Multiple sequence alignment - TraesCS5A01G349400

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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 TraesCS5A01G349400 chr5A 100.000 3402 0 0 1 3402 552512918 552516319 0.000000e+00 6283.0
1 TraesCS5A01G349400 chr5A 79.923 259 37 10 1428 1686 552514282 552514525 3.490000e-40 176.0
2 TraesCS5A01G349400 chr5A 79.923 259 37 10 1365 1608 552514345 552514603 3.490000e-40 176.0
3 TraesCS5A01G349400 chr5A 88.235 51 5 1 499 549 473323476 473323427 3.670000e-05 60.2
4 TraesCS5A01G349400 chr5A 90.698 43 4 0 496 538 658909391 658909433 1.320000e-04 58.4
5 TraesCS5A01G349400 chr5B 89.852 3518 193 59 3 3402 531530962 531534433 0.000000e+00 4368.0
6 TraesCS5A01G349400 chr5B 79.767 257 32 14 1365 1608 531532434 531532683 5.840000e-38 169.0
7 TraesCS5A01G349400 chr5B 78.764 259 31 12 1428 1686 531532371 531532605 5.880000e-33 152.0
8 TraesCS5A01G349400 chr5B 90.698 43 3 1 505 547 59694465 59694506 4.740000e-04 56.5
9 TraesCS5A01G349400 chr5D 91.024 3253 154 57 238 3394 437334863 437338073 0.000000e+00 4263.0
10 TraesCS5A01G349400 chr5D 90.476 189 9 3 3 187 437334673 437334856 1.220000e-59 241.0
11 TraesCS5A01G349400 chr5D 80.309 259 36 11 1365 1608 437336071 437336329 7.500000e-42 182.0
12 TraesCS5A01G349400 chr5D 79.923 259 37 8 1428 1686 437336008 437336251 3.490000e-40 176.0
13 TraesCS5A01G349400 chr4A 100.000 40 0 0 498 537 241015852 241015891 1.310000e-09 75.0
14 TraesCS5A01G349400 chr6D 97.143 35 1 0 511 545 63846470 63846436 3.670000e-05 60.2
15 TraesCS5A01G349400 chr6D 97.059 34 1 0 511 544 63834759 63834726 1.320000e-04 58.4
16 TraesCS5A01G349400 chr7D 88.889 45 5 0 496 540 266247082 266247126 4.740000e-04 56.5


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 TraesCS5A01G349400 chr5A 552512918 552516319 3401 False 2211.666667 6283 86.615333 1 3402 3 chr5A.!!$F2 3401
1 TraesCS5A01G349400 chr5B 531530962 531534433 3471 False 1563.000000 4368 82.794333 3 3402 3 chr5B.!!$F2 3399
2 TraesCS5A01G349400 chr5D 437334673 437338073 3400 False 1215.500000 4263 85.433000 3 3394 4 chr5D.!!$F1 3391

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
741 809 0.107214 GCTCGATGATTTCCCACCCA 60.107 55.0 0.0 0.0 0.0 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2479 2581 0.0982 CTGACCATGATGCAGCGTTG 59.902 55.0 0.0 0.0 0.0 4.1 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
39 45 1.257055 ATTGGATTGGGTTGGGTGCG 61.257 55.000 0.00 0.00 0.00 5.34
83 89 4.487948 CATTTTGCCACATTCTGGTACTG 58.512 43.478 0.00 0.00 42.99 2.74
118 124 9.896645 GAATCCTGATTCATAATGCCTAGAATA 57.103 33.333 13.62 0.00 44.89 1.75
119 125 9.902684 AATCCTGATTCATAATGCCTAGAATAG 57.097 33.333 0.00 0.00 38.80 1.73
120 126 8.670521 TCCTGATTCATAATGCCTAGAATAGA 57.329 34.615 0.00 0.00 42.77 1.98
121 127 9.104713 TCCTGATTCATAATGCCTAGAATAGAA 57.895 33.333 0.00 0.00 42.77 2.10
122 128 9.902684 CCTGATTCATAATGCCTAGAATAGAAT 57.097 33.333 0.00 0.00 42.77 2.40
173 188 9.760077 ACATCCTGTAATTAATTAACCTAGTCG 57.240 33.333 9.48 0.00 0.00 4.18
190 205 1.404035 GTCGTGCCCTGTTTGTTTTCT 59.596 47.619 0.00 0.00 0.00 2.52
195 222 4.554723 CGTGCCCTGTTTGTTTTCTTAGAG 60.555 45.833 0.00 0.00 0.00 2.43
196 223 4.578928 GTGCCCTGTTTGTTTTCTTAGAGA 59.421 41.667 0.00 0.00 0.00 3.10
232 268 7.214467 TCTCAATGTATATATGTGCTCGTCA 57.786 36.000 0.00 0.00 0.00 4.35
255 291 4.025401 CCGCGGTGTGGTTCTTGC 62.025 66.667 19.50 0.00 0.00 4.01
281 317 4.842091 CGTCGACGGGGTTAGCCG 62.842 72.222 29.70 0.00 34.97 5.52
361 398 1.633945 AGGTAGTGGTGGGTTGGATTC 59.366 52.381 0.00 0.00 0.00 2.52
366 403 1.743394 GTGGTGGGTTGGATTCGATTC 59.257 52.381 0.00 0.00 0.00 2.52
522 561 8.292444 AGCTTGCAAAATGGTCTTACATTATA 57.708 30.769 0.00 0.00 40.01 0.98
555 594 2.171725 GTTAGCTTAGCCGTGGCCG 61.172 63.158 7.39 0.00 43.17 6.13
556 595 2.652095 TTAGCTTAGCCGTGGCCGT 61.652 57.895 7.39 0.00 43.17 5.68
557 596 2.567564 TTAGCTTAGCCGTGGCCGTC 62.568 60.000 7.39 0.00 43.17 4.79
575 640 6.481976 TGGCCGTCTTTTTCAGTATATATGTG 59.518 38.462 0.00 0.00 0.00 3.21
603 671 7.095982 GGACGAACAGTTCTTTCTTTTAGAGAG 60.096 40.741 11.60 0.00 35.37 3.20
634 702 7.408756 TTGAGCTAAATCTGCATAAACCATT 57.591 32.000 0.00 0.00 0.00 3.16
637 705 6.809869 AGCTAAATCTGCATAAACCATTTCC 58.190 36.000 0.00 0.00 0.00 3.13
734 802 6.828502 TGTATTGTACTGCTCGATGATTTC 57.171 37.500 0.00 0.00 0.00 2.17
741 809 0.107214 GCTCGATGATTTCCCACCCA 60.107 55.000 0.00 0.00 0.00 4.51
827 897 6.266786 TGAGTACTAGATTGTGACTGGAAACA 59.733 38.462 0.00 0.00 39.59 2.83
901 988 5.808366 TGATGGAGTAACTTGTTCTCTGT 57.192 39.130 10.40 0.00 0.00 3.41
942 1029 7.274904 CCTACTTTGCAAATTTCATCACTGATG 59.725 37.037 13.23 12.25 41.00 3.07
943 1030 6.751157 ACTTTGCAAATTTCATCACTGATGA 58.249 32.000 16.44 16.44 45.78 2.92
944 1031 7.383687 ACTTTGCAAATTTCATCACTGATGAT 58.616 30.769 20.17 6.01 46.52 2.45
969 1059 7.174413 TGTGTAGATTTTGAATCCAGATCCAA 58.826 34.615 0.00 0.00 0.00 3.53
974 1064 5.726980 TTTTGAATCCAGATCCAAGTTGG 57.273 39.130 16.36 16.36 39.43 3.77
1015 1105 2.753043 CCATGGCTGCTGGTGACC 60.753 66.667 0.00 0.00 0.00 4.02
1026 1116 3.236391 GGTGACCACCCACACTCA 58.764 61.111 7.95 0.00 45.68 3.41
1134 1224 2.736670 AAGACAAAGTTGCTGGGACT 57.263 45.000 0.00 0.00 0.00 3.85
1140 1230 0.258774 AAGTTGCTGGGACTGTTGGT 59.741 50.000 0.00 0.00 0.00 3.67
1161 1251 0.618458 TCAAGAGGCCGCAACCTAAT 59.382 50.000 9.88 0.00 41.32 1.73
1191 1284 2.591429 CTGACCAACCAGCACGCA 60.591 61.111 0.00 0.00 0.00 5.24
1424 1517 0.962356 GCTGCTGCTACCACCAATGT 60.962 55.000 8.53 0.00 36.03 2.71
1451 1544 4.225942 TCATACTCCATCAGCTCCTGTTTT 59.774 41.667 0.00 0.00 32.61 2.43
1692 1785 0.332972 AACAATCTCCAGGGAAGGCC 59.667 55.000 0.00 0.00 0.00 5.19
1704 1797 1.566298 GGAAGGCCACTGTCCATCCT 61.566 60.000 5.01 0.00 38.20 3.24
1788 1881 1.961793 TTACGGCTGCCAATACATCC 58.038 50.000 20.29 0.00 0.00 3.51
1790 1883 1.149174 CGGCTGCCAATACATCCCT 59.851 57.895 20.29 0.00 0.00 4.20
1839 1932 0.807667 CTCGTGATGCTGTGGCTACC 60.808 60.000 0.00 0.00 39.59 3.18
1849 1942 1.436336 GTGGCTACCGCTACGACAT 59.564 57.895 0.00 0.00 37.88 3.06
1860 1953 2.391879 GCTACGACATGTAATCCGACC 58.608 52.381 11.17 0.00 31.20 4.79
1875 1968 0.227234 CGACCGATTCGCAAAGATCG 59.773 55.000 0.00 0.00 41.87 3.69
2025 2118 6.486657 ACAACTGCTATCTAAAACATGTGTGT 59.513 34.615 0.00 0.00 41.28 3.72
2091 2184 3.642901 CAAGCATGCCATTGAGCTC 57.357 52.632 15.66 6.82 36.07 4.09
2132 2225 6.696441 TCTCTTAATCGAAGAAGGTACTCC 57.304 41.667 9.16 0.00 43.75 3.85
2163 2263 3.738830 TTTTGCAGCTTTGATCTTGCT 57.261 38.095 0.00 0.00 37.56 3.91
2165 2265 3.293311 TTGCAGCTTTGATCTTGCTTC 57.707 42.857 0.00 2.53 34.51 3.86
2178 2278 6.985117 TGATCTTGCTTCTTAACATTGCTTT 58.015 32.000 0.00 0.00 0.00 3.51
2179 2279 6.864685 TGATCTTGCTTCTTAACATTGCTTTG 59.135 34.615 0.00 0.00 0.00 2.77
2212 2312 5.964751 TGTATTTTCGCACATTGATTCATCG 59.035 36.000 0.00 0.00 0.00 3.84
2233 2333 9.031360 TCATCGTAAATCTGTTTACAATAGCTC 57.969 33.333 10.55 0.00 46.43 4.09
2245 2345 3.326747 ACAATAGCTCGAGTGTTTGACC 58.673 45.455 21.84 3.09 0.00 4.02
2335 2435 2.796483 TTCCACCTGCCGAACATCCG 62.796 60.000 0.00 0.00 0.00 4.18
2409 2509 4.140599 CCGCCGCTGAGAAGAGCT 62.141 66.667 0.00 0.00 36.77 4.09
2426 2528 5.163281 AGAGCTGAAAATCAGATGTCACT 57.837 39.130 11.39 0.00 44.01 3.41
2431 2533 5.305139 TGAAAATCAGATGTCACTGCATG 57.695 39.130 0.00 0.00 37.75 4.06
2440 2542 3.496898 TCACTGCATGACGAGTGTC 57.503 52.632 15.54 0.00 45.71 3.67
2441 2543 0.038251 TCACTGCATGACGAGTGTCC 60.038 55.000 15.54 0.00 44.86 4.02
2442 2544 0.037882 CACTGCATGACGAGTGTCCT 60.038 55.000 0.00 0.00 44.86 3.85
2443 2545 0.037882 ACTGCATGACGAGTGTCCTG 60.038 55.000 0.00 0.00 44.86 3.86
2444 2546 0.244721 CTGCATGACGAGTGTCCTGA 59.755 55.000 0.00 0.00 44.86 3.86
2445 2547 0.038251 TGCATGACGAGTGTCCTGAC 60.038 55.000 0.00 0.00 44.86 3.51
2479 2581 1.671379 GACGAACTCTTGCCACCCC 60.671 63.158 0.00 0.00 0.00 4.95
2513 2615 1.142474 GTCAGCATGTTTTTGCCTGC 58.858 50.000 0.00 0.00 43.83 4.85
2516 2618 0.958091 AGCATGTTTTTGCCTGCGTA 59.042 45.000 0.00 0.00 43.83 4.42
2517 2619 1.545582 AGCATGTTTTTGCCTGCGTAT 59.454 42.857 0.00 0.00 43.83 3.06
2519 2621 2.926159 GCATGTTTTTGCCTGCGTATGT 60.926 45.455 0.00 0.00 36.60 2.29
2520 2622 2.697431 TGTTTTTGCCTGCGTATGTC 57.303 45.000 0.00 0.00 0.00 3.06
2521 2623 1.268352 TGTTTTTGCCTGCGTATGTCC 59.732 47.619 0.00 0.00 0.00 4.02
2612 2735 3.054728 TGCCCGAACTTTGATGGATCTAA 60.055 43.478 0.00 0.00 0.00 2.10
2768 2891 2.715737 TCTTGTTTAATTGCACGGGC 57.284 45.000 0.34 0.34 41.68 6.13
2813 2936 4.156008 GGAACTCCGTCAGCAACAAATAAT 59.844 41.667 0.00 0.00 0.00 1.28
2856 3006 0.107214 ATGCACCCTAACCATGACGG 60.107 55.000 0.00 0.00 42.50 4.79
3069 3219 7.638444 TGGAGAAATGGAGGTTTTACATGATA 58.362 34.615 0.00 0.00 0.00 2.15
3087 3237 5.055642 TGATACCTTGTCACTCAACGTAG 57.944 43.478 0.00 0.00 33.54 3.51
3093 3243 1.534163 TGTCACTCAACGTAGACGGAG 59.466 52.381 7.04 6.87 44.95 4.63
3094 3244 0.520404 TCACTCAACGTAGACGGAGC 59.480 55.000 7.04 0.00 44.95 4.70
3095 3245 0.456312 CACTCAACGTAGACGGAGCC 60.456 60.000 7.04 0.00 44.95 4.70
3174 3324 1.523938 GCATACTGAACCTCGGCCC 60.524 63.158 0.00 0.00 0.00 5.80
3198 3348 1.340248 GAATTGAGCATGGCCATCAGG 59.660 52.381 17.61 6.17 38.23 3.86
3253 3403 1.154197 AGACTTCACGACATCGACGA 58.846 50.000 8.54 0.00 43.02 4.20
3273 3423 4.099120 CGACGTCAAGGAGATCAAACTAG 58.901 47.826 17.16 0.00 0.00 2.57
3311 3461 2.170985 CGCAACAAAGTCGCGGAG 59.829 61.111 6.13 0.00 45.08 4.63
3315 3465 1.156736 CAACAAAGTCGCGGAGGAAT 58.843 50.000 6.13 0.00 0.00 3.01
3316 3466 2.343101 CAACAAAGTCGCGGAGGAATA 58.657 47.619 6.13 0.00 0.00 1.75
3339 3489 2.101783 CTTCCAAGCATACCATTGGCA 58.898 47.619 1.54 0.00 44.67 4.92
3341 3491 1.184431 CCAAGCATACCATTGGCACA 58.816 50.000 1.54 0.00 39.58 4.57
3351 3501 0.592637 CATTGGCACAGCAAAGTCGA 59.407 50.000 0.00 0.00 42.39 4.20
3376 3527 0.871057 AGAAACTTTCAGCAGCGAGC 59.129 50.000 4.34 0.00 46.19 5.03
3394 3545 1.227383 CCTCCATGGGGGTACTTGC 59.773 63.158 24.07 0.00 38.11 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.007039 CCAATCAAATCCACTATCTGTGTCG 59.993 44.000 0.00 0.00 44.81 4.35
1 2 6.115446 TCCAATCAAATCCACTATCTGTGTC 58.885 40.000 0.00 0.00 44.81 3.67
39 45 1.636988 ACCAACTCGTGTAATAGCGC 58.363 50.000 0.00 0.00 0.00 5.92
44 50 4.846779 AAATGCAACCAACTCGTGTAAT 57.153 36.364 0.00 0.00 0.00 1.89
118 124 2.636893 ACTCTGCAGTCAGGTCAATTCT 59.363 45.455 14.67 0.00 40.69 2.40
119 125 2.740981 CACTCTGCAGTCAGGTCAATTC 59.259 50.000 14.67 0.00 40.69 2.17
120 126 2.551721 CCACTCTGCAGTCAGGTCAATT 60.552 50.000 14.67 0.00 40.69 2.32
121 127 1.002888 CCACTCTGCAGTCAGGTCAAT 59.997 52.381 14.67 0.00 40.69 2.57
122 128 0.394192 CCACTCTGCAGTCAGGTCAA 59.606 55.000 14.67 0.00 40.69 3.18
157 164 5.104652 ACAGGGCACGACTAGGTTAATTAAT 60.105 40.000 0.31 0.00 0.00 1.40
158 165 4.223477 ACAGGGCACGACTAGGTTAATTAA 59.777 41.667 0.00 0.00 0.00 1.40
159 166 3.770933 ACAGGGCACGACTAGGTTAATTA 59.229 43.478 0.00 0.00 0.00 1.40
160 167 2.570302 ACAGGGCACGACTAGGTTAATT 59.430 45.455 0.00 0.00 0.00 1.40
173 188 4.578928 TCTCTAAGAAAACAAACAGGGCAC 59.421 41.667 0.00 0.00 0.00 5.01
343 380 1.276989 TCGAATCCAACCCACCACTAC 59.723 52.381 0.00 0.00 0.00 2.73
353 390 4.776743 CATCCAATCGAATCGAATCCAAC 58.223 43.478 10.12 0.00 39.99 3.77
361 398 4.051237 TGTAAGAGCATCCAATCGAATCG 58.949 43.478 0.00 0.00 33.66 3.34
366 403 4.986875 CTCATGTAAGAGCATCCAATCG 57.013 45.455 0.00 0.00 33.66 3.34
522 561 1.409942 GCTAACTACTCCCTCCGTCCT 60.410 57.143 0.00 0.00 0.00 3.85
555 594 8.540492 CGTCCACACATATATACTGAAAAAGAC 58.460 37.037 0.00 0.00 0.00 3.01
556 595 8.471609 TCGTCCACACATATATACTGAAAAAGA 58.528 33.333 0.00 0.00 0.00 2.52
557 596 8.642908 TCGTCCACACATATATACTGAAAAAG 57.357 34.615 0.00 0.00 0.00 2.27
575 640 4.877323 AAAGAAAGAACTGTTCGTCCAC 57.123 40.909 14.35 7.33 34.02 4.02
680 748 6.906848 AGTTCAGCTTCTCTCTACTACCTAT 58.093 40.000 0.00 0.00 0.00 2.57
734 802 2.674380 GTGCAGAGCTTGGGTGGG 60.674 66.667 0.00 0.00 0.00 4.61
741 809 3.347077 AAATGCTAGAGTGCAGAGCTT 57.653 42.857 10.24 2.94 46.71 3.74
827 897 6.805713 ACACAACTGAAATTCCGAAAATTCT 58.194 32.000 9.94 0.00 0.00 2.40
883 970 8.779354 AATATCAACAGAGAACAAGTTACTCC 57.221 34.615 0.00 0.00 0.00 3.85
942 1029 7.500227 TGGATCTGGATTCAAAATCTACACATC 59.500 37.037 0.00 0.00 0.00 3.06
943 1030 7.348815 TGGATCTGGATTCAAAATCTACACAT 58.651 34.615 0.00 0.00 0.00 3.21
944 1031 6.720309 TGGATCTGGATTCAAAATCTACACA 58.280 36.000 0.00 0.00 0.00 3.72
969 1059 0.106519 AGAACTGCAGCCAACCAACT 60.107 50.000 15.27 0.00 0.00 3.16
1015 1105 4.743057 TCTCTGATATTGAGTGTGGGTG 57.257 45.455 6.58 0.00 33.59 4.61
1026 1116 5.125097 CAGTGCTGCCTTTTTCTCTGATATT 59.875 40.000 0.00 0.00 0.00 1.28
1134 1224 0.392461 GCGGCCTCTTGATACCAACA 60.392 55.000 0.00 0.00 0.00 3.33
1140 1230 1.491668 TAGGTTGCGGCCTCTTGATA 58.508 50.000 0.00 0.00 39.94 2.15
1176 1266 3.660111 GGTGCGTGCTGGTTGGTC 61.660 66.667 0.00 0.00 0.00 4.02
1424 1517 2.961741 GGAGCTGATGGAGTATGAGACA 59.038 50.000 0.00 0.00 0.00 3.41
1451 1544 4.426112 CTGCAGCAGGAGACGCGA 62.426 66.667 15.93 0.00 34.74 5.87
1484 1577 2.736978 CTGATGGAGTATGAGACGCAC 58.263 52.381 0.00 0.00 0.00 5.34
1692 1785 3.685139 ACAACACTAGGATGGACAGTG 57.315 47.619 0.00 0.00 44.20 3.66
1704 1797 4.500887 GGACTAGCAGTCACAACAACACTA 60.501 45.833 15.22 0.00 46.79 2.74
1788 1881 5.938125 ACTAGTAGCCACAACATTACAAAGG 59.062 40.000 0.00 0.00 0.00 3.11
1790 1883 7.443477 TGTACTAGTAGCCACAACATTACAAA 58.557 34.615 1.87 0.00 0.00 2.83
1839 1932 2.041966 GTCGGATTACATGTCGTAGCG 58.958 52.381 0.00 0.00 0.00 4.26
1860 1953 1.498865 CCCCCGATCTTTGCGAATCG 61.499 60.000 0.00 0.00 36.41 3.34
1875 1968 2.034878 GCTTTCCAATCTTGATCCCCC 58.965 52.381 0.00 0.00 0.00 5.40
2025 2118 4.127171 GGAGCACTACAGTTCAGACAAAA 58.873 43.478 0.00 0.00 0.00 2.44
2091 2184 2.596419 GAGATTGACTGCTCGTTTCTCG 59.404 50.000 0.00 0.00 41.41 4.04
2132 2225 5.924254 TCAAAGCTGCAAAAATCAGATTGAG 59.076 36.000 1.02 0.00 38.99 3.02
2163 2263 9.039870 CAAATACCAACAAAGCAATGTTAAGAA 57.960 29.630 6.79 0.00 41.44 2.52
2165 2265 8.364129 ACAAATACCAACAAAGCAATGTTAAG 57.636 30.769 6.79 5.03 41.44 1.85
2178 2278 6.073327 TGTGCGAAAATACAAATACCAACA 57.927 33.333 0.00 0.00 0.00 3.33
2179 2279 7.327275 TCAATGTGCGAAAATACAAATACCAAC 59.673 33.333 0.00 0.00 0.00 3.77
2233 2333 1.191647 GTAAGTGCGGTCAAACACTCG 59.808 52.381 0.00 0.00 46.17 4.18
2245 2345 2.747446 AGCAAATAAGGGTGTAAGTGCG 59.253 45.455 0.00 0.00 35.92 5.34
2335 2435 2.143925 GTTGGCTGAGTTGGTAGTGAC 58.856 52.381 0.00 0.00 0.00 3.67
2409 2509 5.005094 TCATGCAGTGACATCTGATTTTCA 58.995 37.500 0.00 0.00 37.61 2.69
2426 2528 4.994744 CAGGACACTCGTCATGCA 57.005 55.556 0.00 0.00 45.87 3.96
2431 2533 0.959553 TTCAGGTCAGGACACTCGTC 59.040 55.000 1.41 0.00 41.80 4.20
2440 2542 2.847327 TGAGAAAGCTTCAGGTCAGG 57.153 50.000 0.00 0.00 0.00 3.86
2441 2543 3.683822 GTCATGAGAAAGCTTCAGGTCAG 59.316 47.826 0.00 0.00 0.00 3.51
2442 2544 3.668447 GTCATGAGAAAGCTTCAGGTCA 58.332 45.455 0.00 0.77 0.00 4.02
2443 2545 2.670414 CGTCATGAGAAAGCTTCAGGTC 59.330 50.000 0.00 0.00 0.00 3.85
2444 2546 2.300152 TCGTCATGAGAAAGCTTCAGGT 59.700 45.455 0.00 0.00 0.00 4.00
2445 2547 2.964740 TCGTCATGAGAAAGCTTCAGG 58.035 47.619 0.00 0.00 0.00 3.86
2479 2581 0.098200 CTGACCATGATGCAGCGTTG 59.902 55.000 0.00 0.00 0.00 4.10
2513 2615 6.018994 GCTACCATTAAGTCTTTGGACATACG 60.019 42.308 9.84 0.00 44.36 3.06
2516 2618 5.882557 CAGCTACCATTAAGTCTTTGGACAT 59.117 40.000 9.84 0.00 44.36 3.06
2517 2619 5.012664 TCAGCTACCATTAAGTCTTTGGACA 59.987 40.000 9.84 0.00 44.36 4.02
2519 2621 5.755409 TCAGCTACCATTAAGTCTTTGGA 57.245 39.130 9.84 0.00 34.52 3.53
2520 2622 5.705441 TGTTCAGCTACCATTAAGTCTTTGG 59.295 40.000 2.26 2.26 36.56 3.28
2521 2623 6.650807 TCTGTTCAGCTACCATTAAGTCTTTG 59.349 38.462 0.00 0.00 0.00 2.77
2612 2735 4.803452 CCTATGGGGTTCATGGTTACATT 58.197 43.478 0.00 0.00 37.30 2.71
2768 2891 0.820891 CCTTGATGGCTTGATCCCCG 60.821 60.000 0.00 0.00 0.00 5.73
2839 2989 2.112815 GCCGTCATGGTTAGGGTGC 61.113 63.158 0.00 0.00 41.21 5.01
2856 3006 6.657836 ACTTGTTATTAATAGTCGTGGTGC 57.342 37.500 0.00 0.00 0.00 5.01
2895 3045 2.037620 GAGCATGCCTGTCCCGATCT 62.038 60.000 15.66 0.00 0.00 2.75
3056 3206 6.653320 TGAGTGACAAGGTATCATGTAAAACC 59.347 38.462 0.00 0.00 0.00 3.27
3087 3237 1.507141 CCATAAATGGCGGCTCCGTC 61.507 60.000 11.43 5.89 45.14 4.79
3174 3324 0.685131 TGGCCATGCTCAATTCAGGG 60.685 55.000 0.00 0.00 38.33 4.45
3218 3368 5.050091 GTGAAGTCTTAGAATGGTGTGTGTG 60.050 44.000 0.00 0.00 0.00 3.82
3222 3372 4.386049 GTCGTGAAGTCTTAGAATGGTGTG 59.614 45.833 0.00 0.00 0.00 3.82
3253 3403 3.368531 GCCTAGTTTGATCTCCTTGACGT 60.369 47.826 0.00 0.00 0.00 4.34
3273 3423 1.153429 AATGGTACGCTCGGAAGCC 60.153 57.895 0.00 0.00 46.34 4.35
3284 3434 1.000717 ACTTTGTTGCGCCAATGGTAC 60.001 47.619 4.18 0.00 0.00 3.34
3298 3448 2.618053 CTTATTCCTCCGCGACTTTGT 58.382 47.619 8.23 0.00 0.00 2.83
3335 3485 1.153269 TGTCGACTTTGCTGTGCCA 60.153 52.632 17.92 0.00 0.00 4.92
3339 3489 1.412710 TCTTCCTGTCGACTTTGCTGT 59.587 47.619 17.92 0.00 0.00 4.40
3341 3491 2.872858 GTTTCTTCCTGTCGACTTTGCT 59.127 45.455 17.92 0.00 0.00 3.91
3351 3501 2.620585 GCTGCTGAAAGTTTCTTCCTGT 59.379 45.455 16.33 0.00 35.30 4.00
3376 3527 1.227383 GCAAGTACCCCCATGGAGG 59.773 63.158 15.22 13.28 38.00 4.30


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

AutoCloner maintained by Alex Coulton.