Multiple sequence alignment - TraesCS3D01G401000

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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 TraesCS3D01G401000 chr3D 100.000 3436 0 0 1 3436 515705494 515708929 0.000000e+00 6346
1 TraesCS3D01G401000 chr3D 93.804 1033 60 4 2406 3436 460018117 460019147 0.000000e+00 1550
2 TraesCS3D01G401000 chr3D 93.153 1037 64 6 2405 3436 303711268 303710234 0.000000e+00 1515
3 TraesCS3D01G401000 chr3A 91.670 2389 136 18 38 2405 649951915 649954261 0.000000e+00 3251
4 TraesCS3D01G401000 chr4D 94.493 1035 52 5 2405 3436 53493336 53492304 0.000000e+00 1591
5 TraesCS3D01G401000 chr4D 93.043 1035 65 7 2406 3436 42204063 42203032 0.000000e+00 1506
6 TraesCS3D01G401000 chr7D 93.714 1034 61 4 2405 3436 531049986 531048955 0.000000e+00 1546
7 TraesCS3D01G401000 chr5D 93.276 1041 64 6 2399 3436 377353637 377352600 0.000000e+00 1530
8 TraesCS3D01G401000 chr5D 93.230 1034 65 5 2406 3436 231395218 231396249 0.000000e+00 1517
9 TraesCS3D01G401000 chr5D 93.147 1036 63 5 2406 3436 301331771 301330739 0.000000e+00 1513
10 TraesCS3D01G401000 chr2D 93.050 1036 67 5 2404 3436 324142249 324143282 0.000000e+00 1509
11 TraesCS3D01G401000 chr2D 82.865 1459 204 19 965 2405 493883340 493881910 0.000000e+00 1267
12 TraesCS3D01G401000 chr2A 82.502 1503 206 25 924 2405 639694683 639696149 0.000000e+00 1266
13 TraesCS3D01G401000 chr6B 81.522 1472 215 27 963 2405 95237658 95236215 0.000000e+00 1158
14 TraesCS3D01G401000 chr6B 80.299 1538 233 29 892 2402 159702427 159703921 0.000000e+00 1098
15 TraesCS3D01G401000 chr6B 78.645 1564 245 45 886 2405 711695132 711693614 0.000000e+00 955
16 TraesCS3D01G401000 chr6B 80.298 939 162 8 1070 2006 665132182 665131265 0.000000e+00 688
17 TraesCS3D01G401000 chr7A 80.454 1499 237 27 929 2405 219396856 219398320 0.000000e+00 1094
18 TraesCS3D01G401000 chr6D 79.974 1528 244 31 892 2402 84084188 84085670 0.000000e+00 1070
19 TraesCS3D01G401000 chr6D 79.926 1350 228 27 1066 2405 466544107 466545423 0.000000e+00 952
20 TraesCS3D01G401000 chr6D 77.610 1456 261 37 983 2405 67326763 67325340 0.000000e+00 822
21 TraesCS3D01G401000 chr6D 77.892 1262 230 32 1168 2405 466528246 466527010 0.000000e+00 739
22 TraesCS3D01G401000 chr6D 79.016 772 127 21 1276 2039 440210496 440209752 2.380000e-136 496
23 TraesCS3D01G401000 chr6D 80.247 405 61 14 928 1315 466528663 466528261 1.560000e-73 287
24 TraesCS3D01G401000 chr6D 79.706 340 36 19 889 1208 440210851 440210525 7.470000e-52 215
25 TraesCS3D01G401000 chr6A 80.274 1460 229 30 963 2402 101354109 101355529 0.000000e+00 1046
26 TraesCS3D01G401000 chr6A 77.622 1354 222 40 1066 2405 84699751 84698465 0.000000e+00 747
27 TraesCS3D01G401000 chr6A 80.769 936 155 10 1073 2005 588354657 588353744 0.000000e+00 708
28 TraesCS3D01G401000 chr6A 79.883 343 33 18 889 1208 588411040 588410711 5.770000e-53 219
29 TraesCS3D01G401000 chr6A 82.432 222 35 3 1795 2014 588410211 588409992 1.260000e-44 191
30 TraesCS3D01G401000 chr3B 88.000 600 42 13 717 1306 678203992 678204571 0.000000e+00 682
31 TraesCS3D01G401000 chr3B 86.192 239 13 12 435 669 678196497 678196719 1.230000e-59 241


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 TraesCS3D01G401000 chr3D 515705494 515708929 3435 False 6346.0 6346 100.0000 1 3436 1 chr3D.!!$F2 3435
1 TraesCS3D01G401000 chr3D 460018117 460019147 1030 False 1550.0 1550 93.8040 2406 3436 1 chr3D.!!$F1 1030
2 TraesCS3D01G401000 chr3D 303710234 303711268 1034 True 1515.0 1515 93.1530 2405 3436 1 chr3D.!!$R1 1031
3 TraesCS3D01G401000 chr3A 649951915 649954261 2346 False 3251.0 3251 91.6700 38 2405 1 chr3A.!!$F1 2367
4 TraesCS3D01G401000 chr4D 53492304 53493336 1032 True 1591.0 1591 94.4930 2405 3436 1 chr4D.!!$R2 1031
5 TraesCS3D01G401000 chr4D 42203032 42204063 1031 True 1506.0 1506 93.0430 2406 3436 1 chr4D.!!$R1 1030
6 TraesCS3D01G401000 chr7D 531048955 531049986 1031 True 1546.0 1546 93.7140 2405 3436 1 chr7D.!!$R1 1031
7 TraesCS3D01G401000 chr5D 377352600 377353637 1037 True 1530.0 1530 93.2760 2399 3436 1 chr5D.!!$R2 1037
8 TraesCS3D01G401000 chr5D 231395218 231396249 1031 False 1517.0 1517 93.2300 2406 3436 1 chr5D.!!$F1 1030
9 TraesCS3D01G401000 chr5D 301330739 301331771 1032 True 1513.0 1513 93.1470 2406 3436 1 chr5D.!!$R1 1030
10 TraesCS3D01G401000 chr2D 324142249 324143282 1033 False 1509.0 1509 93.0500 2404 3436 1 chr2D.!!$F1 1032
11 TraesCS3D01G401000 chr2D 493881910 493883340 1430 True 1267.0 1267 82.8650 965 2405 1 chr2D.!!$R1 1440
12 TraesCS3D01G401000 chr2A 639694683 639696149 1466 False 1266.0 1266 82.5020 924 2405 1 chr2A.!!$F1 1481
13 TraesCS3D01G401000 chr6B 95236215 95237658 1443 True 1158.0 1158 81.5220 963 2405 1 chr6B.!!$R1 1442
14 TraesCS3D01G401000 chr6B 159702427 159703921 1494 False 1098.0 1098 80.2990 892 2402 1 chr6B.!!$F1 1510
15 TraesCS3D01G401000 chr6B 711693614 711695132 1518 True 955.0 955 78.6450 886 2405 1 chr6B.!!$R3 1519
16 TraesCS3D01G401000 chr6B 665131265 665132182 917 True 688.0 688 80.2980 1070 2006 1 chr6B.!!$R2 936
17 TraesCS3D01G401000 chr7A 219396856 219398320 1464 False 1094.0 1094 80.4540 929 2405 1 chr7A.!!$F1 1476
18 TraesCS3D01G401000 chr6D 84084188 84085670 1482 False 1070.0 1070 79.9740 892 2402 1 chr6D.!!$F1 1510
19 TraesCS3D01G401000 chr6D 466544107 466545423 1316 False 952.0 952 79.9260 1066 2405 1 chr6D.!!$F2 1339
20 TraesCS3D01G401000 chr6D 67325340 67326763 1423 True 822.0 822 77.6100 983 2405 1 chr6D.!!$R1 1422
21 TraesCS3D01G401000 chr6D 466527010 466528663 1653 True 513.0 739 79.0695 928 2405 2 chr6D.!!$R3 1477
22 TraesCS3D01G401000 chr6D 440209752 440210851 1099 True 355.5 496 79.3610 889 2039 2 chr6D.!!$R2 1150
23 TraesCS3D01G401000 chr6A 101354109 101355529 1420 False 1046.0 1046 80.2740 963 2402 1 chr6A.!!$F1 1439
24 TraesCS3D01G401000 chr6A 84698465 84699751 1286 True 747.0 747 77.6220 1066 2405 1 chr6A.!!$R1 1339
25 TraesCS3D01G401000 chr6A 588353744 588354657 913 True 708.0 708 80.7690 1073 2005 1 chr6A.!!$R2 932
26 TraesCS3D01G401000 chr6A 588409992 588411040 1048 True 205.0 219 81.1575 889 2014 2 chr6A.!!$R3 1125
27 TraesCS3D01G401000 chr3B 678203992 678204571 579 False 682.0 682 88.0000 717 1306 1 chr3B.!!$F2 589

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
501 506 0.039346 TTGCGATACGACCACGACAA 60.039 50.0 0.0 0.0 42.66 3.18 F
1390 1629 0.321653 GCACGACTCTCCCACCATTT 60.322 55.0 0.0 0.0 0.00 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1774 2019 0.037590 CAGTTCAATTCCCCCGGTCA 59.962 55.000 0.0 0.0 0.00 4.02 R
3166 3496 1.066303 GGACACGATCTCTGCTTCGAT 59.934 52.381 0.0 0.0 38.67 3.59 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
22 23 4.406173 CGTGCGCGTCTGAGAGGT 62.406 66.667 12.43 0.00 0.00 3.85
23 24 2.807045 GTGCGCGTCTGAGAGGTG 60.807 66.667 8.43 11.03 0.00 4.00
24 25 3.295273 TGCGCGTCTGAGAGGTGT 61.295 61.111 15.89 0.00 31.70 4.16
25 26 2.505118 GCGCGTCTGAGAGGTGTC 60.505 66.667 15.89 6.10 31.70 3.67
26 27 2.983930 GCGCGTCTGAGAGGTGTCT 61.984 63.158 15.89 0.00 34.86 3.41
36 37 3.481112 GAGAGGTGTCTCGTCTTCTTC 57.519 52.381 0.00 0.00 44.47 2.87
117 118 2.106938 TGGATGATGGACGCGCTC 59.893 61.111 5.73 2.64 0.00 5.03
157 158 3.530910 CTCGCCGTGGACAAGGGTT 62.531 63.158 6.42 0.00 36.12 4.11
162 163 0.605589 CCGTGGACAAGGGTTCTTCC 60.606 60.000 0.00 0.00 0.00 3.46
180 181 4.214383 CGCTTGCTCGCCACGATG 62.214 66.667 0.00 0.00 34.61 3.84
181 182 4.527157 GCTTGCTCGCCACGATGC 62.527 66.667 0.00 0.00 34.61 3.91
355 356 1.243342 CGCCATGCTTGGAACTGGAA 61.243 55.000 22.21 0.00 46.92 3.53
357 358 1.915141 CCATGCTTGGAACTGGAAGT 58.085 50.000 13.33 0.00 46.92 3.01
396 397 1.324383 CTTACGGTTTTGGGGCTTGT 58.676 50.000 0.00 0.00 0.00 3.16
402 403 0.591659 GTTTTGGGGCTTGTCTCGTC 59.408 55.000 0.00 0.00 0.00 4.20
418 419 2.102588 CTCGTCCCGGTTCTATGGATTT 59.897 50.000 0.00 0.00 0.00 2.17
422 423 4.377897 GTCCCGGTTCTATGGATTTGTAG 58.622 47.826 0.00 0.00 0.00 2.74
425 426 6.014840 GTCCCGGTTCTATGGATTTGTAGATA 60.015 42.308 0.00 0.00 0.00 1.98
426 427 6.210784 TCCCGGTTCTATGGATTTGTAGATAG 59.789 42.308 0.00 0.00 0.00 2.08
501 506 0.039346 TTGCGATACGACCACGACAA 60.039 50.000 0.00 0.00 42.66 3.18
504 509 0.524816 CGATACGACCACGACAAGGG 60.525 60.000 0.00 0.00 42.66 3.95
544 549 2.708216 TCCTTGCCGCTGATAATTCA 57.292 45.000 0.00 0.00 0.00 2.57
550 555 2.224281 TGCCGCTGATAATTCACCCTAG 60.224 50.000 0.00 0.00 0.00 3.02
612 617 4.754667 GCAACCCGTCCCGTCTCC 62.755 72.222 0.00 0.00 0.00 3.71
614 619 4.626402 AACCCGTCCCGTCTCCCA 62.626 66.667 0.00 0.00 0.00 4.37
625 632 4.465446 TCTCCCAGCCTCTCCCGG 62.465 72.222 0.00 0.00 0.00 5.73
687 702 2.111460 TAACACCCCACCACACGC 59.889 61.111 0.00 0.00 0.00 5.34
713 728 3.047280 CGCTGCGGCCAACACTAA 61.047 61.111 15.40 0.00 34.44 2.24
815 830 4.820744 GCCGGCCACCATGACCAT 62.821 66.667 18.11 0.00 0.00 3.55
835 850 1.004440 GCTCTCCTTCGTTGCCACT 60.004 57.895 0.00 0.00 0.00 4.00
841 856 0.608640 CCTTCGTTGCCACTACCTCT 59.391 55.000 0.00 0.00 0.00 3.69
943 972 3.364964 CGGCCTCAATGTAAGTGTTGTTC 60.365 47.826 0.00 0.00 31.21 3.18
1258 1335 4.537936 AAAGCTCGTGTTTTCAGTCTTC 57.462 40.909 0.00 0.00 0.00 2.87
1284 1523 0.391130 TCCTCCAAATCAACCGAGCG 60.391 55.000 0.00 0.00 0.00 5.03
1390 1629 0.321653 GCACGACTCTCCCACCATTT 60.322 55.000 0.00 0.00 0.00 2.32
1422 1661 2.672651 CGTGCCATGTCAGCCCAA 60.673 61.111 0.00 0.00 0.00 4.12
1638 1883 1.956477 TGCAAGCTTTTGGAGTCCTTC 59.044 47.619 11.33 0.00 0.00 3.46
1639 1884 2.234143 GCAAGCTTTTGGAGTCCTTCT 58.766 47.619 11.33 0.00 0.00 2.85
1661 1906 1.355971 TTAACCGATTGCGACTCAGC 58.644 50.000 0.00 0.00 40.82 4.26
1670 1915 2.871182 TGCGACTCAGCGATCTATTT 57.129 45.000 0.00 0.00 40.67 1.40
1761 2006 8.918202 TTGAACTGACATATCTACCAAAACTT 57.082 30.769 0.00 0.00 0.00 2.66
1770 2015 8.387813 ACATATCTACCAAAACTTCAAAGGGTA 58.612 33.333 0.00 0.00 0.00 3.69
1771 2016 9.408648 CATATCTACCAAAACTTCAAAGGGTAT 57.591 33.333 0.00 0.00 31.09 2.73
1773 2018 8.803397 ATCTACCAAAACTTCAAAGGGTATAC 57.197 34.615 0.00 0.00 31.09 1.47
1774 2019 7.981142 TCTACCAAAACTTCAAAGGGTATACT 58.019 34.615 2.25 0.00 31.09 2.12
1775 2020 6.894339 ACCAAAACTTCAAAGGGTATACTG 57.106 37.500 2.25 0.00 0.00 2.74
1776 2021 6.607019 ACCAAAACTTCAAAGGGTATACTGA 58.393 36.000 2.25 0.00 0.00 3.41
1777 2022 6.489022 ACCAAAACTTCAAAGGGTATACTGAC 59.511 38.462 2.25 0.00 0.00 3.51
1778 2023 6.072119 CCAAAACTTCAAAGGGTATACTGACC 60.072 42.308 2.25 0.00 38.93 4.02
1779 2024 4.467198 ACTTCAAAGGGTATACTGACCG 57.533 45.455 2.25 0.00 40.76 4.79
1780 2025 3.197116 ACTTCAAAGGGTATACTGACCGG 59.803 47.826 0.00 0.00 40.76 5.28
1781 2026 2.112998 TCAAAGGGTATACTGACCGGG 58.887 52.381 6.32 0.00 40.76 5.73
1782 2027 1.140252 CAAAGGGTATACTGACCGGGG 59.860 57.143 6.32 0.00 40.76 5.73
1783 2028 0.399519 AAGGGTATACTGACCGGGGG 60.400 60.000 6.32 0.00 40.76 5.40
1784 2029 1.233949 GGGTATACTGACCGGGGGA 59.766 63.158 6.32 0.00 40.76 4.81
1785 2030 0.398948 GGGTATACTGACCGGGGGAA 60.399 60.000 6.32 0.00 40.76 3.97
1786 2031 1.725803 GGTATACTGACCGGGGGAAT 58.274 55.000 6.32 0.00 0.00 3.01
1787 2032 2.052468 GGTATACTGACCGGGGGAATT 58.948 52.381 6.32 0.00 0.00 2.17
1788 2033 2.224450 GGTATACTGACCGGGGGAATTG 60.224 54.545 6.32 0.00 0.00 2.32
1789 2034 1.887797 ATACTGACCGGGGGAATTGA 58.112 50.000 6.32 0.00 0.00 2.57
1790 2035 1.659022 TACTGACCGGGGGAATTGAA 58.341 50.000 6.32 0.00 0.00 2.69
1791 2036 0.037734 ACTGACCGGGGGAATTGAAC 59.962 55.000 6.32 0.00 0.00 3.18
1938 2195 4.546829 TGCTAATGTTCCTTCCGTAAGT 57.453 40.909 0.00 0.00 0.00 2.24
2208 2523 3.909995 TCTGGGTCATCTTTCTGAAGGAA 59.090 43.478 6.30 0.00 33.56 3.36
2247 2562 6.694447 ACAATGTTTATTCTTGAAGCTGCAT 58.306 32.000 0.00 0.00 0.00 3.96
2449 2772 2.582978 GTAGGGGTCCCGAACTGC 59.417 66.667 0.48 0.00 41.95 4.40
2472 2795 3.683340 GTGTTTGAGGATCGAAGGTAACC 59.317 47.826 0.00 0.00 39.66 2.85
2494 2817 2.550208 GGAGACAGGGACACGATGTTTT 60.550 50.000 0.00 0.00 0.00 2.43
2584 2907 6.049955 TGGGGTTTACAAGAGTTGATCTAG 57.950 41.667 0.00 0.00 37.23 2.43
2600 2923 5.788055 GATCTAGCTCGAGATCGTAATGA 57.212 43.478 18.75 2.93 41.79 2.57
2619 2942 8.627403 CGTAATGACTAAACCCTAGATGTCTAA 58.373 37.037 0.00 0.00 0.00 2.10
2646 2971 7.619050 CCTGTATGATTATGATTGCCTCTACT 58.381 38.462 0.00 0.00 0.00 2.57
2657 2982 2.897350 TGCCTCTACTGACTAAACCCA 58.103 47.619 0.00 0.00 0.00 4.51
2737 3062 5.852738 AGAAATCTTCATATCCGAATGCG 57.147 39.130 0.00 0.00 37.24 4.73
2830 3155 1.078708 CATTAGTCCGGCCCACGTT 60.079 57.895 0.00 0.00 42.24 3.99
2832 3157 1.125633 ATTAGTCCGGCCCACGTTAT 58.874 50.000 0.00 0.00 42.24 1.89
2884 3209 1.001760 GACTCCCTCAGTAGCCCCA 59.998 63.158 0.00 0.00 34.41 4.96
3033 3358 1.518056 CCACACACAGCCGCAAAGAT 61.518 55.000 0.00 0.00 0.00 2.40
3111 3437 2.285083 TGCCCGGTCATTATTTCGAAG 58.715 47.619 0.00 0.00 0.00 3.79
3164 3494 0.309302 CGGTTTTCATTGGCACGTCA 59.691 50.000 0.00 0.00 0.00 4.35
3166 3496 2.160615 CGGTTTTCATTGGCACGTCATA 59.839 45.455 0.00 0.00 0.00 2.15
3189 3519 1.617947 AAGCAGAGATCGTGTCCCCC 61.618 60.000 0.00 0.00 0.00 5.40
3226 3556 4.080243 TCATCAATACGGGTGTGGGTAATT 60.080 41.667 0.00 0.00 0.00 1.40
3360 3690 1.563410 CCTTCTTCCTCTCTGCCCATT 59.437 52.381 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.807045 CACCTCTCAGACGCGCAC 60.807 66.667 5.73 0.00 0.00 5.34
7 8 3.268965 GACACCTCTCAGACGCGCA 62.269 63.158 5.73 0.00 0.00 6.09
8 9 2.505118 GACACCTCTCAGACGCGC 60.505 66.667 5.73 0.00 0.00 6.86
9 10 1.135731 GAGACACCTCTCAGACGCG 59.864 63.158 3.53 3.53 42.50 6.01
10 11 1.135731 CGAGACACCTCTCAGACGC 59.864 63.158 0.00 0.00 43.03 5.19
11 12 0.444651 GACGAGACACCTCTCAGACG 59.555 60.000 0.00 0.00 43.03 4.18
12 13 1.816074 AGACGAGACACCTCTCAGAC 58.184 55.000 0.00 0.00 43.03 3.51
13 14 2.039216 AGAAGACGAGACACCTCTCAGA 59.961 50.000 0.00 0.00 43.03 3.27
14 15 2.432444 AGAAGACGAGACACCTCTCAG 58.568 52.381 0.00 0.00 43.03 3.35
15 16 2.570415 AGAAGACGAGACACCTCTCA 57.430 50.000 0.00 0.00 43.03 3.27
16 17 3.078837 AGAAGAAGACGAGACACCTCTC 58.921 50.000 0.00 0.00 39.86 3.20
17 18 3.149005 AGAAGAAGACGAGACACCTCT 57.851 47.619 0.00 0.00 37.28 3.69
18 19 3.366577 GGAAGAAGAAGACGAGACACCTC 60.367 52.174 0.00 0.00 36.08 3.85
19 20 2.559231 GGAAGAAGAAGACGAGACACCT 59.441 50.000 0.00 0.00 0.00 4.00
20 21 2.352912 GGGAAGAAGAAGACGAGACACC 60.353 54.545 0.00 0.00 0.00 4.16
21 22 2.352912 GGGGAAGAAGAAGACGAGACAC 60.353 54.545 0.00 0.00 0.00 3.67
22 23 1.893801 GGGGAAGAAGAAGACGAGACA 59.106 52.381 0.00 0.00 0.00 3.41
23 24 1.135344 CGGGGAAGAAGAAGACGAGAC 60.135 57.143 0.00 0.00 0.00 3.36
24 25 1.174783 CGGGGAAGAAGAAGACGAGA 58.825 55.000 0.00 0.00 0.00 4.04
25 26 0.173708 CCGGGGAAGAAGAAGACGAG 59.826 60.000 0.00 0.00 0.00 4.18
26 27 1.255667 CCCGGGGAAGAAGAAGACGA 61.256 60.000 14.71 0.00 0.00 4.20
27 28 1.218316 CCCGGGGAAGAAGAAGACG 59.782 63.158 14.71 0.00 0.00 4.18
28 29 1.078356 GCCCGGGGAAGAAGAAGAC 60.078 63.158 25.28 0.00 0.00 3.01
29 30 2.656069 CGCCCGGGGAAGAAGAAGA 61.656 63.158 25.28 0.00 0.00 2.87
30 31 2.125106 CGCCCGGGGAAGAAGAAG 60.125 66.667 25.28 0.00 0.00 2.85
31 32 3.712907 CCGCCCGGGGAAGAAGAA 61.713 66.667 25.28 0.00 0.00 2.52
33 34 4.778143 CACCGCCCGGGGAAGAAG 62.778 72.222 25.28 1.77 42.48 2.85
57 58 0.810426 AGCAGCATCACATCGAGCAG 60.810 55.000 0.00 0.00 0.00 4.24
104 105 4.193334 CCGAGAGCGCGTCCATCA 62.193 66.667 8.43 0.00 35.83 3.07
117 118 2.581354 CCCCTCTGCAAGACCGAG 59.419 66.667 0.00 0.00 38.67 4.63
157 158 4.760047 GGCGAGCAAGCGGGAAGA 62.760 66.667 0.00 0.00 38.18 2.87
180 181 1.982073 GCATAACGCAGTGGGTGAGC 61.982 60.000 14.26 13.76 45.00 4.26
181 182 2.089854 GCATAACGCAGTGGGTGAG 58.910 57.895 14.26 7.93 45.00 3.51
343 344 2.678324 GTCTCGACTTCCAGTTCCAAG 58.322 52.381 0.00 0.00 0.00 3.61
402 403 4.682778 TCTACAAATCCATAGAACCGGG 57.317 45.455 6.32 0.00 0.00 5.73
418 419 7.012421 CGCCTATATATGACTGCACTATCTACA 59.988 40.741 0.00 0.00 0.00 2.74
422 423 5.974158 CACGCCTATATATGACTGCACTATC 59.026 44.000 0.00 0.00 0.00 2.08
425 426 3.615110 GCACGCCTATATATGACTGCACT 60.615 47.826 0.00 0.00 0.00 4.40
426 427 2.668457 GCACGCCTATATATGACTGCAC 59.332 50.000 0.00 0.00 0.00 4.57
482 487 0.039346 TTGTCGTGGTCGTATCGCAA 60.039 50.000 0.00 0.00 38.33 4.85
484 489 1.138047 CCTTGTCGTGGTCGTATCGC 61.138 60.000 0.00 0.00 38.33 4.58
485 490 0.524816 CCCTTGTCGTGGTCGTATCG 60.525 60.000 0.00 0.00 38.33 2.92
501 506 1.613630 ACTGGCCGATCAGTTCCCT 60.614 57.895 0.00 0.00 44.74 4.20
544 549 1.762460 CACTGGATCGGCCTAGGGT 60.762 63.158 11.72 0.00 37.63 4.34
550 555 1.776034 GCGAATTCACTGGATCGGCC 61.776 60.000 6.22 0.00 35.91 6.13
612 617 3.151022 GAGACCGGGAGAGGCTGG 61.151 72.222 6.32 0.00 33.69 4.85
614 619 4.824515 CGGAGACCGGGAGAGGCT 62.825 72.222 6.32 0.00 44.15 4.58
651 658 2.770048 AGAAGGGATGGAGGCGGG 60.770 66.667 0.00 0.00 0.00 6.13
810 825 0.173708 AACGAAGGAGAGCGATGGTC 59.826 55.000 0.00 0.00 0.00 4.02
811 826 0.108615 CAACGAAGGAGAGCGATGGT 60.109 55.000 0.00 0.00 0.00 3.55
812 827 1.424493 GCAACGAAGGAGAGCGATGG 61.424 60.000 0.00 0.00 32.03 3.51
813 828 1.424493 GGCAACGAAGGAGAGCGATG 61.424 60.000 0.00 0.00 34.10 3.84
814 829 1.153549 GGCAACGAAGGAGAGCGAT 60.154 57.895 0.00 0.00 0.00 4.58
815 830 2.261671 GGCAACGAAGGAGAGCGA 59.738 61.111 0.00 0.00 0.00 4.93
835 850 3.306088 GCATAATAGCCGAAGCAGAGGTA 60.306 47.826 0.00 0.00 43.56 3.08
943 972 2.886523 TCAATCAGTCAGGCACAAAAGG 59.113 45.455 0.00 0.00 0.00 3.11
1017 1066 0.651031 GCGTCGGATTTAGCTGGAAC 59.349 55.000 0.00 0.00 0.00 3.62
1258 1335 3.426159 CGGTTGATTTGGAGGAATTCACG 60.426 47.826 7.93 0.00 0.00 4.35
1284 1523 2.939103 GTTATCAGTCACATGAGCCACC 59.061 50.000 0.00 0.00 31.44 4.61
1390 1629 1.672030 CACGGGCAACAGATCTGCA 60.672 57.895 22.83 0.00 41.78 4.41
1638 1883 2.734606 TGAGTCGCAATCGGTTAAACAG 59.265 45.455 0.00 0.00 36.13 3.16
1639 1884 2.734606 CTGAGTCGCAATCGGTTAAACA 59.265 45.455 0.00 0.00 36.13 2.83
1661 1906 4.346734 ACTTGCAGCACAAAATAGATCG 57.653 40.909 0.00 0.00 37.96 3.69
1670 1915 2.030893 GCATGTTCTACTTGCAGCACAA 60.031 45.455 11.41 0.00 45.30 3.33
1761 2006 2.112998 CCCGGTCAGTATACCCTTTGA 58.887 52.381 0.00 0.00 36.03 2.69
1770 2015 1.887797 TCAATTCCCCCGGTCAGTAT 58.112 50.000 0.00 0.00 0.00 2.12
1771 2016 1.279846 GTTCAATTCCCCCGGTCAGTA 59.720 52.381 0.00 0.00 0.00 2.74
1772 2017 0.037734 GTTCAATTCCCCCGGTCAGT 59.962 55.000 0.00 0.00 0.00 3.41
1773 2018 0.328258 AGTTCAATTCCCCCGGTCAG 59.672 55.000 0.00 0.00 0.00 3.51
1774 2019 0.037590 CAGTTCAATTCCCCCGGTCA 59.962 55.000 0.00 0.00 0.00 4.02
1775 2020 1.313091 GCAGTTCAATTCCCCCGGTC 61.313 60.000 0.00 0.00 0.00 4.79
1776 2021 1.304134 GCAGTTCAATTCCCCCGGT 60.304 57.895 0.00 0.00 0.00 5.28
1777 2022 0.254747 TAGCAGTTCAATTCCCCCGG 59.745 55.000 0.00 0.00 0.00 5.73
1778 2023 2.348411 ATAGCAGTTCAATTCCCCCG 57.652 50.000 0.00 0.00 0.00 5.73
1779 2024 6.543735 ACTATTATAGCAGTTCAATTCCCCC 58.456 40.000 0.00 0.00 0.00 5.40
1780 2025 7.040409 CCAACTATTATAGCAGTTCAATTCCCC 60.040 40.741 0.00 0.00 32.72 4.81
1781 2026 7.502561 ACCAACTATTATAGCAGTTCAATTCCC 59.497 37.037 0.00 0.00 32.72 3.97
1782 2027 8.451908 ACCAACTATTATAGCAGTTCAATTCC 57.548 34.615 0.00 0.00 32.72 3.01
1785 2030 9.765795 GAGTACCAACTATTATAGCAGTTCAAT 57.234 33.333 0.00 0.00 35.56 2.57
1786 2031 8.978472 AGAGTACCAACTATTATAGCAGTTCAA 58.022 33.333 0.00 0.00 35.56 2.69
1787 2032 8.534954 AGAGTACCAACTATTATAGCAGTTCA 57.465 34.615 0.00 0.00 35.56 3.18
1938 2195 3.358118 TGCAAAATCCAGATGCAGATCA 58.642 40.909 0.00 0.00 44.52 2.92
2040 2342 2.198304 ATTGGCGGAGAAGACCCACC 62.198 60.000 0.00 0.00 0.00 4.61
2136 2451 1.282157 AGTAAGCAGCTTCGGGGATTT 59.718 47.619 12.07 0.00 0.00 2.17
2208 2523 6.655078 AAACATTGTCCAAGCTAAATCACT 57.345 33.333 0.00 0.00 0.00 3.41
2247 2562 1.337823 GCACAGCTCTTTTAGGGACGA 60.338 52.381 0.00 0.00 0.00 4.20
2433 2754 3.072468 CGCAGTTCGGGACCCCTA 61.072 66.667 4.46 0.00 33.78 3.53
2449 2772 2.080286 ACCTTCGATCCTCAAACACG 57.920 50.000 0.00 0.00 0.00 4.49
2472 2795 1.139734 CATCGTGTCCCTGTCTCCG 59.860 63.158 0.00 0.00 0.00 4.63
2494 2817 1.684734 GAGGGCTCGAACCTGGGTA 60.685 63.158 12.67 0.00 38.79 3.69
2584 2907 4.676018 GGTTTAGTCATTACGATCTCGAGC 59.324 45.833 7.81 0.00 43.02 5.03
2600 2923 5.364157 CAGGCTTAGACATCTAGGGTTTAGT 59.636 44.000 0.78 0.00 0.00 2.24
2619 2942 5.013913 AGAGGCAATCATAATCATACAGGCT 59.986 40.000 0.00 0.00 0.00 4.58
2734 3059 2.112928 TGGAAGGCAAGCTTCGCA 59.887 55.556 18.36 0.29 0.00 5.10
2830 3155 4.023137 GGGCGTCCGGGCTATATA 57.977 61.111 3.66 0.00 41.87 0.86
2884 3209 1.347707 TCGTCATTGAAGCCTGGTTCT 59.652 47.619 10.12 0.00 0.00 3.01
2920 3245 2.353011 CCTTGCAATGCCGAAGACAATT 60.353 45.455 1.53 0.00 0.00 2.32
3111 3437 2.483745 GCGGGAGGCTAAAAACGC 59.516 61.111 0.00 0.00 40.19 4.84
3164 3494 3.057876 GGACACGATCTCTGCTTCGATAT 60.058 47.826 0.00 0.00 38.67 1.63
3166 3496 1.066303 GGACACGATCTCTGCTTCGAT 59.934 52.381 0.00 0.00 38.67 3.59
3189 3519 6.744993 CCGTATTGATGAGAATCTCGTGATAG 59.255 42.308 10.07 3.52 34.92 2.08
3197 3527 4.443457 CCACACCCGTATTGATGAGAATCT 60.443 45.833 0.00 0.00 34.92 2.40


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

AutoCloner maintained by Alex Coulton.