Multiple sequence alignment - TraesCS6B01G373000

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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 TraesCS6B01G373000 chr6B 100.000 3684 0 0 1 3684 646244847 646248530 0.000000e+00 6804.0
1 TraesCS6B01G373000 chr6B 87.850 107 9 2 129 235 210610969 210610867 5.000000e-24 122.0
2 TraesCS6B01G373000 chr6D 92.121 1853 121 6 1856 3684 429018099 429019950 0.000000e+00 2590.0
3 TraesCS6B01G373000 chr6D 92.172 1303 80 12 581 1863 429015283 429016583 0.000000e+00 1821.0
4 TraesCS6B01G373000 chr6D 90.359 446 30 6 111 545 429014839 429015282 1.150000e-159 573.0
5 TraesCS6B01G373000 chr6A 93.319 464 29 2 3222 3684 574262280 574262742 0.000000e+00 684.0
6 TraesCS6B01G373000 chr5B 89.205 176 17 2 108 281 477482196 477482371 6.190000e-53 219.0
7 TraesCS6B01G373000 chr2B 89.941 169 14 2 111 278 10767449 10767615 8.010000e-52 215.0
8 TraesCS6B01G373000 chr3B 88.202 178 17 3 105 281 519860830 519860656 3.730000e-50 209.0
9 TraesCS6B01G373000 chr5D 88.372 172 18 2 111 281 77056561 77056391 4.820000e-49 206.0
10 TraesCS6B01G373000 chr5D 75.746 268 38 13 17 281 469506724 469506481 3.890000e-20 110.0
11 TraesCS6B01G373000 chr5D 94.444 36 2 0 75 110 426015623 426015588 5.140000e-04 56.5
12 TraesCS6B01G373000 chr5A 88.439 173 17 2 111 282 566605276 566605106 4.820000e-49 206.0
13 TraesCS6B01G373000 chr5A 87.861 173 20 1 111 282 115095295 115095123 6.240000e-48 202.0
14 TraesCS6B01G373000 chr3A 88.439 173 17 2 111 282 706867973 706867803 4.820000e-49 206.0
15 TraesCS6B01G373000 chr4D 88.372 172 15 4 111 281 504326688 504326521 6.240000e-48 202.0
16 TraesCS6B01G373000 chr4A 87.931 174 18 2 111 283 165816375 165816546 6.240000e-48 202.0
17 TraesCS6B01G373000 chr4A 75.502 249 37 15 17 264 427877600 427877825 2.340000e-17 100.0
18 TraesCS6B01G373000 chr4A 78.626 131 24 2 1619 1747 24557091 24556963 2.360000e-12 84.2
19 TraesCS6B01G373000 chr4A 75.000 196 27 18 63 258 677485806 677485979 1.840000e-08 71.3
20 TraesCS6B01G373000 chr4A 85.000 60 9 0 1621 1680 66910379 66910438 1.100000e-05 62.1
21 TraesCS6B01G373000 chr2D 84.828 145 20 2 140 283 539169665 539169808 1.070000e-30 145.0
22 TraesCS6B01G373000 chr1A 77.528 267 35 19 17 281 362866544 362866301 1.780000e-28 137.0
23 TraesCS6B01G373000 chr1B 91.111 45 4 0 66 110 81378417 81378373 1.100000e-05 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G373000 chr6B 646244847 646248530 3683 False 6804.000000 6804 100.000000 1 3684 1 chr6B.!!$F1 3683
1 TraesCS6B01G373000 chr6D 429014839 429019950 5111 False 1661.333333 2590 91.550667 111 3684 3 chr6D.!!$F1 3573

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
563 575 0.036765 ATGTGCGAACCGTGGTGTAT 60.037 50.0 0.00 0.0 0.00 2.29 F
816 846 0.100861 GGCTAGCTAGTCGAACGCTT 59.899 55.0 21.62 0.0 35.33 4.68 F
1175 1205 0.104120 TCTCGCCGTAATCATGGTGG 59.896 55.0 0.00 0.0 41.06 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1596 1627 0.250901 ACACATCTGGGTTGAGGCAC 60.251 55.0 0.0 0.0 0.00 5.01 R
2441 3996 0.675083 TGCACTTCCAAATGGCACTG 59.325 50.0 0.0 0.0 34.44 3.66 R
2924 4498 0.881118 ACGCAACACAATGGATGGAC 59.119 50.0 0.0 0.0 0.00 4.02 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
24 25 6.716934 ATGTAGTACTCCCTCAATGTAGTG 57.283 41.667 0.00 0.00 0.00 2.74
25 26 4.401519 TGTAGTACTCCCTCAATGTAGTGC 59.598 45.833 0.00 0.00 0.00 4.40
26 27 2.427453 AGTACTCCCTCAATGTAGTGCG 59.573 50.000 0.00 0.00 30.93 5.34
27 28 1.267121 ACTCCCTCAATGTAGTGCGT 58.733 50.000 0.00 0.00 0.00 5.24
28 29 2.453521 ACTCCCTCAATGTAGTGCGTA 58.546 47.619 0.00 0.00 0.00 4.42
29 30 3.031736 ACTCCCTCAATGTAGTGCGTAT 58.968 45.455 0.00 0.00 0.00 3.06
30 31 4.212716 ACTCCCTCAATGTAGTGCGTATA 58.787 43.478 0.00 0.00 0.00 1.47
31 32 4.278669 ACTCCCTCAATGTAGTGCGTATAG 59.721 45.833 0.00 0.00 0.00 1.31
32 33 4.466827 TCCCTCAATGTAGTGCGTATAGA 58.533 43.478 0.00 0.00 0.00 1.98
33 34 5.077564 TCCCTCAATGTAGTGCGTATAGAT 58.922 41.667 0.00 0.00 0.00 1.98
34 35 5.538813 TCCCTCAATGTAGTGCGTATAGATT 59.461 40.000 0.00 0.00 0.00 2.40
35 36 6.041637 TCCCTCAATGTAGTGCGTATAGATTT 59.958 38.462 0.00 0.00 0.00 2.17
36 37 6.706270 CCCTCAATGTAGTGCGTATAGATTTT 59.294 38.462 0.00 0.00 0.00 1.82
37 38 7.226720 CCCTCAATGTAGTGCGTATAGATTTTT 59.773 37.037 0.00 0.00 0.00 1.94
62 63 7.670009 TTTATGTCAGATTTTGCAAAATGGG 57.330 32.000 35.57 26.47 38.64 4.00
63 64 4.952071 TGTCAGATTTTGCAAAATGGGA 57.048 36.364 35.57 27.92 38.64 4.37
64 65 5.486735 TGTCAGATTTTGCAAAATGGGAT 57.513 34.783 35.57 17.22 38.64 3.85
65 66 5.481105 TGTCAGATTTTGCAAAATGGGATC 58.519 37.500 35.57 23.60 38.64 3.36
66 67 5.011840 TGTCAGATTTTGCAAAATGGGATCA 59.988 36.000 35.57 25.47 38.64 2.92
67 68 5.933463 GTCAGATTTTGCAAAATGGGATCAA 59.067 36.000 35.57 15.04 38.64 2.57
68 69 6.091713 GTCAGATTTTGCAAAATGGGATCAAG 59.908 38.462 35.57 19.83 38.64 3.02
69 70 5.935789 CAGATTTTGCAAAATGGGATCAAGT 59.064 36.000 35.57 13.70 38.64 3.16
70 71 6.428771 CAGATTTTGCAAAATGGGATCAAGTT 59.571 34.615 35.57 13.20 38.64 2.66
71 72 6.999871 AGATTTTGCAAAATGGGATCAAGTTT 59.000 30.769 35.57 13.01 38.64 2.66
72 73 8.156165 AGATTTTGCAAAATGGGATCAAGTTTA 58.844 29.630 35.57 6.81 38.64 2.01
73 74 7.727331 TTTTGCAAAATGGGATCAAGTTTAG 57.273 32.000 20.46 0.00 0.00 1.85
74 75 6.662865 TTGCAAAATGGGATCAAGTTTAGA 57.337 33.333 0.00 0.00 0.00 2.10
75 76 6.271488 TGCAAAATGGGATCAAGTTTAGAG 57.729 37.500 0.00 0.00 0.00 2.43
76 77 6.009589 TGCAAAATGGGATCAAGTTTAGAGA 58.990 36.000 0.00 0.00 0.00 3.10
77 78 6.493115 TGCAAAATGGGATCAAGTTTAGAGAA 59.507 34.615 0.00 0.00 0.00 2.87
78 79 7.015098 TGCAAAATGGGATCAAGTTTAGAGAAA 59.985 33.333 0.00 0.00 0.00 2.52
79 80 7.872483 GCAAAATGGGATCAAGTTTAGAGAAAA 59.128 33.333 0.00 0.00 0.00 2.29
80 81 9.762933 CAAAATGGGATCAAGTTTAGAGAAAAA 57.237 29.630 0.00 0.00 0.00 1.94
239 240 7.330946 GTCAAAGTTTGTGAGGCTTAACTTTTT 59.669 33.333 15.08 6.18 44.16 1.94
296 308 2.627217 GGAGTATGGAGGGAACTGGTCT 60.627 54.545 0.00 0.00 44.43 3.85
311 323 1.219393 GTCTAGTGCCTGACTGCCC 59.781 63.158 0.00 0.00 35.96 5.36
321 333 2.262774 CTGACTGCCCAGGGATGTCC 62.263 65.000 21.69 9.76 0.00 4.02
362 374 5.009911 GCCATTTGATGCCATAGTATGACAA 59.990 40.000 11.91 9.11 0.00 3.18
414 426 7.824289 GCTATATATCTCTAAAATGTGTGCCCA 59.176 37.037 0.00 0.00 0.00 5.36
447 459 1.431496 TGACACGATCGAGACGTACA 58.569 50.000 24.34 16.55 42.07 2.90
452 464 1.396301 ACGATCGAGACGTACAAGGAC 59.604 52.381 24.34 0.00 42.17 3.85
472 484 3.448934 ACTTCACATGAGGAGATGGAGT 58.551 45.455 5.33 0.00 0.00 3.85
518 530 0.967662 CCCATGTTTGTGCATGACCA 59.032 50.000 0.00 0.00 46.65 4.02
529 541 2.438975 ATGACCAGGGCACATGCG 60.439 61.111 0.00 0.00 43.26 4.73
545 557 3.126879 CGTGCATGGACGCCACAT 61.127 61.111 26.70 0.00 35.80 3.21
546 558 2.486504 GTGCATGGACGCCACATG 59.513 61.111 0.10 9.45 46.45 3.21
547 559 2.033911 TGCATGGACGCCACATGT 59.966 55.556 13.73 0.00 45.68 3.21
548 560 2.334181 TGCATGGACGCCACATGTG 61.334 57.895 19.31 19.31 45.68 3.21
549 561 2.486504 CATGGACGCCACATGTGC 59.513 61.111 20.81 14.31 40.54 4.57
556 568 3.353836 GCCACATGTGCGAACCGT 61.354 61.111 20.81 0.00 0.00 4.83
557 569 2.555782 CCACATGTGCGAACCGTG 59.444 61.111 20.81 6.27 0.00 4.94
558 570 2.555782 CACATGTGCGAACCGTGG 59.444 61.111 13.94 0.00 0.00 4.94
559 571 2.110213 ACATGTGCGAACCGTGGT 59.890 55.556 0.00 0.00 0.00 4.16
560 572 2.250939 ACATGTGCGAACCGTGGTG 61.251 57.895 0.00 0.00 0.00 4.17
561 573 2.110213 ATGTGCGAACCGTGGTGT 59.890 55.556 0.00 0.00 0.00 4.16
562 574 0.946700 CATGTGCGAACCGTGGTGTA 60.947 55.000 0.00 0.00 0.00 2.90
563 575 0.036765 ATGTGCGAACCGTGGTGTAT 60.037 50.000 0.00 0.00 0.00 2.29
564 576 0.946700 TGTGCGAACCGTGGTGTATG 60.947 55.000 0.00 0.00 0.00 2.39
565 577 0.947180 GTGCGAACCGTGGTGTATGT 60.947 55.000 0.00 0.00 0.00 2.29
566 578 0.249953 TGCGAACCGTGGTGTATGTT 60.250 50.000 0.00 0.00 0.00 2.71
567 579 0.869730 GCGAACCGTGGTGTATGTTT 59.130 50.000 0.00 0.00 0.00 2.83
568 580 2.067766 GCGAACCGTGGTGTATGTTTA 58.932 47.619 0.00 0.00 0.00 2.01
569 581 2.674357 GCGAACCGTGGTGTATGTTTAT 59.326 45.455 0.00 0.00 0.00 1.40
570 582 3.864583 GCGAACCGTGGTGTATGTTTATA 59.135 43.478 0.00 0.00 0.00 0.98
571 583 4.259930 GCGAACCGTGGTGTATGTTTATAC 60.260 45.833 0.00 0.00 39.69 1.47
572 584 4.863689 CGAACCGTGGTGTATGTTTATACA 59.136 41.667 0.00 0.00 45.15 2.29
604 616 2.579201 CGCGGTGGTGAGAAGGAT 59.421 61.111 0.00 0.00 0.00 3.24
605 617 1.813859 CGCGGTGGTGAGAAGGATA 59.186 57.895 0.00 0.00 0.00 2.59
612 624 3.385111 GGTGGTGAGAAGGATAGTAGGTG 59.615 52.174 0.00 0.00 0.00 4.00
645 657 0.528684 GCTCGACATTAGCTCCGCTT 60.529 55.000 0.00 0.00 40.44 4.68
667 679 2.202770 CGGGCATACGCGTACCAA 60.203 61.111 23.19 0.12 46.24 3.67
668 680 2.519175 CGGGCATACGCGTACCAAC 61.519 63.158 23.19 11.96 46.24 3.77
669 681 2.175621 GGGCATACGCGTACCAACC 61.176 63.158 23.19 18.92 39.92 3.77
670 682 1.448189 GGCATACGCGTACCAACCA 60.448 57.895 23.19 0.00 39.92 3.67
685 712 7.359681 GCGTACCAACCAAGGAAAATAATTTTG 60.360 37.037 0.00 0.00 31.94 2.44
712 739 4.435137 TCCCTTCTCCAAAGGTTGATCTA 58.565 43.478 3.32 0.00 35.65 1.98
718 745 7.659390 CCTTCTCCAAAGGTTGATCTATACATC 59.341 40.741 0.00 0.00 32.78 3.06
723 750 4.899352 AGGTTGATCTATACATCCCTGC 57.101 45.455 0.00 0.00 0.00 4.85
773 800 4.506271 GCATCACCCCTAATCATGTGAGAT 60.506 45.833 0.00 0.00 40.70 2.75
788 818 2.924290 GTGAGATCGTACTTCCACAAGC 59.076 50.000 0.00 0.00 32.09 4.01
796 826 0.179018 ACTTCCACAAGCAGGTGACC 60.179 55.000 9.11 0.00 41.32 4.02
797 827 1.227823 TTCCACAAGCAGGTGACCG 60.228 57.895 9.11 0.00 41.32 4.79
816 846 0.100861 GGCTAGCTAGTCGAACGCTT 59.899 55.000 21.62 0.00 35.33 4.68
817 847 1.192793 GCTAGCTAGTCGAACGCTTG 58.807 55.000 21.62 8.71 35.33 4.01
840 870 7.328277 TGTGTAGTAAGCTTGTTTGTTCATT 57.672 32.000 9.86 0.00 0.00 2.57
899 929 5.977635 ACATGTGAAATACCAATCTCGAGA 58.022 37.500 19.19 19.19 0.00 4.04
940 970 4.990257 GCATGTGAGTGCAATCAAACTAT 58.010 39.130 19.78 8.35 44.43 2.12
946 976 6.088824 GTGAGTGCAATCAAACTATCCAAAG 58.911 40.000 19.78 0.00 0.00 2.77
996 1026 1.729586 TACTTGGAGTGGCCTCAACT 58.270 50.000 3.32 0.00 39.64 3.16
1078 1108 4.063689 CCAGCACAAGATAGAGCCATAAG 58.936 47.826 0.00 0.00 0.00 1.73
1095 1125 5.915196 GCCATAAGTCTTGAAGAAACAACAC 59.085 40.000 0.00 0.00 0.00 3.32
1107 1137 8.450578 TGAAGAAACAACACTATTTCATCACT 57.549 30.769 1.68 0.00 37.52 3.41
1137 1167 4.391155 AGCCACCTAAGACTACTATCTCG 58.609 47.826 0.00 0.00 0.00 4.04
1154 1184 7.323420 ACTATCTCGTTTCATCATGAAGAACA 58.677 34.615 12.70 2.82 37.70 3.18
1174 1204 1.934589 TTCTCGCCGTAATCATGGTG 58.065 50.000 0.00 0.00 41.92 4.17
1175 1205 0.104120 TCTCGCCGTAATCATGGTGG 59.896 55.000 0.00 0.00 41.06 4.61
1176 1206 0.179084 CTCGCCGTAATCATGGTGGT 60.179 55.000 0.00 0.00 41.06 4.16
1192 1222 1.488812 GTGGTACTCATGGCCACCATA 59.511 52.381 8.16 0.00 43.15 2.74
1233 1263 9.608718 AGTAGTATTCAGCCCTAATAAGATTCT 57.391 33.333 0.00 0.00 0.00 2.40
1237 1267 4.718961 TCAGCCCTAATAAGATTCTTGCC 58.281 43.478 9.22 0.00 0.00 4.52
1240 1270 3.823304 GCCCTAATAAGATTCTTGCCTGG 59.177 47.826 9.22 6.34 0.00 4.45
1252 1282 1.214305 TTGCCTGGCTCCATACCCTT 61.214 55.000 21.03 0.00 0.00 3.95
1254 1284 1.447643 CCTGGCTCCATACCCTTCG 59.552 63.158 0.00 0.00 0.00 3.79
1290 1320 5.824624 TCTTCATGGCAACCTTCTTATCATC 59.175 40.000 0.00 0.00 0.00 2.92
1300 1330 7.362401 GCAACCTTCTTATCATCTGTCACAATT 60.362 37.037 0.00 0.00 0.00 2.32
1326 1356 1.683943 TACCTTATCCACCGTCCTCG 58.316 55.000 0.00 0.00 0.00 4.63
1340 1370 3.378112 CCGTCCTCGTGTTGTATACCTTA 59.622 47.826 0.00 0.00 35.01 2.69
1372 1402 1.203994 TGCTTCCGACCTAGCAACTAC 59.796 52.381 0.00 0.00 43.88 2.73
1426 1457 8.285394 CACATCCGATTATTTCCAACTCTAATG 58.715 37.037 0.00 0.00 0.00 1.90
1466 1497 5.292834 TCATGAAACGAATGCTTGAGAGATC 59.707 40.000 0.00 0.00 0.00 2.75
1518 1549 2.260822 AGCGCATGGTATATTCCTCCT 58.739 47.619 11.47 0.00 0.00 3.69
1520 1551 2.028112 GCGCATGGTATATTCCTCCTGA 60.028 50.000 0.30 0.00 0.00 3.86
1522 1553 3.617531 CGCATGGTATATTCCTCCTGACC 60.618 52.174 0.00 0.00 0.00 4.02
1533 1564 2.378886 TCCTCCTGACCACTGTCTAAGA 59.621 50.000 0.00 0.00 42.28 2.10
1573 1604 7.781693 AGGCAGAAATGGTCATATTCACTATTT 59.218 33.333 5.88 5.88 37.57 1.40
1574 1605 7.864379 GGCAGAAATGGTCATATTCACTATTTG 59.136 37.037 9.46 1.60 35.68 2.32
1597 1628 8.771920 TTGTGATGAATTATTAGTGAAGACGT 57.228 30.769 0.00 0.00 0.00 4.34
1615 1646 0.250901 GTGCCTCAACCCAGATGTGT 60.251 55.000 0.00 0.00 0.00 3.72
1682 1713 2.617308 CCCTTGCTGACATGATCATGAC 59.383 50.000 36.37 30.54 41.20 3.06
1698 1729 4.797471 TCATGACAAAATTCAAGCTTCGG 58.203 39.130 0.00 0.00 0.00 4.30
1724 1755 0.179062 ATCCGGATTGCACAGCTCTC 60.179 55.000 12.38 0.00 0.00 3.20
1736 1767 0.399091 CAGCTCTCTGGGATGGGGTA 60.399 60.000 0.00 0.00 36.68 3.69
1739 1770 1.879575 CTCTCTGGGATGGGGTACAA 58.120 55.000 0.00 0.00 0.00 2.41
1741 1772 0.178068 CTCTGGGATGGGGTACAACG 59.822 60.000 0.00 0.00 0.00 4.10
1751 1782 1.065272 GGGGTACAACGCAGGGATAAA 60.065 52.381 0.00 0.00 32.03 1.40
1753 1784 2.616842 GGGTACAACGCAGGGATAAATG 59.383 50.000 0.00 0.00 0.00 2.32
1758 1789 3.299050 CGCAGGGATAAATGGCGTA 57.701 52.632 0.00 0.00 42.51 4.42
1767 1798 4.065088 GGATAAATGGCGTAGATCTTGCA 58.935 43.478 18.06 7.69 0.00 4.08
1769 1800 5.182001 GGATAAATGGCGTAGATCTTGCAAT 59.818 40.000 18.06 11.52 0.00 3.56
1863 1894 0.549950 ACATGGGGAGGAAGCATGAG 59.450 55.000 0.00 0.00 0.00 2.90
1864 1895 0.841961 CATGGGGAGGAAGCATGAGA 59.158 55.000 0.00 0.00 0.00 3.27
1865 1896 1.424302 CATGGGGAGGAAGCATGAGAT 59.576 52.381 0.00 0.00 0.00 2.75
1867 1898 1.344803 TGGGGAGGAAGCATGAGATCT 60.345 52.381 0.00 0.00 0.00 2.75
1894 3448 2.099592 ACCAATGCATTATTCCGCACTG 59.900 45.455 12.53 0.00 41.79 3.66
1935 3489 2.218603 TCAACCTCGAGAACAAAAGCC 58.781 47.619 15.71 0.00 0.00 4.35
1981 3535 1.679032 GGAAGTCTACTGGCGCCAAAT 60.679 52.381 32.09 23.50 0.00 2.32
1990 3544 1.227234 GGCGCCAAATACAATGCCC 60.227 57.895 24.80 0.00 36.51 5.36
2010 3564 2.225491 CCACCGTTGTGTATTCCAACAG 59.775 50.000 0.00 0.00 41.76 3.16
2019 3573 5.245531 TGTGTATTCCAACAGGAAGATGAC 58.754 41.667 3.15 1.28 44.23 3.06
2099 3653 6.566079 TCTCAAGGACAATCTCACCATAAT 57.434 37.500 0.00 0.00 0.00 1.28
2117 3671 3.593442 AATTGGACCACTTGTTCTCCA 57.407 42.857 0.00 0.00 0.00 3.86
2172 3727 4.387559 TCATCACACGGAAGTTATTCAACG 59.612 41.667 0.00 0.00 46.40 4.10
2184 3739 0.673644 ATTCAACGCAAGGACCGAGG 60.674 55.000 0.00 0.00 46.39 4.63
2202 3757 3.058155 CGAGGTGTATATCCCTGACTTCG 60.058 52.174 0.00 0.00 0.00 3.79
2208 3763 3.644966 ATATCCCTGACTTCGGCAAAA 57.355 42.857 0.00 0.00 0.00 2.44
2213 3768 1.681264 CCTGACTTCGGCAAAACCTTT 59.319 47.619 0.00 0.00 35.61 3.11
2214 3769 2.543653 CCTGACTTCGGCAAAACCTTTG 60.544 50.000 0.00 0.00 35.61 2.77
2216 3771 2.955660 TGACTTCGGCAAAACCTTTGAT 59.044 40.909 3.35 0.00 35.61 2.57
2245 3800 2.821366 CCATGCTGGTGGACGAGC 60.821 66.667 6.82 6.82 46.09 5.03
2274 3829 2.169832 TGGAGTTCAAAGAAGCCTCG 57.830 50.000 0.00 0.00 0.00 4.63
2275 3830 1.691976 TGGAGTTCAAAGAAGCCTCGA 59.308 47.619 0.00 0.00 0.00 4.04
2283 3838 3.513912 TCAAAGAAGCCTCGACCTATCAA 59.486 43.478 0.00 0.00 0.00 2.57
2286 3841 4.065321 AGAAGCCTCGACCTATCAAATG 57.935 45.455 0.00 0.00 0.00 2.32
2294 3849 4.371786 TCGACCTATCAAATGAGCATGTC 58.628 43.478 0.00 0.00 0.00 3.06
2318 3873 2.939103 GCCATCAAGGATGACACTGTAC 59.061 50.000 7.75 0.00 42.09 2.90
2341 3896 5.546499 ACCGGTATGGGAATACATCAAGTAT 59.454 40.000 4.49 0.00 43.39 2.12
2348 3903 7.067496 TGGGAATACATCAAGTATCTCCTTC 57.933 40.000 0.00 0.00 42.56 3.46
2357 3912 6.968263 TCAAGTATCTCCTTCTGGTATGAG 57.032 41.667 0.00 0.00 34.23 2.90
2368 3923 5.358442 CCTTCTGGTATGAGCTAGCGTATAT 59.642 44.000 9.55 5.29 0.00 0.86
2383 3938 3.120649 GCGTATATTGAAGCTAAAGGCCG 60.121 47.826 0.00 0.00 43.05 6.13
2441 3996 3.146066 TGGATCTGGTTACAAGTGCAAC 58.854 45.455 0.00 0.00 0.00 4.17
2464 4019 0.179129 GCCATTTGGAAGTGCATCCG 60.179 55.000 0.00 0.00 42.76 4.18
2496 4051 2.804986 TGTTGATAGAGCATGGGCAA 57.195 45.000 0.00 0.00 44.61 4.52
2515 4070 1.609208 AATTGCATCCATCGCTACCC 58.391 50.000 0.00 0.00 0.00 3.69
2528 4083 3.220110 TCGCTACCCGATAGATGTCTTT 58.780 45.455 0.00 0.00 41.89 2.52
2594 4166 3.998913 TGGCTTCACTTCATCCATACA 57.001 42.857 0.00 0.00 0.00 2.29
2609 4181 7.995289 TCATCCATACAATATTTGTGGTTGTC 58.005 34.615 14.88 0.00 45.03 3.18
2621 4193 4.019792 TGTGGTTGTCATAAGTGATGCT 57.980 40.909 0.00 0.00 36.60 3.79
2628 4200 8.046708 TGGTTGTCATAAGTGATGCTTATACTT 58.953 33.333 0.00 0.00 45.77 2.24
2656 4228 5.541845 TCTAGACATTGCACTATGGTATGC 58.458 41.667 3.53 0.00 42.40 3.14
2729 4301 7.803279 TTTTCCTCCTCTTCTAAAGAAACAC 57.197 36.000 0.00 0.00 37.02 3.32
2736 4308 9.495572 CTCCTCTTCTAAAGAAACACAAATACT 57.504 33.333 0.00 0.00 37.02 2.12
2816 4390 6.724893 TGAATGGACGATATCTTCACCTAA 57.275 37.500 11.00 0.00 0.00 2.69
2857 4431 0.109342 GCCTCCCGGTCATGAATCAT 59.891 55.000 0.00 0.00 0.00 2.45
2862 4436 0.473755 CCGGTCATGAATCATCCCCA 59.526 55.000 0.00 0.00 0.00 4.96
2867 4441 4.082125 GGTCATGAATCATCCCCATTACC 58.918 47.826 0.00 0.00 30.43 2.85
2869 4443 5.388654 GTCATGAATCATCCCCATTACCTT 58.611 41.667 0.00 0.00 0.00 3.50
2874 4448 6.150332 TGAATCATCCCCATTACCTTCTAGA 58.850 40.000 0.00 0.00 0.00 2.43
2895 4469 6.107901 AGAGGCATCCATATGTTAGTCTTC 57.892 41.667 1.24 0.00 35.38 2.87
2901 4475 8.150945 GGCATCCATATGTTAGTCTTCTCTTTA 58.849 37.037 1.24 0.00 35.38 1.85
2904 4478 8.540507 TCCATATGTTAGTCTTCTCTTTAGCT 57.459 34.615 1.24 0.00 0.00 3.32
2913 4487 4.463186 GTCTTCTCTTTAGCTAGTGGGACA 59.537 45.833 0.00 0.00 0.00 4.02
2924 4498 1.004918 GTGGGACAAGAGTGGACCG 60.005 63.158 0.00 0.00 44.16 4.79
2996 4570 3.515901 ACCATGGGTTCACTTCTAGTCTC 59.484 47.826 18.09 0.00 27.29 3.36
3003 4577 4.477780 GTTCACTTCTAGTCTCGGTTCAG 58.522 47.826 0.00 0.00 0.00 3.02
3040 4614 7.535258 CGAAAAAGAGGTTTCAATACATGAGTG 59.465 37.037 0.00 0.00 39.77 3.51
3049 4623 5.282055 TCAATACATGAGTGGATGGAGAC 57.718 43.478 0.00 0.00 33.04 3.36
3061 4635 2.297315 GGATGGAGACGAGCATATGTCA 59.703 50.000 4.29 0.00 37.58 3.58
3080 4654 4.012895 GTGAACGTGGTGGCAGCG 62.013 66.667 12.58 8.26 0.00 5.18
3095 4669 0.163788 CAGCGGTCAATGTTGTCGAC 59.836 55.000 9.11 9.11 0.00 4.20
3096 4670 0.249699 AGCGGTCAATGTTGTCGACA 60.250 50.000 15.76 15.76 43.71 4.35
3109 4683 2.589720 TGTCGACACTCTAAACCTGGA 58.410 47.619 15.76 0.00 0.00 3.86
3151 4725 0.398318 GGGAACACCTTCACTCTGCT 59.602 55.000 0.00 0.00 35.85 4.24
3153 4727 2.354203 GGGAACACCTTCACTCTGCTAG 60.354 54.545 0.00 0.00 35.85 3.42
3154 4728 2.563179 GGAACACCTTCACTCTGCTAGA 59.437 50.000 0.00 0.00 0.00 2.43
3172 4749 4.867608 GCTAGAAGACAACAACATCCTCTC 59.132 45.833 0.00 0.00 0.00 3.20
3183 4760 3.883830 ACATCCTCTCATGTGAGTCAC 57.116 47.619 20.33 16.68 42.60 3.67
3205 4782 2.337879 GACCCCAATGGCGGCTATCA 62.338 60.000 11.43 0.00 37.83 2.15
3207 4784 0.540365 CCCCAATGGCGGCTATCAAT 60.540 55.000 11.43 0.00 0.00 2.57
3213 4790 1.522668 TGGCGGCTATCAATATGTGC 58.477 50.000 11.43 0.00 0.00 4.57
3214 4791 1.202746 TGGCGGCTATCAATATGTGCA 60.203 47.619 11.43 0.00 0.00 4.57
3235 4812 9.719355 TGTGCACCCTTATTATGTATAAGTATG 57.281 33.333 15.69 0.00 42.77 2.39
3278 4855 2.028112 AGACTACGGAATGCATGTGTGT 60.028 45.455 0.00 0.00 0.00 3.72
3282 4859 5.666462 ACTACGGAATGCATGTGTGTATAA 58.334 37.500 0.00 0.00 29.97 0.98
3283 4860 5.753438 ACTACGGAATGCATGTGTGTATAAG 59.247 40.000 0.00 0.00 29.97 1.73
3284 4861 4.765273 ACGGAATGCATGTGTGTATAAGA 58.235 39.130 0.00 0.00 29.97 2.10
3285 4862 4.570772 ACGGAATGCATGTGTGTATAAGAC 59.429 41.667 0.00 0.00 29.97 3.01
3286 4863 4.570369 CGGAATGCATGTGTGTATAAGACA 59.430 41.667 0.00 0.00 36.33 3.41
3288 4865 6.403092 CGGAATGCATGTGTGTATAAGACAAA 60.403 38.462 0.00 0.00 40.66 2.83
3296 4874 7.987750 TGTGTGTATAAGACAAAAGGCATTA 57.012 32.000 0.00 0.00 40.66 1.90
3333 4911 2.232452 AGAGGTGTTCGAGATGTGGAAG 59.768 50.000 0.00 0.00 0.00 3.46
3337 4915 1.338105 TGTTCGAGATGTGGAAGCAGG 60.338 52.381 0.00 0.00 0.00 4.85
3340 4918 1.817099 GAGATGTGGAAGCAGGGCG 60.817 63.158 0.00 0.00 0.00 6.13
3357 4935 2.031682 GGGCGCATATGAAAGATCACAC 60.032 50.000 10.83 0.00 38.69 3.82
3392 4970 6.496565 ACTCTGGATTCATCGAGAATAAGGAT 59.503 38.462 9.23 2.85 46.76 3.24
3434 5012 3.329929 GGTTGGATGTCGACCTAGTTT 57.670 47.619 14.12 0.00 44.83 2.66
3475 5053 5.238650 ACAATAAGGGACGCATATACAAAGC 59.761 40.000 0.00 0.00 0.00 3.51
3479 5057 1.602377 GGACGCATATACAAAGCACCC 59.398 52.381 0.00 0.00 0.00 4.61
3549 5127 6.658816 TCATGTGGTTTGAAGCTATGTACATT 59.341 34.615 14.77 0.00 0.00 2.71
3569 5147 1.278985 TGACATTGCACCGAGAATCCT 59.721 47.619 0.00 0.00 0.00 3.24
3570 5148 1.936547 GACATTGCACCGAGAATCCTC 59.063 52.381 0.00 0.00 36.08 3.71
3595 5173 6.529125 CGATTGCTTGCAAGATTTAAGAACAT 59.471 34.615 30.39 5.47 0.00 2.71
3622 5200 4.010349 GTTTAGCTCTTGTTAGCCACCAT 58.990 43.478 0.00 0.00 43.86 3.55
3623 5201 5.183228 GTTTAGCTCTTGTTAGCCACCATA 58.817 41.667 0.00 0.00 43.86 2.74
3626 5204 4.010349 AGCTCTTGTTAGCCACCATAAAC 58.990 43.478 0.00 0.00 43.86 2.01
3630 5208 5.321102 TCTTGTTAGCCACCATAAACACAT 58.679 37.500 0.00 0.00 31.92 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.264744 GCACTACATTGAGGGAGTACTACATA 59.735 42.308 7.57 0.00 0.00 2.29
1 2 5.069251 GCACTACATTGAGGGAGTACTACAT 59.931 44.000 7.57 0.00 0.00 2.29
2 3 4.401519 GCACTACATTGAGGGAGTACTACA 59.598 45.833 7.57 0.00 0.00 2.74
3 4 4.497674 CGCACTACATTGAGGGAGTACTAC 60.498 50.000 0.00 0.00 0.00 2.73
4 5 3.630769 CGCACTACATTGAGGGAGTACTA 59.369 47.826 0.00 0.00 0.00 1.82
5 6 2.427453 CGCACTACATTGAGGGAGTACT 59.573 50.000 0.00 0.00 0.00 2.73
6 7 2.165845 ACGCACTACATTGAGGGAGTAC 59.834 50.000 0.00 0.00 30.30 2.73
7 8 2.453521 ACGCACTACATTGAGGGAGTA 58.546 47.619 0.00 0.00 30.30 2.59
8 9 1.267121 ACGCACTACATTGAGGGAGT 58.733 50.000 0.00 0.00 0.00 3.85
9 10 3.735237 ATACGCACTACATTGAGGGAG 57.265 47.619 0.00 0.00 0.00 4.30
10 11 4.466827 TCTATACGCACTACATTGAGGGA 58.533 43.478 0.00 0.00 0.00 4.20
11 12 4.848562 TCTATACGCACTACATTGAGGG 57.151 45.455 0.00 0.00 0.00 4.30
12 13 7.715265 AAAATCTATACGCACTACATTGAGG 57.285 36.000 0.00 0.00 0.00 3.86
36 37 8.566260 CCCATTTTGCAAAATCTGACATAAAAA 58.434 29.630 29.92 3.78 36.52 1.94
37 38 7.935755 TCCCATTTTGCAAAATCTGACATAAAA 59.064 29.630 29.92 4.22 36.52 1.52
38 39 7.448420 TCCCATTTTGCAAAATCTGACATAAA 58.552 30.769 29.92 4.43 36.52 1.40
39 40 7.002250 TCCCATTTTGCAAAATCTGACATAA 57.998 32.000 29.92 10.54 36.52 1.90
40 41 6.602410 TCCCATTTTGCAAAATCTGACATA 57.398 33.333 29.92 11.86 36.52 2.29
41 42 5.486735 TCCCATTTTGCAAAATCTGACAT 57.513 34.783 29.92 9.96 36.52 3.06
42 43 4.952071 TCCCATTTTGCAAAATCTGACA 57.048 36.364 29.92 12.75 36.52 3.58
43 44 5.481105 TGATCCCATTTTGCAAAATCTGAC 58.519 37.500 29.92 21.16 36.52 3.51
44 45 5.741962 TGATCCCATTTTGCAAAATCTGA 57.258 34.783 29.92 26.69 36.52 3.27
45 46 5.935789 ACTTGATCCCATTTTGCAAAATCTG 59.064 36.000 29.92 22.33 36.52 2.90
46 47 6.117975 ACTTGATCCCATTTTGCAAAATCT 57.882 33.333 29.92 16.91 36.52 2.40
47 48 6.806388 AACTTGATCCCATTTTGCAAAATC 57.194 33.333 29.92 21.04 36.52 2.17
48 49 8.156165 TCTAAACTTGATCCCATTTTGCAAAAT 58.844 29.630 27.73 27.73 39.07 1.82
49 50 7.504403 TCTAAACTTGATCCCATTTTGCAAAA 58.496 30.769 25.76 25.76 0.00 2.44
50 51 7.015098 TCTCTAAACTTGATCCCATTTTGCAAA 59.985 33.333 8.05 8.05 0.00 3.68
51 52 6.493115 TCTCTAAACTTGATCCCATTTTGCAA 59.507 34.615 0.00 0.00 0.00 4.08
52 53 6.009589 TCTCTAAACTTGATCCCATTTTGCA 58.990 36.000 0.00 0.00 0.00 4.08
53 54 6.515272 TCTCTAAACTTGATCCCATTTTGC 57.485 37.500 0.00 0.00 0.00 3.68
54 55 9.762933 TTTTTCTCTAAACTTGATCCCATTTTG 57.237 29.630 0.00 0.00 0.00 2.44
195 196 7.213678 ACTTTGACCAAGTTTGTGAAGAAAAA 58.786 30.769 6.75 0.00 43.89 1.94
267 279 3.736094 TCCCTCCATACTCCATCTGTTT 58.264 45.455 0.00 0.00 0.00 2.83
270 282 3.070734 CAGTTCCCTCCATACTCCATCTG 59.929 52.174 0.00 0.00 0.00 2.90
273 285 2.293856 ACCAGTTCCCTCCATACTCCAT 60.294 50.000 0.00 0.00 0.00 3.41
296 308 2.293318 CCTGGGCAGTCAGGCACTA 61.293 63.158 6.99 0.00 46.47 2.74
321 333 2.896801 GCCGTGAAGCACTGTGTGG 61.897 63.158 9.86 3.77 33.64 4.17
322 334 2.633657 GCCGTGAAGCACTGTGTG 59.366 61.111 9.86 0.00 36.51 3.82
352 364 4.213906 TCGTCGTTGTCACTTGTCATACTA 59.786 41.667 0.00 0.00 0.00 1.82
362 374 3.297830 TCATTCATCGTCGTTGTCACT 57.702 42.857 3.38 0.00 0.00 3.41
414 426 4.659111 TCGTGTCATAATATCCCGTGTT 57.341 40.909 0.00 0.00 0.00 3.32
418 430 4.094442 TCTCGATCGTGTCATAATATCCCG 59.906 45.833 15.94 0.00 0.00 5.14
421 433 5.619513 ACGTCTCGATCGTGTCATAATATC 58.380 41.667 15.94 0.00 40.07 1.63
447 459 3.199508 CCATCTCCTCATGTGAAGTCCTT 59.800 47.826 0.00 0.00 0.00 3.36
452 464 4.498850 CGTACTCCATCTCCTCATGTGAAG 60.499 50.000 0.00 0.00 0.00 3.02
472 484 2.892215 TCTATGTGGTTGTGTGGACGTA 59.108 45.455 0.00 0.00 0.00 3.57
529 541 2.334946 ACATGTGGCGTCCATGCAC 61.335 57.895 15.53 0.00 42.74 4.57
545 557 0.946700 CATACACCACGGTTCGCACA 60.947 55.000 0.00 0.00 0.00 4.57
546 558 0.947180 ACATACACCACGGTTCGCAC 60.947 55.000 0.00 0.00 0.00 5.34
547 559 0.249953 AACATACACCACGGTTCGCA 60.250 50.000 0.00 0.00 0.00 5.10
548 560 0.869730 AAACATACACCACGGTTCGC 59.130 50.000 0.00 0.00 0.00 4.70
549 561 4.863689 TGTATAAACATACACCACGGTTCG 59.136 41.667 0.00 0.00 32.58 3.95
550 562 6.913873 ATGTATAAACATACACCACGGTTC 57.086 37.500 0.00 0.00 44.66 3.62
551 563 7.011669 GCTAATGTATAAACATACACCACGGTT 59.988 37.037 0.00 0.00 45.79 4.44
552 564 6.480981 GCTAATGTATAAACATACACCACGGT 59.519 38.462 0.00 0.00 45.79 4.83
553 565 6.480651 TGCTAATGTATAAACATACACCACGG 59.519 38.462 0.00 0.00 45.79 4.94
554 566 7.471657 TGCTAATGTATAAACATACACCACG 57.528 36.000 0.00 0.00 45.79 4.94
555 567 7.226720 AGCTGCTAATGTATAAACATACACCAC 59.773 37.037 0.00 0.00 45.79 4.16
556 568 7.279615 AGCTGCTAATGTATAAACATACACCA 58.720 34.615 0.00 0.00 45.79 4.17
557 569 7.095187 GGAGCTGCTAATGTATAAACATACACC 60.095 40.741 0.15 0.00 45.79 4.16
558 570 7.441157 TGGAGCTGCTAATGTATAAACATACAC 59.559 37.037 6.82 0.00 45.79 2.90
559 571 7.505258 TGGAGCTGCTAATGTATAAACATACA 58.495 34.615 6.82 0.32 45.79 2.29
560 572 7.962964 TGGAGCTGCTAATGTATAAACATAC 57.037 36.000 6.82 0.00 45.79 2.39
561 573 7.119699 GCATGGAGCTGCTAATGTATAAACATA 59.880 37.037 19.93 0.00 42.19 2.29
562 574 6.072286 GCATGGAGCTGCTAATGTATAAACAT 60.072 38.462 19.93 4.70 43.71 2.71
563 575 5.239306 GCATGGAGCTGCTAATGTATAAACA 59.761 40.000 19.93 3.00 41.15 2.83
564 576 5.615544 CGCATGGAGCTGCTAATGTATAAAC 60.616 44.000 19.93 7.02 42.61 2.01
565 577 4.452114 CGCATGGAGCTGCTAATGTATAAA 59.548 41.667 19.93 0.00 42.61 1.40
566 578 3.996363 CGCATGGAGCTGCTAATGTATAA 59.004 43.478 19.93 0.00 42.61 0.98
567 579 3.588955 CGCATGGAGCTGCTAATGTATA 58.411 45.455 19.93 0.00 42.61 1.47
568 580 2.420642 CGCATGGAGCTGCTAATGTAT 58.579 47.619 19.93 3.26 42.61 2.29
569 581 1.869774 CGCATGGAGCTGCTAATGTA 58.130 50.000 19.93 1.30 42.61 2.29
570 582 1.442526 GCGCATGGAGCTGCTAATGT 61.443 55.000 19.93 0.00 42.61 2.71
571 583 1.281960 GCGCATGGAGCTGCTAATG 59.718 57.895 16.52 16.52 42.61 1.90
572 584 2.249535 CGCGCATGGAGCTGCTAAT 61.250 57.895 8.75 0.00 42.61 1.73
573 585 2.891936 CGCGCATGGAGCTGCTAA 60.892 61.111 8.75 0.00 42.61 3.09
574 586 4.897357 CCGCGCATGGAGCTGCTA 62.897 66.667 8.75 0.00 42.61 3.49
591 603 3.385111 CCACCTACTATCCTTCTCACCAC 59.615 52.174 0.00 0.00 0.00 4.16
593 605 3.912248 TCCACCTACTATCCTTCTCACC 58.088 50.000 0.00 0.00 0.00 4.02
604 616 1.366787 TCCCCCAACATCCACCTACTA 59.633 52.381 0.00 0.00 0.00 1.82
605 617 0.120377 TCCCCCAACATCCACCTACT 59.880 55.000 0.00 0.00 0.00 2.57
612 624 1.526917 CGAGCATCCCCCAACATCC 60.527 63.158 0.00 0.00 0.00 3.51
658 670 0.945813 TTTTCCTTGGTTGGTACGCG 59.054 50.000 3.53 3.53 0.00 6.01
664 676 6.261826 TGCACAAAATTATTTTCCTTGGTTGG 59.738 34.615 0.00 0.00 0.00 3.77
665 677 7.256756 TGCACAAAATTATTTTCCTTGGTTG 57.743 32.000 0.00 0.00 0.00 3.77
666 678 7.174772 GGATGCACAAAATTATTTTCCTTGGTT 59.825 33.333 0.00 0.00 0.00 3.67
667 679 6.654582 GGATGCACAAAATTATTTTCCTTGGT 59.345 34.615 0.00 0.00 0.00 3.67
668 680 6.093909 GGGATGCACAAAATTATTTTCCTTGG 59.906 38.462 0.00 0.00 0.00 3.61
669 681 6.880529 AGGGATGCACAAAATTATTTTCCTTG 59.119 34.615 0.00 0.39 0.00 3.61
670 682 7.019656 AGGGATGCACAAAATTATTTTCCTT 57.980 32.000 0.00 0.00 0.00 3.36
685 712 1.272147 ACCTTTGGAGAAGGGATGCAC 60.272 52.381 9.42 0.00 41.71 4.57
712 739 1.426598 CCAATGGGAGCAGGGATGTAT 59.573 52.381 0.00 0.00 35.59 2.29
718 745 2.124570 CGACCAATGGGAGCAGGG 60.125 66.667 3.55 0.00 38.05 4.45
723 750 2.819595 CGTGGCGACCAATGGGAG 60.820 66.667 3.55 0.00 34.18 4.30
773 800 1.045407 ACCTGCTTGTGGAAGTACGA 58.955 50.000 0.00 0.00 0.00 3.43
788 818 1.038130 ACTAGCTAGCCGGTCACCTG 61.038 60.000 20.91 0.00 0.00 4.00
796 826 1.654743 GCGTTCGACTAGCTAGCCG 60.655 63.158 21.86 21.86 0.00 5.52
797 827 0.100861 AAGCGTTCGACTAGCTAGCC 59.899 55.000 20.91 9.02 40.78 3.93
816 846 6.935741 ATGAACAAACAAGCTTACTACACA 57.064 33.333 0.00 0.00 0.00 3.72
817 847 7.414436 TGAATGAACAAACAAGCTTACTACAC 58.586 34.615 0.00 0.00 0.00 2.90
882 912 9.331106 GTTTTTCTTTCTCGAGATTGGTATTTC 57.669 33.333 17.44 0.09 0.00 2.17
895 925 5.116074 GCATGTCATGTGTTTTTCTTTCTCG 59.884 40.000 14.26 0.00 0.00 4.04
899 929 6.533819 CATGCATGTCATGTGTTTTTCTTT 57.466 33.333 18.91 0.00 45.79 2.52
964 994 5.773176 CCACTCCAAGTATTTTGGGTAGTTT 59.227 40.000 6.13 0.00 39.96 2.66
996 1026 1.113788 GGCATGGGCTTTAAGCATCA 58.886 50.000 19.10 15.56 44.75 3.07
1024 1054 2.579684 AAATGAGGACGCGGAGGAGC 62.580 60.000 12.47 0.00 0.00 4.70
1034 1064 5.047377 TGGTTTATGCTTGGAAAATGAGGAC 60.047 40.000 0.00 0.00 0.00 3.85
1078 1108 9.387123 GATGAAATAGTGTTGTTTCTTCAAGAC 57.613 33.333 0.00 0.00 40.38 3.01
1095 1125 8.778358 GGTGGCTAAGATTAAGTGATGAAATAG 58.222 37.037 0.00 0.00 0.00 1.73
1099 1129 6.313519 AGGTGGCTAAGATTAAGTGATGAA 57.686 37.500 0.00 0.00 0.00 2.57
1107 1137 9.878737 ATAGTAGTCTTAGGTGGCTAAGATTAA 57.121 33.333 0.00 0.00 44.59 1.40
1117 1147 6.318144 TGAAACGAGATAGTAGTCTTAGGTGG 59.682 42.308 0.00 0.00 0.00 4.61
1132 1162 7.551974 AGAATGTTCTTCATGATGAAACGAGAT 59.448 33.333 21.74 5.49 35.73 2.75
1137 1167 5.736358 GCGAGAATGTTCTTCATGATGAAAC 59.264 40.000 21.74 16.55 35.73 2.78
1154 1184 2.483876 CACCATGATTACGGCGAGAAT 58.516 47.619 16.62 12.90 0.00 2.40
1174 1204 1.768870 AGTATGGTGGCCATGAGTACC 59.231 52.381 9.72 4.43 44.84 3.34
1175 1205 3.641906 AGTAGTATGGTGGCCATGAGTAC 59.358 47.826 9.72 11.78 44.84 2.73
1176 1206 3.895656 GAGTAGTATGGTGGCCATGAGTA 59.104 47.826 9.72 0.00 44.84 2.59
1213 1243 5.772169 GGCAAGAATCTTATTAGGGCTGAAT 59.228 40.000 0.00 0.00 0.00 2.57
1217 1247 4.446889 CCAGGCAAGAATCTTATTAGGGCT 60.447 45.833 0.00 0.00 0.00 5.19
1233 1263 1.214305 AAGGGTATGGAGCCAGGCAA 61.214 55.000 15.80 0.00 46.47 4.52
1237 1267 0.105039 GTCGAAGGGTATGGAGCCAG 59.895 60.000 0.00 0.00 46.47 4.85
1240 1270 0.105039 CTGGTCGAAGGGTATGGAGC 59.895 60.000 0.00 0.00 0.00 4.70
1252 1282 1.112916 TGAAGAGGTGCACTGGTCGA 61.113 55.000 17.98 0.00 0.00 4.20
1254 1284 1.446907 CATGAAGAGGTGCACTGGTC 58.553 55.000 17.98 11.20 0.00 4.02
1290 1320 7.489113 GGATAAGGTAATGCAAAATTGTGACAG 59.511 37.037 0.00 0.00 0.00 3.51
1300 1330 3.942748 GACGGTGGATAAGGTAATGCAAA 59.057 43.478 0.00 0.00 0.00 3.68
1326 1356 8.758633 AGCATAATCGATAAGGTATACAACAC 57.241 34.615 5.01 0.00 0.00 3.32
1340 1370 2.802816 GTCGGAAGCAAGCATAATCGAT 59.197 45.455 0.00 0.00 0.00 3.59
1426 1457 6.074888 CGTTTCATGAAGTGGACAATGTTTTC 60.075 38.462 8.41 0.00 0.00 2.29
1518 1549 5.047847 CGAGTTTTTCTTAGACAGTGGTCA 58.952 41.667 0.00 0.00 46.80 4.02
1520 1551 4.809426 CACGAGTTTTTCTTAGACAGTGGT 59.191 41.667 0.00 0.00 0.00 4.16
1522 1553 6.420903 TCATCACGAGTTTTTCTTAGACAGTG 59.579 38.462 0.00 0.00 0.00 3.66
1533 1564 3.126001 TCTGCCTCATCACGAGTTTTT 57.874 42.857 0.00 0.00 40.48 1.94
1573 1604 7.201522 GCACGTCTTCACTAATAATTCATCACA 60.202 37.037 0.00 0.00 0.00 3.58
1574 1605 7.119997 GCACGTCTTCACTAATAATTCATCAC 58.880 38.462 0.00 0.00 0.00 3.06
1596 1627 0.250901 ACACATCTGGGTTGAGGCAC 60.251 55.000 0.00 0.00 0.00 5.01
1597 1628 0.478072 AACACATCTGGGTTGAGGCA 59.522 50.000 0.00 0.00 40.71 4.75
1615 1646 5.105917 TGCAGTTGACGATGAGTATGTCTAA 60.106 40.000 0.00 0.00 33.81 2.10
1682 1713 2.295909 TCACCCCGAAGCTTGAATTTTG 59.704 45.455 2.10 0.00 0.00 2.44
1698 1729 1.077787 TGCAATCCGGATGTCACCC 60.078 57.895 19.95 3.66 0.00 4.61
1724 1755 1.451387 GCGTTGTACCCCATCCCAG 60.451 63.158 0.00 0.00 0.00 4.45
1736 1767 1.102978 GCCATTTATCCCTGCGTTGT 58.897 50.000 0.00 0.00 0.00 3.32
1739 1770 4.141144 CGCCATTTATCCCTGCGT 57.859 55.556 0.00 0.00 40.33 5.24
1741 1772 2.543777 TCTACGCCATTTATCCCTGC 57.456 50.000 0.00 0.00 0.00 4.85
1751 1782 4.881273 TGTTTATTGCAAGATCTACGCCAT 59.119 37.500 4.94 10.50 0.00 4.40
1753 1784 4.875544 TGTTTATTGCAAGATCTACGCC 57.124 40.909 4.94 0.00 0.00 5.68
1813 1844 3.118956 CCAGTTAGGATCTCTGTGGACAC 60.119 52.174 0.00 0.00 41.22 3.67
1981 3535 2.635079 CACAACGGTGGGCATTGTA 58.365 52.632 4.97 0.00 41.45 2.41
2010 3564 4.218852 CCTAGATAACCCTCGTCATCTTCC 59.781 50.000 0.00 0.00 0.00 3.46
2019 3573 5.020132 AGATGAATCCCTAGATAACCCTCG 58.980 45.833 0.00 0.00 30.42 4.63
2051 3605 4.956075 CCTTACCAGCAATATCCAAAAGGT 59.044 41.667 0.00 0.00 0.00 3.50
2099 3653 3.020984 GTTTGGAGAACAAGTGGTCCAA 58.979 45.455 10.81 10.81 45.36 3.53
2149 3704 4.387559 CGTTGAATAACTTCCGTGTGATGA 59.612 41.667 0.00 0.00 34.60 2.92
2172 3727 2.288886 GGATATACACCTCGGTCCTTGC 60.289 54.545 0.00 0.00 0.00 4.01
2184 3739 2.364324 TGCCGAAGTCAGGGATATACAC 59.636 50.000 0.00 0.00 0.00 2.90
2208 3763 5.486735 TGGATGCAAAAATGATCAAAGGT 57.513 34.783 0.00 0.00 0.00 3.50
2245 3800 4.498241 TCTTTGAACTCCATCGATCACTG 58.502 43.478 0.00 0.00 0.00 3.66
2274 3829 4.371786 TCGACATGCTCATTTGATAGGTC 58.628 43.478 0.00 0.00 0.00 3.85
2275 3830 4.375272 CTCGACATGCTCATTTGATAGGT 58.625 43.478 0.00 0.00 0.00 3.08
2283 3838 1.134310 TGATGGCTCGACATGCTCATT 60.134 47.619 0.00 0.00 0.00 2.57
2286 3841 0.935898 CTTGATGGCTCGACATGCTC 59.064 55.000 0.00 0.00 0.00 4.26
2294 3849 1.134580 AGTGTCATCCTTGATGGCTCG 60.135 52.381 9.78 0.00 44.06 5.03
2318 3873 4.351874 ACTTGATGTATTCCCATACCGG 57.648 45.455 0.00 0.00 35.25 5.28
2341 3896 3.226777 GCTAGCTCATACCAGAAGGAGA 58.773 50.000 7.70 0.00 38.69 3.71
2348 3903 6.196079 TCAATATACGCTAGCTCATACCAG 57.804 41.667 13.93 0.00 0.00 4.00
2357 3912 5.163943 GCCTTTAGCTTCAATATACGCTAGC 60.164 44.000 4.06 4.06 36.46 3.42
2368 3923 3.009723 CTCATTCGGCCTTTAGCTTCAA 58.990 45.455 0.00 0.00 43.05 2.69
2383 3938 2.573915 ACTTGGTCTCCCTTCCTCATTC 59.426 50.000 0.00 0.00 0.00 2.67
2401 3956 8.096414 CAGATCCAAACCCAATCATTAAAACTT 58.904 33.333 0.00 0.00 0.00 2.66
2412 3967 4.396357 TGTAACCAGATCCAAACCCAAT 57.604 40.909 0.00 0.00 0.00 3.16
2441 3996 0.675083 TGCACTTCCAAATGGCACTG 59.325 50.000 0.00 0.00 34.44 3.66
2450 4005 1.375396 CGACCGGATGCACTTCCAA 60.375 57.895 9.46 0.00 35.34 3.53
2464 4019 5.277538 GCTCTATCAACATTTTGGATCGACC 60.278 44.000 0.00 0.00 39.54 4.79
2496 4051 1.609208 GGGTAGCGATGGATGCAATT 58.391 50.000 0.00 0.00 33.85 2.32
2515 4070 9.929180 TCCATTCCTATTTAAAGACATCTATCG 57.071 33.333 0.00 0.00 0.00 2.92
2528 4083 7.016170 TCGTTCATCCTGATCCATTCCTATTTA 59.984 37.037 0.00 0.00 0.00 1.40
2594 4166 7.975616 GCATCACTTATGACAACCACAAATATT 59.024 33.333 0.00 0.00 37.79 1.28
2628 4200 7.182817 ACCATAGTGCAATGTCTAGAACTTA 57.817 36.000 0.00 0.00 0.00 2.24
2656 4228 1.338105 ACACACACATCCGGAGACATG 60.338 52.381 11.34 5.65 0.00 3.21
2724 4296 8.258708 GGTACATCTAGGAGAGTATTTGTGTTT 58.741 37.037 0.00 0.00 0.00 2.83
2787 4361 4.679373 AGATATCGTCCATTCAAGCACT 57.321 40.909 0.00 0.00 0.00 4.40
2789 4363 4.811024 GTGAAGATATCGTCCATTCAAGCA 59.189 41.667 14.92 0.00 32.13 3.91
2816 4390 2.262774 CTTCGCCTTCCTGCCATCCT 62.263 60.000 0.00 0.00 0.00 3.24
2867 4441 7.178274 AGACTAACATATGGATGCCTCTAGAAG 59.822 40.741 7.80 0.00 36.43 2.85
2869 4443 6.556639 AGACTAACATATGGATGCCTCTAGA 58.443 40.000 7.80 0.00 36.43 2.43
2874 4448 5.843421 AGAGAAGACTAACATATGGATGCCT 59.157 40.000 7.80 0.00 36.43 4.75
2877 4451 9.202273 GCTAAAGAGAAGACTAACATATGGATG 57.798 37.037 7.80 0.00 39.16 3.51
2895 4469 4.464597 ACTCTTGTCCCACTAGCTAAAGAG 59.535 45.833 20.19 20.19 42.98 2.85
2901 4475 1.203187 TCCACTCTTGTCCCACTAGCT 60.203 52.381 0.00 0.00 0.00 3.32
2904 4478 1.640917 GGTCCACTCTTGTCCCACTA 58.359 55.000 0.00 0.00 0.00 2.74
2924 4498 0.881118 ACGCAACACAATGGATGGAC 59.119 50.000 0.00 0.00 0.00 4.02
2961 4535 2.047274 ATGGTCGGACTTGCCACG 60.047 61.111 8.23 0.00 34.84 4.94
2996 4570 1.376037 GCCACCTCCTTCTGAACCG 60.376 63.158 0.00 0.00 0.00 4.44
3003 4577 1.807142 CTCTTTTTCGCCACCTCCTTC 59.193 52.381 0.00 0.00 0.00 3.46
3040 4614 2.297315 TGACATATGCTCGTCTCCATCC 59.703 50.000 1.58 0.00 33.18 3.51
3049 4623 1.854743 CGTTCACCTGACATATGCTCG 59.145 52.381 1.58 0.00 0.00 5.03
3061 4635 2.111043 CTGCCACCACGTTCACCT 59.889 61.111 0.00 0.00 0.00 4.00
3080 4654 2.755650 AGAGTGTCGACAACATTGACC 58.244 47.619 21.95 5.03 40.67 4.02
3083 4657 4.750098 AGGTTTAGAGTGTCGACAACATTG 59.250 41.667 21.95 0.00 40.80 2.82
3084 4658 4.750098 CAGGTTTAGAGTGTCGACAACATT 59.250 41.667 21.95 8.96 40.80 2.71
3109 4683 3.181437 ACCCACGAAACCATCTTTACCTT 60.181 43.478 0.00 0.00 0.00 3.50
3151 4725 6.014242 ACATGAGAGGATGTTGTTGTCTTCTA 60.014 38.462 0.00 0.00 32.38 2.10
3153 4727 4.999950 ACATGAGAGGATGTTGTTGTCTTC 59.000 41.667 0.00 0.00 32.38 2.87
3154 4728 4.758674 CACATGAGAGGATGTTGTTGTCTT 59.241 41.667 0.00 0.00 34.18 3.01
3172 4749 1.079127 GGGTCCCGTGACTCACATG 60.079 63.158 9.84 0.00 41.94 3.21
3261 4838 5.751509 GTCTTATACACACATGCATTCCGTA 59.248 40.000 0.00 0.00 0.00 4.02
3321 4899 1.817099 GCCCTGCTTCCACATCTCG 60.817 63.158 0.00 0.00 0.00 4.04
3333 4911 1.198637 GATCTTTCATATGCGCCCTGC 59.801 52.381 4.18 0.00 46.70 4.85
3337 4915 2.348872 CGTGTGATCTTTCATATGCGCC 60.349 50.000 4.18 0.00 33.56 6.53
3340 4918 5.046529 AGACTCGTGTGATCTTTCATATGC 58.953 41.667 0.00 0.00 33.56 3.14
3372 4950 6.459066 TGTCATCCTTATTCTCGATGAATCC 58.541 40.000 11.69 0.00 42.90 3.01
3374 4952 8.915057 AATTGTCATCCTTATTCTCGATGAAT 57.085 30.769 12.59 12.59 42.90 2.57
3409 4987 0.108329 GGTCGACATCCAACCATCGT 60.108 55.000 18.91 0.00 36.03 3.73
3410 4988 0.175760 AGGTCGACATCCAACCATCG 59.824 55.000 18.91 0.00 35.43 3.84
3430 5008 4.657039 TGTGGGTTCCAAGTAGTAGAAACT 59.343 41.667 0.00 0.00 35.93 2.66
3434 5012 6.070424 CCTTATTGTGGGTTCCAAGTAGTAGA 60.070 42.308 0.00 0.00 34.18 2.59
3465 5043 2.572290 GCCTTCGGGTGCTTTGTATAT 58.428 47.619 0.00 0.00 37.45 0.86
3475 5053 1.551452 TTTTATTGGGCCTTCGGGTG 58.449 50.000 4.53 0.00 37.45 4.61
3479 5057 8.603181 CAAAATTATCTTTTTATTGGGCCTTCG 58.397 33.333 4.53 0.00 0.00 3.79
3549 5127 1.278985 AGGATTCTCGGTGCAATGTCA 59.721 47.619 0.00 0.00 0.00 3.58
3569 5147 5.878332 TCTTAAATCTTGCAAGCAATCGA 57.122 34.783 21.99 10.24 35.20 3.59
3570 5148 5.858049 TGTTCTTAAATCTTGCAAGCAATCG 59.142 36.000 21.99 8.14 35.20 3.34
3579 5157 9.788960 CTAAACCCTAATGTTCTTAAATCTTGC 57.211 33.333 0.00 0.00 0.00 4.01
3595 5173 4.287585 TGGCTAACAAGAGCTAAACCCTAA 59.712 41.667 0.00 0.00 42.43 2.69
3653 5231 5.869579 TCTTGCTTTTGTGGATCTCTAACT 58.130 37.500 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.