Multiple sequence alignment - TraesCS2A01G174200

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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 TraesCS2A01G174200 chr2A 100.000 5055 0 0 1 5055 132616895 132611841 0.000000e+00 9335.0
1 TraesCS2A01G174200 chr2A 97.232 4732 127 4 327 5055 180203877 180199147 0.000000e+00 8010.0
2 TraesCS2A01G174200 chr2A 87.434 565 53 12 3756 4314 705824933 705824381 7.140000e-178 634.0
3 TraesCS2A01G174200 chr4A 97.772 4758 93 6 300 5055 29806142 29801396 0.000000e+00 8187.0
4 TraesCS2A01G174200 chr4A 95.305 1853 77 7 3206 5055 677889651 677887806 0.000000e+00 2931.0
5 TraesCS2A01G174200 chr4A 92.096 291 18 2 1 291 213229103 213228818 6.090000e-109 405.0
6 TraesCS2A01G174200 chr4A 90.378 291 24 1 1 291 213241895 213241609 3.690000e-101 379.0
7 TraesCS2A01G174200 chr4A 85.156 128 14 5 290 415 544591300 544591424 5.310000e-25 126.0
8 TraesCS2A01G174200 chr4A 88.235 85 8 2 276 358 58577647 58577731 3.220000e-17 100.0
9 TraesCS2A01G174200 chr6A 97.275 4293 113 4 766 5055 68546211 68550502 0.000000e+00 7276.0
10 TraesCS2A01G174200 chr6A 95.781 474 18 2 299 770 68533278 68533751 0.000000e+00 763.0
11 TraesCS2A01G174200 chr6A 85.787 197 23 5 363 555 576236119 576235924 2.390000e-48 204.0
12 TraesCS2A01G174200 chr6A 85.787 197 23 5 363 555 576403958 576403763 2.390000e-48 204.0
13 TraesCS2A01G174200 chr1D 96.369 4186 127 15 880 5055 468413311 468417481 0.000000e+00 6865.0
14 TraesCS2A01G174200 chr1D 92.430 568 37 4 299 861 468412755 468413321 0.000000e+00 806.0
15 TraesCS2A01G174200 chr1D 85.756 681 71 16 1502 2166 475823647 475822977 0.000000e+00 697.0
16 TraesCS2A01G174200 chr1D 82.753 632 68 24 1502 2116 475822089 475821482 4.480000e-145 525.0
17 TraesCS2A01G174200 chr1D 82.759 290 39 10 8 291 92915130 92915414 1.090000e-61 248.0
18 TraesCS2A01G174200 chr2D 94.243 3561 172 18 1503 5053 390622137 390625674 0.000000e+00 5409.0
19 TraesCS2A01G174200 chr2D 94.078 1047 49 8 4013 5055 81574413 81573376 0.000000e+00 1578.0
20 TraesCS2A01G174200 chr2D 96.489 940 33 0 2905 3844 81593689 81592750 0.000000e+00 1554.0
21 TraesCS2A01G174200 chr2D 94.324 599 33 1 2905 3503 81598992 81598395 0.000000e+00 917.0
22 TraesCS2A01G174200 chr2D 92.083 581 30 7 1503 2077 81631622 81631052 0.000000e+00 804.0
23 TraesCS2A01G174200 chr6D 93.687 2582 123 16 2481 5053 393958284 393960834 0.000000e+00 3829.0
24 TraesCS2A01G174200 chr6D 86.459 997 102 25 1732 2711 14581081 14582061 0.000000e+00 1062.0
25 TraesCS2A01G174200 chr6D 92.090 708 34 11 1503 2204 393957591 393958282 0.000000e+00 977.0
26 TraesCS2A01G174200 chr6D 86.393 463 58 3 1907 2367 14580429 14580888 7.560000e-138 501.0
27 TraesCS2A01G174200 chr5A 93.934 1154 63 5 3908 5055 219234270 219235422 0.000000e+00 1736.0
28 TraesCS2A01G174200 chr5A 92.664 886 62 2 623 1506 219232183 219233067 0.000000e+00 1273.0
29 TraesCS2A01G174200 chr5A 92.784 291 18 1 1 291 146433769 146434056 7.830000e-113 418.0
30 TraesCS2A01G174200 chr5A 92.440 291 19 1 1 291 146419107 146419394 3.640000e-111 412.0
31 TraesCS2A01G174200 chr5A 88.462 286 26 7 8 291 259955730 259956010 6.270000e-89 339.0
32 TraesCS2A01G174200 chr5A 93.182 220 14 1 3519 3737 401725734 401725953 6.310000e-84 322.0
33 TraesCS2A01G174200 chr5A 100.000 52 0 0 1503 1554 648915467 648915518 4.170000e-16 97.1
34 TraesCS2A01G174200 chr5A 83.824 68 4 6 491 555 243810946 243810883 1.970000e-04 58.4
35 TraesCS2A01G174200 chr7B 93.588 1154 54 13 3908 5055 301889963 301891102 0.000000e+00 1703.0
36 TraesCS2A01G174200 chr7B 92.889 886 60 2 623 1506 301887876 301888760 0.000000e+00 1284.0
37 TraesCS2A01G174200 chr7A 87.054 1344 144 17 3734 5055 95973933 95975268 0.000000e+00 1491.0
38 TraesCS2A01G174200 chr7A 86.791 1340 137 23 3734 5055 104997932 104996615 0.000000e+00 1458.0
39 TraesCS2A01G174200 chr7A 83.118 853 100 27 2726 3568 95972441 95973259 0.000000e+00 737.0
40 TraesCS2A01G174200 chrUn 92.542 885 61 4 623 1506 195343467 195344347 0.000000e+00 1264.0
41 TraesCS2A01G174200 chrUn 92.369 747 54 2 623 1367 350819238 350818493 0.000000e+00 1061.0
42 TraesCS2A01G174200 chrUn 92.369 747 54 2 623 1367 350841958 350841213 0.000000e+00 1061.0
43 TraesCS2A01G174200 chrUn 85.787 197 23 5 363 555 477837834 477838029 2.390000e-48 204.0
44 TraesCS2A01G174200 chr3A 88.356 292 32 2 1 291 278242620 278242330 2.900000e-92 350.0
45 TraesCS2A01G174200 chr3A 88.316 291 30 2 1 291 278250555 278250269 3.750000e-91 346.0
46 TraesCS2A01G174200 chr7D 82.192 292 40 9 6 291 168908422 168908707 1.820000e-59 241.0
47 TraesCS2A01G174200 chr6B 79.851 268 34 14 290 552 50403380 50403632 1.450000e-40 178.0
48 TraesCS2A01G174200 chr5B 83.249 197 28 5 363 555 237129155 237129350 5.200000e-40 176.0
49 TraesCS2A01G174200 chr5B 84.252 127 19 1 289 414 697964365 697964239 6.870000e-24 122.0
50 TraesCS2A01G174200 chr1B 84.328 134 15 5 285 414 495967080 495967211 5.310000e-25 126.0
51 TraesCS2A01G174200 chr1B 77.778 180 32 8 291 467 518905017 518904843 2.490000e-18 104.0
52 TraesCS2A01G174200 chr1A 100.000 52 0 0 1503 1554 96748151 96748100 4.170000e-16 97.1


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 TraesCS2A01G174200 chr2A 132611841 132616895 5054 True 9335.0 9335 100.0000 1 5055 1 chr2A.!!$R1 5054
1 TraesCS2A01G174200 chr2A 180199147 180203877 4730 True 8010.0 8010 97.2320 327 5055 1 chr2A.!!$R2 4728
2 TraesCS2A01G174200 chr2A 705824381 705824933 552 True 634.0 634 87.4340 3756 4314 1 chr2A.!!$R3 558
3 TraesCS2A01G174200 chr4A 29801396 29806142 4746 True 8187.0 8187 97.7720 300 5055 1 chr4A.!!$R1 4755
4 TraesCS2A01G174200 chr4A 677887806 677889651 1845 True 2931.0 2931 95.3050 3206 5055 1 chr4A.!!$R4 1849
5 TraesCS2A01G174200 chr6A 68546211 68550502 4291 False 7276.0 7276 97.2750 766 5055 1 chr6A.!!$F2 4289
6 TraesCS2A01G174200 chr1D 468412755 468417481 4726 False 3835.5 6865 94.3995 299 5055 2 chr1D.!!$F2 4756
7 TraesCS2A01G174200 chr1D 475821482 475823647 2165 True 611.0 697 84.2545 1502 2166 2 chr1D.!!$R1 664
8 TraesCS2A01G174200 chr2D 390622137 390625674 3537 False 5409.0 5409 94.2430 1503 5053 1 chr2D.!!$F1 3550
9 TraesCS2A01G174200 chr2D 81573376 81574413 1037 True 1578.0 1578 94.0780 4013 5055 1 chr2D.!!$R1 1042
10 TraesCS2A01G174200 chr2D 81592750 81593689 939 True 1554.0 1554 96.4890 2905 3844 1 chr2D.!!$R2 939
11 TraesCS2A01G174200 chr2D 81598395 81598992 597 True 917.0 917 94.3240 2905 3503 1 chr2D.!!$R3 598
12 TraesCS2A01G174200 chr2D 81631052 81631622 570 True 804.0 804 92.0830 1503 2077 1 chr2D.!!$R4 574
13 TraesCS2A01G174200 chr6D 393957591 393960834 3243 False 2403.0 3829 92.8885 1503 5053 2 chr6D.!!$F2 3550
14 TraesCS2A01G174200 chr6D 14580429 14582061 1632 False 781.5 1062 86.4260 1732 2711 2 chr6D.!!$F1 979
15 TraesCS2A01G174200 chr5A 219232183 219235422 3239 False 1504.5 1736 93.2990 623 5055 2 chr5A.!!$F6 4432
16 TraesCS2A01G174200 chr7B 301887876 301891102 3226 False 1493.5 1703 93.2385 623 5055 2 chr7B.!!$F1 4432
17 TraesCS2A01G174200 chr7A 104996615 104997932 1317 True 1458.0 1458 86.7910 3734 5055 1 chr7A.!!$R1 1321
18 TraesCS2A01G174200 chr7A 95972441 95975268 2827 False 1114.0 1491 85.0860 2726 5055 2 chr7A.!!$F1 2329
19 TraesCS2A01G174200 chrUn 195343467 195344347 880 False 1264.0 1264 92.5420 623 1506 1 chrUn.!!$F1 883
20 TraesCS2A01G174200 chrUn 350818493 350819238 745 True 1061.0 1061 92.3690 623 1367 1 chrUn.!!$R1 744
21 TraesCS2A01G174200 chrUn 350841213 350841958 745 True 1061.0 1061 92.3690 623 1367 1 chrUn.!!$R2 744

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
203 204 0.605589 GAACCCAGTTTCGGTCCAGG 60.606 60.000 0.00 0.0 31.48 4.45 F
871 879 0.833287 CTCCACATCCCCAAGACGAT 59.167 55.000 0.00 0.0 0.00 3.73 F
1023 1031 0.179176 CTCAGTCGGACTCAAGAGCG 60.179 60.000 7.89 0.0 0.00 5.03 F
2013 3198 1.211457 AGAAGCATCCAATCTCGCCTT 59.789 47.619 0.00 0.0 0.00 4.35 F
2981 4192 0.383231 CGCTGGGGCAATGAATTCTC 59.617 55.000 7.05 0.0 38.60 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1023 1031 0.614979 TGGTGTCCTCTAGTCCAGCC 60.615 60.000 0.00 0.00 0.00 4.85 R
2255 3443 1.133668 GGCTATTCCATGGGCTCAAGT 60.134 52.381 13.02 0.00 33.43 3.16 R
2981 4192 0.532862 ACTGACTCCAACGCACAAGG 60.533 55.000 0.00 0.00 0.00 3.61 R
3153 4376 4.668576 TGTTGAAATCGAGCTAGCTTTG 57.331 40.909 20.42 14.82 0.00 2.77 R
4471 6416 7.663493 TGTGGATACTACACAATCACAAAATGA 59.337 33.333 0.00 0.00 45.05 2.57 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
17 18 4.619227 CGTGTGGTGCGGGAGGTT 62.619 66.667 0.00 0.00 0.00 3.50
18 19 2.978010 GTGTGGTGCGGGAGGTTG 60.978 66.667 0.00 0.00 0.00 3.77
19 20 4.263572 TGTGGTGCGGGAGGTTGG 62.264 66.667 0.00 0.00 0.00 3.77
23 24 4.717313 GTGCGGGAGGTTGGGGAC 62.717 72.222 0.00 0.00 0.00 4.46
29 30 4.410400 GAGGTTGGGGACGGCCTG 62.410 72.222 7.57 0.00 37.23 4.85
30 31 4.974438 AGGTTGGGGACGGCCTGA 62.974 66.667 7.57 0.00 36.01 3.86
31 32 3.728373 GGTTGGGGACGGCCTGAT 61.728 66.667 7.57 0.00 0.00 2.90
33 34 3.727258 TTGGGGACGGCCTGATGG 61.727 66.667 7.57 0.00 0.00 3.51
37 38 2.438434 GGACGGCCTGATGGGTTG 60.438 66.667 0.00 0.00 37.43 3.77
38 39 2.438434 GACGGCCTGATGGGTTGG 60.438 66.667 0.00 0.00 37.43 3.77
39 40 3.995506 GACGGCCTGATGGGTTGGG 62.996 68.421 0.00 0.00 37.43 4.12
61 62 4.047059 CCTGGCAGCGGCAACAAG 62.047 66.667 11.88 2.26 43.71 3.16
62 63 2.979676 CTGGCAGCGGCAACAAGA 60.980 61.111 11.88 0.00 43.71 3.02
63 64 2.974489 CTGGCAGCGGCAACAAGAG 61.974 63.158 11.88 0.00 43.71 2.85
64 65 3.741476 GGCAGCGGCAACAAGAGG 61.741 66.667 11.88 0.00 43.71 3.69
67 68 2.037136 CAGCGGCAACAAGAGGAGG 61.037 63.158 1.45 0.00 0.00 4.30
68 69 2.747855 GCGGCAACAAGAGGAGGG 60.748 66.667 0.00 0.00 0.00 4.30
69 70 2.045926 CGGCAACAAGAGGAGGGG 60.046 66.667 0.00 0.00 0.00 4.79
70 71 2.592993 CGGCAACAAGAGGAGGGGA 61.593 63.158 0.00 0.00 0.00 4.81
71 72 1.301293 GGCAACAAGAGGAGGGGAG 59.699 63.158 0.00 0.00 0.00 4.30
73 74 1.078848 CAACAAGAGGAGGGGAGCG 60.079 63.158 0.00 0.00 0.00 5.03
74 75 1.229209 AACAAGAGGAGGGGAGCGA 60.229 57.895 0.00 0.00 0.00 4.93
76 77 2.042435 AAGAGGAGGGGAGCGAGG 60.042 66.667 0.00 0.00 0.00 4.63
77 78 3.687828 AAGAGGAGGGGAGCGAGGG 62.688 68.421 0.00 0.00 0.00 4.30
78 79 4.467107 GAGGAGGGGAGCGAGGGT 62.467 72.222 0.00 0.00 0.00 4.34
92 93 4.388499 GGGTGGGCGTGTCACGAT 62.388 66.667 28.83 0.00 46.05 3.73
94 95 3.179265 GTGGGCGTGTCACGATCG 61.179 66.667 28.83 14.88 46.05 3.69
96 97 2.879462 GGGCGTGTCACGATCGAC 60.879 66.667 28.83 11.27 46.05 4.20
98 99 3.238241 GCGTGTCACGATCGACCG 61.238 66.667 28.83 15.81 46.05 4.79
99 100 2.477396 CGTGTCACGATCGACCGA 59.523 61.111 24.34 12.15 46.05 4.69
107 108 2.026301 GATCGACCGAGCGGAAGG 59.974 66.667 16.83 4.26 38.96 3.46
140 141 2.361610 CGCTGGGATGTTGGCCTT 60.362 61.111 3.32 0.00 0.00 4.35
142 143 2.353610 GCTGGGATGTTGGCCTTGG 61.354 63.158 3.32 0.00 0.00 3.61
200 201 3.961729 CGAACCCAGTTTCGGTCC 58.038 61.111 0.00 0.00 43.79 4.46
201 202 1.070105 CGAACCCAGTTTCGGTCCA 59.930 57.895 0.00 0.00 43.79 4.02
202 203 0.949105 CGAACCCAGTTTCGGTCCAG 60.949 60.000 0.00 0.00 43.79 3.86
203 204 0.605589 GAACCCAGTTTCGGTCCAGG 60.606 60.000 0.00 0.00 31.48 4.45
204 205 2.359975 CCCAGTTTCGGTCCAGGC 60.360 66.667 0.00 0.00 0.00 4.85
205 206 2.750350 CCAGTTTCGGTCCAGGCT 59.250 61.111 0.00 0.00 0.00 4.58
206 207 1.672356 CCAGTTTCGGTCCAGGCTG 60.672 63.158 7.75 7.75 0.00 4.85
207 208 2.032681 AGTTTCGGTCCAGGCTGC 59.967 61.111 9.56 0.00 0.00 5.25
208 209 3.423154 GTTTCGGTCCAGGCTGCG 61.423 66.667 9.56 7.88 0.00 5.18
209 210 3.936203 TTTCGGTCCAGGCTGCGT 61.936 61.111 9.56 0.00 0.00 5.24
210 211 4.680237 TTCGGTCCAGGCTGCGTG 62.680 66.667 14.97 14.97 0.00 5.34
224 225 4.605967 CGTGCGGCGTTGCTTGTT 62.606 61.111 9.37 0.00 35.36 2.83
225 226 2.278531 GTGCGGCGTTGCTTGTTT 60.279 55.556 9.37 0.00 35.36 2.83
226 227 1.876263 GTGCGGCGTTGCTTGTTTT 60.876 52.632 9.37 0.00 35.36 2.43
227 228 1.153745 TGCGGCGTTGCTTGTTTTT 60.154 47.368 9.37 0.00 35.36 1.94
438 441 1.128200 GGCTGTTTTCCAAAACCCCT 58.872 50.000 11.50 0.00 45.82 4.79
443 446 3.445987 TGTTTTCCAAAACCCCTCTGTT 58.554 40.909 11.50 0.00 45.82 3.16
536 539 2.441532 GGAGGTGACCGATCCCGA 60.442 66.667 0.00 0.00 38.22 5.14
717 725 1.743321 CTCGATCTGCCCCTCCTGAC 61.743 65.000 0.00 0.00 0.00 3.51
719 727 1.690633 GATCTGCCCCTCCTGACCA 60.691 63.158 0.00 0.00 0.00 4.02
770 778 2.283894 TCTCTCCTCAAGGCGCCA 60.284 61.111 31.54 7.07 34.44 5.69
782 790 4.241555 GCGCCACCATCCCGAGAT 62.242 66.667 0.00 0.00 0.00 2.75
815 823 4.147449 CGCTGGAGGTGATCGCCA 62.147 66.667 26.71 11.52 43.16 5.69
845 853 1.072159 GCAGGCTCAACAGTCACCT 59.928 57.895 0.00 0.00 0.00 4.00
871 879 0.833287 CTCCACATCCCCAAGACGAT 59.167 55.000 0.00 0.00 0.00 3.73
889 897 2.460669 GATGTGGAAGAAGCCCCAATT 58.539 47.619 0.00 0.00 33.69 2.32
1023 1031 0.179176 CTCAGTCGGACTCAAGAGCG 60.179 60.000 7.89 0.00 0.00 5.03
1056 1064 2.353704 GGACACCATCGTCTTCACATCA 60.354 50.000 0.00 0.00 36.12 3.07
1240 1248 2.554344 GCAACAAGGGATGGTACCTGAA 60.554 50.000 14.36 0.00 38.63 3.02
1690 2860 7.739498 AGCAGACCTAAAATTTCGAAAACTA 57.261 32.000 15.66 5.82 0.00 2.24
2013 3198 1.211457 AGAAGCATCCAATCTCGCCTT 59.789 47.619 0.00 0.00 0.00 4.35
2070 3256 1.301401 CTCCACACTTCGCCGGAAA 60.301 57.895 5.05 0.00 0.00 3.13
2174 3362 9.461312 AACATATTACCTGCATCTTTTGTTCTA 57.539 29.630 0.00 0.00 0.00 2.10
2255 3443 6.428083 TGGAATAGTTAGTGACCAGTGAAA 57.572 37.500 0.00 0.00 0.00 2.69
2525 3733 5.148651 AGGGTGTAAGCTACAGTAGTTTG 57.851 43.478 17.55 0.00 39.77 2.93
2532 3743 7.376072 GTGTAAGCTACAGTAGTTTGCTTTTTG 59.624 37.037 20.59 0.00 42.29 2.44
2664 3875 2.698274 ACTACAGTGTGATGTGGTGTCA 59.302 45.455 5.88 0.00 42.52 3.58
2752 3963 2.625617 CCTTCCTCTGTTCTAGGCCTCT 60.626 54.545 9.68 0.00 33.84 3.69
2849 4060 2.419011 TACGGGTTGTGGGCATGCTT 62.419 55.000 18.92 0.00 0.00 3.91
2981 4192 0.383231 CGCTGGGGCAATGAATTCTC 59.617 55.000 7.05 0.00 38.60 2.87
3074 4293 2.229784 CCAGTGATCAAAGTTGGAAGCC 59.770 50.000 0.00 0.00 0.00 4.35
3097 4320 5.242434 CCAATGTAAGCTACACAGTTACCA 58.758 41.667 7.13 0.00 42.23 3.25
3153 4376 2.423446 TGGGGCGTAGGAATTTTACC 57.577 50.000 0.00 0.00 0.00 2.85
3313 4537 4.958581 AGTGGAAGATCATGGGGAAATTTC 59.041 41.667 9.83 9.83 0.00 2.17
3767 5570 4.938226 AGGTGTACTGCTCTAAATTGCTTC 59.062 41.667 0.00 0.00 0.00 3.86
3928 5847 8.780249 TGCTAACTAGGATGTTTACTTTTGAAC 58.220 33.333 0.00 0.00 0.00 3.18
3996 5915 8.667076 TTAAACTTTCTTAGCGTAAAAGGTCT 57.333 30.769 8.19 0.00 34.94 3.85
4333 6267 1.202940 ACAAGCCTCTGTTTTCCCTCC 60.203 52.381 0.00 0.00 0.00 4.30
4471 6416 2.328099 GCGCTGGCTTGCAGTACTT 61.328 57.895 0.00 0.00 35.83 2.24
4529 6556 1.523758 CTTAAGTCCGTTGCCTTGCT 58.476 50.000 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.978010 CAACCTCCCGCACCACAC 60.978 66.667 0.00 0.00 0.00 3.82
12 13 4.410400 CAGGCCGTCCCCAACCTC 62.410 72.222 0.00 0.00 0.00 3.85
13 14 4.974438 TCAGGCCGTCCCCAACCT 62.974 66.667 0.00 0.00 0.00 3.50
14 15 3.728373 ATCAGGCCGTCCCCAACC 61.728 66.667 0.00 0.00 0.00 3.77
16 17 3.727258 CCATCAGGCCGTCCCCAA 61.727 66.667 0.00 0.00 0.00 4.12
19 20 3.728373 AACCCATCAGGCCGTCCC 61.728 66.667 0.00 0.00 40.58 4.46
20 21 2.438434 CAACCCATCAGGCCGTCC 60.438 66.667 0.00 0.00 40.58 4.79
21 22 2.438434 CCAACCCATCAGGCCGTC 60.438 66.667 0.00 0.00 40.58 4.79
22 23 4.047125 CCCAACCCATCAGGCCGT 62.047 66.667 0.00 0.00 40.58 5.68
44 45 4.047059 CTTGTTGCCGCTGCCAGG 62.047 66.667 0.00 0.00 36.33 4.45
45 46 2.974489 CTCTTGTTGCCGCTGCCAG 61.974 63.158 0.00 0.00 36.33 4.85
46 47 2.979676 CTCTTGTTGCCGCTGCCA 60.980 61.111 0.00 0.00 36.33 4.92
47 48 3.741476 CCTCTTGTTGCCGCTGCC 61.741 66.667 0.00 0.00 36.33 4.85
49 50 2.037136 CCTCCTCTTGTTGCCGCTG 61.037 63.158 0.00 0.00 0.00 5.18
51 52 2.747855 CCCTCCTCTTGTTGCCGC 60.748 66.667 0.00 0.00 0.00 6.53
53 54 1.301293 CTCCCCTCCTCTTGTTGCC 59.699 63.158 0.00 0.00 0.00 4.52
54 55 1.377856 GCTCCCCTCCTCTTGTTGC 60.378 63.158 0.00 0.00 0.00 4.17
55 56 1.078848 CGCTCCCCTCCTCTTGTTG 60.079 63.158 0.00 0.00 0.00 3.33
56 57 1.229209 TCGCTCCCCTCCTCTTGTT 60.229 57.895 0.00 0.00 0.00 2.83
57 58 1.684049 CTCGCTCCCCTCCTCTTGT 60.684 63.158 0.00 0.00 0.00 3.16
58 59 2.430610 CCTCGCTCCCCTCCTCTTG 61.431 68.421 0.00 0.00 0.00 3.02
59 60 2.042435 CCTCGCTCCCCTCCTCTT 60.042 66.667 0.00 0.00 0.00 2.85
60 61 4.150454 CCCTCGCTCCCCTCCTCT 62.150 72.222 0.00 0.00 0.00 3.69
61 62 4.467107 ACCCTCGCTCCCCTCCTC 62.467 72.222 0.00 0.00 0.00 3.71
62 63 4.787280 CACCCTCGCTCCCCTCCT 62.787 72.222 0.00 0.00 0.00 3.69
76 77 2.813908 GATCGTGACACGCCCACC 60.814 66.667 22.99 6.19 42.21 4.61
77 78 3.179265 CGATCGTGACACGCCCAC 61.179 66.667 22.99 12.07 42.21 4.61
78 79 3.366915 TCGATCGTGACACGCCCA 61.367 61.111 22.99 6.72 42.21 5.36
80 81 2.879462 GGTCGATCGTGACACGCC 60.879 66.667 22.99 13.86 42.21 5.68
81 82 3.238241 CGGTCGATCGTGACACGC 61.238 66.667 22.99 9.21 42.21 5.34
83 84 1.868251 GCTCGGTCGATCGTGACAC 60.868 63.158 23.08 5.52 40.72 3.67
84 85 2.483745 GCTCGGTCGATCGTGACA 59.516 61.111 23.08 0.28 40.72 3.58
86 87 3.872728 CCGCTCGGTCGATCGTGA 61.873 66.667 23.08 10.70 32.67 4.35
87 88 3.391160 TTCCGCTCGGTCGATCGTG 62.391 63.158 19.01 17.09 32.67 4.35
88 89 3.109612 CTTCCGCTCGGTCGATCGT 62.110 63.158 19.01 0.00 32.67 3.73
90 91 2.026301 CCTTCCGCTCGGTCGATC 59.974 66.667 8.28 0.00 36.47 3.69
91 92 4.208686 GCCTTCCGCTCGGTCGAT 62.209 66.667 8.28 0.00 36.47 3.59
123 124 2.361610 AAGGCCAACATCCCAGCG 60.362 61.111 5.01 0.00 0.00 5.18
124 125 2.353610 CCAAGGCCAACATCCCAGC 61.354 63.158 5.01 0.00 0.00 4.85
127 128 3.076916 GCCCAAGGCCAACATCCC 61.077 66.667 5.01 0.00 44.06 3.85
184 185 0.605589 CCTGGACCGAAACTGGGTTC 60.606 60.000 0.00 0.00 38.07 3.62
185 186 1.454539 CCTGGACCGAAACTGGGTT 59.545 57.895 0.00 0.00 38.07 4.11
187 188 2.359975 GCCTGGACCGAAACTGGG 60.360 66.667 0.00 0.00 0.00 4.45
188 189 1.672356 CAGCCTGGACCGAAACTGG 60.672 63.158 0.00 0.00 0.00 4.00
189 190 2.328099 GCAGCCTGGACCGAAACTG 61.328 63.158 0.00 0.00 0.00 3.16
191 192 3.423154 CGCAGCCTGGACCGAAAC 61.423 66.667 0.00 0.00 0.00 2.78
192 193 3.936203 ACGCAGCCTGGACCGAAA 61.936 61.111 0.00 0.00 0.00 3.46
208 209 1.417577 AAAAACAAGCAACGCCGCAC 61.418 50.000 0.00 0.00 0.00 5.34
209 210 1.153745 AAAAACAAGCAACGCCGCA 60.154 47.368 0.00 0.00 0.00 5.69
210 211 3.699671 AAAAACAAGCAACGCCGC 58.300 50.000 0.00 0.00 0.00 6.53
233 234 5.366482 AAGGCCAATTTAGTGTTTGGTTT 57.634 34.783 5.01 0.00 43.54 3.27
234 235 6.487299 TTAAGGCCAATTTAGTGTTTGGTT 57.513 33.333 5.01 0.00 43.54 3.67
235 236 6.487299 TTTAAGGCCAATTTAGTGTTTGGT 57.513 33.333 5.01 0.00 43.54 3.67
236 237 9.665719 ATTATTTAAGGCCAATTTAGTGTTTGG 57.334 29.630 5.01 0.00 44.29 3.28
286 287 9.057089 CGTGCTTTATTATTAGGGAGAGATTTT 57.943 33.333 0.00 0.00 0.00 1.82
289 290 6.497259 TCCGTGCTTTATTATTAGGGAGAGAT 59.503 38.462 0.00 0.00 0.00 2.75
290 291 5.836898 TCCGTGCTTTATTATTAGGGAGAGA 59.163 40.000 0.00 0.00 0.00 3.10
291 292 6.097915 TCCGTGCTTTATTATTAGGGAGAG 57.902 41.667 0.00 0.00 0.00 3.20
292 293 6.681729 ATCCGTGCTTTATTATTAGGGAGA 57.318 37.500 0.00 0.00 0.00 3.71
293 294 6.934645 TCAATCCGTGCTTTATTATTAGGGAG 59.065 38.462 0.00 0.00 0.00 4.30
295 296 6.710744 ACTCAATCCGTGCTTTATTATTAGGG 59.289 38.462 0.00 0.00 0.00 3.53
297 298 8.594881 AGACTCAATCCGTGCTTTATTATTAG 57.405 34.615 0.00 0.00 0.00 1.73
443 446 5.863560 AACTGCGGGTTGAATATTGGATACA 60.864 40.000 0.00 0.00 40.42 2.29
536 539 4.175489 CACCGGATCGAGCGTCGT 62.175 66.667 9.46 0.00 41.35 4.34
770 778 3.157252 AGCGCATCTCGGGATGGT 61.157 61.111 26.15 4.35 46.77 3.55
815 823 2.045926 GCCTGCCAGGTCGACAAT 60.046 61.111 18.91 1.75 37.80 2.71
871 879 1.631405 CAATTGGGGCTTCTTCCACA 58.369 50.000 0.00 0.00 37.86 4.17
909 917 2.282816 CCCCATTGGTGCCGTTGA 60.283 61.111 1.20 0.00 0.00 3.18
920 928 0.722676 TCTACCTCCCAGACCCCATT 59.277 55.000 0.00 0.00 0.00 3.16
1023 1031 0.614979 TGGTGTCCTCTAGTCCAGCC 60.615 60.000 0.00 0.00 0.00 4.85
1056 1064 8.501580 CGCTCATCAAATTCAATAGACATATGT 58.498 33.333 8.43 8.43 0.00 2.29
1307 1315 2.481471 GGCCGCCCTAATTGAGCAC 61.481 63.158 0.00 0.00 0.00 4.40
1604 2774 3.054139 AGGAGCTACATGCATTTGAAGGA 60.054 43.478 0.00 0.00 45.94 3.36
2013 3198 1.894282 TGTTCCGGCAATGCGTCAA 60.894 52.632 0.00 0.00 0.00 3.18
2070 3256 5.305128 TCAAATGGAAAACCTGCAGAAGAAT 59.695 36.000 17.39 0.00 0.00 2.40
2174 3362 5.468540 TTCATCGCATAGCCTAGTACAAT 57.531 39.130 0.00 0.00 0.00 2.71
2255 3443 1.133668 GGCTATTCCATGGGCTCAAGT 60.134 52.381 13.02 0.00 33.43 3.16
2525 3733 5.126396 AGTGCCTTATCAGAACAAAAAGC 57.874 39.130 0.00 0.00 0.00 3.51
2532 3743 8.839310 ACATATATCAAGTGCCTTATCAGAAC 57.161 34.615 0.00 0.00 0.00 3.01
2752 3963 1.228894 AGGAGTGAGGCAAGACGGA 60.229 57.895 0.00 0.00 0.00 4.69
2849 4060 1.699634 CTTTTGTCTCCTCCAGGTCCA 59.300 52.381 0.00 0.00 36.34 4.02
2981 4192 0.532862 ACTGACTCCAACGCACAAGG 60.533 55.000 0.00 0.00 0.00 3.61
3074 4293 5.242434 TGGTAACTGTGTAGCTTACATTGG 58.758 41.667 0.00 0.00 38.21 3.16
3097 4320 7.176589 TGGAAAAACCAACACAAGTAAAGAT 57.823 32.000 0.00 0.00 46.75 2.40
3153 4376 4.668576 TGTTGAAATCGAGCTAGCTTTG 57.331 40.909 20.42 14.82 0.00 2.77
3272 4496 6.968263 TCCACTTTTATTTGTCCATGAACA 57.032 33.333 0.00 0.00 0.00 3.18
3928 5847 8.345565 ACTGCTTTCACAAGTAATGTCTAAAAG 58.654 33.333 0.00 0.00 41.46 2.27
3967 5886 9.887406 CCTTTTACGCTAAGAAAGTTTAATGAA 57.113 29.630 0.00 0.00 0.00 2.57
4471 6416 7.663493 TGTGGATACTACACAATCACAAAATGA 59.337 33.333 0.00 0.00 45.05 2.57


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

AutoCloner maintained by Alex Coulton.