Multiple sequence alignment - TraesCS2A01G171400

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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 TraesCS2A01G171400 chr2A 100.000 4113 0 0 1 4113 126992667 126996779 0.000000e+00 7596.0
1 TraesCS2A01G171400 chr2B 94.352 4143 179 21 1 4113 175455895 175460012 0.000000e+00 6303.0
2 TraesCS2A01G171400 chr5A 90.523 306 24 4 20 323 559787339 559787641 2.300000e-107 399.0
3 TraesCS2A01G171400 chr3D 90.461 304 26 2 20 323 79555400 79555100 8.280000e-107 398.0
4 TraesCS2A01G171400 chr3D 89.189 74 7 1 397 469 474550389 474550316 1.570000e-14 91.6
5 TraesCS2A01G171400 chr6A 88.994 318 29 5 20 335 46549159 46548846 4.990000e-104 388.0
6 TraesCS2A01G171400 chr6A 89.145 304 31 1 20 323 422775948 422776249 1.080000e-100 377.0
7 TraesCS2A01G171400 chr6D 89.286 308 30 2 16 323 454889540 454889236 2.320000e-102 383.0
8 TraesCS2A01G171400 chr6D 88.961 308 31 2 16 323 454923095 454922791 1.080000e-100 377.0
9 TraesCS2A01G171400 chr6D 90.141 71 6 1 397 466 62497433 62497363 1.570000e-14 91.6
10 TraesCS2A01G171400 chr3A 89.216 306 29 3 19 323 703403991 703404293 3.000000e-101 379.0
11 TraesCS2A01G171400 chr3B 89.216 306 27 5 20 323 4554887 4554586 1.080000e-100 377.0
12 TraesCS2A01G171400 chr1B 91.781 73 6 0 397 469 23597202 23597130 7.270000e-18 102.0
13 TraesCS2A01G171400 chr1B 91.781 73 6 0 397 469 23895978 23895906 7.270000e-18 102.0
14 TraesCS2A01G171400 chr4A 91.429 70 6 0 397 466 648377589 648377658 3.380000e-16 97.1
15 TraesCS2A01G171400 chr2D 91.549 71 5 1 397 466 629978282 629978352 3.380000e-16 97.1
16 TraesCS2A01G171400 chr7A 91.304 69 6 0 398 466 12904330 12904398 1.220000e-15 95.3
17 TraesCS2A01G171400 chr7D 90.141 71 6 1 397 466 396381199 396381269 1.570000e-14 91.6


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 TraesCS2A01G171400 chr2A 126992667 126996779 4112 False 7596 7596 100.000 1 4113 1 chr2A.!!$F1 4112
1 TraesCS2A01G171400 chr2B 175455895 175460012 4117 False 6303 6303 94.352 1 4113 1 chr2B.!!$F1 4112

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
257 258 0.107703 AGGGATATGGTGTGCGTGTG 60.108 55.0 0.00 0.0 0.00 3.82 F
1143 1158 0.038526 AGGTTGCCTCGTAAGTCGTG 60.039 55.0 0.00 0.0 40.80 4.35 F
1144 1159 0.038892 GGTTGCCTCGTAAGTCGTGA 60.039 55.0 0.00 0.0 40.80 4.35 F
1151 1166 0.168348 TCGTAAGTCGTGAGAGCAGC 59.832 55.0 0.00 0.0 43.49 5.25 F
2267 2293 0.178767 TCCGTAGACTCCCGATTCGA 59.821 55.0 7.83 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1945 1971 0.179040 CCGGTATTTACATGGGCCGT 60.179 55.0 0.00 0.00 37.76 5.68 R
2400 2426 0.453793 AGCTTCATCTCGGACGACTG 59.546 55.0 0.00 0.00 0.00 3.51 R
2401 2427 0.736053 GAGCTTCATCTCGGACGACT 59.264 55.0 0.00 0.00 0.00 4.18 R
2851 2880 0.750850 ATGCAATCTGAAGCCATGGC 59.249 50.0 30.12 30.12 42.33 4.40 R
3324 3353 0.177836 TGAGGTGTATGGCGGACATG 59.822 55.0 6.59 0.00 40.82 3.21 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
29 30 5.445806 GCAAAATCAATTATGCGAACCAACC 60.446 40.000 0.00 0.00 0.00 3.77
55 56 3.117512 GGTTGGGATGATTAGGTGGACAT 60.118 47.826 0.00 0.00 0.00 3.06
64 65 4.104102 TGATTAGGTGGACATTGGTATCCC 59.896 45.833 0.00 0.00 33.69 3.85
67 68 1.499007 GGTGGACATTGGTATCCCCAT 59.501 52.381 0.00 0.00 44.74 4.00
72 73 1.499007 ACATTGGTATCCCCATCCCAC 59.501 52.381 0.00 0.00 44.74 4.61
93 94 1.073923 CAGGGTTTAAGTCCTGGTGCT 59.926 52.381 14.78 0.00 44.99 4.40
94 95 1.351350 AGGGTTTAAGTCCTGGTGCTC 59.649 52.381 0.00 0.00 31.11 4.26
96 97 1.001633 GGTTTAAGTCCTGGTGCTCGA 59.998 52.381 0.00 0.00 0.00 4.04
106 107 4.034510 GTCCTGGTGCTCGAATTTATTCTG 59.965 45.833 0.00 0.00 34.69 3.02
130 131 5.391629 GGATTTATTTCAGGTTTTCTCGCGT 60.392 40.000 5.77 0.00 0.00 6.01
134 135 2.512485 TCAGGTTTTCTCGCGTTACA 57.488 45.000 5.77 0.00 0.00 2.41
156 157 0.966920 TTCAGTGGGAGGAGACGTTC 59.033 55.000 0.00 0.00 0.00 3.95
169 170 5.517322 GGAGACGTTCCAGTCAACTATAT 57.483 43.478 10.67 0.00 46.01 0.86
180 181 4.681942 CAGTCAACTATATGAAGCGCCTAC 59.318 45.833 2.29 0.00 0.00 3.18
198 199 4.741342 CCTACGGTGACTTCGTAAAATCT 58.259 43.478 0.00 0.00 41.62 2.40
222 223 1.274728 GATGATATGCCGGCTCAGTCT 59.725 52.381 29.70 8.26 0.00 3.24
242 243 0.468214 CTCGGAGGTGCTCATAGGGA 60.468 60.000 0.00 0.00 31.08 4.20
245 246 2.043115 TCGGAGGTGCTCATAGGGATAT 59.957 50.000 0.00 0.00 31.08 1.63
257 258 0.107703 AGGGATATGGTGTGCGTGTG 60.108 55.000 0.00 0.00 0.00 3.82
264 265 2.099446 GTGTGCGTGTGTGCGTTT 59.901 55.556 0.00 0.00 37.81 3.60
268 269 1.457683 TGTGCGTGTGTGCGTTTATAG 59.542 47.619 0.00 0.00 37.81 1.31
282 283 4.442472 GCGTTTATAGGGGTGAGTGTATGT 60.442 45.833 0.00 0.00 0.00 2.29
284 285 5.394883 CGTTTATAGGGGTGAGTGTATGTGT 60.395 44.000 0.00 0.00 0.00 3.72
299 300 5.234329 GTGTATGTGTGTTTATATGAGCGCT 59.766 40.000 11.27 11.27 0.00 5.92
305 306 3.244345 GTGTTTATATGAGCGCTTGCGTA 59.756 43.478 13.26 5.86 45.69 4.42
436 438 8.105829 AGAGTTTGTTTCTCATAGAATGGTCAT 58.894 33.333 0.00 0.00 33.67 3.06
521 523 7.442062 AGAAACAATGCAACCATTCCTAAAAAG 59.558 33.333 0.00 0.00 39.60 2.27
522 524 6.173427 ACAATGCAACCATTCCTAAAAAGT 57.827 33.333 0.00 0.00 39.60 2.66
533 535 4.379339 TCCTAAAAAGTTGCAACCACAC 57.621 40.909 25.62 0.99 0.00 3.82
555 557 8.094548 CACACGGGGATAATTGAATAGAGATAA 58.905 37.037 0.00 0.00 0.00 1.75
574 576 8.628280 AGAGATAATAAAGATCCAAAAGCAAGC 58.372 33.333 0.00 0.00 0.00 4.01
575 577 8.297470 AGATAATAAAGATCCAAAAGCAAGCA 57.703 30.769 0.00 0.00 0.00 3.91
598 600 6.488006 GCATATCTGCTCCCAATAAAAAGAGA 59.512 38.462 0.00 0.00 45.32 3.10
650 652 1.600957 CACATAGCACAGCTGTATGGC 59.399 52.381 24.84 21.52 40.10 4.40
651 653 1.210234 ACATAGCACAGCTGTATGGCA 59.790 47.619 24.84 14.31 40.10 4.92
679 682 2.567615 AGGCCCGTATATTGAGGACATC 59.432 50.000 0.00 0.00 0.00 3.06
693 696 3.618351 AGGACATCTTGCCTCTTGATTG 58.382 45.455 0.00 0.00 0.00 2.67
733 739 9.878667 ATTATGAAATAAAACCCTTTTTACCCG 57.121 29.630 0.00 0.00 42.96 5.28
763 769 5.078411 AGGCGTGCCATAATTATCTCTAG 57.922 43.478 14.29 0.00 38.92 2.43
791 797 4.529897 AGATTATCATCACTTGGCAGCAA 58.470 39.130 0.00 0.00 0.00 3.91
842 848 9.645128 ATCATGGTTGTTCATCATTAAATAGGA 57.355 29.630 0.00 0.00 0.00 2.94
861 867 2.749621 GGAAACATCAGCGACCAAATCT 59.250 45.455 0.00 0.00 0.00 2.40
905 911 9.635520 ATTTTCAGACATCATTTGTGAGAATTC 57.364 29.630 0.00 0.00 39.18 2.17
906 912 6.748333 TCAGACATCATTTGTGAGAATTCC 57.252 37.500 0.65 0.00 39.18 3.01
909 915 7.449395 TCAGACATCATTTGTGAGAATTCCTTT 59.551 33.333 0.65 0.00 39.18 3.11
929 935 8.197592 TCCTTTACTTTTATCACACTCTACCA 57.802 34.615 0.00 0.00 0.00 3.25
951 957 4.344865 TTCCGCTTGAGGCCACCC 62.345 66.667 5.01 0.00 37.74 4.61
973 979 3.068064 TGCACTCATCTCCGGCGA 61.068 61.111 9.30 0.00 0.00 5.54
1011 1017 1.463018 GATCCCCATGCTCCTCCCT 60.463 63.158 0.00 0.00 0.00 4.20
1040 1055 0.251832 ACAGTCGTCACATCCCCTCT 60.252 55.000 0.00 0.00 0.00 3.69
1044 1059 2.025226 AGTCGTCACATCCCCTCTTCTA 60.025 50.000 0.00 0.00 0.00 2.10
1080 1095 1.887707 GCGAATCGATCCACCACCC 60.888 63.158 6.91 0.00 0.00 4.61
1082 1097 1.227556 GAATCGATCCACCACCCCG 60.228 63.158 0.00 0.00 0.00 5.73
1136 1151 1.549170 GGAGAAGAAGGTTGCCTCGTA 59.451 52.381 0.00 0.00 30.89 3.43
1143 1158 0.038526 AGGTTGCCTCGTAAGTCGTG 60.039 55.000 0.00 0.00 40.80 4.35
1144 1159 0.038892 GGTTGCCTCGTAAGTCGTGA 60.039 55.000 0.00 0.00 40.80 4.35
1151 1166 0.168348 TCGTAAGTCGTGAGAGCAGC 59.832 55.000 0.00 0.00 43.49 5.25
1182 1197 1.555075 CAGATTTTGGGGAGGAGACGA 59.445 52.381 0.00 0.00 0.00 4.20
1187 1202 0.687757 TTGGGGAGGAGACGAGGATG 60.688 60.000 0.00 0.00 0.00 3.51
1189 1204 1.834822 GGGAGGAGACGAGGATGGG 60.835 68.421 0.00 0.00 0.00 4.00
1226 1241 6.805713 CCAACAATGGGAAAACCTATATGAC 58.194 40.000 0.00 0.00 43.51 3.06
1252 1267 1.714042 GCGTCAAATTTTCGCGCAAAC 60.714 47.619 19.37 0.00 46.23 2.93
1278 1293 1.992233 GCGAATGCCCAATGCGAGAA 61.992 55.000 0.00 0.00 40.05 2.87
1282 1297 2.589798 ATGCCCAATGCGAGAATTTG 57.410 45.000 0.00 0.00 45.60 2.32
1322 1337 3.373565 GAGGCAGCCGGTTTTGGG 61.374 66.667 5.55 0.00 0.00 4.12
1334 1349 2.751816 CGGTTTTGGGAAGAAGGTTCCT 60.752 50.000 3.87 0.00 38.61 3.36
1391 1406 9.653067 TTTCGGTTTCTTTTGTTTTTCTTTTTC 57.347 25.926 0.00 0.00 0.00 2.29
1653 1675 8.208560 TGTTTTACATTTTATAAAAAGTGCGCG 58.791 29.630 22.68 0.00 36.15 6.86
1665 1687 1.234821 AGTGCGCGGAAGATGAAAAA 58.765 45.000 8.83 0.00 0.00 1.94
1771 1793 3.218453 TCCAAATTTTGCTCGGAGTTCA 58.782 40.909 6.90 0.00 0.00 3.18
1905 1931 0.755698 GGGCTCCCGAGTCTGTCATA 60.756 60.000 0.00 0.00 32.63 2.15
1908 1934 2.103263 GGCTCCCGAGTCTGTCATATTT 59.897 50.000 0.00 0.00 0.00 1.40
1909 1935 3.432326 GGCTCCCGAGTCTGTCATATTTT 60.432 47.826 0.00 0.00 0.00 1.82
1910 1936 3.557595 GCTCCCGAGTCTGTCATATTTTG 59.442 47.826 0.00 0.00 0.00 2.44
1932 1958 9.768215 TTTTGGGGAGAGAATAGAAAAATATGT 57.232 29.630 0.00 0.00 0.00 2.29
2267 2293 0.178767 TCCGTAGACTCCCGATTCGA 59.821 55.000 7.83 0.00 0.00 3.71
2312 2338 0.317519 CGCAGGTTTGGTTCGGAAAC 60.318 55.000 0.00 0.00 33.34 2.78
2411 2437 4.436998 GTGGGGCAGTCGTCCGAG 62.437 72.222 0.00 0.00 38.02 4.63
2412 2438 4.671590 TGGGGCAGTCGTCCGAGA 62.672 66.667 0.00 0.00 38.02 4.04
2413 2439 3.148279 GGGGCAGTCGTCCGAGAT 61.148 66.667 0.00 0.00 38.02 2.75
2414 2440 2.105128 GGGCAGTCGTCCGAGATG 59.895 66.667 0.00 0.00 0.00 2.90
2415 2441 2.415608 GGGCAGTCGTCCGAGATGA 61.416 63.158 6.13 0.00 0.00 2.92
2416 2442 1.511305 GGCAGTCGTCCGAGATGAA 59.489 57.895 6.13 0.00 28.80 2.57
2417 2443 0.526524 GGCAGTCGTCCGAGATGAAG 60.527 60.000 6.13 0.00 28.80 3.02
2418 2444 1.142778 GCAGTCGTCCGAGATGAAGC 61.143 60.000 6.13 0.00 28.80 3.86
2445 2471 0.741915 CCTCTAACTGCTCCGAGACC 59.258 60.000 0.00 0.00 0.00 3.85
2582 2608 6.030228 CGGAGAAACAATATCTTCTTTTGGC 58.970 40.000 0.00 0.00 32.01 4.52
2596 2622 5.384063 TCTTTTGGCAAATGCTTCGATTA 57.616 34.783 14.29 0.00 41.70 1.75
2679 2708 8.784043 GTTGTTGACAAAGATCATACTACCTTT 58.216 33.333 0.00 0.00 37.63 3.11
2851 2880 1.005394 ACGTCTTGGGCCTTACACG 60.005 57.895 4.53 10.53 0.00 4.49
2872 2901 2.821546 CCATGGCTTCAGATTGCATTG 58.178 47.619 0.00 0.00 0.00 2.82
2917 2946 8.034058 ACTATCTGTTGCTGTAAAGAAATGTC 57.966 34.615 0.00 0.00 0.00 3.06
2921 2950 6.542005 TCTGTTGCTGTAAAGAAATGTCTCAA 59.458 34.615 0.00 0.00 30.70 3.02
2970 2999 2.224257 TGCGGCATATTCATGTGCTCTA 60.224 45.455 0.00 0.00 43.38 2.43
3044 3073 5.796424 ACTTCCTTCTCATTTTGCATTGT 57.204 34.783 0.00 0.00 0.00 2.71
3094 3123 5.295292 CCTTCCAATGTTACTGCAGATAGTG 59.705 44.000 23.35 11.98 32.19 2.74
3183 3212 1.078848 GACTCCAGCCGATGCAGTT 60.079 57.895 0.00 0.00 41.13 3.16
3243 3272 2.038164 TGCTGCTGTCTTCAATCAGTCT 59.962 45.455 0.00 0.00 34.57 3.24
3246 3275 2.634453 TGCTGTCTTCAATCAGTCTCCA 59.366 45.455 0.00 0.00 34.57 3.86
3248 3277 3.555795 GCTGTCTTCAATCAGTCTCCACA 60.556 47.826 0.00 0.00 34.57 4.17
3317 3346 5.355596 CACTCATCTTCTACCCTGTTCATC 58.644 45.833 0.00 0.00 0.00 2.92
3324 3353 6.127793 TCTTCTACCCTGTTCATCTACTACC 58.872 44.000 0.00 0.00 0.00 3.18
3414 3443 2.492881 CTGCACCATAATGTTGCTCCAA 59.507 45.455 3.64 0.00 0.00 3.53
3431 3460 1.606668 CCAATAACGTGCAACCTGTGT 59.393 47.619 0.00 0.00 0.00 3.72
3449 3478 5.163622 CCTGTGTTGATATTAAAGCAGTGGG 60.164 44.000 9.73 0.00 0.00 4.61
3509 3538 1.171308 GCTTGCTTCCAGATGCTTCA 58.829 50.000 2.07 0.00 33.23 3.02
3526 3555 4.009675 GCTTCATAGTTCATCACCCACAA 58.990 43.478 0.00 0.00 0.00 3.33
3529 3558 4.009675 TCATAGTTCATCACCCACAAAGC 58.990 43.478 0.00 0.00 0.00 3.51
3597 3626 6.320164 CCAATTACCTCGATCCATTTTTACCA 59.680 38.462 0.00 0.00 0.00 3.25
3630 3659 5.168526 TGGCTTATGCATACGAAATGTTC 57.831 39.130 14.00 0.00 41.91 3.18
3747 3776 1.615883 TCTTCGCTCAGCTCTTGTCTT 59.384 47.619 0.00 0.00 0.00 3.01
3772 3801 6.822667 TGTGATGTGCTCAGTTCAATTATT 57.177 33.333 0.00 0.00 33.51 1.40
3891 3920 4.019321 CCTTACTTCCCTCCACATTCTTCA 60.019 45.833 0.00 0.00 0.00 3.02
3934 3963 6.116126 ACCTGCAAAAGAGAACATATAGGAC 58.884 40.000 0.00 0.00 0.00 3.85
4056 4085 5.971763 TGATATTTATTGGGCCACAACAAC 58.028 37.500 5.23 0.00 42.94 3.32
4080 4109 7.056635 ACATCCAAAAGTAATCTATCCACCAG 58.943 38.462 0.00 0.00 0.00 4.00
4095 4124 9.768215 TCTATCCACCAGATTAAAAAGGAAAAT 57.232 29.630 0.00 0.00 36.33 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 3.241493 CCACAGGTTGGTTCGCATA 57.759 52.632 0.00 0.00 41.10 3.14
29 30 3.282021 CACCTAATCATCCCAACCACAG 58.718 50.000 0.00 0.00 0.00 3.66
83 84 4.034510 CAGAATAAATTCGAGCACCAGGAC 59.965 45.833 0.00 0.00 41.56 3.85
89 90 9.736023 AAATAAATCCAGAATAAATTCGAGCAC 57.264 29.630 0.00 0.00 41.56 4.40
106 107 5.028375 CGCGAGAAAACCTGAAATAAATCC 58.972 41.667 0.00 0.00 0.00 3.01
146 147 1.705873 AGTTGACTGGAACGTCTCCT 58.294 50.000 14.95 0.08 45.64 3.69
156 157 2.802816 GGCGCTTCATATAGTTGACTGG 59.197 50.000 7.64 0.00 0.00 4.00
180 181 4.921515 TCTTGAGATTTTACGAAGTCACCG 59.078 41.667 0.00 0.00 43.93 4.94
198 199 1.693606 TGAGCCGGCATATCATCTTGA 59.306 47.619 31.54 0.00 0.00 3.02
222 223 0.468214 CCCTATGAGCACCTCCGAGA 60.468 60.000 0.00 0.00 0.00 4.04
242 243 1.634757 CGCACACACGCACACCATAT 61.635 55.000 0.00 0.00 0.00 1.78
257 258 2.277084 CACTCACCCCTATAAACGCAC 58.723 52.381 0.00 0.00 0.00 5.34
264 265 4.616553 ACACACATACACTCACCCCTATA 58.383 43.478 0.00 0.00 0.00 1.31
268 269 2.561478 AACACACATACACTCACCCC 57.439 50.000 0.00 0.00 0.00 4.95
282 283 2.030335 CGCAAGCGCTCATATAAACACA 59.970 45.455 12.06 0.00 35.30 3.72
284 285 2.276201 ACGCAAGCGCTCATATAAACA 58.724 42.857 12.06 0.00 44.19 2.83
359 361 2.479566 AAGATGCCGCTTTTCTCTCA 57.520 45.000 0.00 0.00 0.00 3.27
365 367 3.064900 AGAGAGAAAGATGCCGCTTTT 57.935 42.857 2.89 0.00 38.16 2.27
484 486 9.638239 TGGTTGCATTGTTTCTTTAATAGAATC 57.362 29.630 0.00 0.00 42.32 2.52
508 510 4.749598 GTGGTTGCAACTTTTTAGGAATGG 59.250 41.667 27.64 0.00 0.00 3.16
521 523 0.606944 TATCCCCGTGTGGTTGCAAC 60.607 55.000 21.59 21.59 0.00 4.17
522 524 0.110678 TTATCCCCGTGTGGTTGCAA 59.889 50.000 0.00 0.00 0.00 4.08
555 557 8.358148 CAGATATGCTTGCTTTTGGATCTTTAT 58.642 33.333 0.00 0.00 0.00 1.40
574 576 8.512956 CATCTCTTTTTATTGGGAGCAGATATG 58.487 37.037 0.00 0.00 0.00 1.78
575 577 8.223330 ACATCTCTTTTTATTGGGAGCAGATAT 58.777 33.333 0.00 0.00 0.00 1.63
598 600 6.203808 TCTGCTACGTTTAGTATGACACAT 57.796 37.500 0.00 0.00 34.34 3.21
613 615 1.535028 TGTGCCAAACAATCTGCTACG 59.465 47.619 0.00 0.00 35.24 3.51
642 644 0.249489 GCCTCTACGGTGCCATACAG 60.249 60.000 0.00 0.00 34.25 2.74
650 652 1.542492 ATATACGGGCCTCTACGGTG 58.458 55.000 0.84 0.00 34.25 4.94
651 653 1.891150 CAATATACGGGCCTCTACGGT 59.109 52.381 0.84 0.00 34.25 4.83
711 717 6.973460 TCGGGTAAAAAGGGTTTTATTTCA 57.027 33.333 0.00 0.00 40.43 2.69
712 718 8.659925 TTTTCGGGTAAAAAGGGTTTTATTTC 57.340 30.769 0.00 0.00 40.43 2.17
739 745 3.580458 AGAGATAATTATGGCACGCCTCT 59.420 43.478 9.92 3.98 36.94 3.69
740 746 3.931578 AGAGATAATTATGGCACGCCTC 58.068 45.455 9.92 1.69 36.94 4.70
741 747 4.528596 ACTAGAGATAATTATGGCACGCCT 59.471 41.667 9.92 0.00 36.94 5.52
742 748 4.822026 ACTAGAGATAATTATGGCACGCC 58.178 43.478 1.78 0.00 0.00 5.68
743 749 5.715070 AGACTAGAGATAATTATGGCACGC 58.285 41.667 1.78 0.00 0.00 5.34
763 769 5.819379 TGCCAAGTGATGATAATCTTGAGAC 59.181 40.000 0.00 0.00 39.39 3.36
842 848 5.065218 GTGATAGATTTGGTCGCTGATGTTT 59.935 40.000 0.00 0.00 0.00 2.83
905 911 7.063074 CGTGGTAGAGTGTGATAAAAGTAAAGG 59.937 40.741 0.00 0.00 0.00 3.11
906 912 7.811236 TCGTGGTAGAGTGTGATAAAAGTAAAG 59.189 37.037 0.00 0.00 0.00 1.85
909 915 6.822667 TCGTGGTAGAGTGTGATAAAAGTA 57.177 37.500 0.00 0.00 0.00 2.24
929 935 2.048127 GCCTCAAGCGGAACTCGT 60.048 61.111 0.00 0.00 41.72 4.18
951 957 1.153489 CGGAGATGAGTGCAGTGGG 60.153 63.158 0.00 0.00 0.00 4.61
973 979 1.135094 ACGCATCAGATTGATCCCCT 58.865 50.000 0.00 0.00 34.28 4.79
1011 1017 1.593209 GACGACTGTTGGCGACCAA 60.593 57.895 1.61 7.15 41.69 3.67
1040 1055 1.813178 CGAGGTCAGTCAGCAGTAGAA 59.187 52.381 0.00 0.00 0.00 2.10
1044 1059 1.872197 GCTCGAGGTCAGTCAGCAGT 61.872 60.000 15.58 0.00 0.00 4.40
1069 1084 2.120909 CATTGCGGGGTGGTGGATC 61.121 63.158 0.00 0.00 0.00 3.36
1105 1120 1.838073 TTCTTCTCCCCCTTCGCACC 61.838 60.000 0.00 0.00 0.00 5.01
1136 1151 1.018226 GCATGCTGCTCTCACGACTT 61.018 55.000 11.37 0.00 40.96 3.01
1143 1158 3.260483 CGACGGCATGCTGCTCTC 61.260 66.667 26.52 15.25 44.28 3.20
1144 1159 3.997064 GACGACGGCATGCTGCTCT 62.997 63.158 26.52 7.18 44.28 4.09
1151 1166 1.202065 CCAAAATCTGACGACGGCATG 60.202 52.381 2.55 0.00 0.00 4.06
1158 1173 1.555075 CTCCTCCCCAAAATCTGACGA 59.445 52.381 0.00 0.00 0.00 4.20
1159 1174 1.555075 TCTCCTCCCCAAAATCTGACG 59.445 52.381 0.00 0.00 0.00 4.35
1209 1224 5.424757 CAACGAGTCATATAGGTTTTCCCA 58.575 41.667 0.00 0.00 41.86 4.37
1264 1279 0.531657 CCAAATTCTCGCATTGGGCA 59.468 50.000 0.00 0.00 45.17 5.36
1270 1285 1.376609 GCCGACCCAAATTCTCGCAT 61.377 55.000 0.00 0.00 0.00 4.73
1322 1337 3.676093 ACCGATTCAAGGAACCTTCTTC 58.324 45.455 2.84 1.06 33.42 2.87
1640 1662 3.006940 TCATCTTCCGCGCACTTTTTAT 58.993 40.909 8.75 0.00 0.00 1.40
1641 1663 2.418692 TCATCTTCCGCGCACTTTTTA 58.581 42.857 8.75 0.00 0.00 1.52
1653 1675 9.044150 TGAAAACATGAACATTTTTCATCTTCC 57.956 29.630 20.10 1.95 41.85 3.46
1665 1687 9.248291 GTGAACAAATAGTGAAAACATGAACAT 57.752 29.630 0.00 0.00 0.00 2.71
1739 1761 6.122850 AGCAAAATTTGGAGAAAAGCAAAC 57.877 33.333 7.89 0.00 0.00 2.93
1824 1850 9.947669 AAAATGCGATCAAAATTTGAAAATTCA 57.052 22.222 12.75 7.12 43.95 2.57
1873 1899 1.272704 GGGAGCCCCTCTTGACAATTT 60.273 52.381 3.16 0.00 41.34 1.82
1896 1922 5.359194 TCTCTCCCCAAAATATGACAGAC 57.641 43.478 0.00 0.00 0.00 3.51
1932 1958 1.735360 GGCCGTACCACAGCGTATA 59.265 57.895 0.00 0.00 38.86 1.47
1945 1971 0.179040 CCGGTATTTACATGGGCCGT 60.179 55.000 0.00 0.00 37.76 5.68
2074 2100 1.586564 GGAGCGGATCTCGACAACG 60.587 63.158 7.64 0.00 42.82 4.10
2076 2102 1.384989 GGAGGAGCGGATCTCGACAA 61.385 60.000 7.64 0.00 42.82 3.18
2077 2103 1.824329 GGAGGAGCGGATCTCGACA 60.824 63.158 7.64 0.00 42.82 4.35
2312 2338 0.610687 AAGAGACGAAAGCAGGGGAG 59.389 55.000 0.00 0.00 0.00 4.30
2373 2399 1.750399 CCGCCCCATTCTTGACCAG 60.750 63.158 0.00 0.00 0.00 4.00
2398 2424 0.526524 CTTCATCTCGGACGACTGCC 60.527 60.000 0.00 0.00 0.00 4.85
2400 2426 0.453793 AGCTTCATCTCGGACGACTG 59.546 55.000 0.00 0.00 0.00 3.51
2401 2427 0.736053 GAGCTTCATCTCGGACGACT 59.264 55.000 0.00 0.00 0.00 4.18
2402 2428 3.243855 GAGCTTCATCTCGGACGAC 57.756 57.895 0.00 0.00 0.00 4.34
2409 2435 3.211045 AGAGGTAGACGAGCTTCATCTC 58.789 50.000 0.00 0.00 30.63 2.75
2410 2436 3.290948 AGAGGTAGACGAGCTTCATCT 57.709 47.619 0.00 0.00 35.50 2.90
2411 2437 4.577283 AGTTAGAGGTAGACGAGCTTCATC 59.423 45.833 0.00 0.00 35.50 2.92
2412 2438 4.336993 CAGTTAGAGGTAGACGAGCTTCAT 59.663 45.833 0.00 0.00 35.50 2.57
2413 2439 3.690139 CAGTTAGAGGTAGACGAGCTTCA 59.310 47.826 0.00 0.00 35.50 3.02
2414 2440 3.487879 GCAGTTAGAGGTAGACGAGCTTC 60.488 52.174 0.00 0.00 35.50 3.86
2415 2441 2.424246 GCAGTTAGAGGTAGACGAGCTT 59.576 50.000 0.00 0.00 35.50 3.74
2416 2442 2.018515 GCAGTTAGAGGTAGACGAGCT 58.981 52.381 0.00 0.00 39.10 4.09
2417 2443 2.018515 AGCAGTTAGAGGTAGACGAGC 58.981 52.381 0.00 0.00 0.00 5.03
2418 2444 2.614983 GGAGCAGTTAGAGGTAGACGAG 59.385 54.545 0.00 0.00 0.00 4.18
2445 2471 2.815647 GTTGGCTCGCTTCTCCGG 60.816 66.667 0.00 0.00 0.00 5.14
2477 2503 1.342076 TGATTACTCCGACCTGGCTCT 60.342 52.381 0.00 0.00 37.80 4.09
2582 2608 7.760131 ATTCATGGTTTAATCGAAGCATTTG 57.240 32.000 0.00 0.00 43.11 2.32
2596 2622 5.996513 TGTAATTGCAGCAAATTCATGGTTT 59.003 32.000 12.97 0.88 32.16 3.27
2679 2708 6.360370 ACTAGTTGCAGGATTCAGACTTAA 57.640 37.500 0.00 0.00 0.00 1.85
2851 2880 0.750850 ATGCAATCTGAAGCCATGGC 59.249 50.000 30.12 30.12 42.33 4.40
2917 2946 3.268330 CATATGGCGATGGATCCTTGAG 58.732 50.000 14.23 4.45 0.00 3.02
2921 2950 3.198635 CCTAACATATGGCGATGGATCCT 59.801 47.826 14.23 0.00 0.00 3.24
3044 3073 2.026915 AGATGCACATAGTGTCCAGCAA 60.027 45.455 0.00 0.00 31.96 3.91
3183 3212 1.075970 ATCTAGAGGCAGGGTCGCA 60.076 57.895 0.00 0.00 0.00 5.10
3243 3272 1.131303 AGGTTGTCGGGGATTGTGGA 61.131 55.000 0.00 0.00 0.00 4.02
3246 3275 1.683441 GGAGGTTGTCGGGGATTGT 59.317 57.895 0.00 0.00 0.00 2.71
3248 3277 2.987125 CGGAGGTTGTCGGGGATT 59.013 61.111 0.00 0.00 0.00 3.01
3317 3346 2.626266 TGTATGGCGGACATGGTAGTAG 59.374 50.000 6.59 0.00 40.82 2.57
3324 3353 0.177836 TGAGGTGTATGGCGGACATG 59.822 55.000 6.59 0.00 40.82 3.21
3431 3460 6.245408 ACTCAACCCACTGCTTTAATATCAA 58.755 36.000 0.00 0.00 0.00 2.57
3449 3478 1.927895 CCATCGAGGCTGTACTCAAC 58.072 55.000 0.00 0.00 37.34 3.18
3509 3538 4.307032 AGCTTTGTGGGTGATGAACTAT 57.693 40.909 0.00 0.00 0.00 2.12
3526 3555 1.211456 AGCTTCATGGGAGCTAGCTT 58.789 50.000 20.42 0.00 38.99 3.74
3529 3558 3.577848 AGTCATAGCTTCATGGGAGCTAG 59.422 47.826 25.37 19.61 43.24 3.42
3597 3626 6.919662 CGTATGCATAAGCCAAATCAAAAGAT 59.080 34.615 8.28 0.00 41.13 2.40
3630 3659 1.378531 TTCCTTCGGCCATTTCATCG 58.621 50.000 2.24 0.00 0.00 3.84
3718 3747 1.472376 GCTGAGCGAAGAAGGTAGCAT 60.472 52.381 0.00 0.00 0.00 3.79
3747 3776 5.518848 AATTGAACTGAGCACATCACAAA 57.481 34.783 0.00 0.00 33.22 2.83
3822 3851 8.231692 TCAAACACATGACTCCTAAATTTCAA 57.768 30.769 0.00 0.00 0.00 2.69
3891 3920 6.956435 TGCAGGTCCTATATGTTCTCATAGAT 59.044 38.462 0.00 0.00 39.49 1.98
4056 4085 7.282585 TCTGGTGGATAGATTACTTTTGGATG 58.717 38.462 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.