Multiple sequence alignment - TraesCS6A01G259600

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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 TraesCS6A01G259600 chr6A 100.000 3709 0 0 1 3709 482621930 482618222 0.000000e+00 6850
1 TraesCS6A01G259600 chr6D 96.070 3257 103 9 175 3427 342474521 342471286 0.000000e+00 5282
2 TraesCS6A01G259600 chr6D 87.654 243 23 6 3474 3709 342471195 342470953 3.650000e-70 276
3 TraesCS6A01G259600 chr6D 81.041 269 42 8 3070 3334 123158968 123159231 4.860000e-49 206
4 TraesCS6A01G259600 chr6B 91.048 3787 179 70 3 3709 516881932 516878226 0.000000e+00 4968
5 TraesCS6A01G259600 chr6B 80.074 271 43 8 3070 3334 217168994 217169259 1.360000e-44 191
6 TraesCS6A01G259600 chr2D 90.132 456 13 8 1057 1493 114646639 114647081 6.950000e-157 564
7 TraesCS6A01G259600 chr2D 84.175 594 72 17 1661 2240 500362593 500363178 1.160000e-154 556
8 TraesCS6A01G259600 chr2D 77.481 262 54 5 3072 3331 477418291 477418033 6.420000e-33 152
9 TraesCS6A01G259600 chr2A 84.444 585 75 14 1661 2240 645311345 645311918 2.500000e-156 562
10 TraesCS6A01G259600 chr2A 85.906 149 16 5 3469 3615 157925644 157925499 1.780000e-33 154
11 TraesCS6A01G259600 chr2A 78.175 252 45 10 3089 3336 140514843 140515088 6.420000e-33 152
12 TraesCS6A01G259600 chr2B 85.130 538 65 13 1703 2234 588067380 588067908 1.520000e-148 536
13 TraesCS6A01G259600 chr2B 84.516 155 20 4 3463 3615 201471880 201472032 2.310000e-32 150
14 TraesCS6A01G259600 chrUn 88.319 351 37 3 1725 2073 365429968 365429620 5.730000e-113 418
15 TraesCS6A01G259600 chr4B 88.319 351 37 3 1725 2073 641891314 641890966 5.730000e-113 418
16 TraesCS6A01G259600 chr5A 87.749 351 39 3 1725 2073 679875216 679874868 1.240000e-109 407
17 TraesCS6A01G259600 chr5A 86.350 337 46 0 1722 2058 685432403 685432739 5.850000e-98 368
18 TraesCS6A01G259600 chr3A 83.028 218 34 3 3084 3300 51742486 51742271 1.050000e-45 195
19 TraesCS6A01G259600 chr4A 88.667 150 13 4 3469 3615 154525488 154525340 2.940000e-41 180
20 TraesCS6A01G259600 chr4D 88.158 152 15 3 3463 3612 319243486 319243636 1.060000e-40 178
21 TraesCS6A01G259600 chr7D 78.358 268 49 9 3071 3334 11245685 11245423 8.240000e-37 165
22 TraesCS6A01G259600 chr3B 77.860 271 49 9 3069 3334 161300847 161301111 1.380000e-34 158


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 TraesCS6A01G259600 chr6A 482618222 482621930 3708 True 6850 6850 100.000 1 3709 1 chr6A.!!$R1 3708
1 TraesCS6A01G259600 chr6D 342470953 342474521 3568 True 2779 5282 91.862 175 3709 2 chr6D.!!$R1 3534
2 TraesCS6A01G259600 chr6B 516878226 516881932 3706 True 4968 4968 91.048 3 3709 1 chr6B.!!$R1 3706
3 TraesCS6A01G259600 chr2D 500362593 500363178 585 False 556 556 84.175 1661 2240 1 chr2D.!!$F2 579
4 TraesCS6A01G259600 chr2A 645311345 645311918 573 False 562 562 84.444 1661 2240 1 chr2A.!!$F2 579
5 TraesCS6A01G259600 chr2B 588067380 588067908 528 False 536 536 85.130 1703 2234 1 chr2B.!!$F2 531

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
135 136 0.037232 GAGTGTCCTTACGCCAGCTT 60.037 55.000 0.0 0.0 36.76 3.74 F
150 151 0.462047 AGCTTAACTCCGAATGCCCG 60.462 55.000 0.0 0.0 0.00 6.13 F
1005 1017 0.543277 CTGCCACATCCCAGAGCTAA 59.457 55.000 0.0 0.0 0.00 3.09 F
1565 1593 1.471501 CGCGAGATCCCTTTCATGACA 60.472 52.381 0.0 0.0 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1404 1432 1.153168 ATCCCGATTCGCCAACAGG 60.153 57.895 0.00 0.00 0.00 4.00 R
1405 1433 2.016961 CATCCCGATTCGCCAACAG 58.983 57.895 0.00 0.00 0.00 3.16 R
2423 2463 0.037512 TTTCGATTACCGGCACCGAA 60.038 50.000 11.42 14.64 42.83 4.30 R
3467 3561 0.039618 TCAAAACTGCCATCCTCCCC 59.960 55.000 0.00 0.00 0.00 4.81 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
44 45 0.755686 ATGGGAGAGAAGATGACCGC 59.244 55.000 0.00 0.00 0.00 5.68
45 46 1.330655 TGGGAGAGAAGATGACCGCC 61.331 60.000 0.00 0.00 0.00 6.13
46 47 1.330655 GGGAGAGAAGATGACCGCCA 61.331 60.000 0.00 0.00 0.00 5.69
47 48 0.755686 GGAGAGAAGATGACCGCCAT 59.244 55.000 0.00 0.00 38.43 4.40
48 49 1.539929 GGAGAGAAGATGACCGCCATG 60.540 57.143 0.00 0.00 35.17 3.66
49 50 0.467384 AGAGAAGATGACCGCCATGG 59.533 55.000 7.63 7.63 46.41 3.66
50 51 0.465705 GAGAAGATGACCGCCATGGA 59.534 55.000 18.40 0.00 42.00 3.41
51 52 0.179000 AGAAGATGACCGCCATGGAC 59.821 55.000 18.40 5.97 42.00 4.02
65 66 2.643551 CATGGACTCATGGGTAACACC 58.356 52.381 0.00 0.00 45.19 4.16
69 70 1.813753 CTCATGGGTAACACCGGCG 60.814 63.158 0.00 0.00 39.83 6.46
81 82 3.917760 CCGGCGTCCTCCTCATCC 61.918 72.222 6.01 0.00 0.00 3.51
83 84 2.721167 CGGCGTCCTCCTCATCCAA 61.721 63.158 0.00 0.00 0.00 3.53
86 87 1.587547 GCGTCCTCCTCATCCAAATC 58.412 55.000 0.00 0.00 0.00 2.17
88 89 2.831333 CGTCCTCCTCATCCAAATCAG 58.169 52.381 0.00 0.00 0.00 2.90
90 91 2.774234 GTCCTCCTCATCCAAATCAGGA 59.226 50.000 0.00 0.00 43.01 3.86
114 115 7.781324 AGAATCCAAAACATACATTGACCTT 57.219 32.000 0.00 0.00 0.00 3.50
115 116 7.605449 AGAATCCAAAACATACATTGACCTTG 58.395 34.615 0.00 0.00 0.00 3.61
119 120 5.243730 CCAAAACATACATTGACCTTGGAGT 59.756 40.000 0.00 0.00 35.60 3.85
124 125 2.057922 ACATTGACCTTGGAGTGTCCT 58.942 47.619 0.00 0.00 37.46 3.85
127 128 3.764237 TTGACCTTGGAGTGTCCTTAC 57.236 47.619 0.00 0.00 37.46 2.34
131 132 0.320374 CTTGGAGTGTCCTTACGCCA 59.680 55.000 0.00 0.00 46.65 5.69
135 136 0.037232 GAGTGTCCTTACGCCAGCTT 60.037 55.000 0.00 0.00 36.76 3.74
136 137 1.203994 GAGTGTCCTTACGCCAGCTTA 59.796 52.381 0.00 0.00 36.76 3.09
137 138 1.621814 AGTGTCCTTACGCCAGCTTAA 59.378 47.619 0.00 0.00 36.76 1.85
138 139 1.730612 GTGTCCTTACGCCAGCTTAAC 59.269 52.381 0.00 0.00 0.00 2.01
142 143 1.278238 CTTACGCCAGCTTAACTCCG 58.722 55.000 0.00 0.00 0.00 4.63
150 151 0.462047 AGCTTAACTCCGAATGCCCG 60.462 55.000 0.00 0.00 0.00 6.13
156 157 2.515991 TCCGAATGCCCGATTGCC 60.516 61.111 0.00 0.00 0.00 4.52
157 158 2.828095 CCGAATGCCCGATTGCCA 60.828 61.111 0.00 0.00 0.00 4.92
192 199 2.960129 GCGACCGCATTCCTACCG 60.960 66.667 9.73 0.00 41.49 4.02
196 203 0.663568 GACCGCATTCCTACCGATCG 60.664 60.000 8.51 8.51 0.00 3.69
210 217 1.548973 CGATCGAAATTCCTCGCCCG 61.549 60.000 10.26 0.00 38.73 6.13
231 239 2.639327 GGCCCATGACAAGCCACAC 61.639 63.158 9.08 0.00 46.34 3.82
236 244 2.158986 CCCATGACAAGCCACACAAAAA 60.159 45.455 0.00 0.00 0.00 1.94
238 246 4.128643 CCATGACAAGCCACACAAAAATT 58.871 39.130 0.00 0.00 0.00 1.82
250 258 6.037610 GCCACACAAAAATTATGGTGTTCAAA 59.962 34.615 6.28 0.00 42.16 2.69
251 259 7.405769 CCACACAAAAATTATGGTGTTCAAAC 58.594 34.615 6.28 0.00 42.16 2.93
278 286 1.336755 GAGGCAGACGAGATCTTCTCC 59.663 57.143 0.00 1.32 40.34 3.71
301 309 7.888424 TCCTTCCACATCATGCAATTATTATG 58.112 34.615 0.00 0.00 0.00 1.90
376 384 1.746220 ACTTGCCTACACGAGAGCTAG 59.254 52.381 0.00 0.00 33.59 3.42
749 760 2.820059 AAACACAGCGAGATGACTCA 57.180 45.000 0.00 0.00 42.72 3.41
755 766 2.257894 CAGCGAGATGACTCACTTCAC 58.742 52.381 0.00 0.00 42.72 3.18
759 770 3.612717 GCGAGATGACTCACTTCACTTCA 60.613 47.826 0.00 0.00 42.72 3.02
760 771 3.917380 CGAGATGACTCACTTCACTTCAC 59.083 47.826 0.00 0.00 42.72 3.18
766 777 4.099419 TGACTCACTTCACTTCACTAAGCA 59.901 41.667 0.00 0.00 36.05 3.91
811 823 6.498651 AGTGAGTTCAAGGAAGAGGAATCTTA 59.501 38.462 0.00 0.00 0.00 2.10
999 1011 1.152819 CATCCCTGCCACATCCCAG 60.153 63.158 0.00 0.00 0.00 4.45
1005 1017 0.543277 CTGCCACATCCCAGAGCTAA 59.457 55.000 0.00 0.00 0.00 3.09
1208 1236 2.158856 ACATGCTATAGCTCTGCTGCAA 60.159 45.455 24.61 2.19 38.29 4.08
1404 1432 2.242708 TGGTCTTCCTCCTCTCCTCTAC 59.757 54.545 0.00 0.00 34.23 2.59
1405 1433 2.423803 GGTCTTCCTCCTCTCCTCTACC 60.424 59.091 0.00 0.00 0.00 3.18
1406 1434 2.512476 GTCTTCCTCCTCTCCTCTACCT 59.488 54.545 0.00 0.00 0.00 3.08
1565 1593 1.471501 CGCGAGATCCCTTTCATGACA 60.472 52.381 0.00 0.00 0.00 3.58
1573 1601 2.031919 TTTCATGACAGCCGCGGT 59.968 55.556 28.70 11.01 0.00 5.68
2012 2049 1.507174 GGACACCGTCTCCTTCTCG 59.493 63.158 0.00 0.00 32.47 4.04
2402 2442 1.733758 CGGCGTAAGTGTAACCGCA 60.734 57.895 0.00 0.00 44.84 5.69
2423 2463 2.284625 TCCCCAGTGGTGCTCGAT 60.285 61.111 8.74 0.00 34.77 3.59
2624 2664 0.687757 TGCTAGAGTTCCCCTCGCAT 60.688 55.000 0.00 0.00 45.44 4.73
2687 2727 1.078214 CAAGAGGGAGGCGCATTCA 60.078 57.895 10.83 0.00 0.00 2.57
2800 2840 9.591792 TCACTTCTCATGTGATTCAGTTATAAG 57.408 33.333 0.00 0.00 39.23 1.73
2951 2991 5.013079 AGTGTCATCTCTTGTCCACCATTAA 59.987 40.000 0.00 0.00 32.35 1.40
2954 2994 7.552687 GTGTCATCTCTTGTCCACCATTAATTA 59.447 37.037 0.00 0.00 0.00 1.40
2955 2995 8.274322 TGTCATCTCTTGTCCACCATTAATTAT 58.726 33.333 0.00 0.00 0.00 1.28
2956 2996 9.125026 GTCATCTCTTGTCCACCATTAATTATT 57.875 33.333 0.00 0.00 0.00 1.40
2957 2997 9.699410 TCATCTCTTGTCCACCATTAATTATTT 57.301 29.630 0.00 0.00 0.00 1.40
2962 3002 7.898636 TCTTGTCCACCATTAATTATTTTCCCT 59.101 33.333 0.00 0.00 0.00 4.20
3008 3049 3.229276 TGCCCATGTTTAGCAAAATCG 57.771 42.857 0.00 0.00 32.56 3.34
3056 3100 4.033817 ACATTTGTCCGTGTGCAAATTTTG 59.966 37.500 4.72 4.72 41.62 2.44
3343 3417 4.986054 ACTGGAGGAGTACGAGAGATAT 57.014 45.455 0.00 0.00 30.86 1.63
3349 3423 6.042897 TGGAGGAGTACGAGAGATATGAGTTA 59.957 42.308 0.00 0.00 0.00 2.24
3365 3439 9.970395 GATATGAGTTAAATCCATCAAAATGCA 57.030 29.630 0.00 0.00 0.00 3.96
3369 3443 7.488792 TGAGTTAAATCCATCAAAATGCATTCG 59.511 33.333 13.38 7.43 0.00 3.34
3371 3445 5.341872 AAATCCATCAAAATGCATTCGGA 57.658 34.783 13.38 13.40 0.00 4.55
3401 3475 8.574251 ACCAGCACTACACATTAATAATTCAA 57.426 30.769 0.00 0.00 0.00 2.69
3427 3501 2.678190 GCTAACTGGCGACCATTCTCTT 60.678 50.000 0.00 0.00 30.82 2.85
3459 3553 5.949354 TGACAATTTTAGTTGTATCAGGGGG 59.051 40.000 0.00 0.00 42.08 5.40
3460 3554 5.899278 ACAATTTTAGTTGTATCAGGGGGT 58.101 37.500 0.00 0.00 40.35 4.95
3461 3555 5.714806 ACAATTTTAGTTGTATCAGGGGGTG 59.285 40.000 0.00 0.00 40.35 4.61
3462 3556 5.530176 ATTTTAGTTGTATCAGGGGGTGT 57.470 39.130 0.00 0.00 0.00 4.16
3464 3558 5.327737 TTTAGTTGTATCAGGGGGTGTTT 57.672 39.130 0.00 0.00 0.00 2.83
3467 3561 3.895041 AGTTGTATCAGGGGGTGTTTTTG 59.105 43.478 0.00 0.00 0.00 2.44
3468 3562 2.883026 TGTATCAGGGGGTGTTTTTGG 58.117 47.619 0.00 0.00 0.00 3.28
3469 3563 2.176045 GTATCAGGGGGTGTTTTTGGG 58.824 52.381 0.00 0.00 0.00 4.12
3470 3564 0.178906 ATCAGGGGGTGTTTTTGGGG 60.179 55.000 0.00 0.00 0.00 4.96
3471 3565 1.234529 CAGGGGGTGTTTTTGGGGA 59.765 57.895 0.00 0.00 0.00 4.81
3472 3566 0.831711 CAGGGGGTGTTTTTGGGGAG 60.832 60.000 0.00 0.00 0.00 4.30
3473 3567 1.535444 GGGGGTGTTTTTGGGGAGG 60.535 63.158 0.00 0.00 0.00 4.30
3477 3577 1.266178 GGTGTTTTTGGGGAGGATGG 58.734 55.000 0.00 0.00 0.00 3.51
3480 3580 0.897621 GTTTTTGGGGAGGATGGCAG 59.102 55.000 0.00 0.00 0.00 4.85
3485 3585 0.251742 TGGGGAGGATGGCAGTTTTG 60.252 55.000 0.00 0.00 0.00 2.44
3497 3619 2.951726 GCAGTTTTGAGCCTTCATTCC 58.048 47.619 0.00 0.00 32.27 3.01
3506 3628 3.194116 TGAGCCTTCATTCCAGAAAATGC 59.806 43.478 0.00 0.00 36.72 3.56
3517 3639 2.289010 CCAGAAAATGCCAGGTTGTTCC 60.289 50.000 0.00 0.00 0.00 3.62
3605 3730 1.468565 CGAACGGTCGCCAGATAAGAA 60.469 52.381 11.19 0.00 41.08 2.52
3613 3739 3.383825 GTCGCCAGATAAGAAGGTCCTAA 59.616 47.826 0.00 0.00 0.00 2.69
3616 3742 5.243283 TCGCCAGATAAGAAGGTCCTAATAC 59.757 44.000 0.00 0.00 0.00 1.89
3620 3746 7.993758 GCCAGATAAGAAGGTCCTAATACTTTT 59.006 37.037 0.00 0.00 0.00 2.27
3623 3749 8.422566 AGATAAGAAGGTCCTAATACTTTTCCG 58.577 37.037 0.00 0.00 0.00 4.30
3626 3752 7.486407 AGAAGGTCCTAATACTTTTCCGTAA 57.514 36.000 0.00 0.00 0.00 3.18
3683 3809 0.814010 AATATCCGCACAACTCGGCC 60.814 55.000 0.00 0.00 46.05 6.13
3688 3814 2.356553 GCACAACTCGGCCGTACA 60.357 61.111 27.15 4.62 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 1.209504 CGGTGTTACCCATGAGTCCAT 59.790 52.381 0.00 0.00 33.75 3.41
47 48 0.611200 CGGTGTTACCCATGAGTCCA 59.389 55.000 0.00 0.00 33.75 4.02
48 49 0.107848 CCGGTGTTACCCATGAGTCC 60.108 60.000 0.00 0.00 33.75 3.85
49 50 0.743345 GCCGGTGTTACCCATGAGTC 60.743 60.000 1.90 0.00 33.75 3.36
50 51 1.298667 GCCGGTGTTACCCATGAGT 59.701 57.895 1.90 0.00 33.75 3.41
51 52 1.813753 CGCCGGTGTTACCCATGAG 60.814 63.158 6.91 0.00 33.75 2.90
64 65 3.917760 GGATGAGGAGGACGCCGG 61.918 72.222 0.00 0.00 0.00 6.13
65 66 2.238847 TTTGGATGAGGAGGACGCCG 62.239 60.000 0.00 0.00 0.00 6.46
69 70 2.774234 TCCTGATTTGGATGAGGAGGAC 59.226 50.000 0.00 0.00 40.26 3.85
81 82 7.829725 TGTATGTTTTGGATTCTCCTGATTTG 58.170 34.615 0.00 0.00 37.46 2.32
83 84 8.472413 CAATGTATGTTTTGGATTCTCCTGATT 58.528 33.333 0.00 0.00 37.46 2.57
86 87 7.253422 GTCAATGTATGTTTTGGATTCTCCTG 58.747 38.462 0.00 0.00 37.46 3.86
88 89 6.378280 AGGTCAATGTATGTTTTGGATTCTCC 59.622 38.462 0.00 0.00 36.96 3.71
90 91 7.309990 CCAAGGTCAATGTATGTTTTGGATTCT 60.310 37.037 0.00 0.00 37.19 2.40
97 98 5.833131 ACACTCCAAGGTCAATGTATGTTTT 59.167 36.000 0.00 0.00 0.00 2.43
101 102 3.941483 GGACACTCCAAGGTCAATGTATG 59.059 47.826 0.00 0.00 36.28 2.39
114 115 1.972198 CTGGCGTAAGGACACTCCA 59.028 57.895 0.00 0.00 39.61 3.86
115 116 1.448013 GCTGGCGTAAGGACACTCC 60.448 63.158 0.00 0.00 36.58 3.85
119 120 1.621814 AGTTAAGCTGGCGTAAGGACA 59.378 47.619 1.60 0.00 38.28 4.02
124 125 0.889994 TCGGAGTTAAGCTGGCGTAA 59.110 50.000 0.00 0.00 0.00 3.18
127 128 0.652592 CATTCGGAGTTAAGCTGGCG 59.347 55.000 0.00 0.00 0.00 5.69
131 132 0.462047 CGGGCATTCGGAGTTAAGCT 60.462 55.000 0.00 0.00 0.00 3.74
135 136 1.948104 CAATCGGGCATTCGGAGTTA 58.052 50.000 0.00 0.00 0.00 2.24
136 137 1.376609 GCAATCGGGCATTCGGAGTT 61.377 55.000 0.00 0.00 0.00 3.01
137 138 1.819632 GCAATCGGGCATTCGGAGT 60.820 57.895 0.00 0.00 0.00 3.85
138 139 2.546494 GGCAATCGGGCATTCGGAG 61.546 63.158 0.00 0.00 42.77 4.63
150 151 6.455360 TTGGATGTTTCTATTCTGGCAATC 57.545 37.500 0.00 0.00 0.00 2.67
156 157 5.504665 GGTCGCATTGGATGTTTCTATTCTG 60.505 44.000 0.00 0.00 0.00 3.02
157 158 4.576463 GGTCGCATTGGATGTTTCTATTCT 59.424 41.667 0.00 0.00 0.00 2.40
186 193 2.662700 CGAGGAATTTCGATCGGTAGG 58.337 52.381 16.41 0.00 43.03 3.18
192 199 0.529992 ACGGGCGAGGAATTTCGATC 60.530 55.000 3.75 0.00 43.03 3.69
196 203 1.800681 CCAACGGGCGAGGAATTTC 59.199 57.895 0.00 0.00 0.00 2.17
210 217 2.973082 GGCTTGTCATGGGCCAAC 59.027 61.111 11.89 5.71 44.69 3.77
217 224 6.128499 CCATAATTTTTGTGTGGCTTGTCATG 60.128 38.462 0.00 0.00 0.00 3.07
255 263 0.736053 AAGATCTCGTCTGCCTCGAC 59.264 55.000 0.00 0.00 37.23 4.20
257 265 1.002900 GAGAAGATCTCGTCTGCCTCG 60.003 57.143 1.53 0.00 37.23 4.63
278 286 8.789762 TCTCATAATAATTGCATGATGTGGAAG 58.210 33.333 0.00 0.00 41.68 3.46
504 515 1.957177 GCTTTATAAAGGGCAGAGGGC 59.043 52.381 23.37 6.04 37.92 5.19
612 623 3.627577 TCTCTTTGTGAAAGAAGGTGTGC 59.372 43.478 0.00 0.00 46.13 4.57
749 760 3.397482 CAGCTGCTTAGTGAAGTGAAGT 58.603 45.455 0.00 0.00 34.90 3.01
755 766 0.801251 GTGGCAGCTGCTTAGTGAAG 59.199 55.000 35.82 0.00 41.70 3.02
759 770 0.322008 GGAAGTGGCAGCTGCTTAGT 60.322 55.000 35.82 24.48 41.70 2.24
760 771 0.321919 TGGAAGTGGCAGCTGCTTAG 60.322 55.000 35.82 0.25 41.70 2.18
766 777 1.298014 GCTAGTGGAAGTGGCAGCT 59.702 57.895 0.00 0.00 44.05 4.24
1208 1236 1.402259 CTCGAGAATAGACACTGCGGT 59.598 52.381 6.58 0.00 0.00 5.68
1343 1371 3.817647 AGCAACTACAAAAGAGCTTCCTG 59.182 43.478 0.00 0.00 36.98 3.86
1404 1432 1.153168 ATCCCGATTCGCCAACAGG 60.153 57.895 0.00 0.00 0.00 4.00
1405 1433 2.016961 CATCCCGATTCGCCAACAG 58.983 57.895 0.00 0.00 0.00 3.16
1406 1434 2.112198 GCATCCCGATTCGCCAACA 61.112 57.895 0.00 0.00 0.00 3.33
1650 1678 2.911928 GGGAGGGCTACTTCCAGC 59.088 66.667 1.88 0.00 45.18 4.85
2066 2103 4.083862 GGGTCTCTGGTGTCGGCC 62.084 72.222 0.00 0.00 0.00 6.13
2423 2463 0.037512 TTTCGATTACCGGCACCGAA 60.038 50.000 11.42 14.64 42.83 4.30
2524 2564 1.134818 TGCCATAATTGCTCGACTCGT 60.135 47.619 0.00 0.00 0.00 4.18
2687 2727 1.411977 CACAGATCGAGATCCAAGCCT 59.588 52.381 9.27 0.00 38.58 4.58
2800 2840 1.598924 GCTGCCGCTATCATCAAAAGC 60.599 52.381 0.00 0.00 0.00 3.51
2902 2942 9.933723 CTGATTTGGGAGAAAAACATTAATCTT 57.066 29.630 0.00 0.00 0.00 2.40
2951 2991 5.134725 AGCACATGGAGAGGGAAAATAAT 57.865 39.130 0.00 0.00 0.00 1.28
2954 2994 3.094572 CAAGCACATGGAGAGGGAAAAT 58.905 45.455 0.00 0.00 0.00 1.82
2955 2995 2.158475 ACAAGCACATGGAGAGGGAAAA 60.158 45.455 0.00 0.00 0.00 2.29
2956 2996 1.425066 ACAAGCACATGGAGAGGGAAA 59.575 47.619 0.00 0.00 0.00 3.13
2957 2997 1.067295 ACAAGCACATGGAGAGGGAA 58.933 50.000 0.00 0.00 0.00 3.97
2958 2998 0.325933 CACAAGCACATGGAGAGGGA 59.674 55.000 0.00 0.00 0.00 4.20
2959 2999 1.310933 GCACAAGCACATGGAGAGGG 61.311 60.000 0.00 0.00 41.58 4.30
2962 3002 1.202794 TGAAGCACAAGCACATGGAGA 60.203 47.619 0.00 0.00 45.49 3.71
3008 3049 5.648178 TCATATGTATGAAATGGGCATGC 57.352 39.130 9.90 9.90 39.58 4.06
3056 3100 5.364157 AGGAAGTACTATGAGACCATGAACC 59.636 44.000 0.00 0.00 34.31 3.62
3310 3384 9.023962 TCGTACTCCTCCAGTTACTTTTTATTA 57.976 33.333 0.00 0.00 36.43 0.98
3320 3394 4.774660 ATCTCTCGTACTCCTCCAGTTA 57.225 45.455 0.00 0.00 36.43 2.24
3326 3400 7.966246 TTAACTCATATCTCTCGTACTCCTC 57.034 40.000 0.00 0.00 0.00 3.71
3327 3401 8.927675 ATTTAACTCATATCTCTCGTACTCCT 57.072 34.615 0.00 0.00 0.00 3.69
3343 3417 7.488792 CGAATGCATTTTGATGGATTTAACTCA 59.511 33.333 14.33 0.00 41.59 3.41
3349 3423 5.111293 GTCCGAATGCATTTTGATGGATTT 58.889 37.500 14.33 0.00 41.59 2.17
3365 3439 1.981256 AGTGCTGGTTTTGTCCGAAT 58.019 45.000 0.00 0.00 0.00 3.34
3367 3441 1.139256 TGTAGTGCTGGTTTTGTCCGA 59.861 47.619 0.00 0.00 0.00 4.55
3369 3443 2.294074 TGTGTAGTGCTGGTTTTGTCC 58.706 47.619 0.00 0.00 0.00 4.02
3371 3445 6.648879 ATTAATGTGTAGTGCTGGTTTTGT 57.351 33.333 0.00 0.00 0.00 2.83
3401 3475 1.975660 TGGTCGCCAGTTAGCTTTTT 58.024 45.000 0.00 0.00 0.00 1.94
3434 3528 6.435904 CCCCCTGATACAACTAAAATTGTCAA 59.564 38.462 0.00 0.00 41.89 3.18
3459 3553 0.608130 GCCATCCTCCCCAAAAACAC 59.392 55.000 0.00 0.00 0.00 3.32
3460 3554 0.189574 TGCCATCCTCCCCAAAAACA 59.810 50.000 0.00 0.00 0.00 2.83
3461 3555 0.897621 CTGCCATCCTCCCCAAAAAC 59.102 55.000 0.00 0.00 0.00 2.43
3462 3556 0.486879 ACTGCCATCCTCCCCAAAAA 59.513 50.000 0.00 0.00 0.00 1.94
3464 3558 0.486879 AAACTGCCATCCTCCCCAAA 59.513 50.000 0.00 0.00 0.00 3.28
3467 3561 0.039618 TCAAAACTGCCATCCTCCCC 59.960 55.000 0.00 0.00 0.00 4.81
3468 3562 1.467920 CTCAAAACTGCCATCCTCCC 58.532 55.000 0.00 0.00 0.00 4.30
3469 3563 0.813821 GCTCAAAACTGCCATCCTCC 59.186 55.000 0.00 0.00 0.00 4.30
3477 3577 2.297033 TGGAATGAAGGCTCAAAACTGC 59.703 45.455 0.00 0.00 34.49 4.40
3480 3580 4.853924 TTCTGGAATGAAGGCTCAAAAC 57.146 40.909 0.00 0.00 34.49 2.43
3485 3585 3.429960 GGCATTTTCTGGAATGAAGGCTC 60.430 47.826 2.04 0.00 38.93 4.70
3497 3619 2.607771 CGGAACAACCTGGCATTTTCTG 60.608 50.000 0.00 0.00 36.31 3.02
3506 3628 2.290641 CAGTTTCTTCGGAACAACCTGG 59.709 50.000 0.00 0.00 36.31 4.45
3517 3639 1.873591 CAAGGGGTGACAGTTTCTTCG 59.126 52.381 0.00 0.00 0.00 3.79
3542 3665 6.034044 TGCAAACGTTTTGATCACAGTTTTAC 59.966 34.615 11.66 9.16 30.56 2.01
3605 3730 6.610075 TGTTACGGAAAAGTATTAGGACCT 57.390 37.500 0.00 0.00 0.00 3.85
3613 3739 9.609346 AAGTAATAGCATGTTACGGAAAAGTAT 57.391 29.630 0.00 0.00 37.18 2.12
3616 3742 7.692291 CACAAGTAATAGCATGTTACGGAAAAG 59.308 37.037 0.00 0.00 37.18 2.27
3620 3746 5.968254 TCACAAGTAATAGCATGTTACGGA 58.032 37.500 0.00 0.00 37.18 4.69
3623 3749 8.251750 TCAGTTCACAAGTAATAGCATGTTAC 57.748 34.615 0.00 0.00 33.32 2.50
3626 3752 9.618890 AATATCAGTTCACAAGTAATAGCATGT 57.381 29.630 0.00 0.00 0.00 3.21
3683 3809 0.872451 TAACGCGCCATCCATGTACG 60.872 55.000 5.73 0.00 0.00 3.67
3688 3814 2.186826 GGCTTAACGCGCCATCCAT 61.187 57.895 5.73 0.00 46.77 3.41


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

AutoCloner maintained by Alex Coulton.