Multiple sequence alignment - TraesCS2D01G355100

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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 TraesCS2D01G355100 chr2D 100.000 3362 0 0 1 3362 457256804 457253443 0.000000e+00 6209
1 TraesCS2D01G355100 chr2B 93.808 3004 97 38 65 3028 538013096 538010142 0.000000e+00 4434
2 TraesCS2D01G355100 chr2B 94.286 175 4 2 3193 3362 538009805 538009632 2.570000e-66 263
3 TraesCS2D01G355100 chr2B 95.575 113 4 1 3094 3205 538010028 538009916 2.670000e-41 180
4 TraesCS2D01G355100 chr2B 88.288 111 8 3 3213 3322 544755591 544755697 9.790000e-26 128
5 TraesCS2D01G355100 chr2A 94.161 2586 78 28 57 2615 600530915 600528376 0.000000e+00 3871
6 TraesCS2D01G355100 chr2A 91.728 544 28 11 2647 3184 600527145 600526613 0.000000e+00 739
7 TraesCS2D01G355100 chr2A 95.620 137 5 1 3200 3335 600519268 600519132 5.650000e-53 219
8 TraesCS2D01G355100 chr6D 83.531 1348 190 19 1023 2363 288541795 288540473 0.000000e+00 1230
9 TraesCS2D01G355100 chr6B 82.864 1348 199 19 1023 2363 448668256 448666934 0.000000e+00 1181
10 TraesCS2D01G355100 chr6A 82.725 1343 196 23 1026 2360 437021237 437022551 0.000000e+00 1162
11 TraesCS2D01G355100 chrUn 100.000 395 0 0 1154 1548 479365959 479365565 0.000000e+00 730
12 TraesCS2D01G355100 chr1A 75.915 328 56 19 1179 1493 551680384 551680067 2.700000e-31 147


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 TraesCS2D01G355100 chr2D 457253443 457256804 3361 True 6209.000000 6209 100.000000 1 3362 1 chr2D.!!$R1 3361
1 TraesCS2D01G355100 chr2B 538009632 538013096 3464 True 1625.666667 4434 94.556333 65 3362 3 chr2B.!!$R1 3297
2 TraesCS2D01G355100 chr2A 600526613 600530915 4302 True 2305.000000 3871 92.944500 57 3184 2 chr2A.!!$R2 3127
3 TraesCS2D01G355100 chr6D 288540473 288541795 1322 True 1230.000000 1230 83.531000 1023 2363 1 chr6D.!!$R1 1340
4 TraesCS2D01G355100 chr6B 448666934 448668256 1322 True 1181.000000 1181 82.864000 1023 2363 1 chr6B.!!$R1 1340
5 TraesCS2D01G355100 chr6A 437021237 437022551 1314 False 1162.000000 1162 82.725000 1026 2360 1 chr6A.!!$F1 1334

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
227 228 0.036022 ACAGAAGCAGGCAGGAAGAC 59.964 55.0 0.0 0.00 0.00 3.01 F
234 235 0.321671 CAGGCAGGAAGACGAGGAAA 59.678 55.0 0.0 0.00 0.00 3.13 F
322 323 0.809241 CAGAGTTGGAGATGCTCGCC 60.809 60.0 0.0 0.19 36.83 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1848 1890 1.739929 CACCATGAGCGCGTTGGTA 60.740 57.895 24.79 1.86 41.77 3.25 R
1905 1947 2.115291 GTCCCGGAAATCCAGCAGC 61.115 63.158 0.73 0.00 35.14 5.25 R
2383 2428 4.427661 ACCGCGAGCTGAGCAGAC 62.428 66.667 8.23 0.00 34.19 3.51 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
38 39 8.824159 ATAACATCGATTGAGACTTAATGAGG 57.176 34.615 0.00 1.08 0.00 3.86
39 40 6.227298 ACATCGATTGAGACTTAATGAGGT 57.773 37.500 0.00 1.63 0.00 3.85
40 41 6.045318 ACATCGATTGAGACTTAATGAGGTG 58.955 40.000 0.00 1.36 0.00 4.00
41 42 5.661056 TCGATTGAGACTTAATGAGGTGT 57.339 39.130 0.00 0.00 0.00 4.16
42 43 5.651530 TCGATTGAGACTTAATGAGGTGTC 58.348 41.667 0.00 0.00 0.00 3.67
43 44 5.185056 TCGATTGAGACTTAATGAGGTGTCA 59.815 40.000 0.00 0.00 34.67 3.58
44 45 5.518128 CGATTGAGACTTAATGAGGTGTCAG 59.482 44.000 0.00 0.00 37.13 3.51
45 46 5.808366 TTGAGACTTAATGAGGTGTCAGT 57.192 39.130 0.00 0.00 37.13 3.41
46 47 5.392767 TGAGACTTAATGAGGTGTCAGTC 57.607 43.478 0.00 0.00 35.66 3.51
47 48 4.082733 TGAGACTTAATGAGGTGTCAGTCG 60.083 45.833 0.00 0.00 35.66 4.18
48 49 4.079970 AGACTTAATGAGGTGTCAGTCGA 58.920 43.478 0.00 0.00 35.66 4.20
49 50 4.082679 AGACTTAATGAGGTGTCAGTCGAC 60.083 45.833 7.70 7.70 42.93 4.20
50 51 2.913777 TAATGAGGTGTCAGTCGACG 57.086 50.000 10.46 5.48 45.80 5.12
51 52 0.243907 AATGAGGTGTCAGTCGACGG 59.756 55.000 10.46 10.03 45.80 4.79
52 53 0.608308 ATGAGGTGTCAGTCGACGGA 60.608 55.000 14.65 14.65 45.80 4.69
53 54 1.235281 TGAGGTGTCAGTCGACGGAG 61.235 60.000 18.96 8.90 45.80 4.63
54 55 0.954449 GAGGTGTCAGTCGACGGAGA 60.954 60.000 18.96 15.10 45.80 3.71
55 56 0.536687 AGGTGTCAGTCGACGGAGAA 60.537 55.000 18.96 7.73 45.80 2.87
178 179 0.400525 CAGGGGCAGGAATAGAGGGA 60.401 60.000 0.00 0.00 0.00 4.20
192 193 3.825908 AGAGGGAAAATAGGCCAACAA 57.174 42.857 5.01 0.00 0.00 2.83
204 205 4.058721 AGGCCAACAAAAAGTAAGCAAG 57.941 40.909 5.01 0.00 31.76 4.01
213 214 8.707839 CAACAAAAAGTAAGCAAGAAAACAGAA 58.292 29.630 0.00 0.00 0.00 3.02
227 228 0.036022 ACAGAAGCAGGCAGGAAGAC 59.964 55.000 0.00 0.00 0.00 3.01
228 229 1.018226 CAGAAGCAGGCAGGAAGACG 61.018 60.000 0.00 0.00 0.00 4.18
229 230 1.188219 AGAAGCAGGCAGGAAGACGA 61.188 55.000 0.00 0.00 0.00 4.20
230 231 0.739112 GAAGCAGGCAGGAAGACGAG 60.739 60.000 0.00 0.00 0.00 4.18
231 232 2.125350 GCAGGCAGGAAGACGAGG 60.125 66.667 0.00 0.00 0.00 4.63
232 233 2.650116 GCAGGCAGGAAGACGAGGA 61.650 63.158 0.00 0.00 0.00 3.71
233 234 1.975327 CAGGCAGGAAGACGAGGAA 59.025 57.895 0.00 0.00 0.00 3.36
234 235 0.321671 CAGGCAGGAAGACGAGGAAA 59.678 55.000 0.00 0.00 0.00 3.13
235 236 1.056660 AGGCAGGAAGACGAGGAAAA 58.943 50.000 0.00 0.00 0.00 2.29
236 237 1.002544 AGGCAGGAAGACGAGGAAAAG 59.997 52.381 0.00 0.00 0.00 2.27
237 238 1.002087 GGCAGGAAGACGAGGAAAAGA 59.998 52.381 0.00 0.00 0.00 2.52
321 322 1.427592 GCAGAGTTGGAGATGCTCGC 61.428 60.000 0.00 0.00 35.78 5.03
322 323 0.809241 CAGAGTTGGAGATGCTCGCC 60.809 60.000 0.00 0.19 36.83 5.54
323 324 1.522580 GAGTTGGAGATGCTCGCCC 60.523 63.158 4.11 0.00 35.30 6.13
324 325 2.244117 GAGTTGGAGATGCTCGCCCA 62.244 60.000 4.11 0.00 35.30 5.36
325 326 1.153086 GTTGGAGATGCTCGCCCAT 60.153 57.895 4.11 0.00 35.30 4.00
326 327 1.153107 TTGGAGATGCTCGCCCATG 60.153 57.895 4.11 0.00 35.30 3.66
327 328 1.913951 TTGGAGATGCTCGCCCATGT 61.914 55.000 0.00 0.00 35.30 3.21
441 442 2.027751 GCGCCGGTCTAAGCCTAG 59.972 66.667 1.90 0.00 0.00 3.02
443 444 2.491022 CGCCGGTCTAAGCCTAGCT 61.491 63.158 1.90 0.00 42.56 3.32
589 590 5.584649 TGACTACAAGTTTCTCCACAGTTTG 59.415 40.000 0.00 0.00 0.00 2.93
604 605 7.164803 TCCACAGTTTGTTTTTCCTTTTTGAT 58.835 30.769 0.00 0.00 0.00 2.57
605 606 7.663493 TCCACAGTTTGTTTTTCCTTTTTGATT 59.337 29.630 0.00 0.00 0.00 2.57
606 607 7.750014 CCACAGTTTGTTTTTCCTTTTTGATTG 59.250 33.333 0.00 0.00 0.00 2.67
614 615 8.881743 TGTTTTTCCTTTTTGATTGTTGATGAG 58.118 29.630 0.00 0.00 0.00 2.90
678 679 1.761784 ACTAGATTCAGGCAGGAGCAG 59.238 52.381 0.00 0.00 44.61 4.24
689 690 1.135575 GCAGGAGCAGAAAATTCCACG 60.136 52.381 0.00 0.00 41.58 4.94
778 801 2.413142 GCAGCACCATCTCTTGCCC 61.413 63.158 0.00 0.00 39.75 5.36
919 953 2.444256 CCCCACCCGATTCTCCTCC 61.444 68.421 0.00 0.00 0.00 4.30
1548 1590 3.392595 CTACCTCGACGCGTCCACC 62.393 68.421 31.84 9.75 0.00 4.61
1551 1593 4.778415 CTCGACGCGTCCACCCTG 62.778 72.222 31.84 17.50 0.00 4.45
1905 1947 1.019278 CGGACAACTGTTCCATCGGG 61.019 60.000 0.00 0.00 0.00 5.14
2069 2111 2.747686 GTTCCTGGACCTGCGGAA 59.252 61.111 0.00 6.43 34.61 4.30
2383 2428 3.429141 CAGCCTGCTCTGCGTTGG 61.429 66.667 0.00 0.00 0.00 3.77
2398 2443 3.921767 TTGGTCTGCTCAGCTCGCG 62.922 63.158 0.00 0.00 0.00 5.87
2406 2451 1.803519 CTCAGCTCGCGGTGACTTC 60.804 63.158 6.13 0.00 42.30 3.01
2417 2462 1.266175 CGGTGACTTCAGTCGTACTGT 59.734 52.381 12.62 0.00 46.03 3.55
2418 2463 2.481568 CGGTGACTTCAGTCGTACTGTA 59.518 50.000 12.62 5.07 46.03 2.74
2419 2464 3.666374 CGGTGACTTCAGTCGTACTGTAC 60.666 52.174 7.90 7.90 46.03 2.90
2420 2465 3.501445 GGTGACTTCAGTCGTACTGTACT 59.499 47.826 15.35 0.00 46.03 2.73
2421 2466 4.692625 GGTGACTTCAGTCGTACTGTACTA 59.307 45.833 15.35 2.25 46.03 1.82
2509 2554 3.813443 ACACCTAACTGATGATGATGGC 58.187 45.455 0.00 0.00 0.00 4.40
2600 2646 5.300034 GGTTTCTAACCCGGAAAAGAGAAAA 59.700 40.000 0.73 0.00 46.12 2.29
2611 2657 7.015877 CCGGAAAAGAGAAAATTTCGACTAAG 58.984 38.462 0.00 0.00 36.60 2.18
2659 3903 4.037208 CGCATGCCATCCTTCTAATTCTTT 59.963 41.667 13.15 0.00 0.00 2.52
2662 3906 6.406177 GCATGCCATCCTTCTAATTCTTTTCA 60.406 38.462 6.36 0.00 0.00 2.69
2664 3908 7.722949 TGCCATCCTTCTAATTCTTTTCATT 57.277 32.000 0.00 0.00 0.00 2.57
2668 3912 8.411683 CCATCCTTCTAATTCTTTTCATTGGAG 58.588 37.037 0.00 0.00 0.00 3.86
2710 3954 2.728846 CGTTGCCCTGTCAAAATCATCG 60.729 50.000 0.00 0.00 0.00 3.84
2738 3982 6.150140 AGGTTGATTCTCAGCAAAGTATGTTC 59.850 38.462 0.00 0.00 28.47 3.18
2912 4157 3.696548 TGTCGGCCACAATATTTAATGCA 59.303 39.130 2.24 0.00 29.30 3.96
2913 4158 4.158579 TGTCGGCCACAATATTTAATGCAA 59.841 37.500 2.24 0.00 29.30 4.08
2927 4172 9.941325 ATATTTAATGCAAAATTGGAACAGTGA 57.059 25.926 0.00 0.00 42.39 3.41
2929 4174 4.942761 ATGCAAAATTGGAACAGTGACT 57.057 36.364 0.00 0.00 42.39 3.41
2937 4182 3.876274 TGGAACAGTGACTCTATCTGC 57.124 47.619 0.00 0.00 33.12 4.26
2946 4191 6.153510 ACAGTGACTCTATCTGCTTCACATAA 59.846 38.462 0.00 0.00 39.26 1.90
2947 4192 6.696583 CAGTGACTCTATCTGCTTCACATAAG 59.303 42.308 0.00 0.00 39.26 1.73
2948 4193 6.379703 AGTGACTCTATCTGCTTCACATAAGT 59.620 38.462 0.00 0.00 39.26 2.24
2950 4195 8.356657 GTGACTCTATCTGCTTCACATAAGTAT 58.643 37.037 0.00 0.00 37.20 2.12
2951 4196 9.574516 TGACTCTATCTGCTTCACATAAGTATA 57.425 33.333 0.00 0.00 0.00 1.47
2952 4197 9.834628 GACTCTATCTGCTTCACATAAGTATAC 57.165 37.037 0.00 0.00 0.00 1.47
2953 4198 9.355916 ACTCTATCTGCTTCACATAAGTATACA 57.644 33.333 5.50 0.00 0.00 2.29
2981 4228 5.063438 TCTGTCACGTGTTTCTTTCTTTGAG 59.937 40.000 16.51 0.00 0.00 3.02
2989 4238 9.849166 ACGTGTTTCTTTCTTTGAGAAAATAAA 57.151 25.926 4.84 5.83 42.95 1.40
3042 4291 6.542370 TCAAAGAGTTTAGAAACAGACCCAAG 59.458 38.462 7.82 0.00 41.30 3.61
3043 4292 5.632034 AGAGTTTAGAAACAGACCCAAGT 57.368 39.130 7.82 0.00 41.30 3.16
3127 4455 5.160641 TGTAATCTTTCATTTGCGGCTTTC 58.839 37.500 0.00 0.00 0.00 2.62
3276 4727 0.409484 ATGGCTTTGGCAAGGTAGGT 59.591 50.000 11.21 0.00 42.43 3.08
3312 4763 1.909700 TTGAGTTCATTCCTGTGGCC 58.090 50.000 0.00 0.00 0.00 5.36
3337 4793 3.254657 GCCGTAGTGCAGAGATCTAGAAT 59.745 47.826 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 9.914131 CCTCATTAAGTCTCAATCGATGTTATA 57.086 33.333 0.00 0.00 0.00 0.98
13 14 8.424918 ACCTCATTAAGTCTCAATCGATGTTAT 58.575 33.333 0.00 0.00 0.00 1.89
14 15 7.706607 CACCTCATTAAGTCTCAATCGATGTTA 59.293 37.037 0.00 0.00 0.00 2.41
15 16 6.536582 CACCTCATTAAGTCTCAATCGATGTT 59.463 38.462 0.00 0.00 0.00 2.71
16 17 6.045318 CACCTCATTAAGTCTCAATCGATGT 58.955 40.000 0.00 0.00 0.00 3.06
17 18 6.045318 ACACCTCATTAAGTCTCAATCGATG 58.955 40.000 0.00 0.00 0.00 3.84
18 19 6.127338 TGACACCTCATTAAGTCTCAATCGAT 60.127 38.462 0.00 0.00 32.41 3.59
19 20 5.185056 TGACACCTCATTAAGTCTCAATCGA 59.815 40.000 0.00 0.00 32.41 3.59
20 21 5.410924 TGACACCTCATTAAGTCTCAATCG 58.589 41.667 0.00 0.00 32.41 3.34
21 22 6.402222 ACTGACACCTCATTAAGTCTCAATC 58.598 40.000 0.00 0.00 32.41 2.67
22 23 6.365970 ACTGACACCTCATTAAGTCTCAAT 57.634 37.500 0.00 0.00 32.41 2.57
23 24 5.564848 CGACTGACACCTCATTAAGTCTCAA 60.565 44.000 0.00 0.00 32.41 3.02
24 25 4.082733 CGACTGACACCTCATTAAGTCTCA 60.083 45.833 0.00 0.00 32.41 3.27
25 26 4.156190 TCGACTGACACCTCATTAAGTCTC 59.844 45.833 0.00 0.00 32.41 3.36
26 27 4.079970 TCGACTGACACCTCATTAAGTCT 58.920 43.478 0.00 0.00 32.41 3.24
27 28 4.167268 GTCGACTGACACCTCATTAAGTC 58.833 47.826 8.70 0.00 44.82 3.01
28 29 3.366070 CGTCGACTGACACCTCATTAAGT 60.366 47.826 14.70 0.00 45.80 2.24
29 30 3.172050 CGTCGACTGACACCTCATTAAG 58.828 50.000 14.70 0.00 45.80 1.85
30 31 2.094906 CCGTCGACTGACACCTCATTAA 60.095 50.000 14.70 0.00 45.80 1.40
31 32 1.471287 CCGTCGACTGACACCTCATTA 59.529 52.381 14.70 0.00 45.80 1.90
32 33 0.243907 CCGTCGACTGACACCTCATT 59.756 55.000 14.70 0.00 45.80 2.57
33 34 0.608308 TCCGTCGACTGACACCTCAT 60.608 55.000 14.70 0.00 45.80 2.90
34 35 1.228033 TCCGTCGACTGACACCTCA 60.228 57.895 14.70 0.00 45.80 3.86
35 36 0.954449 TCTCCGTCGACTGACACCTC 60.954 60.000 14.70 0.00 45.80 3.85
36 37 0.536687 TTCTCCGTCGACTGACACCT 60.537 55.000 14.70 0.00 45.80 4.00
37 38 0.526662 ATTCTCCGTCGACTGACACC 59.473 55.000 14.70 0.00 45.80 4.16
38 39 2.349297 AATTCTCCGTCGACTGACAC 57.651 50.000 14.70 0.00 45.80 3.67
39 40 3.253921 TGTTAATTCTCCGTCGACTGACA 59.746 43.478 14.70 3.19 45.80 3.58
40 41 3.829948 TGTTAATTCTCCGTCGACTGAC 58.170 45.455 14.70 0.41 41.91 3.51
41 42 4.216902 TCTTGTTAATTCTCCGTCGACTGA 59.783 41.667 14.70 11.91 0.00 3.41
42 43 4.323868 GTCTTGTTAATTCTCCGTCGACTG 59.676 45.833 14.70 7.40 0.00 3.51
43 44 4.217983 AGTCTTGTTAATTCTCCGTCGACT 59.782 41.667 14.70 0.00 0.00 4.18
44 45 4.323868 CAGTCTTGTTAATTCTCCGTCGAC 59.676 45.833 5.18 5.18 0.00 4.20
45 46 4.022589 ACAGTCTTGTTAATTCTCCGTCGA 60.023 41.667 0.00 0.00 32.28 4.20
46 47 4.235360 ACAGTCTTGTTAATTCTCCGTCG 58.765 43.478 0.00 0.00 32.28 5.12
47 48 6.541111 AAACAGTCTTGTTAATTCTCCGTC 57.459 37.500 0.00 0.00 46.54 4.79
48 49 7.439381 TCTAAACAGTCTTGTTAATTCTCCGT 58.561 34.615 0.00 0.00 46.54 4.69
49 50 7.884816 TCTAAACAGTCTTGTTAATTCTCCG 57.115 36.000 0.00 0.00 46.54 4.63
54 55 9.529325 GGCTTTTTCTAAACAGTCTTGTTAATT 57.471 29.630 0.00 0.00 46.54 1.40
55 56 8.141909 GGGCTTTTTCTAAACAGTCTTGTTAAT 58.858 33.333 0.00 0.00 46.54 1.40
163 164 4.657013 CCTATTTTCCCTCTATTCCTGCC 58.343 47.826 0.00 0.00 0.00 4.85
178 179 6.587273 TGCTTACTTTTTGTTGGCCTATTTT 58.413 32.000 3.32 0.00 0.00 1.82
192 193 6.630071 TGCTTCTGTTTTCTTGCTTACTTTT 58.370 32.000 0.00 0.00 0.00 2.27
204 205 1.609208 TCCTGCCTGCTTCTGTTTTC 58.391 50.000 0.00 0.00 0.00 2.29
213 214 2.654079 CCTCGTCTTCCTGCCTGCT 61.654 63.158 0.00 0.00 0.00 4.24
230 231 2.403586 CGGCGCGGAATCTTTTCC 59.596 61.111 9.72 0.00 46.85 3.13
260 261 3.949754 GACTCTGCCAAATCCAATCATCA 59.050 43.478 0.00 0.00 0.00 3.07
326 327 0.175073 GTACCGACCTGACATGGGAC 59.825 60.000 0.00 0.00 0.00 4.46
327 328 0.040646 AGTACCGACCTGACATGGGA 59.959 55.000 0.00 0.00 0.00 4.37
459 460 2.439701 TACTCGGCCCGACCTGAG 60.440 66.667 0.00 0.00 41.79 3.35
460 461 2.753043 GTACTCGGCCCGACCTGA 60.753 66.667 0.00 0.00 35.61 3.86
461 462 4.189188 CGTACTCGGCCCGACCTG 62.189 72.222 0.00 0.00 35.61 4.00
462 463 4.729918 ACGTACTCGGCCCGACCT 62.730 66.667 0.00 0.00 41.85 3.85
463 464 4.487412 CACGTACTCGGCCCGACC 62.487 72.222 0.00 0.00 41.85 4.79
464 465 4.487412 CCACGTACTCGGCCCGAC 62.487 72.222 0.00 0.00 41.85 4.79
589 590 9.097257 TCTCATCAACAATCAAAAAGGAAAAAC 57.903 29.630 0.00 0.00 0.00 2.43
604 605 4.323417 ACGCATAACCTTCTCATCAACAA 58.677 39.130 0.00 0.00 0.00 2.83
605 606 3.937814 ACGCATAACCTTCTCATCAACA 58.062 40.909 0.00 0.00 0.00 3.33
606 607 4.492570 CGAACGCATAACCTTCTCATCAAC 60.493 45.833 0.00 0.00 0.00 3.18
614 615 2.991190 TCTTGTCGAACGCATAACCTTC 59.009 45.455 0.00 0.00 0.00 3.46
689 690 3.141488 TCTCCGCTTCTCTCCGGC 61.141 66.667 0.00 0.00 44.01 6.13
804 827 2.645730 TCGCTGCTGTTGTTTTTGTT 57.354 40.000 0.00 0.00 0.00 2.83
939 973 2.033602 CCCCCAACCAACCTCGAC 59.966 66.667 0.00 0.00 0.00 4.20
949 983 1.452108 CCATTCGCTCTCCCCCAAC 60.452 63.158 0.00 0.00 0.00 3.77
1848 1890 1.739929 CACCATGAGCGCGTTGGTA 60.740 57.895 24.79 1.86 41.77 3.25
1905 1947 2.115291 GTCCCGGAAATCCAGCAGC 61.115 63.158 0.73 0.00 35.14 5.25
2383 2428 4.427661 ACCGCGAGCTGAGCAGAC 62.428 66.667 8.23 0.00 34.19 3.51
2406 2451 6.731335 ACAACAAGTGTAGTACAGTACGACTG 60.731 42.308 20.69 14.58 44.89 3.51
2539 2585 6.402222 CACTCTAGTGCTCCAGTTAAGATTT 58.598 40.000 0.00 0.00 39.39 2.17
2588 2634 9.808808 GTACTTAGTCGAAATTTTCTCTTTTCC 57.191 33.333 7.50 0.00 0.00 3.13
2600 2646 3.065371 CCCCGTACGTACTTAGTCGAAAT 59.935 47.826 22.55 0.00 0.00 2.17
2611 2657 0.319297 GGATGATGCCCCGTACGTAC 60.319 60.000 15.90 15.90 0.00 3.67
2659 3903 2.743664 CGACAACAGATGCTCCAATGAA 59.256 45.455 0.00 0.00 0.00 2.57
2662 3906 1.742761 CCGACAACAGATGCTCCAAT 58.257 50.000 0.00 0.00 0.00 3.16
2664 3908 1.375908 GCCGACAACAGATGCTCCA 60.376 57.895 0.00 0.00 0.00 3.86
2668 3912 0.376152 CTGATGCCGACAACAGATGC 59.624 55.000 2.76 0.00 46.63 3.91
2738 3982 7.571026 CGAAAGATATCCTTTAGCATTCACAG 58.429 38.462 0.00 0.00 44.63 3.66
2912 4157 6.150140 GCAGATAGAGTCACTGTTCCAATTTT 59.850 38.462 11.56 0.00 34.60 1.82
2913 4158 5.645497 GCAGATAGAGTCACTGTTCCAATTT 59.355 40.000 11.56 0.00 34.60 1.82
2927 4172 9.355916 TGTATACTTATGTGAAGCAGATAGAGT 57.644 33.333 4.17 0.00 0.00 3.24
2946 4191 7.656137 AGAAACACGTGACAGAAAATGTATACT 59.344 33.333 25.01 0.00 44.17 2.12
2947 4192 7.793902 AGAAACACGTGACAGAAAATGTATAC 58.206 34.615 25.01 0.00 44.17 1.47
2948 4193 7.956420 AGAAACACGTGACAGAAAATGTATA 57.044 32.000 25.01 0.00 44.17 1.47
2950 4195 6.671614 AAGAAACACGTGACAGAAAATGTA 57.328 33.333 25.01 0.00 44.17 2.29
2952 4197 6.258160 AGAAAGAAACACGTGACAGAAAATG 58.742 36.000 25.01 0.00 0.00 2.32
2953 4198 6.436843 AGAAAGAAACACGTGACAGAAAAT 57.563 33.333 25.01 0.69 0.00 1.82
2954 4199 5.873179 AGAAAGAAACACGTGACAGAAAA 57.127 34.783 25.01 0.00 0.00 2.29
2955 4200 5.873179 AAGAAAGAAACACGTGACAGAAA 57.127 34.783 25.01 0.00 0.00 2.52
3009 4258 9.508567 CTGTTTCTAAACTCTTTGAAAGAAAGG 57.491 33.333 9.15 0.31 39.59 3.11
3018 4267 6.318900 ACTTGGGTCTGTTTCTAAACTCTTTG 59.681 38.462 7.09 0.00 39.59 2.77
3037 4286 1.073923 AGCAGAAACCAGGTACTTGGG 59.926 52.381 26.16 10.41 34.60 4.12
3042 4291 2.256117 ACACAGCAGAAACCAGGTAC 57.744 50.000 0.00 0.00 0.00 3.34
3043 4292 2.438021 AGAACACAGCAGAAACCAGGTA 59.562 45.455 0.00 0.00 0.00 3.08
3312 4763 0.317436 GATCTCTGCACTACGGCTCG 60.317 60.000 0.00 0.00 34.04 5.03


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

AutoCloner maintained by Alex Coulton.