Multiple sequence alignment - TraesCS3D01G391100

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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 TraesCS3D01G391100 chr3D 100.000 2823 0 0 1 2823 506062934 506060112 0.000000e+00 5214.0
1 TraesCS3D01G391100 chr3D 98.123 1012 16 2 1 1010 506110476 506109466 0.000000e+00 1760.0
2 TraesCS3D01G391100 chr3D 93.291 313 0 1 1026 1338 506109482 506109191 2.580000e-120 442.0
3 TraesCS3D01G391100 chr3D 94.077 287 16 1 2537 2823 542386430 542386715 4.320000e-118 435.0
4 TraesCS3D01G391100 chr3D 93.080 289 20 0 2535 2823 549246574 549246862 9.350000e-115 424.0
5 TraesCS3D01G391100 chr3D 92.734 289 20 1 2535 2823 76940832 76941119 1.560000e-112 416.0
6 TraesCS3D01G391100 chr3B 90.770 1246 60 29 688 1916 667779690 667778483 0.000000e+00 1613.0
7 TraesCS3D01G391100 chr3B 92.496 693 27 11 1 668 622385977 622385285 0.000000e+00 968.0
8 TraesCS3D01G391100 chr3B 87.783 221 24 3 2325 2545 667772931 667772714 3.610000e-64 255.0
9 TraesCS3D01G391100 chr3B 88.500 200 23 0 2090 2289 667773128 667772929 2.810000e-60 243.0
10 TraesCS3D01G391100 chr3A 95.597 863 23 3 1031 1893 644705152 644704305 0.000000e+00 1369.0
11 TraesCS3D01G391100 chr3A 90.606 660 53 5 1888 2538 644699452 644698793 0.000000e+00 867.0
12 TraesCS3D01G391100 chr3A 92.683 287 21 0 2537 2823 56672928 56673214 5.630000e-112 414.0
13 TraesCS3D01G391100 chr5D 94.891 685 18 9 1 668 458676199 458676883 0.000000e+00 1055.0
14 TraesCS3D01G391100 chr5D 93.380 287 18 1 2537 2823 50860616 50860901 9.350000e-115 424.0
15 TraesCS3D01G391100 chr7B 93.869 685 25 10 1 668 65900631 65901315 0.000000e+00 1016.0
16 TraesCS3D01G391100 chr7B 91.825 685 28 10 1 668 743734330 743733657 0.000000e+00 929.0
17 TraesCS3D01G391100 chr7B 81.250 160 20 7 1159 1309 630662734 630662576 1.370000e-23 121.0
18 TraesCS3D01G391100 chr4A 93.869 685 25 9 1 668 708624108 708624792 0.000000e+00 1016.0
19 TraesCS3D01G391100 chr1B 93.869 685 25 9 1 668 360329238 360328554 0.000000e+00 1016.0
20 TraesCS3D01G391100 chr1B 92.733 688 30 10 1 668 360582910 360583597 0.000000e+00 976.0
21 TraesCS3D01G391100 chr1B 80.583 515 78 13 1027 1527 567979831 567979325 7.380000e-101 377.0
22 TraesCS3D01G391100 chr1B 80.810 469 71 9 1070 1527 568006558 568006098 1.610000e-92 350.0
23 TraesCS3D01G391100 chr4D 92.833 293 20 1 2531 2823 3792708 3792999 9.350000e-115 424.0
24 TraesCS3D01G391100 chr1A 93.617 282 15 3 2537 2818 524115540 524115262 4.350000e-113 418.0
25 TraesCS3D01G391100 chr1A 92.734 289 19 2 2535 2823 592161597 592161883 1.560000e-112 416.0
26 TraesCS3D01G391100 chr1A 79.537 518 80 13 1025 1527 516727347 516726841 2.080000e-91 346.0
27 TraesCS3D01G391100 chr1A 79.304 517 78 16 1027 1527 516740336 516739833 4.510000e-88 335.0
28 TraesCS3D01G391100 chr4B 92.683 287 21 0 2537 2823 43232280 43231994 5.630000e-112 414.0
29 TraesCS3D01G391100 chr1D 80.087 462 71 10 1078 1527 420379908 420379456 9.750000e-85 324.0
30 TraesCS3D01G391100 chr6B 97.015 134 3 1 209 341 5184245 5184112 1.020000e-54 224.0
31 TraesCS3D01G391100 chr6B 86.957 115 8 4 395 502 5184113 5183999 3.820000e-24 122.0
32 TraesCS3D01G391100 chr5B 84.076 157 18 7 519 668 512208337 512208493 8.150000e-31 145.0
33 TraesCS3D01G391100 chr5A 83.766 154 18 7 522 668 644141070 644140917 3.790000e-29 139.0
34 TraesCS3D01G391100 chr7D 81.250 160 20 8 1159 1309 572850973 572850815 1.370000e-23 121.0
35 TraesCS3D01G391100 chr6A 88.462 78 7 2 764 841 480016025 480015950 2.990000e-15 93.5
36 TraesCS3D01G391100 chr2B 87.273 55 2 5 2509 2563 673288257 673288306 1.090000e-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 TraesCS3D01G391100 chr3D 506060112 506062934 2822 True 5214 5214 100.000 1 2823 1 chr3D.!!$R1 2822
1 TraesCS3D01G391100 chr3D 506109191 506110476 1285 True 1101 1760 95.707 1 1338 2 chr3D.!!$R2 1337
2 TraesCS3D01G391100 chr3B 667778483 667779690 1207 True 1613 1613 90.770 688 1916 1 chr3B.!!$R2 1228
3 TraesCS3D01G391100 chr3B 622385285 622385977 692 True 968 968 92.496 1 668 1 chr3B.!!$R1 667
4 TraesCS3D01G391100 chr3A 644704305 644705152 847 True 1369 1369 95.597 1031 1893 1 chr3A.!!$R2 862
5 TraesCS3D01G391100 chr3A 644698793 644699452 659 True 867 867 90.606 1888 2538 1 chr3A.!!$R1 650
6 TraesCS3D01G391100 chr5D 458676199 458676883 684 False 1055 1055 94.891 1 668 1 chr5D.!!$F2 667
7 TraesCS3D01G391100 chr7B 65900631 65901315 684 False 1016 1016 93.869 1 668 1 chr7B.!!$F1 667
8 TraesCS3D01G391100 chr7B 743733657 743734330 673 True 929 929 91.825 1 668 1 chr7B.!!$R2 667
9 TraesCS3D01G391100 chr4A 708624108 708624792 684 False 1016 1016 93.869 1 668 1 chr4A.!!$F1 667
10 TraesCS3D01G391100 chr1B 360328554 360329238 684 True 1016 1016 93.869 1 668 1 chr1B.!!$R1 667
11 TraesCS3D01G391100 chr1B 360582910 360583597 687 False 976 976 92.733 1 668 1 chr1B.!!$F1 667
12 TraesCS3D01G391100 chr1B 567979325 567979831 506 True 377 377 80.583 1027 1527 1 chr1B.!!$R2 500
13 TraesCS3D01G391100 chr1A 516726841 516727347 506 True 346 346 79.537 1025 1527 1 chr1A.!!$R1 502
14 TraesCS3D01G391100 chr1A 516739833 516740336 503 True 335 335 79.304 1027 1527 1 chr1A.!!$R2 500

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
289 297 0.250209 CACCAACTGCACTGCTCTCT 60.25 55.0 1.98 0.0 0.0 3.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2080 2138 0.445436 CATGAGACTGGCGTCAAAGC 59.555 55.0 11.04 0.0 42.73 3.51 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
81 83 2.102252 CAGCTACAACCTGATCTCTCCC 59.898 54.545 0.00 0.00 32.03 4.30
174 176 6.862209 AGTAATTCAACAAGCACTTGAACAA 58.138 32.000 16.95 6.32 42.93 2.83
289 297 0.250209 CACCAACTGCACTGCTCTCT 60.250 55.000 1.98 0.00 0.00 3.10
474 492 0.375803 GTTGTCACGTGGTTCGCTTT 59.624 50.000 17.00 0.00 44.19 3.51
520 538 1.963985 ACTGGCCCAAGAAGAGAGAT 58.036 50.000 0.00 0.00 0.00 2.75
992 1030 1.623811 GAGGAGAGCACCACCAGTTTA 59.376 52.381 0.00 0.00 0.00 2.01
993 1031 1.348036 AGGAGAGCACCACCAGTTTAC 59.652 52.381 0.00 0.00 0.00 2.01
994 1032 1.071699 GGAGAGCACCACCAGTTTACA 59.928 52.381 0.00 0.00 0.00 2.41
995 1033 2.143925 GAGAGCACCACCAGTTTACAC 58.856 52.381 0.00 0.00 0.00 2.90
996 1034 1.488812 AGAGCACCACCAGTTTACACA 59.511 47.619 0.00 0.00 0.00 3.72
997 1035 1.602377 GAGCACCACCAGTTTACACAC 59.398 52.381 0.00 0.00 0.00 3.82
998 1036 1.065053 AGCACCACCAGTTTACACACA 60.065 47.619 0.00 0.00 0.00 3.72
999 1037 1.064952 GCACCACCAGTTTACACACAC 59.935 52.381 0.00 0.00 0.00 3.82
1000 1038 2.360844 CACCACCAGTTTACACACACA 58.639 47.619 0.00 0.00 0.00 3.72
1001 1039 2.096819 CACCACCAGTTTACACACACAC 59.903 50.000 0.00 0.00 0.00 3.82
1002 1040 2.290387 ACCACCAGTTTACACACACACA 60.290 45.455 0.00 0.00 0.00 3.72
1003 1041 2.096819 CCACCAGTTTACACACACACAC 59.903 50.000 0.00 0.00 0.00 3.82
1004 1042 2.744741 CACCAGTTTACACACACACACA 59.255 45.455 0.00 0.00 0.00 3.72
1005 1043 3.189495 CACCAGTTTACACACACACACAA 59.811 43.478 0.00 0.00 0.00 3.33
1006 1044 3.189702 ACCAGTTTACACACACACACAAC 59.810 43.478 0.00 0.00 0.00 3.32
1007 1045 3.189495 CCAGTTTACACACACACACAACA 59.811 43.478 0.00 0.00 0.00 3.33
1008 1046 4.155449 CAGTTTACACACACACACAACAC 58.845 43.478 0.00 0.00 0.00 3.32
1009 1047 3.815962 AGTTTACACACACACACAACACA 59.184 39.130 0.00 0.00 0.00 3.72
1010 1048 3.815337 TTACACACACACACAACACAC 57.185 42.857 0.00 0.00 0.00 3.82
1011 1049 1.598882 ACACACACACACAACACACA 58.401 45.000 0.00 0.00 0.00 3.72
1012 1050 1.265635 ACACACACACACAACACACAC 59.734 47.619 0.00 0.00 0.00 3.82
1013 1051 1.265365 CACACACACACAACACACACA 59.735 47.619 0.00 0.00 0.00 3.72
1014 1052 1.265635 ACACACACACAACACACACAC 59.734 47.619 0.00 0.00 0.00 3.82
1015 1053 1.265365 CACACACACAACACACACACA 59.735 47.619 0.00 0.00 0.00 3.72
1016 1054 1.265635 ACACACACAACACACACACAC 59.734 47.619 0.00 0.00 0.00 3.82
1017 1055 1.265365 CACACACAACACACACACACA 59.735 47.619 0.00 0.00 0.00 3.72
1018 1056 1.265635 ACACACAACACACACACACAC 59.734 47.619 0.00 0.00 0.00 3.82
1019 1057 1.265365 CACACAACACACACACACACA 59.735 47.619 0.00 0.00 0.00 3.72
1020 1058 1.265635 ACACAACACACACACACACAC 59.734 47.619 0.00 0.00 0.00 3.82
1021 1059 1.265365 CACAACACACACACACACACA 59.735 47.619 0.00 0.00 0.00 3.72
1022 1060 1.265635 ACAACACACACACACACACAC 59.734 47.619 0.00 0.00 0.00 3.82
1023 1061 1.265365 CAACACACACACACACACACA 59.735 47.619 0.00 0.00 0.00 3.72
1671 1723 1.583054 GTTGCCACGTCTTCTTCACT 58.417 50.000 0.00 0.00 0.00 3.41
1764 1816 4.016113 GGAACCTCAAATAATGCGTGTC 57.984 45.455 0.00 0.00 0.00 3.67
1843 1901 1.931172 CAATTAACGGAGGGCGTACTG 59.069 52.381 0.00 0.00 0.00 2.74
1976 2034 6.430000 GCTCAATCACTAAGTGGTTTTCCTTA 59.570 38.462 0.00 0.00 34.35 2.69
2003 2061 1.308998 CCGGAGCATAAATCCACACC 58.691 55.000 0.00 0.00 36.57 4.16
2009 2067 5.124776 CGGAGCATAAATCCACACCTTTTAA 59.875 40.000 0.00 0.00 36.57 1.52
2054 2112 6.378280 GGTGTCCCAATCTTACAATGAGAAAT 59.622 38.462 0.00 0.00 0.00 2.17
2079 2137 2.616960 TGTCGATTTGGATGGAGAACG 58.383 47.619 0.00 0.00 0.00 3.95
2080 2138 1.933853 GTCGATTTGGATGGAGAACGG 59.066 52.381 0.00 0.00 0.00 4.44
2116 2174 7.439356 CAGTCTCATGAATATTACCGTCAATGT 59.561 37.037 0.00 0.00 0.00 2.71
2117 2175 7.987458 AGTCTCATGAATATTACCGTCAATGTT 59.013 33.333 0.00 0.00 0.00 2.71
2124 2188 2.481289 TACCGTCAATGTTGGATGCA 57.519 45.000 0.00 0.00 0.00 3.96
2169 2234 6.877322 GGTCTACCTGCAAGTAATAAAAGACA 59.123 38.462 13.23 0.00 0.00 3.41
2188 2253 5.139727 AGACAATCAAGAATGTGGTGGAAA 58.860 37.500 0.00 0.00 0.00 3.13
2349 2414 2.759560 GCGGCCAATGGGGTTGAT 60.760 61.111 2.24 0.00 40.37 2.57
2352 2417 2.734720 GGCCAATGGGGTTGATGCC 61.735 63.158 0.00 0.00 40.37 4.40
2379 2444 4.549458 CAATGACAGCAAACAACCCTAAG 58.451 43.478 0.00 0.00 0.00 2.18
2381 2446 3.626930 TGACAGCAAACAACCCTAAGTT 58.373 40.909 0.00 0.00 40.16 2.66
2391 2456 4.851843 ACAACCCTAAGTTATACAAGGCC 58.148 43.478 0.00 0.00 36.18 5.19
2397 2462 5.280521 CCCTAAGTTATACAAGGCCCATAGG 60.281 48.000 0.00 0.00 0.00 2.57
2401 2466 4.104261 AGTTATACAAGGCCCATAGGGTTC 59.896 45.833 0.00 0.00 46.51 3.62
2461 2526 0.881118 TGAAATTCGGGCACTTCTGC 59.119 50.000 0.00 0.00 43.41 4.26
2477 2542 6.089954 GCACTTCTGCCATATTTTCAGAAAAC 59.910 38.462 10.62 0.00 43.60 2.43
2479 2544 7.816031 CACTTCTGCCATATTTTCAGAAAACAT 59.184 33.333 10.62 1.76 43.60 2.71
2512 2578 3.435105 AAATTCTCAAGCAAACGCACA 57.565 38.095 0.00 0.00 0.00 4.57
2528 2594 2.159881 CGCACAGTAGTTAGGCGTTTTC 60.160 50.000 0.00 0.00 42.51 2.29
2533 2599 6.705782 CACAGTAGTTAGGCGTTTTCATATG 58.294 40.000 0.00 0.00 0.00 1.78
2534 2600 6.312918 CACAGTAGTTAGGCGTTTTCATATGT 59.687 38.462 1.90 0.00 0.00 2.29
2536 2602 8.036575 ACAGTAGTTAGGCGTTTTCATATGTTA 58.963 33.333 1.90 0.00 0.00 2.41
2537 2603 8.540492 CAGTAGTTAGGCGTTTTCATATGTTAG 58.460 37.037 1.90 0.00 0.00 2.34
2538 2604 8.472413 AGTAGTTAGGCGTTTTCATATGTTAGA 58.528 33.333 1.90 0.00 0.00 2.10
2539 2605 7.772332 AGTTAGGCGTTTTCATATGTTAGAG 57.228 36.000 1.90 0.00 0.00 2.43
2540 2606 6.258068 AGTTAGGCGTTTTCATATGTTAGAGC 59.742 38.462 1.90 4.87 0.00 4.09
2541 2607 4.513442 AGGCGTTTTCATATGTTAGAGCA 58.487 39.130 1.90 0.00 0.00 4.26
2542 2608 4.941263 AGGCGTTTTCATATGTTAGAGCAA 59.059 37.500 1.90 0.00 0.00 3.91
2543 2609 5.028375 GGCGTTTTCATATGTTAGAGCAAC 58.972 41.667 1.90 0.00 37.67 4.17
2544 2610 5.163754 GGCGTTTTCATATGTTAGAGCAACT 60.164 40.000 1.90 0.00 38.05 3.16
2545 2611 5.960105 GCGTTTTCATATGTTAGAGCAACTC 59.040 40.000 1.90 0.00 38.05 3.01
2546 2612 6.183360 GCGTTTTCATATGTTAGAGCAACTCT 60.183 38.462 1.90 2.23 43.83 3.24
2547 2613 7.010183 GCGTTTTCATATGTTAGAGCAACTCTA 59.990 37.037 1.90 0.16 41.50 2.43
2548 2614 8.535592 CGTTTTCATATGTTAGAGCAACTCTAG 58.464 37.037 1.90 0.00 42.92 2.43
2549 2615 8.331742 GTTTTCATATGTTAGAGCAACTCTAGC 58.668 37.037 10.50 10.50 42.92 3.42
2553 2619 4.442375 TGTTAGAGCAACTCTAGCAGAC 57.558 45.455 14.73 7.03 44.88 3.51
2554 2620 3.193691 TGTTAGAGCAACTCTAGCAGACC 59.806 47.826 14.73 0.00 44.88 3.85
2555 2621 1.190643 AGAGCAACTCTAGCAGACCC 58.809 55.000 0.00 0.00 39.28 4.46
2556 2622 0.176910 GAGCAACTCTAGCAGACCCC 59.823 60.000 0.00 0.00 0.00 4.95
2557 2623 1.153549 GCAACTCTAGCAGACCCCG 60.154 63.158 0.00 0.00 0.00 5.73
2558 2624 1.153549 CAACTCTAGCAGACCCCGC 60.154 63.158 0.00 0.00 0.00 6.13
2559 2625 1.609501 AACTCTAGCAGACCCCGCA 60.610 57.895 0.00 0.00 0.00 5.69
2560 2626 1.192146 AACTCTAGCAGACCCCGCAA 61.192 55.000 0.00 0.00 0.00 4.85
2561 2627 1.192146 ACTCTAGCAGACCCCGCAAA 61.192 55.000 0.00 0.00 0.00 3.68
2562 2628 0.036388 CTCTAGCAGACCCCGCAAAA 60.036 55.000 0.00 0.00 0.00 2.44
2563 2629 0.321298 TCTAGCAGACCCCGCAAAAC 60.321 55.000 0.00 0.00 0.00 2.43
2564 2630 0.605319 CTAGCAGACCCCGCAAAACA 60.605 55.000 0.00 0.00 0.00 2.83
2565 2631 0.887387 TAGCAGACCCCGCAAAACAC 60.887 55.000 0.00 0.00 0.00 3.32
2566 2632 2.637025 CAGACCCCGCAAAACACG 59.363 61.111 0.00 0.00 0.00 4.49
2567 2633 3.284449 AGACCCCGCAAAACACGC 61.284 61.111 0.00 0.00 0.00 5.34
2568 2634 3.587933 GACCCCGCAAAACACGCA 61.588 61.111 0.00 0.00 0.00 5.24
2569 2635 3.536498 GACCCCGCAAAACACGCAG 62.536 63.158 0.00 0.00 0.00 5.18
2570 2636 3.283684 CCCCGCAAAACACGCAGA 61.284 61.111 0.00 0.00 0.00 4.26
2571 2637 2.051345 CCCGCAAAACACGCAGAC 60.051 61.111 0.00 0.00 0.00 3.51
2572 2638 2.051345 CCGCAAAACACGCAGACC 60.051 61.111 0.00 0.00 0.00 3.85
2573 2639 2.051345 CGCAAAACACGCAGACCC 60.051 61.111 0.00 0.00 0.00 4.46
2574 2640 2.051345 GCAAAACACGCAGACCCG 60.051 61.111 0.00 0.00 0.00 5.28
2575 2641 2.051345 CAAAACACGCAGACCCGC 60.051 61.111 0.00 0.00 0.00 6.13
2576 2642 2.515057 AAAACACGCAGACCCGCA 60.515 55.556 0.00 0.00 0.00 5.69
2577 2643 2.115911 AAAACACGCAGACCCGCAA 61.116 52.632 0.00 0.00 0.00 4.85
2578 2644 1.658686 AAAACACGCAGACCCGCAAA 61.659 50.000 0.00 0.00 0.00 3.68
2579 2645 1.658686 AAACACGCAGACCCGCAAAA 61.659 50.000 0.00 0.00 0.00 2.44
2580 2646 1.452145 AACACGCAGACCCGCAAAAT 61.452 50.000 0.00 0.00 0.00 1.82
2581 2647 1.285641 CACGCAGACCCGCAAAATT 59.714 52.632 0.00 0.00 0.00 1.82
2582 2648 0.729140 CACGCAGACCCGCAAAATTC 60.729 55.000 0.00 0.00 0.00 2.17
2583 2649 1.154035 CGCAGACCCGCAAAATTCC 60.154 57.895 0.00 0.00 0.00 3.01
2584 2650 1.154035 GCAGACCCGCAAAATTCCG 60.154 57.895 0.00 0.00 0.00 4.30
2585 2651 1.506262 CAGACCCGCAAAATTCCGG 59.494 57.895 0.00 0.00 43.97 5.14
2586 2652 2.180769 GACCCGCAAAATTCCGGC 59.819 61.111 0.00 0.00 43.05 6.13
2593 2659 2.105323 GCAAAATTCCGGCGAGTATG 57.895 50.000 9.30 0.41 0.00 2.39
2594 2660 1.859998 GCAAAATTCCGGCGAGTATGC 60.860 52.381 9.30 7.54 0.00 3.14
2595 2661 0.655733 AAAATTCCGGCGAGTATGCG 59.344 50.000 9.30 0.00 35.06 4.73
2596 2662 1.157870 AAATTCCGGCGAGTATGCGG 61.158 55.000 9.30 0.00 35.06 5.69
2613 2679 2.892640 GGCTCGGCCCAATTTTCC 59.107 61.111 0.00 0.00 44.06 3.13
2614 2680 2.489751 GCTCGGCCCAATTTTCCG 59.510 61.111 0.00 4.00 44.16 4.30
2615 2681 3.063743 GCTCGGCCCAATTTTCCGG 62.064 63.158 0.00 0.00 43.10 5.14
2616 2682 3.063743 CTCGGCCCAATTTTCCGGC 62.064 63.158 0.00 2.83 43.10 6.13
2619 2685 2.578664 GCCCAATTTTCCGGCCAG 59.421 61.111 2.24 0.00 36.63 4.85
2620 2686 1.981853 GCCCAATTTTCCGGCCAGA 60.982 57.895 2.24 0.00 36.63 3.86
2621 2687 1.540435 GCCCAATTTTCCGGCCAGAA 61.540 55.000 2.24 0.00 36.63 3.02
2622 2688 0.246360 CCCAATTTTCCGGCCAGAAC 59.754 55.000 0.00 0.00 0.00 3.01
2623 2689 0.965439 CCAATTTTCCGGCCAGAACA 59.035 50.000 0.00 0.00 0.00 3.18
2624 2690 1.067635 CCAATTTTCCGGCCAGAACAG 60.068 52.381 0.00 0.00 0.00 3.16
2625 2691 1.885887 CAATTTTCCGGCCAGAACAGA 59.114 47.619 0.00 0.00 0.00 3.41
2626 2692 1.826385 ATTTTCCGGCCAGAACAGAG 58.174 50.000 0.00 0.00 0.00 3.35
2627 2693 0.889186 TTTTCCGGCCAGAACAGAGC 60.889 55.000 0.00 0.00 0.00 4.09
2628 2694 2.748058 TTTCCGGCCAGAACAGAGCC 62.748 60.000 0.00 0.00 43.53 4.70
2629 2695 4.785453 CCGGCCAGAACAGAGCCC 62.785 72.222 2.24 0.00 44.13 5.19
2632 2698 4.704833 GCCAGAACAGAGCCCGCA 62.705 66.667 0.00 0.00 0.00 5.69
2633 2699 2.270205 CCAGAACAGAGCCCGCAT 59.730 61.111 0.00 0.00 0.00 4.73
2634 2700 1.522092 CCAGAACAGAGCCCGCATA 59.478 57.895 0.00 0.00 0.00 3.14
2635 2701 0.811616 CCAGAACAGAGCCCGCATAC 60.812 60.000 0.00 0.00 0.00 2.39
2636 2702 0.176680 CAGAACAGAGCCCGCATACT 59.823 55.000 0.00 0.00 0.00 2.12
2637 2703 0.461961 AGAACAGAGCCCGCATACTC 59.538 55.000 0.00 0.00 0.00 2.59
2638 2704 0.872021 GAACAGAGCCCGCATACTCG 60.872 60.000 0.00 0.00 37.99 4.18
2639 2705 2.659897 CAGAGCCCGCATACTCGC 60.660 66.667 0.00 0.00 37.99 5.03
2640 2706 3.917760 AGAGCCCGCATACTCGCC 61.918 66.667 0.00 0.00 37.99 5.54
2641 2707 4.971125 GAGCCCGCATACTCGCCC 62.971 72.222 0.00 0.00 0.00 6.13
2655 2721 4.386951 GCCCGGCCCGCAAAATTT 62.387 61.111 0.00 0.00 0.00 1.82
2656 2722 2.345617 CCCGGCCCGCAAAATTTT 59.654 55.556 0.00 0.00 0.00 1.82
2657 2723 1.302112 CCCGGCCCGCAAAATTTTT 60.302 52.632 0.00 0.00 0.00 1.94
2687 2753 4.025401 CAAACCGCACGCCCTGAC 62.025 66.667 0.00 0.00 0.00 3.51
2693 2759 4.530857 GCACGCCCTGACCGCTAT 62.531 66.667 0.00 0.00 0.00 2.97
2694 2760 3.125607 CACGCCCTGACCGCTATA 58.874 61.111 0.00 0.00 0.00 1.31
2695 2761 1.440060 CACGCCCTGACCGCTATAA 59.560 57.895 0.00 0.00 0.00 0.98
2696 2762 0.874607 CACGCCCTGACCGCTATAAC 60.875 60.000 0.00 0.00 0.00 1.89
2697 2763 1.041447 ACGCCCTGACCGCTATAACT 61.041 55.000 0.00 0.00 0.00 2.24
2698 2764 0.597637 CGCCCTGACCGCTATAACTG 60.598 60.000 0.00 0.00 0.00 3.16
2699 2765 0.880718 GCCCTGACCGCTATAACTGC 60.881 60.000 0.00 0.00 0.00 4.40
2716 2782 3.227667 CGGTTTCGCGACTCGTTT 58.772 55.556 9.15 0.00 39.67 3.60
2717 2783 1.154908 CGGTTTCGCGACTCGTTTG 60.155 57.895 9.15 0.00 39.67 2.93
2718 2784 1.438222 GGTTTCGCGACTCGTTTGC 60.438 57.895 9.15 0.00 39.67 3.68
2739 2805 2.327200 GGTTCAAACCCTATCCCTCG 57.673 55.000 0.10 0.00 43.43 4.63
2740 2806 1.664873 GTTCAAACCCTATCCCTCGC 58.335 55.000 0.00 0.00 0.00 5.03
2741 2807 0.544697 TTCAAACCCTATCCCTCGCC 59.455 55.000 0.00 0.00 0.00 5.54
2742 2808 1.227556 CAAACCCTATCCCTCGCCG 60.228 63.158 0.00 0.00 0.00 6.46
2743 2809 1.688187 AAACCCTATCCCTCGCCGT 60.688 57.895 0.00 0.00 0.00 5.68
2744 2810 1.683418 AAACCCTATCCCTCGCCGTC 61.683 60.000 0.00 0.00 0.00 4.79
2745 2811 3.671411 CCCTATCCCTCGCCGTCG 61.671 72.222 0.00 0.00 0.00 5.12
2746 2812 4.344474 CCTATCCCTCGCCGTCGC 62.344 72.222 0.00 0.00 35.26 5.19
2747 2813 4.344474 CTATCCCTCGCCGTCGCC 62.344 72.222 0.00 0.00 35.26 5.54
2765 2831 4.162690 GAGCCACGCGATTCCCCT 62.163 66.667 15.93 0.00 0.00 4.79
2766 2832 3.682292 GAGCCACGCGATTCCCCTT 62.682 63.158 15.93 0.00 0.00 3.95
2767 2833 3.202706 GCCACGCGATTCCCCTTC 61.203 66.667 15.93 0.00 0.00 3.46
2768 2834 2.513897 CCACGCGATTCCCCTTCC 60.514 66.667 15.93 0.00 0.00 3.46
2769 2835 2.513897 CACGCGATTCCCCTTCCC 60.514 66.667 15.93 0.00 0.00 3.97
2770 2836 3.793888 ACGCGATTCCCCTTCCCC 61.794 66.667 15.93 0.00 0.00 4.81
2771 2837 4.564110 CGCGATTCCCCTTCCCCC 62.564 72.222 0.00 0.00 0.00 5.40
2772 2838 3.097162 GCGATTCCCCTTCCCCCT 61.097 66.667 0.00 0.00 0.00 4.79
2773 2839 3.121406 GCGATTCCCCTTCCCCCTC 62.121 68.421 0.00 0.00 0.00 4.30
2774 2840 1.384643 CGATTCCCCTTCCCCCTCT 60.385 63.158 0.00 0.00 0.00 3.69
2775 2841 1.411651 CGATTCCCCTTCCCCCTCTC 61.412 65.000 0.00 0.00 0.00 3.20
2776 2842 1.006227 ATTCCCCTTCCCCCTCTCC 59.994 63.158 0.00 0.00 0.00 3.71
2777 2843 1.848835 ATTCCCCTTCCCCCTCTCCA 61.849 60.000 0.00 0.00 0.00 3.86
2778 2844 2.692741 CCCCTTCCCCCTCTCCAC 60.693 72.222 0.00 0.00 0.00 4.02
2779 2845 2.124996 CCCTTCCCCCTCTCCACA 59.875 66.667 0.00 0.00 0.00 4.17
2780 2846 1.308216 CCCTTCCCCCTCTCCACAT 60.308 63.158 0.00 0.00 0.00 3.21
2781 2847 0.921256 CCCTTCCCCCTCTCCACATT 60.921 60.000 0.00 0.00 0.00 2.71
2782 2848 1.002857 CCTTCCCCCTCTCCACATTT 58.997 55.000 0.00 0.00 0.00 2.32
2783 2849 1.064389 CCTTCCCCCTCTCCACATTTC 60.064 57.143 0.00 0.00 0.00 2.17
2784 2850 1.918957 CTTCCCCCTCTCCACATTTCT 59.081 52.381 0.00 0.00 0.00 2.52
2785 2851 1.584724 TCCCCCTCTCCACATTTCTC 58.415 55.000 0.00 0.00 0.00 2.87
2786 2852 0.179000 CCCCCTCTCCACATTTCTCG 59.821 60.000 0.00 0.00 0.00 4.04
2787 2853 0.462759 CCCCTCTCCACATTTCTCGC 60.463 60.000 0.00 0.00 0.00 5.03
2788 2854 0.462759 CCCTCTCCACATTTCTCGCC 60.463 60.000 0.00 0.00 0.00 5.54
2789 2855 0.807667 CCTCTCCACATTTCTCGCCG 60.808 60.000 0.00 0.00 0.00 6.46
2790 2856 0.108615 CTCTCCACATTTCTCGCCGT 60.109 55.000 0.00 0.00 0.00 5.68
2791 2857 0.108804 TCTCCACATTTCTCGCCGTC 60.109 55.000 0.00 0.00 0.00 4.79
2792 2858 1.413767 CTCCACATTTCTCGCCGTCG 61.414 60.000 0.00 0.00 0.00 5.12
2793 2859 2.452813 CCACATTTCTCGCCGTCGG 61.453 63.158 6.99 6.99 36.13 4.79
2794 2860 1.736645 CACATTTCTCGCCGTCGGT 60.737 57.895 13.94 0.00 36.13 4.69
2795 2861 1.736645 ACATTTCTCGCCGTCGGTG 60.737 57.895 18.95 18.95 36.13 4.94
2796 2862 1.445410 CATTTCTCGCCGTCGGTGA 60.445 57.895 25.20 25.20 40.17 4.02
2797 2863 1.445582 ATTTCTCGCCGTCGGTGAC 60.446 57.895 23.33 0.00 37.29 3.67
2798 2864 2.830704 ATTTCTCGCCGTCGGTGACC 62.831 60.000 23.33 0.00 37.29 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 83 2.202623 GCCTGGAGTGTAGCGACG 60.203 66.667 0.00 0.00 0.00 5.12
118 120 9.032420 GCTGGTTGATTAACTTATACTCAGTAC 57.968 37.037 0.00 0.00 36.99 2.73
174 176 2.353803 GCCTTCAACTACATCTCCGTGT 60.354 50.000 0.00 0.00 36.13 4.49
461 479 0.534203 ATGGACAAAGCGAACCACGT 60.534 50.000 0.00 0.00 44.60 4.49
992 1030 1.265635 GTGTGTGTTGTGTGTGTGTGT 59.734 47.619 0.00 0.00 0.00 3.72
993 1031 1.265365 TGTGTGTGTTGTGTGTGTGTG 59.735 47.619 0.00 0.00 0.00 3.82
994 1032 1.265635 GTGTGTGTGTTGTGTGTGTGT 59.734 47.619 0.00 0.00 0.00 3.72
995 1033 1.265365 TGTGTGTGTGTTGTGTGTGTG 59.735 47.619 0.00 0.00 0.00 3.82
996 1034 1.265635 GTGTGTGTGTGTTGTGTGTGT 59.734 47.619 0.00 0.00 0.00 3.72
997 1035 1.265365 TGTGTGTGTGTGTTGTGTGTG 59.735 47.619 0.00 0.00 0.00 3.82
998 1036 1.265635 GTGTGTGTGTGTGTTGTGTGT 59.734 47.619 0.00 0.00 0.00 3.72
999 1037 1.265365 TGTGTGTGTGTGTGTTGTGTG 59.735 47.619 0.00 0.00 0.00 3.82
1000 1038 1.265635 GTGTGTGTGTGTGTGTTGTGT 59.734 47.619 0.00 0.00 0.00 3.72
1001 1039 1.265365 TGTGTGTGTGTGTGTGTTGTG 59.735 47.619 0.00 0.00 0.00 3.33
1002 1040 1.265635 GTGTGTGTGTGTGTGTGTTGT 59.734 47.619 0.00 0.00 0.00 3.32
1003 1041 1.265365 TGTGTGTGTGTGTGTGTGTTG 59.735 47.619 0.00 0.00 0.00 3.33
1004 1042 1.265635 GTGTGTGTGTGTGTGTGTGTT 59.734 47.619 0.00 0.00 0.00 3.32
1005 1043 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1006 1044 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1007 1045 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1008 1046 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1009 1047 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1010 1048 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1011 1049 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1012 1050 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1013 1051 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1014 1052 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1015 1053 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1016 1054 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1017 1055 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1018 1056 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1019 1057 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1020 1058 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1021 1059 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1022 1060 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1023 1061 1.265635 GTTGTGTGTGTGTGTGTGTGT 59.734 47.619 0.00 0.00 0.00 3.72
1347 1390 2.813908 GTAGCCGCAGAACCCGTG 60.814 66.667 0.00 0.00 0.00 4.94
1403 1446 3.266230 CTTGATGTTGGCGCGGCAA 62.266 57.895 39.80 39.80 0.00 4.52
1671 1723 2.032377 CGAAGAAAACGCAAACTAGCCA 60.032 45.455 0.00 0.00 0.00 4.75
1778 1836 5.296035 GGATTACAAAGATTACAAGGACGGG 59.704 44.000 0.00 0.00 0.00 5.28
1835 1893 5.975939 CCTAAAGATAACACTACAGTACGCC 59.024 44.000 0.00 0.00 0.00 5.68
1843 1901 9.685828 CAGAGATTAGCCTAAAGATAACACTAC 57.314 37.037 0.00 0.00 0.00 2.73
1976 2034 0.988832 TTTATGCTCCGGGACACCTT 59.011 50.000 0.00 0.00 33.28 3.50
2014 2072 2.301346 GACACCCATGCCCTTATCAAG 58.699 52.381 0.00 0.00 0.00 3.02
2030 2088 6.817765 TTTCTCATTGTAAGATTGGGACAC 57.182 37.500 0.00 0.00 39.29 3.67
2043 2101 9.357652 CCAAATCGACAAAATATTTCTCATTGT 57.642 29.630 0.10 1.67 36.96 2.71
2054 2112 6.183360 CGTTCTCCATCCAAATCGACAAAATA 60.183 38.462 0.00 0.00 0.00 1.40
2080 2138 0.445436 CATGAGACTGGCGTCAAAGC 59.555 55.000 11.04 0.00 42.73 3.51
2092 2150 7.715265 ACATTGACGGTAATATTCATGAGAC 57.285 36.000 0.00 0.00 0.00 3.36
2103 2161 3.351740 TGCATCCAACATTGACGGTAAT 58.648 40.909 0.00 0.00 0.00 1.89
2116 2174 2.689471 GTCATGCTAACCATGCATCCAA 59.311 45.455 0.00 0.00 46.80 3.53
2117 2175 2.300433 GTCATGCTAACCATGCATCCA 58.700 47.619 0.00 0.00 46.80 3.41
2124 2188 3.624777 CCTTCTTGGTCATGCTAACCAT 58.375 45.455 5.64 0.00 45.89 3.55
2166 2231 5.221224 TGTTTCCACCACATTCTTGATTGTC 60.221 40.000 0.00 0.00 0.00 3.18
2169 2234 5.867903 TTGTTTCCACCACATTCTTGATT 57.132 34.783 0.00 0.00 0.00 2.57
2179 2244 5.679638 GCAATATCCAGATTGTTTCCACCAC 60.680 44.000 0.00 0.00 38.77 4.16
2184 2249 4.576463 ACTCGCAATATCCAGATTGTTTCC 59.424 41.667 0.00 0.00 38.77 3.13
2188 2253 7.468141 TCTATACTCGCAATATCCAGATTGT 57.532 36.000 0.00 0.00 38.77 2.71
2230 2295 2.286772 GCACCTTTGTGTACTCCGTTTG 60.287 50.000 0.00 0.00 44.65 2.93
2284 2349 8.697507 AGATCAACCTCATAGTGTTTTCTTTT 57.302 30.769 0.00 0.00 0.00 2.27
2315 2380 1.481802 CCGCCACCCCTTAGTCCTATA 60.482 57.143 0.00 0.00 0.00 1.31
2349 2414 0.251698 TTGCTGTCATTGGATGGGCA 60.252 50.000 0.00 0.00 0.00 5.36
2352 2417 3.319755 GTTGTTTGCTGTCATTGGATGG 58.680 45.455 0.00 0.00 0.00 3.51
2355 2420 1.686052 GGGTTGTTTGCTGTCATTGGA 59.314 47.619 0.00 0.00 0.00 3.53
2391 2456 6.094881 ACACAAATAACAATCGAACCCTATGG 59.905 38.462 0.00 0.00 37.80 2.74
2397 2462 4.541779 TGCACACAAATAACAATCGAACC 58.458 39.130 0.00 0.00 0.00 3.62
2491 2556 3.779759 TGTGCGTTTGCTTGAGAATTTT 58.220 36.364 0.00 0.00 43.34 1.82
2492 2557 3.181487 ACTGTGCGTTTGCTTGAGAATTT 60.181 39.130 0.00 0.00 43.34 1.82
2493 2558 2.358898 ACTGTGCGTTTGCTTGAGAATT 59.641 40.909 0.00 0.00 43.34 2.17
2494 2559 1.949525 ACTGTGCGTTTGCTTGAGAAT 59.050 42.857 0.00 0.00 43.34 2.40
2500 2566 2.806244 CCTAACTACTGTGCGTTTGCTT 59.194 45.455 3.29 0.00 43.34 3.91
2512 2578 8.472413 TCTAACATATGAAAACGCCTAACTACT 58.528 33.333 10.38 0.00 0.00 2.57
2528 2594 6.640499 GTCTGCTAGAGTTGCTCTAACATATG 59.360 42.308 0.00 0.00 41.74 1.78
2533 2599 3.429684 GGGTCTGCTAGAGTTGCTCTAAC 60.430 52.174 7.22 4.03 41.74 2.34
2534 2600 2.761208 GGGTCTGCTAGAGTTGCTCTAA 59.239 50.000 7.22 0.00 41.74 2.10
2536 2602 1.190643 GGGTCTGCTAGAGTTGCTCT 58.809 55.000 4.02 4.02 43.83 4.09
2537 2603 0.176910 GGGGTCTGCTAGAGTTGCTC 59.823 60.000 0.00 0.00 0.00 4.26
2538 2604 1.608717 CGGGGTCTGCTAGAGTTGCT 61.609 60.000 0.00 0.00 0.00 3.91
2539 2605 1.153549 CGGGGTCTGCTAGAGTTGC 60.154 63.158 0.00 0.00 0.00 4.17
2540 2606 1.153549 GCGGGGTCTGCTAGAGTTG 60.154 63.158 0.00 0.00 0.00 3.16
2541 2607 1.192146 TTGCGGGGTCTGCTAGAGTT 61.192 55.000 0.00 0.00 0.00 3.01
2542 2608 1.192146 TTTGCGGGGTCTGCTAGAGT 61.192 55.000 0.00 0.00 0.00 3.24
2543 2609 0.036388 TTTTGCGGGGTCTGCTAGAG 60.036 55.000 0.00 0.00 0.00 2.43
2544 2610 0.321298 GTTTTGCGGGGTCTGCTAGA 60.321 55.000 0.00 0.00 0.00 2.43
2545 2611 0.605319 TGTTTTGCGGGGTCTGCTAG 60.605 55.000 0.30 0.00 0.00 3.42
2546 2612 0.887387 GTGTTTTGCGGGGTCTGCTA 60.887 55.000 0.30 0.00 0.00 3.49
2547 2613 2.193536 GTGTTTTGCGGGGTCTGCT 61.194 57.895 0.30 0.00 0.00 4.24
2548 2614 2.335011 GTGTTTTGCGGGGTCTGC 59.665 61.111 0.00 0.00 0.00 4.26
2549 2615 2.637025 CGTGTTTTGCGGGGTCTG 59.363 61.111 0.00 0.00 0.00 3.51
2550 2616 3.284449 GCGTGTTTTGCGGGGTCT 61.284 61.111 0.00 0.00 0.00 3.85
2551 2617 3.536498 CTGCGTGTTTTGCGGGGTC 62.536 63.158 0.00 0.00 35.04 4.46
2552 2618 3.591835 CTGCGTGTTTTGCGGGGT 61.592 61.111 0.00 0.00 35.04 4.95
2553 2619 3.283684 TCTGCGTGTTTTGCGGGG 61.284 61.111 0.00 0.00 39.23 5.73
2554 2620 2.051345 GTCTGCGTGTTTTGCGGG 60.051 61.111 0.00 0.00 39.23 6.13
2555 2621 2.051345 GGTCTGCGTGTTTTGCGG 60.051 61.111 0.00 0.00 40.13 5.69
2556 2622 2.051345 GGGTCTGCGTGTTTTGCG 60.051 61.111 0.00 0.00 34.24 4.85
2557 2623 2.051345 CGGGTCTGCGTGTTTTGC 60.051 61.111 0.00 0.00 0.00 3.68
2558 2624 2.051345 GCGGGTCTGCGTGTTTTG 60.051 61.111 0.00 0.00 0.00 2.44
2559 2625 1.658686 TTTGCGGGTCTGCGTGTTTT 61.659 50.000 0.00 0.00 37.81 2.43
2560 2626 1.658686 TTTTGCGGGTCTGCGTGTTT 61.659 50.000 0.00 0.00 37.81 2.83
2561 2627 1.452145 ATTTTGCGGGTCTGCGTGTT 61.452 50.000 0.00 0.00 37.81 3.32
2562 2628 1.452145 AATTTTGCGGGTCTGCGTGT 61.452 50.000 0.00 0.00 37.81 4.49
2563 2629 0.729140 GAATTTTGCGGGTCTGCGTG 60.729 55.000 0.00 0.00 37.81 5.34
2564 2630 1.579429 GAATTTTGCGGGTCTGCGT 59.421 52.632 0.00 0.00 37.81 5.24
2565 2631 1.154035 GGAATTTTGCGGGTCTGCG 60.154 57.895 0.00 0.00 37.81 5.18
2566 2632 1.154035 CGGAATTTTGCGGGTCTGC 60.154 57.895 0.00 0.00 38.41 4.26
2574 2640 1.859998 GCATACTCGCCGGAATTTTGC 60.860 52.381 5.05 2.38 0.00 3.68
2575 2641 1.594518 CGCATACTCGCCGGAATTTTG 60.595 52.381 5.05 0.00 0.00 2.44
2576 2642 0.655733 CGCATACTCGCCGGAATTTT 59.344 50.000 5.05 0.00 0.00 1.82
2577 2643 1.157870 CCGCATACTCGCCGGAATTT 61.158 55.000 5.05 0.00 44.55 1.82
2578 2644 1.594293 CCGCATACTCGCCGGAATT 60.594 57.895 5.05 0.00 44.55 2.17
2579 2645 2.029073 CCGCATACTCGCCGGAAT 59.971 61.111 5.05 0.00 44.55 3.01
2580 2646 4.215742 CCCGCATACTCGCCGGAA 62.216 66.667 5.05 0.00 44.55 4.30
2587 2653 4.971125 GGCCGAGCCCGCATACTC 62.971 72.222 3.73 0.00 44.06 2.59
2603 2669 0.246360 GTTCTGGCCGGAAAATTGGG 59.754 55.000 28.65 0.00 0.00 4.12
2604 2670 0.965439 TGTTCTGGCCGGAAAATTGG 59.035 50.000 28.65 0.00 0.00 3.16
2605 2671 1.885887 TCTGTTCTGGCCGGAAAATTG 59.114 47.619 28.65 17.36 0.00 2.32
2606 2672 2.162681 CTCTGTTCTGGCCGGAAAATT 58.837 47.619 28.65 0.00 0.00 1.82
2607 2673 1.826385 CTCTGTTCTGGCCGGAAAAT 58.174 50.000 28.65 0.00 0.00 1.82
2608 2674 0.889186 GCTCTGTTCTGGCCGGAAAA 60.889 55.000 28.65 22.57 0.00 2.29
2609 2675 1.302511 GCTCTGTTCTGGCCGGAAA 60.303 57.895 28.65 16.90 0.00 3.13
2610 2676 2.347490 GCTCTGTTCTGGCCGGAA 59.653 61.111 23.60 23.60 0.00 4.30
2611 2677 3.706373 GGCTCTGTTCTGGCCGGA 61.706 66.667 11.27 11.27 36.37 5.14
2612 2678 4.785453 GGGCTCTGTTCTGGCCGG 62.785 72.222 4.71 4.71 46.10 6.13
2615 2681 2.593468 TATGCGGGCTCTGTTCTGGC 62.593 60.000 0.00 0.00 0.00 4.85
2616 2682 0.811616 GTATGCGGGCTCTGTTCTGG 60.812 60.000 0.00 0.00 0.00 3.86
2617 2683 0.176680 AGTATGCGGGCTCTGTTCTG 59.823 55.000 0.00 0.00 0.00 3.02
2618 2684 0.461961 GAGTATGCGGGCTCTGTTCT 59.538 55.000 0.00 0.00 0.00 3.01
2619 2685 0.872021 CGAGTATGCGGGCTCTGTTC 60.872 60.000 0.00 0.00 0.00 3.18
2620 2686 1.141881 CGAGTATGCGGGCTCTGTT 59.858 57.895 0.00 0.00 0.00 3.16
2621 2687 2.808315 CGAGTATGCGGGCTCTGT 59.192 61.111 0.00 0.00 0.00 3.41
2622 2688 2.659897 GCGAGTATGCGGGCTCTG 60.660 66.667 0.00 0.00 0.00 3.35
2623 2689 3.917760 GGCGAGTATGCGGGCTCT 61.918 66.667 0.00 0.00 35.06 4.09
2624 2690 4.971125 GGGCGAGTATGCGGGCTC 62.971 72.222 0.00 0.00 35.06 4.70
2638 2704 3.892740 AAAATTTTGCGGGCCGGGC 62.893 57.895 29.48 22.00 0.00 6.13
2639 2705 1.302112 AAAAATTTTGCGGGCCGGG 60.302 52.632 29.48 0.00 0.00 5.73
2640 2706 4.370182 AAAAATTTTGCGGGCCGG 57.630 50.000 29.48 9.71 0.00 6.13
2670 2736 4.025401 GTCAGGGCGTGCGGTTTG 62.025 66.667 1.51 0.00 0.00 2.93
2676 2742 2.638330 TTATAGCGGTCAGGGCGTGC 62.638 60.000 1.51 0.00 35.00 5.34
2677 2743 0.874607 GTTATAGCGGTCAGGGCGTG 60.875 60.000 0.00 0.00 35.00 5.34
2678 2744 1.041447 AGTTATAGCGGTCAGGGCGT 61.041 55.000 0.00 0.00 35.00 5.68
2679 2745 0.597637 CAGTTATAGCGGTCAGGGCG 60.598 60.000 0.00 0.00 35.00 6.13
2680 2746 0.880718 GCAGTTATAGCGGTCAGGGC 60.881 60.000 0.00 0.00 0.00 5.19
2681 2747 3.290776 GCAGTTATAGCGGTCAGGG 57.709 57.895 0.00 0.00 0.00 4.45
2699 2765 1.154908 CAAACGAGTCGCGAAACCG 60.155 57.895 12.06 17.10 44.57 4.44
2700 2766 1.438222 GCAAACGAGTCGCGAAACC 60.438 57.895 12.06 0.00 44.57 3.27
2701 2767 4.095355 GCAAACGAGTCGCGAAAC 57.905 55.556 12.06 7.09 44.57 2.78
2706 2772 3.291167 GAACCCGCAAACGAGTCGC 62.291 63.158 13.59 0.00 43.93 5.19
2707 2773 1.492319 TTGAACCCGCAAACGAGTCG 61.492 55.000 11.85 11.85 43.93 4.18
2708 2774 0.658897 TTTGAACCCGCAAACGAGTC 59.341 50.000 0.00 0.00 43.93 3.36
2709 2775 0.379316 GTTTGAACCCGCAAACGAGT 59.621 50.000 0.00 0.00 45.40 4.18
2710 2776 3.157922 GTTTGAACCCGCAAACGAG 57.842 52.632 0.00 0.00 45.40 4.18
2721 2787 1.664873 GCGAGGGATAGGGTTTGAAC 58.335 55.000 0.00 0.00 0.00 3.18
2722 2788 0.544697 GGCGAGGGATAGGGTTTGAA 59.455 55.000 0.00 0.00 0.00 2.69
2723 2789 1.682451 CGGCGAGGGATAGGGTTTGA 61.682 60.000 0.00 0.00 0.00 2.69
2724 2790 1.227556 CGGCGAGGGATAGGGTTTG 60.228 63.158 0.00 0.00 0.00 2.93
2725 2791 1.683418 GACGGCGAGGGATAGGGTTT 61.683 60.000 16.62 0.00 0.00 3.27
2726 2792 2.042230 ACGGCGAGGGATAGGGTT 60.042 61.111 16.62 0.00 0.00 4.11
2727 2793 2.521224 GACGGCGAGGGATAGGGT 60.521 66.667 16.62 0.00 0.00 4.34
2728 2794 3.671411 CGACGGCGAGGGATAGGG 61.671 72.222 16.62 0.00 40.82 3.53
2729 2795 4.344474 GCGACGGCGAGGGATAGG 62.344 72.222 18.90 0.00 40.82 2.57
2730 2796 4.344474 GGCGACGGCGAGGGATAG 62.344 72.222 18.90 0.00 41.24 2.08
2748 2814 3.682292 AAGGGGAATCGCGTGGCTC 62.682 63.158 5.77 0.00 0.00 4.70
2749 2815 3.682292 GAAGGGGAATCGCGTGGCT 62.682 63.158 5.77 0.00 0.00 4.75
2750 2816 3.202706 GAAGGGGAATCGCGTGGC 61.203 66.667 5.77 0.00 0.00 5.01
2751 2817 2.513897 GGAAGGGGAATCGCGTGG 60.514 66.667 5.77 0.00 0.00 4.94
2752 2818 2.513897 GGGAAGGGGAATCGCGTG 60.514 66.667 5.77 0.00 0.00 5.34
2753 2819 3.793888 GGGGAAGGGGAATCGCGT 61.794 66.667 5.77 0.00 0.00 6.01
2754 2820 4.564110 GGGGGAAGGGGAATCGCG 62.564 72.222 0.00 0.00 0.00 5.87
2755 2821 3.097162 AGGGGGAAGGGGAATCGC 61.097 66.667 0.00 0.00 0.00 4.58
2756 2822 1.384643 AGAGGGGGAAGGGGAATCG 60.385 63.158 0.00 0.00 0.00 3.34
2757 2823 1.063070 GGAGAGGGGGAAGGGGAATC 61.063 65.000 0.00 0.00 0.00 2.52
2758 2824 1.006227 GGAGAGGGGGAAGGGGAAT 59.994 63.158 0.00 0.00 0.00 3.01
2759 2825 2.459710 GGAGAGGGGGAAGGGGAA 59.540 66.667 0.00 0.00 0.00 3.97
2760 2826 2.879490 TGGAGAGGGGGAAGGGGA 60.879 66.667 0.00 0.00 0.00 4.81
2761 2827 2.692741 GTGGAGAGGGGGAAGGGG 60.693 72.222 0.00 0.00 0.00 4.79
2762 2828 0.921256 AATGTGGAGAGGGGGAAGGG 60.921 60.000 0.00 0.00 0.00 3.95
2763 2829 1.002857 AAATGTGGAGAGGGGGAAGG 58.997 55.000 0.00 0.00 0.00 3.46
2764 2830 1.918957 AGAAATGTGGAGAGGGGGAAG 59.081 52.381 0.00 0.00 0.00 3.46
2765 2831 1.916181 GAGAAATGTGGAGAGGGGGAA 59.084 52.381 0.00 0.00 0.00 3.97
2766 2832 1.584724 GAGAAATGTGGAGAGGGGGA 58.415 55.000 0.00 0.00 0.00 4.81
2767 2833 0.179000 CGAGAAATGTGGAGAGGGGG 59.821 60.000 0.00 0.00 0.00 5.40
2768 2834 0.462759 GCGAGAAATGTGGAGAGGGG 60.463 60.000 0.00 0.00 0.00 4.79
2769 2835 0.462759 GGCGAGAAATGTGGAGAGGG 60.463 60.000 0.00 0.00 0.00 4.30
2770 2836 0.807667 CGGCGAGAAATGTGGAGAGG 60.808 60.000 0.00 0.00 0.00 3.69
2771 2837 0.108615 ACGGCGAGAAATGTGGAGAG 60.109 55.000 16.62 0.00 0.00 3.20
2772 2838 0.108804 GACGGCGAGAAATGTGGAGA 60.109 55.000 16.62 0.00 0.00 3.71
2773 2839 1.413767 CGACGGCGAGAAATGTGGAG 61.414 60.000 16.62 0.00 40.82 3.86
2774 2840 1.445410 CGACGGCGAGAAATGTGGA 60.445 57.895 16.62 0.00 40.82 4.02
2775 2841 2.452813 CCGACGGCGAGAAATGTGG 61.453 63.158 15.16 0.00 40.82 4.17
2776 2842 1.736645 ACCGACGGCGAGAAATGTG 60.737 57.895 15.16 0.00 40.82 3.21
2777 2843 1.736645 CACCGACGGCGAGAAATGT 60.737 57.895 15.16 0.00 40.82 2.71
2778 2844 1.445410 TCACCGACGGCGAGAAATG 60.445 57.895 15.16 1.83 40.82 2.32
2779 2845 1.445582 GTCACCGACGGCGAGAAAT 60.446 57.895 15.16 0.00 40.82 2.17
2780 2846 2.049802 GTCACCGACGGCGAGAAA 60.050 61.111 15.16 0.00 40.82 2.52
2781 2847 4.047059 GGTCACCGACGGCGAGAA 62.047 66.667 15.16 0.00 40.82 2.87


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

AutoCloner maintained by Alex Coulton.