Multiple sequence alignment - TraesCS5A01G233500

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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 TraesCS5A01G233500 chr5A 100.000 5186 0 0 1 5186 448830108 448835293 0.000000e+00 9577.0
1 TraesCS5A01G233500 chr5A 98.214 56 1 0 4834 4889 1242090 1242035 1.190000e-16 99.0
2 TraesCS5A01G233500 chr5A 89.333 75 7 1 4823 4896 647165554 647165480 5.530000e-15 93.5
3 TraesCS5A01G233500 chr5B 93.593 4027 156 39 858 4830 409055330 409059308 0.000000e+00 5914.0
4 TraesCS5A01G233500 chr5B 80.323 742 108 18 80 815 409054300 409055009 1.280000e-145 527.0
5 TraesCS5A01G233500 chr5B 92.359 301 16 3 4889 5186 409059318 409059614 6.210000e-114 422.0
6 TraesCS5A01G233500 chr5D 93.929 3179 129 23 1691 4836 348742572 348745719 0.000000e+00 4743.0
7 TraesCS5A01G233500 chr5D 93.020 831 36 6 835 1662 348741764 348742575 0.000000e+00 1194.0
8 TraesCS5A01G233500 chr5D 87.298 496 58 2 1 491 348740785 348741280 3.510000e-156 562.0
9 TraesCS5A01G233500 chr5D 95.667 300 7 2 4889 5186 348745724 348746019 1.310000e-130 477.0
10 TraesCS5A01G233500 chr4D 93.651 63 4 0 4828 4890 149761067 149761129 1.540000e-15 95.3
11 TraesCS5A01G233500 chr4D 93.651 63 4 0 4828 4890 149794435 149794497 1.540000e-15 95.3
12 TraesCS5A01G233500 chr4D 93.651 63 4 0 4828 4890 149828552 149828614 1.540000e-15 95.3
13 TraesCS5A01G233500 chr4D 90.000 70 5 2 4822 4890 36413224 36413292 7.150000e-14 89.8
14 TraesCS5A01G233500 chr4D 100.000 29 0 0 585 613 356963336 356963364 3.000000e-03 54.7
15 TraesCS5A01G233500 chr2A 92.537 67 3 2 4834 4898 157931452 157931518 1.540000e-15 95.3
16 TraesCS5A01G233500 chr2A 100.000 28 0 0 586 613 466323787 466323814 9.000000e-03 52.8
17 TraesCS5A01G233500 chr6D 92.537 67 1 4 4834 4898 131426757 131426821 5.530000e-15 93.5
18 TraesCS5A01G233500 chr3A 91.176 68 5 1 4834 4900 693337535 693337468 1.990000e-14 91.6
19 TraesCS5A01G233500 chr7D 100.000 29 0 0 585 613 145618691 145618719 3.000000e-03 54.7
20 TraesCS5A01G233500 chr3B 100.000 29 0 0 585 613 775959250 775959278 3.000000e-03 54.7
21 TraesCS5A01G233500 chr2B 100.000 29 0 0 585 613 263882961 263882933 3.000000e-03 54.7


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 TraesCS5A01G233500 chr5A 448830108 448835293 5185 False 9577.000000 9577 100.000000 1 5186 1 chr5A.!!$F1 5185
1 TraesCS5A01G233500 chr5B 409054300 409059614 5314 False 2287.666667 5914 88.758333 80 5186 3 chr5B.!!$F1 5106
2 TraesCS5A01G233500 chr5D 348740785 348746019 5234 False 1744.000000 4743 92.478500 1 5186 4 chr5D.!!$F1 5185

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
381 383 0.098200 GCGGCCTTGGAAAACGATAC 59.902 55.000 0.00 0.0 0.00 2.24 F
382 384 0.730840 CGGCCTTGGAAAACGATACC 59.269 55.000 0.00 0.0 0.00 2.73 F
1267 1646 0.469705 TCAAATTGGGGCTGTGCTGT 60.470 50.000 0.00 0.0 0.00 4.40 F
1288 1667 1.141657 ACTGTTGGCTTGAGCTCTTGA 59.858 47.619 16.19 0.0 41.70 3.02 F
2908 3347 0.249868 CTGGAAGGTGCTTCGTGACA 60.250 55.000 0.00 0.0 40.99 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1268 1647 1.141657 TCAAGAGCTCAAGCCAACAGT 59.858 47.619 17.77 0.00 43.38 3.55 R
1422 1801 1.153549 CAGTAAGCTCGAGCCCCAC 60.154 63.158 32.94 25.65 43.38 4.61 R
2908 3347 0.034670 GCTCCAATCCTCCAAGCAGT 60.035 55.000 0.00 0.00 33.21 4.40 R
2960 3399 7.497925 AGAAATGAGAAGAAGTAACCACAAC 57.502 36.000 0.00 0.00 0.00 3.32 R
4284 4726 0.320858 TTCGTGAAGTAATGCGGCCA 60.321 50.000 2.24 0.00 0.00 5.36 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
47 48 2.361610 CAAGGCGCATCCCCAAGT 60.362 61.111 10.83 0.00 34.51 3.16
53 54 2.971598 CGCATCCCCAAGTCCTGGT 61.972 63.158 0.00 0.00 44.76 4.00
67 68 1.833630 TCCTGGTTGAGGAGTATGCAG 59.166 52.381 0.00 0.00 46.96 4.41
76 77 1.075374 AGGAGTATGCAGGCAACCAAA 59.925 47.619 0.00 0.00 37.17 3.28
78 79 2.162681 GAGTATGCAGGCAACCAAACT 58.837 47.619 0.00 0.00 37.17 2.66
99 100 2.890474 CCTTAACGGCGCTCGCAT 60.890 61.111 16.36 9.52 44.11 4.73
122 123 2.771943 ACCTCATCGTTCACCACCATAT 59.228 45.455 0.00 0.00 0.00 1.78
143 144 9.416794 CCATATATATCAGCGAATTGATCTACC 57.583 37.037 0.00 0.00 38.65 3.18
149 150 3.069586 CAGCGAATTGATCTACCCCTACA 59.930 47.826 0.00 0.00 0.00 2.74
155 156 2.239400 TGATCTACCCCTACATCTGCG 58.761 52.381 0.00 0.00 0.00 5.18
161 162 1.360551 CCCTACATCTGCGACTCCG 59.639 63.158 0.00 0.00 39.16 4.63
167 168 2.049185 ATCTGCGACTCCGTGAGCT 61.049 57.895 0.00 0.00 38.24 4.09
178 179 0.794473 CCGTGAGCTTTAAACCCGTC 59.206 55.000 0.00 0.00 0.00 4.79
181 182 1.458445 GTGAGCTTTAAACCCGTCGTC 59.542 52.381 0.00 0.00 0.00 4.20
183 184 2.289195 TGAGCTTTAAACCCGTCGTCAT 60.289 45.455 0.00 0.00 0.00 3.06
184 185 2.073816 AGCTTTAAACCCGTCGTCATG 58.926 47.619 0.00 0.00 0.00 3.07
186 187 2.481185 GCTTTAAACCCGTCGTCATGAA 59.519 45.455 0.00 0.00 0.00 2.57
195 196 4.042398 CCCGTCGTCATGAACTAATACTG 58.958 47.826 0.00 0.00 0.00 2.74
289 290 7.988904 AATGTCAAAATTTTGCAACCATTTG 57.011 28.000 23.36 17.55 38.05 2.32
361 363 2.028112 ACATAGTGTGAACATGCGGAGT 60.028 45.455 0.00 0.00 0.00 3.85
363 365 1.207593 GTGTGAACATGCGGAGTGC 59.792 57.895 0.00 0.00 46.70 4.40
381 383 0.098200 GCGGCCTTGGAAAACGATAC 59.902 55.000 0.00 0.00 0.00 2.24
382 384 0.730840 CGGCCTTGGAAAACGATACC 59.269 55.000 0.00 0.00 0.00 2.73
386 388 2.089201 CCTTGGAAAACGATACCCACC 58.911 52.381 0.00 0.00 0.00 4.61
401 403 1.212688 CCCACCTGACCTATCATGCAA 59.787 52.381 0.00 0.00 33.22 4.08
409 411 5.766670 CCTGACCTATCATGCAACAATATGT 59.233 40.000 0.00 0.00 33.22 2.29
436 438 1.300697 ACAACTCGAAGGCCGTGTC 60.301 57.895 0.00 0.00 43.20 3.67
446 448 4.980805 GCCGTGTCGCCTGTTGGA 62.981 66.667 0.00 0.00 34.57 3.53
456 458 0.743097 GCCTGTTGGATGCAAGATCC 59.257 55.000 0.00 0.00 38.66 3.36
480 486 2.742116 GCCGGATGCCAACCCTAGA 61.742 63.158 5.05 0.00 0.00 2.43
487 493 3.769300 GGATGCCAACCCTAGAAACAAAT 59.231 43.478 0.00 0.00 0.00 2.32
491 497 6.339587 TGCCAACCCTAGAAACAAATTAAG 57.660 37.500 0.00 0.00 0.00 1.85
493 499 6.723977 TGCCAACCCTAGAAACAAATTAAGAT 59.276 34.615 0.00 0.00 0.00 2.40
518 614 1.583556 TAATCTGAGCTCCTTGGCCA 58.416 50.000 12.15 0.00 0.00 5.36
521 617 1.453379 CTGAGCTCCTTGGCCATGG 60.453 63.158 28.04 28.04 0.00 3.66
536 632 1.414181 CCATGGCAAGACGGATACTCT 59.586 52.381 0.00 0.00 0.00 3.24
541 637 2.025155 GCAAGACGGATACTCTCTCCA 58.975 52.381 0.00 0.00 32.72 3.86
562 658 6.774673 TCCAATCCATATTAATTACCGCTCA 58.225 36.000 0.00 0.00 0.00 4.26
563 659 6.653320 TCCAATCCATATTAATTACCGCTCAC 59.347 38.462 0.00 0.00 0.00 3.51
564 660 6.429692 CCAATCCATATTAATTACCGCTCACA 59.570 38.462 0.00 0.00 0.00 3.58
565 661 7.121168 CCAATCCATATTAATTACCGCTCACAT 59.879 37.037 0.00 0.00 0.00 3.21
566 662 7.615582 ATCCATATTAATTACCGCTCACATG 57.384 36.000 0.00 0.00 0.00 3.21
568 664 6.873605 TCCATATTAATTACCGCTCACATGAG 59.126 38.462 0.00 4.43 44.75 2.90
590 686 2.811431 CGGAGCGGCAATTAATATGGAA 59.189 45.455 1.45 0.00 0.00 3.53
592 688 3.364964 GGAGCGGCAATTAATATGGAACG 60.365 47.826 1.45 0.00 0.00 3.95
593 689 2.552315 AGCGGCAATTAATATGGAACGG 59.448 45.455 1.45 0.00 0.00 4.44
595 691 3.364964 GCGGCAATTAATATGGAACGGAG 60.365 47.826 0.00 0.00 0.00 4.63
596 692 3.188460 CGGCAATTAATATGGAACGGAGG 59.812 47.826 0.00 0.00 0.00 4.30
601 697 6.743208 GCAATTAATATGGAACGGAGGGAGTA 60.743 42.308 0.00 0.00 0.00 2.59
612 708 2.685522 CGGAGGGAGTAGCTCTTTCTCT 60.686 54.545 0.00 0.00 0.00 3.10
645 741 3.103793 CGCAAGAAAACAGTACCATCG 57.896 47.619 0.00 0.00 43.02 3.84
646 742 2.734606 CGCAAGAAAACAGTACCATCGA 59.265 45.455 0.00 0.00 43.02 3.59
647 743 3.181530 CGCAAGAAAACAGTACCATCGAG 60.182 47.826 0.00 0.00 43.02 4.04
648 744 3.994392 GCAAGAAAACAGTACCATCGAGA 59.006 43.478 0.00 0.00 0.00 4.04
655 751 6.541111 AAACAGTACCATCGAGAAAGTTTC 57.459 37.500 7.57 7.57 0.00 2.78
667 763 4.212214 CGAGAAAGTTTCTTCAGACTTGGG 59.788 45.833 18.96 0.00 40.87 4.12
668 764 5.368989 GAGAAAGTTTCTTCAGACTTGGGA 58.631 41.667 18.96 0.00 40.87 4.37
669 765 5.755849 AGAAAGTTTCTTCAGACTTGGGAA 58.244 37.500 12.50 0.00 36.36 3.97
671 767 6.836007 AGAAAGTTTCTTCAGACTTGGGAATT 59.164 34.615 12.50 0.00 36.36 2.17
672 768 6.396829 AAGTTTCTTCAGACTTGGGAATTG 57.603 37.500 0.00 0.00 34.96 2.32
673 769 5.449553 AGTTTCTTCAGACTTGGGAATTGT 58.550 37.500 0.00 0.00 0.00 2.71
674 770 6.601332 AGTTTCTTCAGACTTGGGAATTGTA 58.399 36.000 0.00 0.00 0.00 2.41
681 777 5.705441 TCAGACTTGGGAATTGTATTGTCAC 59.295 40.000 0.00 0.00 0.00 3.67
682 778 5.707298 CAGACTTGGGAATTGTATTGTCACT 59.293 40.000 0.00 0.00 0.00 3.41
685 781 6.248433 ACTTGGGAATTGTATTGTCACTGAT 58.752 36.000 0.00 0.00 0.00 2.90
696 792 3.792047 CACTGATGCGTGTGGGCG 61.792 66.667 0.00 0.00 35.06 6.13
712 808 2.358267 TGGGCGTGTTGTTACGATTTTT 59.642 40.909 2.14 0.00 46.46 1.94
715 811 3.792421 GGCGTGTTGTTACGATTTTTGTT 59.208 39.130 2.14 0.00 46.46 2.83
720 816 7.317177 CGTGTTGTTACGATTTTTGTTCTTTC 58.683 34.615 0.00 0.00 46.46 2.62
752 849 7.978099 AATTAATAACCTGGCAATCCTCTTT 57.022 32.000 0.00 0.00 0.00 2.52
756 853 6.775594 ATAACCTGGCAATCCTCTTTAAAC 57.224 37.500 0.00 0.00 0.00 2.01
764 861 6.151648 TGGCAATCCTCTTTAAACAGATTGAG 59.848 38.462 22.40 11.37 44.14 3.02
765 862 6.151817 GGCAATCCTCTTTAAACAGATTGAGT 59.848 38.462 22.40 3.92 44.14 3.41
790 887 8.722394 GTCCATTAGACTCTGGTTTAAAGAAAG 58.278 37.037 4.39 0.00 42.69 2.62
899 1275 1.663643 CGTACGATTTCCATGTGTGGG 59.336 52.381 10.44 0.00 46.06 4.61
1028 1404 2.513897 CTCGACGGCCCAAATCCC 60.514 66.667 0.00 0.00 0.00 3.85
1045 1421 2.683475 CCCCATTCCTCACCACCC 59.317 66.667 0.00 0.00 0.00 4.61
1242 1621 1.509463 CGCGGCAGAAGGTACTGTA 59.491 57.895 0.00 0.00 40.86 2.74
1264 1643 2.735126 CGTAATCAAATTGGGGCTGTGC 60.735 50.000 0.00 0.00 0.00 4.57
1265 1644 1.648116 AATCAAATTGGGGCTGTGCT 58.352 45.000 0.00 0.00 0.00 4.40
1266 1645 0.899720 ATCAAATTGGGGCTGTGCTG 59.100 50.000 0.00 0.00 0.00 4.41
1267 1646 0.469705 TCAAATTGGGGCTGTGCTGT 60.470 50.000 0.00 0.00 0.00 4.40
1268 1647 1.202989 TCAAATTGGGGCTGTGCTGTA 60.203 47.619 0.00 0.00 0.00 2.74
1288 1667 1.141657 ACTGTTGGCTTGAGCTCTTGA 59.858 47.619 16.19 0.00 41.70 3.02
1289 1668 2.224606 CTGTTGGCTTGAGCTCTTGAA 58.775 47.619 16.19 0.00 41.70 2.69
1290 1669 2.224606 TGTTGGCTTGAGCTCTTGAAG 58.775 47.619 16.19 11.38 41.70 3.02
1305 1684 7.865707 AGCTCTTGAAGTAATTGTTACAGTTG 58.134 34.615 3.33 0.00 38.60 3.16
1306 1685 7.499232 AGCTCTTGAAGTAATTGTTACAGTTGT 59.501 33.333 3.33 0.00 38.60 3.32
1307 1686 8.770828 GCTCTTGAAGTAATTGTTACAGTTGTA 58.229 33.333 3.33 0.00 38.60 2.41
1381 1760 3.112709 GAGCTTGCCACCGACGAC 61.113 66.667 0.00 0.00 0.00 4.34
1422 1801 3.829601 GAGATCCTCTATGGTACCAGGTG 59.170 52.174 21.41 14.98 37.07 4.00
1453 1832 4.666237 GAGCTTACTGATTGTTCCAATGC 58.334 43.478 0.00 0.00 0.00 3.56
1454 1833 4.338879 AGCTTACTGATTGTTCCAATGCT 58.661 39.130 0.00 0.00 0.00 3.79
1455 1834 4.157289 AGCTTACTGATTGTTCCAATGCTG 59.843 41.667 0.00 0.00 0.00 4.41
1456 1835 4.082571 GCTTACTGATTGTTCCAATGCTGT 60.083 41.667 0.00 0.94 0.00 4.40
1457 1836 5.565439 GCTTACTGATTGTTCCAATGCTGTT 60.565 40.000 0.00 0.00 0.00 3.16
1458 1837 4.942761 ACTGATTGTTCCAATGCTGTTT 57.057 36.364 0.00 0.00 0.00 2.83
1459 1838 7.517614 TTACTGATTGTTCCAATGCTGTTTA 57.482 32.000 0.00 0.00 0.00 2.01
1666 2052 3.581755 CATGCTTTGCTGCACAATTAGT 58.418 40.909 0.00 0.00 46.33 2.24
1667 2053 3.287312 TGCTTTGCTGCACAATTAGTC 57.713 42.857 0.00 0.00 38.31 2.59
1668 2054 2.622470 TGCTTTGCTGCACAATTAGTCA 59.378 40.909 0.00 0.00 38.31 3.41
1669 2055 3.067883 TGCTTTGCTGCACAATTAGTCAA 59.932 39.130 0.00 0.00 38.31 3.18
1670 2056 4.050553 GCTTTGCTGCACAATTAGTCAAA 58.949 39.130 0.00 0.00 38.31 2.69
1671 2057 4.687483 GCTTTGCTGCACAATTAGTCAAAT 59.313 37.500 0.00 0.00 38.31 2.32
1672 2058 5.863397 GCTTTGCTGCACAATTAGTCAAATA 59.137 36.000 0.00 0.00 38.31 1.40
1673 2059 6.532657 GCTTTGCTGCACAATTAGTCAAATAT 59.467 34.615 0.00 0.00 38.31 1.28
1674 2060 7.701924 GCTTTGCTGCACAATTAGTCAAATATA 59.298 33.333 0.00 0.00 38.31 0.86
1675 2061 9.740239 CTTTGCTGCACAATTAGTCAAATATAT 57.260 29.630 0.00 0.00 38.31 0.86
1676 2062 9.734620 TTTGCTGCACAATTAGTCAAATATATC 57.265 29.630 0.00 0.00 38.31 1.63
1677 2063 8.681486 TGCTGCACAATTAGTCAAATATATCT 57.319 30.769 0.00 0.00 0.00 1.98
1678 2064 9.777297 TGCTGCACAATTAGTCAAATATATCTA 57.223 29.630 0.00 0.00 0.00 1.98
2011 2444 4.137543 GACCTGATCACTTTCCTGTGTTT 58.862 43.478 0.00 0.00 38.90 2.83
2013 2446 3.885297 CCTGATCACTTTCCTGTGTTTGT 59.115 43.478 0.00 0.00 38.90 2.83
2027 2460 4.917385 TGTGTTTGTATAATGGGACTGCT 58.083 39.130 0.00 0.00 0.00 4.24
2070 2506 9.948964 CAATATCTACCTGTCATATTCCAATGA 57.051 33.333 0.00 0.00 33.48 2.57
2115 2551 5.825593 TGGTTCTGTGTCTCCTTATTCTT 57.174 39.130 0.00 0.00 0.00 2.52
2148 2584 3.524541 GCCCAGTGCTAAAATCAATTGG 58.475 45.455 5.42 0.00 36.87 3.16
2161 2597 4.824479 ATCAATTGGAAAAAGGCCGAAT 57.176 36.364 5.42 0.00 0.00 3.34
2171 2607 3.615224 AAAGGCCGAATACCGTTTCTA 57.385 42.857 0.00 0.00 36.31 2.10
2185 2621 4.226761 CCGTTTCTATTGTTGCTTTGGAC 58.773 43.478 0.00 0.00 0.00 4.02
2287 2723 3.409026 AGGTCAGTCAAGTAGGCTTTG 57.591 47.619 0.00 0.00 31.49 2.77
2294 2730 4.162320 CAGTCAAGTAGGCTTTGATCCCTA 59.838 45.833 5.02 0.00 31.49 3.53
2301 2737 7.192852 AGTAGGCTTTGATCCCTATATCATG 57.807 40.000 0.00 0.00 35.84 3.07
2322 2758 8.481492 TCATGCAAAAATGTATCCCTGATTAT 57.519 30.769 0.00 0.00 0.00 1.28
2361 2797 2.501723 AGTCGACCTGATATGGTTTGCT 59.498 45.455 13.01 0.00 41.00 3.91
2499 2936 1.990060 TAGTGCAGACCTGGAGGCC 60.990 63.158 0.00 0.00 39.32 5.19
2532 2969 6.143206 TCTACACCTCCTGGATGAATATTCA 58.857 40.000 20.07 20.07 37.99 2.57
2539 2976 6.883217 CCTCCTGGATGAATATTCAAGGTATG 59.117 42.308 24.42 17.93 41.13 2.39
2545 2982 9.725019 TGGATGAATATTCAAGGTATGTACATC 57.275 33.333 21.50 9.86 41.13 3.06
2606 3043 8.829373 ATTTCCCTGGGATATATGAAAATAGC 57.171 34.615 17.93 0.00 0.00 2.97
2652 3090 5.634859 CGCTGCAATCTGTTTCCTTTTAAAT 59.365 36.000 0.00 0.00 0.00 1.40
2655 3093 7.060383 TGCAATCTGTTTCCTTTTAAATGGA 57.940 32.000 16.72 16.72 0.00 3.41
2656 3094 7.678837 TGCAATCTGTTTCCTTTTAAATGGAT 58.321 30.769 20.21 5.08 32.92 3.41
2908 3347 0.249868 CTGGAAGGTGCTTCGTGACA 60.250 55.000 0.00 0.00 40.99 3.58
2960 3399 9.930693 ACTAGAAAGTACATTCTTGAAGGTTAG 57.069 33.333 22.88 12.91 40.13 2.34
3192 3632 6.213600 AGTTAGCCAAGAGACTATCTGGAAAA 59.786 38.462 1.92 0.00 38.67 2.29
3340 3780 7.543868 GCGCAATAGATAGAACTTCATATCTGT 59.456 37.037 0.30 9.36 38.78 3.41
3375 3815 3.268023 AGCTCTTGTTCTATTTCCCCG 57.732 47.619 0.00 0.00 0.00 5.73
3492 3932 6.378280 CCAGAAGTAATGCCTTTACCATTTCT 59.622 38.462 3.70 4.38 41.01 2.52
3565 4005 3.260884 GCAGCTAGGCAGGTAATACCATA 59.739 47.826 12.54 0.00 41.95 2.74
3906 4348 8.843308 TGATCTGATCAAATTAAATTCCCCTT 57.157 30.769 17.56 0.00 36.11 3.95
3907 4349 9.270707 TGATCTGATCAAATTAAATTCCCCTTT 57.729 29.630 17.56 0.00 36.11 3.11
3908 4350 9.538508 GATCTGATCAAATTAAATTCCCCTTTG 57.461 33.333 12.66 0.00 0.00 2.77
3909 4351 7.330262 TCTGATCAAATTAAATTCCCCTTTGC 58.670 34.615 0.00 0.00 0.00 3.68
3943 4385 1.234821 TTTTGCCTGTAAGTCGCCTG 58.765 50.000 0.00 0.00 0.00 4.85
3951 4393 1.000145 GTAAGTCGCCTGCTAACTGC 59.000 55.000 0.00 0.00 43.25 4.40
4043 4485 4.160329 TCGGGACAGATTATGCTAGGATT 58.840 43.478 0.65 0.00 0.00 3.01
4088 4530 4.563580 GCTCAGGTGAGGTTCACTTTATCA 60.564 45.833 9.03 0.00 46.19 2.15
4089 4531 5.738909 CTCAGGTGAGGTTCACTTTATCAT 58.261 41.667 8.89 0.00 46.19 2.45
4091 4533 4.878397 CAGGTGAGGTTCACTTTATCATCC 59.122 45.833 8.89 0.00 46.19 3.51
4093 4535 5.251700 AGGTGAGGTTCACTTTATCATCCTT 59.748 40.000 8.89 0.00 46.19 3.36
4094 4536 5.586643 GGTGAGGTTCACTTTATCATCCTTC 59.413 44.000 8.89 0.00 46.19 3.46
4096 4538 6.536941 GTGAGGTTCACTTTATCATCCTTCTC 59.463 42.308 2.08 0.00 43.73 2.87
4098 4540 6.648192 AGGTTCACTTTATCATCCTTCTCAG 58.352 40.000 0.00 0.00 0.00 3.35
4106 4548 3.464720 TCATCCTTCTCAGGTCTCAGT 57.535 47.619 0.00 0.00 41.69 3.41
4119 4561 3.199508 AGGTCTCAGTAGCTGCATTGATT 59.800 43.478 4.12 0.00 0.00 2.57
4124 4566 6.649973 GTCTCAGTAGCTGCATTGATTCATAT 59.350 38.462 4.12 0.00 0.00 1.78
4134 4576 4.678287 GCATTGATTCATATGTCGCCTTTG 59.322 41.667 1.90 0.00 0.00 2.77
4182 4624 6.693545 CGTGTTACCTAGAATCTCATGAAGAC 59.306 42.308 0.00 0.00 36.65 3.01
4187 4629 5.954752 ACCTAGAATCTCATGAAGACTGACA 59.045 40.000 0.00 0.00 36.65 3.58
4194 4636 3.657634 TCATGAAGACTGACAAGAGCAC 58.342 45.455 0.00 0.00 0.00 4.40
4201 4643 4.649692 AGACTGACAAGAGCACAATCATT 58.350 39.130 0.00 0.00 0.00 2.57
4237 4679 0.615331 TGGGCACTCTGATCTTGTCC 59.385 55.000 0.00 0.00 35.43 4.02
4292 4734 1.315690 CAGATCATTTCTGGCCGCAT 58.684 50.000 0.00 0.00 46.89 4.73
4297 4739 2.722094 TCATTTCTGGCCGCATTACTT 58.278 42.857 0.00 0.00 0.00 2.24
4312 4756 2.065993 TACTTCACGAAGCTCTGCAC 57.934 50.000 6.71 0.00 41.99 4.57
4315 4759 0.319900 TTCACGAAGCTCTGCACCTC 60.320 55.000 0.00 0.00 0.00 3.85
4317 4761 1.013005 CACGAAGCTCTGCACCTCTG 61.013 60.000 0.00 0.00 0.00 3.35
4318 4762 1.447489 CGAAGCTCTGCACCTCTGG 60.447 63.158 0.00 0.00 0.00 3.86
4323 4767 1.261238 GCTCTGCACCTCTGGGTAGT 61.261 60.000 0.00 0.00 45.41 2.73
4365 4809 1.202698 GCAGATGGTAGGTAGCAAGGG 60.203 57.143 0.00 0.00 37.24 3.95
4370 4814 0.466124 GGTAGGTAGCAAGGGCAGAG 59.534 60.000 0.00 0.00 44.61 3.35
4381 4825 0.767375 AGGGCAGAGAAGAACAGCAA 59.233 50.000 0.00 0.00 0.00 3.91
4384 4828 1.534595 GGCAGAGAAGAACAGCAACAG 59.465 52.381 0.00 0.00 0.00 3.16
4387 4831 3.303659 GCAGAGAAGAACAGCAACAGTTC 60.304 47.826 0.00 0.00 44.32 3.01
4388 4832 3.873361 CAGAGAAGAACAGCAACAGTTCA 59.127 43.478 8.54 0.00 45.93 3.18
4389 4833 4.025061 CAGAGAAGAACAGCAACAGTTCAG 60.025 45.833 8.54 0.00 45.93 3.02
4392 4836 0.312102 GAACAGCAACAGTTCAGCCC 59.688 55.000 0.00 0.00 43.64 5.19
4393 4837 0.106519 AACAGCAACAGTTCAGCCCT 60.107 50.000 0.00 0.00 0.00 5.19
4395 4839 0.595095 CAGCAACAGTTCAGCCCTTC 59.405 55.000 0.00 0.00 0.00 3.46
4396 4840 0.183492 AGCAACAGTTCAGCCCTTCA 59.817 50.000 0.00 0.00 0.00 3.02
4397 4841 1.032014 GCAACAGTTCAGCCCTTCAA 58.968 50.000 0.00 0.00 0.00 2.69
4403 4869 3.571401 ACAGTTCAGCCCTTCAAATTCAG 59.429 43.478 0.00 0.00 0.00 3.02
4407 4873 2.756760 TCAGCCCTTCAAATTCAGATGC 59.243 45.455 0.00 0.00 0.00 3.91
4409 4875 1.745087 GCCCTTCAAATTCAGATGCGA 59.255 47.619 0.00 0.00 0.00 5.10
4422 4888 6.983474 TTCAGATGCGAGAATTTGATTGTA 57.017 33.333 0.00 0.00 0.00 2.41
4427 4893 4.732784 TGCGAGAATTTGATTGTAAAGCC 58.267 39.130 0.00 0.00 0.00 4.35
4644 5117 2.207590 GTAAAATAACGGCTCCCCTCG 58.792 52.381 0.00 0.00 0.00 4.63
4677 5150 1.742750 GCGCCCTACCTTTCAGTTAGG 60.743 57.143 0.00 0.00 38.79 2.69
4730 5203 5.904750 TGCTCATACCAGCCATCCATATATA 59.095 40.000 0.00 0.00 38.80 0.86
4732 5205 7.102346 GCTCATACCAGCCATCCATATATATC 58.898 42.308 0.00 0.00 32.76 1.63
4733 5206 7.038445 GCTCATACCAGCCATCCATATATATCT 60.038 40.741 0.00 0.00 32.76 1.98
4734 5207 8.803600 TCATACCAGCCATCCATATATATCTT 57.196 34.615 0.00 0.00 0.00 2.40
4735 5208 9.897040 TCATACCAGCCATCCATATATATCTTA 57.103 33.333 0.00 0.00 0.00 2.10
4798 5275 1.083489 TGCCGATCACCGATGTTTTC 58.917 50.000 0.00 0.00 41.76 2.29
4832 5309 4.673061 CGTTCATCGGAGCAGTATCTATCC 60.673 50.000 0.00 0.00 35.71 2.59
4836 5313 3.413327 TCGGAGCAGTATCTATCCACTC 58.587 50.000 0.00 0.00 0.00 3.51
4837 5314 2.490115 CGGAGCAGTATCTATCCACTCC 59.510 54.545 0.00 0.00 39.06 3.85
4838 5315 2.829120 GGAGCAGTATCTATCCACTCCC 59.171 54.545 0.00 0.00 36.95 4.30
4840 5317 3.761752 GAGCAGTATCTATCCACTCCCTC 59.238 52.174 0.00 0.00 0.00 4.30
4841 5318 3.401002 AGCAGTATCTATCCACTCCCTCT 59.599 47.826 0.00 0.00 0.00 3.69
4842 5319 3.509575 GCAGTATCTATCCACTCCCTCTG 59.490 52.174 0.00 0.00 0.00 3.35
4843 5320 4.735369 CAGTATCTATCCACTCCCTCTGT 58.265 47.826 0.00 0.00 0.00 3.41
4844 5321 4.764823 CAGTATCTATCCACTCCCTCTGTC 59.235 50.000 0.00 0.00 0.00 3.51
4845 5322 2.757894 TCTATCCACTCCCTCTGTCC 57.242 55.000 0.00 0.00 0.00 4.02
4846 5323 1.218196 TCTATCCACTCCCTCTGTCCC 59.782 57.143 0.00 0.00 0.00 4.46
4847 5324 1.015609 TATCCACTCCCTCTGTCCCA 58.984 55.000 0.00 0.00 0.00 4.37
4848 5325 0.119155 ATCCACTCCCTCTGTCCCAA 59.881 55.000 0.00 0.00 0.00 4.12
4849 5326 0.104672 TCCACTCCCTCTGTCCCAAA 60.105 55.000 0.00 0.00 0.00 3.28
4850 5327 0.771127 CCACTCCCTCTGTCCCAAAA 59.229 55.000 0.00 0.00 0.00 2.44
4851 5328 1.355720 CCACTCCCTCTGTCCCAAAAT 59.644 52.381 0.00 0.00 0.00 1.82
4852 5329 2.225117 CCACTCCCTCTGTCCCAAAATT 60.225 50.000 0.00 0.00 0.00 1.82
4853 5330 3.084786 CACTCCCTCTGTCCCAAAATTC 58.915 50.000 0.00 0.00 0.00 2.17
4854 5331 2.989571 ACTCCCTCTGTCCCAAAATTCT 59.010 45.455 0.00 0.00 0.00 2.40
4855 5332 3.399305 ACTCCCTCTGTCCCAAAATTCTT 59.601 43.478 0.00 0.00 0.00 2.52
4856 5333 3.760684 CTCCCTCTGTCCCAAAATTCTTG 59.239 47.826 0.00 0.00 0.00 3.02
4857 5334 3.140144 TCCCTCTGTCCCAAAATTCTTGT 59.860 43.478 0.00 0.00 0.00 3.16
4858 5335 3.507622 CCCTCTGTCCCAAAATTCTTGTC 59.492 47.826 0.00 0.00 0.00 3.18
4859 5336 4.401925 CCTCTGTCCCAAAATTCTTGTCT 58.598 43.478 0.00 0.00 0.00 3.41
4860 5337 4.829492 CCTCTGTCCCAAAATTCTTGTCTT 59.171 41.667 0.00 0.00 0.00 3.01
4861 5338 6.003950 CCTCTGTCCCAAAATTCTTGTCTTA 58.996 40.000 0.00 0.00 0.00 2.10
4862 5339 6.150140 CCTCTGTCCCAAAATTCTTGTCTTAG 59.850 42.308 0.00 0.00 0.00 2.18
4863 5340 6.837312 TCTGTCCCAAAATTCTTGTCTTAGA 58.163 36.000 0.00 0.00 0.00 2.10
4864 5341 7.461749 TCTGTCCCAAAATTCTTGTCTTAGAT 58.538 34.615 0.00 0.00 0.00 1.98
4865 5342 7.944554 TCTGTCCCAAAATTCTTGTCTTAGATT 59.055 33.333 0.00 0.00 0.00 2.40
4866 5343 8.477419 TGTCCCAAAATTCTTGTCTTAGATTT 57.523 30.769 0.00 0.00 0.00 2.17
4867 5344 8.359642 TGTCCCAAAATTCTTGTCTTAGATTTG 58.640 33.333 0.00 0.00 29.84 2.32
4868 5345 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
4869 5346 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
4870 5347 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
4946 5423 1.136891 TCTGTGATATGTGCCTCACCG 59.863 52.381 0.00 0.00 40.83 4.94
5001 5478 5.066634 TGAAGATGGTCGTGCAAAGTTTTTA 59.933 36.000 0.00 0.00 0.00 1.52
5087 5567 1.863454 GTGAATGAGCGCCATGTCTAG 59.137 52.381 2.29 0.00 35.24 2.43
5088 5568 0.864455 GAATGAGCGCCATGTCTAGC 59.136 55.000 2.29 0.00 35.24 3.42
5089 5569 0.467384 AATGAGCGCCATGTCTAGCT 59.533 50.000 2.29 0.00 43.33 3.32
5090 5570 1.332195 ATGAGCGCCATGTCTAGCTA 58.668 50.000 2.29 0.00 40.39 3.32
5171 5651 1.215423 AGCTTTCTAAATCCCGGGCAT 59.785 47.619 18.49 7.71 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.361610 ACTTGGGGATGCGCCTTG 60.362 61.111 4.18 0.00 37.37 3.61
32 33 4.115199 GGACTTGGGGATGCGCCT 62.115 66.667 4.18 0.00 37.37 5.52
34 35 2.825836 CAGGACTTGGGGATGCGC 60.826 66.667 0.00 0.00 0.00 6.09
53 54 1.340017 GGTTGCCTGCATACTCCTCAA 60.340 52.381 0.00 0.00 0.00 3.02
67 68 1.886886 TAAGGACGAGTTTGGTTGCC 58.113 50.000 0.00 0.00 0.00 4.52
90 91 2.587194 ATGAGGTGATGCGAGCGC 60.587 61.111 8.08 8.08 42.35 5.92
95 96 0.647410 GTGAACGATGAGGTGATGCG 59.353 55.000 0.00 0.00 0.00 4.73
99 100 0.320374 GGTGGTGAACGATGAGGTGA 59.680 55.000 0.00 0.00 0.00 4.02
122 123 5.958380 AGGGGTAGATCAATTCGCTGATATA 59.042 40.000 0.00 0.00 36.15 0.86
143 144 1.360551 CGGAGTCGCAGATGTAGGG 59.639 63.158 0.00 0.00 40.67 3.53
149 150 1.599606 AAGCTCACGGAGTCGCAGAT 61.600 55.000 0.00 0.00 41.61 2.90
155 156 2.074576 GGGTTTAAAGCTCACGGAGTC 58.925 52.381 16.40 0.00 41.61 3.36
161 162 1.458445 GACGACGGGTTTAAAGCTCAC 59.542 52.381 16.40 7.52 0.00 3.51
167 168 3.731089 AGTTCATGACGACGGGTTTAAA 58.269 40.909 0.00 0.00 0.00 1.52
178 179 7.582435 ACAACTTCAGTATTAGTTCATGACG 57.418 36.000 0.00 0.00 32.50 4.35
361 363 0.321741 TATCGTTTTCCAAGGCCGCA 60.322 50.000 0.00 0.00 0.00 5.69
363 365 0.730840 GGTATCGTTTTCCAAGGCCG 59.269 55.000 0.00 0.00 0.00 6.13
370 372 2.353323 GTCAGGTGGGTATCGTTTTCC 58.647 52.381 0.00 0.00 0.00 3.13
372 374 1.982958 AGGTCAGGTGGGTATCGTTTT 59.017 47.619 0.00 0.00 0.00 2.43
381 383 0.839277 TGCATGATAGGTCAGGTGGG 59.161 55.000 0.00 0.00 38.37 4.61
382 384 2.292267 GTTGCATGATAGGTCAGGTGG 58.708 52.381 0.00 0.00 38.37 4.61
386 388 6.484308 TCACATATTGTTGCATGATAGGTCAG 59.516 38.462 0.00 0.00 37.87 3.51
409 411 2.610479 GCCTTCGAGTTGTGATCACTCA 60.610 50.000 25.55 10.52 0.00 3.41
436 438 0.379669 GATCTTGCATCCAACAGGCG 59.620 55.000 0.00 0.00 33.06 5.52
456 458 2.823593 TTGGCATCCGGCATGACG 60.824 61.111 15.88 15.88 44.85 4.35
491 497 8.093927 GGCCAAGGAGCTCAGATTATATATATC 58.906 40.741 17.19 0.00 0.00 1.63
493 499 6.902974 TGGCCAAGGAGCTCAGATTATATATA 59.097 38.462 17.19 0.00 0.00 0.86
501 507 0.183014 CATGGCCAAGGAGCTCAGAT 59.817 55.000 10.96 0.00 0.00 2.90
512 608 2.497792 ATCCGTCTTGCCATGGCCAA 62.498 55.000 33.44 24.06 41.09 4.52
518 614 2.625790 GAGAGAGTATCCGTCTTGCCAT 59.374 50.000 0.00 0.00 33.66 4.40
521 617 2.025155 TGGAGAGAGTATCCGTCTTGC 58.975 52.381 0.00 0.00 39.91 4.01
525 621 3.223435 TGGATTGGAGAGAGTATCCGTC 58.777 50.000 0.00 0.00 39.52 4.79
527 623 6.537453 AATATGGATTGGAGAGAGTATCCG 57.463 41.667 0.00 0.00 39.52 4.18
536 632 7.016153 AGCGGTAATTAATATGGATTGGAGA 57.984 36.000 0.00 0.00 0.00 3.71
541 637 7.882791 TCATGTGAGCGGTAATTAATATGGATT 59.117 33.333 0.00 0.00 0.00 3.01
562 658 3.687321 ATTGCCGCTCCGCTCATGT 62.687 57.895 0.00 0.00 0.00 3.21
563 659 1.159713 TAATTGCCGCTCCGCTCATG 61.160 55.000 0.00 0.00 0.00 3.07
564 660 0.463654 TTAATTGCCGCTCCGCTCAT 60.464 50.000 0.00 0.00 0.00 2.90
565 661 0.463654 ATTAATTGCCGCTCCGCTCA 60.464 50.000 0.00 0.00 0.00 4.26
566 662 1.508632 TATTAATTGCCGCTCCGCTC 58.491 50.000 0.00 0.00 0.00 5.03
568 664 1.135689 CCATATTAATTGCCGCTCCGC 60.136 52.381 0.00 0.00 0.00 5.54
569 665 2.422597 TCCATATTAATTGCCGCTCCG 58.577 47.619 0.00 0.00 0.00 4.63
570 666 3.364964 CGTTCCATATTAATTGCCGCTCC 60.365 47.826 0.00 0.00 0.00 4.70
576 672 4.394729 TCCCTCCGTTCCATATTAATTGC 58.605 43.478 0.00 0.00 0.00 3.56
590 686 1.006162 AGAAAGAGCTACTCCCTCCGT 59.994 52.381 0.00 0.00 0.00 4.69
592 688 3.026707 AGAGAAAGAGCTACTCCCTCC 57.973 52.381 0.00 0.00 31.76 4.30
593 689 3.767131 ACAAGAGAAAGAGCTACTCCCTC 59.233 47.826 0.00 0.00 0.00 4.30
595 691 4.021016 TGAACAAGAGAAAGAGCTACTCCC 60.021 45.833 0.00 0.00 0.00 4.30
596 692 5.140747 TGAACAAGAGAAAGAGCTACTCC 57.859 43.478 0.00 0.00 0.00 3.85
601 697 3.080319 GGCATGAACAAGAGAAAGAGCT 58.920 45.455 0.00 0.00 0.00 4.09
631 727 6.766467 AGAAACTTTCTCGATGGTACTGTTTT 59.234 34.615 0.00 0.00 34.07 2.43
637 733 6.089685 GTCTGAAGAAACTTTCTCGATGGTAC 59.910 42.308 4.46 0.00 39.61 3.34
639 735 4.991687 GTCTGAAGAAACTTTCTCGATGGT 59.008 41.667 4.46 0.00 39.61 3.55
640 736 5.233988 AGTCTGAAGAAACTTTCTCGATGG 58.766 41.667 4.46 0.00 39.61 3.51
641 737 6.347240 CCAAGTCTGAAGAAACTTTCTCGATG 60.347 42.308 4.46 0.44 39.61 3.84
642 738 5.698545 CCAAGTCTGAAGAAACTTTCTCGAT 59.301 40.000 4.46 0.00 39.61 3.59
643 739 5.050490 CCAAGTCTGAAGAAACTTTCTCGA 58.950 41.667 4.46 0.41 39.61 4.04
644 740 4.212214 CCCAAGTCTGAAGAAACTTTCTCG 59.788 45.833 4.46 0.00 39.61 4.04
645 741 5.368989 TCCCAAGTCTGAAGAAACTTTCTC 58.631 41.667 4.46 0.45 39.61 2.87
646 742 5.373812 TCCCAAGTCTGAAGAAACTTTCT 57.626 39.130 0.00 0.00 43.15 2.52
647 743 6.641169 ATTCCCAAGTCTGAAGAAACTTTC 57.359 37.500 0.00 0.00 33.53 2.62
648 744 6.381133 ACAATTCCCAAGTCTGAAGAAACTTT 59.619 34.615 0.00 0.00 33.53 2.66
655 751 6.430925 TGACAATACAATTCCCAAGTCTGAAG 59.569 38.462 0.00 0.00 0.00 3.02
667 763 5.023920 CACGCATCAGTGACAATACAATTC 58.976 41.667 0.00 0.00 44.43 2.17
668 764 4.455533 ACACGCATCAGTGACAATACAATT 59.544 37.500 0.00 0.00 44.43 2.32
669 765 4.002982 ACACGCATCAGTGACAATACAAT 58.997 39.130 0.00 0.00 44.43 2.71
671 767 2.736192 CACACGCATCAGTGACAATACA 59.264 45.455 0.00 0.00 44.43 2.29
672 768 2.094258 CCACACGCATCAGTGACAATAC 59.906 50.000 0.00 0.00 44.43 1.89
673 769 2.345876 CCACACGCATCAGTGACAATA 58.654 47.619 0.00 0.00 44.43 1.90
674 770 1.159285 CCACACGCATCAGTGACAAT 58.841 50.000 0.00 0.00 44.43 2.71
681 777 3.792047 CACGCCCACACGCATCAG 61.792 66.667 0.00 0.00 36.19 2.90
682 778 4.617520 ACACGCCCACACGCATCA 62.618 61.111 0.00 0.00 36.19 3.07
696 792 8.389586 AGAAAGAACAAAAATCGTAACAACAC 57.610 30.769 0.00 0.00 0.00 3.32
744 841 7.020827 TGGACTCAATCTGTTTAAAGAGGAT 57.979 36.000 12.06 2.77 0.00 3.24
764 861 8.617290 TTTCTTTAAACCAGAGTCTAATGGAC 57.383 34.615 9.98 0.00 44.80 4.02
765 862 8.656806 TCTTTCTTTAAACCAGAGTCTAATGGA 58.343 33.333 9.98 0.00 39.02 3.41
851 1054 3.191371 CCCAGTTTCATGGCAAAGACTAC 59.809 47.826 0.00 0.00 39.17 2.73
877 1253 1.663643 CACACATGGAAATCGTACGGG 59.336 52.381 16.52 0.00 0.00 5.28
899 1275 2.631545 ACCTGTATAAGATACGGCCACC 59.368 50.000 2.24 0.00 0.00 4.61
1028 1404 2.683475 GGGTGGTGAGGAATGGGG 59.317 66.667 0.00 0.00 0.00 4.96
1045 1421 1.376037 GCGAGGACTGGAAAGTGGG 60.376 63.158 0.00 0.00 0.00 4.61
1181 1560 3.059982 CACAGGCAGGGAGAACGA 58.940 61.111 0.00 0.00 0.00 3.85
1242 1621 2.491693 CACAGCCCCAATTTGATTACGT 59.508 45.455 0.00 0.00 0.00 3.57
1264 1643 2.072298 GAGCTCAAGCCAACAGTACAG 58.928 52.381 9.40 0.00 43.38 2.74
1265 1644 1.694150 AGAGCTCAAGCCAACAGTACA 59.306 47.619 17.77 0.00 43.38 2.90
1266 1645 2.464157 AGAGCTCAAGCCAACAGTAC 57.536 50.000 17.77 0.00 43.38 2.73
1267 1646 2.368548 TCAAGAGCTCAAGCCAACAGTA 59.631 45.455 17.77 0.00 43.38 2.74
1268 1647 1.141657 TCAAGAGCTCAAGCCAACAGT 59.858 47.619 17.77 0.00 43.38 3.55
1289 1668 9.720769 AGCATACTTACAACTGTAACAATTACT 57.279 29.630 0.00 0.00 35.75 2.24
1305 1684 5.885912 TCATCCCCTTCAAAAGCATACTTAC 59.114 40.000 0.00 0.00 34.05 2.34
1306 1685 6.073447 TCATCCCCTTCAAAAGCATACTTA 57.927 37.500 0.00 0.00 34.05 2.24
1307 1686 4.934356 TCATCCCCTTCAAAAGCATACTT 58.066 39.130 0.00 0.00 37.90 2.24
1308 1687 4.591321 TCATCCCCTTCAAAAGCATACT 57.409 40.909 0.00 0.00 0.00 2.12
1381 1760 1.447489 CTCCAGTTCCAGCAGCTCG 60.447 63.158 0.00 0.00 0.00 5.03
1422 1801 1.153549 CAGTAAGCTCGAGCCCCAC 60.154 63.158 32.94 25.65 43.38 4.61
1453 1832 8.436200 GTTATCTCAGTGCTAAACAGTAAACAG 58.564 37.037 0.00 0.00 0.00 3.16
1454 1833 8.148351 AGTTATCTCAGTGCTAAACAGTAAACA 58.852 33.333 0.00 0.00 0.00 2.83
1455 1834 8.436200 CAGTTATCTCAGTGCTAAACAGTAAAC 58.564 37.037 0.00 0.00 0.00 2.01
1456 1835 8.364894 TCAGTTATCTCAGTGCTAAACAGTAAA 58.635 33.333 0.00 0.00 0.00 2.01
1457 1836 7.892609 TCAGTTATCTCAGTGCTAAACAGTAA 58.107 34.615 0.00 0.00 0.00 2.24
1458 1837 7.462571 TCAGTTATCTCAGTGCTAAACAGTA 57.537 36.000 0.00 0.00 0.00 2.74
1459 1838 6.346477 TCAGTTATCTCAGTGCTAAACAGT 57.654 37.500 0.00 0.00 0.00 3.55
1677 2063 8.918658 CGTTACTACTTTGTAATCAAGCAACTA 58.081 33.333 0.00 0.00 35.27 2.24
1678 2064 7.570691 GCGTTACTACTTTGTAATCAAGCAACT 60.571 37.037 0.00 0.00 35.27 3.16
1679 2065 6.518736 GCGTTACTACTTTGTAATCAAGCAAC 59.481 38.462 0.00 0.00 35.27 4.17
1680 2066 6.425721 AGCGTTACTACTTTGTAATCAAGCAA 59.574 34.615 0.00 0.00 35.27 3.91
1681 2067 5.929992 AGCGTTACTACTTTGTAATCAAGCA 59.070 36.000 0.00 0.00 35.27 3.91
1682 2068 6.404712 AGCGTTACTACTTTGTAATCAAGC 57.595 37.500 0.00 0.00 35.27 4.01
1683 2069 8.378421 GGTTAGCGTTACTACTTTGTAATCAAG 58.622 37.037 0.00 0.00 35.27 3.02
1684 2070 7.062138 CGGTTAGCGTTACTACTTTGTAATCAA 59.938 37.037 0.00 0.00 35.27 2.57
1685 2071 6.527722 CGGTTAGCGTTACTACTTTGTAATCA 59.472 38.462 0.00 0.00 35.27 2.57
1686 2072 6.506984 GCGGTTAGCGTTACTACTTTGTAATC 60.507 42.308 5.55 0.00 33.97 1.75
1687 2073 5.289434 GCGGTTAGCGTTACTACTTTGTAAT 59.711 40.000 5.55 0.00 33.97 1.89
1688 2074 4.621034 GCGGTTAGCGTTACTACTTTGTAA 59.379 41.667 5.55 0.00 35.41 2.41
1689 2075 4.165779 GCGGTTAGCGTTACTACTTTGTA 58.834 43.478 5.55 0.00 35.41 2.41
1895 2328 6.805713 TGGAAAAAGAAACAAAGGAGATGAC 58.194 36.000 0.00 0.00 0.00 3.06
2011 2444 6.094881 GCTTTTTGTAGCAGTCCCATTATACA 59.905 38.462 0.00 0.00 40.89 2.29
2013 2446 6.318648 CAGCTTTTTGTAGCAGTCCCATTATA 59.681 38.462 0.00 0.00 43.68 0.98
2027 2460 6.980593 AGATATTGCACAACAGCTTTTTGTA 58.019 32.000 9.63 0.00 35.38 2.41
2040 2473 7.161404 GGAATATGACAGGTAGATATTGCACA 58.839 38.462 0.00 0.00 33.15 4.57
2042 2475 7.315066 TGGAATATGACAGGTAGATATTGCA 57.685 36.000 10.93 10.93 37.78 4.08
2148 2584 3.189910 AGAAACGGTATTCGGCCTTTTTC 59.810 43.478 0.00 0.00 44.45 2.29
2161 2597 5.049267 GTCCAAAGCAACAATAGAAACGGTA 60.049 40.000 0.00 0.00 0.00 4.02
2171 2607 4.188462 TCGATATCGTCCAAAGCAACAAT 58.812 39.130 23.61 0.00 40.80 2.71
2185 2621 6.148645 TGAAAAGATCTCTCTCCTCGATATCG 59.851 42.308 19.14 19.14 41.45 2.92
2294 2730 8.660295 ATCAGGGATACATTTTTGCATGATAT 57.340 30.769 0.00 0.00 33.81 1.63
2322 2758 7.781693 AGGTCGACTTCTACAGGGTAATTAATA 59.218 37.037 16.46 0.00 0.00 0.98
2499 2936 5.914033 TCCAGGAGGTGTAGAAATATTTCG 58.086 41.667 19.86 4.48 37.97 3.46
2532 2969 7.878495 TCCCCAAAATAAGATGTACATACCTT 58.122 34.615 8.71 11.27 0.00 3.50
2545 2982 7.039714 GGCATCCTTATACTTCCCCAAAATAAG 60.040 40.741 0.00 0.00 32.42 1.73
2553 2990 1.003233 CGGGCATCCTTATACTTCCCC 59.997 57.143 0.00 0.00 0.00 4.81
2606 3043 7.167635 CAGCGTATCTGGTTACATAGTTTACAG 59.832 40.741 0.00 0.00 39.15 2.74
2681 3119 7.222224 GCAATAGCGCCGATTACTAGTTAATAT 59.778 37.037 2.29 0.00 29.85 1.28
2902 3341 0.036952 ATCCTCCAAGCAGTGTCACG 60.037 55.000 0.00 0.00 0.00 4.35
2903 3342 1.808945 CAATCCTCCAAGCAGTGTCAC 59.191 52.381 0.00 0.00 0.00 3.67
2908 3347 0.034670 GCTCCAATCCTCCAAGCAGT 60.035 55.000 0.00 0.00 33.21 4.40
2960 3399 7.497925 AGAAATGAGAAGAAGTAACCACAAC 57.502 36.000 0.00 0.00 0.00 3.32
3340 3780 6.049955 ACAAGAGCTTATACTAGGCAAACA 57.950 37.500 0.00 0.00 32.53 2.83
3375 3815 2.747396 TGCCAATGCATTTTCCAGAC 57.253 45.000 9.83 0.00 44.23 3.51
3479 3919 3.288092 GCCACCCTAGAAATGGTAAAGG 58.712 50.000 8.22 0.00 35.79 3.11
3492 3932 2.040009 GCAGCTAATCGGCCACCCTA 62.040 60.000 2.24 0.00 0.00 3.53
3673 4114 7.956420 AAAACTTGACATCTGTATGTACGAA 57.044 32.000 0.00 0.00 46.49 3.85
3832 4273 3.842732 AAAATAGGCGGTAACAGCAAC 57.157 42.857 0.00 0.00 37.75 4.17
3906 4348 4.558178 CAAAATACTCCATGTGCAAGCAA 58.442 39.130 0.00 0.00 0.00 3.91
3907 4349 3.614630 GCAAAATACTCCATGTGCAAGCA 60.615 43.478 0.00 0.00 31.63 3.91
3908 4350 2.925563 GCAAAATACTCCATGTGCAAGC 59.074 45.455 0.00 0.00 31.63 4.01
3909 4351 3.194116 AGGCAAAATACTCCATGTGCAAG 59.806 43.478 0.00 0.00 32.50 4.01
4043 4485 0.321564 AAGCGTAGATTGCCTGCACA 60.322 50.000 0.00 0.00 31.35 4.57
4088 4530 3.052944 AGCTACTGAGACCTGAGAAGGAT 60.053 47.826 0.00 0.00 0.00 3.24
4089 4531 2.310349 AGCTACTGAGACCTGAGAAGGA 59.690 50.000 0.00 0.00 0.00 3.36
4091 4533 2.159254 GCAGCTACTGAGACCTGAGAAG 60.159 54.545 0.00 0.00 32.44 2.85
4093 4535 1.272147 TGCAGCTACTGAGACCTGAGA 60.272 52.381 0.00 0.00 32.44 3.27
4094 4536 1.180907 TGCAGCTACTGAGACCTGAG 58.819 55.000 0.00 0.00 32.44 3.35
4096 4538 2.093816 TCAATGCAGCTACTGAGACCTG 60.094 50.000 0.00 0.00 32.44 4.00
4098 4540 2.680312 TCAATGCAGCTACTGAGACC 57.320 50.000 0.00 0.00 32.44 3.85
4106 4548 4.152938 GCGACATATGAATCAATGCAGCTA 59.847 41.667 10.38 0.00 0.00 3.32
4119 4561 5.079689 TCTGTAACAAAGGCGACATATGA 57.920 39.130 10.38 0.00 0.00 2.15
4124 4566 2.734606 CGAATCTGTAACAAAGGCGACA 59.265 45.455 0.00 0.00 0.00 4.35
4134 4576 2.186076 CGAGTGAGCCGAATCTGTAAC 58.814 52.381 0.00 0.00 0.00 2.50
4182 4624 4.201753 CGGTAATGATTGTGCTCTTGTCAG 60.202 45.833 0.00 0.00 0.00 3.51
4187 4629 3.270877 GTCCGGTAATGATTGTGCTCTT 58.729 45.455 0.00 0.00 0.00 2.85
4194 4636 2.643551 AGGCTTGTCCGGTAATGATTG 58.356 47.619 0.00 0.00 40.77 2.67
4201 4643 0.899720 CCAGTTAGGCTTGTCCGGTA 59.100 55.000 0.00 0.00 40.77 4.02
4237 4679 4.142609 ACACTATGGAGCTGTAATGGTG 57.857 45.455 12.21 12.21 38.38 4.17
4282 4724 0.739462 CGTGAAGTAATGCGGCCAGA 60.739 55.000 2.24 0.00 0.00 3.86
4284 4726 0.320858 TTCGTGAAGTAATGCGGCCA 60.321 50.000 2.24 0.00 0.00 5.36
4287 4729 1.324736 GAGCTTCGTGAAGTAATGCGG 59.675 52.381 11.01 0.00 40.45 5.69
4292 4734 2.404215 GTGCAGAGCTTCGTGAAGTAA 58.596 47.619 11.01 0.00 40.45 2.24
4297 4739 1.181741 AGAGGTGCAGAGCTTCGTGA 61.182 55.000 0.00 0.00 0.00 4.35
4312 4756 4.588951 TGTTATCTATGCACTACCCAGAGG 59.411 45.833 0.00 0.00 40.04 3.69
4315 4759 5.777802 CTCTGTTATCTATGCACTACCCAG 58.222 45.833 0.00 0.00 0.00 4.45
4317 4761 4.039245 TGCTCTGTTATCTATGCACTACCC 59.961 45.833 0.00 0.00 0.00 3.69
4318 4762 5.201713 TGCTCTGTTATCTATGCACTACC 57.798 43.478 0.00 0.00 0.00 3.18
4320 4764 6.707608 CCAATTGCTCTGTTATCTATGCACTA 59.292 38.462 0.00 0.00 0.00 2.74
4323 4767 4.276678 GCCAATTGCTCTGTTATCTATGCA 59.723 41.667 0.00 0.00 36.87 3.96
4365 4809 2.216898 ACTGTTGCTGTTCTTCTCTGC 58.783 47.619 0.00 0.00 0.00 4.26
4370 4814 2.287248 GGCTGAACTGTTGCTGTTCTTC 60.287 50.000 15.98 9.66 40.99 2.87
4381 4825 3.565307 TGAATTTGAAGGGCTGAACTGT 58.435 40.909 0.00 0.00 0.00 3.55
4384 4828 4.741342 CATCTGAATTTGAAGGGCTGAAC 58.259 43.478 0.00 0.00 0.00 3.18
4387 4831 2.479049 CGCATCTGAATTTGAAGGGCTG 60.479 50.000 0.00 0.00 0.00 4.85
4388 4832 1.747355 CGCATCTGAATTTGAAGGGCT 59.253 47.619 0.00 0.00 0.00 5.19
4389 4833 1.745087 TCGCATCTGAATTTGAAGGGC 59.255 47.619 0.00 0.00 0.00 5.19
4397 4841 6.860080 ACAATCAAATTCTCGCATCTGAATT 58.140 32.000 0.00 0.00 42.52 2.17
4403 4869 5.456822 GGCTTTACAATCAAATTCTCGCATC 59.543 40.000 0.00 0.00 0.00 3.91
4407 4873 6.538742 TCCTAGGCTTTACAATCAAATTCTCG 59.461 38.462 2.96 0.00 0.00 4.04
4409 4875 8.650143 TTTCCTAGGCTTTACAATCAAATTCT 57.350 30.769 2.96 0.00 0.00 2.40
4422 4888 5.183904 CACTATGCTGTTTTTCCTAGGCTTT 59.816 40.000 2.96 0.00 0.00 3.51
4427 4893 5.352569 CCTGACACTATGCTGTTTTTCCTAG 59.647 44.000 0.00 0.00 0.00 3.02
4475 4941 7.640630 CGTGAGCTATTTGTCAAGTACTACTAG 59.359 40.741 0.00 0.00 0.00 2.57
4476 4942 7.335171 TCGTGAGCTATTTGTCAAGTACTACTA 59.665 37.037 0.00 0.00 0.00 1.82
4477 4943 6.150641 TCGTGAGCTATTTGTCAAGTACTACT 59.849 38.462 0.00 0.00 0.00 2.57
4478 4944 6.320171 TCGTGAGCTATTTGTCAAGTACTAC 58.680 40.000 0.00 0.00 0.00 2.73
4479 4945 6.505044 TCGTGAGCTATTTGTCAAGTACTA 57.495 37.500 0.00 0.00 0.00 1.82
4480 4946 5.386958 TCGTGAGCTATTTGTCAAGTACT 57.613 39.130 0.00 0.00 0.00 2.73
4481 4947 7.166142 GTCTATCGTGAGCTATTTGTCAAGTAC 59.834 40.741 0.00 0.00 0.00 2.73
4482 4948 7.148137 TGTCTATCGTGAGCTATTTGTCAAGTA 60.148 37.037 0.00 0.00 0.00 2.24
4483 4949 6.037098 GTCTATCGTGAGCTATTTGTCAAGT 58.963 40.000 0.00 0.00 0.00 3.16
4644 5117 2.381725 AGGGCGCAGTAGTTTAAGAC 57.618 50.000 10.83 0.00 0.00 3.01
4677 5150 1.495951 CCAACGAAGTACGCCTTGC 59.504 57.895 0.00 0.00 45.00 4.01
4730 5203 7.056006 TGCAACCATATCATGTGTCTTAAGAT 58.944 34.615 8.75 0.00 0.00 2.40
4732 5205 6.682423 TGCAACCATATCATGTGTCTTAAG 57.318 37.500 0.00 0.00 0.00 1.85
4733 5206 6.018016 CGATGCAACCATATCATGTGTCTTAA 60.018 38.462 0.00 0.00 0.00 1.85
4734 5207 5.466393 CGATGCAACCATATCATGTGTCTTA 59.534 40.000 0.00 0.00 0.00 2.10
4735 5208 4.274214 CGATGCAACCATATCATGTGTCTT 59.726 41.667 0.00 0.00 0.00 3.01
4782 5255 1.014352 GGGGAAAACATCGGTGATCG 58.986 55.000 0.65 0.00 40.90 3.69
4788 5261 2.112815 GCGAGGGGGAAAACATCGG 61.113 63.158 0.00 0.00 34.11 4.18
4798 5275 4.143333 ATGAACGTCGCGAGGGGG 62.143 66.667 29.83 13.40 0.00 5.40
4832 5309 2.887151 ATTTTGGGACAGAGGGAGTG 57.113 50.000 0.00 0.00 42.39 3.51
4836 5313 3.500343 ACAAGAATTTTGGGACAGAGGG 58.500 45.455 5.68 0.00 42.39 4.30
4837 5314 4.401925 AGACAAGAATTTTGGGACAGAGG 58.598 43.478 5.68 0.00 42.39 3.69
4838 5315 6.936900 TCTAAGACAAGAATTTTGGGACAGAG 59.063 38.462 5.68 0.00 42.39 3.35
4840 5317 7.693969 ATCTAAGACAAGAATTTTGGGACAG 57.306 36.000 5.68 0.00 42.39 3.51
4841 5318 8.359642 CAAATCTAAGACAAGAATTTTGGGACA 58.640 33.333 5.68 0.00 28.49 4.02
4842 5319 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
4843 5320 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
4844 5321 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
4885 5362 7.119846 AGCAAAACCAGCATCTAAACTAGTTAG 59.880 37.037 8.92 7.09 40.67 2.34
4886 5363 6.940298 AGCAAAACCAGCATCTAAACTAGTTA 59.060 34.615 8.92 0.00 0.00 2.24
4887 5364 5.770162 AGCAAAACCAGCATCTAAACTAGTT 59.230 36.000 1.12 1.12 0.00 2.24
4888 5365 5.316987 AGCAAAACCAGCATCTAAACTAGT 58.683 37.500 0.00 0.00 0.00 2.57
4889 5366 5.886960 AGCAAAACCAGCATCTAAACTAG 57.113 39.130 0.00 0.00 0.00 2.57
4890 5367 6.374333 CCTAAGCAAAACCAGCATCTAAACTA 59.626 38.462 0.00 0.00 0.00 2.24
4891 5368 5.183904 CCTAAGCAAAACCAGCATCTAAACT 59.816 40.000 0.00 0.00 0.00 2.66
4936 5413 0.814010 ACTTGTTGACGGTGAGGCAC 60.814 55.000 0.00 0.00 37.81 5.01
4946 5423 1.378531 TCACCAGTGCACTTGTTGAC 58.621 50.000 20.22 0.00 0.00 3.18
5001 5478 5.107607 CGCGTTCTCACATGTAAAGTTTAGT 60.108 40.000 0.00 0.00 0.00 2.24
5087 5567 2.695666 TGCATCCTTCTAGACCACTAGC 59.304 50.000 0.00 0.00 43.97 3.42
5088 5568 4.262377 CCATGCATCCTTCTAGACCACTAG 60.262 50.000 0.00 0.00 45.21 2.57
5089 5569 3.643320 CCATGCATCCTTCTAGACCACTA 59.357 47.826 0.00 0.00 0.00 2.74
5090 5570 2.437281 CCATGCATCCTTCTAGACCACT 59.563 50.000 0.00 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.