379 2671 1.000843 GGTTTAGCAGCTTGGGGTTTG 59.999 52.381 0.00 0.00 0.00 2.93
2757 3051 5.734720 ACATAGTCCAGTTGACCATTACTG 58.265 41.667 0.00 0.00 45.68 2.74
2861 3155 3.760151 GGTAAAAGCAAGAACCGGGTTAT 59.240 43.478 13.38 6.85 0.00 1.89
3170 3464 3.370840 TCTTATGGCCATTTGCTCACT 57.629 42.857 26.37 0.00 40.92 3.41
3353 3647 2.029518 CCTCGCATGCGGCTATGA 59.970 61.111 37.18 17.88 41.67 2.15
3400 3694 1.898574 CAAAGGAACACAGCCGGCT 60.899 57.895 27.08 27.08 0.00 5.52
3512 3807 1.264045 GGCTCTTCTGTCAGGCTCCT 61.264 60.000 0.00 0.00 32.47 3.69
3892 4196 2.429930 CCTTTCCACCCGCAGTCA 59.570 61.111 0.00 0.00 0.00 3.41
4256 4560 1.732917 TGCACCAAAGCAAGTTCGG 59.267 52.632 0.00 0.00 42.46 4.30
4679 4983 1.656441 CCAGCTGTGAACAAGGTGC 59.344 57.895 13.81 0.00 0.00 5.01
4807 5111 1.819632 CAAGCCTATCGGTGCACCC 60.820 63.158 29.95 14.67 0.00 4.61
5288 5592 7.880195 CCATGTTGGTTGGTGGAATTTTTATTA 59.120 33.333 0.00 0.00 33.53 0.98
5289 5593 9.447157 CATGTTGGTTGGTGGAATTTTTATTAT 57.553 29.630 0.00 0.00 0.00 1.28
5652 5957 6.460676 GGCTTTGATGATCCTCAAATTACAGG 60.461 42.308 21.65 12.68 42.54 4.00
5731 6036 8.301252 TGGAAGTCAATGAAAATGATGATCAT 57.699 30.769 8.25 8.25 39.09 2.45
6216 6524 4.142609 TCTCTTATGGAACTGACATGCC 57.857 45.455 0.00 0.00 0.00 4.40
6340 6648 3.181485 CCTCGGTCTCCAGAAATACTCAC 60.181 52.174 0.00 0.00 0.00 3.51
6832 7140 1.338579 CCTCCAGCAAGAGAAGGTGAC 60.339 57.143 4.67 0.00 36.64 3.67
7132 7440 2.034939 CAGACCAGCATTGCAAACTCAA 59.965 45.455 11.91 0.00 0.00 3.02
7306 7614 5.571784 ACCAACATAGTCATTCTGCATTG 57.428 39.130 0.00 0.00 0.00 2.82
7364 7672 3.646162 TCCTCTTCCAAGTGTTCAAGCTA 59.354 43.478 0.00 0.00 0.00 3.32
7663 7971 3.744940 AGGGAGAATTTTGCTGGATCA 57.255 42.857 0.00 0.00 0.00 2.92
7741 8049 1.381928 TACATCTCACCCCGTCTCGC 61.382 60.000 0.00 0.00 0.00 5.03
8203 8513 5.236263 TGCAGTATATGTTGCCAAGATAACG 59.764 40.000 0.00 0.00 39.54 3.18
8212 8522 5.703592 TGTTGCCAAGATAACGTAATGAACT 59.296 36.000 0.00 0.00 0.00 3.01
8213 8523 6.874664 TGTTGCCAAGATAACGTAATGAACTA 59.125 34.615 0.00 0.00 0.00 2.24
8214 8524 7.064134 TGTTGCCAAGATAACGTAATGAACTAG 59.936 37.037 0.00 0.00 0.00 2.57
8405 8716 4.024048 CGACCATTGTTGCTAACTGAAACT 60.024 41.667 0.00 0.00 35.23 2.66
8406 8717 5.505654 CGACCATTGTTGCTAACTGAAACTT 60.506 40.000 0.00 0.00 35.23 2.66
8407 8718 6.220726 ACCATTGTTGCTAACTGAAACTTT 57.779 33.333 0.00 0.00 35.23 2.66
8706 9018 6.063496 ACCCTAAACCTACCTCTTCAATTC 57.937 41.667 0.00 0.00 0.00 2.17
8772 9084 2.258591 CGATCCCATCTACCGCGG 59.741 66.667 26.86 26.86 0.00 6.46
8848 9292 0.465705 AGCTAGCCATGCACATACGT 59.534 50.000 12.13 0.00 0.00 3.57
8849 9293 0.583438 GCTAGCCATGCACATACGTG 59.417 55.000 2.29 0.00 46.56 4.49
8861 9305 3.743521 CACATACGTGGGATCCATCAAT 58.256 45.455 15.23 0.00 39.64 2.57
8904 9348 3.186047 GCCGCGCGAACACTACAT 61.186 61.111 34.63 0.00 0.00 2.29
9110 9595 1.971167 GGCCGCCACAACTTCATGA 60.971 57.895 3.91 0.00 0.00 3.07
9249 9751 4.441792 CGTATCATCATTGGTGGACTCAA 58.558 43.478 0.00 0.00 0.00 3.02
9280 9782 4.502106 AGGGCCTCCTTCTTACCC 57.498 61.111 0.00 0.00 41.56 3.69
9532 10035 3.433314 GCTCATTGATCACATCCTCACCT 60.433 47.826 0.00 0.00 0.00 4.00
9533 10036 4.378774 CTCATTGATCACATCCTCACCTC 58.621 47.826 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 5.622180 TCACTCGAGACCTATATAGCAGTT 58.378 41.667 21.68 0.00 0.00 3.16
30 31 5.012251 TCTCACTCGAGACCTATATAGCAGT 59.988 44.000 21.68 0.00 43.55 4.40
189 190 6.653320 CAGTGCTTGTTATCCCTTACAACTTA 59.347 38.462 0.00 0.00 31.46 2.24
191 192 5.003804 CAGTGCTTGTTATCCCTTACAACT 58.996 41.667 0.00 0.00 31.46 3.16
272 274 4.104102 TGACCCAGAAACATTAGACTTGGT 59.896 41.667 0.00 0.00 32.41 3.67
300 303 7.063308 GCTTCAATCAGAAACACAAAAAGTTCA 59.937 33.333 0.00 0.00 35.40 3.18
301 304 7.276438 AGCTTCAATCAGAAACACAAAAAGTTC 59.724 33.333 0.00 0.00 35.40 3.01
429 432 3.706086 ACCAAGATTGCAGAGGTTGTTTT 59.294 39.130 0.00 0.00 0.00 2.43
582 586 2.147958 TGTGGTCTGTTGGCGAATAAC 58.852 47.619 0.00 0.00 0.00 1.89
583 587 2.552599 TGTGGTCTGTTGGCGAATAA 57.447 45.000 0.00 0.00 0.00 1.40
584 588 2.779755 ATGTGGTCTGTTGGCGAATA 57.220 45.000 0.00 0.00 0.00 1.75
585 589 2.779755 TATGTGGTCTGTTGGCGAAT 57.220 45.000 0.00 0.00 0.00 3.34
604 608 0.392060 TGTCGCAATGCAGAGCTGAT 60.392 50.000 5.91 0.00 0.00 2.90
631 635 2.521996 CGTGTATCGTCGGTTGAATGA 58.478 47.619 0.00 0.00 34.52 2.57
674 678 3.688694 AAGAACCACGGTTATGCTGTA 57.311 42.857 0.34 0.00 38.60 2.74
677 681 4.281898 AGTAAAGAACCACGGTTATGCT 57.718 40.909 0.34 0.00 38.60 3.79
681 685 7.416817 GCTTTTTAAGTAAAGAACCACGGTTA 58.583 34.615 0.34 0.00 38.60 2.85
728 732 1.711375 TCCAGAGAGATATAGGCCGGT 59.289 52.381 1.90 0.00 0.00 5.28
816 822 1.278637 GAAACACCAACCACTCGCG 59.721 57.895 0.00 0.00 0.00 5.87
1196 1213 3.695830 ATCTCAAGAAACGGGCTAACA 57.304 42.857 0.00 0.00 0.00 2.41
1204 1221 2.996621 AGCGGAGAAATCTCAAGAAACG 59.003 45.455 12.21 6.48 44.60 3.60
1206 1223 3.753272 CCAAGCGGAGAAATCTCAAGAAA 59.247 43.478 12.21 0.00 44.60 2.52
1265 1282 1.338655 GAAAGAGGGGAGCTAGCGTAG 59.661 57.143 9.55 0.00 0.00 3.51
1314 1331 3.031964 GATCCACGCACAGCACAGC 62.032 63.158 0.00 0.00 0.00 4.40
1316 1333 1.374631 GAGATCCACGCACAGCACA 60.375 57.895 0.00 0.00 0.00 4.57
1632 1916 1.483827 GGAGGGAGGGGTAGTTTAACG 59.516 57.143 0.00 0.00 0.00 3.18
1669 1953 8.292444 TGTTGATGGGGAAATAAATAGACAAG 57.708 34.615 0.00 0.00 0.00 3.16
1684 1968 1.818674 GGTACTGCTTTGTTGATGGGG 59.181 52.381 0.00 0.00 0.00 4.96
1753 2038 5.116084 AGGATTTGCAGAAAGGCAGTATA 57.884 39.130 0.00 0.00 45.88 1.47
1894 2180 3.557264 GGGGTGGAAGACAAGTTACTCTG 60.557 52.174 0.00 0.00 0.00 3.35
1922 2208 0.396556 GAGTGGAGAGGGGGAGAGAC 60.397 65.000 0.00 0.00 0.00 3.36
2011 2297 4.671831 ACCCATGTTATTTCATGTCCACA 58.328 39.130 0.00 0.00 42.29 4.17
2314 2606 8.001292 CCAATAATCAGAAAGGTCCCTCTTATT 58.999 37.037 4.31 4.31 0.00 1.40
2355 2647 2.024414 CCCCAAGCTGCTAAACCATAC 58.976 52.381 0.90 0.00 0.00 2.39
2379 2671 9.087424 GCAAATCCACCATTTTAAGAAGATAAC 57.913 33.333 0.00 0.00 31.79 1.89
2539 2831 4.034285 TCAGTTTCTTGGATCCTTTCCC 57.966 45.455 14.23 0.00 44.77 3.97
2705 2997 4.143094 GGAAGAAAAAGGAGACGAACATCG 60.143 45.833 0.00 0.00 46.93 3.84
2757 3051 9.565213 ACGTATATATAGTATTCAAACGGCTTC 57.435 33.333 0.00 0.00 32.47 3.86
2933 3227 6.599638 GCTTCAAGAATGGGTGTCTTATTACT 59.400 38.462 0.00 0.00 33.53 2.24
3054 3348 4.357947 TGTGGCTCCGTCACTCGC 62.358 66.667 0.08 0.00 39.12 5.03
3170 3464 3.435275 AGGTCTGATAGTTGCACTCTCA 58.565 45.455 0.00 0.00 31.69 3.27
3892 4196 1.334869 CGCTTCAAGCAAAGTTCCAGT 59.665 47.619 10.73 0.00 42.58 4.00
4205 4509 7.037730 ATCTTCCTGATATGCTTGTATAGCCTT 60.038 37.037 0.00 0.00 40.45 4.35
4256 4560 1.079750 GTCGAGCAACCTCTGTCCC 60.080 63.158 0.00 0.00 35.90 4.46
4679 4983 2.415512 GGCTACGGTTCTTAGTGCAAAG 59.584 50.000 0.00 0.00 0.00 2.77
4798 5102 2.113139 AAGACCAAGGGTGCACCG 59.887 61.111 29.08 17.70 46.96 4.94
4807 5111 1.479323 CCATCATTGCCCAAGACCAAG 59.521 52.381 0.00 0.00 0.00 3.61
5290 5594 9.337396 TGCGATTTGGTAGATAAATTCAGTAAT 57.663 29.630 0.00 0.00 0.00 1.89
5447 5752 2.094675 AGGTTTCTGTGTATGCATGGC 58.905 47.619 10.16 2.61 0.00 4.40
5571 5876 3.519107 TCCAGGTTTCATGCTATCTGACA 59.481 43.478 8.28 0.00 0.00 3.58
5590 5895 4.735369 TCCTAGCCAATTTCTTTGTTCCA 58.265 39.130 0.00 0.00 33.15 3.53
5652 5957 8.178313 GTGAAGAAAATGCCTCAGTATAACTTC 58.822 37.037 0.00 0.00 0.00 3.01
5731 6036 8.704849 TGAATAATCTTGAAGAACCCTTTTCA 57.295 30.769 0.00 1.33 31.62 2.69
6340 6648 1.159713 TTGCACTGCAACAGTCCTCG 61.160 55.000 12.59 0.00 43.43 4.63
6832 7140 3.077359 CAACTTCTCCTTAGCCAACTGG 58.923 50.000 0.00 0.00 38.53 4.00
7064 7372 5.455899 GGGAGCTCATGGAAGATTCAGTTAT 60.456 44.000 17.19 0.00 0.00 1.89
7132 7440 2.436646 CTTGGCGGCGATGGAAGT 60.437 61.111 12.98 0.00 0.00 3.01
7306 7614 2.159184 TGCTGATGGAGTTCTGTCGATC 60.159 50.000 0.00 0.00 33.50 3.69
7364 7672 1.115326 GGAGGCCCAACAAAGTTGCT 61.115 55.000 0.00 0.00 0.00 3.91
7504 7812 2.481854 CTTCTGCATTCAGGAGGATCG 58.518 52.381 0.00 0.00 41.38 3.69
7663 7971 4.136051 CAAACATTGGGAAAACAGGCATT 58.864 39.130 0.00 0.00 0.00 3.56
7741 8049 2.046892 CCTTGTGGAGGCTGGACG 60.047 66.667 0.00 0.00 39.09 4.79
8031 8339 7.394359 AGTGAAATGTATGCTTGGTCACTATTT 59.606 33.333 11.77 0.00 41.71 1.40
8212 8522 9.602568 TTATTCTCCGTGTAATGCAAATTACTA 57.397 29.630 10.67 0.00 37.76 1.82
8213 8523 8.395633 GTTATTCTCCGTGTAATGCAAATTACT 58.604 33.333 10.67 0.00 37.76 2.24
8214 8524 8.178964 TGTTATTCTCCGTGTAATGCAAATTAC 58.821 33.333 3.67 3.67 37.49 1.89
8470 8781 5.878406 AGGTACTCCACAGATCCTTAATG 57.122 43.478 0.00 0.00 35.89 1.90
8706 9018 2.417516 CCGACCTGGCTGATACCG 59.582 66.667 0.00 0.00 0.00 4.02
8838 9187 0.836606 ATGGATCCCACGTATGTGCA 59.163 50.000 9.90 2.36 45.04 4.57
8848 9292 2.940158 CAAGCAGATTGATGGATCCCA 58.060 47.619 9.90 0.00 41.83 4.37
8849 9293 1.612463 GCAAGCAGATTGATGGATCCC 59.388 52.381 9.90 0.00 41.83 3.85
8903 9347 1.368950 CGGATGGATCAGGCGACAT 59.631 57.895 0.00 0.00 0.00 3.06
8904 9348 2.814604 CGGATGGATCAGGCGACA 59.185 61.111 0.00 0.00 0.00 4.35
9110 9595 4.195334 GGCGATGCCTCCCCACAT 62.195 66.667 0.00 0.00 46.69 3.21
9173 9675 1.811266 CCGACAGCGATGGTCTTGG 60.811 63.158 5.32 0.00 40.82 3.61
9249 9751 0.915364 GGCCCTTGACCTTCTGATCT 59.085 55.000 0.00 0.00 0.00 2.75
9280 9782 1.750930 CGATGTCCTCCTCCATGGG 59.249 63.158 13.02 2.26 36.20 4.00


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

AutoCloner maintained by Alex Coulton.