Multiple sequence alignment - TraesCS2D01G421400

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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 TraesCS2D01G421400 chr2D 100.000 4780 0 0 1 4780 534957227 534962006 0.000000e+00 8828.0
1 TraesCS2D01G421400 chr2A 91.580 2779 119 42 93 2813 678192030 678194751 0.000000e+00 3729.0
2 TraesCS2D01G421400 chr2A 97.134 977 27 1 2966 3942 678195109 678196084 0.000000e+00 1648.0
3 TraesCS2D01G421400 chr2A 90.840 393 33 1 4391 4780 678198050 678198442 1.520000e-144 523.0
4 TraesCS2D01G421400 chr2A 86.704 361 39 7 2452 2807 339108485 339108841 4.480000e-105 392.0
5 TraesCS2D01G421400 chr2A 85.286 367 45 7 2452 2813 325794450 325794088 2.100000e-98 370.0
6 TraesCS2D01G421400 chr2A 84.783 368 49 6 2809 3175 339108885 339109246 3.520000e-96 363.0
7 TraesCS2D01G421400 chr2A 81.761 477 28 18 3969 4401 678196393 678196854 1.270000e-90 344.0
8 TraesCS2D01G421400 chr2A 97.727 176 4 0 2809 2984 678194790 678194965 2.160000e-78 303.0
9 TraesCS2D01G421400 chr2B 90.053 1498 74 30 773 2232 636211914 636213374 0.000000e+00 1871.0
10 TraesCS2D01G421400 chr2B 92.896 1295 66 18 2966 4250 636214192 636215470 0.000000e+00 1858.0
11 TraesCS2D01G421400 chr2B 91.603 655 31 9 1 635 636210839 636211489 0.000000e+00 883.0
12 TraesCS2D01G421400 chr2B 93.139 583 34 5 2233 2813 636213613 636214191 0.000000e+00 850.0
13 TraesCS2D01G421400 chr2B 85.266 319 33 5 4330 4636 636215588 636215904 2.780000e-82 316.0
14 TraesCS2D01G421400 chr2B 88.679 159 12 2 4623 4780 636216257 636216410 6.320000e-44 189.0
15 TraesCS2D01G421400 chr6A 86.207 348 39 7 2471 2813 511287361 511287018 7.560000e-98 368.0
16 TraesCS2D01G421400 chr5D 86.217 341 39 6 2469 2805 21305986 21306322 3.520000e-96 363.0
17 TraesCS2D01G421400 chr5D 85.950 121 12 5 1085 1204 488236780 488236664 1.810000e-24 124.0
18 TraesCS2D01G421400 chr7D 85.449 323 34 8 2452 2769 175872782 175873096 1.660000e-84 324.0
19 TraesCS2D01G421400 chr4B 83.429 350 48 8 2469 2813 413483831 413483487 2.780000e-82 316.0
20 TraesCS2D01G421400 chr3B 87.179 234 26 3 2469 2701 29355672 29355442 3.670000e-66 263.0
21 TraesCS2D01G421400 chr6B 84.286 210 13 8 8 216 700079056 700079246 2.270000e-43 187.0
22 TraesCS2D01G421400 chr5B 83.616 177 21 6 3096 3270 415051891 415052061 4.950000e-35 159.0
23 TraesCS2D01G421400 chr5B 85.616 146 14 3 3862 4007 415052059 415052197 3.850000e-31 147.0
24 TraesCS2D01G421400 chr5B 85.950 121 12 5 1085 1204 600940161 600940045 1.810000e-24 124.0
25 TraesCS2D01G421400 chr5A 86.777 121 11 5 1085 1204 608989730 608989614 3.880000e-26 130.0
26 TraesCS2D01G421400 chr5A 77.099 131 23 5 4269 4399 619461121 619460998 8.580000e-08 69.4
27 TraesCS2D01G421400 chr4A 79.394 165 22 11 1084 1241 80174236 80174395 6.540000e-19 106.0
28 TraesCS2D01G421400 chr4A 87.013 77 10 0 3650 3726 80177823 80177899 2.370000e-13 87.9
29 TraesCS2D01G421400 chr4D 87.013 77 10 0 3650 3726 408810328 408810404 2.370000e-13 87.9


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 TraesCS2D01G421400 chr2D 534957227 534962006 4779 False 8828.0 8828 100.000000 1 4780 1 chr2D.!!$F1 4779
1 TraesCS2D01G421400 chr2A 678192030 678198442 6412 False 1309.4 3729 91.808400 93 4780 5 chr2A.!!$F2 4687
2 TraesCS2D01G421400 chr2A 339108485 339109246 761 False 377.5 392 85.743500 2452 3175 2 chr2A.!!$F1 723
3 TraesCS2D01G421400 chr2B 636210839 636216410 5571 False 994.5 1871 90.272667 1 4780 6 chr2B.!!$F1 4779

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
543 574 1.202830 AGGCCGTTGATGGTGTGTTAA 60.203 47.619 0.00 0.0 0.00 2.01 F
1280 1618 1.268640 GCGATTCGTGGTCTCTAGGAC 60.269 57.143 8.03 3.5 43.79 3.85 F
1686 2069 0.112995 TTTGACCCTGCCTTGCTCAT 59.887 50.000 0.00 0.0 0.00 2.90 F
2213 2601 2.795329 CTTACCAGCTTGGGTGTCATT 58.205 47.619 5.99 0.0 43.37 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1673 2055 0.245539 CACCAAATGAGCAAGGCAGG 59.754 55.000 0.00 0.00 0.00 4.85 R
2115 2503 0.333993 AGGGGCACATGAGCTGAAAT 59.666 50.000 14.91 0.00 34.17 2.17 R
3474 4308 2.519302 GTGCAACACAGGCCCTGT 60.519 61.111 11.57 11.57 46.51 4.00 R
3989 5105 1.594397 GCTTTGCTTTGCTTGTGTTCC 59.406 47.619 0.00 0.00 0.00 3.62 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
55 56 1.222300 CCACGAACACATCCAAACGA 58.778 50.000 0.00 0.00 0.00 3.85
61 62 1.674359 ACACATCCAAACGACAGCAA 58.326 45.000 0.00 0.00 0.00 3.91
64 65 1.873591 ACATCCAAACGACAGCAAGTC 59.126 47.619 0.00 0.00 44.02 3.01
112 113 4.318121 GCTACTCGATTTGCAAGGAATACG 60.318 45.833 0.00 1.39 0.00 3.06
115 116 2.942376 TCGATTTGCAAGGAATACGCAT 59.058 40.909 0.00 0.00 35.19 4.73
125 126 2.105477 AGGAATACGCATGCTTCTCCAT 59.895 45.455 20.75 8.64 0.00 3.41
182 183 2.358615 GCCGCATCGCATATCCCA 60.359 61.111 0.00 0.00 0.00 4.37
216 219 1.377229 CAAGGTAACGGGGGAGCAA 59.623 57.895 0.00 0.00 46.39 3.91
243 247 1.429825 CGCTACACGGTGAGGAGAG 59.570 63.158 16.29 6.93 38.44 3.20
244 248 1.810532 GCTACACGGTGAGGAGAGG 59.189 63.158 16.29 0.00 0.00 3.69
245 249 1.668101 GCTACACGGTGAGGAGAGGG 61.668 65.000 16.29 0.00 0.00 4.30
543 574 1.202830 AGGCCGTTGATGGTGTGTTAA 60.203 47.619 0.00 0.00 0.00 2.01
621 652 2.743183 GCTGCGGACATAAACCAGAGAT 60.743 50.000 0.00 0.00 0.00 2.75
674 727 2.204306 CCTTCCCCCACCTCCCTT 60.204 66.667 0.00 0.00 0.00 3.95
682 735 2.124996 CACCTCCCTTCCCCCTCA 59.875 66.667 0.00 0.00 0.00 3.86
770 823 1.617947 GGTCTGGTGGAGCGGATTCT 61.618 60.000 0.00 0.00 32.59 2.40
776 1112 2.109181 GGAGCGGATTCTTCCCGG 59.891 66.667 0.00 0.00 46.55 5.73
829 1165 2.417097 ACCTGCGCTGGTTTTTGC 59.583 55.556 30.90 0.00 36.89 3.68
917 1254 3.842126 CTGCGTGCGATCCGTGTG 61.842 66.667 0.00 0.00 0.00 3.82
918 1255 4.656117 TGCGTGCGATCCGTGTGT 62.656 61.111 0.00 0.00 0.00 3.72
960 1297 2.614057 CGGTTGCTGTCTTTTCTGTCTT 59.386 45.455 0.00 0.00 0.00 3.01
1022 1359 2.383527 CGAACCTGCAGTCTTCCGC 61.384 63.158 13.81 0.00 0.00 5.54
1024 1361 2.456287 GAACCTGCAGTCTTCCGCCT 62.456 60.000 13.81 0.00 0.00 5.52
1194 1531 2.044252 AACGCCCTCCTCGAGCTA 60.044 61.111 6.99 0.00 0.00 3.32
1197 1534 2.631580 CGCCCTCCTCGAGCTATCC 61.632 68.421 6.99 0.00 0.00 2.59
1219 1556 4.415332 TCCGTCGCGTGCTCTTCC 62.415 66.667 5.77 0.00 0.00 3.46
1261 1599 1.595929 TCACGAGGACGGGTTTTGC 60.596 57.895 0.00 0.00 44.00 3.68
1271 1609 1.847890 CGGGTTTTGCGATTCGTGGT 61.848 55.000 8.03 0.00 0.00 4.16
1280 1618 1.268640 GCGATTCGTGGTCTCTAGGAC 60.269 57.143 8.03 3.50 43.79 3.85
1292 1651 4.957327 GGTCTCTAGGACTTACCATGAAGT 59.043 45.833 0.00 0.00 43.97 3.01
1302 1661 2.768253 ACCATGAAGTGAGCGATTGA 57.232 45.000 0.00 0.00 0.00 2.57
1383 1743 9.219603 TCATTAGCATGCTATATAAGGTGTTTC 57.780 33.333 27.35 0.00 0.00 2.78
1402 1762 5.531659 TGTTTCGTAAGGCCAAAGTAAATCA 59.468 36.000 5.01 0.00 38.47 2.57
1403 1763 6.039493 TGTTTCGTAAGGCCAAAGTAAATCAA 59.961 34.615 5.01 0.00 38.47 2.57
1506 1871 2.863740 TGCTTCAGGTATGCGTAATTCG 59.136 45.455 0.00 0.00 43.12 3.34
1559 1926 8.855110 TGCTTCAAATTACATAAAAGAACTGGA 58.145 29.630 0.00 0.00 0.00 3.86
1586 1965 8.647796 AGCTATGTACCTTATGCTGTGTTTATA 58.352 33.333 0.00 0.00 0.00 0.98
1620 1999 8.531982 ACTGTGAAAGCAGTCACTATTCTATTA 58.468 33.333 17.55 0.00 45.63 0.98
1686 2069 0.112995 TTTGACCCTGCCTTGCTCAT 59.887 50.000 0.00 0.00 0.00 2.90
1830 2213 6.303839 TCAGGTACAGCTCCAAATAAAAAGT 58.696 36.000 0.00 0.00 0.00 2.66
1831 2214 6.206634 TCAGGTACAGCTCCAAATAAAAAGTG 59.793 38.462 0.00 0.00 0.00 3.16
1832 2215 5.476945 AGGTACAGCTCCAAATAAAAAGTGG 59.523 40.000 0.00 0.00 0.00 4.00
1833 2216 4.871933 ACAGCTCCAAATAAAAAGTGGG 57.128 40.909 0.00 0.00 32.95 4.61
1834 2217 3.578282 ACAGCTCCAAATAAAAAGTGGGG 59.422 43.478 0.00 0.00 35.86 4.96
1835 2218 3.578282 CAGCTCCAAATAAAAAGTGGGGT 59.422 43.478 0.00 0.00 35.15 4.95
1864 2252 6.815089 ACATTCACAAAATTGCTTGAAGGTA 58.185 32.000 12.26 0.00 36.83 3.08
1877 2265 5.883673 TGCTTGAAGGTACCCATGTTATTAC 59.116 40.000 8.74 0.00 0.00 1.89
2115 2503 3.903714 TCTCTCTGTCCTCCATTTGTTCA 59.096 43.478 0.00 0.00 0.00 3.18
2213 2601 2.795329 CTTACCAGCTTGGGTGTCATT 58.205 47.619 5.99 0.00 43.37 2.57
2353 2979 5.754890 ACCAATGAAGCTTCATGTTGTTTTC 59.245 36.000 36.16 4.71 46.60 2.29
2411 3037 4.631234 AGGTCACAAGGGATACATCCTTA 58.369 43.478 8.14 0.00 46.35 2.69
2430 3056 8.500773 CATCCTTATTACTTTGTTGTGTAACGT 58.499 33.333 0.00 0.00 42.39 3.99
2432 3058 9.539825 TCCTTATTACTTTGTTGTGTAACGTAA 57.460 29.630 0.00 0.00 42.39 3.18
2602 3228 7.112122 TGCAGGTTGATGATACTGAAGTTATT 58.888 34.615 0.00 0.00 32.86 1.40
2714 3340 6.039941 ACCATCTCAATCCTCGTCTAAAGTAG 59.960 42.308 0.00 0.00 0.00 2.57
3149 3983 6.260271 GCCAAACAGGGTCTTATACAGATAAC 59.740 42.308 0.00 0.00 38.09 1.89
3467 4301 4.799564 TCCCATGTGCTAATTTTTGTCC 57.200 40.909 0.00 0.00 0.00 4.02
3474 4308 3.576550 GTGCTAATTTTTGTCCTTCCCCA 59.423 43.478 0.00 0.00 0.00 4.96
3620 4454 9.086336 CAAATAAAATGAAATGTAGTTGCCGAT 57.914 29.630 0.00 0.00 0.00 4.18
3624 4458 4.200838 TGAAATGTAGTTGCCGATCAGA 57.799 40.909 0.00 0.00 0.00 3.27
3637 4471 4.037565 TGCCGATCAGAATACTAATCGTGT 59.962 41.667 0.00 0.00 41.24 4.49
3780 4614 4.019051 TGGATCACATGATGGGGATATGAC 60.019 45.833 0.00 0.00 34.37 3.06
3828 4662 9.778741 ACAACAATAATAGAGTCTCTTGTGAAA 57.221 29.630 7.89 0.00 0.00 2.69
3868 4702 1.028905 CTTCCCTCAGCCGTCTAGAG 58.971 60.000 0.00 0.00 0.00 2.43
3937 4797 3.717400 TGTTGTTTGTGTGTGTGTGTT 57.283 38.095 0.00 0.00 0.00 3.32
3989 5105 6.119536 TGGTTTGCTTATCCTGTAATACTGG 58.880 40.000 9.72 9.72 38.41 4.00
4005 5121 0.746063 CTGGGAACACAAGCAAAGCA 59.254 50.000 0.00 0.00 35.60 3.91
4020 5136 2.867975 CAAAGCAAAGCTGTTTTCTGGG 59.132 45.455 0.00 0.00 39.62 4.45
4049 5168 2.997485 AGGTCTTGCAGCGATTTTTC 57.003 45.000 0.00 0.00 0.00 2.29
4052 5171 3.057946 AGGTCTTGCAGCGATTTTTCTTC 60.058 43.478 0.00 0.00 0.00 2.87
4194 5317 2.264794 CCCTTTCAGACGGACCCG 59.735 66.667 6.94 6.94 46.03 5.28
4220 5343 5.351458 TCCATGAGACTTTCATATCACACG 58.649 41.667 0.00 0.00 44.76 4.49
4229 5352 5.408604 ACTTTCATATCACACGGAAACTCAC 59.591 40.000 0.00 0.00 0.00 3.51
4264 5400 3.054503 GCCTGCTGCTGTGAGGTG 61.055 66.667 0.00 0.00 36.87 4.00
4267 5403 1.070275 CTGCTGCTGTGAGGTGACA 59.930 57.895 0.00 0.00 0.00 3.58
4287 5423 2.802816 CAGGTTCGAGTCCAGAAAACAG 59.197 50.000 10.54 0.00 0.00 3.16
4303 5439 6.980397 CAGAAAACAGCCTCTTGTAAAAATGT 59.020 34.615 0.00 0.00 0.00 2.71
4304 5440 7.168135 CAGAAAACAGCCTCTTGTAAAAATGTC 59.832 37.037 0.00 0.00 0.00 3.06
4326 5487 3.606153 CGAAGAAGGTTGCGTACAAAAGG 60.606 47.826 0.00 0.00 37.58 3.11
4338 5499 1.115326 ACAAAAGGCCCAAGGTGCTC 61.115 55.000 0.00 0.00 0.00 4.26
4343 5504 4.329545 GCCCAAGGTGCTCGGACA 62.330 66.667 0.00 0.00 0.00 4.02
4349 5510 2.047179 GGTGCTCGGACACTTCCC 60.047 66.667 8.33 0.00 38.99 3.97
4350 5511 2.047179 GTGCTCGGACACTTCCCC 60.047 66.667 2.01 0.00 38.99 4.81
4360 5563 1.079543 CACTTCCCCTGACTCTGCG 60.080 63.158 0.00 0.00 0.00 5.18
4380 5583 2.575532 GCAAGTGGGAGCTATATGCAA 58.424 47.619 0.00 0.00 45.94 4.08
4424 6832 2.783135 GAGCATCTTCAACAAGTCCCA 58.217 47.619 0.00 0.00 0.00 4.37
4434 6842 2.558359 CAACAAGTCCCATTTCCTGGTC 59.442 50.000 0.00 0.00 44.30 4.02
4518 6929 5.826643 TCCTTGTATAATCAGCCCAACTTT 58.173 37.500 0.00 0.00 0.00 2.66
4531 6942 5.762218 CAGCCCAACTTTTCCTCTATCTATG 59.238 44.000 0.00 0.00 0.00 2.23
4535 6955 5.132816 CCAACTTTTCCTCTATCTATGGGGT 59.867 44.000 0.00 0.00 0.00 4.95
4573 6993 1.075536 CCTTCCCCTAAAAGTGCCACT 59.924 52.381 0.00 0.00 0.00 4.00
4582 7002 1.174712 AAAGTGCCACTTCAGCGCAT 61.175 50.000 11.11 0.00 43.21 4.73
4637 7423 0.965363 CCCTAAAAGTGCCACGCCAT 60.965 55.000 0.00 0.00 0.00 4.40
4646 7432 0.680601 TGCCACGCCATCACATCATT 60.681 50.000 0.00 0.00 0.00 2.57
4650 7436 1.009335 CGCCATCACATCATTGCCG 60.009 57.895 0.00 0.00 0.00 5.69
4658 7444 0.618458 ACATCATTGCCGTACCCACT 59.382 50.000 0.00 0.00 0.00 4.00
4659 7445 1.016627 CATCATTGCCGTACCCACTG 58.983 55.000 0.00 0.00 0.00 3.66
4674 7460 4.640855 CTGTGTCGCGACCACCGT 62.641 66.667 34.34 0.00 41.15 4.83
4715 7501 3.209097 CCGCCCGCCATAAACCAG 61.209 66.667 0.00 0.00 0.00 4.00
4717 7503 2.043980 CGCCCGCCATAAACCAGTT 61.044 57.895 0.00 0.00 0.00 3.16
4731 7517 7.282450 CCATAAACCAGTTATAGGTGGAGTTTC 59.718 40.741 8.98 0.00 39.86 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 8.937634 AGGTTACTACTGTGGTAATTTTATCG 57.062 34.615 17.85 0.00 32.78 2.92
19 20 2.357009 CGTGGTGCGATAGGTTACTACT 59.643 50.000 0.00 0.00 44.77 2.57
47 48 0.468226 AGGACTTGCTGTCGTTTGGA 59.532 50.000 4.78 0.00 46.24 3.53
55 56 0.034059 CGGTCAGAAGGACTTGCTGT 59.966 55.000 0.00 0.00 46.16 4.40
61 62 1.048601 TCTTTGCGGTCAGAAGGACT 58.951 50.000 0.00 0.00 46.16 3.85
64 65 2.280628 GGTATCTTTGCGGTCAGAAGG 58.719 52.381 0.00 0.00 0.00 3.46
112 113 1.022735 CTGTCCATGGAGAAGCATGC 58.977 55.000 16.81 10.51 0.00 4.06
115 116 2.475155 AGATCTGTCCATGGAGAAGCA 58.525 47.619 16.81 8.74 0.00 3.91
125 126 4.503817 GCCATGTATGCTTAGATCTGTCCA 60.504 45.833 5.18 0.00 0.00 4.02
173 174 1.898574 CCGGGTGCTTGGGATATGC 60.899 63.158 0.00 0.00 0.00 3.14
202 203 0.037160 TTCCTTTGCTCCCCCGTTAC 59.963 55.000 0.00 0.00 0.00 2.50
203 204 0.326927 CTTCCTTTGCTCCCCCGTTA 59.673 55.000 0.00 0.00 0.00 3.18
216 219 1.215647 CCGTGTAGCGCTCTTCCTT 59.784 57.895 16.34 0.00 39.71 3.36
235 238 2.693017 GCTCTCCCCCTCTCCTCA 59.307 66.667 0.00 0.00 0.00 3.86
243 247 1.915983 CAGGTAAAGGCTCTCCCCC 59.084 63.158 0.00 0.00 0.00 5.40
244 248 1.224870 GCAGGTAAAGGCTCTCCCC 59.775 63.158 0.00 0.00 0.00 4.81
245 249 2.302019 AGCAGGTAAAGGCTCTCCC 58.698 57.895 0.00 0.00 34.76 4.30
613 644 5.249393 GGATCTCTCTCTCTCTATCTCTGGT 59.751 48.000 0.00 0.00 0.00 4.00
621 652 2.903784 CGAGGGGATCTCTCTCTCTCTA 59.096 54.545 8.79 0.00 40.30 2.43
674 727 4.715130 CCGGTGACCTGAGGGGGA 62.715 72.222 2.38 0.00 40.03 4.81
747 800 2.427245 CCGCTCCACCAGACCCTAG 61.427 68.421 0.00 0.00 0.00 3.02
770 823 0.679002 AGTTCGATCGACTCCGGGAA 60.679 55.000 19.26 0.00 36.24 3.97
830 1166 1.666580 GGGACGGATCGAGGAATCC 59.333 63.158 0.00 0.00 41.63 3.01
914 1251 2.267426 CAATCGAGTCGCCATTACACA 58.733 47.619 7.92 0.00 0.00 3.72
916 1253 1.206132 ACCAATCGAGTCGCCATTACA 59.794 47.619 7.92 0.00 0.00 2.41
917 1254 1.935933 ACCAATCGAGTCGCCATTAC 58.064 50.000 7.92 0.00 0.00 1.89
918 1255 2.276201 CAACCAATCGAGTCGCCATTA 58.724 47.619 7.92 0.00 0.00 1.90
960 1297 3.585862 GAGCACCGTCACTAATTTCTCA 58.414 45.455 0.00 0.00 0.00 3.27
1022 1359 3.687828 AAGGAGGAGGGCTCGGAGG 62.688 68.421 7.20 0.00 0.00 4.30
1024 1361 2.042843 GAAGGAGGAGGGCTCGGA 60.043 66.667 0.00 0.00 0.00 4.55
1194 1531 3.379445 ACGCGACGGACCTTGGAT 61.379 61.111 15.93 0.00 0.00 3.41
1219 1556 1.202428 GGCGCTAGAACCCTAGAACTG 60.202 57.143 7.64 0.00 44.00 3.16
1261 1599 2.759538 GTCCTAGAGACCACGAATCG 57.240 55.000 0.00 0.00 39.84 3.34
1271 1609 5.827756 TCACTTCATGGTAAGTCCTAGAGA 58.172 41.667 0.00 0.00 37.61 3.10
1280 1618 4.183865 TCAATCGCTCACTTCATGGTAAG 58.816 43.478 0.00 0.00 0.00 2.34
1292 1651 5.401550 CCAAAATTAAGCTTCAATCGCTCA 58.598 37.500 0.00 0.00 36.56 4.26
1302 1661 4.041444 TCATGGCAACCCAAAATTAAGCTT 59.959 37.500 3.48 3.48 46.14 3.74
1383 1743 6.970613 GGTTATTGATTTACTTTGGCCTTACG 59.029 38.462 3.32 0.00 0.00 3.18
1506 1871 9.109393 TGCAAACCATAAACATAGAAGATAGAC 57.891 33.333 0.00 0.00 0.00 2.59
1559 1926 5.359194 ACACAGCATAAGGTACATAGCTT 57.641 39.130 8.32 8.32 45.08 3.74
1586 1965 3.885484 CTGCTTTCACAGTTCGACAAT 57.115 42.857 0.00 0.00 32.78 2.71
1620 1999 2.038387 AGTGCCGACTTGAAAACACT 57.962 45.000 0.00 0.00 33.71 3.55
1673 2055 0.245539 CACCAAATGAGCAAGGCAGG 59.754 55.000 0.00 0.00 0.00 4.85
1686 2069 6.531503 TTCCAAGTTGTCAAATACACCAAA 57.468 33.333 1.45 0.00 38.00 3.28
1835 2218 8.883954 TTCAAGCAATTTTGTGAATGTAATCA 57.116 26.923 0.00 0.00 0.00 2.57
1864 2252 9.906660 CGCAATAATAAATGTAATAACATGGGT 57.093 29.630 0.00 0.00 45.79 4.51
2064 2452 8.447787 AAATGAATCGCTAACAACAACAATAC 57.552 30.769 0.00 0.00 0.00 1.89
2115 2503 0.333993 AGGGGCACATGAGCTGAAAT 59.666 50.000 14.91 0.00 34.17 2.17
2213 2601 6.969993 AAAATTACCTTAACAAGAGCACCA 57.030 33.333 0.00 0.00 0.00 4.17
2261 2887 7.762615 CAGAGTTGGATGCATCATACAAAATTT 59.237 33.333 27.25 7.91 44.91 1.82
2307 2933 7.685481 TGGTTGTAGAATTAGTGAAAGGATCA 58.315 34.615 0.00 0.00 35.05 2.92
2498 3124 4.782019 TTGGAAACACATGCAGTATTCC 57.218 40.909 17.05 17.05 42.67 3.01
2573 3199 4.193865 TCAGTATCATCAACCTGCATGTG 58.806 43.478 0.00 0.00 0.00 3.21
3149 3983 7.814587 TGGAATGACAGCTATACATTTATCTCG 59.185 37.037 11.55 0.00 34.94 4.04
3474 4308 2.519302 GTGCAACACAGGCCCTGT 60.519 61.111 11.57 11.57 46.51 4.00
3538 4372 3.445008 AGCATGACTCACCCTAAGAGAA 58.555 45.455 0.00 0.00 36.91 2.87
3599 4433 6.150976 TCTGATCGGCAACTACATTTCATTTT 59.849 34.615 0.00 0.00 0.00 1.82
3605 4439 6.349300 AGTATTCTGATCGGCAACTACATTT 58.651 36.000 0.00 0.00 0.00 2.32
3608 4442 6.459670 TTAGTATTCTGATCGGCAACTACA 57.540 37.500 0.00 0.00 0.00 2.74
3609 4443 7.569677 GATTAGTATTCTGATCGGCAACTAC 57.430 40.000 0.00 0.00 29.47 2.73
3637 4471 9.706691 GGTCATCCTTCGTTTCAGATATATAAA 57.293 33.333 0.00 0.00 0.00 1.40
3780 4614 3.005684 TGAATTGCAGCAACTAAACTGGG 59.994 43.478 10.85 0.00 34.38 4.45
3828 4662 4.507342 AGATAATCTTCCCCTACCTGCAT 58.493 43.478 0.00 0.00 0.00 3.96
3868 4702 2.434359 GACACCGCACAGCCTACC 60.434 66.667 0.00 0.00 0.00 3.18
3937 4797 2.223782 GCTGCTGTTGATGTTTCCACAA 60.224 45.455 0.00 0.00 36.16 3.33
3989 5105 1.594397 GCTTTGCTTTGCTTGTGTTCC 59.406 47.619 0.00 0.00 0.00 3.62
4005 5121 2.174685 AACCCCCAGAAAACAGCTTT 57.825 45.000 0.00 0.00 0.00 3.51
4220 5343 5.689383 TTTGTCTAATGCAGTGAGTTTCC 57.311 39.130 0.00 0.00 0.00 3.13
4229 5352 2.426024 AGGCATGCTTTGTCTAATGCAG 59.574 45.455 18.92 1.90 46.10 4.41
4264 5400 2.801111 GTTTTCTGGACTCGAACCTGTC 59.199 50.000 9.25 2.43 0.00 3.51
4267 5403 2.807108 GCTGTTTTCTGGACTCGAACCT 60.807 50.000 9.25 0.00 0.00 3.50
4287 5423 5.607119 TCTTCGACATTTTTACAAGAGGC 57.393 39.130 0.00 0.00 0.00 4.70
4303 5439 2.512485 TTGTACGCAACCTTCTTCGA 57.488 45.000 0.00 0.00 0.00 3.71
4304 5440 3.541711 CTTTTGTACGCAACCTTCTTCG 58.458 45.455 0.00 0.00 33.82 3.79
4326 5487 4.329545 TGTCCGAGCACCTTGGGC 62.330 66.667 0.00 0.00 39.94 5.36
4338 5499 0.900647 AGAGTCAGGGGAAGTGTCCG 60.901 60.000 0.00 0.00 46.04 4.79
4343 5504 2.948720 GCGCAGAGTCAGGGGAAGT 61.949 63.158 0.30 0.00 0.00 3.01
4349 5510 2.031516 CCACTTGCGCAGAGTCAGG 61.032 63.158 11.31 11.58 0.00 3.86
4350 5511 2.031516 CCCACTTGCGCAGAGTCAG 61.032 63.158 11.31 7.44 0.00 3.51
4360 5563 2.260844 TGCATATAGCTCCCACTTGC 57.739 50.000 0.00 0.00 45.94 4.01
4434 6842 0.400213 TTGGGCACAACTCACCCTAG 59.600 55.000 0.00 0.00 44.56 3.02
4518 6929 7.780822 AGATCTTTACCCCATAGATAGAGGAA 58.219 38.462 0.00 0.00 0.00 3.36
4531 6942 5.105023 AGGTTTACGAGAAGATCTTTACCCC 60.105 44.000 9.87 0.00 0.00 4.95
4535 6955 6.351626 GGGGAAGGTTTACGAGAAGATCTTTA 60.352 42.308 9.87 0.00 0.00 1.85
4573 6993 1.978080 ATGGTGGCAATGCGCTGAA 60.978 52.632 9.73 0.00 41.91 3.02
4582 7002 3.173953 AGATCTTTTCCATGGTGGCAA 57.826 42.857 12.58 0.00 37.47 4.52
4637 7423 0.615850 TGGGTACGGCAATGATGTGA 59.384 50.000 0.00 0.00 0.00 3.58
4646 7432 2.738480 GACACAGTGGGTACGGCA 59.262 61.111 0.00 0.00 0.00 5.69
4650 7436 1.731969 GTCGCGACACAGTGGGTAC 60.732 63.158 33.09 2.01 0.00 3.34
4658 7444 4.634133 GACGGTGGTCGCGACACA 62.634 66.667 37.26 28.72 43.89 3.72
4674 7460 0.739462 CAGCGGCTTACAATGGACGA 60.739 55.000 0.00 0.00 0.00 4.20
4715 7501 5.664457 TCCCCTTAGAAACTCCACCTATAAC 59.336 44.000 0.00 0.00 0.00 1.89
4717 7503 5.042827 AGTCCCCTTAGAAACTCCACCTATA 60.043 44.000 0.00 0.00 0.00 1.31
4731 7517 3.433740 GCACCTCCAATAAGTCCCCTTAG 60.434 52.174 0.00 0.00 36.63 2.18


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

AutoCloner maintained by Alex Coulton.