Multiple sequence alignment - TraesCS7D01G186300

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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 TraesCS7D01G186300 chr7D 100.000 2768 0 0 1 2768 139082678 139085445 0.000000e+00 5112.0
1 TraesCS7D01G186300 chr7D 82.546 2074 248 51 1 2038 548096732 548094737 0.000000e+00 1720.0
2 TraesCS7D01G186300 chr7D 83.600 1439 121 50 755 2162 548089302 548087948 0.000000e+00 1243.0
3 TraesCS7D01G186300 chr7D 81.361 338 44 7 2168 2496 548093446 548093119 9.840000e-65 257.0
4 TraesCS7D01G186300 chr7D 77.083 336 44 17 1845 2169 548561796 548562109 2.210000e-36 163.0
5 TraesCS7D01G186300 chr7D 93.506 77 3 2 2099 2174 548326351 548326426 2.250000e-21 113.0
6 TraesCS7D01G186300 chr7D 84.694 98 13 2 2074 2170 573970411 573970507 2.270000e-16 97.1
7 TraesCS7D01G186300 chr7D 84.286 70 9 2 520 587 363909276 363909207 1.780000e-07 67.6
8 TraesCS7D01G186300 chr7A 93.925 1432 72 6 753 2171 138982195 138983624 0.000000e+00 2148.0
9 TraesCS7D01G186300 chr7A 92.513 561 28 7 2222 2768 138983751 138984311 0.000000e+00 791.0
10 TraesCS7D01G186300 chr7A 87.368 665 65 11 803 1457 630436345 630437000 0.000000e+00 745.0
11 TraesCS7D01G186300 chr7A 89.147 258 25 1 1550 1807 631954241 631953987 4.450000e-83 318.0
12 TraesCS7D01G186300 chr7A 93.182 176 12 0 1847 2022 169953674 169953499 2.730000e-65 259.0
13 TraesCS7D01G186300 chr7A 95.000 60 3 0 2167 2226 631848784 631848725 8.160000e-16 95.3
14 TraesCS7D01G186300 chr7A 75.573 131 25 5 462 589 103211456 103211582 1.070000e-04 58.4
15 TraesCS7D01G186300 chr7B 81.110 2234 268 69 1 2163 591074138 591071988 0.000000e+00 1646.0
16 TraesCS7D01G186300 chr7B 82.538 1466 117 49 586 2022 589916110 589917465 0.000000e+00 1160.0
17 TraesCS7D01G186300 chr7B 82.691 1375 137 47 799 2151 591577022 591578317 0.000000e+00 1127.0
18 TraesCS7D01G186300 chr7B 82.977 1122 120 36 435 1516 591160026 591158936 0.000000e+00 948.0
19 TraesCS7D01G186300 chr7B 89.481 751 49 13 755 1483 591279458 591278716 0.000000e+00 922.0
20 TraesCS7D01G186300 chr7B 88.149 751 59 15 755 1483 591228329 591227587 0.000000e+00 867.0
21 TraesCS7D01G186300 chr7B 83.645 642 55 22 1529 2162 591147745 591147146 2.410000e-155 558.0
22 TraesCS7D01G186300 chr7B 83.022 642 59 24 1529 2162 591227580 591226981 1.130000e-148 536.0
23 TraesCS7D01G186300 chr7B 83.022 642 59 22 1529 2162 591278709 591278110 1.130000e-148 536.0
24 TraesCS7D01G186300 chr7B 77.695 269 40 9 2314 2570 591147003 591146743 2.220000e-31 147.0
25 TraesCS7D01G186300 chr7B 92.208 77 4 2 2099 2174 348751317 348751242 1.050000e-19 108.0
26 TraesCS7D01G186300 chr7B 78.947 171 23 5 2308 2466 591277975 591277806 1.360000e-18 104.0
27 TraesCS7D01G186300 chr7B 77.838 185 28 7 2308 2480 591226846 591226663 4.880000e-18 102.0
28 TraesCS7D01G186300 chr7B 76.389 216 32 13 1976 2173 633002260 633002474 6.310000e-17 99.0
29 TraesCS7D01G186300 chr7B 89.610 77 5 3 2099 2174 591055662 591055588 8.160000e-16 95.3
30 TraesCS7D01G186300 chr7B 93.443 61 3 1 2167 2226 591055538 591055478 3.800000e-14 89.8
31 TraesCS7D01G186300 chr7B 93.333 60 3 1 2167 2226 569480242 569480184 1.370000e-13 87.9
32 TraesCS7D01G186300 chr2B 92.105 76 4 2 2099 2173 49036099 49036173 3.770000e-19 106.0
33 TraesCS7D01G186300 chr2B 89.610 77 6 2 2099 2174 33601710 33601785 2.270000e-16 97.1
34 TraesCS7D01G186300 chr2B 89.610 77 6 2 2099 2174 742367445 742367370 2.270000e-16 97.1
35 TraesCS7D01G186300 chr5D 79.798 99 16 4 502 600 412622747 412622653 4.950000e-08 69.4


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 TraesCS7D01G186300 chr7D 139082678 139085445 2767 False 5112.000000 5112 100.000000 1 2768 1 chr7D.!!$F1 2767
1 TraesCS7D01G186300 chr7D 548087948 548096732 8784 True 1073.333333 1720 82.502333 1 2496 3 chr7D.!!$R2 2495
2 TraesCS7D01G186300 chr7A 138982195 138984311 2116 False 1469.500000 2148 93.219000 753 2768 2 chr7A.!!$F3 2015
3 TraesCS7D01G186300 chr7A 630436345 630437000 655 False 745.000000 745 87.368000 803 1457 1 chr7A.!!$F2 654
4 TraesCS7D01G186300 chr7B 591071988 591074138 2150 True 1646.000000 1646 81.110000 1 2163 1 chr7B.!!$R3 2162
5 TraesCS7D01G186300 chr7B 589916110 589917465 1355 False 1160.000000 1160 82.538000 586 2022 1 chr7B.!!$F1 1436
6 TraesCS7D01G186300 chr7B 591577022 591578317 1295 False 1127.000000 1127 82.691000 799 2151 1 chr7B.!!$F2 1352
7 TraesCS7D01G186300 chr7B 591158936 591160026 1090 True 948.000000 948 82.977000 435 1516 1 chr7B.!!$R4 1081
8 TraesCS7D01G186300 chr7B 591277806 591279458 1652 True 520.666667 922 83.816667 755 2466 3 chr7B.!!$R8 1711
9 TraesCS7D01G186300 chr7B 591226663 591228329 1666 True 501.666667 867 83.003000 755 2480 3 chr7B.!!$R7 1725
10 TraesCS7D01G186300 chr7B 591146743 591147745 1002 True 352.500000 558 80.670000 1529 2570 2 chr7B.!!$R6 1041

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
148 152 0.033920 CGATGAGAATGGCCGGATCA 59.966 55.0 5.05 2.18 0.0 2.92 F
150 154 0.109342 ATGAGAATGGCCGGATCACC 59.891 55.0 5.05 0.00 0.0 4.02 F
402 418 0.321653 GTGGCGTTTGAGATGGAGGT 60.322 55.0 0.00 0.00 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1628 8432 0.249398 TTTAGCGTCCTCTGCTTCCC 59.751 55.000 0.00 0.0 43.71 3.97 R
1753 8560 1.849039 AGAGCCCTAAGCCATGTGAAT 59.151 47.619 0.00 0.0 45.47 2.57 R
2278 9193 1.337167 GCCAGTTCAAACCATGGAAGC 60.337 52.381 21.47 2.9 34.60 3.86 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
37 38 0.036164 CGTGTTGAGGATGGAACCCA 59.964 55.000 0.00 0.00 38.19 4.51
45 46 0.748450 GGATGGAACCCATACGACGA 59.252 55.000 0.00 0.00 45.26 4.20
48 49 1.875364 GGAACCCATACGACGACGC 60.875 63.158 7.30 0.00 43.96 5.19
49 50 1.875364 GAACCCATACGACGACGCC 60.875 63.158 7.30 0.00 43.96 5.68
67 71 4.338539 GTCGTCGAGGTGCACCGT 62.339 66.667 29.68 18.18 42.08 4.83
90 94 3.941188 CGGATATGGCAGGCGGGT 61.941 66.667 0.00 0.00 0.00 5.28
107 111 1.217244 GTAACCGACGAGCCCATGT 59.783 57.895 0.00 0.00 0.00 3.21
140 144 2.890109 GCGGCAGCGATGAGAATGG 61.890 63.158 4.02 0.00 0.00 3.16
145 149 2.108976 GCGATGAGAATGGCCGGA 59.891 61.111 5.05 0.00 0.00 5.14
148 152 0.033920 CGATGAGAATGGCCGGATCA 59.966 55.000 5.05 2.18 0.00 2.92
150 154 0.109342 ATGAGAATGGCCGGATCACC 59.891 55.000 5.05 0.00 0.00 4.02
177 181 0.531532 CCTAGCATGAGAAGGGCACG 60.532 60.000 0.00 0.00 0.00 5.34
178 182 1.153369 TAGCATGAGAAGGGCACGC 60.153 57.895 0.00 0.00 0.00 5.34
180 184 2.758089 GCATGAGAAGGGCACGCTG 61.758 63.158 0.00 0.00 0.00 5.18
181 185 2.437359 ATGAGAAGGGCACGCTGC 60.437 61.111 1.92 1.92 44.08 5.25
203 207 0.394565 GGCCTAGGCGACAATGAGAT 59.605 55.000 27.24 0.00 43.06 2.75
217 221 3.470520 GAGATCAGTCTCCGCATCG 57.529 57.895 0.00 0.00 44.20 3.84
230 234 2.436646 CATCGGCGTTCTTGGGCT 60.437 61.111 6.85 0.00 0.00 5.19
231 235 2.436646 ATCGGCGTTCTTGGGCTG 60.437 61.111 6.85 0.00 36.88 4.85
271 275 4.223964 GCGGCGGCGACATCTTTC 62.224 66.667 36.87 10.85 0.00 2.62
274 278 2.464459 GGCGGCGACATCTTTCTGG 61.464 63.158 12.98 0.00 0.00 3.86
281 285 1.338105 CGACATCTTTCTGGTCTGCCA 60.338 52.381 0.00 0.00 43.73 4.92
283 287 1.081892 CATCTTTCTGGTCTGCCACG 58.918 55.000 0.00 0.00 40.46 4.94
294 298 1.191489 TCTGCCACGACCTTCATCCA 61.191 55.000 0.00 0.00 0.00 3.41
298 302 1.811266 CACGACCTTCATCCAGCCG 60.811 63.158 0.00 0.00 0.00 5.52
300 304 2.990479 GACCTTCATCCAGCCGGT 59.010 61.111 1.90 0.00 0.00 5.28
310 314 4.821589 CAGCCGGTCCTCTTCGCC 62.822 72.222 1.90 0.00 0.00 5.54
317 321 1.080974 GTCCTCTTCGCCGTTTCGA 60.081 57.895 0.00 0.00 36.60 3.71
372 388 2.131709 GCATGGCATGGGCAGACAT 61.132 57.895 27.48 0.00 42.43 3.06
390 406 3.894947 GTTGTTGGCCGTGGCGTT 61.895 61.111 4.53 0.00 43.06 4.84
392 408 3.417275 TTGTTGGCCGTGGCGTTTG 62.417 57.895 4.53 0.00 43.06 2.93
393 409 3.587933 GTTGGCCGTGGCGTTTGA 61.588 61.111 4.53 0.00 43.06 2.69
395 411 3.758973 TTGGCCGTGGCGTTTGAGA 62.759 57.895 4.53 0.00 43.06 3.27
402 418 0.321653 GTGGCGTTTGAGATGGAGGT 60.322 55.000 0.00 0.00 0.00 3.85
403 419 0.400213 TGGCGTTTGAGATGGAGGTT 59.600 50.000 0.00 0.00 0.00 3.50
433 449 2.980233 GGGTGCATCGCCTATGGC 60.980 66.667 0.00 0.00 46.75 4.40
454 470 1.549950 GCAAGGGTGGGAGGATTTTGA 60.550 52.381 0.00 0.00 0.00 2.69
501 517 1.019278 CCCATTGACGAACGGGTCAG 61.019 60.000 6.38 0.00 46.68 3.51
505 522 2.993264 GACGAACGGGTCAGGGGA 60.993 66.667 0.00 0.00 36.91 4.81
508 525 2.280552 CGAACGGGTCAGGGGAGAA 61.281 63.158 0.00 0.00 0.00 2.87
509 526 1.295746 GAACGGGTCAGGGGAGAAC 59.704 63.158 0.00 0.00 0.00 3.01
511 528 1.481056 AACGGGTCAGGGGAGAACAG 61.481 60.000 0.00 0.00 0.00 3.16
512 529 2.660064 CGGGTCAGGGGAGAACAGG 61.660 68.421 0.00 0.00 0.00 4.00
520 537 2.125225 GGAGAACAGGGGGAGGGT 59.875 66.667 0.00 0.00 0.00 4.34
524 541 2.928396 AACAGGGGGAGGGTGTCG 60.928 66.667 0.00 0.00 0.00 4.35
525 542 3.786866 AACAGGGGGAGGGTGTCGT 62.787 63.158 0.00 0.00 0.00 4.34
533 550 3.682292 GAGGGTGTCGTGGGCATCC 62.682 68.421 0.00 0.00 37.39 3.51
545 562 3.545481 GCATCCGCGTCGACACAG 61.545 66.667 17.16 5.66 0.00 3.66
550 567 4.337060 CGCGTCGACACAGACCCA 62.337 66.667 17.16 0.00 37.85 4.51
553 570 2.048127 GTCGACACAGACCCAGCC 60.048 66.667 11.55 0.00 35.22 4.85
573 590 1.678425 CCAAATTTGGGCCGGAAATGG 60.678 52.381 26.87 10.05 44.70 3.16
574 591 0.617935 AAATTTGGGCCGGAAATGGG 59.382 50.000 5.05 0.00 0.00 4.00
579 596 2.034999 GGCCGGAAATGGGTCACA 59.965 61.111 5.05 0.00 0.00 3.58
589 606 4.039124 GGAAATGGGTCACAACAGACAAAT 59.961 41.667 0.00 0.00 40.29 2.32
592 609 5.705609 ATGGGTCACAACAGACAAATAAC 57.294 39.130 0.00 0.00 40.29 1.89
595 612 5.596361 TGGGTCACAACAGACAAATAACAAT 59.404 36.000 0.00 0.00 40.29 2.71
599 616 7.589954 GGTCACAACAGACAAATAACAATACAC 59.410 37.037 0.00 0.00 40.29 2.90
608 625 8.763356 AGACAAATAACAATACACGTTCGTTTA 58.237 29.630 0.00 0.00 0.00 2.01
627 644 0.460284 ACGTCTCCGCATTTAGCTGG 60.460 55.000 0.00 0.00 42.61 4.85
670 691 2.186826 GGACGCGGATGAAATGGGG 61.187 63.158 12.47 0.00 0.00 4.96
675 696 3.226537 GGATGAAATGGGGCGCCC 61.227 66.667 38.57 38.57 45.71 6.13
676 697 2.123726 GATGAAATGGGGCGCCCT 60.124 61.111 42.70 25.80 45.70 5.19
691 712 0.615850 GCCCTGTTAGAGCTGACCTT 59.384 55.000 0.00 0.00 0.00 3.50
704 725 2.093658 GCTGACCTTAATGTCGGGAGAA 60.094 50.000 18.02 0.00 41.12 2.87
737 758 1.473965 GGAGGATTTGCATCTGAGCGA 60.474 52.381 0.00 0.00 37.31 4.93
738 759 2.283298 GAGGATTTGCATCTGAGCGAA 58.717 47.619 0.00 0.00 41.80 4.70
740 761 2.093288 AGGATTTGCATCTGAGCGAAGA 60.093 45.455 0.00 0.00 40.96 2.87
741 762 2.877168 GGATTTGCATCTGAGCGAAGAT 59.123 45.455 0.00 0.00 40.96 2.40
746 767 1.485397 CATCTGAGCGAAGATGGACG 58.515 55.000 18.73 0.00 46.57 4.79
868 959 1.133407 GTAGTGGAGCTCGACTTCCAG 59.867 57.143 32.38 0.00 36.35 3.86
899 1006 4.740695 GCGTACTACATCCACAAGAGAATC 59.259 45.833 0.00 0.00 0.00 2.52
912 1019 3.467374 AGAGAATCCATCGCTTTCCTC 57.533 47.619 0.00 0.00 34.10 3.71
931 1039 1.377202 GATCGCCAACCTTCTGCCA 60.377 57.895 0.00 0.00 0.00 4.92
957 1071 2.883828 CGGGACAAGAGCACCACCT 61.884 63.158 0.00 0.00 0.00 4.00
1072 1198 1.069090 GCCTTCGACTGTGTGGACA 59.931 57.895 0.00 0.00 0.00 4.02
1457 8258 2.579787 GATCACCGTCGGTCAGCG 60.580 66.667 15.67 3.19 31.02 5.18
1483 8284 1.586564 GTCTCCGCCGATTCTGACG 60.587 63.158 0.00 0.00 0.00 4.35
1522 8326 2.125552 TCATGAAGACGGCGGCAG 60.126 61.111 18.30 0.00 0.00 4.85
1523 8327 2.434884 CATGAAGACGGCGGCAGT 60.435 61.111 18.30 5.21 0.00 4.40
1525 8329 2.942796 ATGAAGACGGCGGCAGTCA 61.943 57.895 29.73 19.02 40.84 3.41
1628 8432 0.604511 AAGTTCCGCCAAGGTTACCG 60.605 55.000 0.00 0.00 41.99 4.02
1644 8448 3.764466 CGGGAAGCAGAGGACGCT 61.764 66.667 0.00 0.00 42.98 5.07
1727 8531 1.000521 CCAGCTCCATGGCCAAGAA 60.001 57.895 10.96 0.00 32.48 2.52
1728 8532 1.035932 CCAGCTCCATGGCCAAGAAG 61.036 60.000 10.96 8.51 32.48 2.85
1729 8533 1.035932 CAGCTCCATGGCCAAGAAGG 61.036 60.000 10.96 10.24 41.84 3.46
1753 8560 2.142357 CTTCGTGGTCAGGACGCAGA 62.142 60.000 0.00 0.00 32.68 4.26
1820 8627 8.139350 TCTAAACTCGTGTCATCTCACTTTTTA 58.861 33.333 0.00 0.00 36.33 1.52
1822 8629 7.730364 AACTCGTGTCATCTCACTTTTTAAT 57.270 32.000 0.00 0.00 36.33 1.40
1902 8716 1.860676 AATGCAGTTGCTTGCTTGTG 58.139 45.000 5.62 0.00 44.38 3.33
1926 8740 7.602644 GTGTGTTCTGTACATGATCTAAGGAAA 59.397 37.037 0.00 0.00 39.39 3.13
2035 8850 6.890663 AAGATGTGTTTGTGTCAAATTGTG 57.109 33.333 0.00 0.00 0.00 3.33
2111 8936 4.934001 TCTCATCTTCATGTTCAGACTTGC 59.066 41.667 0.00 0.00 32.55 4.01
2129 8961 2.823984 TGCAGTCCAAGTTGCAATTTG 58.176 42.857 23.59 23.59 46.42 2.32
2130 8962 2.429971 TGCAGTCCAAGTTGCAATTTGA 59.570 40.909 29.86 16.31 46.42 2.69
2131 8963 3.118847 TGCAGTCCAAGTTGCAATTTGAA 60.119 39.130 29.86 12.68 46.42 2.69
2137 8969 6.993902 AGTCCAAGTTGCAATTTGAATCAATT 59.006 30.769 29.86 9.93 0.00 2.32
2183 9081 3.056250 TGCTGTTTCTTGAGGTTTGCAAA 60.056 39.130 8.05 8.05 0.00 3.68
2196 9094 5.783111 AGGTTTGCAAATTGGATTGTACTC 58.217 37.500 16.21 0.00 32.80 2.59
2243 9158 4.287766 ACAACTAAAAGCTGGACTAGGG 57.712 45.455 0.00 0.00 0.00 3.53
2244 9159 3.010420 CAACTAAAAGCTGGACTAGGGC 58.990 50.000 0.00 0.00 0.00 5.19
2278 9193 6.549912 TCATCTGAGTGTCAAATCACAAAG 57.450 37.500 0.00 0.00 40.37 2.77
2283 9198 4.036734 TGAGTGTCAAATCACAAAGCTTCC 59.963 41.667 0.00 0.00 40.37 3.46
2296 9211 4.326504 AAAGCTTCCATGGTTTGAACTG 57.673 40.909 12.58 0.00 36.46 3.16
2302 9217 3.979911 TCCATGGTTTGAACTGGCATAT 58.020 40.909 12.58 0.00 0.00 1.78
2303 9218 5.122707 TCCATGGTTTGAACTGGCATATA 57.877 39.130 12.58 0.00 0.00 0.86
2306 9221 7.293828 TCCATGGTTTGAACTGGCATATATTA 58.706 34.615 12.58 0.00 0.00 0.98
2382 9313 1.078848 AGCTCGTGGCATCCTTCAC 60.079 57.895 0.00 0.00 44.79 3.18
2419 9358 7.690256 AGTTATATGATCCCCCTTTCATACAC 58.310 38.462 0.00 0.00 37.58 2.90
2471 9410 5.142639 CCCTGATTTGGTTCATATCCACAT 58.857 41.667 0.00 0.00 34.45 3.21
2520 9459 7.004555 TCATAGTCACCACTGATAAACAACT 57.995 36.000 0.00 0.00 33.62 3.16
2572 9511 9.199645 TCCTTTCTATTGCCAAATGATTCATAA 57.800 29.630 0.00 0.00 0.00 1.90
2592 9531 8.603898 TCATAATACCTGGACTTCAAACTAGA 57.396 34.615 0.00 0.00 0.00 2.43
2615 9554 2.282180 GGTGTCCCGCCACAATGT 60.282 61.111 0.00 0.00 37.06 2.71
2643 9582 4.006989 CACGGAATCCTACAAAATGACCA 58.993 43.478 0.00 0.00 0.00 4.02
2686 9625 2.106566 ACCACATTGGCTTGACACAAA 58.893 42.857 0.00 0.00 42.67 2.83
2699 9638 5.509501 GCTTGACACAAAAATTCATCCTCCA 60.510 40.000 0.00 0.00 0.00 3.86
2702 9641 5.774184 TGACACAAAAATTCATCCTCCATCA 59.226 36.000 0.00 0.00 0.00 3.07
2739 9678 3.454375 TCGTGTTTCCTTCAGAGTCAAC 58.546 45.455 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.857038 AACACGACCTGGGTGCGT 61.857 61.111 0.00 1.94 38.98 5.24
10 11 0.836400 ATCCTCAACACGACCTGGGT 60.836 55.000 0.00 0.00 0.00 4.51
15 16 1.439679 GTTCCATCCTCAACACGACC 58.560 55.000 0.00 0.00 0.00 4.79
55 56 2.430921 GAGTCACGGTGCACCTCG 60.431 66.667 32.28 22.38 0.00 4.63
67 71 1.758440 GCCTGCCATATCCGGAGTCA 61.758 60.000 11.34 0.00 0.00 3.41
90 94 0.390603 CAACATGGGCTCGTCGGTTA 60.391 55.000 0.00 0.00 0.00 2.85
119 123 2.584261 ATTCTCATCGCTGCCGCTGT 62.584 55.000 0.00 0.00 32.77 4.40
124 128 2.550101 GGCCATTCTCATCGCTGCC 61.550 63.158 0.00 0.00 0.00 4.85
127 131 1.762522 ATCCGGCCATTCTCATCGCT 61.763 55.000 2.24 0.00 0.00 4.93
132 136 1.526887 GGTGATCCGGCCATTCTCA 59.473 57.895 2.24 0.00 0.00 3.27
145 149 1.367840 GCTAGGGATTCGCGGTGAT 59.632 57.895 6.13 0.00 0.00 3.06
148 152 1.069765 CATGCTAGGGATTCGCGGT 59.930 57.895 6.13 0.00 0.00 5.68
150 154 0.315251 TCTCATGCTAGGGATTCGCG 59.685 55.000 0.00 0.00 0.00 5.87
151 155 2.411904 CTTCTCATGCTAGGGATTCGC 58.588 52.381 0.00 0.00 0.00 4.70
180 184 4.752879 TTGTCGCCTAGGCCACGC 62.753 66.667 28.09 15.16 35.02 5.34
181 185 2.173669 CATTGTCGCCTAGGCCACG 61.174 63.158 28.09 14.38 35.02 4.94
182 186 0.811616 CTCATTGTCGCCTAGGCCAC 60.812 60.000 28.09 25.57 37.98 5.01
183 187 0.975556 TCTCATTGTCGCCTAGGCCA 60.976 55.000 28.09 18.00 37.98 5.36
184 188 0.394565 ATCTCATTGTCGCCTAGGCC 59.605 55.000 28.09 15.42 37.98 5.19
185 189 1.069204 TGATCTCATTGTCGCCTAGGC 59.931 52.381 24.75 24.75 37.85 3.93
186 190 2.363680 ACTGATCTCATTGTCGCCTAGG 59.636 50.000 3.67 3.67 0.00 3.02
187 191 3.317711 AGACTGATCTCATTGTCGCCTAG 59.682 47.826 0.00 0.00 34.92 3.02
188 192 3.291584 AGACTGATCTCATTGTCGCCTA 58.708 45.455 0.00 0.00 34.92 3.93
189 193 2.106566 AGACTGATCTCATTGTCGCCT 58.893 47.619 0.00 0.00 34.92 5.52
274 278 0.741221 GGATGAAGGTCGTGGCAGAC 60.741 60.000 8.11 8.11 40.25 3.51
281 285 2.579201 CGGCTGGATGAAGGTCGT 59.421 61.111 0.00 0.00 0.00 4.34
283 287 1.153349 GACCGGCTGGATGAAGGTC 60.153 63.158 21.41 0.00 43.55 3.85
286 290 1.144936 GAGGACCGGCTGGATGAAG 59.855 63.158 21.41 0.00 39.21 3.02
298 302 2.092882 CGAAACGGCGAAGAGGACC 61.093 63.158 16.62 0.00 0.00 4.46
300 304 1.080974 GTCGAAACGGCGAAGAGGA 60.081 57.895 16.62 0.61 42.55 3.71
317 321 3.459063 GCCGAAGTAGAGGGCCGT 61.459 66.667 0.00 0.00 41.01 5.68
367 383 1.172180 CCACGGCCAACAACATGTCT 61.172 55.000 2.24 0.00 0.00 3.41
369 385 2.855514 GCCACGGCCAACAACATGT 61.856 57.895 2.24 0.00 34.56 3.21
374 390 3.141488 AAACGCCACGGCCAACAA 61.141 55.556 2.24 0.00 37.98 2.83
390 406 0.389817 CGTCGCAACCTCCATCTCAA 60.390 55.000 0.00 0.00 0.00 3.02
392 408 1.519455 CCGTCGCAACCTCCATCTC 60.519 63.158 0.00 0.00 0.00 2.75
393 409 2.579201 CCGTCGCAACCTCCATCT 59.421 61.111 0.00 0.00 0.00 2.90
395 411 4.096003 CCCCGTCGCAACCTCCAT 62.096 66.667 0.00 0.00 0.00 3.41
413 429 1.168407 CCATAGGCGATGCACCCAAG 61.168 60.000 1.62 0.00 33.79 3.61
433 449 0.611896 AAAATCCTCCCACCCTTGCG 60.612 55.000 0.00 0.00 0.00 4.85
441 457 2.578021 CCTCTTCCTCAAAATCCTCCCA 59.422 50.000 0.00 0.00 0.00 4.37
486 502 2.738480 CCCTGACCCGTTCGTCAA 59.262 61.111 0.00 0.00 42.06 3.18
501 517 2.692741 CCTCCCCCTGTTCTCCCC 60.693 72.222 0.00 0.00 0.00 4.81
505 522 1.539124 GACACCCTCCCCCTGTTCT 60.539 63.158 0.00 0.00 0.00 3.01
508 525 4.250170 ACGACACCCTCCCCCTGT 62.250 66.667 0.00 0.00 0.00 4.00
509 526 3.706373 CACGACACCCTCCCCCTG 61.706 72.222 0.00 0.00 0.00 4.45
533 550 4.337060 TGGGTCTGTGTCGACGCG 62.337 66.667 23.01 17.32 46.31 6.01
573 590 7.589954 GTGTATTGTTATTTGTCTGTTGTGACC 59.410 37.037 0.00 0.00 36.21 4.02
574 591 7.320324 CGTGTATTGTTATTTGTCTGTTGTGAC 59.680 37.037 0.00 0.00 37.47 3.67
579 596 7.067116 CGAACGTGTATTGTTATTTGTCTGTT 58.933 34.615 0.00 0.00 0.00 3.16
627 644 3.488573 TCCGCGCGGATAAAAACC 58.511 55.556 45.37 0.00 39.76 3.27
645 662 2.475098 TTCATCCGCGTCCGTTTCGA 62.475 55.000 4.92 0.00 0.00 3.71
647 664 0.725117 ATTTCATCCGCGTCCGTTTC 59.275 50.000 4.92 0.00 0.00 2.78
670 691 1.811679 GTCAGCTCTAACAGGGCGC 60.812 63.158 0.00 0.00 0.00 6.53
675 696 4.800993 CGACATTAAGGTCAGCTCTAACAG 59.199 45.833 19.31 0.00 37.66 3.16
676 697 4.381612 CCGACATTAAGGTCAGCTCTAACA 60.382 45.833 19.31 0.00 37.66 2.41
691 712 4.202121 CCGATTCTTCTTCTCCCGACATTA 60.202 45.833 0.00 0.00 0.00 1.90
704 725 2.182516 ATCCTCCACCCGATTCTTCT 57.817 50.000 0.00 0.00 0.00 2.85
737 758 0.107508 CACCATCCAGCGTCCATCTT 60.108 55.000 0.00 0.00 0.00 2.40
738 759 1.524002 CACCATCCAGCGTCCATCT 59.476 57.895 0.00 0.00 0.00 2.90
740 761 2.591753 CCACCATCCAGCGTCCAT 59.408 61.111 0.00 0.00 0.00 3.41
741 762 4.408821 GCCACCATCCAGCGTCCA 62.409 66.667 0.00 0.00 0.00 4.02
824 915 1.143183 GTCGGATTAAGGAGGCGCA 59.857 57.895 10.83 0.00 0.00 6.09
868 959 5.835257 TGTGGATGTAGTACGCTTATAACC 58.165 41.667 0.00 0.00 0.00 2.85
912 1019 2.464459 GGCAGAAGGTTGGCGATCG 61.464 63.158 11.69 11.69 33.76 3.69
931 1039 3.530910 CTCTTGTCCCGCGGGTGTT 62.531 63.158 41.57 0.00 36.47 3.32
941 1049 1.205893 CTAGAGGTGGTGCTCTTGTCC 59.794 57.143 0.00 0.00 0.00 4.02
957 1071 2.375509 TCTGTCCTCTGTGTGACCTAGA 59.624 50.000 0.00 0.00 0.00 2.43
1072 1198 4.115199 GGAGGGCTTGATGGCGGT 62.115 66.667 0.00 0.00 42.84 5.68
1255 1390 4.170062 CGTGGAAGCCAGCATGCG 62.170 66.667 13.01 7.31 32.34 4.73
1403 1538 0.658536 GCTGACGTTGTCAAGCTTGC 60.659 55.000 21.99 16.43 42.26 4.01
1457 8258 3.499737 CGGCGGAGACATGTTGCC 61.500 66.667 17.45 17.45 42.29 4.52
1483 8284 2.453638 GCGCCTTCGTCTTGGCTAC 61.454 63.158 0.00 0.00 46.42 3.58
1501 8305 2.885644 CGCCGTCTTCATGACCGG 60.886 66.667 18.62 18.62 42.49 5.28
1522 8326 3.786635 ACGCATCCTTTCTGATAGTGAC 58.213 45.455 0.00 0.00 0.00 3.67
1523 8327 3.181475 GGACGCATCCTTTCTGATAGTGA 60.181 47.826 0.00 0.00 42.45 3.41
1525 8329 2.223829 CGGACGCATCCTTTCTGATAGT 60.224 50.000 0.00 0.00 43.73 2.12
1565 8369 4.834453 CGGAGCAGAGGCCAGCAG 62.834 72.222 5.01 0.00 42.56 4.24
1628 8432 0.249398 TTTAGCGTCCTCTGCTTCCC 59.751 55.000 0.00 0.00 43.71 3.97
1753 8560 1.849039 AGAGCCCTAAGCCATGTGAAT 59.151 47.619 0.00 0.00 45.47 2.57
1902 8716 8.723942 ATTTCCTTAGATCATGTACAGAACAC 57.276 34.615 0.33 0.00 42.09 3.32
1937 8751 5.585500 TTGTAAAACCGAATCTCACTTCG 57.415 39.130 0.00 0.00 45.79 3.79
2035 8850 5.528690 TGATTGCTTAGGTATGTGCAGAATC 59.471 40.000 0.00 0.00 36.75 2.52
2111 8936 5.291178 TGATTCAAATTGCAACTTGGACTG 58.709 37.500 19.53 0.00 0.00 3.51
2151 8983 5.472820 CCTCAAGAAACAGCAAGAAGAGAAT 59.527 40.000 0.00 0.00 0.00 2.40
2163 8995 5.006941 CCAATTTGCAAACCTCAAGAAACAG 59.993 40.000 15.41 0.00 0.00 3.16
2183 9081 6.349611 GCAATCTGTGTTGAGTACAATCCAAT 60.350 38.462 0.00 0.00 38.80 3.16
2196 9094 4.548494 TGCTTTGTATGCAATCTGTGTTG 58.452 39.130 0.00 0.00 37.51 3.33
2223 9121 3.010420 GCCCTAGTCCAGCTTTTAGTTG 58.990 50.000 0.00 0.00 0.00 3.16
2243 9158 5.181748 ACACTCAGATGAAACTAGGAATGC 58.818 41.667 0.00 0.00 0.00 3.56
2244 9159 6.401394 TGACACTCAGATGAAACTAGGAATG 58.599 40.000 0.00 0.00 0.00 2.67
2278 9193 1.337167 GCCAGTTCAAACCATGGAAGC 60.337 52.381 21.47 2.90 34.60 3.86
2283 9198 9.985730 AATTAATATATGCCAGTTCAAACCATG 57.014 29.630 0.00 0.00 0.00 3.66
2302 9217 7.338449 ACCGAAGAAGGCAAAAGCTAATTAATA 59.662 33.333 0.00 0.00 33.69 0.98
2303 9218 6.152831 ACCGAAGAAGGCAAAAGCTAATTAAT 59.847 34.615 0.00 0.00 33.69 1.40
2306 9221 3.826729 ACCGAAGAAGGCAAAAGCTAATT 59.173 39.130 0.00 0.00 33.69 1.40
2382 9313 8.848182 GGGGATCATATAACTATTACCTCTACG 58.152 40.741 0.00 0.00 0.00 3.51
2405 9344 1.087771 GCGTCGTGTATGAAAGGGGG 61.088 60.000 0.00 0.00 0.00 5.40
2419 9358 0.992072 CCAGTAATGTCACTGCGTCG 59.008 55.000 0.00 0.00 43.82 5.12
2471 9410 2.435805 GTGATGATTGGCTCTCCTGGTA 59.564 50.000 0.00 0.00 0.00 3.25
2520 9459 4.553144 GGGGTGTGAGTCCCTGTA 57.447 61.111 0.96 0.00 44.07 2.74
2572 9511 5.336531 CGTGTCTAGTTTGAAGTCCAGGTAT 60.337 44.000 0.00 0.00 0.00 2.73
2615 9554 4.610605 TTTGTAGGATTCCGTGAGTCAA 57.389 40.909 0.00 0.00 0.00 3.18
2643 9582 5.296531 GTGAAACCCAAATCAGCAATTGTTT 59.703 36.000 7.40 0.00 0.00 2.83
2686 9625 3.931907 TCGGTGATGGAGGATGAATTT 57.068 42.857 0.00 0.00 0.00 1.82
2699 9638 2.159393 CGATGGTTGCAAATTCGGTGAT 60.159 45.455 15.39 0.00 0.00 3.06
2702 9641 1.068610 CACGATGGTTGCAAATTCGGT 60.069 47.619 22.81 9.10 32.35 4.69


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

AutoCloner maintained by Alex Coulton.