Multiple sequence alignment - TraesCS5D01G371000

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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 TraesCS5D01G371000 chr5D 100.000 4991 0 0 1 4991 445493373 445488383 0.000000e+00 9217.0
1 TraesCS5D01G371000 chr5D 80.640 1250 208 18 1008 2240 436980991 436982223 0.000000e+00 937.0
2 TraesCS5D01G371000 chr5D 84.105 648 94 3 2468 3112 445404372 445403731 7.100000e-173 617.0
3 TraesCS5D01G371000 chr5D 83.554 377 54 6 3358 3728 553912598 553912972 3.700000e-91 346.0
4 TraesCS5D01G371000 chr5D 83.918 342 50 3 3362 3702 436983273 436983610 6.230000e-84 322.0
5 TraesCS5D01G371000 chr5D 75.421 594 85 31 3476 4057 445317028 445316484 1.080000e-56 231.0
6 TraesCS5D01G371000 chr5B 93.636 1697 96 2 1680 3364 543299438 543297742 0.000000e+00 2525.0
7 TraesCS5D01G371000 chr5B 96.320 951 23 3 3404 4354 543297747 543296809 0.000000e+00 1552.0
8 TraesCS5D01G371000 chr5B 90.121 1073 47 25 87 1125 543300934 543299887 0.000000e+00 1339.0
9 TraesCS5D01G371000 chr5B 79.567 1248 223 19 1009 2240 531192392 531193623 0.000000e+00 863.0
10 TraesCS5D01G371000 chr5B 90.575 626 32 17 4384 4991 543294697 543294081 0.000000e+00 804.0
11 TraesCS5D01G371000 chr5B 98.448 451 7 0 1199 1649 543299889 543299439 0.000000e+00 795.0
12 TraesCS5D01G371000 chr5B 84.568 648 91 3 2468 3112 543244964 543244323 7.050000e-178 634.0
13 TraesCS5D01G371000 chr5B 81.558 629 107 6 2455 3081 531193741 531194362 1.240000e-140 510.0
14 TraesCS5D01G371000 chr5B 76.967 877 168 25 1385 2240 543274602 543273739 2.100000e-128 470.0
15 TraesCS5D01G371000 chr5B 78.887 611 116 7 1016 1618 543282493 543281888 7.780000e-108 401.0
16 TraesCS5D01G371000 chr5B 86.885 305 34 2 3402 3703 543270185 543269884 2.230000e-88 337.0
17 TraesCS5D01G371000 chr5B 84.257 343 49 3 3362 3703 531194673 531195011 3.720000e-86 329.0
18 TraesCS5D01G371000 chr5B 95.082 61 3 0 3 63 658101839 658101779 4.110000e-16 97.1
19 TraesCS5D01G371000 chr5B 86.585 82 8 1 3959 4037 542950407 542950326 2.480000e-13 87.9
20 TraesCS5D01G371000 chr4D 81.571 2024 280 43 1074 3069 2973625 2975583 0.000000e+00 1585.0
21 TraesCS5D01G371000 chr4D 80.635 1260 205 27 1008 2240 1687325 1688572 0.000000e+00 939.0
22 TraesCS5D01G371000 chr4D 81.931 642 74 23 3386 3993 2975740 2976373 5.770000e-139 505.0
23 TraesCS5D01G371000 chr4D 78.889 630 102 18 2451 3075 1688855 1689458 1.010000e-106 398.0
24 TraesCS5D01G371000 chr4D 88.040 301 34 2 3408 3707 1689605 1689904 6.150000e-94 355.0
25 TraesCS5D01G371000 chr4D 88.344 163 19 0 4093 4255 2976561 2976723 3.940000e-46 196.0
26 TraesCS5D01G371000 chr5A 80.562 1245 212 18 1008 2240 552267420 552268646 0.000000e+00 931.0
27 TraesCS5D01G371000 chr5A 84.877 648 89 3 2468 3112 563255048 563254407 0.000000e+00 645.0
28 TraesCS5D01G371000 chr5A 81.790 637 107 6 2455 3089 552268791 552269420 4.430000e-145 525.0
29 TraesCS5D01G371000 chr5A 85.671 328 41 6 3408 3734 552300432 552300754 1.720000e-89 340.0
30 TraesCS5D01G371000 chr5A 85.586 111 12 2 3950 4057 562889456 562889347 4.080000e-21 113.0
31 TraesCS5D01G371000 chrUn 79.837 1101 157 36 324 1398 63573878 63572817 0.000000e+00 743.0
32 TraesCS5D01G371000 chrUn 80.658 972 134 29 453 1398 411621333 411620390 0.000000e+00 704.0
33 TraesCS5D01G371000 chrUn 95.122 287 11 2 4705 4991 396038014 396037731 2.740000e-122 449.0
34 TraesCS5D01G371000 chrUn 92.565 269 19 1 4432 4700 467260718 467260985 7.840000e-103 385.0
35 TraesCS5D01G371000 chrUn 89.157 249 22 4 87 330 63574408 63574160 6.280000e-79 305.0
36 TraesCS5D01G371000 chrUn 86.076 158 18 3 4133 4286 51689915 51690072 3.090000e-37 167.0
37 TraesCS5D01G371000 chrUn 73.445 418 79 17 2609 3022 310057855 310057466 1.460000e-25 128.0
38 TraesCS5D01G371000 chr1B 83.453 695 109 4 1007 1698 553015698 553015007 4.210000e-180 641.0
39 TraesCS5D01G371000 chr1B 84.969 326 46 3 3411 3734 553013242 553012918 1.340000e-85 327.0
40 TraesCS5D01G371000 chr1B 90.566 53 5 0 1 53 309119288 309119340 2.490000e-08 71.3
41 TraesCS5D01G371000 chr1D 82.038 579 103 1 1010 1588 410460387 410459810 4.490000e-135 492.0
42 TraesCS5D01G371000 chr4B 86.076 158 18 3 4133 4286 2207406 2207563 3.090000e-37 167.0
43 TraesCS5D01G371000 chr4B 86.076 158 18 3 4133 4286 2236837 2236994 3.090000e-37 167.0
44 TraesCS5D01G371000 chr3B 93.651 63 4 0 1 63 764057005 764057067 1.480000e-15 95.3
45 TraesCS5D01G371000 chr3B 93.023 43 3 0 1 43 309403638 309403596 4.170000e-06 63.9
46 TraesCS5D01G371000 chr3B 94.444 36 0 2 1 34 736935476 736935441 3.000000e-03 54.7
47 TraesCS5D01G371000 chr2D 92.982 57 4 0 3 59 256865911 256865967 3.200000e-12 84.2
48 TraesCS5D01G371000 chr4A 91.071 56 4 1 722 777 602894690 602894636 1.930000e-09 75.0
49 TraesCS5D01G371000 chr3A 82.192 73 7 5 1 68 691249672 691249601 1.940000e-04 58.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G371000 chr5D 445488383 445493373 4990 True 9217.000000 9217 100.000000 1 4991 1 chr5D.!!$R3 4990
1 TraesCS5D01G371000 chr5D 436980991 436983610 2619 False 629.500000 937 82.279000 1008 3702 2 chr5D.!!$F2 2694
2 TraesCS5D01G371000 chr5D 445403731 445404372 641 True 617.000000 617 84.105000 2468 3112 1 chr5D.!!$R2 644
3 TraesCS5D01G371000 chr5D 445316484 445317028 544 True 231.000000 231 75.421000 3476 4057 1 chr5D.!!$R1 581
4 TraesCS5D01G371000 chr5B 543294081 543300934 6853 True 1403.000000 2525 93.820000 87 4991 5 chr5B.!!$R6 4904
5 TraesCS5D01G371000 chr5B 543244323 543244964 641 True 634.000000 634 84.568000 2468 3112 1 chr5B.!!$R2 644
6 TraesCS5D01G371000 chr5B 531192392 531195011 2619 False 567.333333 863 81.794000 1009 3703 3 chr5B.!!$F1 2694
7 TraesCS5D01G371000 chr5B 543269884 543274602 4718 True 403.500000 470 81.926000 1385 3703 2 chr5B.!!$R5 2318
8 TraesCS5D01G371000 chr5B 543281888 543282493 605 True 401.000000 401 78.887000 1016 1618 1 chr5B.!!$R3 602
9 TraesCS5D01G371000 chr4D 2973625 2976723 3098 False 762.000000 1585 83.948667 1074 4255 3 chr4D.!!$F2 3181
10 TraesCS5D01G371000 chr4D 1687325 1689904 2579 False 564.000000 939 82.521333 1008 3707 3 chr4D.!!$F1 2699
11 TraesCS5D01G371000 chr5A 552267420 552269420 2000 False 728.000000 931 81.176000 1008 3089 2 chr5A.!!$F2 2081
12 TraesCS5D01G371000 chr5A 563254407 563255048 641 True 645.000000 645 84.877000 2468 3112 1 chr5A.!!$R2 644
13 TraesCS5D01G371000 chrUn 411620390 411621333 943 True 704.000000 704 80.658000 453 1398 1 chrUn.!!$R3 945
14 TraesCS5D01G371000 chrUn 63572817 63574408 1591 True 524.000000 743 84.497000 87 1398 2 chrUn.!!$R4 1311
15 TraesCS5D01G371000 chr1B 553012918 553015698 2780 True 484.000000 641 84.211000 1007 3734 2 chr1B.!!$R1 2727
16 TraesCS5D01G371000 chr1D 410459810 410460387 577 True 492.000000 492 82.038000 1010 1588 1 chr1D.!!$R1 578

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
576 898 0.030235 TCTTGTACGCATCCGATCCG 59.970 55.0 0.00 0.00 38.29 4.18 F
735 1071 0.321653 ACGATCAGGTCTTTGCCACC 60.322 55.0 0.00 0.00 0.00 4.61 F
1677 2056 0.112995 TTGAGCCTGGCAACCATCTT 59.887 50.0 22.65 0.00 30.82 2.40 F
1678 2057 0.322816 TGAGCCTGGCAACCATCTTC 60.323 55.0 22.65 7.40 30.82 2.87 F
2585 3394 0.468029 CAGTATTGGGGGTCCATGGC 60.468 60.0 6.96 1.78 43.63 4.40 F
3373 7032 0.035630 GCCCACAGAATGCAGAGAGT 60.036 55.0 0.00 0.00 42.53 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1658 2037 0.112995 AAGATGGTTGCCAGGCTCAA 59.887 50.0 14.15 0.0 36.75 3.02 R
1709 2121 0.249073 CTGATAGTCGGCCTCAACGG 60.249 60.0 0.00 0.0 0.00 4.44 R
3151 6618 0.035439 ATTTTGGCGTCGGACCAGAT 60.035 50.0 1.91 0.0 38.73 2.90 R
3363 7022 0.036952 CCGGTGACAACTCTCTGCAT 60.037 55.0 0.00 0.0 0.00 3.96 R
3938 7648 0.107703 CGTAGATGCACCACCACCAT 60.108 55.0 0.00 0.0 0.00 3.55 R
4721 10658 0.448990 TTGCATCATCAACGCTCTGC 59.551 50.0 0.00 0.0 0.00 4.26 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
296 299 2.202703 CCCTTTCCTCCGTACGCG 60.203 66.667 10.49 3.53 37.95 6.01
379 673 1.674322 CCCATTCGTTTCCGCCACT 60.674 57.895 0.00 0.00 0.00 4.00
391 685 1.375908 CGCCACTTTAGCTGGAGCA 60.376 57.895 0.00 0.00 45.16 4.26
392 686 1.364626 CGCCACTTTAGCTGGAGCAG 61.365 60.000 0.00 0.00 45.16 4.24
393 687 0.322008 GCCACTTTAGCTGGAGCAGT 60.322 55.000 0.00 0.00 45.16 4.40
449 770 3.551496 TTGCTTGGCCTCGACTGGG 62.551 63.158 3.32 0.00 0.00 4.45
455 776 2.184579 GCCTCGACTGGGTACTGC 59.815 66.667 0.00 0.00 0.00 4.40
456 777 2.352032 GCCTCGACTGGGTACTGCT 61.352 63.158 0.00 0.00 0.00 4.24
480 801 1.248785 TGTGGTCTCGGGTACTCAGC 61.249 60.000 0.00 0.00 0.00 4.26
489 810 1.404843 GGGTACTCAGCCTCACTAGG 58.595 60.000 0.00 0.00 46.76 3.02
508 829 8.704668 TCACTAGGTAGCTGATGAATATTTTGA 58.295 33.333 4.27 0.00 0.00 2.69
523 844 8.100791 TGAATATTTTGAGCCAAGTGTACTAGT 58.899 33.333 0.00 0.00 0.00 2.57
525 846 9.601217 AATATTTTGAGCCAAGTGTACTAGTAG 57.399 33.333 1.87 0.00 0.00 2.57
526 847 6.659745 TTTTGAGCCAAGTGTACTAGTAGA 57.340 37.500 1.87 0.00 0.00 2.59
528 849 6.852420 TTGAGCCAAGTGTACTAGTAGAAT 57.148 37.500 1.87 0.00 0.00 2.40
530 851 7.949690 TGAGCCAAGTGTACTAGTAGAATTA 57.050 36.000 11.79 0.00 0.00 1.40
531 852 7.997482 TGAGCCAAGTGTACTAGTAGAATTAG 58.003 38.462 11.79 6.83 0.00 1.73
532 853 7.614583 TGAGCCAAGTGTACTAGTAGAATTAGT 59.385 37.037 11.79 1.21 35.62 2.24
533 854 9.118300 GAGCCAAGTGTACTAGTAGAATTAGTA 57.882 37.037 11.79 0.00 33.60 1.82
564 886 8.539674 GTTTTGATGGTTGTGATTTTCTTGTAC 58.460 33.333 0.00 0.00 0.00 2.90
572 894 3.369756 GTGATTTTCTTGTACGCATCCGA 59.630 43.478 0.00 0.00 38.29 4.55
573 895 4.034048 GTGATTTTCTTGTACGCATCCGAT 59.966 41.667 0.00 0.00 38.29 4.18
574 896 4.270084 TGATTTTCTTGTACGCATCCGATC 59.730 41.667 0.00 0.00 38.29 3.69
575 897 2.218953 TTCTTGTACGCATCCGATCC 57.781 50.000 0.00 0.00 38.29 3.36
576 898 0.030235 TCTTGTACGCATCCGATCCG 59.970 55.000 0.00 0.00 38.29 4.18
644 973 8.807948 ATATATATGATTAACCACCCTTGTGC 57.192 34.615 0.00 0.00 41.35 4.57
645 974 2.666272 TGATTAACCACCCTTGTGCA 57.334 45.000 0.00 0.00 41.35 4.57
726 1062 3.309954 GTCTTGCCAAATACGATCAGGTC 59.690 47.826 0.00 0.00 0.00 3.85
735 1071 0.321653 ACGATCAGGTCTTTGCCACC 60.322 55.000 0.00 0.00 0.00 4.61
790 1126 3.431673 AGGCAAAAGGAGAAGAAGAGG 57.568 47.619 0.00 0.00 0.00 3.69
791 1127 2.982488 AGGCAAAAGGAGAAGAAGAGGA 59.018 45.455 0.00 0.00 0.00 3.71
792 1128 3.078097 GGCAAAAGGAGAAGAAGAGGAC 58.922 50.000 0.00 0.00 0.00 3.85
793 1129 3.496870 GGCAAAAGGAGAAGAAGAGGACA 60.497 47.826 0.00 0.00 0.00 4.02
794 1130 4.331108 GCAAAAGGAGAAGAAGAGGACAT 58.669 43.478 0.00 0.00 0.00 3.06
795 1131 4.394610 GCAAAAGGAGAAGAAGAGGACATC 59.605 45.833 0.00 0.00 0.00 3.06
796 1132 5.555017 CAAAAGGAGAAGAAGAGGACATCA 58.445 41.667 0.00 0.00 0.00 3.07
797 1133 5.832539 AAAGGAGAAGAAGAGGACATCAA 57.167 39.130 0.00 0.00 0.00 2.57
798 1134 4.817318 AGGAGAAGAAGAGGACATCAAC 57.183 45.455 0.00 0.00 0.00 3.18
799 1135 3.517500 AGGAGAAGAAGAGGACATCAACC 59.482 47.826 0.00 0.00 0.00 3.77
800 1136 3.261897 GGAGAAGAAGAGGACATCAACCA 59.738 47.826 0.00 0.00 0.00 3.67
801 1137 4.249661 GAGAAGAAGAGGACATCAACCAC 58.750 47.826 0.00 0.00 0.00 4.16
864 1212 1.131883 GCACAGTAGCATCCAAAGCAG 59.868 52.381 0.00 0.00 0.00 4.24
934 1289 1.138859 CTGCTGGTTCCGGTCATATCA 59.861 52.381 0.00 0.00 0.00 2.15
1139 1498 4.730949 TTCCTTCCTTGTACAGATACGG 57.269 45.455 0.00 0.00 33.60 4.02
1497 1862 2.040278 CCCCAGGCTCTCAGGAGT 59.960 66.667 0.00 0.00 41.38 3.85
1649 2028 3.213206 TCAAGCACAAGAAGGTGATGT 57.787 42.857 0.00 0.00 41.32 3.06
1650 2029 2.880268 TCAAGCACAAGAAGGTGATGTG 59.120 45.455 0.00 0.97 45.54 3.21
1651 2030 1.901591 AGCACAAGAAGGTGATGTGG 58.098 50.000 7.19 0.00 43.54 4.17
1652 2031 1.609208 GCACAAGAAGGTGATGTGGT 58.391 50.000 7.19 0.00 43.54 4.16
1653 2032 1.956477 GCACAAGAAGGTGATGTGGTT 59.044 47.619 7.19 0.00 43.54 3.67
1654 2033 2.287788 GCACAAGAAGGTGATGTGGTTG 60.288 50.000 7.19 0.00 43.54 3.77
1655 2034 3.213506 CACAAGAAGGTGATGTGGTTGA 58.786 45.455 0.00 0.00 41.32 3.18
1656 2035 3.003689 CACAAGAAGGTGATGTGGTTGAC 59.996 47.826 0.00 0.00 41.32 3.18
1657 2036 2.554032 CAAGAAGGTGATGTGGTTGACC 59.446 50.000 0.00 0.00 0.00 4.02
1658 2037 2.057922 AGAAGGTGATGTGGTTGACCT 58.942 47.619 1.34 0.00 40.71 3.85
1660 2039 2.276732 AGGTGATGTGGTTGACCTTG 57.723 50.000 1.34 0.00 35.12 3.61
1661 2040 1.774254 AGGTGATGTGGTTGACCTTGA 59.226 47.619 1.34 0.00 35.12 3.02
1662 2041 2.154462 GGTGATGTGGTTGACCTTGAG 58.846 52.381 1.34 0.00 36.82 3.02
1663 2042 1.537202 GTGATGTGGTTGACCTTGAGC 59.463 52.381 1.34 0.00 36.82 4.26
1664 2043 1.168714 GATGTGGTTGACCTTGAGCC 58.831 55.000 1.34 0.00 36.82 4.70
1665 2044 0.773644 ATGTGGTTGACCTTGAGCCT 59.226 50.000 1.34 0.00 36.82 4.58
1666 2045 0.179020 TGTGGTTGACCTTGAGCCTG 60.179 55.000 1.34 0.00 36.82 4.85
1667 2046 0.890996 GTGGTTGACCTTGAGCCTGG 60.891 60.000 1.34 0.00 36.82 4.45
1668 2047 1.973812 GGTTGACCTTGAGCCTGGC 60.974 63.158 11.65 11.65 0.00 4.85
1669 2048 1.228245 GTTGACCTTGAGCCTGGCA 60.228 57.895 22.65 0.00 0.00 4.92
1670 2049 0.823356 GTTGACCTTGAGCCTGGCAA 60.823 55.000 22.65 6.35 0.00 4.52
1671 2050 0.823356 TTGACCTTGAGCCTGGCAAC 60.823 55.000 22.65 14.69 0.00 4.17
1672 2051 1.973812 GACCTTGAGCCTGGCAACC 60.974 63.158 22.65 10.00 0.00 3.77
1673 2052 2.115910 CCTTGAGCCTGGCAACCA 59.884 61.111 22.65 12.61 0.00 3.67
1674 2053 1.304713 CCTTGAGCCTGGCAACCAT 60.305 57.895 22.65 0.00 30.82 3.55
1675 2054 1.318158 CCTTGAGCCTGGCAACCATC 61.318 60.000 22.65 9.73 30.82 3.51
1676 2055 0.323178 CTTGAGCCTGGCAACCATCT 60.323 55.000 22.65 0.00 30.82 2.90
1677 2056 0.112995 TTGAGCCTGGCAACCATCTT 59.887 50.000 22.65 0.00 30.82 2.40
1678 2057 0.322816 TGAGCCTGGCAACCATCTTC 60.323 55.000 22.65 7.40 30.82 2.87
1709 2121 2.437359 AGAAGACGCTGCCATGGC 60.437 61.111 30.54 30.54 42.35 4.40
1823 2238 5.393135 GGAGAAGCTGCCTAAACCAAATAAC 60.393 44.000 0.00 0.00 0.00 1.89
1837 2267 4.338682 ACCAAATAACAAGCCGTTACAACA 59.661 37.500 0.00 0.00 42.82 3.33
1843 2273 2.164624 ACAAGCCGTTACAACAAAAGCA 59.835 40.909 0.00 0.00 0.00 3.91
1845 2275 3.011949 AGCCGTTACAACAAAAGCATG 57.988 42.857 0.00 0.00 0.00 4.06
1846 2276 2.058057 GCCGTTACAACAAAAGCATGG 58.942 47.619 0.00 0.00 0.00 3.66
1855 2288 8.699749 GTTACAACAAAAGCATGGAAGAAATAC 58.300 33.333 0.00 0.00 0.00 1.89
1876 2309 3.935203 ACAAAGGCGAGTTGATGACTATG 59.065 43.478 5.76 0.00 39.19 2.23
1968 2401 3.857052 TGAATTCATCTGGGTACGTGAC 58.143 45.455 3.38 0.00 0.00 3.67
2311 2762 1.528129 GGAAGCCAGTTCTGGTTCTG 58.472 55.000 18.42 0.00 35.25 3.02
2466 3272 5.886960 AGGCACTCTTAAATAGCTTTGTG 57.113 39.130 0.00 0.00 0.00 3.33
2500 3306 4.406456 TCTGGTATGGTTCTTTGCATGTT 58.594 39.130 0.00 0.00 0.00 2.71
2520 3326 0.846693 ACAAAAGGCACTCCTCCTGT 59.153 50.000 0.00 0.00 43.40 4.00
2528 3334 1.484240 GCACTCCTCCTGTAAGATGCT 59.516 52.381 0.00 0.00 34.07 3.79
2534 3340 2.288702 CCTCCTGTAAGATGCTCATCGG 60.289 54.545 4.41 0.43 42.48 4.18
2536 3342 1.270518 CCTGTAAGATGCTCATCGGGG 60.271 57.143 4.41 1.35 42.48 5.73
2541 3347 2.267174 AGATGCTCATCGGGGAATTG 57.733 50.000 4.41 0.00 42.48 2.32
2545 3351 2.091541 TGCTCATCGGGGAATTGTTTC 58.908 47.619 0.00 0.00 0.00 2.78
2560 3366 6.460953 GGAATTGTTTCACTGCAAGGACTTTA 60.461 38.462 0.00 0.00 39.30 1.85
2585 3394 0.468029 CAGTATTGGGGGTCCATGGC 60.468 60.000 6.96 1.78 43.63 4.40
2586 3395 0.923729 AGTATTGGGGGTCCATGGCA 60.924 55.000 6.96 0.00 43.63 4.92
2633 3442 3.265791 CAGAGTTGGTTCTGGAGTATGC 58.734 50.000 0.00 0.00 40.69 3.14
2827 6047 1.539157 TTACCACATTGGCGCATCAA 58.461 45.000 10.83 5.49 42.67 2.57
3002 6225 2.617308 CTGAGATGTTATTGCCTGGCAG 59.383 50.000 22.17 7.75 40.61 4.85
3032 6255 5.182001 GGAATCTGTTCACAACTGCTAATGT 59.818 40.000 0.00 0.00 36.01 2.71
3105 6506 2.822215 GGACGGGCCTTCTCTCATA 58.178 57.895 10.13 0.00 0.00 2.15
3134 6601 8.899887 ATCTTGGGGAGAAAAGATTCAAATTA 57.100 30.769 0.00 0.00 39.55 1.40
3136 6603 6.850752 TGGGGAGAAAAGATTCAAATTACC 57.149 37.500 0.00 0.00 38.06 2.85
3138 6605 5.650703 GGGGAGAAAAGATTCAAATTACCGA 59.349 40.000 0.00 0.00 38.06 4.69
3192 6836 3.209410 GAAATGGCGTGAGGAGATCAAT 58.791 45.455 0.00 0.00 40.43 2.57
3296 6955 4.774660 ATGCAGAGACAATCTCCAAGAT 57.225 40.909 2.18 0.00 44.42 2.40
3300 6959 4.452825 CAGAGACAATCTCCAAGATGCAT 58.547 43.478 0.00 0.00 44.42 3.96
3318 6977 2.812591 GCATCCCACAGAATGCATAGAG 59.187 50.000 0.00 0.00 42.53 2.43
3322 6981 3.264193 TCCCACAGAATGCATAGAGTTGT 59.736 43.478 0.00 0.00 42.53 3.32
3343 7002 4.023365 TGTCATCAGATGCAGAGATACTCG 60.023 45.833 5.41 0.00 35.36 4.18
3361 7020 2.987547 CCAAGGTGCAGCCCACAG 60.988 66.667 13.29 0.00 46.50 3.66
3362 7021 2.113774 CAAGGTGCAGCCCACAGA 59.886 61.111 13.29 0.00 46.50 3.41
3363 7022 1.529010 CAAGGTGCAGCCCACAGAA 60.529 57.895 13.29 0.00 46.50 3.02
3364 7023 0.896940 CAAGGTGCAGCCCACAGAAT 60.897 55.000 13.29 0.00 46.50 2.40
3365 7024 0.896940 AAGGTGCAGCCCACAGAATG 60.897 55.000 13.29 0.00 46.50 2.67
3366 7025 2.570181 GTGCAGCCCACAGAATGC 59.430 61.111 0.00 0.00 44.06 3.56
3367 7026 2.115695 TGCAGCCCACAGAATGCA 59.884 55.556 0.00 0.00 45.82 3.96
3368 7027 1.974875 TGCAGCCCACAGAATGCAG 60.975 57.895 0.00 0.00 43.34 4.41
3369 7028 1.676635 GCAGCCCACAGAATGCAGA 60.677 57.895 0.00 0.00 42.53 4.26
3370 7029 1.654954 GCAGCCCACAGAATGCAGAG 61.655 60.000 0.00 0.00 42.53 3.35
3371 7030 0.035725 CAGCCCACAGAATGCAGAGA 60.036 55.000 0.00 0.00 42.53 3.10
3372 7031 0.252479 AGCCCACAGAATGCAGAGAG 59.748 55.000 0.00 0.00 42.53 3.20
3373 7032 0.035630 GCCCACAGAATGCAGAGAGT 60.036 55.000 0.00 0.00 42.53 3.24
3374 7033 1.612726 GCCCACAGAATGCAGAGAGTT 60.613 52.381 0.00 0.00 42.53 3.01
3375 7034 2.082231 CCCACAGAATGCAGAGAGTTG 58.918 52.381 0.00 0.00 42.53 3.16
3376 7035 2.551721 CCCACAGAATGCAGAGAGTTGT 60.552 50.000 0.00 0.00 42.53 3.32
3377 7036 2.740981 CCACAGAATGCAGAGAGTTGTC 59.259 50.000 0.00 0.00 42.53 3.18
3378 7037 3.396560 CACAGAATGCAGAGAGTTGTCA 58.603 45.455 0.00 0.00 42.53 3.58
3379 7038 3.186001 CACAGAATGCAGAGAGTTGTCAC 59.814 47.826 0.00 0.00 42.53 3.67
3380 7039 2.740981 CAGAATGCAGAGAGTTGTCACC 59.259 50.000 0.00 0.00 0.00 4.02
3381 7040 1.728971 GAATGCAGAGAGTTGTCACCG 59.271 52.381 0.00 0.00 0.00 4.94
3382 7041 0.036952 ATGCAGAGAGTTGTCACCGG 60.037 55.000 0.00 0.00 0.00 5.28
3383 7042 1.374758 GCAGAGAGTTGTCACCGGG 60.375 63.158 6.32 0.00 0.00 5.73
3384 7043 1.374758 CAGAGAGTTGTCACCGGGC 60.375 63.158 6.32 0.00 0.00 6.13
3385 7044 2.432628 GAGAGTTGTCACCGGGCG 60.433 66.667 6.32 0.00 0.00 6.13
3386 7045 3.222354 GAGAGTTGTCACCGGGCGT 62.222 63.158 6.32 0.00 0.00 5.68
3387 7046 3.041940 GAGTTGTCACCGGGCGTG 61.042 66.667 6.32 0.00 44.50 5.34
3388 7047 4.619227 AGTTGTCACCGGGCGTGG 62.619 66.667 6.32 0.00 43.23 4.94
3389 7048 4.612412 GTTGTCACCGGGCGTGGA 62.612 66.667 6.32 0.00 43.23 4.02
3390 7049 3.862991 TTGTCACCGGGCGTGGAA 61.863 61.111 6.32 0.00 43.23 3.53
3391 7050 3.402095 TTGTCACCGGGCGTGGAAA 62.402 57.895 6.32 0.00 43.23 3.13
3392 7051 3.351416 GTCACCGGGCGTGGAAAC 61.351 66.667 6.32 0.00 43.23 2.78
3393 7052 3.862991 TCACCGGGCGTGGAAACA 61.863 61.111 6.32 0.00 43.23 2.83
3394 7053 2.671619 CACCGGGCGTGGAAACAT 60.672 61.111 6.32 0.00 46.14 2.71
3395 7054 1.376166 CACCGGGCGTGGAAACATA 60.376 57.895 6.32 0.00 46.14 2.29
3918 7628 0.109342 CACCCTTCAGGCACTCAAGT 59.891 55.000 0.00 0.00 33.57 3.16
3945 7655 2.360852 GCTGCTGCTGATGGTGGT 60.361 61.111 10.92 0.00 36.03 4.16
3946 7656 2.697761 GCTGCTGCTGATGGTGGTG 61.698 63.158 10.92 0.00 36.03 4.17
4134 7966 0.657840 GTTACTCCACGGATGCATGC 59.342 55.000 11.82 11.82 0.00 4.06
4255 8087 4.846779 TTGCTACCCAATTGTCAGAAAC 57.153 40.909 4.43 0.00 0.00 2.78
4266 8098 3.266510 TGTCAGAAACTGAAGTGCTGT 57.733 42.857 2.98 0.00 42.46 4.40
4288 8120 3.439857 TTTCTCCCTCAACCTCCAATG 57.560 47.619 0.00 0.00 0.00 2.82
4289 8121 2.044793 TCTCCCTCAACCTCCAATGT 57.955 50.000 0.00 0.00 0.00 2.71
4335 8167 1.272554 GGGAGGGGATGGAAAGACGT 61.273 60.000 0.00 0.00 0.00 4.34
4354 8186 2.921121 CGTTACTGCTGCTGACGAAATA 59.079 45.455 13.69 0.00 35.90 1.40
4355 8187 3.241678 CGTTACTGCTGCTGACGAAATAC 60.242 47.826 13.69 0.51 35.90 1.89
4356 8188 1.726853 ACTGCTGCTGACGAAATACC 58.273 50.000 13.69 0.00 0.00 2.73
4357 8189 0.647410 CTGCTGCTGACGAAATACCG 59.353 55.000 0.00 0.00 0.00 4.02
4358 8190 0.739462 TGCTGCTGACGAAATACCGG 60.739 55.000 0.00 0.00 0.00 5.28
4359 8191 2.006772 CTGCTGACGAAATACCGGC 58.993 57.895 0.00 0.00 38.24 6.13
4360 8192 0.739462 CTGCTGACGAAATACCGGCA 60.739 55.000 0.00 0.00 46.52 5.69
4365 8197 1.274167 TGACGAAATACCGGCAGAGTT 59.726 47.619 0.00 0.00 43.46 3.01
4372 8204 1.471119 TACCGGCAGAGTTACCTGAG 58.529 55.000 0.00 0.00 36.29 3.35
4384 8216 6.825721 CAGAGTTACCTGAGAAATTATTGCCT 59.174 38.462 0.00 0.00 36.29 4.75
4385 8217 7.011857 CAGAGTTACCTGAGAAATTATTGCCTC 59.988 40.741 0.00 0.00 36.29 4.70
4386 8218 6.963322 AGTTACCTGAGAAATTATTGCCTCT 58.037 36.000 8.37 0.00 0.00 3.69
4423 10343 2.773487 TGGAAATAACCCGTGTCTGTG 58.227 47.619 0.00 0.00 0.00 3.66
4463 10383 3.349927 TGATTCTGATTTGCCCAGTCAG 58.650 45.455 0.00 0.00 40.48 3.51
4481 10401 6.283694 CAGTCAGCTTATTACTGCTATCCAA 58.716 40.000 3.19 0.00 37.81 3.53
4483 10403 6.763610 AGTCAGCTTATTACTGCTATCCAAAC 59.236 38.462 0.00 0.00 37.81 2.93
4485 10405 4.511826 AGCTTATTACTGCTATCCAAACGC 59.488 41.667 0.00 0.00 37.81 4.84
4493 10413 1.400494 GCTATCCAAACGCCGTGATTT 59.600 47.619 0.00 0.00 0.00 2.17
4495 10415 3.672241 GCTATCCAAACGCCGTGATTTTT 60.672 43.478 0.00 0.00 0.00 1.94
4577 10514 0.037975 GTTCAACCATGCCAAGGCTG 60.038 55.000 12.96 7.93 42.51 4.85
4676 10613 5.653507 TCATAATGCAATGCAGTTTTCCTC 58.346 37.500 14.79 0.00 43.65 3.71
4721 10658 2.856346 CGTCGCGCCATCCGTAAAG 61.856 63.158 0.00 0.00 39.71 1.85
4736 10673 2.604914 CGTAAAGCAGAGCGTTGATGAT 59.395 45.455 0.52 0.00 32.01 2.45
4745 10683 2.677836 GAGCGTTGATGATGCAAAGGTA 59.322 45.455 0.00 0.00 42.96 3.08
4758 10696 3.288809 CAAAGGTAAGGTTGCAGCTTC 57.711 47.619 0.00 0.00 37.16 3.86
4795 10733 9.046296 CAGGGAAATCTTATAACTGTGATGTAC 57.954 37.037 0.00 0.00 0.00 2.90
4799 10737 9.378551 GAAATCTTATAACTGTGATGTACCACA 57.621 33.333 5.08 5.08 43.98 4.17
4821 10759 4.080015 CAGGTAACCAAAGACATGGGGATA 60.080 45.833 0.00 0.00 45.18 2.59
4822 10760 4.731929 AGGTAACCAAAGACATGGGGATAT 59.268 41.667 0.00 0.00 45.18 1.63
4823 10761 4.827284 GGTAACCAAAGACATGGGGATATG 59.173 45.833 0.00 0.00 45.18 1.78
4830 10768 1.630878 GACATGGGGATATGGAGGACC 59.369 57.143 0.00 0.00 32.32 4.46
4832 10770 2.352371 CATGGGGATATGGAGGACCTT 58.648 52.381 0.00 0.00 37.04 3.50
4840 10778 1.434513 ATGGAGGACCTTGGCCAACA 61.435 55.000 16.05 9.78 37.04 3.33
4855 10793 0.167470 CAACAAGGCGTCAGATGCTG 59.833 55.000 14.44 8.29 0.00 4.41
4876 10814 3.054582 TGGAGCATCATGAAGAAGAAGCT 60.055 43.478 0.00 0.84 36.25 3.74
4944 10882 8.443953 ACCAGCTGAATAATCTGAGAAATTAC 57.556 34.615 17.39 0.00 0.00 1.89
4964 10902 6.680148 TTACTATCTGCTTATACATGGGCA 57.320 37.500 0.00 0.00 0.00 5.36
4979 10917 1.312815 GGGCATAATCCTGTGTCTGC 58.687 55.000 0.00 0.00 0.00 4.26
4985 10923 4.769688 CATAATCCTGTGTCTGCCTTACA 58.230 43.478 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 9.881529 CGAATACTGATACTACCTTCTTACTTC 57.118 37.037 0.00 0.00 0.00 3.01
65 66 9.624373 TCGAATACTGATACTACCTTCTTACTT 57.376 33.333 0.00 0.00 0.00 2.24
66 67 9.796180 ATCGAATACTGATACTACCTTCTTACT 57.204 33.333 0.00 0.00 0.00 2.24
67 68 9.828852 CATCGAATACTGATACTACCTTCTTAC 57.171 37.037 0.00 0.00 0.00 2.34
68 69 8.512956 GCATCGAATACTGATACTACCTTCTTA 58.487 37.037 0.00 0.00 0.00 2.10
69 70 7.371936 GCATCGAATACTGATACTACCTTCTT 58.628 38.462 0.00 0.00 0.00 2.52
70 71 6.071840 GGCATCGAATACTGATACTACCTTCT 60.072 42.308 0.00 0.00 0.00 2.85
71 72 6.094061 GGCATCGAATACTGATACTACCTTC 58.906 44.000 0.00 0.00 0.00 3.46
72 73 5.047235 GGGCATCGAATACTGATACTACCTT 60.047 44.000 0.00 0.00 0.00 3.50
73 74 4.463186 GGGCATCGAATACTGATACTACCT 59.537 45.833 0.00 0.00 0.00 3.08
74 75 4.219944 TGGGCATCGAATACTGATACTACC 59.780 45.833 0.00 0.00 0.00 3.18
75 76 5.162075 GTGGGCATCGAATACTGATACTAC 58.838 45.833 0.00 0.00 0.00 2.73
76 77 4.082949 CGTGGGCATCGAATACTGATACTA 60.083 45.833 0.00 0.00 0.00 1.82
77 78 3.305403 CGTGGGCATCGAATACTGATACT 60.305 47.826 0.00 0.00 0.00 2.12
78 79 2.987149 CGTGGGCATCGAATACTGATAC 59.013 50.000 0.00 0.00 0.00 2.24
79 80 2.888414 TCGTGGGCATCGAATACTGATA 59.112 45.455 0.00 0.00 34.36 2.15
80 81 1.686587 TCGTGGGCATCGAATACTGAT 59.313 47.619 0.00 0.00 34.36 2.90
81 82 1.067060 CTCGTGGGCATCGAATACTGA 59.933 52.381 0.00 0.00 36.89 3.41
82 83 1.491670 CTCGTGGGCATCGAATACTG 58.508 55.000 0.00 0.00 36.89 2.74
83 84 0.249489 GCTCGTGGGCATCGAATACT 60.249 55.000 0.00 0.00 36.89 2.12
84 85 1.222115 GGCTCGTGGGCATCGAATAC 61.222 60.000 0.00 0.00 40.53 1.89
85 86 1.069090 GGCTCGTGGGCATCGAATA 59.931 57.895 0.00 0.00 40.53 1.75
317 321 3.057547 CTGGGCAGTCGAGTCGAGG 62.058 68.421 17.12 12.49 36.23 4.63
348 642 6.294286 GGAAACGAATGGGAATAAACACAAGA 60.294 38.462 0.00 0.00 0.00 3.02
379 673 1.406069 GCTGCTACTGCTCCAGCTAAA 60.406 52.381 4.74 0.00 46.28 1.85
391 685 1.550976 GAACACCAGGTAGCTGCTACT 59.449 52.381 31.90 18.94 37.16 2.57
392 686 1.275291 TGAACACCAGGTAGCTGCTAC 59.725 52.381 27.44 27.44 36.33 3.58
393 687 1.639722 TGAACACCAGGTAGCTGCTA 58.360 50.000 16.62 5.02 0.00 3.49
449 770 2.678324 GAGACCACAGACAAGCAGTAC 58.322 52.381 0.00 0.00 0.00 2.73
455 776 1.067776 GTACCCGAGACCACAGACAAG 60.068 57.143 0.00 0.00 0.00 3.16
456 777 0.963962 GTACCCGAGACCACAGACAA 59.036 55.000 0.00 0.00 0.00 3.18
489 810 6.624352 TGGCTCAAAATATTCATCAGCTAC 57.376 37.500 0.00 0.00 0.00 3.58
508 829 7.957992 ACTAATTCTACTAGTACACTTGGCT 57.042 36.000 0.00 0.00 0.00 4.75
530 851 9.612066 AAATCACAACCATCAAAACATTTTACT 57.388 25.926 0.00 0.00 0.00 2.24
533 854 9.176460 AGAAAATCACAACCATCAAAACATTTT 57.824 25.926 0.00 0.00 0.00 1.82
572 894 3.922366 GGATCCCAATCCCCGGAT 58.078 61.111 0.73 0.00 45.11 4.18
642 971 9.047371 CCTATAAATTGATTGAAATTGCATGCA 57.953 29.630 18.46 18.46 30.21 3.96
643 972 9.263538 TCCTATAAATTGATTGAAATTGCATGC 57.736 29.630 11.82 11.82 30.21 4.06
735 1071 5.545658 TTTGCTAAAGACTAAAGCCATCG 57.454 39.130 6.52 0.00 35.33 3.84
790 1126 1.781555 CGTGCTCGTGGTTGATGTC 59.218 57.895 0.00 0.00 0.00 3.06
791 1127 3.951332 CGTGCTCGTGGTTGATGT 58.049 55.556 0.00 0.00 0.00 3.06
801 1137 3.416119 TTAGTATTCCTCACGTGCTCG 57.584 47.619 11.67 6.63 43.34 5.03
864 1212 0.971959 TGGAATGTGGAGGGCATTGC 60.972 55.000 0.00 0.00 42.46 3.56
1139 1498 4.263462 TGCCCAGGTATGACATCCATATTC 60.263 45.833 0.00 0.00 39.69 1.75
1431 1796 4.870426 ACGACGAATAAACAGATTGATGCT 59.130 37.500 0.00 0.00 0.00 3.79
1497 1862 3.450817 TGACTAGGCTGTTAATGCTAGCA 59.549 43.478 21.85 21.85 39.15 3.49
1649 2028 1.455849 CCAGGCTCAAGGTCAACCA 59.544 57.895 1.33 0.00 38.89 3.67
1650 2029 1.973812 GCCAGGCTCAAGGTCAACC 60.974 63.158 3.29 0.00 0.00 3.77
1651 2030 0.823356 TTGCCAGGCTCAAGGTCAAC 60.823 55.000 14.15 0.00 0.00 3.18
1652 2031 0.823356 GTTGCCAGGCTCAAGGTCAA 60.823 55.000 14.15 0.00 0.00 3.18
1653 2032 1.228245 GTTGCCAGGCTCAAGGTCA 60.228 57.895 14.15 0.00 0.00 4.02
1654 2033 1.973812 GGTTGCCAGGCTCAAGGTC 60.974 63.158 14.15 0.00 0.00 3.85
1655 2034 2.085343 ATGGTTGCCAGGCTCAAGGT 62.085 55.000 14.15 0.00 36.75 3.50
1656 2035 1.304713 ATGGTTGCCAGGCTCAAGG 60.305 57.895 14.15 0.00 36.75 3.61
1657 2036 0.323178 AGATGGTTGCCAGGCTCAAG 60.323 55.000 14.15 0.00 36.75 3.02
1658 2037 0.112995 AAGATGGTTGCCAGGCTCAA 59.887 50.000 14.15 0.00 36.75 3.02
1659 2038 0.322816 GAAGATGGTTGCCAGGCTCA 60.323 55.000 14.15 9.02 36.75 4.26
1660 2039 1.034292 GGAAGATGGTTGCCAGGCTC 61.034 60.000 14.15 5.81 36.75 4.70
1661 2040 1.000396 GGAAGATGGTTGCCAGGCT 60.000 57.895 14.15 0.00 36.75 4.58
1662 2041 1.000396 AGGAAGATGGTTGCCAGGC 60.000 57.895 3.66 3.66 36.75 4.85
1663 2042 0.329261 TGAGGAAGATGGTTGCCAGG 59.671 55.000 0.00 0.00 36.75 4.45
1664 2043 2.089980 CTTGAGGAAGATGGTTGCCAG 58.910 52.381 0.00 0.00 36.75 4.85
1665 2044 1.887956 GCTTGAGGAAGATGGTTGCCA 60.888 52.381 0.00 0.00 38.19 4.92
1666 2045 0.813821 GCTTGAGGAAGATGGTTGCC 59.186 55.000 0.00 0.00 0.00 4.52
1667 2046 1.200948 GTGCTTGAGGAAGATGGTTGC 59.799 52.381 0.00 0.00 0.00 4.17
1668 2047 2.507484 TGTGCTTGAGGAAGATGGTTG 58.493 47.619 0.00 0.00 0.00 3.77
1669 2048 2.957402 TGTGCTTGAGGAAGATGGTT 57.043 45.000 0.00 0.00 0.00 3.67
1670 2049 2.553904 CCTTGTGCTTGAGGAAGATGGT 60.554 50.000 0.00 0.00 34.91 3.55
1671 2050 2.089980 CCTTGTGCTTGAGGAAGATGG 58.910 52.381 0.00 0.00 34.91 3.51
1672 2051 3.008330 CTCCTTGTGCTTGAGGAAGATG 58.992 50.000 4.50 0.00 41.33 2.90
1673 2052 2.909006 TCTCCTTGTGCTTGAGGAAGAT 59.091 45.455 4.50 0.00 41.33 2.40
1674 2053 2.329267 TCTCCTTGTGCTTGAGGAAGA 58.671 47.619 4.50 2.64 41.33 2.87
1675 2054 2.847327 TCTCCTTGTGCTTGAGGAAG 57.153 50.000 4.50 0.00 41.33 3.46
1676 2055 2.705658 TCTTCTCCTTGTGCTTGAGGAA 59.294 45.455 4.50 0.00 41.33 3.36
1677 2056 2.037772 GTCTTCTCCTTGTGCTTGAGGA 59.962 50.000 3.17 3.17 39.69 3.71
1678 2057 2.421619 GTCTTCTCCTTGTGCTTGAGG 58.578 52.381 0.00 0.00 0.00 3.86
1709 2121 0.249073 CTGATAGTCGGCCTCAACGG 60.249 60.000 0.00 0.00 0.00 4.44
1711 2123 2.979130 GCTGATAGTCGGCCTCAAC 58.021 57.895 0.00 0.00 42.80 3.18
1823 2238 2.803451 TGCTTTTGTTGTAACGGCTTG 58.197 42.857 0.00 0.00 0.00 4.01
1837 2267 5.934043 GCCTTTGTATTTCTTCCATGCTTTT 59.066 36.000 0.00 0.00 0.00 2.27
1843 2273 4.589908 ACTCGCCTTTGTATTTCTTCCAT 58.410 39.130 0.00 0.00 0.00 3.41
1845 2275 4.454504 TCAACTCGCCTTTGTATTTCTTCC 59.545 41.667 0.00 0.00 0.00 3.46
1846 2276 5.607119 TCAACTCGCCTTTGTATTTCTTC 57.393 39.130 0.00 0.00 0.00 2.87
1855 2288 4.183865 TCATAGTCATCAACTCGCCTTTG 58.816 43.478 0.00 0.00 39.55 2.77
2311 2762 4.647399 TGCCTGTTTATATTTAGCAACCCC 59.353 41.667 0.00 0.00 0.00 4.95
2466 3272 5.193099 ACCATACCAGATTATATTGGCCC 57.807 43.478 0.00 0.00 38.03 5.80
2520 3326 3.136443 ACAATTCCCCGATGAGCATCTTA 59.864 43.478 8.66 0.00 35.72 2.10
2528 3334 3.081061 CAGTGAAACAATTCCCCGATGA 58.919 45.455 0.00 0.00 41.43 2.92
2534 3340 2.627699 TCCTTGCAGTGAAACAATTCCC 59.372 45.455 0.00 0.00 41.43 3.97
2536 3342 4.574599 AGTCCTTGCAGTGAAACAATTC 57.425 40.909 0.00 0.00 41.43 2.17
2541 3347 5.915196 GTCAATAAAGTCCTTGCAGTGAAAC 59.085 40.000 0.00 0.00 0.00 2.78
2545 3351 3.820467 TGGTCAATAAAGTCCTTGCAGTG 59.180 43.478 0.00 0.00 0.00 3.66
2576 3385 3.884704 TTGCAGGGTGCCATGGACC 62.885 63.158 18.40 19.15 44.23 4.46
2577 3386 2.283101 TTGCAGGGTGCCATGGAC 60.283 61.111 18.40 10.81 44.23 4.02
2585 3394 1.101049 AACGGTTGAGTTGCAGGGTG 61.101 55.000 0.00 0.00 32.39 4.61
2586 3395 1.101049 CAACGGTTGAGTTGCAGGGT 61.101 55.000 15.66 0.00 43.87 4.34
2633 3442 2.027192 TGATCTTCCCACCCTTTCTTCG 60.027 50.000 0.00 0.00 0.00 3.79
2679 3494 2.917933 CCCCTGCGATCATTGAACTTA 58.082 47.619 0.00 0.00 0.00 2.24
2808 5978 1.201181 GTTGATGCGCCAATGTGGTAA 59.799 47.619 4.18 0.00 40.46 2.85
2827 6047 1.002257 TGGCGCATTGGTGATCTGT 60.002 52.632 10.83 0.00 0.00 3.41
3002 6225 2.380084 TGTGAACAGATTCCGCCTAC 57.620 50.000 0.00 0.00 33.49 3.18
3099 6500 5.409590 TTCTCCCCAAGATCTCTATGAGA 57.590 43.478 0.00 3.39 43.20 3.27
3105 6506 5.490357 TGAATCTTTTCTCCCCAAGATCTCT 59.510 40.000 0.00 0.00 38.55 3.10
3134 6601 6.318900 GGACCAGATCTTCAAAATATTTCGGT 59.681 38.462 0.10 0.00 0.00 4.69
3136 6603 6.257849 TCGGACCAGATCTTCAAAATATTTCG 59.742 38.462 0.10 0.00 0.00 3.46
3138 6605 6.037172 CGTCGGACCAGATCTTCAAAATATTT 59.963 38.462 1.91 0.00 0.00 1.40
3151 6618 0.035439 ATTTTGGCGTCGGACCAGAT 60.035 50.000 1.91 0.00 38.73 2.90
3155 6622 0.594110 TTTCATTTTGGCGTCGGACC 59.406 50.000 1.91 0.00 0.00 4.46
3192 6836 3.838244 ACTGTTTGCACAAGTCCTCTA 57.162 42.857 0.00 0.00 30.36 2.43
3300 6959 3.264193 ACAACTCTATGCATTCTGTGGGA 59.736 43.478 3.54 0.00 0.00 4.37
3318 6977 5.599732 AGTATCTCTGCATCTGATGACAAC 58.400 41.667 21.30 11.92 0.00 3.32
3322 6981 3.057666 GCGAGTATCTCTGCATCTGATGA 60.058 47.826 21.30 5.83 33.08 2.92
3361 7020 1.728971 CGGTGACAACTCTCTGCATTC 59.271 52.381 0.00 0.00 0.00 2.67
3362 7021 1.609061 CCGGTGACAACTCTCTGCATT 60.609 52.381 0.00 0.00 0.00 3.56
3363 7022 0.036952 CCGGTGACAACTCTCTGCAT 60.037 55.000 0.00 0.00 0.00 3.96
3364 7023 1.367471 CCGGTGACAACTCTCTGCA 59.633 57.895 0.00 0.00 0.00 4.41
3365 7024 1.374758 CCCGGTGACAACTCTCTGC 60.375 63.158 0.00 0.00 0.00 4.26
3366 7025 1.374758 GCCCGGTGACAACTCTCTG 60.375 63.158 0.00 0.00 0.00 3.35
3367 7026 2.932234 CGCCCGGTGACAACTCTCT 61.932 63.158 0.00 0.00 0.00 3.10
3368 7027 2.432628 CGCCCGGTGACAACTCTC 60.433 66.667 0.00 0.00 0.00 3.20
3369 7028 3.231736 ACGCCCGGTGACAACTCT 61.232 61.111 4.58 0.00 0.00 3.24
3377 7036 0.746563 ATATGTTTCCACGCCCGGTG 60.747 55.000 0.00 0.00 46.57 4.94
3378 7037 0.746563 CATATGTTTCCACGCCCGGT 60.747 55.000 0.00 0.00 0.00 5.28
3379 7038 2.021722 CATATGTTTCCACGCCCGG 58.978 57.895 0.00 0.00 0.00 5.73
3380 7039 1.355210 GCATATGTTTCCACGCCCG 59.645 57.895 4.29 0.00 0.00 6.13
3381 7040 0.814457 TTGCATATGTTTCCACGCCC 59.186 50.000 4.29 0.00 0.00 6.13
3382 7041 1.472480 AGTTGCATATGTTTCCACGCC 59.528 47.619 4.29 0.00 0.00 5.68
3383 7042 2.919666 AGTTGCATATGTTTCCACGC 57.080 45.000 4.29 0.00 0.00 5.34
3384 7043 4.153296 TGTGTAGTTGCATATGTTTCCACG 59.847 41.667 4.29 0.00 0.00 4.94
3385 7044 5.621197 TGTGTAGTTGCATATGTTTCCAC 57.379 39.130 4.29 5.27 0.00 4.02
3386 7045 5.182950 CCTTGTGTAGTTGCATATGTTTCCA 59.817 40.000 4.29 0.00 0.00 3.53
3387 7046 5.183140 ACCTTGTGTAGTTGCATATGTTTCC 59.817 40.000 4.29 0.00 0.00 3.13
3388 7047 6.254281 ACCTTGTGTAGTTGCATATGTTTC 57.746 37.500 4.29 0.00 0.00 2.78
3389 7048 6.648879 AACCTTGTGTAGTTGCATATGTTT 57.351 33.333 4.29 0.00 0.00 2.83
3390 7049 6.648879 AAACCTTGTGTAGTTGCATATGTT 57.351 33.333 4.29 0.00 0.00 2.71
3391 7050 6.648879 AAAACCTTGTGTAGTTGCATATGT 57.351 33.333 4.29 0.00 0.00 2.29
3392 7051 8.458052 TGATAAAACCTTGTGTAGTTGCATATG 58.542 33.333 0.00 0.00 0.00 1.78
3393 7052 8.574251 TGATAAAACCTTGTGTAGTTGCATAT 57.426 30.769 0.00 0.00 0.00 1.78
3394 7053 7.987750 TGATAAAACCTTGTGTAGTTGCATA 57.012 32.000 0.00 0.00 0.00 3.14
3395 7054 6.892658 TGATAAAACCTTGTGTAGTTGCAT 57.107 33.333 0.00 0.00 0.00 3.96
3918 7628 4.631773 GCAGCAGCTTCATGAGGA 57.368 55.556 9.36 0.00 37.91 3.71
3938 7648 0.107703 CGTAGATGCACCACCACCAT 60.108 55.000 0.00 0.00 0.00 3.55
3939 7649 1.295101 CGTAGATGCACCACCACCA 59.705 57.895 0.00 0.00 0.00 4.17
3940 7650 0.739813 GACGTAGATGCACCACCACC 60.740 60.000 0.00 0.00 0.00 4.61
3941 7651 0.246635 AGACGTAGATGCACCACCAC 59.753 55.000 0.00 0.00 0.00 4.16
3942 7652 0.530744 GAGACGTAGATGCACCACCA 59.469 55.000 0.00 0.00 0.00 4.17
3943 7653 0.525668 CGAGACGTAGATGCACCACC 60.526 60.000 0.00 0.00 0.00 4.61
3944 7654 0.525668 CCGAGACGTAGATGCACCAC 60.526 60.000 0.00 0.00 0.00 4.16
3945 7655 1.807226 CCGAGACGTAGATGCACCA 59.193 57.895 0.00 0.00 0.00 4.17
3946 7656 1.589196 GCCGAGACGTAGATGCACC 60.589 63.158 0.00 0.00 0.00 5.01
3997 7713 6.169557 TCAAACTGGACTAGTGCTTTTCTA 57.830 37.500 15.92 3.52 40.26 2.10
4084 7916 5.052481 CCATACGACAGACATGATCATTGT 58.948 41.667 5.16 8.39 0.00 2.71
4134 7966 3.804036 TGCTATAGAATTCAACACGGGG 58.196 45.455 8.44 0.00 0.00 5.73
4255 8087 3.217626 AGGGAGAAAAACAGCACTTCAG 58.782 45.455 0.00 0.00 0.00 3.02
4266 8098 3.963476 TTGGAGGTTGAGGGAGAAAAA 57.037 42.857 0.00 0.00 0.00 1.94
4288 8120 8.690884 AGCATGTATCTATCTGGTATATCACAC 58.309 37.037 0.00 0.00 0.00 3.82
4289 8121 8.829373 AGCATGTATCTATCTGGTATATCACA 57.171 34.615 0.00 0.00 0.00 3.58
4335 8167 3.259064 GGTATTTCGTCAGCAGCAGTAA 58.741 45.455 0.00 0.00 0.00 2.24
4365 8197 9.920946 AATAAAGAGGCAATAATTTCTCAGGTA 57.079 29.630 0.00 0.00 0.00 3.08
4414 10334 2.159787 GCAGATTGCTAACACAGACACG 60.160 50.000 0.00 0.00 40.96 4.49
4437 10357 4.240096 CTGGGCAAATCAGAATCAAACAC 58.760 43.478 0.00 0.00 34.36 3.32
4463 10383 4.319549 GGCGTTTGGATAGCAGTAATAAGC 60.320 45.833 0.00 0.00 0.00 3.09
4508 10428 9.767684 CGTTGCAACAAATCTTGTAGATATAAA 57.232 29.630 28.01 0.00 44.59 1.40
4509 10429 8.941977 ACGTTGCAACAAATCTTGTAGATATAA 58.058 29.630 28.01 0.00 44.59 0.98
4510 10430 8.487313 ACGTTGCAACAAATCTTGTAGATATA 57.513 30.769 28.01 0.00 44.59 0.86
4533 10470 1.872952 TGTTCTTGTGATGGAGCAACG 59.127 47.619 0.00 0.00 0.00 4.10
4577 10514 2.011540 ACGCGAAGAAGGAAATCTCC 57.988 50.000 15.93 0.00 42.81 3.71
4615 10552 7.637709 TGTGTCTGATATATACAAATCACGC 57.362 36.000 0.00 0.00 0.00 5.34
4616 10553 8.650714 CCATGTGTCTGATATATACAAATCACG 58.349 37.037 0.00 0.00 0.00 4.35
4619 10556 8.939929 CCACCATGTGTCTGATATATACAAATC 58.060 37.037 0.00 0.00 0.00 2.17
4676 10613 0.533755 GGCACTGGATGATTCGAGGG 60.534 60.000 0.00 0.00 34.45 4.30
4721 10658 0.448990 TTGCATCATCAACGCTCTGC 59.551 50.000 0.00 0.00 0.00 4.26
4745 10683 0.756442 TGCAAGGAAGCTGCAACCTT 60.756 50.000 19.38 19.38 46.47 3.50
4795 10733 2.819608 CCATGTCTTTGGTTACCTGTGG 59.180 50.000 2.07 0.00 31.74 4.17
4799 10737 2.354328 TCCCCATGTCTTTGGTTACCT 58.646 47.619 2.07 0.00 34.77 3.08
4821 10759 1.384191 GTTGGCCAAGGTCCTCCAT 59.616 57.895 21.21 0.00 35.89 3.41
4822 10760 1.650242 TTGTTGGCCAAGGTCCTCCA 61.650 55.000 21.21 8.67 35.89 3.86
4823 10761 0.895559 CTTGTTGGCCAAGGTCCTCC 60.896 60.000 21.21 5.65 45.70 4.30
4840 10778 1.220206 CTCCAGCATCTGACGCCTT 59.780 57.895 0.00 0.00 32.44 4.35
4855 10793 3.312973 CAGCTTCTTCTTCATGATGCTCC 59.687 47.826 0.00 0.00 40.25 4.70
4892 10830 5.357257 TCTTCAGTTTGTTGACAGGTAGAC 58.643 41.667 0.00 0.00 0.00 2.59
4944 10882 7.443575 GGATTATGCCCATGTATAAGCAGATAG 59.556 40.741 10.18 0.00 37.23 2.08
4950 10888 5.124457 CACAGGATTATGCCCATGTATAAGC 59.876 44.000 0.00 0.00 35.51 3.09
4951 10889 6.240894 ACACAGGATTATGCCCATGTATAAG 58.759 40.000 0.00 0.00 33.40 1.73
4952 10890 6.044287 AGACACAGGATTATGCCCATGTATAA 59.956 38.462 0.00 0.00 34.23 0.98
4953 10891 5.547666 AGACACAGGATTATGCCCATGTATA 59.452 40.000 0.00 0.00 0.00 1.47
4954 10892 4.352001 AGACACAGGATTATGCCCATGTAT 59.648 41.667 0.00 0.00 0.00 2.29
4959 10897 1.408683 GCAGACACAGGATTATGCCCA 60.409 52.381 0.00 0.00 0.00 5.36
4961 10899 1.312815 GGCAGACACAGGATTATGCC 58.687 55.000 0.00 0.00 45.61 4.40
4964 10902 4.770795 GTGTAAGGCAGACACAGGATTAT 58.229 43.478 14.79 0.00 45.36 1.28


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

AutoCloner maintained by Alex Coulton.