Multiple sequence alignment - TraesCS5A01G144600

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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 TraesCS5A01G144600 chr5A 100.000 6172 0 0 1 6172 320558753 320564924 0.000000e+00 11398.0
1 TraesCS5A01G144600 chr5D 94.760 4561 137 50 93 4574 233973687 233969150 0.000000e+00 7005.0
2 TraesCS5A01G144600 chr5D 95.278 953 26 7 4570 5509 233969104 233968158 0.000000e+00 1493.0
3 TraesCS5A01G144600 chr5D 95.380 303 13 1 5722 6024 233967168 233966867 1.200000e-131 481.0
4 TraesCS5A01G144600 chr5D 91.597 119 7 2 6054 6172 233966872 233966757 1.780000e-35 161.0
5 TraesCS5A01G144600 chr5D 85.417 144 4 5 5524 5667 233967762 233967636 3.880000e-27 134.0
6 TraesCS5A01G144600 chr5B 93.992 4544 171 45 79 4574 270859695 270864184 0.000000e+00 6785.0
7 TraesCS5A01G144600 chr5B 94.328 1093 44 7 4570 5650 270864230 270865316 0.000000e+00 1659.0
8 TraesCS5A01G144600 chr5B 96.943 229 6 1 5843 6070 270865603 270865831 3.490000e-102 383.0
9 TraesCS5A01G144600 chr5B 94.650 243 12 1 5602 5844 270865317 270865558 5.840000e-100 375.0
10 TraesCS5A01G144600 chr4B 85.775 471 61 6 2327 2794 147382253 147381786 1.550000e-135 494.0
11 TraesCS5A01G144600 chr4B 88.021 192 22 1 3313 3503 147381337 147381146 6.230000e-55 226.0
12 TraesCS5A01G144600 chr4B 92.000 75 5 1 1063 1137 147383195 147383122 3.040000e-18 104.0
13 TraesCS5A01G144600 chr4D 85.563 471 61 7 2327 2794 103254840 103254374 2.590000e-133 486.0
14 TraesCS5A01G144600 chr4D 83.951 405 51 6 4108 4511 103252932 103252541 5.840000e-100 375.0
15 TraesCS5A01G144600 chr4D 88.542 192 21 1 3313 3503 103253945 103253754 1.340000e-56 231.0
16 TraesCS5A01G144600 chr4D 92.000 75 5 1 1063 1137 103255764 103255691 3.040000e-18 104.0
17 TraesCS5A01G144600 chr4A 85.256 468 62 7 2327 2791 471918724 471919187 5.600000e-130 475.0
18 TraesCS5A01G144600 chr4A 83.704 405 52 6 4108 4511 471920858 471921249 2.720000e-98 370.0
19 TraesCS5A01G144600 chr4A 88.360 189 21 1 3313 3500 471919639 471919827 6.230000e-55 226.0
20 TraesCS5A01G144600 chr4A 92.000 75 5 1 1063 1137 471917798 471917871 3.040000e-18 104.0
21 TraesCS5A01G144600 chr7A 92.857 84 5 1 1 84 91007768 91007850 3.020000e-23 121.0
22 TraesCS5A01G144600 chr7A 93.671 79 5 0 1 79 80326299 80326221 1.090000e-22 119.0
23 TraesCS5A01G144600 chr7A 90.588 85 6 2 1 84 6271062 6270979 1.820000e-20 111.0
24 TraesCS5A01G144600 chr2D 92.771 83 6 0 1 83 21007758 21007676 3.020000e-23 121.0
25 TraesCS5A01G144600 chrUn 91.765 85 6 1 1 84 343885163 343885247 3.910000e-22 117.0
26 TraesCS5A01G144600 chr7B 92.683 82 5 1 1 82 686615992 686615912 3.910000e-22 117.0
27 TraesCS5A01G144600 chr3D 92.683 82 4 1 1 82 410995961 410995882 3.910000e-22 117.0
28 TraesCS5A01G144600 chr3D 90.769 65 4 1 6054 6116 478537159 478537223 1.100000e-12 86.1
29 TraesCS5A01G144600 chr2B 92.683 82 5 1 1 82 732891760 732891840 3.910000e-22 117.0
30 TraesCS5A01G144600 chr6A 91.566 83 6 1 1 82 611066407 611066325 5.060000e-21 113.0


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 TraesCS5A01G144600 chr5A 320558753 320564924 6171 False 11398.000000 11398 100.000000 1 6172 1 chr5A.!!$F1 6171
1 TraesCS5A01G144600 chr5D 233966757 233973687 6930 True 1854.800000 7005 92.486400 93 6172 5 chr5D.!!$R1 6079
2 TraesCS5A01G144600 chr5B 270859695 270865831 6136 False 2300.500000 6785 94.978250 79 6070 4 chr5B.!!$F1 5991
3 TraesCS5A01G144600 chr4B 147381146 147383195 2049 True 274.666667 494 88.598667 1063 3503 3 chr4B.!!$R1 2440
4 TraesCS5A01G144600 chr4D 103252541 103255764 3223 True 299.000000 486 87.514000 1063 4511 4 chr4D.!!$R1 3448
5 TraesCS5A01G144600 chr4A 471917798 471921249 3451 False 293.750000 475 87.330000 1063 4511 4 chr4A.!!$F1 3448

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
149 150 0.539986 TGGTTTACCCATCCGCTCTC 59.460 55.000 0.00 0.00 38.72 3.20 F
690 731 0.605589 AAAGCGAGCTACCACCAACC 60.606 55.000 0.00 0.00 0.00 3.77 F
1265 1333 0.672401 GTGGAATCGCCGGAAGAACA 60.672 55.000 5.05 2.23 40.66 3.18 F
1609 1845 0.952010 GCATTTGCTGCCCAAGTTGG 60.952 55.000 15.52 15.52 45.66 3.77 F
1620 1856 2.517959 CCCAAGTTGGCATTCTTCTCA 58.482 47.619 17.07 0.00 35.79 3.27 F
2752 3109 5.549347 TGTACATTGGCATGCTGAAAATTT 58.451 33.333 18.92 8.39 33.05 1.82 F
4124 5110 1.104577 CCTCAGAGACCGCTACTCCC 61.105 65.000 0.00 0.00 35.27 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1219 1287 0.673985 TCCATAACGCGGATCTCAGG 59.326 55.000 12.47 2.76 0.00 3.86 R
1637 1880 4.951715 AGCAGGATTTATGATGCAAGAACA 59.048 37.500 0.00 0.00 41.14 3.18 R
3053 3470 1.047034 ACTCGGGGGCTACGCTTATT 61.047 55.000 0.00 0.00 0.00 1.40 R
3068 3485 1.467734 AGTAACTACAGGCACGACTCG 59.532 52.381 0.00 0.00 0.00 4.18 R
3575 4034 2.283298 AGCATGACGATGGTGTTGATC 58.717 47.619 0.00 0.00 38.90 2.92 R
4564 5551 1.063616 CTCAGATCATGCAGTTTGGCG 59.936 52.381 0.00 0.00 36.28 5.69 R
5270 6319 0.863957 AACGAAAAACAACAGCGGCG 60.864 50.000 0.51 0.51 0.00 6.46 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
20 21 3.177997 GCCTTGTGTGGTGAATTTTGT 57.822 42.857 0.00 0.00 0.00 2.83
21 22 4.314740 GCCTTGTGTGGTGAATTTTGTA 57.685 40.909 0.00 0.00 0.00 2.41
22 23 4.688021 GCCTTGTGTGGTGAATTTTGTAA 58.312 39.130 0.00 0.00 0.00 2.41
23 24 5.296748 GCCTTGTGTGGTGAATTTTGTAAT 58.703 37.500 0.00 0.00 0.00 1.89
24 25 5.177327 GCCTTGTGTGGTGAATTTTGTAATG 59.823 40.000 0.00 0.00 0.00 1.90
25 26 6.511416 CCTTGTGTGGTGAATTTTGTAATGA 58.489 36.000 0.00 0.00 0.00 2.57
26 27 6.983307 CCTTGTGTGGTGAATTTTGTAATGAA 59.017 34.615 0.00 0.00 0.00 2.57
27 28 7.042791 CCTTGTGTGGTGAATTTTGTAATGAAC 60.043 37.037 0.00 0.00 0.00 3.18
28 29 5.974158 TGTGTGGTGAATTTTGTAATGAACG 59.026 36.000 0.00 0.00 0.00 3.95
29 30 6.183360 TGTGTGGTGAATTTTGTAATGAACGA 60.183 34.615 0.00 0.00 0.00 3.85
30 31 6.861055 GTGTGGTGAATTTTGTAATGAACGAT 59.139 34.615 0.00 0.00 0.00 3.73
31 32 7.381139 GTGTGGTGAATTTTGTAATGAACGATT 59.619 33.333 0.00 0.00 0.00 3.34
32 33 7.380870 TGTGGTGAATTTTGTAATGAACGATTG 59.619 33.333 0.00 0.00 0.00 2.67
33 34 7.381139 GTGGTGAATTTTGTAATGAACGATTGT 59.619 33.333 0.00 0.00 0.00 2.71
34 35 8.568794 TGGTGAATTTTGTAATGAACGATTGTA 58.431 29.630 0.00 0.00 0.00 2.41
35 36 9.400638 GGTGAATTTTGTAATGAACGATTGTAA 57.599 29.630 0.00 0.00 0.00 2.41
65 66 9.709495 CATTATTAATTGATTAATGTGTGGGGG 57.291 33.333 15.73 0.00 41.58 5.40
149 150 0.539986 TGGTTTACCCATCCGCTCTC 59.460 55.000 0.00 0.00 38.72 3.20
189 190 3.955551 TGGAAAAGGGTTACCACTTGTTC 59.044 43.478 2.98 10.00 40.13 3.18
200 201 6.127394 GGTTACCACTTGTTCCTAAAACCAAA 60.127 38.462 0.00 0.00 35.15 3.28
201 202 7.418139 GGTTACCACTTGTTCCTAAAACCAAAT 60.418 37.037 0.00 0.00 35.15 2.32
203 204 6.578944 ACCACTTGTTCCTAAAACCAAATTC 58.421 36.000 0.00 0.00 0.00 2.17
236 267 4.764679 TTATGCAAGATCAAAGCGTTGT 57.235 36.364 12.18 0.01 36.07 3.32
244 275 2.341846 TCAAAGCGTTGTCTTTCCCT 57.658 45.000 12.18 0.00 34.31 4.20
357 388 6.211184 TCTGTTGAAATGGCAGGTAAATCATT 59.789 34.615 0.00 0.00 0.00 2.57
379 410 6.463995 TTATTGTTCACTTGCCAAAGAACT 57.536 33.333 17.82 6.67 40.62 3.01
387 418 3.383505 ACTTGCCAAAGAACTGTAAACCC 59.616 43.478 0.00 0.00 36.84 4.11
390 421 3.117663 TGCCAAAGAACTGTAAACCCTCT 60.118 43.478 0.00 0.00 0.00 3.69
391 422 3.889538 GCCAAAGAACTGTAAACCCTCTT 59.110 43.478 0.00 0.00 0.00 2.85
392 423 4.341235 GCCAAAGAACTGTAAACCCTCTTT 59.659 41.667 0.00 0.00 36.92 2.52
394 425 6.629515 GCCAAAGAACTGTAAACCCTCTTTTT 60.630 38.462 1.29 0.00 34.84 1.94
452 489 2.806244 ACTCGTGAAAGAATTGTTCCGG 59.194 45.455 0.00 0.00 0.00 5.14
469 506 2.305927 TCCGGAGCAAGAGGAATCTTTT 59.694 45.455 0.00 0.00 0.00 2.27
495 532 3.139029 GGTGGATCCGTCTGTTCAC 57.861 57.895 7.39 0.00 0.00 3.18
508 546 3.492011 GTCTGTTCACGGTTCGTACATTT 59.508 43.478 0.00 0.00 38.32 2.32
589 627 6.697892 CCTGTTTCTACGATGGAGACTAATTC 59.302 42.308 0.00 0.00 0.00 2.17
602 640 4.036518 AGACTAATTCTGCATCTCCTGGT 58.963 43.478 0.00 0.00 31.12 4.00
610 648 7.992754 ATTCTGCATCTCCTGGTTATTAATC 57.007 36.000 0.00 0.00 0.00 1.75
612 650 6.763355 TCTGCATCTCCTGGTTATTAATCTC 58.237 40.000 0.00 0.00 0.00 2.75
618 656 8.646004 CATCTCCTGGTTATTAATCTCTGAAGA 58.354 37.037 0.00 0.00 35.54 2.87
647 685 1.476110 CCATACCGGTACCACATTGGG 60.476 57.143 18.55 6.20 43.37 4.12
679 720 4.019919 TCAGCAATATGAAAAAGCGAGC 57.980 40.909 0.00 0.00 0.00 5.03
690 731 0.605589 AAAGCGAGCTACCACCAACC 60.606 55.000 0.00 0.00 0.00 3.77
691 732 2.436115 GCGAGCTACCACCAACCC 60.436 66.667 0.00 0.00 0.00 4.11
699 740 3.268334 AGCTACCACCAACCCATTATGAA 59.732 43.478 0.00 0.00 0.00 2.57
700 741 3.380320 GCTACCACCAACCCATTATGAAC 59.620 47.826 0.00 0.00 0.00 3.18
813 873 1.474677 CCCATCACTCATCAGTCCTGC 60.475 57.143 0.00 0.00 0.00 4.85
937 997 3.941657 GACACACCTCTCCGCTGCC 62.942 68.421 0.00 0.00 0.00 4.85
953 1021 2.738743 CTGCCTCTCCTCTCTTCTCTT 58.261 52.381 0.00 0.00 0.00 2.85
983 1051 1.288350 CTCAAGGATGAAGCTCGCTG 58.712 55.000 0.00 0.00 34.49 5.18
1048 1116 4.659172 CAAGAGCCCCGCCAACCA 62.659 66.667 0.00 0.00 0.00 3.67
1075 1143 3.453679 AAGCGAGACGAGGAGGGC 61.454 66.667 0.00 0.00 0.00 5.19
1265 1333 0.672401 GTGGAATCGCCGGAAGAACA 60.672 55.000 5.05 2.23 40.66 3.18
1329 1397 3.357079 CCGGCTGGTGACTTGTGC 61.357 66.667 2.29 0.00 0.00 4.57
1360 1428 2.370349 GGCTTTCTTTCTTCTAGGGCC 58.630 52.381 0.00 0.00 0.00 5.80
1609 1845 0.952010 GCATTTGCTGCCCAAGTTGG 60.952 55.000 15.52 15.52 45.66 3.77
1620 1856 2.517959 CCCAAGTTGGCATTCTTCTCA 58.482 47.619 17.07 0.00 35.79 3.27
1637 1880 7.560796 TCTTCTCACCTTCCTTATCTTCTTT 57.439 36.000 0.00 0.00 0.00 2.52
2176 2529 7.247929 TCTATGTACTACATGAGTGAGTTCG 57.752 40.000 11.39 0.00 39.53 3.95
2178 2531 6.701145 ATGTACTACATGAGTGAGTTCGAT 57.299 37.500 0.00 0.00 37.45 3.59
2738 3095 7.042725 CCTGATAGTGTTTACGATGTACATTGG 60.043 40.741 24.01 15.12 0.00 3.16
2752 3109 5.549347 TGTACATTGGCATGCTGAAAATTT 58.451 33.333 18.92 8.39 33.05 1.82
3022 3439 7.148052 TGGAAACTGGAAAATTCGTAAGTTGAA 60.148 33.333 7.72 0.00 39.48 2.69
3053 3470 9.071221 GTTATTTTTATCGTGCATGTGAATGAA 57.929 29.630 5.68 0.00 0.00 2.57
3575 4034 2.802816 CCCCGATTCTTTCTCTAATGCG 59.197 50.000 0.00 0.00 0.00 4.73
4075 5051 8.728088 AACTTGTATATGAAACAGCGAAAAAG 57.272 30.769 0.00 0.00 0.00 2.27
4124 5110 1.104577 CCTCAGAGACCGCTACTCCC 61.105 65.000 0.00 0.00 35.27 4.30
4519 5506 7.283580 CGGTATTACCCTCATTTTCCAACAATA 59.716 37.037 7.29 0.00 33.75 1.90
4564 5551 2.985957 AATGCCACAATGCCATTACC 57.014 45.000 0.00 0.00 0.00 2.85
4566 5553 1.226945 GCCACAATGCCATTACCGC 60.227 57.895 0.00 0.00 0.00 5.68
4573 5610 0.817013 ATGCCATTACCGCCAAACTG 59.183 50.000 0.00 0.00 0.00 3.16
4662 5710 5.679792 AAAATTATTTTTCGAGGCGATACGC 59.320 36.000 7.62 7.62 40.41 4.42
4772 5821 1.202818 AGCTTTGGTGTGGTCCTTCTC 60.203 52.381 0.00 0.00 0.00 2.87
5046 6095 2.300967 GGTGGGAGTGATGGAGCCA 61.301 63.158 0.00 0.00 0.00 4.75
5060 6109 1.228552 AGCCATTGTTCAAGCCGGT 60.229 52.632 1.90 0.00 0.00 5.28
5088 6137 1.333931 CTGACTATAGAGTTCGCCGCA 59.666 52.381 6.78 0.00 35.45 5.69
5219 6268 1.486310 CCTACCCACTGCTGCAATAGA 59.514 52.381 3.02 0.00 0.00 1.98
5265 6314 5.478233 TTCCGATGTGTAAATTTGATCCG 57.522 39.130 0.00 0.00 0.00 4.18
5266 6315 3.311322 TCCGATGTGTAAATTTGATCCGC 59.689 43.478 0.00 0.00 0.00 5.54
5270 6319 0.247894 TGTAAATTTGATCCGCGCGC 60.248 50.000 27.36 23.91 0.00 6.86
5425 6475 1.480137 CAAGAGTGGTTGGTTGGCAAA 59.520 47.619 0.00 0.00 0.00 3.68
5428 6478 1.412343 GAGTGGTTGGTTGGCAAATGT 59.588 47.619 0.00 0.00 0.00 2.71
5571 7004 5.707764 AGTTCTTGGTCATTTCCTTTCTAGC 59.292 40.000 0.00 0.00 0.00 3.42
5586 7019 8.596781 TCCTTTCTAGCAAGAATTAGAGTACT 57.403 34.615 3.47 0.00 41.36 2.73
5607 7040 3.758023 CTGGAGTATGTTGCATGGTTTCA 59.242 43.478 0.00 0.00 0.00 2.69
5613 7046 3.029320 TGTTGCATGGTTTCAGATTGC 57.971 42.857 0.00 0.00 0.00 3.56
5619 7052 0.178967 TGGTTTCAGATTGCCTGGCA 60.179 50.000 19.30 19.30 43.12 4.92
5751 7646 6.775594 ACTAGTAGTTGTCTATGCACATGA 57.224 37.500 0.00 0.00 0.00 3.07
5766 7661 1.610522 ACATGACTTGAGCTGGTTTGC 59.389 47.619 0.00 0.00 0.00 3.68
5772 7667 2.156917 CTTGAGCTGGTTTGCTGATCA 58.843 47.619 0.00 0.00 44.17 2.92
5775 7670 3.954200 TGAGCTGGTTTGCTGATCAATA 58.046 40.909 0.00 0.00 44.17 1.90
5833 7728 4.037208 GCCGGTCATTCTCAATCAATTCAT 59.963 41.667 1.90 0.00 0.00 2.57
5914 7855 5.469760 CGCTCCCATTACATTTACATGATCA 59.530 40.000 0.00 0.00 34.11 2.92
6052 7994 6.942005 TGTATATGTCCATGGATTGATGTTCC 59.058 38.462 19.62 1.65 0.00 3.62
6073 8015 4.099419 TCCTTTTCTTTTGAAGCCCAGAAC 59.901 41.667 0.00 0.00 39.88 3.01
6074 8016 4.371786 CTTTTCTTTTGAAGCCCAGAACC 58.628 43.478 0.00 0.00 39.88 3.62
6081 8023 1.275291 TGAAGCCCAGAACCGTAGAAG 59.725 52.381 0.00 0.00 0.00 2.85
6161 8103 7.656412 AGCAAAAAGAAAAACCAAACAAATGT 58.344 26.923 0.00 0.00 0.00 2.71
6169 8111 6.739331 AAAACCAAACAAATGTCCTATCCA 57.261 33.333 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 6.511416 TCATTACAAAATTCACCACACAAGG 58.489 36.000 0.00 0.00 0.00 3.61
2 3 7.305935 CGTTCATTACAAAATTCACCACACAAG 60.306 37.037 0.00 0.00 0.00 3.16
3 4 6.473778 CGTTCATTACAAAATTCACCACACAA 59.526 34.615 0.00 0.00 0.00 3.33
4 5 5.974158 CGTTCATTACAAAATTCACCACACA 59.026 36.000 0.00 0.00 0.00 3.72
6 7 6.378710 TCGTTCATTACAAAATTCACCACA 57.621 33.333 0.00 0.00 0.00 4.17
8 9 7.429633 ACAATCGTTCATTACAAAATTCACCA 58.570 30.769 0.00 0.00 0.00 4.17
9 10 7.867445 ACAATCGTTCATTACAAAATTCACC 57.133 32.000 0.00 0.00 0.00 4.02
39 40 9.709495 CCCCCACACATTAATCAATTAATAATG 57.291 33.333 7.48 10.60 40.07 1.90
137 138 3.470888 AACCGGAGAGCGGATGGG 61.471 66.667 9.46 0.00 0.00 4.00
159 160 5.047590 GTGGTAACCCTTTTCCAACCTTATG 60.048 44.000 0.00 0.00 34.22 1.90
176 177 6.453926 TTGGTTTTAGGAACAAGTGGTAAC 57.546 37.500 0.00 0.00 0.00 2.50
178 179 7.201929 GGAATTTGGTTTTAGGAACAAGTGGTA 60.202 37.037 0.00 0.00 0.00 3.25
214 223 5.048782 AGACAACGCTTTGATCTTGCATAAA 60.049 36.000 10.27 0.00 36.48 1.40
220 229 4.222114 GGAAAGACAACGCTTTGATCTTG 58.778 43.478 10.27 0.00 38.16 3.02
236 267 5.308825 CAGCTACAGAAGAAAAGGGAAAGA 58.691 41.667 0.00 0.00 0.00 2.52
244 275 4.567747 GGGGAATCCAGCTACAGAAGAAAA 60.568 45.833 0.09 0.00 35.00 2.29
333 364 5.389859 TGATTTACCTGCCATTTCAACAG 57.610 39.130 0.00 0.00 0.00 3.16
357 388 5.359576 ACAGTTCTTTGGCAAGTGAACAATA 59.640 36.000 30.83 6.62 40.62 1.90
396 427 6.826231 TCATGGACTTGACTTGACTAACAAAA 59.174 34.615 0.00 0.00 38.08 2.44
399 430 5.541845 CTCATGGACTTGACTTGACTAACA 58.458 41.667 0.00 0.00 0.00 2.41
400 431 4.390297 GCTCATGGACTTGACTTGACTAAC 59.610 45.833 0.00 0.00 0.00 2.34
401 432 4.040339 TGCTCATGGACTTGACTTGACTAA 59.960 41.667 0.00 0.00 0.00 2.24
403 434 2.369860 TGCTCATGGACTTGACTTGACT 59.630 45.455 0.00 0.00 0.00 3.41
404 435 2.771089 TGCTCATGGACTTGACTTGAC 58.229 47.619 0.00 0.00 0.00 3.18
408 439 3.430042 ACAATGCTCATGGACTTGACT 57.570 42.857 0.00 0.00 0.00 3.41
409 440 3.503363 TGAACAATGCTCATGGACTTGAC 59.497 43.478 0.00 0.00 0.00 3.18
452 489 2.821969 TGCCAAAAGATTCCTCTTGCTC 59.178 45.455 0.00 0.00 40.93 4.26
487 524 3.374220 AATGTACGAACCGTGAACAGA 57.626 42.857 1.93 0.00 41.39 3.41
589 627 6.649973 CAGAGATTAATAACCAGGAGATGCAG 59.350 42.308 0.00 0.00 0.00 4.41
610 648 5.525378 CGGTATGGAGGAAAAATCTTCAGAG 59.475 44.000 0.00 0.00 0.00 3.35
612 650 4.576463 CCGGTATGGAGGAAAAATCTTCAG 59.424 45.833 0.00 0.00 42.00 3.02
618 656 3.524380 TGGTACCGGTATGGAGGAAAAAT 59.476 43.478 19.19 0.00 42.00 1.82
679 720 4.855340 AGTTCATAATGGGTTGGTGGTAG 58.145 43.478 0.00 0.00 0.00 3.18
733 775 4.142790 TCAAAAAGTACCACCGCCATTTA 58.857 39.130 0.00 0.00 0.00 1.40
792 852 1.140452 CAGGACTGATGAGTGATGGGG 59.860 57.143 0.00 0.00 30.16 4.96
813 873 1.067060 TCACTTGTGACGAGTGACAGG 59.933 52.381 27.29 6.28 46.21 4.00
937 997 4.164988 AGGAGAGAAGAGAAGAGAGGAGAG 59.835 50.000 0.00 0.00 0.00 3.20
1048 1116 3.923864 TCTCGCTTGCGGTGTGGT 61.924 61.111 15.10 0.00 0.00 4.16
1075 1143 1.153289 CCGCAGTTCCCCATCTCTG 60.153 63.158 0.00 0.00 0.00 3.35
1219 1287 0.673985 TCCATAACGCGGATCTCAGG 59.326 55.000 12.47 2.76 0.00 3.86
1265 1333 5.399301 CGTCACAAAAATCGAAGCAAAGAAT 59.601 36.000 0.00 0.00 0.00 2.40
1315 1383 4.030452 GCCGCACAAGTCACCAGC 62.030 66.667 0.00 0.00 0.00 4.85
1329 1397 1.644786 AAGAAAGCCCGAATTCGCCG 61.645 55.000 22.36 14.60 38.18 6.46
1609 1845 5.679601 AGATAAGGAAGGTGAGAAGAATGC 58.320 41.667 0.00 0.00 0.00 3.56
1620 1856 6.207614 GCAAGAACAAAGAAGATAAGGAAGGT 59.792 38.462 0.00 0.00 0.00 3.50
1637 1880 4.951715 AGCAGGATTTATGATGCAAGAACA 59.048 37.500 0.00 0.00 41.14 3.18
1928 2276 6.382859 TGGCTTGGACTATGTTTCTGAGTATA 59.617 38.462 0.00 0.00 0.00 1.47
1929 2277 5.189736 TGGCTTGGACTATGTTTCTGAGTAT 59.810 40.000 0.00 0.00 0.00 2.12
2144 2497 6.262049 ACTCATGTAGTACATAGAGCTGAGTG 59.738 42.308 24.20 9.50 38.66 3.51
2282 2638 5.418524 TGTTAGTGCCATTTATGCATCAGTT 59.581 36.000 0.19 0.00 41.46 3.16
3022 3439 8.085296 TCACATGCACGATAAAAATAACCTTTT 58.915 29.630 0.00 0.00 33.22 2.27
3053 3470 1.047034 ACTCGGGGGCTACGCTTATT 61.047 55.000 0.00 0.00 0.00 1.40
3068 3485 1.467734 AGTAACTACAGGCACGACTCG 59.532 52.381 0.00 0.00 0.00 4.18
3106 3523 6.773976 ATGTTTCCAAATCCAATACACGAT 57.226 33.333 0.00 0.00 0.00 3.73
3294 3743 8.836413 TGAGTAACACATTGAGAACTTTTTAGG 58.164 33.333 0.00 0.00 0.00 2.69
3575 4034 2.283298 AGCATGACGATGGTGTTGATC 58.717 47.619 0.00 0.00 38.90 2.92
4046 5022 9.601971 TTTCGCTGTTTCATATACAAGTTTAAC 57.398 29.630 0.00 0.00 0.00 2.01
4075 5051 4.822350 ACAAGAGAAGGAGTTAGCAAAACC 59.178 41.667 0.00 0.00 0.00 3.27
4115 5101 2.125178 CCAGGGTAAGGGAGTAGCG 58.875 63.158 0.00 0.00 0.00 4.26
4124 5110 1.580059 TCCTAGTTGCCCAGGGTAAG 58.420 55.000 9.76 0.00 32.40 2.34
4295 5282 8.985315 ATTTCTGATGGATATGCAAAGAACTA 57.015 30.769 19.02 10.54 0.00 2.24
4552 5539 1.204467 AGTTTGGCGGTAATGGCATTG 59.796 47.619 22.57 7.30 44.53 2.82
4553 5540 1.204467 CAGTTTGGCGGTAATGGCATT 59.796 47.619 18.01 18.01 44.53 3.56
4564 5551 1.063616 CTCAGATCATGCAGTTTGGCG 59.936 52.381 0.00 0.00 36.28 5.69
4566 5553 4.035324 GTGATCTCAGATCATGCAGTTTGG 59.965 45.833 20.49 0.00 0.00 3.28
4772 5821 4.504916 CGCCCTGTCAGGAGCTCG 62.505 72.222 21.23 13.24 37.67 5.03
4862 5911 0.398696 TTTGGTGAAGCCGCCTCTTA 59.601 50.000 0.00 0.00 43.32 2.10
5046 6095 3.365535 GCCACCGGCTTGAACAAT 58.634 55.556 0.00 0.00 46.69 2.71
5060 6109 1.860240 ACTCTATAGTCAGGGAGGCCA 59.140 52.381 5.01 0.00 0.00 5.36
5088 6137 2.032681 GCTGTTTCCGGTCAGGCT 59.967 61.111 19.29 0.00 40.77 4.58
5219 6268 1.613437 GCTTGCAATGTACAACTGGGT 59.387 47.619 0.00 0.00 0.00 4.51
5270 6319 0.863957 AACGAAAAACAACAGCGGCG 60.864 50.000 0.51 0.51 0.00 6.46
5274 6323 3.000773 CAGCAGAAACGAAAAACAACAGC 60.001 43.478 0.00 0.00 0.00 4.40
5425 6475 9.561069 GACATAACTTCCATAGTTCCATAACAT 57.439 33.333 0.00 0.00 43.67 2.71
5428 6478 8.544622 TGTGACATAACTTCCATAGTTCCATAA 58.455 33.333 0.00 0.00 43.67 1.90
5571 7004 9.307121 CAACATACTCCAGTACTCTAATTCTTG 57.693 37.037 0.00 0.00 32.72 3.02
5586 7019 3.758023 CTGAAACCATGCAACATACTCCA 59.242 43.478 0.00 0.00 0.00 3.86
5613 7046 1.675310 TTCGACAGCCATTGCCAGG 60.675 57.895 0.00 0.00 38.69 4.45
5619 7052 2.093500 TGATGCTAGTTCGACAGCCATT 60.093 45.455 9.64 0.00 36.95 3.16
5751 7646 2.157738 GATCAGCAAACCAGCTCAAGT 58.842 47.619 0.00 0.00 44.54 3.16
5833 7728 8.353684 CACCACACCAATTTACTAATTTACACA 58.646 33.333 0.00 0.00 31.63 3.72
6052 7994 4.371786 GGTTCTGGGCTTCAAAAGAAAAG 58.628 43.478 0.00 0.00 30.85 2.27
6118 8060 9.691362 CTTTTTGCTTGTAAATATGTAGTGGTT 57.309 29.630 0.00 0.00 0.00 3.67
6119 8061 9.073475 TCTTTTTGCTTGTAAATATGTAGTGGT 57.927 29.630 0.00 0.00 0.00 4.16
6120 8062 9.906660 TTCTTTTTGCTTGTAAATATGTAGTGG 57.093 29.630 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.