Multiple sequence alignment - TraesCS4B01G174300

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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 TraesCS4B01G174300 chr4B 100.000 6685 0 0 1 6685 382204984 382211668 0.000000e+00 12345.0
1 TraesCS4B01G174300 chr4B 98.472 2029 29 2 4657 6684 382231584 382233611 0.000000e+00 3574.0
2 TraesCS4B01G174300 chr4B 89.201 463 40 5 6232 6685 664556718 664556257 2.710000e-158 569.0
3 TraesCS4B01G174300 chr4B 82.124 386 54 9 6176 6553 117078698 117078320 3.890000e-82 316.0
4 TraesCS4B01G174300 chr4D 96.272 4265 105 29 1129 5349 305981368 305985622 0.000000e+00 6946.0
5 TraesCS4B01G174300 chr4D 97.756 713 9 2 5342 6047 305985645 305986357 0.000000e+00 1221.0
6 TraesCS4B01G174300 chr4D 86.850 981 45 24 1 931 305980054 305981000 0.000000e+00 1020.0
7 TraesCS4B01G174300 chr4D 90.323 155 8 5 976 1124 305981146 305981299 5.290000e-46 196.0
8 TraesCS4B01G174300 chr4A 95.662 2282 58 19 1129 3384 171208226 171205960 0.000000e+00 3627.0
9 TraesCS4B01G174300 chr4A 96.789 1962 54 6 3392 5349 171205920 171203964 0.000000e+00 3265.0
10 TraesCS4B01G174300 chr4A 97.046 677 16 1 5345 6017 171203938 171203262 0.000000e+00 1136.0
11 TraesCS4B01G174300 chr4A 85.920 696 25 27 466 1124 171208960 171208301 0.000000e+00 675.0
12 TraesCS4B01G174300 chr4A 84.561 421 22 9 1 391 171209493 171209086 1.760000e-100 377.0
13 TraesCS4B01G174300 chr1B 82.038 579 92 9 6115 6685 359410445 359409871 3.630000e-132 483.0
14 TraesCS4B01G174300 chr5A 85.928 469 41 18 6218 6685 456070915 456071359 1.690000e-130 477.0
15 TraesCS4B01G174300 chr3D 91.496 341 26 1 6345 6685 498870590 498870927 3.650000e-127 466.0
16 TraesCS4B01G174300 chr1D 82.766 470 75 6 6218 6684 40176507 40176041 1.340000e-111 414.0
17 TraesCS4B01G174300 chr1D 89.506 324 26 3 6370 6685 46392585 46392908 2.900000e-108 403.0
18 TraesCS4B01G174300 chr3B 79.725 582 81 22 6115 6685 768732935 768732380 2.920000e-103 387.0
19 TraesCS4B01G174300 chrUn 82.124 386 54 9 6176 6553 395017424 395017802 3.890000e-82 316.0
20 TraesCS4B01G174300 chr7D 82.817 355 55 2 6332 6685 445455074 445455423 5.030000e-81 313.0
21 TraesCS4B01G174300 chr2D 100.000 29 0 0 6070 6098 306300867 306300839 3.000000e-03 54.7
22 TraesCS4B01G174300 chr2B 100.000 29 0 0 6070 6098 374248987 374248959 3.000000e-03 54.7
23 TraesCS4B01G174300 chr2A 100.000 28 0 0 6070 6097 385340250 385340223 1.200000e-02 52.8


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 TraesCS4B01G174300 chr4B 382204984 382211668 6684 False 12345.00 12345 100.00000 1 6685 1 chr4B.!!$F1 6684
1 TraesCS4B01G174300 chr4B 382231584 382233611 2027 False 3574.00 3574 98.47200 4657 6684 1 chr4B.!!$F2 2027
2 TraesCS4B01G174300 chr4D 305980054 305986357 6303 False 2345.75 6946 92.80025 1 6047 4 chr4D.!!$F1 6046
3 TraesCS4B01G174300 chr4A 171203262 171209493 6231 True 1816.00 3627 91.99560 1 6017 5 chr4A.!!$R1 6016
4 TraesCS4B01G174300 chr1B 359409871 359410445 574 True 483.00 483 82.03800 6115 6685 1 chr1B.!!$R1 570
5 TraesCS4B01G174300 chr3B 768732380 768732935 555 True 387.00 387 79.72500 6115 6685 1 chr3B.!!$R1 570

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
566 650 0.038435 TGCAATCCATTTGGCGTGTG 60.038 50.000 0.00 0.0 35.75 3.82 F
1230 1539 0.322008 CTCCTGCGCTTCCTTCCTTT 60.322 55.000 9.73 0.0 0.00 3.11 F
1231 1540 0.606401 TCCTGCGCTTCCTTCCTTTG 60.606 55.000 9.73 0.0 0.00 2.77 F
2509 2827 1.302285 CATGGAGCTGGTGAGGCTT 59.698 57.895 0.00 0.0 40.40 4.35 F
3866 4240 0.881118 TTGAAAGGAACATGCGCCTC 59.119 50.000 4.18 0.0 32.07 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1951 2269 0.603065 TCAGCGTCTCTTGCTTAGCA 59.397 50.000 1.39 1.39 41.72 3.49 R
2509 2827 1.078497 CATGAAGTACGCCTGCCCA 60.078 57.895 0.00 0.00 0.00 5.36 R
2775 3093 1.434513 ATCAAACCCCAGCCCAGACA 61.435 55.000 0.00 0.00 0.00 3.41 R
4300 4678 1.402511 GCGACTTCAAAAAGCTGCAG 58.597 50.000 10.11 10.11 36.47 4.41 R
6199 6646 0.178900 GGAGAATAGGGGACGGGGAT 60.179 60.000 0.00 0.00 0.00 3.85 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
33 34 1.881973 GTGGTTTACGGGGACTTTTCC 59.118 52.381 0.00 0.00 41.95 3.13
58 59 2.738846 CGAGGGTTTGATGTCAACTCTG 59.261 50.000 0.00 0.00 35.28 3.35
59 60 3.744660 GAGGGTTTGATGTCAACTCTGT 58.255 45.455 0.00 0.00 35.28 3.41
60 61 4.560716 CGAGGGTTTGATGTCAACTCTGTA 60.561 45.833 0.00 0.00 35.28 2.74
61 62 4.899502 AGGGTTTGATGTCAACTCTGTAG 58.100 43.478 0.00 0.00 35.28 2.74
62 63 4.348168 AGGGTTTGATGTCAACTCTGTAGT 59.652 41.667 0.00 0.00 37.65 2.73
63 64 5.542635 AGGGTTTGATGTCAACTCTGTAGTA 59.457 40.000 0.00 0.00 33.75 1.82
64 65 6.213600 AGGGTTTGATGTCAACTCTGTAGTAT 59.786 38.462 0.00 0.00 33.75 2.12
65 66 7.399191 AGGGTTTGATGTCAACTCTGTAGTATA 59.601 37.037 0.00 0.00 33.75 1.47
66 67 7.707035 GGGTTTGATGTCAACTCTGTAGTATAG 59.293 40.741 0.00 0.00 33.75 1.31
67 68 8.251721 GGTTTGATGTCAACTCTGTAGTATAGT 58.748 37.037 0.00 0.00 33.75 2.12
68 69 9.077674 GTTTGATGTCAACTCTGTAGTATAGTG 57.922 37.037 0.00 0.00 33.75 2.74
132 154 2.108566 CCTCCATGGAGCAGAGCG 59.891 66.667 32.97 16.45 40.69 5.03
160 182 3.431415 TCCTCTGTCAAGATTCTTCCGA 58.569 45.455 0.00 0.00 0.00 4.55
223 253 2.412089 GGCACTTGTTCATCTGACGTAC 59.588 50.000 0.00 0.00 0.00 3.67
254 284 3.499072 ACGTTGACTTGATTCGAAACG 57.501 42.857 0.00 7.60 44.28 3.60
267 297 3.595709 TCGAAACGAAACGCAGAAAAT 57.404 38.095 0.00 0.00 31.06 1.82
278 308 2.554032 ACGCAGAAAATAAAGCAGCAGT 59.446 40.909 0.00 0.00 0.00 4.40
370 403 6.549364 TGAAATGACTTTTCTTTAGCCCTTGA 59.451 34.615 13.25 0.00 43.50 3.02
391 424 8.450964 CCTTGATTTATGTGGGCTTAATATACG 58.549 37.037 0.00 0.00 0.00 3.06
392 425 7.915293 TGATTTATGTGGGCTTAATATACGG 57.085 36.000 0.00 0.00 0.00 4.02
393 426 6.882140 TGATTTATGTGGGCTTAATATACGGG 59.118 38.462 0.00 0.00 0.00 5.28
394 427 6.436738 TTTATGTGGGCTTAATATACGGGA 57.563 37.500 0.00 0.00 0.00 5.14
422 470 4.886247 TTAAATCTCGCCCAAAATACGG 57.114 40.909 0.00 0.00 0.00 4.02
444 524 5.461526 GGAGAATTAGAAACTGGTTGCAAC 58.538 41.667 21.59 21.59 0.00 4.17
458 539 3.862845 GGTTGCAACCTGTTTGTTTGTAG 59.137 43.478 36.26 0.00 45.75 2.74
460 541 5.393243 GGTTGCAACCTGTTTGTTTGTAGTA 60.393 40.000 36.26 0.00 45.75 1.82
461 542 6.270064 GTTGCAACCTGTTTGTTTGTAGTAT 58.730 36.000 19.15 0.00 37.54 2.12
462 543 6.458232 TGCAACCTGTTTGTTTGTAGTATT 57.542 33.333 0.00 0.00 37.54 1.89
463 544 6.269315 TGCAACCTGTTTGTTTGTAGTATTG 58.731 36.000 0.00 0.00 37.54 1.90
541 625 2.951676 TCGATGAGACGATGATCGAC 57.048 50.000 22.88 15.75 43.74 4.20
566 650 0.038435 TGCAATCCATTTGGCGTGTG 60.038 50.000 0.00 0.00 35.75 3.82
751 843 1.088306 CGCTACTCCGAGTCTGTCTT 58.912 55.000 3.74 0.00 0.00 3.01
772 864 6.365247 GTCTTCGTATGACAGCTTTGTTTCTA 59.635 38.462 0.00 0.00 34.80 2.10
787 879 9.908152 GCTTTGTTTCTACACTAATTAAACCAT 57.092 29.630 0.00 0.00 32.98 3.55
854 950 7.284489 ACAAAATTAACAGCTCACTTAGTTGGA 59.716 33.333 0.00 0.00 40.53 3.53
881 977 3.576861 TCCCTTGTCTTCTGTCTTCTCA 58.423 45.455 0.00 0.00 0.00 3.27
914 1019 7.865706 TCCTAATCAAATTTCTACTTGCCTC 57.134 36.000 0.00 0.00 0.00 4.70
974 1164 8.423906 TTTATTGCTAGACTATTAGAGGAGGG 57.576 38.462 0.00 0.00 0.00 4.30
1023 1230 2.043227 CCCAAAACCCAAAGCCTACAA 58.957 47.619 0.00 0.00 0.00 2.41
1024 1231 2.224185 CCCAAAACCCAAAGCCTACAAC 60.224 50.000 0.00 0.00 0.00 3.32
1025 1232 2.432510 CCAAAACCCAAAGCCTACAACA 59.567 45.455 0.00 0.00 0.00 3.33
1081 1296 2.427095 GTGCTTTTGTCCTCACCAACTT 59.573 45.455 0.00 0.00 0.00 2.66
1153 1438 3.036091 AGCAGCCCATCTTTAATGCAAT 58.964 40.909 0.00 0.00 36.15 3.56
1213 1522 0.458889 CACTGCTCTGCTCTGCTCTC 60.459 60.000 0.00 0.00 0.00 3.20
1216 1525 1.142314 GCTCTGCTCTGCTCTCCTG 59.858 63.158 0.00 0.00 0.00 3.86
1217 1526 1.142314 CTCTGCTCTGCTCTCCTGC 59.858 63.158 0.00 0.00 0.00 4.85
1230 1539 0.322008 CTCCTGCGCTTCCTTCCTTT 60.322 55.000 9.73 0.00 0.00 3.11
1231 1540 0.606401 TCCTGCGCTTCCTTCCTTTG 60.606 55.000 9.73 0.00 0.00 2.77
1678 1996 4.856607 CTCGCCTTCGTCCTCGCC 62.857 72.222 0.00 0.00 36.96 5.54
1714 2032 4.112341 GCGTACGAGGACTGGCGT 62.112 66.667 21.65 0.00 43.86 5.68
1748 2066 2.888534 GCGCCGAGAATAACCGCA 60.889 61.111 0.00 0.00 43.67 5.69
1765 2083 3.071206 ATCGCCGCTGTCCTGTCT 61.071 61.111 0.00 0.00 0.00 3.41
1773 2091 4.988716 TGTCCTGTCTCCCGGCGT 62.989 66.667 6.01 0.00 0.00 5.68
1774 2092 2.753043 GTCCTGTCTCCCGGCGTA 60.753 66.667 6.01 0.00 0.00 4.42
1794 2112 2.124320 CGCCCAATTCGTCCCCAT 60.124 61.111 0.00 0.00 0.00 4.00
1948 2266 3.938289 GAGTCCAACCTAAAGACTCGT 57.062 47.619 3.85 0.00 44.98 4.18
1951 2269 5.963594 GAGTCCAACCTAAAGACTCGTTAT 58.036 41.667 3.85 0.00 44.98 1.89
2283 2601 2.182791 CATCGTGCTCTGCTCGGT 59.817 61.111 12.76 4.30 44.06 4.69
2385 2703 2.045926 CAAGGTCGGCAAGGAGGG 60.046 66.667 0.00 0.00 0.00 4.30
2389 2707 2.044946 GTCGGCAAGGAGGGCAAT 60.045 61.111 0.00 0.00 0.00 3.56
2431 2749 3.788766 GCGGCGCAGATCGTGTTT 61.789 61.111 29.21 0.00 41.07 2.83
2509 2827 1.302285 CATGGAGCTGGTGAGGCTT 59.698 57.895 0.00 0.00 40.40 4.35
2553 2871 2.430244 CGCCAAGCTGTACGACGT 60.430 61.111 5.52 5.52 0.00 4.34
2677 2995 3.950794 GATGGAGTTCCGGTGCGCA 62.951 63.158 5.66 5.66 39.43 6.09
2775 3093 5.892119 TCAGTAAATTCTATCGAGTGGAGGT 59.108 40.000 0.00 0.00 0.00 3.85
2818 3136 2.622452 CCTTTGATTCATGGCAGAGGGT 60.622 50.000 10.73 0.00 33.90 4.34
2960 3278 1.334960 CGTGCAACACCATTGTTCCTC 60.335 52.381 0.00 0.00 44.57 3.71
3064 3385 2.403586 GCGGCGTATGGCTTTGTC 59.596 61.111 9.37 0.00 42.94 3.18
3067 3388 1.705337 CGGCGTATGGCTTTGTCCTG 61.705 60.000 6.95 0.00 42.94 3.86
3199 3523 8.606602 GGGAATTTTGCTTTCATTTCATGATAC 58.393 33.333 0.00 0.00 39.39 2.24
3200 3524 9.374838 GGAATTTTGCTTTCATTTCATGATACT 57.625 29.630 0.00 0.00 39.39 2.12
3213 3537 7.801716 TTTCATGATACTATACAGTTTGCCC 57.198 36.000 0.00 0.00 36.14 5.36
3233 3557 4.691216 GCCCTTAGTTTGTGTCTTCTAGTG 59.309 45.833 0.00 0.00 0.00 2.74
3342 3684 4.142600 GCAACCGCAGAACTTCAGATATTT 60.143 41.667 0.00 0.00 38.36 1.40
3390 3764 4.350368 TGACTGCAATAGGTTGAGTTGA 57.650 40.909 0.00 0.00 37.53 3.18
3405 3779 8.414003 AGGTTGAGTTGATTTCCTTAGTTTTTC 58.586 33.333 0.00 0.00 0.00 2.29
3406 3780 7.378728 GGTTGAGTTGATTTCCTTAGTTTTTCG 59.621 37.037 0.00 0.00 0.00 3.46
3506 3880 6.090223 CACAAAACATTTAATCGCCTTTACCC 59.910 38.462 0.00 0.00 0.00 3.69
3740 4114 1.337821 GAACACTCGTCATCGGTGTC 58.662 55.000 0.00 0.00 44.18 3.67
3752 4126 1.969862 CGGTGTCCGGGAACTTAGT 59.030 57.895 0.00 0.00 44.15 2.24
3797 4171 1.848652 TGGCTTACGAGAAGGCTAGT 58.151 50.000 21.94 0.00 42.57 2.57
3824 4198 4.723309 CCTTATTAGGCAGAGGCAATCTT 58.277 43.478 0.00 0.00 43.71 2.40
3866 4240 0.881118 TTGAAAGGAACATGCGCCTC 59.119 50.000 4.18 0.00 32.07 4.70
4196 4570 4.510340 GTCTACATTTTTGACACAGACCGT 59.490 41.667 0.00 0.00 0.00 4.83
4416 4794 2.802816 GCGAACAAGTGACATGACTCTT 59.197 45.455 0.00 2.83 0.00 2.85
4478 4856 3.254166 TCAGCACTTTCATCTTTTGCTCC 59.746 43.478 0.00 0.00 41.60 4.70
4550 4928 5.836898 AGGTGCAAATGATGTATCCATGATT 59.163 36.000 0.00 0.00 36.60 2.57
4649 5027 4.225042 GGGCAATTTAGATTTTTGGTCCCT 59.775 41.667 0.00 0.00 0.00 4.20
4652 5030 6.379988 GGCAATTTAGATTTTTGGTCCCTCTA 59.620 38.462 0.00 0.00 0.00 2.43
6105 6552 0.323178 ACTTACCTCTCTTCCCGCGA 60.323 55.000 8.23 0.00 0.00 5.87
6212 6659 4.892291 GGCCATCCCCGTCCCCTA 62.892 72.222 0.00 0.00 0.00 3.53
6224 6677 0.568697 GTCCCCTATTCTCCCCTCCT 59.431 60.000 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 1.001974 TGACATCAAACCCTCGACTGG 59.998 52.381 0.00 0.00 0.00 4.00
33 34 2.455674 TGACATCAAACCCTCGACTG 57.544 50.000 0.00 0.00 0.00 3.51
58 59 5.510674 CCGCGCAATATGTACACTATACTAC 59.489 44.000 8.75 0.00 0.00 2.73
59 60 5.412286 TCCGCGCAATATGTACACTATACTA 59.588 40.000 8.75 0.00 0.00 1.82
60 61 4.216902 TCCGCGCAATATGTACACTATACT 59.783 41.667 8.75 0.00 0.00 2.12
61 62 4.478699 TCCGCGCAATATGTACACTATAC 58.521 43.478 8.75 0.00 0.00 1.47
62 63 4.380128 CCTCCGCGCAATATGTACACTATA 60.380 45.833 8.75 0.00 0.00 1.31
63 64 3.575630 CTCCGCGCAATATGTACACTAT 58.424 45.455 8.75 0.00 0.00 2.12
64 65 2.287970 CCTCCGCGCAATATGTACACTA 60.288 50.000 8.75 0.00 0.00 2.74
65 66 1.538204 CCTCCGCGCAATATGTACACT 60.538 52.381 8.75 0.00 0.00 3.55
66 67 0.859232 CCTCCGCGCAATATGTACAC 59.141 55.000 8.75 0.00 0.00 2.90
67 68 0.462375 ACCTCCGCGCAATATGTACA 59.538 50.000 8.75 0.00 0.00 2.90
68 69 1.260561 CAACCTCCGCGCAATATGTAC 59.739 52.381 8.75 0.00 0.00 2.90
132 154 4.588528 AGAATCTTGACAGAGGATAGCTCC 59.411 45.833 0.00 0.00 42.43 4.70
160 182 5.048364 TGTTGGACGCAAACATATTTTAGCT 60.048 36.000 0.00 0.00 32.71 3.32
217 244 0.638746 CGTTCGCAATGGAGTACGTC 59.361 55.000 0.00 0.00 34.07 4.34
223 253 1.148310 AGTCAACGTTCGCAATGGAG 58.852 50.000 0.00 0.00 0.00 3.86
254 284 3.980775 TGCTGCTTTATTTTCTGCGTTTC 59.019 39.130 0.00 0.00 0.00 2.78
267 297 0.250295 ACGCCAAGACTGCTGCTTTA 60.250 50.000 0.00 0.00 0.00 1.85
278 308 1.269883 TGACTTTTCGCTACGCCAAGA 60.270 47.619 5.38 0.00 0.00 3.02
370 403 7.023171 TCCCGTATATTAAGCCCACATAAAT 57.977 36.000 0.00 0.00 0.00 1.40
391 424 3.813724 GGGCGAGATTTAATTGTACTCCC 59.186 47.826 0.00 0.00 0.00 4.30
392 425 4.448210 TGGGCGAGATTTAATTGTACTCC 58.552 43.478 0.00 0.00 0.00 3.85
393 426 6.431198 TTTGGGCGAGATTTAATTGTACTC 57.569 37.500 0.00 0.00 0.00 2.59
394 427 6.827586 TTTTGGGCGAGATTTAATTGTACT 57.172 33.333 0.00 0.00 0.00 2.73
396 429 7.411274 CGTATTTTGGGCGAGATTTAATTGTA 58.589 34.615 0.00 0.00 0.00 2.41
398 431 5.685511 CCGTATTTTGGGCGAGATTTAATTG 59.314 40.000 0.00 0.00 0.00 2.32
444 524 5.183140 CCTCCCAATACTACAAACAAACAGG 59.817 44.000 0.00 0.00 0.00 4.00
482 566 4.451150 TCATCGAGGGTGTGCCGC 62.451 66.667 0.00 0.00 34.97 6.53
541 625 1.202604 GCCAAATGGATTGCAGATGGG 60.203 52.381 2.98 0.00 37.73 4.00
622 706 1.069500 GTCATTTTCGTCGGGTTGGTG 60.069 52.381 0.00 0.00 0.00 4.17
667 757 2.434359 CGAAAGTGGGGAGACGGC 60.434 66.667 0.00 0.00 0.00 5.68
751 843 5.404366 GTGTAGAAACAAAGCTGTCATACGA 59.596 40.000 0.00 0.00 37.36 3.43
805 897 9.563748 TTGTTTATAGGCGGCTTAATATAACTT 57.436 29.630 19.76 0.00 0.00 2.66
806 898 9.563748 TTTGTTTATAGGCGGCTTAATATAACT 57.436 29.630 19.76 0.00 0.00 2.24
812 904 9.524106 GTTAATTTTGTTTATAGGCGGCTTAAT 57.476 29.630 19.76 8.33 0.00 1.40
813 905 8.521176 TGTTAATTTTGTTTATAGGCGGCTTAA 58.479 29.630 19.76 12.70 0.00 1.85
854 950 5.511386 AGACAGAAGACAAGGGAATGAAT 57.489 39.130 0.00 0.00 0.00 2.57
914 1019 7.429633 AGTAATCGGATTAGTCAAGTCATCAG 58.570 38.462 10.60 0.00 0.00 2.90
955 1145 5.386924 TCAACCCTCCTCTAATAGTCTAGC 58.613 45.833 0.00 0.00 0.00 3.42
964 1154 4.026744 CTCATGACTCAACCCTCCTCTAA 58.973 47.826 0.00 0.00 0.00 2.10
965 1155 3.269643 TCTCATGACTCAACCCTCCTCTA 59.730 47.826 0.00 0.00 0.00 2.43
967 1157 2.167487 GTCTCATGACTCAACCCTCCTC 59.833 54.545 0.00 0.00 39.94 3.71
968 1158 2.183679 GTCTCATGACTCAACCCTCCT 58.816 52.381 0.00 0.00 39.94 3.69
969 1159 1.902508 TGTCTCATGACTCAACCCTCC 59.097 52.381 0.00 0.00 43.29 4.30
970 1160 3.196469 TCATGTCTCATGACTCAACCCTC 59.804 47.826 8.14 0.00 43.29 4.30
971 1161 3.176411 TCATGTCTCATGACTCAACCCT 58.824 45.455 8.14 0.00 43.29 4.34
972 1162 3.196469 TCTCATGTCTCATGACTCAACCC 59.804 47.826 8.14 0.00 43.29 4.11
974 1164 4.159321 TCCTCTCATGTCTCATGACTCAAC 59.841 45.833 8.14 0.00 43.29 3.18
1023 1230 0.041982 GAGGGAGGGAGAGACCTTGT 59.958 60.000 0.00 0.00 42.10 3.16
1024 1231 1.040339 CGAGGGAGGGAGAGACCTTG 61.040 65.000 0.00 0.00 42.10 3.61
1025 1232 1.308326 CGAGGGAGGGAGAGACCTT 59.692 63.158 0.00 0.00 42.10 3.50
1081 1296 2.170607 CGCTTAAAATCTGGGAGAGGGA 59.829 50.000 0.00 0.00 0.00 4.20
1124 1339 4.124943 ATGGGCTGCTGCTGAGGG 62.125 66.667 15.64 0.00 39.59 4.30
1125 1340 2.516460 GATGGGCTGCTGCTGAGG 60.516 66.667 15.64 0.00 39.59 3.86
1127 1342 0.620030 TAAAGATGGGCTGCTGCTGA 59.380 50.000 15.64 2.63 39.59 4.26
1153 1438 2.954318 GTGGGAGTAACTATGGCGAGTA 59.046 50.000 0.00 0.00 0.00 2.59
1213 1522 1.878775 CAAAGGAAGGAAGCGCAGG 59.121 57.895 11.47 0.00 0.00 4.85
1216 1525 1.503994 GAGCAAAGGAAGGAAGCGC 59.496 57.895 0.00 0.00 0.00 5.92
1217 1526 1.308783 GGGAGCAAAGGAAGGAAGCG 61.309 60.000 0.00 0.00 0.00 4.68
1230 1539 2.031120 CAAGAAACAAACAGGGGAGCA 58.969 47.619 0.00 0.00 0.00 4.26
1231 1540 2.306847 TCAAGAAACAAACAGGGGAGC 58.693 47.619 0.00 0.00 0.00 4.70
1748 2066 3.069980 GAGACAGGACAGCGGCGAT 62.070 63.158 12.98 0.00 0.00 4.58
1773 2091 2.188469 GGACGAATTGGGCGCCTA 59.812 61.111 28.56 19.98 0.00 3.93
1774 2092 4.796495 GGGACGAATTGGGCGCCT 62.796 66.667 28.56 5.85 0.00 5.52
1794 2112 2.649034 GGACGTGCTTCCACTCGA 59.351 61.111 0.00 0.00 39.86 4.04
1948 2266 3.119137 TCAGCGTCTCTTGCTTAGCATAA 60.119 43.478 8.05 0.00 41.72 1.90
1951 2269 0.603065 TCAGCGTCTCTTGCTTAGCA 59.397 50.000 1.39 1.39 41.72 3.49
2167 2485 1.817099 CAGCATCGCCTTGGTCTCC 60.817 63.158 0.00 0.00 0.00 3.71
2385 2703 5.515626 CCGTAGTAGTTGTAGTTCTCATTGC 59.484 44.000 0.00 0.00 0.00 3.56
2389 2707 4.074259 TGCCGTAGTAGTTGTAGTTCTCA 58.926 43.478 0.00 0.00 0.00 3.27
2431 2749 1.271856 TGACCGCCATGAGGAAGTTA 58.728 50.000 13.11 0.00 36.89 2.24
2509 2827 1.078497 CATGAAGTACGCCTGCCCA 60.078 57.895 0.00 0.00 0.00 5.36
2518 2836 1.868519 GCGTCCCGGATCATGAAGTAC 60.869 57.143 0.73 0.00 0.00 2.73
2553 2871 1.572085 GAACCTCGAGTCGGACGACA 61.572 60.000 24.48 5.52 46.76 4.35
2775 3093 1.434513 ATCAAACCCCAGCCCAGACA 61.435 55.000 0.00 0.00 0.00 3.41
2840 3158 2.264794 GTCGACCTTCACCGGCAT 59.735 61.111 3.51 0.00 0.00 4.40
2960 3278 2.228059 GTCAGGGCCATCAATGATCAG 58.772 52.381 6.18 0.00 0.00 2.90
3085 3406 3.126001 AGGACGTCAATGACAATGTGT 57.874 42.857 18.91 2.37 32.09 3.72
3199 3523 6.430000 ACACAAACTAAGGGCAAACTGTATAG 59.570 38.462 0.00 0.00 0.00 1.31
3200 3524 6.300703 ACACAAACTAAGGGCAAACTGTATA 58.699 36.000 0.00 0.00 0.00 1.47
3201 3525 5.137551 ACACAAACTAAGGGCAAACTGTAT 58.862 37.500 0.00 0.00 0.00 2.29
3213 3537 4.982916 ACGCACTAGAAGACACAAACTAAG 59.017 41.667 0.00 0.00 0.00 2.18
3233 3557 0.900421 AACCTCCCCAACTAGTACGC 59.100 55.000 0.00 0.00 0.00 4.42
3342 3684 5.381757 ACCAATGTTAGTTTAGGTGAAGCA 58.618 37.500 0.00 0.00 0.00 3.91
3390 3764 8.398878 TGAATGTACCGAAAAACTAAGGAAAT 57.601 30.769 0.00 0.00 0.00 2.17
3506 3880 3.664276 CGTCAAACCTGCACAATAAGTCG 60.664 47.826 0.00 0.00 0.00 4.18
3740 4114 2.164624 CTCTGACTGACTAAGTTCCCGG 59.835 54.545 0.00 0.00 40.07 5.73
3752 4126 2.630098 CCACTCCTGAAACTCTGACTGA 59.370 50.000 0.00 0.00 0.00 3.41
3803 4177 5.619220 AGAAGATTGCCTCTGCCTAATAAG 58.381 41.667 0.00 0.00 36.33 1.73
3824 4198 4.735132 GCGGCCACACTGCGTAGA 62.735 66.667 7.78 0.00 41.87 2.59
4085 4459 5.163754 CCGAAGTTTGTTAACCATGGAGATC 60.164 44.000 21.47 6.77 34.71 2.75
4300 4678 1.402511 GCGACTTCAAAAAGCTGCAG 58.597 50.000 10.11 10.11 36.47 4.41
4441 4819 7.120579 TGAAAGTGCTGAACTAGTTTGAAAGAA 59.879 33.333 10.02 0.00 38.56 2.52
4442 4820 6.597672 TGAAAGTGCTGAACTAGTTTGAAAGA 59.402 34.615 10.02 0.00 38.56 2.52
4443 4821 6.785191 TGAAAGTGCTGAACTAGTTTGAAAG 58.215 36.000 10.02 6.85 38.56 2.62
4649 5027 5.185454 CAGTGGCCATGAACTAACAATAGA 58.815 41.667 9.72 0.00 33.15 1.98
4652 5030 3.091545 CCAGTGGCCATGAACTAACAAT 58.908 45.455 9.72 0.00 0.00 2.71
6199 6646 0.178900 GGAGAATAGGGGACGGGGAT 60.179 60.000 0.00 0.00 0.00 3.85
6206 6653 0.568192 CAGGAGGGGAGAATAGGGGA 59.432 60.000 0.00 0.00 0.00 4.81
6212 6659 0.983378 CGGGAACAGGAGGGGAGAAT 60.983 60.000 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.