Multiple sequence alignment - TraesCS2A01G445200

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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 TraesCS2A01G445200 chr2A 100.000 2334 0 0 1 2334 694956570 694954237 0.000000e+00 4311.0
1 TraesCS2A01G445200 chr2A 79.980 1019 85 50 654 1617 694976940 694975986 1.960000e-180 641.0
2 TraesCS2A01G445200 chr2B 83.398 1807 167 56 618 2334 661779018 661777255 0.000000e+00 1552.0
3 TraesCS2A01G445200 chr2B 78.739 809 82 42 654 1396 661833731 661832947 2.110000e-125 459.0
4 TraesCS2A01G445200 chr2B 92.143 140 7 4 4 141 661834972 661834835 6.580000e-46 195.0
5 TraesCS2A01G445200 chr2B 88.889 162 11 4 453 608 661834168 661834008 2.370000e-45 193.0
6 TraesCS2A01G445200 chr2B 81.579 190 18 6 256 443 661834315 661834141 8.700000e-30 141.0
7 TraesCS2A01G445200 chr2D 81.687 1316 113 47 493 1716 555224272 555222993 0.000000e+00 977.0
8 TraesCS2A01G445200 chr2D 94.833 329 11 1 2006 2334 555222672 555222350 2.070000e-140 508.0
9 TraesCS2A01G445200 chr2D 86.705 173 11 8 1 165 555225795 555225627 5.120000e-42 182.0
10 TraesCS2A01G445200 chr2D 87.805 82 5 1 165 241 555224866 555224785 8.880000e-15 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 TraesCS2A01G445200 chr2A 694954237 694956570 2333 True 4311.00 4311 100.0000 1 2334 1 chr2A.!!$R1 2333
1 TraesCS2A01G445200 chr2A 694975986 694976940 954 True 641.00 641 79.9800 654 1617 1 chr2A.!!$R2 963
2 TraesCS2A01G445200 chr2B 661777255 661779018 1763 True 1552.00 1552 83.3980 618 2334 1 chr2B.!!$R1 1716
3 TraesCS2A01G445200 chr2B 661832947 661834972 2025 True 247.00 459 85.3375 4 1396 4 chr2B.!!$R2 1392
4 TraesCS2A01G445200 chr2D 555222350 555225795 3445 True 439.65 977 87.7575 1 2334 4 chr2D.!!$R1 2333

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
823 2264 0.238289 AAGCAAAATCGAGGCACGTG 59.762 50.0 12.28 12.28 43.13 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1631 3172 0.941542 ACATTTTGTCGACCACGGTG 59.058 50.0 14.12 8.16 40.21 4.94 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
34 35 1.672881 CTGTTGAGGGAAATCGATGGC 59.327 52.381 0.00 0.00 0.00 4.40
63 66 2.287849 GGAAGCCTGAACTGCTGTTTTC 60.288 50.000 10.54 9.35 39.48 2.29
68 71 3.796844 GCCTGAACTGCTGTTTTCCTTTC 60.797 47.826 10.54 0.00 36.39 2.62
69 72 3.633986 CCTGAACTGCTGTTTTCCTTTCT 59.366 43.478 10.54 0.00 36.39 2.52
87 95 4.670896 TTCTTTTTCAGGCAGGGAAAAG 57.329 40.909 13.54 13.54 42.99 2.27
108 116 1.229428 CCTGAACTTGCGAAGAAGCA 58.771 50.000 3.37 0.00 46.54 3.91
133 141 4.288105 TGTTTTGGTTTCATGGGCCATAAT 59.712 37.500 20.73 0.00 31.71 1.28
145 157 2.202395 CCATAATGCGGGCCCCTTG 61.202 63.158 18.66 2.81 0.00 3.61
151 163 4.115199 GCGGGCCCCTTGAGATGT 62.115 66.667 18.66 0.00 0.00 3.06
155 167 2.048603 GGCCCCTTGAGATGTGCAC 61.049 63.158 10.75 10.75 0.00 4.57
187 960 3.803082 CCCTGATTGGCACACGCG 61.803 66.667 3.53 3.53 39.29 6.01
188 961 3.803082 CCTGATTGGCACACGCGG 61.803 66.667 12.47 1.27 39.29 6.46
189 962 2.741985 CTGATTGGCACACGCGGA 60.742 61.111 12.47 0.00 39.29 5.54
196 981 2.435234 GCACACGCGGAATACCCA 60.435 61.111 12.47 0.00 34.14 4.51
197 982 2.461110 GCACACGCGGAATACCCAG 61.461 63.158 12.47 0.00 34.14 4.45
241 1026 3.495806 GGTTTGGCATTCCACATTTCCAA 60.496 43.478 0.00 0.00 43.33 3.53
242 1027 4.133078 GTTTGGCATTCCACATTTCCAAA 58.867 39.130 0.00 0.00 43.33 3.28
244 1029 3.237746 TGGCATTCCACATTTCCAAAGA 58.762 40.909 0.00 0.00 37.47 2.52
245 1030 3.839490 TGGCATTCCACATTTCCAAAGAT 59.161 39.130 0.00 0.00 37.47 2.40
246 1031 5.022122 TGGCATTCCACATTTCCAAAGATA 58.978 37.500 0.00 0.00 37.47 1.98
247 1032 5.105392 TGGCATTCCACATTTCCAAAGATAC 60.105 40.000 0.00 0.00 37.47 2.24
248 1033 5.036737 GCATTCCACATTTCCAAAGATACG 58.963 41.667 0.00 0.00 0.00 3.06
250 1035 6.624861 GCATTCCACATTTCCAAAGATACGAA 60.625 38.462 0.00 0.00 0.00 3.85
254 1039 5.391950 CCACATTTCCAAAGATACGAAGTGG 60.392 44.000 0.00 0.00 45.73 4.00
285 1448 2.380410 GCCGCACGTGACGAGAATT 61.380 57.895 26.33 0.00 0.00 2.17
287 1450 0.732880 CCGCACGTGACGAGAATTCT 60.733 55.000 26.33 7.95 0.00 2.40
320 1483 1.289160 CCAGGAAAGGACATCTGGGA 58.711 55.000 0.00 0.00 42.12 4.37
321 1484 1.635487 CCAGGAAAGGACATCTGGGAA 59.365 52.381 0.00 0.00 42.12 3.97
322 1485 2.619074 CCAGGAAAGGACATCTGGGAAC 60.619 54.545 0.00 0.00 42.12 3.62
323 1486 1.279271 AGGAAAGGACATCTGGGAACG 59.721 52.381 0.00 0.00 0.00 3.95
324 1487 1.278127 GGAAAGGACATCTGGGAACGA 59.722 52.381 0.00 0.00 0.00 3.85
325 1488 2.347731 GAAAGGACATCTGGGAACGAC 58.652 52.381 0.00 0.00 0.00 4.34
326 1489 0.613777 AAGGACATCTGGGAACGACC 59.386 55.000 0.00 0.00 38.08 4.79
349 1512 1.715030 CGCGCGCTTTTAATGTACTC 58.285 50.000 30.48 0.00 0.00 2.59
363 1526 0.456312 GTACTCCGCGACCTGTGAAG 60.456 60.000 8.23 0.00 0.00 3.02
372 1535 4.717629 CCTGTGAAGCCGACGCGA 62.718 66.667 15.93 0.00 41.18 5.87
422 1585 4.202574 CCAGGGCCACACACACCA 62.203 66.667 6.18 0.00 0.00 4.17
423 1586 2.906897 CAGGGCCACACACACCAC 60.907 66.667 6.18 0.00 0.00 4.16
424 1587 4.204028 AGGGCCACACACACCACC 62.204 66.667 6.18 0.00 0.00 4.61
425 1588 4.514585 GGGCCACACACACCACCA 62.515 66.667 4.39 0.00 0.00 4.17
426 1589 3.216292 GGCCACACACACCACCAC 61.216 66.667 0.00 0.00 0.00 4.16
427 1590 3.216292 GCCACACACACCACCACC 61.216 66.667 0.00 0.00 0.00 4.61
428 1591 2.273776 CCACACACACCACCACCA 59.726 61.111 0.00 0.00 0.00 4.17
429 1592 2.118404 CCACACACACCACCACCAC 61.118 63.158 0.00 0.00 0.00 4.16
430 1593 2.118404 CACACACACCACCACCACC 61.118 63.158 0.00 0.00 0.00 4.61
431 1594 2.273776 CACACACCACCACCACCA 59.726 61.111 0.00 0.00 0.00 4.17
432 1595 2.118404 CACACACCACCACCACCAC 61.118 63.158 0.00 0.00 0.00 4.16
433 1596 2.518349 CACACCACCACCACCACC 60.518 66.667 0.00 0.00 0.00 4.61
434 1597 3.018193 ACACCACCACCACCACCA 61.018 61.111 0.00 0.00 0.00 4.17
435 1598 2.518349 CACCACCACCACCACCAC 60.518 66.667 0.00 0.00 0.00 4.16
436 1599 4.183858 ACCACCACCACCACCACG 62.184 66.667 0.00 0.00 0.00 4.94
437 1600 3.867783 CCACCACCACCACCACGA 61.868 66.667 0.00 0.00 0.00 4.35
438 1601 2.590575 CACCACCACCACCACGAC 60.591 66.667 0.00 0.00 0.00 4.34
439 1602 4.230002 ACCACCACCACCACGACG 62.230 66.667 0.00 0.00 0.00 5.12
440 1603 3.918977 CCACCACCACCACGACGA 61.919 66.667 0.00 0.00 0.00 4.20
441 1604 2.660552 CACCACCACCACGACGAC 60.661 66.667 0.00 0.00 0.00 4.34
442 1605 4.274700 ACCACCACCACGACGACG 62.275 66.667 5.58 5.58 45.75 5.12
443 1606 3.968568 CCACCACCACGACGACGA 61.969 66.667 15.32 0.00 42.66 4.20
444 1607 2.728383 CACCACCACGACGACGAC 60.728 66.667 15.32 0.00 42.66 4.34
445 1608 4.318021 ACCACCACGACGACGACG 62.318 66.667 17.60 17.60 42.66 5.12
446 1609 4.016629 CCACCACGACGACGACGA 62.017 66.667 25.15 0.00 42.66 4.20
447 1610 2.794166 CACCACGACGACGACGAC 60.794 66.667 25.15 7.02 42.66 4.34
481 1644 3.299977 CCGACACCACCAGGACGA 61.300 66.667 0.00 0.00 38.69 4.20
571 1740 1.597854 TTCAGGTGCAGGTTCAGCG 60.598 57.895 0.00 0.00 39.28 5.18
685 2096 3.202829 TGTGTTCTGGACAAGTTACCC 57.797 47.619 0.00 0.00 40.65 3.69
694 2116 0.608640 ACAAGTTACCCGGAGCTGAG 59.391 55.000 0.73 0.00 0.00 3.35
756 2184 2.490902 CCCCTTACTTGCTTTCCCTTGT 60.491 50.000 0.00 0.00 0.00 3.16
771 2202 1.608717 CTTGTACTGGAGGCGCCTCT 61.609 60.000 45.55 32.85 42.38 3.69
789 2228 2.989840 CTCTCGTACTCAAAGCACCAAG 59.010 50.000 0.00 0.00 0.00 3.61
821 2262 1.529826 GCTAAGCAAAATCGAGGCACG 60.530 52.381 0.00 0.00 44.09 5.34
822 2263 1.732259 CTAAGCAAAATCGAGGCACGT 59.268 47.619 3.89 0.00 43.13 4.49
823 2264 0.238289 AAGCAAAATCGAGGCACGTG 59.762 50.000 12.28 12.28 43.13 4.49
824 2265 0.602638 AGCAAAATCGAGGCACGTGA 60.603 50.000 22.23 0.00 43.13 4.35
825 2266 0.447801 GCAAAATCGAGGCACGTGAT 59.552 50.000 22.23 6.57 43.13 3.06
826 2267 1.529826 GCAAAATCGAGGCACGTGATC 60.530 52.381 22.23 15.14 43.13 2.92
827 2268 1.062587 CAAAATCGAGGCACGTGATCC 59.937 52.381 22.23 12.28 43.13 3.36
841 2282 4.796231 ATCCAGCCGACGCGTGAC 62.796 66.667 20.70 5.38 41.18 3.67
858 2299 3.673338 CGTGACATTCAGAGAAGCGTAAA 59.327 43.478 0.00 0.00 0.00 2.01
879 2322 3.923017 AAAAATGCAGATATAGCCGGC 57.077 42.857 21.89 21.89 0.00 6.13
880 2323 1.442769 AAATGCAGATATAGCCGGCG 58.557 50.000 23.20 5.73 0.00 6.46
881 2324 0.321671 AATGCAGATATAGCCGGCGT 59.678 50.000 23.20 16.91 0.00 5.68
882 2325 0.390340 ATGCAGATATAGCCGGCGTG 60.390 55.000 23.20 13.58 0.00 5.34
884 2327 0.600255 GCAGATATAGCCGGCGTGTT 60.600 55.000 23.20 5.85 0.00 3.32
885 2328 1.336517 GCAGATATAGCCGGCGTGTTA 60.337 52.381 23.20 8.40 0.00 2.41
886 2329 2.596452 CAGATATAGCCGGCGTGTTAG 58.404 52.381 23.20 6.03 0.00 2.34
887 2330 2.030185 CAGATATAGCCGGCGTGTTAGT 60.030 50.000 23.20 3.61 0.00 2.24
888 2331 2.030185 AGATATAGCCGGCGTGTTAGTG 60.030 50.000 23.20 0.00 0.00 2.74
889 2332 0.249155 TATAGCCGGCGTGTTAGTGC 60.249 55.000 23.20 0.00 0.00 4.40
890 2333 1.956629 ATAGCCGGCGTGTTAGTGCT 61.957 55.000 23.20 8.02 0.00 4.40
891 2334 1.314534 TAGCCGGCGTGTTAGTGCTA 61.315 55.000 23.20 6.92 0.00 3.49
892 2335 2.450345 GCCGGCGTGTTAGTGCTAC 61.450 63.158 12.58 0.00 0.00 3.58
893 2336 2.156446 CCGGCGTGTTAGTGCTACG 61.156 63.158 6.01 0.00 40.52 3.51
894 2337 1.443194 CGGCGTGTTAGTGCTACGT 60.443 57.895 0.00 0.00 39.79 3.57
906 2349 4.650754 AGTGCTACGTATCTCGGAATTT 57.349 40.909 0.00 0.00 44.69 1.82
908 2351 4.097437 AGTGCTACGTATCTCGGAATTTGA 59.903 41.667 0.00 0.00 44.69 2.69
918 2361 2.878406 CTCGGAATTTGACGGCCATAAT 59.122 45.455 2.24 0.00 0.00 1.28
920 2363 4.647611 TCGGAATTTGACGGCCATAATAT 58.352 39.130 2.24 0.00 0.00 1.28
921 2364 5.795972 TCGGAATTTGACGGCCATAATATA 58.204 37.500 2.24 0.00 0.00 0.86
922 2365 6.231951 TCGGAATTTGACGGCCATAATATAA 58.768 36.000 2.24 0.00 0.00 0.98
923 2366 6.370442 TCGGAATTTGACGGCCATAATATAAG 59.630 38.462 2.24 0.00 0.00 1.73
938 2393 5.746990 AATATAAGAAGTATCAGCCGGCT 57.253 39.130 27.08 27.08 0.00 5.52
961 2416 1.299165 CGTCCCAATCCGAGCGTAG 60.299 63.158 0.00 0.00 0.00 3.51
992 2466 1.583495 CCAGCCGTGTAGTCGAGACA 61.583 60.000 5.99 0.00 0.00 3.41
1029 2503 4.803426 GTGAGCTCCCCGTCGCTG 62.803 72.222 12.15 0.00 36.45 5.18
1120 2621 4.492160 TCGTGCCGCTCATCGTCC 62.492 66.667 0.00 0.00 36.19 4.79
1144 2645 0.241213 CTGCTTCGTCGTCCTCTTCA 59.759 55.000 0.00 0.00 0.00 3.02
1198 2703 2.084101 GTCGCGCGTGTGTGTGATA 61.084 57.895 30.98 2.41 45.87 2.15
1202 2707 0.442310 GCGCGTGTGTGTGATACATT 59.558 50.000 8.43 0.00 42.24 2.71
1205 2710 2.348362 CGCGTGTGTGTGATACATTCAT 59.652 45.455 0.00 0.00 42.24 2.57
1226 2731 2.736721 TCAAACGTCTTGATACAGCTGC 59.263 45.455 15.27 0.00 0.00 5.25
1259 2764 1.370172 GCTCTGCATTATGCTGCGC 60.370 57.895 19.65 19.65 45.31 6.09
1358 2867 1.825474 GACCAAGGAAGGAGACGATCA 59.175 52.381 0.00 0.00 0.00 2.92
1444 2968 4.462508 TCTTGATCTCAGCTGTGTTAGG 57.537 45.455 14.67 3.49 0.00 2.69
1473 2998 0.867753 GTACTGATCTCGCTGCACCG 60.868 60.000 0.00 0.00 0.00 4.94
1484 3011 3.263261 TCGCTGCACCGATAATAAAACA 58.737 40.909 0.00 0.00 31.36 2.83
1503 3030 5.530519 AACACATACAGAACGCAATAGTG 57.469 39.130 0.00 0.00 0.00 2.74
1547 3081 1.602323 GGTTTCATGGTCCGGTGCA 60.602 57.895 0.00 0.00 0.00 4.57
1569 3103 5.481105 CAATTTGGCCACTCATAATTGTGT 58.519 37.500 23.21 0.00 33.63 3.72
1570 3104 6.629128 CAATTTGGCCACTCATAATTGTGTA 58.371 36.000 23.21 0.00 33.63 2.90
1594 3128 3.888930 TGAACAAACCTCTCACCATTTCC 59.111 43.478 0.00 0.00 0.00 3.13
1598 3132 0.250513 ACCTCTCACCATTTCCTCGC 59.749 55.000 0.00 0.00 0.00 5.03
1618 3159 4.526650 TCGCTGAAGAGGGTATATAATGCA 59.473 41.667 0.00 0.00 33.81 3.96
1624 3165 6.155221 TGAAGAGGGTATATAATGCAGCCTAG 59.845 42.308 0.00 0.00 40.19 3.02
1630 3171 7.846823 AGGGTATATAATGCAGCCTAGTTCTAT 59.153 37.037 0.00 0.00 38.38 1.98
1631 3172 8.145122 GGGTATATAATGCAGCCTAGTTCTATC 58.855 40.741 0.00 0.00 0.00 2.08
1638 3180 2.032620 AGCCTAGTTCTATCACCGTGG 58.967 52.381 0.00 0.00 0.00 4.94
1644 3186 1.200716 GTTCTATCACCGTGGTCGACA 59.799 52.381 18.91 0.27 39.71 4.35
1672 3214 0.884704 GGTGTCTGATGTTGCCACGT 60.885 55.000 0.00 0.00 0.00 4.49
1678 3220 1.666553 GATGTTGCCACGTGGTCGA 60.667 57.895 33.92 22.69 40.62 4.20
1717 3259 1.172175 TCACAGCACAGCACAACAAA 58.828 45.000 0.00 0.00 0.00 2.83
1718 3260 1.750206 TCACAGCACAGCACAACAAAT 59.250 42.857 0.00 0.00 0.00 2.32
1719 3261 2.166050 TCACAGCACAGCACAACAAATT 59.834 40.909 0.00 0.00 0.00 1.82
1720 3262 3.379688 TCACAGCACAGCACAACAAATTA 59.620 39.130 0.00 0.00 0.00 1.40
1721 3263 4.111198 CACAGCACAGCACAACAAATTAA 58.889 39.130 0.00 0.00 0.00 1.40
1722 3264 4.565962 CACAGCACAGCACAACAAATTAAA 59.434 37.500 0.00 0.00 0.00 1.52
1729 3271 7.623089 GCACAGCACAACAAATTAAAACAAAGA 60.623 33.333 0.00 0.00 0.00 2.52
1762 3304 7.903995 AGTTGTTTTCAGCAAAAGAATGAAA 57.096 28.000 0.00 0.00 37.17 2.69
1784 3326 2.510238 GCCAGCAGCACTCTACCG 60.510 66.667 0.00 0.00 42.97 4.02
1816 3362 2.743928 CGCCCACACTTCTGGCTC 60.744 66.667 0.00 0.00 43.12 4.70
1853 3419 4.374689 TGGGCAACACAAGTATTCCTAA 57.625 40.909 0.00 0.00 39.74 2.69
1996 3620 6.728200 AGGTGAATATCATACGCAAACATTG 58.272 36.000 0.00 0.00 0.00 2.82
2003 3627 3.812609 TCATACGCAAACATTGTGACACT 59.187 39.130 7.20 0.00 43.66 3.55
2122 3746 2.294074 ACAATACAGCAACCACAACGT 58.706 42.857 0.00 0.00 0.00 3.99
2124 3748 3.042189 CAATACAGCAACCACAACGTTG 58.958 45.455 26.20 26.20 44.87 4.10
2129 3753 1.938814 CAACCACAACGTTGCAGCG 60.939 57.895 27.61 21.95 36.96 5.18
2176 3802 8.298030 TGTCTATTTACATTCATGTATCAGCG 57.702 34.615 0.45 0.00 42.32 5.18
2219 3845 0.952010 GCGCAGGTTCCGGTTTCTTA 60.952 55.000 0.30 0.00 0.00 2.10
2220 3846 1.076332 CGCAGGTTCCGGTTTCTTAG 58.924 55.000 0.00 0.00 0.00 2.18
2221 3847 1.450025 GCAGGTTCCGGTTTCTTAGG 58.550 55.000 0.00 0.00 0.00 2.69
2222 3848 1.002773 GCAGGTTCCGGTTTCTTAGGA 59.997 52.381 0.00 0.00 0.00 2.94
2223 3849 2.551504 GCAGGTTCCGGTTTCTTAGGAA 60.552 50.000 0.00 0.00 41.28 3.36
2224 3850 3.335579 CAGGTTCCGGTTTCTTAGGAAG 58.664 50.000 0.00 0.00 43.80 3.46
2227 3853 3.001414 GTTCCGGTTTCTTAGGAAGAGC 58.999 50.000 0.00 0.00 43.80 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 2.490903 CAGTTCAGGCTTCCATTTCCAG 59.509 50.000 0.00 0.00 0.00 3.86
63 66 2.597455 TCCCTGCCTGAAAAAGAAAGG 58.403 47.619 0.00 0.00 0.00 3.11
68 71 2.548707 GCCTTTTCCCTGCCTGAAAAAG 60.549 50.000 6.59 0.00 40.19 2.27
69 72 1.416030 GCCTTTTCCCTGCCTGAAAAA 59.584 47.619 6.59 0.00 40.19 1.94
87 95 0.519077 CTTCTTCGCAAGTTCAGGCC 59.481 55.000 0.00 0.00 39.48 5.19
108 116 2.441001 TGGCCCATGAAACCAAAACATT 59.559 40.909 0.00 0.00 0.00 2.71
133 141 4.113815 CATCTCAAGGGGCCCGCA 62.114 66.667 18.95 3.68 0.00 5.69
141 153 2.604914 GTCATACGTGCACATCTCAAGG 59.395 50.000 18.64 0.00 0.00 3.61
145 157 1.200483 CGGTCATACGTGCACATCTC 58.800 55.000 18.64 1.61 0.00 2.75
155 167 0.319555 CAGGGCCATACGGTCATACG 60.320 60.000 6.18 0.00 39.40 3.06
180 953 2.461110 GCTGGGTATTCCGCGTGTG 61.461 63.158 4.92 0.00 38.76 3.82
187 960 4.349930 TCTTAGTTATGGGCTGGGTATTCC 59.650 45.833 0.00 0.00 0.00 3.01
188 961 5.163237 TGTCTTAGTTATGGGCTGGGTATTC 60.163 44.000 0.00 0.00 0.00 1.75
189 962 4.724798 TGTCTTAGTTATGGGCTGGGTATT 59.275 41.667 0.00 0.00 0.00 1.89
196 981 6.496911 ACCAAAAATTGTCTTAGTTATGGGCT 59.503 34.615 0.00 0.00 0.00 5.19
197 982 6.697395 ACCAAAAATTGTCTTAGTTATGGGC 58.303 36.000 0.00 0.00 0.00 5.36
241 1026 0.107654 GCTGGGCCACTTCGTATCTT 60.108 55.000 0.00 0.00 0.00 2.40
242 1027 0.978146 AGCTGGGCCACTTCGTATCT 60.978 55.000 0.00 0.00 0.00 1.98
244 1029 0.107654 GAAGCTGGGCCACTTCGTAT 60.108 55.000 23.57 5.43 33.56 3.06
245 1030 1.295423 GAAGCTGGGCCACTTCGTA 59.705 57.895 23.57 0.00 33.56 3.43
246 1031 2.032681 GAAGCTGGGCCACTTCGT 59.967 61.111 23.57 8.05 33.56 3.85
247 1032 1.172180 TTTGAAGCTGGGCCACTTCG 61.172 55.000 27.98 13.24 44.24 3.79
248 1033 0.600057 CTTTGAAGCTGGGCCACTTC 59.400 55.000 27.64 27.64 42.15 3.01
250 1035 4.507969 CTTTGAAGCTGGGCCACT 57.492 55.556 0.00 1.86 0.00 4.00
269 1432 0.635731 GAGAATTCTCGTCACGTGCG 59.364 55.000 19.31 21.12 32.78 5.34
329 1492 0.247537 AGTACATTAAAAGCGCGCGC 60.248 50.000 45.10 45.10 42.33 6.86
330 1493 1.591394 GGAGTACATTAAAAGCGCGCG 60.591 52.381 28.44 28.44 0.00 6.86
331 1494 1.591394 CGGAGTACATTAAAAGCGCGC 60.591 52.381 26.66 26.66 0.00 6.86
332 1495 1.591394 GCGGAGTACATTAAAAGCGCG 60.591 52.381 0.00 0.00 0.00 6.86
333 1496 1.591394 CGCGGAGTACATTAAAAGCGC 60.591 52.381 0.00 0.00 39.90 5.92
337 1500 3.255725 CAGGTCGCGGAGTACATTAAAA 58.744 45.455 6.13 0.00 0.00 1.52
363 1526 4.117372 CTTTGTCGTCGCGTCGGC 62.117 66.667 22.72 22.72 35.91 5.54
372 1535 4.927782 TGCTGGCCGCTTTGTCGT 62.928 61.111 18.14 0.00 40.11 4.34
421 1584 2.590575 GTCGTGGTGGTGGTGGTG 60.591 66.667 0.00 0.00 0.00 4.17
422 1585 4.230002 CGTCGTGGTGGTGGTGGT 62.230 66.667 0.00 0.00 0.00 4.16
423 1586 3.918977 TCGTCGTGGTGGTGGTGG 61.919 66.667 0.00 0.00 0.00 4.61
424 1587 2.660552 GTCGTCGTGGTGGTGGTG 60.661 66.667 0.00 0.00 0.00 4.17
425 1588 4.274700 CGTCGTCGTGGTGGTGGT 62.275 66.667 0.00 0.00 0.00 4.16
426 1589 3.968568 TCGTCGTCGTGGTGGTGG 61.969 66.667 1.33 0.00 38.33 4.61
427 1590 2.728383 GTCGTCGTCGTGGTGGTG 60.728 66.667 1.33 0.00 38.33 4.17
428 1591 4.318021 CGTCGTCGTCGTGGTGGT 62.318 66.667 3.67 0.00 38.33 4.16
429 1592 4.016629 TCGTCGTCGTCGTGGTGG 62.017 66.667 11.41 0.00 38.33 4.61
430 1593 2.794166 GTCGTCGTCGTCGTGGTG 60.794 66.667 11.41 0.00 38.33 4.17
431 1594 4.360027 CGTCGTCGTCGTCGTGGT 62.360 66.667 12.51 0.00 41.73 4.16
432 1595 4.063230 TCGTCGTCGTCGTCGTGG 62.063 66.667 18.44 5.42 45.27 4.94
433 1596 2.857992 GTCGTCGTCGTCGTCGTG 60.858 66.667 18.44 6.23 45.27 4.35
434 1597 4.400776 CGTCGTCGTCGTCGTCGT 62.401 66.667 18.87 0.00 45.27 4.34
435 1598 4.108437 TCGTCGTCGTCGTCGTCG 62.108 66.667 20.39 20.39 45.27 5.12
436 1599 2.566765 GTCGTCGTCGTCGTCGTC 60.567 66.667 18.44 11.28 45.27 4.20
437 1600 4.400776 CGTCGTCGTCGTCGTCGT 62.401 66.667 18.87 0.00 45.27 4.34
438 1601 4.108437 TCGTCGTCGTCGTCGTCG 62.108 66.667 20.39 20.39 45.27 5.12
439 1602 2.566765 GTCGTCGTCGTCGTCGTC 60.567 66.667 18.44 11.28 45.27 4.20
440 1603 4.400776 CGTCGTCGTCGTCGTCGT 62.401 66.667 18.87 0.00 45.27 4.34
441 1604 4.108437 TCGTCGTCGTCGTCGTCG 62.108 66.667 20.39 20.39 45.27 5.12
442 1605 2.566765 GTCGTCGTCGTCGTCGTC 60.567 66.667 18.44 11.28 45.27 4.20
443 1606 4.400776 CGTCGTCGTCGTCGTCGT 62.401 66.667 18.87 0.00 45.27 4.34
444 1607 4.108437 TCGTCGTCGTCGTCGTCG 62.108 66.667 20.39 20.39 45.27 5.12
445 1608 2.566765 GTCGTCGTCGTCGTCGTC 60.567 66.667 18.44 11.28 45.27 4.20
446 1609 3.330077 TGTCGTCGTCGTCGTCGT 61.330 61.111 18.44 0.00 45.27 4.34
447 1610 2.857992 GTGTCGTCGTCGTCGTCG 60.858 66.667 14.18 14.18 46.06 5.12
448 1611 2.498466 GGTGTCGTCGTCGTCGTC 60.498 66.667 11.41 6.94 38.33 4.20
449 1612 4.360027 CGGTGTCGTCGTCGTCGT 62.360 66.667 11.41 0.00 38.33 4.34
450 1613 4.063230 TCGGTGTCGTCGTCGTCG 62.063 66.667 5.50 5.50 38.33 5.12
451 1614 2.498466 GTCGGTGTCGTCGTCGTC 60.498 66.667 1.33 0.00 38.33 4.20
452 1615 3.271586 TGTCGGTGTCGTCGTCGT 61.272 61.111 1.33 0.00 38.33 4.34
453 1616 2.794166 GTGTCGGTGTCGTCGTCG 60.794 66.667 0.00 0.00 37.69 5.12
481 1644 2.289444 ACACGACGATGGTGAAAAGGAT 60.289 45.455 0.00 0.00 38.73 3.24
485 1648 1.868498 GGAACACGACGATGGTGAAAA 59.132 47.619 0.00 0.00 38.73 2.29
539 1702 1.974236 ACCTGAACCTGAACCTGAGAG 59.026 52.381 0.00 0.00 0.00 3.20
584 1753 4.771356 CGCCGGTCACATCGACGT 62.771 66.667 1.90 0.00 46.42 4.34
608 1777 4.248842 CACCAGTGGCCGTGTCCA 62.249 66.667 9.78 0.00 0.00 4.02
610 1779 4.927782 TGCACCAGTGGCCGTGTC 62.928 66.667 9.78 3.92 32.40 3.67
611 1780 4.935495 CTGCACCAGTGGCCGTGT 62.935 66.667 9.78 0.00 32.40 4.49
745 2173 1.950954 GCCTCCAGTACAAGGGAAAGC 60.951 57.143 10.04 8.39 32.98 3.51
756 2184 2.261430 TACGAGAGGCGCCTCCAGTA 62.261 60.000 44.91 40.39 46.04 2.74
771 2202 1.508632 GCTTGGTGCTTTGAGTACGA 58.491 50.000 0.00 0.00 38.95 3.43
789 2228 0.667993 TGCTTAGCACCAACAACAGC 59.332 50.000 1.39 0.00 31.71 4.40
798 2239 1.202188 GCCTCGATTTTGCTTAGCACC 60.202 52.381 6.34 0.00 38.71 5.01
821 2262 4.796231 ACGCGTCGGCTGGATCAC 62.796 66.667 5.58 0.00 36.88 3.06
822 2263 4.794439 CACGCGTCGGCTGGATCA 62.794 66.667 9.86 0.00 36.88 2.92
823 2264 4.492160 TCACGCGTCGGCTGGATC 62.492 66.667 9.86 0.00 36.88 3.36
824 2265 4.796231 GTCACGCGTCGGCTGGAT 62.796 66.667 9.86 0.00 36.88 3.41
827 2268 3.071459 GAATGTCACGCGTCGGCTG 62.071 63.158 9.86 0.00 36.88 4.85
832 2273 1.651138 CTTCTCTGAATGTCACGCGTC 59.349 52.381 9.86 0.00 0.00 5.19
865 2308 0.600255 AACACGCCGGCTATATCTGC 60.600 55.000 26.68 0.00 0.00 4.26
866 2309 2.030185 ACTAACACGCCGGCTATATCTG 60.030 50.000 26.68 9.51 0.00 2.90
867 2310 2.030185 CACTAACACGCCGGCTATATCT 60.030 50.000 26.68 6.36 0.00 1.98
870 2313 0.249155 GCACTAACACGCCGGCTATA 60.249 55.000 26.68 10.76 0.00 1.31
872 2315 1.314534 TAGCACTAACACGCCGGCTA 61.315 55.000 26.68 9.08 33.10 3.93
874 2317 2.125832 TAGCACTAACACGCCGGC 60.126 61.111 19.07 19.07 0.00 6.13
875 2318 2.156446 CGTAGCACTAACACGCCGG 61.156 63.158 0.00 0.00 0.00 6.13
876 2319 0.179192 TACGTAGCACTAACACGCCG 60.179 55.000 0.00 0.00 39.23 6.46
877 2320 2.114825 GATACGTAGCACTAACACGCC 58.885 52.381 5.84 0.00 39.23 5.68
878 2321 3.034562 GAGATACGTAGCACTAACACGC 58.965 50.000 14.09 0.00 39.23 5.34
879 2322 3.278303 CGAGATACGTAGCACTAACACG 58.722 50.000 14.09 3.52 41.32 4.49
880 2323 3.310774 TCCGAGATACGTAGCACTAACAC 59.689 47.826 14.09 0.00 40.78 3.32
881 2324 3.534554 TCCGAGATACGTAGCACTAACA 58.465 45.455 14.09 0.00 40.78 2.41
882 2325 4.542662 TTCCGAGATACGTAGCACTAAC 57.457 45.455 14.09 0.00 40.78 2.34
884 2327 5.297527 TCAAATTCCGAGATACGTAGCACTA 59.702 40.000 14.09 0.00 40.78 2.74
885 2328 4.097437 TCAAATTCCGAGATACGTAGCACT 59.903 41.667 14.09 6.52 40.78 4.40
886 2329 4.206609 GTCAAATTCCGAGATACGTAGCAC 59.793 45.833 14.09 5.85 40.78 4.40
887 2330 4.357142 GTCAAATTCCGAGATACGTAGCA 58.643 43.478 14.09 0.00 40.78 3.49
888 2331 3.421231 CGTCAAATTCCGAGATACGTAGC 59.579 47.826 1.72 1.72 40.78 3.58
889 2332 3.973135 CCGTCAAATTCCGAGATACGTAG 59.027 47.826 0.08 0.00 40.78 3.51
890 2333 3.793129 GCCGTCAAATTCCGAGATACGTA 60.793 47.826 0.00 0.00 40.78 3.57
891 2334 2.805845 CCGTCAAATTCCGAGATACGT 58.194 47.619 0.00 0.00 40.78 3.57
892 2335 1.521423 GCCGTCAAATTCCGAGATACG 59.479 52.381 0.00 0.00 42.18 3.06
893 2336 1.865340 GGCCGTCAAATTCCGAGATAC 59.135 52.381 0.00 0.00 0.00 2.24
894 2337 1.483004 TGGCCGTCAAATTCCGAGATA 59.517 47.619 0.00 0.00 0.00 1.98
906 2349 8.129496 TGATACTTCTTATATTATGGCCGTCA 57.871 34.615 0.00 0.00 0.00 4.35
908 2351 7.042335 GCTGATACTTCTTATATTATGGCCGT 58.958 38.462 1.35 1.35 0.00 5.68
918 2361 4.799586 GCAAGCCGGCTGATACTTCTTATA 60.800 45.833 33.60 0.00 0.00 0.98
920 2363 2.741878 GCAAGCCGGCTGATACTTCTTA 60.742 50.000 33.60 0.00 0.00 2.10
921 2364 2.014068 GCAAGCCGGCTGATACTTCTT 61.014 52.381 33.60 7.91 0.00 2.52
922 2365 0.462759 GCAAGCCGGCTGATACTTCT 60.463 55.000 33.60 8.83 0.00 2.85
923 2366 0.744414 TGCAAGCCGGCTGATACTTC 60.744 55.000 33.60 9.02 34.04 3.01
938 2393 1.375396 CTCGGATTGGGACGTGCAA 60.375 57.895 9.96 0.00 0.00 4.08
961 2416 1.299926 CGGCTGGGACTGTATACGC 60.300 63.158 0.00 0.00 0.00 4.42
962 2417 0.248907 CACGGCTGGGACTGTATACG 60.249 60.000 0.00 0.00 0.00 3.06
963 2418 0.822164 ACACGGCTGGGACTGTATAC 59.178 55.000 0.00 0.00 0.00 1.47
964 2419 2.304092 CTACACGGCTGGGACTGTATA 58.696 52.381 0.00 0.00 0.00 1.47
965 2420 1.112113 CTACACGGCTGGGACTGTAT 58.888 55.000 0.00 0.00 0.00 2.29
969 2424 2.341101 CGACTACACGGCTGGGACT 61.341 63.158 0.00 0.00 0.00 3.85
970 2425 2.181021 CGACTACACGGCTGGGAC 59.819 66.667 0.00 0.00 0.00 4.46
972 2427 2.044555 TCTCGACTACACGGCTGGG 61.045 63.158 0.00 0.00 0.00 4.45
975 2430 1.874562 GTGTCTCGACTACACGGCT 59.125 57.895 9.79 0.00 38.03 5.52
992 2466 2.430610 GGCCTCTGCATCCTCTCGT 61.431 63.158 0.00 0.00 40.13 4.18
999 2473 2.202987 CTCACCGGCCTCTGCATC 60.203 66.667 0.00 0.00 40.13 3.91
1027 2501 2.815647 GTCCTCGAAAGCGGGCAG 60.816 66.667 0.00 0.00 41.12 4.85
1029 2503 4.430765 TCGTCCTCGAAAGCGGGC 62.431 66.667 0.00 0.00 43.34 6.13
1034 2508 1.668101 CTCCCCCTCGTCCTCGAAAG 61.668 65.000 0.00 0.00 45.61 2.62
1035 2509 1.681327 CTCCCCCTCGTCCTCGAAA 60.681 63.158 0.00 0.00 45.61 3.46
1040 2514 4.077180 GGTCCTCCCCCTCGTCCT 62.077 72.222 0.00 0.00 0.00 3.85
1120 2621 1.803519 GGACGACGAAGCAGAGCAG 60.804 63.158 0.00 0.00 0.00 4.24
1144 2645 3.083997 GGGGACGTGGGAGCAGAT 61.084 66.667 0.00 0.00 0.00 2.90
1191 2696 6.408858 AGACGTTTGATGAATGTATCACAC 57.591 37.500 0.00 0.00 41.93 3.82
1194 2699 7.848223 ATCAAGACGTTTGATGAATGTATCA 57.152 32.000 18.74 0.00 43.67 2.15
1195 2700 8.817100 TGTATCAAGACGTTTGATGAATGTATC 58.183 33.333 24.04 11.76 39.30 2.24
1198 2703 6.402550 GCTGTATCAAGACGTTTGATGAATGT 60.403 38.462 24.04 9.84 39.30 2.71
1202 2707 4.627035 CAGCTGTATCAAGACGTTTGATGA 59.373 41.667 24.04 13.20 39.30 2.92
1205 2710 2.736721 GCAGCTGTATCAAGACGTTTGA 59.263 45.455 16.64 13.12 0.00 2.69
1226 2731 1.516821 GAGCTCAGAGTCAGCAGCG 60.517 63.158 9.40 0.00 39.56 5.18
1266 2771 4.631377 TCGACATATCTGCAGACCAAAAAG 59.369 41.667 20.97 8.42 0.00 2.27
1268 2773 4.183865 CTCGACATATCTGCAGACCAAAA 58.816 43.478 20.97 2.67 0.00 2.44
1269 2774 3.785486 CTCGACATATCTGCAGACCAAA 58.215 45.455 20.97 5.41 0.00 3.28
1270 2775 2.481969 GCTCGACATATCTGCAGACCAA 60.482 50.000 20.97 8.21 0.00 3.67
1271 2776 1.067669 GCTCGACATATCTGCAGACCA 59.932 52.381 20.97 10.68 0.00 4.02
1358 2867 2.902486 TCAGTCCTTGAGCTCTTGTCAT 59.098 45.455 16.19 0.00 0.00 3.06
1473 2998 9.716507 ATTGCGTTCTGTATGTGTTTTATTATC 57.283 29.630 0.00 0.00 0.00 1.75
1515 3044 5.718130 ACCATGAAACCAACATGATGAGAAT 59.282 36.000 4.25 0.00 45.22 2.40
1547 3081 5.743636 ACACAATTATGAGTGGCCAAATT 57.256 34.783 7.24 6.78 39.99 1.82
1569 3103 4.974645 ATGGTGAGAGGTTTGTTCACTA 57.025 40.909 4.15 0.00 40.71 2.74
1570 3104 3.864789 ATGGTGAGAGGTTTGTTCACT 57.135 42.857 4.15 0.00 40.71 3.41
1594 3128 5.105752 GCATTATATACCCTCTTCAGCGAG 58.894 45.833 0.00 0.00 0.00 5.03
1598 3132 5.046014 AGGCTGCATTATATACCCTCTTCAG 60.046 44.000 0.50 0.00 0.00 3.02
1612 3153 4.262036 CGGTGATAGAACTAGGCTGCATTA 60.262 45.833 0.50 0.00 0.00 1.90
1618 3159 2.032620 CCACGGTGATAGAACTAGGCT 58.967 52.381 10.28 0.00 0.00 4.58
1624 3165 1.200716 TGTCGACCACGGTGATAGAAC 59.799 52.381 14.12 2.11 40.21 3.01
1630 3171 1.222300 CATTTTGTCGACCACGGTGA 58.778 50.000 14.12 0.00 40.21 4.02
1631 3172 0.941542 ACATTTTGTCGACCACGGTG 59.058 50.000 14.12 8.16 40.21 4.94
1644 3186 3.140325 ACATCAGACACCGGACATTTT 57.860 42.857 9.46 0.00 0.00 1.82
1672 3214 1.663739 CCGAGTGGAAGTTCGACCA 59.336 57.895 13.72 0.00 39.06 4.02
1678 3220 1.122019 AGAGTGGCCGAGTGGAAGTT 61.122 55.000 0.00 0.00 37.49 2.66
1686 3228 1.739562 GCTGTGAAGAGTGGCCGAG 60.740 63.158 0.00 0.00 0.00 4.63
1784 3326 1.569479 GGGCGTGCAAGAGTTCACTC 61.569 60.000 2.99 0.00 43.17 3.51
1787 3329 1.891919 GTGGGCGTGCAAGAGTTCA 60.892 57.895 2.99 0.00 0.00 3.18
1833 3399 4.076394 TGTTAGGAATACTTGTGTTGCCC 58.924 43.478 0.00 0.00 0.00 5.36
1839 3405 4.695455 CCACCACTGTTAGGAATACTTGTG 59.305 45.833 0.00 0.00 0.00 3.33
1973 3597 6.414694 CACAATGTTTGCGTATGATATTCACC 59.585 38.462 0.00 0.00 0.00 4.02
2045 3669 6.238814 GGACCGAAAGAGTTTGGAATTTGTAA 60.239 38.462 0.00 0.00 40.45 2.41
2101 3725 3.468770 ACGTTGTGGTTGCTGTATTGTA 58.531 40.909 0.00 0.00 0.00 2.41
2122 3746 3.376540 GGTTGTTTAATTCACGCTGCAA 58.623 40.909 0.00 0.00 0.00 4.08
2124 3748 2.287909 TGGGTTGTTTAATTCACGCTGC 60.288 45.455 0.00 0.00 0.00 5.25
2129 3753 6.924111 ACATGAGATGGGTTGTTTAATTCAC 58.076 36.000 0.00 0.00 33.60 3.18
2176 3802 6.985645 GCAGGGATTGATACTATGATGATCTC 59.014 42.308 0.00 0.00 0.00 2.75
2219 3845 4.093291 CCCGCTGCTGCTCTTCCT 62.093 66.667 14.03 0.00 36.97 3.36
2220 3846 4.400961 ACCCGCTGCTGCTCTTCC 62.401 66.667 14.03 0.00 36.97 3.46
2221 3847 3.123620 CACCCGCTGCTGCTCTTC 61.124 66.667 14.03 0.00 36.97 2.87
2222 3848 4.711949 CCACCCGCTGCTGCTCTT 62.712 66.667 14.03 0.00 36.97 2.85
2240 3872 1.807165 CAGTGATGCGTCTCCACCG 60.807 63.158 7.58 0.00 0.00 4.94
2255 3887 4.656112 CCCATTACAGTAGAGGATTCCAGT 59.344 45.833 5.29 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.