Multiple sequence alignment - TraesCS3D01G158500

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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 TraesCS3D01G158500 chr3D 100.000 4511 0 0 1 4511 126982764 126978254 0.000000e+00 8331.0
1 TraesCS3D01G158500 chr3D 80.769 130 23 1 31 160 431624002 431624129 2.870000e-17 100.0
2 TraesCS3D01G158500 chr3A 94.944 2492 93 11 958 3423 137612045 137609561 0.000000e+00 3873.0
3 TraesCS3D01G158500 chr3A 88.028 710 60 16 3811 4511 137609059 137608366 0.000000e+00 817.0
4 TraesCS3D01G158500 chr3A 87.952 581 41 11 216 795 594646206 594645654 0.000000e+00 658.0
5 TraesCS3D01G158500 chr3A 79.630 324 35 16 3448 3760 137609493 137609190 2.130000e-48 204.0
6 TraesCS3D01G158500 chr3A 83.051 118 18 1 43 160 568968807 568968922 6.170000e-19 106.0
7 TraesCS3D01G158500 chr3A 86.022 93 7 2 863 949 468958822 468958914 1.340000e-15 95.3
8 TraesCS3D01G158500 chr3B 96.307 1408 47 2 2016 3418 181321032 181319625 0.000000e+00 2307.0
9 TraesCS3D01G158500 chr3B 90.949 1127 63 15 953 2052 181322153 181321039 0.000000e+00 1480.0
10 TraesCS3D01G158500 chr3B 88.400 819 37 13 4 795 434417164 434416377 0.000000e+00 933.0
11 TraesCS3D01G158500 chr3B 87.981 832 36 12 1 795 829507308 829508112 0.000000e+00 924.0
12 TraesCS3D01G158500 chr3B 85.826 769 79 18 3757 4511 181319211 181318459 0.000000e+00 789.0
13 TraesCS3D01G158500 chr3B 90.071 141 14 0 4371 4511 60830050 60829910 2.770000e-42 183.0
14 TraesCS3D01G158500 chr3B 88.235 85 7 1 868 949 514126809 514126725 1.030000e-16 99.0
15 TraesCS3D01G158500 chr3B 86.170 94 6 2 863 949 757951605 757951512 1.340000e-15 95.3
16 TraesCS3D01G158500 chr3B 90.566 53 4 1 806 857 181322210 181322158 8.100000e-08 69.4
17 TraesCS3D01G158500 chr7D 91.409 582 21 9 213 792 22089343 22089897 0.000000e+00 771.0
18 TraesCS3D01G158500 chr2D 90.893 582 24 9 213 792 577713561 577714115 0.000000e+00 754.0
19 TraesCS3D01G158500 chr2D 86.000 100 7 2 857 949 150675551 150675650 2.870000e-17 100.0
20 TraesCS3D01G158500 chr7A 90.534 581 27 8 213 792 9363232 9363785 0.000000e+00 743.0
21 TraesCS3D01G158500 chr7A 88.468 581 39 8 216 795 711925108 711924555 0.000000e+00 676.0
22 TraesCS3D01G158500 chr7A 88.559 472 23 8 216 684 61568267 61567824 1.100000e-150 544.0
23 TraesCS3D01G158500 chr7A 88.858 359 29 6 436 792 169967701 169968050 8.960000e-117 431.0
24 TraesCS3D01G158500 chr6B 90.361 581 29 8 213 792 679325108 679325662 0.000000e+00 737.0
25 TraesCS3D01G158500 chr6B 90.426 470 23 7 216 684 679290250 679289802 2.320000e-167 599.0
26 TraesCS3D01G158500 chr6B 91.034 145 13 0 4365 4509 88270920 88271064 3.560000e-46 196.0
27 TraesCS3D01G158500 chr6B 89.796 147 15 0 4365 4511 88284006 88284152 5.960000e-44 189.0
28 TraesCS3D01G158500 chr6B 86.022 93 12 1 857 949 592979056 592979147 1.030000e-16 99.0
29 TraesCS3D01G158500 chr6B 85.870 92 6 3 865 949 11300326 11300417 1.730000e-14 91.6
30 TraesCS3D01G158500 chr6B 85.870 92 6 3 865 949 12748738 12748829 1.730000e-14 91.6
31 TraesCS3D01G158500 chr6D 85.800 500 47 7 1 477 414111971 414112469 4.030000e-140 508.0
32 TraesCS3D01G158500 chr6D 90.780 141 13 0 4371 4511 26606019 26605879 5.960000e-44 189.0
33 TraesCS3D01G158500 chr5B 89.796 147 15 0 4365 4511 287785372 287785518 5.960000e-44 189.0
34 TraesCS3D01G158500 chr4D 89.130 92 8 1 857 948 480993121 480993210 3.690000e-21 113.0
35 TraesCS3D01G158500 chr4A 86.517 89 5 3 868 949 563451293 563451205 1.730000e-14 91.6


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G158500 chr3D 126978254 126982764 4510 True 8331.000000 8331 100.000 1 4511 1 chr3D.!!$R1 4510
1 TraesCS3D01G158500 chr3A 137608366 137612045 3679 True 1631.333333 3873 87.534 958 4511 3 chr3A.!!$R2 3553
2 TraesCS3D01G158500 chr3A 594645654 594646206 552 True 658.000000 658 87.952 216 795 1 chr3A.!!$R1 579
3 TraesCS3D01G158500 chr3B 181318459 181322210 3751 True 1161.350000 2307 90.912 806 4511 4 chr3B.!!$R5 3705
4 TraesCS3D01G158500 chr3B 434416377 434417164 787 True 933.000000 933 88.400 4 795 1 chr3B.!!$R2 791
5 TraesCS3D01G158500 chr3B 829507308 829508112 804 False 924.000000 924 87.981 1 795 1 chr3B.!!$F1 794
6 TraesCS3D01G158500 chr7D 22089343 22089897 554 False 771.000000 771 91.409 213 792 1 chr7D.!!$F1 579
7 TraesCS3D01G158500 chr2D 577713561 577714115 554 False 754.000000 754 90.893 213 792 1 chr2D.!!$F2 579
8 TraesCS3D01G158500 chr7A 9363232 9363785 553 False 743.000000 743 90.534 213 792 1 chr7A.!!$F1 579
9 TraesCS3D01G158500 chr7A 711924555 711925108 553 True 676.000000 676 88.468 216 795 1 chr7A.!!$R2 579
10 TraesCS3D01G158500 chr6B 679325108 679325662 554 False 737.000000 737 90.361 213 792 1 chr6B.!!$F6 579

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
854 895 0.032615 TTCCCCTGGCAAAACACAGT 60.033 50.0 0.00 0.00 32.90 3.55 F
1533 1592 0.108019 TCCTCTCCGATTCGATCCGA 59.892 55.0 7.83 0.00 0.00 4.55 F
1615 1674 0.960364 GTGTGGTAGGTGTGCCATGG 60.960 60.0 7.63 7.63 41.04 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1720 1784 1.473434 GCAGGGAACAGCTAACGCTAT 60.473 52.381 0.00 0.0 46.99 2.97 R
3445 3593 0.737219 GCAATCACCTGACATCAGCC 59.263 55.000 3.18 0.0 42.47 4.85 R
3596 3756 1.001641 GGGCCAGAGCTCACAACAT 60.002 57.895 17.77 0.0 40.27 2.71 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
117 118 3.114616 CAGAGACCGCGGTTGCTG 61.115 66.667 32.60 32.60 39.65 4.41
153 154 5.559227 TCACAAAATCGATGAAATGCTACG 58.441 37.500 0.00 0.00 0.00 3.51
180 181 0.893270 TGGTGATTTGCTGGAACCGG 60.893 55.000 0.00 0.00 33.41 5.28
328 362 1.742761 CACGGATGCTTCAACCTGAT 58.257 50.000 1.64 0.00 0.00 2.90
334 368 4.070716 GGATGCTTCAACCTGATATGGAG 58.929 47.826 1.64 0.00 0.00 3.86
375 409 0.250597 AGAAGTTACAACCGGTGGCC 60.251 55.000 8.52 0.00 0.00 5.36
441 475 1.318576 AAAAGCTTCACCCGTGGAAG 58.681 50.000 0.00 0.00 43.59 3.46
462 496 1.895020 ATGCTTCAACCGGCGTAGGA 61.895 55.000 6.01 0.00 34.73 2.94
463 497 1.375013 GCTTCAACCGGCGTAGGAA 60.375 57.895 6.01 5.19 34.73 3.36
464 498 0.952010 GCTTCAACCGGCGTAGGAAA 60.952 55.000 6.01 0.00 34.73 3.13
465 499 1.734163 CTTCAACCGGCGTAGGAAAT 58.266 50.000 6.01 0.00 34.73 2.17
466 500 1.396996 CTTCAACCGGCGTAGGAAATG 59.603 52.381 6.01 0.00 34.73 2.32
467 501 0.609151 TCAACCGGCGTAGGAAATGA 59.391 50.000 6.01 0.00 34.73 2.57
468 502 1.208535 TCAACCGGCGTAGGAAATGAT 59.791 47.619 6.01 0.00 34.73 2.45
469 503 2.014128 CAACCGGCGTAGGAAATGATT 58.986 47.619 6.01 0.00 34.73 2.57
470 504 1.949465 ACCGGCGTAGGAAATGATTC 58.051 50.000 6.01 0.00 34.73 2.52
471 505 1.208535 ACCGGCGTAGGAAATGATTCA 59.791 47.619 6.01 0.00 37.29 2.57
472 506 2.285083 CCGGCGTAGGAAATGATTCAA 58.715 47.619 6.01 0.00 37.29 2.69
473 507 2.031683 CCGGCGTAGGAAATGATTCAAC 59.968 50.000 6.01 0.00 37.29 3.18
474 508 2.031683 CGGCGTAGGAAATGATTCAACC 59.968 50.000 0.00 0.00 37.29 3.77
475 509 2.031683 GGCGTAGGAAATGATTCAACCG 59.968 50.000 0.00 0.00 37.29 4.44
476 510 2.031683 GCGTAGGAAATGATTCAACCGG 59.968 50.000 0.00 0.00 37.29 5.28
477 511 2.031683 CGTAGGAAATGATTCAACCGGC 59.968 50.000 0.00 0.00 37.29 6.13
478 512 2.214376 AGGAAATGATTCAACCGGCA 57.786 45.000 0.00 0.00 37.29 5.69
479 513 2.738743 AGGAAATGATTCAACCGGCAT 58.261 42.857 0.00 0.00 37.29 4.40
480 514 3.897239 AGGAAATGATTCAACCGGCATA 58.103 40.909 0.00 0.00 37.29 3.14
481 515 3.885297 AGGAAATGATTCAACCGGCATAG 59.115 43.478 0.00 0.00 37.29 2.23
482 516 3.004734 GGAAATGATTCAACCGGCATAGG 59.995 47.826 0.00 0.00 37.29 2.57
486 520 3.897239 TGATTCAACCGGCATAGGAAAT 58.103 40.909 0.00 0.00 34.73 2.17
501 535 2.108952 AGGAAATGCTTCAACCAGAGGT 59.891 45.455 0.00 0.00 37.65 3.85
608 647 4.814294 CGACGGCGAGGGAAAGGG 62.814 72.222 16.62 0.00 40.82 3.95
680 719 2.125713 ACACATCGCGCCGAATGA 60.126 55.556 16.31 1.94 39.99 2.57
694 733 2.270923 CGAATGAATCTGAAGCGTGGA 58.729 47.619 0.00 0.00 0.00 4.02
724 765 4.039245 GGAAGAAGATGATATGACGTGGGA 59.961 45.833 0.00 0.00 0.00 4.37
795 836 2.626780 GCTGACCGGGCCAAACTTC 61.627 63.158 3.83 0.00 0.00 3.01
796 837 1.971695 CTGACCGGGCCAAACTTCC 60.972 63.158 3.83 0.00 0.00 3.46
797 838 3.053896 GACCGGGCCAAACTTCCG 61.054 66.667 6.32 0.00 43.05 4.30
804 845 2.739287 CCAAACTTCCGGCGCGTA 60.739 61.111 8.43 0.00 0.00 4.42
805 846 2.104253 CCAAACTTCCGGCGCGTAT 61.104 57.895 8.43 0.00 0.00 3.06
806 847 1.347221 CAAACTTCCGGCGCGTATC 59.653 57.895 8.43 0.00 0.00 2.24
807 848 1.079681 AAACTTCCGGCGCGTATCA 60.080 52.632 8.43 0.00 0.00 2.15
808 849 1.356527 AAACTTCCGGCGCGTATCAC 61.357 55.000 8.43 0.00 0.00 3.06
809 850 2.104331 CTTCCGGCGCGTATCACT 59.896 61.111 8.43 0.00 0.00 3.41
810 851 2.202690 TTCCGGCGCGTATCACTG 60.203 61.111 8.43 0.00 0.00 3.66
850 891 3.582164 AGTAATTTCCCCTGGCAAAACA 58.418 40.909 0.00 0.00 0.00 2.83
854 895 0.032615 TTCCCCTGGCAAAACACAGT 60.033 50.000 0.00 0.00 32.90 3.55
857 898 1.478654 CCCCTGGCAAAACACAGTACT 60.479 52.381 0.00 0.00 32.90 2.73
859 900 3.561313 CCCCTGGCAAAACACAGTACTAT 60.561 47.826 0.00 0.00 32.90 2.12
860 901 4.323945 CCCCTGGCAAAACACAGTACTATA 60.324 45.833 0.00 0.00 32.90 1.31
861 902 5.437060 CCCTGGCAAAACACAGTACTATAT 58.563 41.667 0.00 0.00 32.90 0.86
862 903 5.296780 CCCTGGCAAAACACAGTACTATATG 59.703 44.000 0.00 0.00 32.90 1.78
864 905 6.597672 CCTGGCAAAACACAGTACTATATGAA 59.402 38.462 0.00 0.00 32.90 2.57
865 906 7.283127 CCTGGCAAAACACAGTACTATATGAAT 59.717 37.037 0.00 0.00 32.90 2.57
866 907 9.325198 CTGGCAAAACACAGTACTATATGAATA 57.675 33.333 0.00 0.00 0.00 1.75
867 908 9.845740 TGGCAAAACACAGTACTATATGAATAT 57.154 29.630 0.00 0.00 0.00 1.28
933 974 8.006027 AGTTAAATTGTCGTTCTAAAACTACGC 58.994 33.333 0.00 0.00 34.64 4.42
934 975 4.557276 ATTGTCGTTCTAAAACTACGCG 57.443 40.909 3.53 3.53 34.64 6.01
935 976 3.266541 TGTCGTTCTAAAACTACGCGA 57.733 42.857 15.93 0.00 34.64 5.87
936 977 3.626977 TGTCGTTCTAAAACTACGCGAA 58.373 40.909 15.93 0.00 34.64 4.70
937 978 4.229096 TGTCGTTCTAAAACTACGCGAAT 58.771 39.130 15.93 0.00 34.64 3.34
938 979 4.088923 TGTCGTTCTAAAACTACGCGAATG 59.911 41.667 15.93 4.47 34.64 2.67
939 980 4.321745 GTCGTTCTAAAACTACGCGAATGA 59.678 41.667 15.93 0.49 35.40 2.57
940 981 4.321745 TCGTTCTAAAACTACGCGAATGAC 59.678 41.667 15.93 0.00 35.40 3.06
941 982 4.322804 CGTTCTAAAACTACGCGAATGACT 59.677 41.667 15.93 0.00 32.95 3.41
942 983 5.164119 CGTTCTAAAACTACGCGAATGACTT 60.164 40.000 15.93 0.94 32.95 3.01
943 984 6.032775 CGTTCTAAAACTACGCGAATGACTTA 59.967 38.462 15.93 2.18 32.95 2.24
944 985 7.253552 CGTTCTAAAACTACGCGAATGACTTAT 60.254 37.037 15.93 0.00 32.95 1.73
945 986 8.378421 GTTCTAAAACTACGCGAATGACTTATT 58.622 33.333 15.93 0.00 32.36 1.40
946 987 8.112099 TCTAAAACTACGCGAATGACTTATTC 57.888 34.615 15.93 0.00 41.46 1.75
947 988 6.715344 AAAACTACGCGAATGACTTATTCA 57.285 33.333 15.93 0.00 44.42 2.57
948 989 5.697848 AACTACGCGAATGACTTATTCAC 57.302 39.130 15.93 0.00 44.42 3.18
951 992 2.943865 CGCGAATGACTTATTCACGTG 58.056 47.619 9.94 9.94 43.04 4.49
952 993 2.285026 CGCGAATGACTTATTCACGTGG 60.285 50.000 17.00 0.90 43.04 4.94
953 994 2.671396 GCGAATGACTTATTCACGTGGT 59.329 45.455 17.00 4.73 44.42 4.16
954 995 3.861113 GCGAATGACTTATTCACGTGGTA 59.139 43.478 17.00 6.60 44.42 3.25
993 1034 0.865769 CGCACTCACAACCTACCAAC 59.134 55.000 0.00 0.00 0.00 3.77
1280 1339 1.153005 CTACGACTACCCCTCCGCT 60.153 63.158 0.00 0.00 0.00 5.52
1355 1414 4.430765 GTCGTCCACGGCCACGAT 62.431 66.667 17.77 0.00 46.13 3.73
1492 1551 1.318158 ACGCAGGTAGTAGTTCCCCG 61.318 60.000 3.38 3.38 0.00 5.73
1494 1553 1.328430 GCAGGTAGTAGTTCCCCGCT 61.328 60.000 0.00 0.00 0.00 5.52
1533 1592 0.108019 TCCTCTCCGATTCGATCCGA 59.892 55.000 7.83 0.00 0.00 4.55
1615 1674 0.960364 GTGTGGTAGGTGTGCCATGG 60.960 60.000 7.63 7.63 41.04 3.66
1683 1746 4.336433 TCAGTAAGGAATTGCTATGCTTGC 59.664 41.667 0.00 0.00 32.48 4.01
1720 1784 2.642154 TTTTGCCAAGTCCCGTAGAA 57.358 45.000 0.00 0.00 0.00 2.10
1805 1869 3.088532 TGTCACAACTCACAAAGCCTTT 58.911 40.909 0.00 0.00 0.00 3.11
1900 1964 9.671279 TGTTGTCACAATGATCTATCTGTAATT 57.329 29.630 0.00 0.00 0.00 1.40
2055 2165 7.910584 TGAACATATGAGGCATATCATAGTGT 58.089 34.615 10.38 10.68 43.52 3.55
2287 2397 1.108776 CTGGAATTGCTGTCATGGGG 58.891 55.000 0.00 0.00 0.00 4.96
2344 2454 1.766864 TGGGTTTCGACCACAGGGA 60.767 57.895 0.00 0.00 38.05 4.20
2459 2569 4.970662 TTGCTCCATGTTATTCTGCTTC 57.029 40.909 0.00 0.00 0.00 3.86
2582 2692 4.081531 TCAGCATTGAAAATCCCAACCATC 60.082 41.667 0.00 0.00 0.00 3.51
2651 2761 5.509670 CGTCCTGCTCTATCCATACATTGAA 60.510 44.000 0.00 0.00 0.00 2.69
2832 2945 5.724328 TGACAACTTAAAACAATTGTGCCA 58.276 33.333 12.82 0.00 35.47 4.92
2839 2952 7.973601 ACTTAAAACAATTGTGCCAAAAGAAG 58.026 30.769 12.82 9.54 0.00 2.85
2862 2975 3.937706 CCTAGTCAAATCTGCCACTTGAG 59.062 47.826 0.00 0.00 30.00 3.02
2885 2998 2.479049 GCTACGCATCGTCTTGGTCTTA 60.479 50.000 0.00 0.00 41.54 2.10
2922 3036 7.945033 TCACCATGCAAAAAGAAAAAGATAC 57.055 32.000 0.00 0.00 0.00 2.24
3110 3225 6.048509 CCCAGAAATTTTACCATGTTATGCC 58.951 40.000 0.00 0.00 0.00 4.40
3116 3231 8.860780 AAATTTTACCATGTTATGCCATTTGT 57.139 26.923 0.00 0.00 0.00 2.83
3160 3277 4.624364 TGCCTGCAGGTGACACCG 62.624 66.667 32.81 14.38 44.90 4.94
3211 3328 2.076863 AGTGTCATTAACAAGGCGCTC 58.923 47.619 7.64 0.00 40.31 5.03
3256 3373 4.778143 CGGTCTTTCCCTGGCCCG 62.778 72.222 0.00 0.00 0.00 6.13
3433 3581 8.870075 AGTTAAATCTATCAAACTGAAAGCCT 57.130 30.769 0.00 0.00 37.60 4.58
3434 3582 9.301897 AGTTAAATCTATCAAACTGAAAGCCTT 57.698 29.630 0.00 0.00 37.60 4.35
3435 3583 9.914131 GTTAAATCTATCAAACTGAAAGCCTTT 57.086 29.630 0.00 0.00 37.60 3.11
3436 3584 9.912634 TTAAATCTATCAAACTGAAAGCCTTTG 57.087 29.630 0.00 0.00 37.60 2.77
3458 3618 2.165167 CAATGTTGGCTGATGTCAGGT 58.835 47.619 11.66 0.00 43.94 4.00
3466 3626 1.131883 GCTGATGTCAGGTGATTGCAC 59.868 52.381 11.66 0.00 43.94 4.57
3488 3648 5.062934 CACGTATCGTCTGCCTTTGAATAAA 59.937 40.000 0.00 0.00 38.32 1.40
3489 3649 5.815740 ACGTATCGTCTGCCTTTGAATAAAT 59.184 36.000 0.00 0.00 33.69 1.40
3551 3711 3.302365 TTTCAATTTGGCAGCTGCTAC 57.698 42.857 35.82 21.98 41.70 3.58
3554 3714 3.684908 TCAATTTGGCAGCTGCTACTTA 58.315 40.909 35.82 19.17 41.70 2.24
3555 3715 4.078537 TCAATTTGGCAGCTGCTACTTAA 58.921 39.130 35.82 22.52 41.70 1.85
3558 3718 4.927978 TTTGGCAGCTGCTACTTAAAAA 57.072 36.364 35.82 18.50 41.70 1.94
3561 3721 4.078537 TGGCAGCTGCTACTTAAAAATGA 58.921 39.130 35.82 0.39 41.70 2.57
3570 3730 7.133891 TGCTACTTAAAAATGAGACTTGAGC 57.866 36.000 0.00 0.00 0.00 4.26
3596 3756 3.874383 TTTGATGGTGAAAGGGACTGA 57.126 42.857 0.00 0.00 40.86 3.41
3607 3767 1.356124 AGGGACTGATGTTGTGAGCT 58.644 50.000 0.00 0.00 37.18 4.09
3608 3768 1.277557 AGGGACTGATGTTGTGAGCTC 59.722 52.381 6.82 6.82 37.18 4.09
3609 3769 1.277557 GGGACTGATGTTGTGAGCTCT 59.722 52.381 16.19 0.00 0.00 4.09
3610 3770 2.344950 GGACTGATGTTGTGAGCTCTG 58.655 52.381 16.19 0.00 0.00 3.35
3611 3771 2.344950 GACTGATGTTGTGAGCTCTGG 58.655 52.381 16.19 0.00 0.00 3.86
3614 3774 1.001641 ATGTTGTGAGCTCTGGCCC 60.002 57.895 16.19 0.00 39.73 5.80
3622 3782 0.324943 GAGCTCTGGCCCTACACAAA 59.675 55.000 6.43 0.00 39.73 2.83
3649 3809 9.736023 GAGTGAACTCTGTCAACAAAATAAATT 57.264 29.630 3.13 0.00 39.81 1.82
3650 3810 9.520204 AGTGAACTCTGTCAACAAAATAAATTG 57.480 29.630 0.00 0.00 36.37 2.32
3651 3811 8.755018 GTGAACTCTGTCAACAAAATAAATTGG 58.245 33.333 0.00 0.00 34.56 3.16
3652 3812 7.437862 TGAACTCTGTCAACAAAATAAATTGGC 59.562 33.333 0.00 0.00 34.56 4.52
3653 3813 7.054491 ACTCTGTCAACAAAATAAATTGGCT 57.946 32.000 0.00 0.00 34.56 4.75
3654 3814 6.925165 ACTCTGTCAACAAAATAAATTGGCTG 59.075 34.615 0.00 0.00 34.56 4.85
3672 3849 0.184692 TGTGGGCAATTGTCTGGTCA 59.815 50.000 10.38 0.00 0.00 4.02
3673 3850 1.327303 GTGGGCAATTGTCTGGTCAA 58.673 50.000 10.38 0.00 0.00 3.18
3674 3851 1.270550 GTGGGCAATTGTCTGGTCAAG 59.729 52.381 10.38 0.00 0.00 3.02
3675 3852 1.133513 TGGGCAATTGTCTGGTCAAGT 60.134 47.619 10.38 0.00 0.00 3.16
3676 3853 2.107378 TGGGCAATTGTCTGGTCAAGTA 59.893 45.455 10.38 0.00 0.00 2.24
3677 3854 3.153919 GGGCAATTGTCTGGTCAAGTAA 58.846 45.455 10.38 0.00 0.00 2.24
3678 3855 3.763897 GGGCAATTGTCTGGTCAAGTAAT 59.236 43.478 10.38 0.00 0.00 1.89
3685 3862 7.923414 ATTGTCTGGTCAAGTAATAAGAACC 57.077 36.000 0.00 0.00 0.00 3.62
3687 3864 6.833041 TGTCTGGTCAAGTAATAAGAACCAA 58.167 36.000 0.00 0.00 0.00 3.67
3689 3866 7.776030 TGTCTGGTCAAGTAATAAGAACCAAAA 59.224 33.333 0.00 0.00 0.00 2.44
3744 3921 6.414732 TGTTCTTCCAGTTATCCGATTCATT 58.585 36.000 0.00 0.00 0.00 2.57
3753 3930 7.416664 CCAGTTATCCGATTCATTGACCATTTT 60.417 37.037 0.00 0.00 0.00 1.82
3754 3931 7.645340 CAGTTATCCGATTCATTGACCATTTTC 59.355 37.037 0.00 0.00 0.00 2.29
3788 4009 6.640518 ACAAGTACACCGTCTAATTCATGAT 58.359 36.000 0.00 0.00 0.00 2.45
3809 4030 5.652014 TGATCAACTCAGACCAACAAACTTT 59.348 36.000 0.00 0.00 0.00 2.66
3842 4099 4.433186 TTGTTGTACATACATTGGCAGC 57.567 40.909 0.00 0.00 35.89 5.25
3845 4102 4.279420 TGTTGTACATACATTGGCAGCAAA 59.721 37.500 0.00 0.00 35.89 3.68
3846 4103 5.047448 TGTTGTACATACATTGGCAGCAAAT 60.047 36.000 0.00 0.00 35.89 2.32
3876 4139 0.726827 CATGTACGCCGACAAGCATT 59.273 50.000 0.00 0.00 31.83 3.56
3883 4146 1.982073 GCCGACAAGCATTCTTCGGG 61.982 60.000 10.64 0.00 46.10 5.14
3884 4147 1.369091 CCGACAAGCATTCTTCGGGG 61.369 60.000 0.83 0.00 43.65 5.73
3885 4148 1.803289 GACAAGCATTCTTCGGGGC 59.197 57.895 0.00 0.00 0.00 5.80
3891 4154 1.648467 GCATTCTTCGGGGCACTGTC 61.648 60.000 0.00 0.00 0.00 3.51
3893 4156 1.207089 CATTCTTCGGGGCACTGTCTA 59.793 52.381 0.00 0.00 0.00 2.59
3894 4157 1.344065 TTCTTCGGGGCACTGTCTAA 58.656 50.000 0.00 0.00 0.00 2.10
3895 4158 1.344065 TCTTCGGGGCACTGTCTAAA 58.656 50.000 0.00 0.00 0.00 1.85
3937 4200 1.815003 CAGGAACATCTTGCAGAACCC 59.185 52.381 0.00 0.00 0.00 4.11
3959 4222 2.687200 ATGCCCGTGTGCCTCCTA 60.687 61.111 0.00 0.00 0.00 2.94
3970 4233 2.225467 GTGCCTCCTAAATCCTCATGC 58.775 52.381 0.00 0.00 0.00 4.06
3997 4261 1.024271 AACCATGGGCAATCGAATCG 58.976 50.000 18.09 0.00 0.00 3.34
3998 4262 0.180171 ACCATGGGCAATCGAATCGA 59.820 50.000 18.09 8.12 41.13 3.59
3999 4263 1.308047 CCATGGGCAATCGAATCGAA 58.692 50.000 10.12 0.00 39.99 3.71
4000 4264 1.881973 CCATGGGCAATCGAATCGAAT 59.118 47.619 10.12 0.00 39.99 3.34
4001 4265 2.351060 CCATGGGCAATCGAATCGAATG 60.351 50.000 15.60 15.60 39.99 2.67
4002 4266 2.036958 TGGGCAATCGAATCGAATGT 57.963 45.000 19.98 2.14 38.77 2.71
4009 4273 1.006086 TCGAATCGAATGTGCGCATT 58.994 45.000 24.87 24.87 46.99 3.56
4015 4279 3.106242 TCGAATGTGCGCATTACCTAT 57.894 42.857 24.68 2.20 44.61 2.57
4045 4309 3.055819 ACAAACATACATGCGAGACCTCT 60.056 43.478 0.00 0.00 0.00 3.69
4074 4338 1.667724 GCAGCGCTGTATGACATTCTT 59.332 47.619 35.80 0.00 0.00 2.52
4081 4345 6.477033 AGCGCTGTATGACATTCTTTAGTTAG 59.523 38.462 10.39 0.00 0.00 2.34
4101 4365 4.913335 AGAATATTGGCATGTTCAGCTG 57.087 40.909 7.63 7.63 33.88 4.24
4107 4371 4.339872 TTGGCATGTTCAGCTGATTTTT 57.660 36.364 19.04 0.00 0.00 1.94
4132 4409 4.627611 AGACATCAAGTATGCACAATGC 57.372 40.909 0.00 0.00 45.29 3.56
4141 4418 3.422303 GCACAATGCGCCGAGTCA 61.422 61.111 4.18 0.00 31.71 3.41
4161 4438 7.255277 CGAGTCAACTGGATGAGTAGATGAATA 60.255 40.741 0.00 0.00 33.17 1.75
4166 4443 9.605275 CAACTGGATGAGTAGATGAATAAGAAA 57.395 33.333 0.00 0.00 33.09 2.52
4171 4448 9.691362 GGATGAGTAGATGAATAAGAAACTCTC 57.309 37.037 0.00 0.00 34.41 3.20
4178 4455 7.507829 AGATGAATAAGAAACTCTCCATGAGG 58.492 38.462 0.00 0.00 46.72 3.86
4180 4457 7.257790 TGAATAAGAAACTCTCCATGAGGAA 57.742 36.000 0.00 0.00 45.19 3.36
4185 4462 1.880340 CTCTCCATGAGGAACGCGC 60.880 63.158 5.73 0.00 45.19 6.86
4187 4464 3.699955 CTCCATGAGGAACGCGCGA 62.700 63.158 39.36 14.00 45.19 5.87
4189 4466 2.809174 CATGAGGAACGCGCGACA 60.809 61.111 39.36 25.05 0.00 4.35
4240 4517 9.696917 AATGAATCTCTTGTACCAAAAATGAAC 57.303 29.630 0.00 0.00 0.00 3.18
4284 4561 4.927267 AATCCTGGAGTAATCACCAACA 57.073 40.909 1.52 0.00 34.19 3.33
4317 4594 1.218047 CGGATCTTTCTCACCGCCA 59.782 57.895 0.00 0.00 38.98 5.69
4347 4624 0.895100 TTTCGCCTGCTTGCTCCAAT 60.895 50.000 0.00 0.00 0.00 3.16
4440 4717 0.903942 CAACCATGGTGATTTGGGGG 59.096 55.000 20.60 0.00 37.32 5.40
4453 4730 1.541275 TTGGGGGAGAAGAGGGTTTT 58.459 50.000 0.00 0.00 0.00 2.43
4458 4735 2.555448 GGGGAGAAGAGGGTTTTCTTGG 60.555 54.545 0.00 0.00 37.53 3.61
4508 4785 4.593206 TCTGTGTATCAAACCAAGAGGACT 59.407 41.667 0.00 0.00 38.69 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.401552 CCACCACTGCACCATTAATCG 59.598 52.381 0.00 0.00 0.00 3.34
41 42 5.448904 CGTGATGATGGTTGCAATATTGTCA 60.449 40.000 16.61 11.18 0.00 3.58
48 49 4.426416 CAAATCGTGATGATGGTTGCAAT 58.574 39.130 0.59 0.00 37.39 3.56
117 118 0.541764 TTTGTGATGGGGGTGCTTCC 60.542 55.000 0.00 0.00 0.00 3.46
180 181 1.004745 TCACCATTGAGGGAGGAAAGC 59.995 52.381 0.00 0.00 43.89 3.51
181 182 2.619074 GGTCACCATTGAGGGAGGAAAG 60.619 54.545 0.00 0.00 43.89 2.62
310 344 3.470709 CATATCAGGTTGAAGCATCCGT 58.529 45.455 0.00 0.00 0.00 4.69
312 346 4.070716 CTCCATATCAGGTTGAAGCATCC 58.929 47.826 0.00 0.00 0.00 3.51
328 362 5.003804 GGTGAGTTGAAGCTTTTCTCCATA 58.996 41.667 17.47 3.85 0.00 2.74
334 368 4.642429 TCCTAGGTGAGTTGAAGCTTTTC 58.358 43.478 9.08 0.00 0.00 2.29
375 409 2.490328 TGCCTGTTGAAGCTTTTTCG 57.510 45.000 0.00 0.00 0.00 3.46
462 496 3.897239 TCCTATGCCGGTTGAATCATTT 58.103 40.909 1.90 0.00 0.00 2.32
463 497 3.576078 TCCTATGCCGGTTGAATCATT 57.424 42.857 1.90 0.00 0.00 2.57
464 498 3.576078 TTCCTATGCCGGTTGAATCAT 57.424 42.857 1.90 0.00 0.00 2.45
465 499 3.358111 TTTCCTATGCCGGTTGAATCA 57.642 42.857 1.90 0.00 0.00 2.57
466 500 3.550842 GCATTTCCTATGCCGGTTGAATC 60.551 47.826 1.90 0.00 39.01 2.52
467 501 2.362077 GCATTTCCTATGCCGGTTGAAT 59.638 45.455 1.90 0.00 39.01 2.57
468 502 1.748493 GCATTTCCTATGCCGGTTGAA 59.252 47.619 1.90 0.00 39.01 2.69
469 503 1.064758 AGCATTTCCTATGCCGGTTGA 60.065 47.619 1.90 0.00 45.59 3.18
470 504 1.392589 AGCATTTCCTATGCCGGTTG 58.607 50.000 1.90 0.00 45.59 3.77
471 505 2.024414 GAAGCATTTCCTATGCCGGTT 58.976 47.619 1.90 0.00 45.59 4.44
472 506 1.064758 TGAAGCATTTCCTATGCCGGT 60.065 47.619 1.90 0.00 45.59 5.28
473 507 1.679139 TGAAGCATTTCCTATGCCGG 58.321 50.000 0.00 0.00 45.59 6.13
474 508 2.223572 GGTTGAAGCATTTCCTATGCCG 60.224 50.000 6.15 0.00 45.59 5.69
475 509 2.760092 TGGTTGAAGCATTTCCTATGCC 59.240 45.455 6.15 0.00 45.59 4.40
476 510 3.696051 TCTGGTTGAAGCATTTCCTATGC 59.304 43.478 0.00 1.61 44.85 3.14
477 511 4.337555 CCTCTGGTTGAAGCATTTCCTATG 59.662 45.833 0.00 0.00 32.09 2.23
478 512 4.018050 ACCTCTGGTTGAAGCATTTCCTAT 60.018 41.667 0.00 0.00 27.29 2.57
479 513 3.330701 ACCTCTGGTTGAAGCATTTCCTA 59.669 43.478 0.00 0.00 27.29 2.94
480 514 2.108952 ACCTCTGGTTGAAGCATTTCCT 59.891 45.455 0.00 0.00 27.29 3.36
481 515 2.519013 ACCTCTGGTTGAAGCATTTCC 58.481 47.619 0.00 0.00 27.29 3.13
482 516 5.705609 TTAACCTCTGGTTGAAGCATTTC 57.294 39.130 11.78 0.00 46.35 2.17
604 643 2.044946 GGAAGCATCCACGCCCTT 60.045 61.111 2.32 0.00 45.79 3.95
680 719 0.539051 CCCTCTCCACGCTTCAGATT 59.461 55.000 0.00 0.00 0.00 2.40
694 733 5.779771 GTCATATCATCTTCTTCCTCCCTCT 59.220 44.000 0.00 0.00 0.00 3.69
797 838 4.530857 AGGGCAGTGATACGCGCC 62.531 66.667 5.73 0.00 44.10 6.53
798 839 1.644786 AAAAGGGCAGTGATACGCGC 61.645 55.000 5.73 0.00 41.08 6.86
799 840 1.647346 TAAAAGGGCAGTGATACGCG 58.353 50.000 3.53 3.53 0.00 6.01
800 841 4.632538 AAATAAAAGGGCAGTGATACGC 57.367 40.909 0.00 0.00 0.00 4.42
801 842 7.531716 TGTAAAAATAAAAGGGCAGTGATACG 58.468 34.615 0.00 0.00 0.00 3.06
802 843 8.520351 ACTGTAAAAATAAAAGGGCAGTGATAC 58.480 33.333 0.00 0.00 35.06 2.24
803 844 8.644374 ACTGTAAAAATAAAAGGGCAGTGATA 57.356 30.769 0.00 0.00 35.06 2.15
804 845 7.539034 ACTGTAAAAATAAAAGGGCAGTGAT 57.461 32.000 0.00 0.00 35.06 3.06
805 846 6.969993 ACTGTAAAAATAAAAGGGCAGTGA 57.030 33.333 0.00 0.00 35.06 3.41
806 847 7.882179 ACTACTGTAAAAATAAAAGGGCAGTG 58.118 34.615 0.00 0.00 36.72 3.66
807 848 9.577222 TTACTACTGTAAAAATAAAAGGGCAGT 57.423 29.630 0.00 0.00 35.90 4.40
907 948 8.006027 GCGTAGTTTTAGAACGACAATTTAACT 58.994 33.333 9.48 0.00 40.20 2.24
908 949 7.004718 CGCGTAGTTTTAGAACGACAATTTAAC 59.995 37.037 9.48 0.00 40.20 2.01
909 950 7.003072 CGCGTAGTTTTAGAACGACAATTTAA 58.997 34.615 9.48 0.00 40.20 1.52
910 951 6.362016 TCGCGTAGTTTTAGAACGACAATTTA 59.638 34.615 5.77 0.00 40.20 1.40
911 952 5.175491 TCGCGTAGTTTTAGAACGACAATTT 59.825 36.000 5.77 0.00 40.20 1.82
912 953 4.681025 TCGCGTAGTTTTAGAACGACAATT 59.319 37.500 5.77 0.00 40.20 2.32
913 954 4.229096 TCGCGTAGTTTTAGAACGACAAT 58.771 39.130 5.77 0.00 40.20 2.71
914 955 3.626977 TCGCGTAGTTTTAGAACGACAA 58.373 40.909 5.77 0.00 40.20 3.18
915 956 3.266541 TCGCGTAGTTTTAGAACGACA 57.733 42.857 5.77 0.00 40.20 4.35
916 957 4.321745 TCATTCGCGTAGTTTTAGAACGAC 59.678 41.667 5.77 0.04 40.75 4.34
917 958 4.321745 GTCATTCGCGTAGTTTTAGAACGA 59.678 41.667 5.77 0.00 40.75 3.85
918 959 4.322804 AGTCATTCGCGTAGTTTTAGAACG 59.677 41.667 5.77 0.00 40.75 3.95
919 960 5.758570 AGTCATTCGCGTAGTTTTAGAAC 57.241 39.130 5.77 0.00 35.97 3.01
920 961 8.470040 AATAAGTCATTCGCGTAGTTTTAGAA 57.530 30.769 5.77 0.00 0.00 2.10
921 962 7.756272 TGAATAAGTCATTCGCGTAGTTTTAGA 59.244 33.333 5.77 0.00 45.25 2.10
922 963 7.839837 GTGAATAAGTCATTCGCGTAGTTTTAG 59.160 37.037 5.77 0.00 45.25 1.85
923 964 7.669098 GTGAATAAGTCATTCGCGTAGTTTTA 58.331 34.615 5.77 0.20 45.25 1.52
924 965 6.531439 GTGAATAAGTCATTCGCGTAGTTTT 58.469 36.000 5.77 0.00 45.25 2.43
925 966 6.091123 GTGAATAAGTCATTCGCGTAGTTT 57.909 37.500 5.77 0.00 45.25 2.66
926 967 5.697848 GTGAATAAGTCATTCGCGTAGTT 57.302 39.130 5.77 2.59 45.25 2.24
932 973 2.671396 ACCACGTGAATAAGTCATTCGC 59.329 45.455 19.30 1.37 45.25 4.70
933 974 5.337554 TCTACCACGTGAATAAGTCATTCG 58.662 41.667 19.30 0.00 45.25 3.34
934 975 6.237490 CGTTCTACCACGTGAATAAGTCATTC 60.237 42.308 19.30 0.00 43.01 2.67
935 976 5.575606 CGTTCTACCACGTGAATAAGTCATT 59.424 40.000 19.30 0.00 38.90 2.57
936 977 5.100259 CGTTCTACCACGTGAATAAGTCAT 58.900 41.667 19.30 0.00 38.90 3.06
937 978 4.478699 CGTTCTACCACGTGAATAAGTCA 58.521 43.478 19.30 0.00 35.34 3.41
938 979 3.302699 GCGTTCTACCACGTGAATAAGTC 59.697 47.826 19.30 0.98 42.43 3.01
939 980 3.248266 GCGTTCTACCACGTGAATAAGT 58.752 45.455 19.30 8.45 42.43 2.24
940 981 3.247442 TGCGTTCTACCACGTGAATAAG 58.753 45.455 19.30 8.50 42.43 1.73
941 982 3.300852 TGCGTTCTACCACGTGAATAA 57.699 42.857 19.30 2.73 42.43 1.40
942 983 3.300852 TTGCGTTCTACCACGTGAATA 57.699 42.857 19.30 8.22 42.43 1.75
943 984 2.157834 TTGCGTTCTACCACGTGAAT 57.842 45.000 19.30 7.37 42.43 2.57
944 985 1.593933 GTTTGCGTTCTACCACGTGAA 59.406 47.619 19.30 3.51 42.43 3.18
945 986 1.210870 GTTTGCGTTCTACCACGTGA 58.789 50.000 19.30 0.00 42.43 4.35
946 987 0.233848 GGTTTGCGTTCTACCACGTG 59.766 55.000 9.08 9.08 42.43 4.49
947 988 0.881600 GGGTTTGCGTTCTACCACGT 60.882 55.000 0.00 0.00 42.43 4.49
948 989 0.601841 AGGGTTTGCGTTCTACCACG 60.602 55.000 0.00 0.00 43.36 4.94
949 990 1.265905 CAAGGGTTTGCGTTCTACCAC 59.734 52.381 0.00 0.00 33.51 4.16
950 991 1.600023 CAAGGGTTTGCGTTCTACCA 58.400 50.000 0.00 0.00 33.51 3.25
1280 1339 4.034258 GCGGAGTCGACGTGGACA 62.034 66.667 28.83 0.00 39.42 4.02
1355 1414 1.316969 GGAGATGGGGAGGGTGGTA 59.683 63.158 0.00 0.00 0.00 3.25
1533 1592 6.877236 ACGGCAATTTAATTTCAATCTCCAT 58.123 32.000 0.00 0.00 0.00 3.41
1615 1674 3.021695 GGTAAATAGGGGGAGTGCAAAC 58.978 50.000 0.00 0.00 0.00 2.93
1683 1746 1.710013 AATTAGTGCCGTCACACGAG 58.290 50.000 0.00 0.00 46.05 4.18
1707 1770 2.865343 ACGCTATTCTACGGGACTTG 57.135 50.000 0.00 0.00 0.00 3.16
1708 1771 3.243334 GCTAACGCTATTCTACGGGACTT 60.243 47.826 0.00 0.00 0.00 3.01
1709 1772 2.292845 GCTAACGCTATTCTACGGGACT 59.707 50.000 0.00 0.00 0.00 3.85
1720 1784 1.473434 GCAGGGAACAGCTAACGCTAT 60.473 52.381 0.00 0.00 46.99 2.97
1840 1904 9.162793 CGATCAATTGAACTTTATTAGCACATC 57.837 33.333 13.09 0.00 0.00 3.06
1900 1964 8.756486 ACCTCCTTTTTAGCTTAAAAACTACA 57.244 30.769 11.41 0.00 41.28 2.74
1903 1967 8.301252 TGAACCTCCTTTTTAGCTTAAAAACT 57.699 30.769 11.41 0.00 41.28 2.66
1904 1968 8.410912 TCTGAACCTCCTTTTTAGCTTAAAAAC 58.589 33.333 11.41 2.24 41.28 2.43
2055 2165 9.524496 ACACATCTAGATACCGTATTACCAATA 57.476 33.333 4.54 0.00 0.00 1.90
2057 2167 7.503230 TGACACATCTAGATACCGTATTACCAA 59.497 37.037 4.54 0.00 0.00 3.67
2344 2454 8.322091 ACCTTTATAGCACTATCAACTGTCTTT 58.678 33.333 0.00 0.00 0.00 2.52
2459 2569 4.799678 CTGTCTCTACAACCTGTACACAG 58.200 47.826 2.23 2.23 38.23 3.66
2620 2730 5.392767 TGGATAGAGCAGGACGAATAATC 57.607 43.478 0.00 0.00 0.00 1.75
2631 2741 7.384477 TCAGATTCAATGTATGGATAGAGCAG 58.616 38.462 0.00 0.00 0.00 4.24
2832 2945 4.460731 GGCAGATTTGACTAGGCTTCTTTT 59.539 41.667 0.00 0.00 0.00 2.27
2839 2952 2.409948 AGTGGCAGATTTGACTAGGC 57.590 50.000 0.00 0.00 31.73 3.93
2885 2998 9.499479 TTTTTGCATGGTGATAACAAAATATGT 57.501 25.926 0.00 0.00 46.82 2.29
3110 3225 0.877071 ACTTGAGCTCGGCACAAATG 59.123 50.000 9.64 0.00 38.48 2.32
3116 3231 0.966179 TTGTAGACTTGAGCTCGGCA 59.034 50.000 9.64 0.00 0.00 5.69
3160 3277 2.346545 GCCGAATTGCTTGCAGAATTTC 59.653 45.455 0.00 0.00 0.00 2.17
3211 3328 3.583806 CACCTCTTGCTTGTAGTCTGAG 58.416 50.000 0.00 0.00 0.00 3.35
3256 3373 4.569564 GTGATTTTATACGGGGTGTGACTC 59.430 45.833 0.00 0.00 0.00 3.36
3432 3580 2.289195 ACATCAGCCAACATTGCCAAAG 60.289 45.455 0.00 0.00 0.00 2.77
3433 3581 1.693062 ACATCAGCCAACATTGCCAAA 59.307 42.857 0.00 0.00 0.00 3.28
3434 3582 1.273048 GACATCAGCCAACATTGCCAA 59.727 47.619 0.00 0.00 0.00 4.52
3435 3583 0.889994 GACATCAGCCAACATTGCCA 59.110 50.000 0.00 0.00 0.00 4.92
3436 3584 0.889994 TGACATCAGCCAACATTGCC 59.110 50.000 0.00 0.00 0.00 4.52
3438 3586 2.094906 CACCTGACATCAGCCAACATTG 60.095 50.000 3.18 0.00 42.47 2.82
3439 3587 2.165167 CACCTGACATCAGCCAACATT 58.835 47.619 3.18 0.00 42.47 2.71
3441 3589 0.764271 TCACCTGACATCAGCCAACA 59.236 50.000 3.18 0.00 42.47 3.33
3444 3592 1.951895 GCAATCACCTGACATCAGCCA 60.952 52.381 3.18 0.00 42.47 4.75
3445 3593 0.737219 GCAATCACCTGACATCAGCC 59.263 55.000 3.18 0.00 42.47 4.85
3446 3594 1.131883 GTGCAATCACCTGACATCAGC 59.868 52.381 3.18 0.00 42.47 4.26
3453 3613 1.203758 ACGATACGTGCAATCACCTGA 59.796 47.619 0.00 0.00 39.18 3.86
3458 3618 1.277326 GCAGACGATACGTGCAATCA 58.723 50.000 0.00 0.00 41.37 2.57
3466 3626 5.712217 TTTATTCAAAGGCAGACGATACG 57.288 39.130 0.00 0.00 0.00 3.06
3538 3698 4.522405 TCATTTTTAAGTAGCAGCTGCCAA 59.478 37.500 34.39 20.82 43.38 4.52
3540 3700 4.396166 TCTCATTTTTAAGTAGCAGCTGCC 59.604 41.667 34.39 20.47 43.38 4.85
3558 3718 7.395489 ACCATCAAATTAAAGCTCAAGTCTCAT 59.605 33.333 0.00 0.00 0.00 2.90
3561 3721 6.716628 TCACCATCAAATTAAAGCTCAAGTCT 59.283 34.615 0.00 0.00 0.00 3.24
3570 3730 7.039784 TCAGTCCCTTTCACCATCAAATTAAAG 60.040 37.037 0.00 0.00 0.00 1.85
3575 3735 4.387026 TCAGTCCCTTTCACCATCAAAT 57.613 40.909 0.00 0.00 0.00 2.32
3579 3739 3.356529 ACATCAGTCCCTTTCACCATC 57.643 47.619 0.00 0.00 0.00 3.51
3581 3741 2.174639 ACAACATCAGTCCCTTTCACCA 59.825 45.455 0.00 0.00 0.00 4.17
3596 3756 1.001641 GGGCCAGAGCTCACAACAT 60.002 57.895 17.77 0.00 40.27 2.71
3607 3767 1.347707 CACTCTTTGTGTAGGGCCAGA 59.652 52.381 6.18 0.00 41.53 3.86
3608 3768 1.347707 TCACTCTTTGTGTAGGGCCAG 59.652 52.381 6.18 0.00 46.27 4.85
3609 3769 1.429930 TCACTCTTTGTGTAGGGCCA 58.570 50.000 6.18 0.00 46.27 5.36
3610 3770 2.152016 GTTCACTCTTTGTGTAGGGCC 58.848 52.381 0.00 0.00 46.27 5.80
3611 3771 3.067833 GAGTTCACTCTTTGTGTAGGGC 58.932 50.000 0.00 0.00 46.27 5.19
3629 3789 6.925165 CAGCCAATTTATTTTGTTGACAGAGT 59.075 34.615 0.00 0.00 0.00 3.24
3639 3799 3.672808 TGCCCACAGCCAATTTATTTTG 58.327 40.909 0.00 0.00 42.71 2.44
3640 3800 4.363991 TTGCCCACAGCCAATTTATTTT 57.636 36.364 0.00 0.00 42.71 1.82
3644 3804 2.636893 ACAATTGCCCACAGCCAATTTA 59.363 40.909 5.05 0.00 42.71 1.40
3645 3805 1.420891 ACAATTGCCCACAGCCAATTT 59.579 42.857 5.05 0.00 42.71 1.82
3646 3806 1.002315 GACAATTGCCCACAGCCAATT 59.998 47.619 5.05 0.00 42.71 2.32
3648 3808 0.469705 AGACAATTGCCCACAGCCAA 60.470 50.000 5.05 0.00 42.71 4.52
3649 3809 1.153524 AGACAATTGCCCACAGCCA 59.846 52.632 5.05 0.00 42.71 4.75
3650 3810 1.588082 CAGACAATTGCCCACAGCC 59.412 57.895 5.05 0.00 42.71 4.85
3651 3811 1.181098 ACCAGACAATTGCCCACAGC 61.181 55.000 5.05 0.00 44.14 4.40
3652 3812 0.883833 GACCAGACAATTGCCCACAG 59.116 55.000 5.05 0.00 0.00 3.66
3653 3813 0.184692 TGACCAGACAATTGCCCACA 59.815 50.000 5.05 0.00 0.00 4.17
3654 3814 1.270550 CTTGACCAGACAATTGCCCAC 59.729 52.381 5.05 0.00 0.00 4.61
3664 3841 7.739498 TTTGGTTCTTATTACTTGACCAGAC 57.261 36.000 0.00 0.00 0.00 3.51
3689 3866 8.723942 AGATTGAAACAGCTCGTATCTATTTT 57.276 30.769 0.00 0.00 0.00 1.82
3699 3876 9.416794 AGAACATATATAGATTGAAACAGCTCG 57.583 33.333 0.00 0.00 0.00 5.03
3753 3930 8.836268 AGACGGTGTACTTGTATTTTATTTGA 57.164 30.769 0.00 0.00 0.00 2.69
3768 3989 6.757010 AGTTGATCATGAATTAGACGGTGTAC 59.243 38.462 0.00 0.00 0.00 2.90
3788 4009 5.253330 AGAAAGTTTGTTGGTCTGAGTTGA 58.747 37.500 0.00 0.00 0.00 3.18
3828 4085 2.896168 GCATTTGCTGCCAATGTATGT 58.104 42.857 22.52 0.00 45.66 2.29
3842 4099 5.333339 GGCGTACATGTATACTGAGCATTTG 60.333 44.000 9.18 0.00 0.00 2.32
3845 4102 3.611766 CGGCGTACATGTATACTGAGCAT 60.612 47.826 9.18 0.00 0.00 3.79
3846 4103 2.287368 CGGCGTACATGTATACTGAGCA 60.287 50.000 9.18 0.00 0.00 4.26
3876 4139 1.275291 CTTTAGACAGTGCCCCGAAGA 59.725 52.381 0.00 0.00 0.00 2.87
3883 4146 5.470098 TCAGAATTTGACTTTAGACAGTGCC 59.530 40.000 0.00 0.00 0.00 5.01
3884 4147 6.425114 TCTCAGAATTTGACTTTAGACAGTGC 59.575 38.462 0.00 0.00 0.00 4.40
3885 4148 7.953158 TCTCAGAATTTGACTTTAGACAGTG 57.047 36.000 0.00 0.00 0.00 3.66
3891 4154 9.670719 GTTTCCTTTCTCAGAATTTGACTTTAG 57.329 33.333 0.00 0.00 0.00 1.85
3893 4156 8.066612 TGTTTCCTTTCTCAGAATTTGACTTT 57.933 30.769 0.00 0.00 0.00 2.66
3894 4157 7.201857 CCTGTTTCCTTTCTCAGAATTTGACTT 60.202 37.037 0.00 0.00 0.00 3.01
3895 4158 6.264067 CCTGTTTCCTTTCTCAGAATTTGACT 59.736 38.462 0.00 0.00 0.00 3.41
3947 4210 1.207089 TGAGGATTTAGGAGGCACACG 59.793 52.381 0.00 0.00 0.00 4.49
3954 4217 4.125703 GACAGTGCATGAGGATTTAGGAG 58.874 47.826 0.00 0.00 0.00 3.69
3959 4222 3.256631 GGTTTGACAGTGCATGAGGATTT 59.743 43.478 0.00 0.00 0.00 2.17
3970 4233 1.039068 TTGCCCATGGTTTGACAGTG 58.961 50.000 11.73 0.00 0.00 3.66
4074 4338 7.775093 AGCTGAACATGCCAATATTCTAACTAA 59.225 33.333 0.00 0.00 0.00 2.24
4081 4345 4.906065 TCAGCTGAACATGCCAATATTC 57.094 40.909 15.67 0.00 0.00 1.75
4107 4371 7.028962 GCATTGTGCATACTTGATGTCTTAAA 58.971 34.615 0.00 0.00 44.26 1.52
4128 4405 2.034879 CCAGTTGACTCGGCGCATT 61.035 57.895 10.83 0.00 0.00 3.56
4130 4407 2.942796 ATCCAGTTGACTCGGCGCA 61.943 57.895 10.83 0.00 0.00 6.09
4132 4409 0.803768 CTCATCCAGTTGACTCGGCG 60.804 60.000 0.00 0.00 0.00 6.46
4133 4410 0.247736 ACTCATCCAGTTGACTCGGC 59.752 55.000 0.00 0.00 26.56 5.54
4134 4411 3.017442 TCTACTCATCCAGTTGACTCGG 58.983 50.000 0.00 0.00 36.43 4.63
4135 4412 4.336713 TCATCTACTCATCCAGTTGACTCG 59.663 45.833 0.00 0.00 39.34 4.18
4136 4413 5.843673 TCATCTACTCATCCAGTTGACTC 57.156 43.478 0.00 0.00 39.34 3.36
4137 4414 6.805016 ATTCATCTACTCATCCAGTTGACT 57.195 37.500 0.00 0.00 39.34 3.41
4138 4415 8.417106 TCTTATTCATCTACTCATCCAGTTGAC 58.583 37.037 0.00 0.00 39.34 3.18
4141 4418 9.606631 GTTTCTTATTCATCTACTCATCCAGTT 57.393 33.333 0.00 0.00 36.43 3.16
4161 4438 3.866449 GCGTTCCTCATGGAGAGTTTCTT 60.866 47.826 0.00 0.00 44.24 2.52
4166 4443 1.513158 CGCGTTCCTCATGGAGAGT 59.487 57.895 0.00 0.00 44.24 3.24
4171 4448 3.554692 GTCGCGCGTTCCTCATGG 61.555 66.667 30.98 0.00 0.00 3.66
4178 4455 4.122515 GAGCACTGTCGCGCGTTC 62.123 66.667 30.98 23.04 36.85 3.95
4180 4457 3.336715 TATGAGCACTGTCGCGCGT 62.337 57.895 30.98 8.38 36.85 6.01
4185 4462 1.391485 GCACAAGTATGAGCACTGTCG 59.609 52.381 0.00 0.00 42.02 4.35
4187 4464 2.847327 AGCACAAGTATGAGCACTGT 57.153 45.000 1.38 0.00 44.47 3.55
4189 4466 3.251729 CACAAAGCACAAGTATGAGCACT 59.748 43.478 1.38 0.00 44.47 4.40
4224 4501 6.514212 CGACATGAGGTTCATTTTTGGTACAA 60.514 38.462 0.00 0.00 38.30 2.41
4240 4517 3.997021 ACAAAGTTTAGCTCGACATGAGG 59.003 43.478 0.00 0.00 45.38 3.86
4284 4561 0.968405 ATCCGCTGTTTGTTGCCAAT 59.032 45.000 0.00 0.00 0.00 3.16
4347 4624 6.713762 ACAATGGATGACTTGACAAAAGAA 57.286 33.333 0.00 0.00 0.00 2.52
4436 4713 1.373536 AGAAAACCCTCTTCTCCCCC 58.626 55.000 0.00 0.00 0.00 5.40
4440 4717 5.770162 TGATTTCCAAGAAAACCCTCTTCTC 59.230 40.000 0.00 0.00 33.25 2.87
4453 4730 5.988310 AGCATGAACAATGATTTCCAAGA 57.012 34.783 0.00 0.00 38.72 3.02


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

AutoCloner maintained by Alex Coulton.