Multiple sequence alignment - TraesCS3D01G263200

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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 TraesCS3D01G263200 chr3D 100.000 5120 0 0 1 5120 365328276 365333395 0.000000e+00 9455.0
1 TraesCS3D01G263200 chr3D 100.000 29 0 0 5 33 540150528 540150500 3.000000e-03 54.7
2 TraesCS3D01G263200 chr3A 93.541 4490 176 46 147 4571 487431025 487435465 0.000000e+00 6580.0
3 TraesCS3D01G263200 chr3B 95.358 2736 75 18 1542 4243 475827862 475830579 0.000000e+00 4301.0
4 TraesCS3D01G263200 chr3B 93.447 763 26 8 754 1500 475826975 475827729 0.000000e+00 1110.0
5 TraesCS3D01G263200 chr3B 85.567 582 54 13 4568 5120 592852556 592853136 2.660000e-162 582.0
6 TraesCS3D01G263200 chr3B 83.156 564 72 8 4578 5120 85170792 85170231 1.280000e-135 494.0
7 TraesCS3D01G263200 chr3B 94.921 315 16 0 4243 4557 475832862 475833176 1.280000e-135 494.0
8 TraesCS3D01G263200 chr3B 100.000 29 0 0 5 33 16067468 16067440 3.000000e-03 54.7
9 TraesCS3D01G263200 chr3B 100.000 29 0 0 5 33 25240863 25240891 3.000000e-03 54.7
10 TraesCS3D01G263200 chr1A 88.725 541 49 6 4590 5119 78546453 78545914 0.000000e+00 651.0
11 TraesCS3D01G263200 chr5A 88.192 542 44 12 4588 5119 601243599 601243068 3.360000e-176 628.0
12 TraesCS3D01G263200 chr1D 87.796 549 50 7 4588 5119 315546835 315546287 1.210000e-175 627.0
13 TraesCS3D01G263200 chr2B 86.726 565 43 16 4587 5119 109076367 109075803 2.640000e-167 599.0
14 TraesCS3D01G263200 chr2B 86.059 538 58 12 4588 5119 53059340 53058814 3.460000e-156 562.0
15 TraesCS3D01G263200 chr2B 75.000 224 40 14 91 304 144246357 144246574 7.060000e-14 89.8
16 TraesCS3D01G263200 chr2A 87.716 464 39 10 4673 5119 71111520 71111058 4.540000e-145 525.0
17 TraesCS3D01G263200 chr2A 96.721 61 2 0 4587 4647 71111580 71111520 9.070000e-18 102.0
18 TraesCS3D01G263200 chr1B 83.964 555 62 16 4593 5120 645533709 645534263 1.640000e-139 507.0
19 TraesCS3D01G263200 chr6B 80.505 277 28 14 4582 4835 345222618 345222345 6.770000e-44 189.0
20 TraesCS3D01G263200 chr5B 78.341 217 27 14 4582 4779 14936590 14936375 6.960000e-24 122.0
21 TraesCS3D01G263200 chr5B 93.671 79 4 1 4568 4646 432987348 432987425 3.240000e-22 117.0
22 TraesCS3D01G263200 chr6D 90.541 74 4 3 4582 4654 221848190 221848119 1.520000e-15 95.3
23 TraesCS3D01G263200 chr5D 100.000 29 0 0 5 33 361915120 361915092 3.000000e-03 54.7
24 TraesCS3D01G263200 chr4D 90.476 42 3 1 1 42 423595071 423595031 3.000000e-03 54.7


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 TraesCS3D01G263200 chr3D 365328276 365333395 5119 False 9455.000000 9455 100.000000 1 5120 1 chr3D.!!$F1 5119
1 TraesCS3D01G263200 chr3A 487431025 487435465 4440 False 6580.000000 6580 93.541000 147 4571 1 chr3A.!!$F1 4424
2 TraesCS3D01G263200 chr3B 475826975 475833176 6201 False 1968.333333 4301 94.575333 754 4557 3 chr3B.!!$F3 3803
3 TraesCS3D01G263200 chr3B 592852556 592853136 580 False 582.000000 582 85.567000 4568 5120 1 chr3B.!!$F2 552
4 TraesCS3D01G263200 chr3B 85170231 85170792 561 True 494.000000 494 83.156000 4578 5120 1 chr3B.!!$R2 542
5 TraesCS3D01G263200 chr1A 78545914 78546453 539 True 651.000000 651 88.725000 4590 5119 1 chr1A.!!$R1 529
6 TraesCS3D01G263200 chr5A 601243068 601243599 531 True 628.000000 628 88.192000 4588 5119 1 chr5A.!!$R1 531
7 TraesCS3D01G263200 chr1D 315546287 315546835 548 True 627.000000 627 87.796000 4588 5119 1 chr1D.!!$R1 531
8 TraesCS3D01G263200 chr2B 109075803 109076367 564 True 599.000000 599 86.726000 4587 5119 1 chr2B.!!$R2 532
9 TraesCS3D01G263200 chr2B 53058814 53059340 526 True 562.000000 562 86.059000 4588 5119 1 chr2B.!!$R1 531
10 TraesCS3D01G263200 chr2A 71111058 71111580 522 True 313.500000 525 92.218500 4587 5119 2 chr2A.!!$R1 532
11 TraesCS3D01G263200 chr1B 645533709 645534263 554 False 507.000000 507 83.964000 4593 5120 1 chr1B.!!$F1 527

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
810 853 0.032130 ATCACACGCTCACAGTCGTT 59.968 50.000 0.00 0.00 36.73 3.85 F
1502 1579 1.000506 GCCACTCGTGTCTAGGTTTGA 59.999 52.381 0.00 0.00 0.00 2.69 F
1869 2021 2.228822 CCCTGGCGGAAATGCAATATAC 59.771 50.000 0.00 0.00 36.28 1.47 F
1947 2099 2.740981 GCTGGAAAGATGGCATCTATCG 59.259 50.000 29.02 16.44 39.08 2.92 F
3173 3351 2.746904 TGAACTAATGACATTGGGTGCG 59.253 45.455 15.12 0.00 0.00 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1985 2137 4.111577 AGTTTCCTCAATACTCCATGGGA 58.888 43.478 13.02 0.0 0.00 4.37 R
3486 3664 1.336440 TGCCACAAATGAACCAACGAG 59.664 47.619 0.00 0.0 0.00 4.18 R
3648 3830 2.478134 CACTGAGAAGCGAAAACAGAGG 59.522 50.000 0.00 0.0 33.53 3.69 R
3778 3960 4.074970 AGGTACATGAGAAAAAGGTGCAG 58.925 43.478 0.00 0.0 0.00 4.41 R
5068 7624 0.303493 GAACGACACAAAAGAGCGCA 59.697 50.000 11.47 0.0 0.00 6.09 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
47 48 9.764363 AAAAATGTTTGCCCAAGTTTTTAAAAA 57.236 22.222 9.31 9.31 29.87 1.94
104 105 7.644986 AAAAATGACGAAAACAAGTGTTTGA 57.355 28.000 10.05 0.00 46.47 2.69
105 106 6.869421 AAATGACGAAAACAAGTGTTTGAG 57.131 33.333 10.05 9.51 46.47 3.02
106 107 5.811399 ATGACGAAAACAAGTGTTTGAGA 57.189 34.783 10.05 0.00 46.47 3.27
107 108 5.614923 TGACGAAAACAAGTGTTTGAGAA 57.385 34.783 10.05 0.92 46.47 2.87
108 109 6.003234 TGACGAAAACAAGTGTTTGAGAAA 57.997 33.333 10.05 0.00 46.47 2.52
109 110 6.439599 TGACGAAAACAAGTGTTTGAGAAAA 58.560 32.000 10.05 0.00 46.47 2.29
110 111 6.918569 TGACGAAAACAAGTGTTTGAGAAAAA 59.081 30.769 10.05 0.00 46.47 1.94
111 112 7.596995 TGACGAAAACAAGTGTTTGAGAAAAAT 59.403 29.630 10.05 0.00 46.47 1.82
112 113 8.305441 ACGAAAACAAGTGTTTGAGAAAAATT 57.695 26.923 10.05 0.00 46.47 1.82
113 114 8.220434 ACGAAAACAAGTGTTTGAGAAAAATTG 58.780 29.630 10.05 0.00 46.47 2.32
114 115 7.687757 CGAAAACAAGTGTTTGAGAAAAATTGG 59.312 33.333 10.05 0.00 46.47 3.16
115 116 8.614469 AAAACAAGTGTTTGAGAAAAATTGGA 57.386 26.923 10.05 0.00 46.47 3.53
116 117 8.614469 AAACAAGTGTTTGAGAAAAATTGGAA 57.386 26.923 8.58 0.00 45.55 3.53
117 118 8.791327 AACAAGTGTTTGAGAAAAATTGGAAT 57.209 26.923 0.00 0.00 37.73 3.01
118 119 9.883142 AACAAGTGTTTGAGAAAAATTGGAATA 57.117 25.926 0.00 0.00 37.73 1.75
119 120 9.883142 ACAAGTGTTTGAGAAAAATTGGAATAA 57.117 25.926 0.00 0.00 37.73 1.40
251 252 9.676195 TCATGTATGTGAAAAGTGTTAAACATG 57.324 29.630 0.00 0.00 40.96 3.21
273 274 8.408601 ACATGTACAAGAAAATATTCCTGATGC 58.591 33.333 4.87 0.00 36.12 3.91
279 280 8.000709 ACAAGAAAATATTCCTGATGCATAGGA 58.999 33.333 16.41 16.41 42.43 2.94
475 503 9.203421 TGTACATTTTGTAGAAGTAGACATGTG 57.797 33.333 1.15 0.00 32.84 3.21
569 600 7.712205 AGACAAAGAAAAACCAAGAAATCATGG 59.288 33.333 3.25 3.25 40.34 3.66
574 605 8.437360 AGAAAAACCAAGAAATCATGGAAAAC 57.563 30.769 11.37 0.38 38.06 2.43
575 606 7.498900 AGAAAAACCAAGAAATCATGGAAAACC 59.501 33.333 11.37 0.00 38.06 3.27
576 607 5.885449 AACCAAGAAATCATGGAAAACCA 57.115 34.783 11.37 0.00 38.06 3.67
578 609 4.901250 ACCAAGAAATCATGGAAAACCAGT 59.099 37.500 11.37 0.00 38.06 4.00
579 610 5.221501 ACCAAGAAATCATGGAAAACCAGTG 60.222 40.000 11.37 0.00 38.06 3.66
580 611 5.010922 CCAAGAAATCATGGAAAACCAGTGA 59.989 40.000 0.00 0.00 36.89 3.41
581 612 6.462768 CCAAGAAATCATGGAAAACCAGTGAA 60.463 38.462 0.00 0.00 36.89 3.18
582 613 6.336842 AGAAATCATGGAAAACCAGTGAAG 57.663 37.500 0.00 0.00 0.00 3.02
583 614 6.070656 AGAAATCATGGAAAACCAGTGAAGA 58.929 36.000 0.00 0.00 0.00 2.87
585 616 6.729690 AATCATGGAAAACCAGTGAAGAAA 57.270 33.333 0.00 0.00 0.00 2.52
586 617 5.514274 TCATGGAAAACCAGTGAAGAAAC 57.486 39.130 0.00 0.00 0.00 2.78
587 618 4.952957 TCATGGAAAACCAGTGAAGAAACA 59.047 37.500 0.00 0.00 0.00 2.83
661 692 9.586435 AGAAAACATAAAACCTGAAGAAAACAG 57.414 29.630 0.00 0.00 35.43 3.16
673 704 1.792118 GAAAACAGTGTGGGCCGGAC 61.792 60.000 5.05 0.00 0.00 4.79
722 753 3.814005 CTGTAAGCCCATTACTACCGT 57.186 47.619 0.08 0.00 43.61 4.83
724 755 2.168936 TGTAAGCCCATTACTACCGTGG 59.831 50.000 0.08 0.00 43.61 4.94
725 756 1.575419 AAGCCCATTACTACCGTGGA 58.425 50.000 0.00 0.00 34.94 4.02
726 757 0.828677 AGCCCATTACTACCGTGGAC 59.171 55.000 0.00 0.00 34.94 4.02
751 782 1.203050 AGCAGCCTGGCCTTTAAGAAA 60.203 47.619 16.57 0.00 0.00 2.52
781 812 4.410400 GGGCCGGTCCAGGTCAAG 62.410 72.222 23.50 0.00 37.71 3.02
804 847 1.805943 CCATTCAATCACACGCTCACA 59.194 47.619 0.00 0.00 0.00 3.58
808 851 0.436150 CAATCACACGCTCACAGTCG 59.564 55.000 0.00 0.00 0.00 4.18
810 853 0.032130 ATCACACGCTCACAGTCGTT 59.968 50.000 0.00 0.00 36.73 3.85
882 925 2.992114 AAGCCGGCAGTCTCGACT 60.992 61.111 31.54 0.00 43.61 4.18
883 926 2.995872 AAGCCGGCAGTCTCGACTC 61.996 63.158 31.54 0.00 40.20 3.36
884 927 3.444805 GCCGGCAGTCTCGACTCT 61.445 66.667 24.80 0.00 40.20 3.24
885 928 2.795297 CCGGCAGTCTCGACTCTC 59.205 66.667 0.00 0.00 40.20 3.20
886 929 2.401592 CGGCAGTCTCGACTCTCG 59.598 66.667 0.00 1.01 40.20 4.04
888 931 1.426223 GGCAGTCTCGACTCTCGAC 59.574 63.158 0.00 0.00 44.82 4.20
1449 1506 7.390440 TGAAATTACTCATGATTTCGGAGTGTT 59.610 33.333 12.53 6.79 41.49 3.32
1452 1509 2.604914 CTCATGATTTCGGAGTGTTCGG 59.395 50.000 0.00 0.00 0.00 4.30
1502 1579 1.000506 GCCACTCGTGTCTAGGTTTGA 59.999 52.381 0.00 0.00 0.00 2.69
1510 1587 3.791887 CGTGTCTAGGTTTGAGATAAGCG 59.208 47.826 0.00 0.00 0.00 4.68
1547 1695 5.702865 ACACTTGAATGCACATTGTATGTC 58.297 37.500 0.00 0.00 42.70 3.06
1814 1966 5.019470 GGATTCTGAATTGACCTTCCCTTT 58.981 41.667 4.11 0.00 0.00 3.11
1869 2021 2.228822 CCCTGGCGGAAATGCAATATAC 59.771 50.000 0.00 0.00 36.28 1.47
1947 2099 2.740981 GCTGGAAAGATGGCATCTATCG 59.259 50.000 29.02 16.44 39.08 2.92
1985 2137 9.863650 TCTTAAGCTAGTAATATCAGGTACACT 57.136 33.333 0.00 0.00 0.00 3.55
2130 2300 5.047377 AGCTTCTTTTCCTTTGTGTGACAAA 60.047 36.000 2.14 2.14 44.91 2.83
2908 3079 7.754625 TGTTTAGTGTTTACAACCTTTCTGAC 58.245 34.615 0.00 0.00 0.00 3.51
2976 3149 8.756864 GTTAGCACTTGATGATACTAACTTAGC 58.243 37.037 0.00 0.00 37.53 3.09
2982 3155 7.766278 ACTTGATGATACTAACTTAGCCAAGTG 59.234 37.037 0.00 0.00 44.41 3.16
3036 3209 8.216423 AGCAATCTACAAGACATCCATCTTTAT 58.784 33.333 0.00 0.00 36.78 1.40
3173 3351 2.746904 TGAACTAATGACATTGGGTGCG 59.253 45.455 15.12 0.00 0.00 5.34
3372 3550 7.625828 AAATTAGTAAGTACCTTGACCATGC 57.374 36.000 0.00 0.00 0.00 4.06
3648 3830 8.774890 ACTGAAATGCTATAGATCATGATCAC 57.225 34.615 31.99 18.04 40.22 3.06
3659 3841 5.114780 AGATCATGATCACCTCTGTTTTCG 58.885 41.667 31.99 0.00 40.22 3.46
3745 3927 5.833131 TGAACTTTTGAAGGCTACAAAGGAT 59.167 36.000 14.18 7.30 38.25 3.24
3757 3939 4.932200 GCTACAAAGGATATCGAATCCCAG 59.068 45.833 17.64 12.42 38.98 4.45
3778 3960 6.127897 CCCAGTTGGAAAAAGTCAGTATCATC 60.128 42.308 0.00 0.00 37.39 2.92
3848 4035 3.760684 ACCTGAATCAAGAAGCAACCATC 59.239 43.478 0.00 0.00 0.00 3.51
3854 4041 3.002791 TCAAGAAGCAACCATCGTCATC 58.997 45.455 0.00 0.00 0.00 2.92
3914 4101 7.426456 CACTTCGTACATGTTATTGCAGATTTC 59.574 37.037 2.30 0.00 0.00 2.17
4012 4199 2.561569 CCAACACGAAAGACAAGACCT 58.438 47.619 0.00 0.00 0.00 3.85
4077 4264 2.710377 CCTGATGACCGGATTTCAACA 58.290 47.619 9.46 5.84 0.00 3.33
4179 4366 1.401552 CATGGTTTCGTTGATCGGCAT 59.598 47.619 0.00 0.00 40.32 4.40
4229 4420 9.787532 ATGAATCAAATAATAAAACTCGGTGTG 57.212 29.630 0.00 0.00 0.00 3.82
4298 6772 4.558226 TTCAGGAACATGCTGTACAGAT 57.442 40.909 27.08 13.59 37.12 2.90
4453 6927 3.317149 GGAACACCGTTTTTCCTTTAGCT 59.683 43.478 0.00 0.00 38.65 3.32
4467 6941 0.991146 TTAGCTTGTCCAGGGCATCA 59.009 50.000 0.00 0.00 0.00 3.07
4529 7004 6.707440 TCCTACAGAGAGACAATGAAGATC 57.293 41.667 0.00 0.00 0.00 2.75
4549 7024 3.734463 TCGGTGTTCTTGAAGCAATACA 58.266 40.909 0.00 0.00 0.00 2.29
4563 7038 3.256631 AGCAATACAGGCCAAGAAAGTTG 59.743 43.478 5.01 1.65 0.00 3.16
4574 7049 2.206576 AGAAAGTTGGCCATCTCCAC 57.793 50.000 16.70 6.59 35.50 4.02
4731 7247 1.519719 CTTCTTCTCCTCTGCCCGG 59.480 63.158 0.00 0.00 0.00 5.73
4771 7300 4.680237 CTTCTGGTGGCGGCGTGA 62.680 66.667 9.37 0.00 0.00 4.35
4829 7366 2.359107 CTGCTGGTCGTGCATGGT 60.359 61.111 5.98 0.00 39.86 3.55
4965 7517 1.651770 TGGATCCTACTTCCAGTCCCT 59.348 52.381 14.23 0.00 38.35 4.20
5095 7651 5.220681 GCTCTTTTGTGTCGTTCTCTTCTTT 60.221 40.000 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 9.764363 TTTTTAAAAACTTGGGCAAACATTTTT 57.236 22.222 9.31 8.75 34.56 1.94
80 81 7.596995 TCTCAAACACTTGTTTTCGTCATTTTT 59.403 29.630 4.56 0.00 45.07 1.94
81 82 7.087639 TCTCAAACACTTGTTTTCGTCATTTT 58.912 30.769 4.56 0.00 45.07 1.82
82 83 6.616947 TCTCAAACACTTGTTTTCGTCATTT 58.383 32.000 4.56 0.00 45.07 2.32
83 84 6.189677 TCTCAAACACTTGTTTTCGTCATT 57.810 33.333 4.56 0.00 45.07 2.57
84 85 5.811399 TCTCAAACACTTGTTTTCGTCAT 57.189 34.783 4.56 0.00 45.07 3.06
85 86 5.614923 TTCTCAAACACTTGTTTTCGTCA 57.385 34.783 4.56 0.00 45.07 4.35
86 87 6.921332 TTTTCTCAAACACTTGTTTTCGTC 57.079 33.333 4.56 0.00 45.07 4.20
87 88 7.883229 ATTTTTCTCAAACACTTGTTTTCGT 57.117 28.000 4.56 0.00 45.07 3.85
88 89 7.687757 CCAATTTTTCTCAAACACTTGTTTTCG 59.312 33.333 4.56 0.16 45.07 3.46
89 90 8.716909 TCCAATTTTTCTCAAACACTTGTTTTC 58.283 29.630 4.56 0.00 45.07 2.29
90 91 8.614469 TCCAATTTTTCTCAAACACTTGTTTT 57.386 26.923 4.56 0.00 45.07 2.43
92 93 8.791327 ATTCCAATTTTTCTCAAACACTTGTT 57.209 26.923 0.00 0.00 40.50 2.83
93 94 9.883142 TTATTCCAATTTTTCTCAAACACTTGT 57.117 25.926 0.00 0.00 33.94 3.16
247 248 8.408601 GCATCAGGAATATTTTCTTGTACATGT 58.591 33.333 2.69 2.69 39.34 3.21
248 249 8.407832 TGCATCAGGAATATTTTCTTGTACATG 58.592 33.333 0.00 0.00 39.34 3.21
249 250 8.523915 TGCATCAGGAATATTTTCTTGTACAT 57.476 30.769 0.00 0.00 39.34 2.29
250 251 7.936496 TGCATCAGGAATATTTTCTTGTACA 57.064 32.000 7.66 0.00 39.34 2.90
372 376 9.569122 AATAAGTGGTGTACATCTTTTTACTGT 57.431 29.630 7.81 0.00 0.00 3.55
493 522 6.162777 CCAGTTTTTCACAGGTTTTCTTTGA 58.837 36.000 0.00 0.00 30.97 2.69
496 525 4.020662 TGCCAGTTTTTCACAGGTTTTCTT 60.021 37.500 0.00 0.00 34.40 2.52
539 570 9.371136 GATTTCTTGGTTTTTCTTTGTCTCTTT 57.629 29.630 0.00 0.00 0.00 2.52
551 582 7.115414 TGGTTTTCCATGATTTCTTGGTTTTT 58.885 30.769 11.10 0.00 46.22 1.94
569 600 7.883229 TTTCTTTGTTTCTTCACTGGTTTTC 57.117 32.000 0.00 0.00 0.00 2.29
574 605 4.265320 GCGTTTTCTTTGTTTCTTCACTGG 59.735 41.667 0.00 0.00 0.00 4.00
575 606 4.028509 CGCGTTTTCTTTGTTTCTTCACTG 60.029 41.667 0.00 0.00 0.00 3.66
576 607 4.095610 CGCGTTTTCTTTGTTTCTTCACT 58.904 39.130 0.00 0.00 0.00 3.41
578 609 4.343811 TCGCGTTTTCTTTGTTTCTTCA 57.656 36.364 5.77 0.00 0.00 3.02
579 610 5.674215 TTTCGCGTTTTCTTTGTTTCTTC 57.326 34.783 5.77 0.00 0.00 2.87
580 611 6.293618 GTTTTTCGCGTTTTCTTTGTTTCTT 58.706 32.000 5.77 0.00 0.00 2.52
581 612 5.164031 GGTTTTTCGCGTTTTCTTTGTTTCT 60.164 36.000 5.77 0.00 0.00 2.52
582 613 5.010749 GGTTTTTCGCGTTTTCTTTGTTTC 58.989 37.500 5.77 0.00 0.00 2.78
583 614 4.433152 CGGTTTTTCGCGTTTTCTTTGTTT 60.433 37.500 5.77 0.00 0.00 2.83
585 616 2.595095 CGGTTTTTCGCGTTTTCTTTGT 59.405 40.909 5.77 0.00 0.00 2.83
586 617 2.035259 CCGGTTTTTCGCGTTTTCTTTG 60.035 45.455 5.77 0.00 0.00 2.77
587 618 2.186891 CCGGTTTTTCGCGTTTTCTTT 58.813 42.857 5.77 0.00 0.00 2.52
641 672 6.697019 CCACACTGTTTTCTTCAGGTTTTATG 59.303 38.462 0.00 0.00 37.25 1.90
643 674 5.126384 CCCACACTGTTTTCTTCAGGTTTTA 59.874 40.000 0.00 0.00 37.25 1.52
648 679 1.338020 GCCCACACTGTTTTCTTCAGG 59.662 52.381 0.00 0.00 37.25 3.86
706 737 1.208776 GTCCACGGTAGTAATGGGCTT 59.791 52.381 0.00 0.00 35.13 4.35
721 752 4.008933 AGGCTGCTCGGTGTCCAC 62.009 66.667 0.00 0.00 0.00 4.02
722 753 4.007644 CAGGCTGCTCGGTGTCCA 62.008 66.667 0.00 0.00 0.00 4.02
781 812 1.139520 GCGTGTGATTGAATGGGCC 59.860 57.895 0.00 0.00 0.00 5.80
808 851 2.267961 CCACTCCCCCGTGCTAAC 59.732 66.667 0.00 0.00 33.60 2.34
810 853 2.682494 GACCACTCCCCCGTGCTA 60.682 66.667 0.00 0.00 33.60 3.49
818 861 0.245539 TCGACGATTTGACCACTCCC 59.754 55.000 0.00 0.00 0.00 4.30
820 863 2.400399 TGTTCGACGATTTGACCACTC 58.600 47.619 0.00 0.00 0.00 3.51
882 925 1.909141 GCGTCGTCTCCTTGTCGAGA 61.909 60.000 0.00 0.00 36.95 4.04
883 926 1.512310 GCGTCGTCTCCTTGTCGAG 60.512 63.158 0.00 0.00 36.95 4.04
884 927 2.559840 GCGTCGTCTCCTTGTCGA 59.440 61.111 0.00 0.00 34.21 4.20
885 928 2.504244 GGCGTCGTCTCCTTGTCG 60.504 66.667 0.00 0.00 0.00 4.35
886 929 1.733399 GTGGCGTCGTCTCCTTGTC 60.733 63.158 0.00 0.00 0.00 3.18
887 930 2.338984 GTGGCGTCGTCTCCTTGT 59.661 61.111 0.00 0.00 0.00 3.16
888 931 2.432628 GGTGGCGTCGTCTCCTTG 60.433 66.667 10.60 0.00 0.00 3.61
925 968 1.005332 CTCTGAGAGGAGAGGGACACA 59.995 57.143 0.36 0.00 36.57 3.72
926 969 1.005450 ACTCTGAGAGGAGAGGGACAC 59.995 57.143 14.83 0.00 43.42 3.67
927 970 1.283613 GACTCTGAGAGGAGAGGGACA 59.716 57.143 14.83 0.00 43.42 4.02
928 971 1.564348 AGACTCTGAGAGGAGAGGGAC 59.436 57.143 14.83 0.00 43.42 4.46
1396 1453 2.080286 AATGGTACTGCGTGTGAGTC 57.920 50.000 0.00 0.00 0.00 3.36
1449 1506 7.278424 GCAGTACAACTATACAAAATAACCCGA 59.722 37.037 0.00 0.00 0.00 5.14
1452 1509 7.901377 CACGCAGTACAACTATACAAAATAACC 59.099 37.037 0.00 0.00 41.61 2.85
1502 1579 0.181114 TGCTGCCCATTCGCTTATCT 59.819 50.000 0.00 0.00 0.00 1.98
1510 1587 1.470098 CAAGTGTAGTGCTGCCCATTC 59.530 52.381 0.00 0.00 0.00 2.67
1547 1695 3.742290 CTCAAGCAACAGAGCAACG 57.258 52.632 0.00 0.00 36.85 4.10
1814 1966 5.016173 ACCAAATACAAGCAGCCTGAATAA 58.984 37.500 0.00 0.00 0.00 1.40
1947 2099 6.146601 ACTAGCTTAAGATACCGGTCTTTC 57.853 41.667 12.40 7.24 39.15 2.62
1985 2137 4.111577 AGTTTCCTCAATACTCCATGGGA 58.888 43.478 13.02 0.00 0.00 4.37
2130 2300 6.896021 TTCTACAGAAACAGCACTACTACT 57.104 37.500 0.00 0.00 0.00 2.57
2131 2301 8.535690 AAATTCTACAGAAACAGCACTACTAC 57.464 34.615 0.00 0.00 37.61 2.73
2132 2302 8.988934 CAAAATTCTACAGAAACAGCACTACTA 58.011 33.333 0.00 0.00 37.61 1.82
2133 2303 7.715249 TCAAAATTCTACAGAAACAGCACTACT 59.285 33.333 0.00 0.00 37.61 2.57
2134 2304 7.861630 TCAAAATTCTACAGAAACAGCACTAC 58.138 34.615 0.00 0.00 37.61 2.73
2135 2305 7.931407 TCTCAAAATTCTACAGAAACAGCACTA 59.069 33.333 0.00 0.00 37.61 2.74
2136 2306 6.767902 TCTCAAAATTCTACAGAAACAGCACT 59.232 34.615 0.00 0.00 37.61 4.40
2137 2307 6.853362 GTCTCAAAATTCTACAGAAACAGCAC 59.147 38.462 0.00 0.00 37.61 4.40
2138 2308 6.017109 GGTCTCAAAATTCTACAGAAACAGCA 60.017 38.462 0.00 0.00 37.61 4.41
2139 2309 6.017109 TGGTCTCAAAATTCTACAGAAACAGC 60.017 38.462 0.00 0.00 37.61 4.40
3018 3191 5.586243 CACGGAATAAAGATGGATGTCTTGT 59.414 40.000 0.00 0.00 38.41 3.16
3036 3209 7.160049 TCATAACTGGTTGTTATAACACGGAA 58.840 34.615 17.85 0.57 46.69 4.30
3038 3211 6.971527 TCATAACTGGTTGTTATAACACGG 57.028 37.500 17.85 14.21 46.69 4.94
3173 3351 6.599638 AGAGCCTTGTAATAAAGATGGTGAAC 59.400 38.462 0.00 0.00 0.00 3.18
3372 3550 8.611757 CAAACCAAGTTGAAGAAAATAAAAGGG 58.388 33.333 3.87 0.00 0.00 3.95
3481 3659 2.223479 ACAAATGAACCAACGAGTGTGC 60.223 45.455 0.00 0.00 0.00 4.57
3486 3664 1.336440 TGCCACAAATGAACCAACGAG 59.664 47.619 0.00 0.00 0.00 4.18
3648 3830 2.478134 CACTGAGAAGCGAAAACAGAGG 59.522 50.000 0.00 0.00 33.53 3.69
3757 3939 6.072508 TGCAGATGATACTGACTTTTTCCAAC 60.073 38.462 0.00 0.00 39.94 3.77
3778 3960 4.074970 AGGTACATGAGAAAAAGGTGCAG 58.925 43.478 0.00 0.00 0.00 4.41
3848 4035 6.568869 ACTTCCAGAATAAGAAGAGATGACG 58.431 40.000 6.75 0.00 41.69 4.35
3914 4101 6.376299 TCCATGAAGAATCAACAATGGAGAAG 59.624 38.462 0.00 0.00 39.49 2.85
4012 4199 2.573462 AGGCACCTTCATAGAGCTTCAA 59.427 45.455 0.00 0.00 0.00 2.69
4077 4264 2.947652 CGAAATGATGTCCTTGATGGCT 59.052 45.455 0.00 0.00 35.26 4.75
4179 4366 5.009631 CCAATGTTAAGTGGACCAGAATGA 58.990 41.667 0.00 0.00 44.62 2.57
4216 4403 1.541670 GGCCTCACACACCGAGTTTTA 60.542 52.381 0.00 0.00 0.00 1.52
4250 6724 1.598132 CAGCAGAGAATTCCATGCTCG 59.402 52.381 24.70 18.09 45.57 5.03
4328 6802 9.469807 TGCTAACAAATTAATGAAAACGTGAAT 57.530 25.926 0.00 0.00 0.00 2.57
4431 6905 3.317149 AGCTAAAGGAAAAACGGTGTTCC 59.683 43.478 15.13 15.13 43.17 3.62
4453 6927 1.361204 TCTCTTGATGCCCTGGACAA 58.639 50.000 0.00 0.00 0.00 3.18
4529 7004 3.120199 CCTGTATTGCTTCAAGAACACCG 60.120 47.826 0.00 0.00 0.00 4.94
4823 7360 1.153549 GGAGAGGACGACACCATGC 60.154 63.158 0.00 0.00 0.00 4.06
4829 7366 2.680352 GCCCAGGAGAGGACGACA 60.680 66.667 0.00 0.00 0.00 4.35
4857 7394 2.836636 TGGAGAGCTCTACACCAGAT 57.163 50.000 25.36 0.00 30.33 2.90
4965 7517 1.806461 GATCGCCGCCATCTCTACCA 61.806 60.000 0.00 0.00 0.00 3.25
5068 7624 0.303493 GAACGACACAAAAGAGCGCA 59.697 50.000 11.47 0.00 0.00 6.09
5095 7651 2.766263 ACTTCTCCATGGCGATGTCTTA 59.234 45.455 15.54 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.