Multiple sequence alignment - TraesCS7A01G096400

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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 TraesCS7A01G096400 chr7A 100.000 3594 0 0 1 3594 59286699 59290292 0.000000e+00 6637.0
1 TraesCS7A01G096400 chr7A 81.645 2882 323 125 16 2796 59348229 59351005 0.000000e+00 2202.0
2 TraesCS7A01G096400 chr7A 87.164 1153 85 34 1 1141 59227828 59228929 0.000000e+00 1251.0
3 TraesCS7A01G096400 chr7A 89.412 935 68 21 1781 2708 59229625 59230535 0.000000e+00 1149.0
4 TraesCS7A01G096400 chr7A 83.504 879 110 24 1617 2469 59202427 59203296 0.000000e+00 787.0
5 TraesCS7A01G096400 chr7A 93.532 402 26 0 1182 1583 59229024 59229425 1.850000e-167 599.0
6 TraesCS7A01G096400 chr7A 83.633 611 51 21 969 1542 59201818 59202416 2.460000e-146 529.0
7 TraesCS7A01G096400 chr7A 84.242 495 52 17 1 483 59200967 59201447 3.270000e-125 459.0
8 TraesCS7A01G096400 chr7A 83.106 367 29 10 550 912 59201458 59201795 1.620000e-78 303.0
9 TraesCS7A01G096400 chr7A 91.603 131 6 2 1609 1734 59229493 59229623 3.690000e-40 176.0
10 TraesCS7A01G096400 chr7A 86.792 159 12 4 2537 2695 59203416 59203565 6.170000e-38 169.0
11 TraesCS7A01G096400 chr7A 86.275 102 11 3 2790 2889 510494081 510494181 1.360000e-19 108.0
12 TraesCS7A01G096400 chr7D 93.167 2810 136 29 1 2789 55373600 55376374 0.000000e+00 4074.0
13 TraesCS7A01G096400 chr7D 81.065 1558 144 81 111 1595 55386662 55388141 0.000000e+00 1103.0
14 TraesCS7A01G096400 chr7D 81.436 1212 146 43 1609 2789 55388201 55389364 0.000000e+00 918.0
15 TraesCS7A01G096400 chr7D 83.560 882 107 23 1616 2469 55267838 55268709 0.000000e+00 791.0
16 TraesCS7A01G096400 chr7D 82.633 881 115 26 1616 2469 55250760 55251629 0.000000e+00 745.0
17 TraesCS7A01G096400 chr7D 88.870 575 26 13 2939 3507 55376354 55376896 0.000000e+00 673.0
18 TraesCS7A01G096400 chr7D 80.289 761 74 30 180 922 55249440 55250142 4.140000e-139 505.0
19 TraesCS7A01G096400 chr7D 82.373 590 59 29 989 1542 55250170 55250750 4.200000e-129 472.0
20 TraesCS7A01G096400 chr7D 81.333 600 60 22 549 1140 55266807 55267362 1.180000e-119 440.0
21 TraesCS7A01G096400 chr7D 83.200 500 55 18 1 483 55266310 55266797 7.130000e-117 431.0
22 TraesCS7A01G096400 chr7D 88.462 364 29 7 1184 1541 55267471 55267827 9.220000e-116 427.0
23 TraesCS7A01G096400 chr7D 85.185 189 25 3 1 187 55249068 55249255 1.320000e-44 191.0
24 TraesCS7A01G096400 chr7D 97.436 39 1 0 3556 3594 55376894 55376932 2.320000e-07 67.6
25 TraesCS7A01G096400 chr4A 83.068 880 104 28 1609 2460 671639812 671640674 0.000000e+00 758.0
26 TraesCS7A01G096400 chr4A 83.353 847 70 45 578 1408 671638830 671639621 0.000000e+00 717.0
27 TraesCS7A01G096400 chr4A 83.097 704 96 13 1774 2460 671524512 671525209 1.420000e-173 619.0
28 TraesCS7A01G096400 chr4A 86.120 598 39 16 314 908 671596408 671596964 3.970000e-169 604.0
29 TraesCS7A01G096400 chr4A 83.415 609 64 16 965 1551 671596987 671597580 6.830000e-147 531.0
30 TraesCS7A01G096400 chr4A 81.208 596 78 19 1609 2175 671597703 671598293 1.970000e-122 449.0
31 TraesCS7A01G096400 chr4A 80.532 601 74 18 549 1140 671522851 671523417 4.290000e-114 422.0
32 TraesCS7A01G096400 chr4A 88.187 364 30 7 1184 1541 671523519 671523875 4.290000e-114 422.0
33 TraesCS7A01G096400 chr4A 80.228 526 53 30 2210 2708 671598295 671598796 7.390000e-92 348.0
34 TraesCS7A01G096400 chr4A 82.135 431 40 22 111 516 671638380 671638798 5.750000e-88 335.0
35 TraesCS7A01G096400 chr4A 89.883 257 19 5 2534 2789 671641004 671641254 1.240000e-84 324.0
36 TraesCS7A01G096400 chr4A 89.947 189 11 6 1 185 671595881 671596065 1.670000e-58 237.0
37 TraesCS7A01G096400 chr4A 93.939 132 8 0 1477 1608 671639641 671639772 2.190000e-47 200.0
38 TraesCS7A01G096400 chr4A 88.050 159 10 4 2537 2695 671525590 671525739 2.850000e-41 180.0
39 TraesCS7A01G096400 chr4A 88.889 90 7 2 2801 2888 627294701 627294613 1.360000e-19 108.0
40 TraesCS7A01G096400 chr5B 93.000 100 7 0 2789 2888 21036371 21036470 2.890000e-31 147.0
41 TraesCS7A01G096400 chr6B 90.000 90 7 1 2801 2888 20742045 20742134 8.150000e-22 115.0
42 TraesCS7A01G096400 chr4B 89.888 89 9 0 2800 2888 229527556 229527468 8.150000e-22 115.0
43 TraesCS7A01G096400 chr4B 82.883 111 17 2 2790 2899 5531185 5531294 8.210000e-17 99.0
44 TraesCS7A01G096400 chr4B 82.569 109 17 2 2798 2904 51675715 51675823 1.060000e-15 95.3
45 TraesCS7A01G096400 chrUn 87.000 100 11 2 2801 2899 162260417 162260515 1.050000e-20 111.0
46 TraesCS7A01G096400 chr5D 96.774 62 1 1 2889 2949 558721817 558721756 6.350000e-18 102.0
47 TraesCS7A01G096400 chr3A 83.333 102 13 4 2801 2900 681554486 681554387 1.370000e-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 TraesCS7A01G096400 chr7A 59286699 59290292 3593 False 6637.000000 6637 100.000000 1 3594 1 chr7A.!!$F1 3593
1 TraesCS7A01G096400 chr7A 59348229 59351005 2776 False 2202.000000 2202 81.645000 16 2796 1 chr7A.!!$F2 2780
2 TraesCS7A01G096400 chr7A 59227828 59230535 2707 False 793.750000 1251 90.427750 1 2708 4 chr7A.!!$F5 2707
3 TraesCS7A01G096400 chr7A 59200967 59203565 2598 False 449.400000 787 84.255400 1 2695 5 chr7A.!!$F4 2694
4 TraesCS7A01G096400 chr7D 55373600 55376932 3332 False 1604.866667 4074 93.157667 1 3594 3 chr7D.!!$F3 3593
5 TraesCS7A01G096400 chr7D 55386662 55389364 2702 False 1010.500000 1103 81.250500 111 2789 2 chr7D.!!$F4 2678
6 TraesCS7A01G096400 chr7D 55266310 55268709 2399 False 522.250000 791 84.138750 1 2469 4 chr7D.!!$F2 2468
7 TraesCS7A01G096400 chr7D 55249068 55251629 2561 False 478.250000 745 82.620000 1 2469 4 chr7D.!!$F1 2468
8 TraesCS7A01G096400 chr4A 671638380 671641254 2874 False 466.800000 758 86.475600 111 2789 5 chr4A.!!$F3 2678
9 TraesCS7A01G096400 chr4A 671595881 671598796 2915 False 433.800000 604 84.183600 1 2708 5 chr4A.!!$F2 2707
10 TraesCS7A01G096400 chr4A 671522851 671525739 2888 False 410.750000 619 84.966500 549 2695 4 chr4A.!!$F1 2146

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
661 1167 0.108233 GGCTCTCTGGTCTCTGCAAG 60.108 60.0 0.0 0.0 0.00 4.01 F
662 1168 0.607620 GCTCTCTGGTCTCTGCAAGT 59.392 55.0 0.0 0.0 33.76 3.16 F
1309 2114 0.716591 AGGGACCACAGATCCTGGTA 59.283 55.0 11.8 0.0 42.42 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1777 3202 0.539669 GTTGGCTACTTGGCTGGGTT 60.540 55.000 0.00 0.00 42.34 4.11 R
2056 3491 1.404035 CCGTCGACCAGTGATGTATGA 59.596 52.381 10.58 0.00 0.00 2.15 R
2892 4734 0.305922 GCTGAGATGGCCGAATTTCG 59.694 55.000 11.81 11.81 40.07 3.46 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
149 164 5.308825 TCTTTTTCTGACCATTCTGACTCC 58.691 41.667 0.00 0.00 29.96 3.85
230 556 3.795688 AATGGACTTCTTTCTGGCAGA 57.204 42.857 14.43 14.43 0.00 4.26
281 613 2.659063 CGCCATGTCCTCCACCTCA 61.659 63.158 0.00 0.00 0.00 3.86
282 614 1.685224 GCCATGTCCTCCACCTCAA 59.315 57.895 0.00 0.00 0.00 3.02
293 625 2.744202 CTCCACCTCAAACCAAATCTCG 59.256 50.000 0.00 0.00 0.00 4.04
306 638 4.570772 ACCAAATCTCGTTACATGGATTCG 59.429 41.667 0.00 0.00 0.00 3.34
307 639 4.024893 CCAAATCTCGTTACATGGATTCGG 60.025 45.833 0.00 0.00 0.00 4.30
342 788 6.331369 TGTATGAGCGATTATGACTGATCA 57.669 37.500 0.00 0.00 39.83 2.92
483 952 1.446907 CAGGAAGCTTCATCAACGCT 58.553 50.000 27.02 10.70 35.09 5.07
486 958 0.449388 GAAGCTTCATCAACGCTGGG 59.551 55.000 21.67 0.00 33.64 4.45
541 1021 2.926165 GACGCGCGTCCTAGTTATAAT 58.074 47.619 44.30 16.21 39.08 1.28
589 1071 0.175073 ACACGTCGAAGCCTATTCCC 59.825 55.000 0.00 0.00 0.00 3.97
614 1115 5.719085 ACACACATAAATCTCAGTCTCCTCT 59.281 40.000 0.00 0.00 0.00 3.69
615 1116 6.127479 ACACACATAAATCTCAGTCTCCTCTC 60.127 42.308 0.00 0.00 0.00 3.20
616 1117 5.362430 ACACATAAATCTCAGTCTCCTCTCC 59.638 44.000 0.00 0.00 0.00 3.71
617 1118 5.598005 CACATAAATCTCAGTCTCCTCTCCT 59.402 44.000 0.00 0.00 0.00 3.69
618 1119 6.775142 CACATAAATCTCAGTCTCCTCTCCTA 59.225 42.308 0.00 0.00 0.00 2.94
619 1120 7.451255 CACATAAATCTCAGTCTCCTCTCCTAT 59.549 40.741 0.00 0.00 0.00 2.57
620 1121 7.669722 ACATAAATCTCAGTCTCCTCTCCTATC 59.330 40.741 0.00 0.00 0.00 2.08
631 1132 3.201487 TCCTCTCCTATCCGCCGATATAA 59.799 47.826 0.00 0.00 30.49 0.98
655 1161 3.409026 TTTTTCTGGCTCTCTGGTCTC 57.591 47.619 0.00 0.00 0.00 3.36
656 1162 2.317371 TTTCTGGCTCTCTGGTCTCT 57.683 50.000 0.00 0.00 0.00 3.10
657 1163 1.554836 TTCTGGCTCTCTGGTCTCTG 58.445 55.000 0.00 0.00 0.00 3.35
658 1164 0.969917 TCTGGCTCTCTGGTCTCTGC 60.970 60.000 0.00 0.00 0.00 4.26
659 1165 1.228988 TGGCTCTCTGGTCTCTGCA 60.229 57.895 0.00 0.00 0.00 4.41
660 1166 0.833409 TGGCTCTCTGGTCTCTGCAA 60.833 55.000 0.00 0.00 0.00 4.08
661 1167 0.108233 GGCTCTCTGGTCTCTGCAAG 60.108 60.000 0.00 0.00 0.00 4.01
662 1168 0.607620 GCTCTCTGGTCTCTGCAAGT 59.392 55.000 0.00 0.00 33.76 3.16
663 1169 1.404047 GCTCTCTGGTCTCTGCAAGTC 60.404 57.143 0.00 0.00 33.76 3.01
664 1170 2.170166 CTCTCTGGTCTCTGCAAGTCT 58.830 52.381 0.00 0.00 33.76 3.24
665 1171 2.562298 CTCTCTGGTCTCTGCAAGTCTT 59.438 50.000 0.00 0.00 33.76 3.01
666 1172 2.560542 TCTCTGGTCTCTGCAAGTCTTC 59.439 50.000 0.00 0.00 33.76 2.87
667 1173 1.270826 TCTGGTCTCTGCAAGTCTTCG 59.729 52.381 0.00 0.00 33.76 3.79
681 1187 2.143925 GTCTTCGGTCTTCACCAAAGG 58.856 52.381 0.00 0.00 44.02 3.11
705 1215 4.515191 GTGAGGCTGTGTTTGACATTTCTA 59.485 41.667 0.00 0.00 32.74 2.10
712 1222 4.219033 GTGTTTGACATTTCTAACGCTGG 58.781 43.478 11.01 0.00 41.75 4.85
945 1492 1.133792 GTGAGAGAGGAGGAGGAGAGG 60.134 61.905 0.00 0.00 0.00 3.69
1164 1752 8.652810 ATGCTTGTTCATTTATTTGGATAAGC 57.347 30.769 7.13 7.13 37.79 3.09
1221 1992 1.882623 CTCTCTTCTTTGGGTTGTGGC 59.117 52.381 0.00 0.00 0.00 5.01
1309 2114 0.716591 AGGGACCACAGATCCTGGTA 59.283 55.000 11.80 0.00 42.42 3.25
1520 2370 1.134753 TGCAAAACCAGTCAAGCACAG 59.865 47.619 0.00 0.00 0.00 3.66
1769 2722 5.132043 ACTAGTTAGCTCCCAGTAGTCAT 57.868 43.478 0.00 0.00 0.00 3.06
1777 3202 9.021807 GTTAGCTCCCAGTAGTCATATATACAA 57.978 37.037 0.00 0.00 0.00 2.41
2056 3491 4.778143 GCCGTTGGCTCACCGGAT 62.778 66.667 9.46 0.00 46.69 4.18
2151 3604 3.729108 ACATGGGAGAAGAGATCAAGGA 58.271 45.455 0.00 0.00 0.00 3.36
2276 3729 0.036732 TGTGGTGACATTGAGCCCTC 59.963 55.000 0.00 0.00 46.14 4.30
2352 3811 0.541863 ATGGCGAAGAACCCGAGAAT 59.458 50.000 0.00 0.00 0.00 2.40
2358 3817 0.974383 AAGAACCCGAGAATCACCGT 59.026 50.000 0.00 0.00 33.17 4.83
2511 4297 7.230849 AGAACTTGAATGGTAAATGCATGAA 57.769 32.000 0.00 0.00 0.00 2.57
2532 4373 5.887598 TGAAAGGGATGTGGAAACTCATATG 59.112 40.000 0.00 0.00 44.12 1.78
2533 4374 3.825328 AGGGATGTGGAAACTCATATGC 58.175 45.455 0.00 0.00 44.12 3.14
2674 4515 3.857038 ACCGTCGCAACAGGGTGT 61.857 61.111 0.00 0.00 33.15 4.16
2720 4562 9.669353 GTATATTCACTGCAATACATCCAAAAG 57.331 33.333 0.00 0.00 0.00 2.27
2729 4571 5.512232 GCAATACATCCAAAAGAACCCCAAA 60.512 40.000 0.00 0.00 0.00 3.28
2781 4623 3.801594 GTGTTTCGCAAACCAAACATGAT 59.198 39.130 0.00 0.00 42.81 2.45
2789 4631 4.448732 GCAAACCAAACATGATGAAGAACC 59.551 41.667 0.00 0.00 0.00 3.62
2790 4632 5.739935 GCAAACCAAACATGATGAAGAACCT 60.740 40.000 0.00 0.00 0.00 3.50
2791 4633 5.458041 AACCAAACATGATGAAGAACCTG 57.542 39.130 0.00 0.00 0.00 4.00
2792 4634 4.473444 ACCAAACATGATGAAGAACCTGT 58.527 39.130 0.00 0.00 0.00 4.00
2793 4635 4.279169 ACCAAACATGATGAAGAACCTGTG 59.721 41.667 0.00 0.00 0.00 3.66
2794 4636 4.279169 CCAAACATGATGAAGAACCTGTGT 59.721 41.667 0.00 0.00 0.00 3.72
2795 4637 5.221303 CCAAACATGATGAAGAACCTGTGTT 60.221 40.000 0.00 0.00 37.42 3.32
2796 4638 6.275335 CAAACATGATGAAGAACCTGTGTTT 58.725 36.000 0.00 0.00 38.60 2.83
2797 4639 6.469782 AACATGATGAAGAACCTGTGTTTT 57.530 33.333 0.00 0.00 33.97 2.43
2798 4640 5.835257 ACATGATGAAGAACCTGTGTTTTG 58.165 37.500 0.00 0.00 33.97 2.44
2799 4641 5.593909 ACATGATGAAGAACCTGTGTTTTGA 59.406 36.000 0.00 0.00 33.97 2.69
2800 4642 6.096705 ACATGATGAAGAACCTGTGTTTTGAA 59.903 34.615 0.00 0.00 33.97 2.69
2801 4643 6.713762 TGATGAAGAACCTGTGTTTTGAAT 57.286 33.333 0.00 0.00 33.97 2.57
2802 4644 7.111247 TGATGAAGAACCTGTGTTTTGAATT 57.889 32.000 0.00 0.00 33.97 2.17
2803 4645 7.555087 TGATGAAGAACCTGTGTTTTGAATTT 58.445 30.769 0.00 0.00 33.97 1.82
2804 4646 7.706179 TGATGAAGAACCTGTGTTTTGAATTTC 59.294 33.333 0.00 0.00 33.97 2.17
2805 4647 6.033341 TGAAGAACCTGTGTTTTGAATTTCG 58.967 36.000 0.00 0.00 33.97 3.46
2806 4648 4.932146 AGAACCTGTGTTTTGAATTTCGG 58.068 39.130 0.00 0.00 33.97 4.30
2807 4649 3.092334 ACCTGTGTTTTGAATTTCGGC 57.908 42.857 0.00 0.00 0.00 5.54
2808 4650 2.223947 ACCTGTGTTTTGAATTTCGGCC 60.224 45.455 0.00 0.00 0.00 6.13
2809 4651 2.050691 CTGTGTTTTGAATTTCGGCCG 58.949 47.619 22.12 22.12 0.00 6.13
2810 4652 1.676529 TGTGTTTTGAATTTCGGCCGA 59.323 42.857 27.28 27.28 0.00 5.54
2811 4653 2.099263 TGTGTTTTGAATTTCGGCCGAA 59.901 40.909 35.81 35.81 0.00 4.30
2812 4654 3.243569 TGTGTTTTGAATTTCGGCCGAAT 60.244 39.130 38.89 26.73 33.79 3.34
2813 4655 3.738791 GTGTTTTGAATTTCGGCCGAATT 59.261 39.130 38.89 31.79 33.79 2.17
2814 4656 4.210328 GTGTTTTGAATTTCGGCCGAATTT 59.790 37.500 38.89 37.01 33.79 1.82
2815 4657 4.446051 TGTTTTGAATTTCGGCCGAATTTC 59.554 37.500 41.52 41.52 41.25 2.17
2816 4658 2.535934 TGAATTTCGGCCGAATTTCG 57.464 45.000 41.19 17.36 42.55 3.46
2826 4668 1.934463 CGAATTTCGGCCATCTCGG 59.066 57.895 10.95 0.00 36.00 4.63
2845 4687 2.271944 GCCTGGGGCGAAATATACTT 57.728 50.000 0.00 0.00 39.62 2.24
2846 4688 2.583143 GCCTGGGGCGAAATATACTTT 58.417 47.619 0.00 0.00 39.62 2.66
2847 4689 2.552743 GCCTGGGGCGAAATATACTTTC 59.447 50.000 0.00 0.00 39.62 2.62
2848 4690 3.146847 CCTGGGGCGAAATATACTTTCC 58.853 50.000 0.00 0.00 0.00 3.13
2849 4691 3.434453 CCTGGGGCGAAATATACTTTCCA 60.434 47.826 0.00 0.00 0.00 3.53
2850 4692 3.815401 CTGGGGCGAAATATACTTTCCAG 59.185 47.826 0.00 0.00 34.22 3.86
2851 4693 2.552743 GGGGCGAAATATACTTTCCAGC 59.447 50.000 0.00 0.00 0.00 4.85
2852 4694 2.223377 GGGCGAAATATACTTTCCAGCG 59.777 50.000 0.00 0.00 0.00 5.18
2853 4695 3.128349 GGCGAAATATACTTTCCAGCGA 58.872 45.455 0.00 0.00 0.00 4.93
2854 4696 3.558418 GGCGAAATATACTTTCCAGCGAA 59.442 43.478 0.00 0.00 0.00 4.70
2855 4697 4.034742 GGCGAAATATACTTTCCAGCGAAA 59.965 41.667 0.00 0.00 36.55 3.46
2856 4698 5.448089 GGCGAAATATACTTTCCAGCGAAAA 60.448 40.000 0.00 0.00 37.53 2.29
2857 4699 6.025280 GCGAAATATACTTTCCAGCGAAAAA 58.975 36.000 0.00 0.00 37.53 1.94
2896 4738 7.793927 AATTTTAGTCAAATTTTGGCCGAAA 57.206 28.000 20.60 20.60 41.57 3.46
2897 4739 7.977789 ATTTTAGTCAAATTTTGGCCGAAAT 57.022 28.000 23.22 23.22 35.39 2.17
2898 4740 7.793927 TTTTAGTCAAATTTTGGCCGAAATT 57.206 28.000 30.49 30.49 40.06 1.82
2899 4741 7.414814 TTTAGTCAAATTTTGGCCGAAATTC 57.585 32.000 34.05 24.56 38.04 2.17
2900 4742 3.987220 AGTCAAATTTTGGCCGAAATTCG 59.013 39.130 34.05 27.03 38.04 3.34
2911 4753 0.305922 CGAAATTCGGCCATCTCAGC 59.694 55.000 7.61 0.00 36.00 4.26
2928 4770 3.137484 GCCTGGGGCGAAAAATTTC 57.863 52.632 0.00 0.00 39.62 2.17
2929 4771 0.320050 GCCTGGGGCGAAAAATTTCA 59.680 50.000 6.69 0.00 39.62 2.69
2930 4772 1.939381 GCCTGGGGCGAAAAATTTCAC 60.939 52.381 6.69 0.00 39.62 3.18
2931 4773 1.342819 CCTGGGGCGAAAAATTTCACA 59.657 47.619 6.69 0.00 37.01 3.58
2932 4774 2.224161 CCTGGGGCGAAAAATTTCACAA 60.224 45.455 6.69 0.00 37.01 3.33
2933 4775 3.462021 CTGGGGCGAAAAATTTCACAAA 58.538 40.909 6.69 0.00 37.01 2.83
2934 4776 3.198872 TGGGGCGAAAAATTTCACAAAC 58.801 40.909 6.69 0.00 37.01 2.93
2935 4777 2.546368 GGGGCGAAAAATTTCACAAACC 59.454 45.455 6.69 1.24 37.01 3.27
2936 4778 2.546368 GGGCGAAAAATTTCACAAACCC 59.454 45.455 6.69 4.95 37.01 4.11
2937 4779 3.198872 GGCGAAAAATTTCACAAACCCA 58.801 40.909 6.69 0.00 37.01 4.51
2938 4780 3.623510 GGCGAAAAATTTCACAAACCCAA 59.376 39.130 6.69 0.00 37.01 4.12
2939 4781 4.095036 GGCGAAAAATTTCACAAACCCAAA 59.905 37.500 6.69 0.00 37.01 3.28
2940 4782 5.392057 GGCGAAAAATTTCACAAACCCAAAA 60.392 36.000 6.69 0.00 37.01 2.44
2941 4783 6.261859 GCGAAAAATTTCACAAACCCAAAAT 58.738 32.000 6.69 0.00 37.01 1.82
2942 4784 6.413526 GCGAAAAATTTCACAAACCCAAAATC 59.586 34.615 6.69 0.00 37.01 2.17
2943 4785 7.467623 CGAAAAATTTCACAAACCCAAAATCA 58.532 30.769 6.69 0.00 37.01 2.57
2944 4786 7.965107 CGAAAAATTTCACAAACCCAAAATCAA 59.035 29.630 6.69 0.00 37.01 2.57
2945 4787 9.631452 GAAAAATTTCACAAACCCAAAATCAAA 57.369 25.926 1.11 0.00 37.15 2.69
2946 4788 8.978564 AAAATTTCACAAACCCAAAATCAAAC 57.021 26.923 0.00 0.00 0.00 2.93
2947 4789 6.691754 ATTTCACAAACCCAAAATCAAACC 57.308 33.333 0.00 0.00 0.00 3.27
2948 4790 5.428184 TTCACAAACCCAAAATCAAACCT 57.572 34.783 0.00 0.00 0.00 3.50
2949 4791 5.428184 TCACAAACCCAAAATCAAACCTT 57.572 34.783 0.00 0.00 0.00 3.50
2950 4792 5.181748 TCACAAACCCAAAATCAAACCTTG 58.818 37.500 0.00 0.00 0.00 3.61
2951 4793 3.944650 ACAAACCCAAAATCAAACCTTGC 59.055 39.130 0.00 0.00 0.00 4.01
2952 4794 2.524569 ACCCAAAATCAAACCTTGCG 57.475 45.000 0.00 0.00 0.00 4.85
2953 4795 2.035632 ACCCAAAATCAAACCTTGCGA 58.964 42.857 0.00 0.00 0.00 5.10
2954 4796 2.432510 ACCCAAAATCAAACCTTGCGAA 59.567 40.909 0.00 0.00 0.00 4.70
2955 4797 3.059166 CCCAAAATCAAACCTTGCGAAG 58.941 45.455 0.00 0.00 0.00 3.79
2956 4798 3.243704 CCCAAAATCAAACCTTGCGAAGA 60.244 43.478 0.00 0.00 0.00 2.87
2957 4799 4.367450 CCAAAATCAAACCTTGCGAAGAA 58.633 39.130 0.00 0.00 0.00 2.52
2958 4800 4.209080 CCAAAATCAAACCTTGCGAAGAAC 59.791 41.667 0.00 0.00 0.00 3.01
2972 4814 4.092821 TGCGAAGAACTATACATGTGTTGC 59.907 41.667 9.11 4.84 0.00 4.17
2991 4833 0.592637 CTTCCAAACATCGCAGTGCA 59.407 50.000 16.83 2.61 0.00 4.57
3043 4885 8.615878 AATTAACCCTAAACCAAAAATGCTTC 57.384 30.769 0.00 0.00 0.00 3.86
3081 4923 6.180472 CCAAACTTGACCAAGACCTATACAT 58.820 40.000 15.84 0.00 40.79 2.29
3102 4946 5.301551 ACATGTGTTGCTTTAATGTCAGGAA 59.698 36.000 0.00 0.00 0.00 3.36
3124 4968 2.511600 GCGCCGGCTAACAGATGT 60.512 61.111 26.68 0.00 35.83 3.06
3127 4971 1.865865 CGCCGGCTAACAGATGTATT 58.134 50.000 26.68 0.00 0.00 1.89
3128 4972 2.864882 GCGCCGGCTAACAGATGTATTA 60.865 50.000 26.68 0.00 35.83 0.98
3136 4980 7.435488 CCGGCTAACAGATGTATTATATACAGC 59.565 40.741 6.91 6.91 34.38 4.40
3195 5040 7.148639 GCTCGACACTTACAGATCAAAAATGTA 60.149 37.037 0.00 0.00 0.00 2.29
3196 5041 8.771920 TCGACACTTACAGATCAAAAATGTAT 57.228 30.769 0.00 0.00 30.03 2.29
3197 5042 9.863845 TCGACACTTACAGATCAAAAATGTATA 57.136 29.630 0.00 0.00 30.03 1.47
3198 5043 9.901724 CGACACTTACAGATCAAAAATGTATAC 57.098 33.333 0.00 0.00 30.03 1.47
3210 5055 8.514330 TCAAAAATGTATACAACCCCAGATAC 57.486 34.615 10.14 0.00 0.00 2.24
3213 5058 4.289837 TGTATACAACCCCAGATACCCT 57.710 45.455 2.20 0.00 0.00 4.34
3217 5062 3.169512 ACAACCCCAGATACCCTTTTG 57.830 47.619 0.00 0.00 0.00 2.44
3218 5063 2.449345 ACAACCCCAGATACCCTTTTGT 59.551 45.455 0.00 0.00 0.00 2.83
3219 5064 3.658705 ACAACCCCAGATACCCTTTTGTA 59.341 43.478 0.00 0.00 0.00 2.41
3235 5082 6.127338 CCCTTTTGTAAAATTCAGGGAGATCC 60.127 42.308 6.12 0.00 33.66 3.36
3275 5122 5.992217 GGTTTCCAGCGAGATCTAATTATGT 59.008 40.000 0.00 0.00 0.00 2.29
3277 5124 5.048153 TCCAGCGAGATCTAATTATGTCG 57.952 43.478 0.00 3.95 43.39 4.35
3320 5167 6.930731 ACGTATTCTTATGTTTGCCCAAAAT 58.069 32.000 0.00 0.00 31.33 1.82
3326 5174 6.763355 TCTTATGTTTGCCCAAAATTAGCAA 58.237 32.000 0.00 0.00 44.32 3.91
3369 5217 6.929049 CGTATATTTCTCAAGTGGATGCCTAA 59.071 38.462 0.00 0.00 0.00 2.69
3389 5237 9.914834 TGCCTAATACAGTTCATATTTAAGGTT 57.085 29.630 0.00 0.00 0.00 3.50
3400 5248 9.569167 GTTCATATTTAAGGTTCAAAACTAGCC 57.431 33.333 0.00 0.00 0.00 3.93
3408 5256 5.876357 AGGTTCAAAACTAGCCAGTATCAA 58.124 37.500 0.00 0.00 33.48 2.57
3417 5265 2.279173 AGCCAGTATCAAGTTCCCCTT 58.721 47.619 0.00 0.00 0.00 3.95
3418 5266 2.239907 AGCCAGTATCAAGTTCCCCTTC 59.760 50.000 0.00 0.00 0.00 3.46
3423 5271 5.538433 CCAGTATCAAGTTCCCCTTCAAAAA 59.462 40.000 0.00 0.00 0.00 1.94
3445 5293 3.503365 AGTACTAGTACCAAGTGGCACA 58.497 45.455 25.97 0.00 39.32 4.57
3468 5316 4.630894 TCAACTAAATTAAGCCGCCATG 57.369 40.909 0.00 0.00 0.00 3.66
3472 5320 0.894141 AAATTAAGCCGCCATGTGCA 59.106 45.000 6.92 0.00 41.33 4.57
3473 5321 1.113788 AATTAAGCCGCCATGTGCAT 58.886 45.000 0.00 0.00 41.33 3.96
3504 5352 2.579201 CGGCGTCCAGACTCCATT 59.421 61.111 7.53 0.00 36.01 3.16
3505 5353 1.672854 CCGGCGTCCAGACTCCATTA 61.673 60.000 6.01 0.00 36.01 1.90
3506 5354 0.174845 CGGCGTCCAGACTCCATTAA 59.825 55.000 7.53 0.00 36.01 1.40
3507 5355 1.202533 CGGCGTCCAGACTCCATTAAT 60.203 52.381 7.53 0.00 36.01 1.40
3508 5356 2.484889 GGCGTCCAGACTCCATTAATC 58.515 52.381 1.92 0.00 36.27 1.75
3509 5357 2.158957 GGCGTCCAGACTCCATTAATCA 60.159 50.000 1.92 0.00 36.27 2.57
3510 5358 3.531538 GCGTCCAGACTCCATTAATCAA 58.468 45.455 0.00 0.00 0.00 2.57
3511 5359 3.557595 GCGTCCAGACTCCATTAATCAAG 59.442 47.826 0.00 0.00 0.00 3.02
3512 5360 3.557595 CGTCCAGACTCCATTAATCAAGC 59.442 47.826 0.00 0.00 0.00 4.01
3513 5361 3.557595 GTCCAGACTCCATTAATCAAGCG 59.442 47.826 0.00 0.00 0.00 4.68
3514 5362 3.197766 TCCAGACTCCATTAATCAAGCGT 59.802 43.478 0.00 0.00 0.00 5.07
3515 5363 3.941483 CCAGACTCCATTAATCAAGCGTT 59.059 43.478 0.00 0.00 0.00 4.84
3516 5364 4.201851 CCAGACTCCATTAATCAAGCGTTG 60.202 45.833 0.00 0.00 0.00 4.10
3517 5365 3.941483 AGACTCCATTAATCAAGCGTTGG 59.059 43.478 0.00 0.00 0.00 3.77
3518 5366 3.938963 GACTCCATTAATCAAGCGTTGGA 59.061 43.478 0.00 0.00 0.00 3.53
3519 5367 4.542662 CTCCATTAATCAAGCGTTGGAG 57.457 45.455 2.65 2.65 42.92 3.86
3520 5368 2.682856 TCCATTAATCAAGCGTTGGAGC 59.317 45.455 0.00 0.00 37.41 4.70
3521 5369 2.539547 CCATTAATCAAGCGTTGGAGCG 60.540 50.000 0.00 0.00 43.00 5.03
3544 5392 4.179599 GGGGAGGGAGGGAGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
3545 5393 4.890306 GGGAGGGAGGGAGGGAGC 62.890 77.778 0.00 0.00 0.00 4.70
3546 5394 3.773154 GGAGGGAGGGAGGGAGCT 61.773 72.222 0.00 0.00 0.00 4.09
3547 5395 2.404750 GGAGGGAGGGAGGGAGCTA 61.405 68.421 0.00 0.00 0.00 3.32
3548 5396 1.155155 GAGGGAGGGAGGGAGCTAG 59.845 68.421 0.00 0.00 0.00 3.42
3549 5397 2.525629 GGGAGGGAGGGAGCTAGC 60.526 72.222 6.62 6.62 0.00 3.42
3550 5398 2.915137 GGAGGGAGGGAGCTAGCG 60.915 72.222 9.55 0.00 0.00 4.26
3551 5399 2.915137 GAGGGAGGGAGCTAGCGG 60.915 72.222 9.55 0.00 0.00 5.52
3552 5400 4.548513 AGGGAGGGAGCTAGCGGG 62.549 72.222 9.55 0.00 0.00 6.13
3583 5431 2.353607 GCACGTAGCCGGAGATCG 60.354 66.667 5.05 6.42 38.78 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
144 159 6.317789 TGTCACAGAAAATGAATTGGAGTC 57.682 37.500 0.00 0.00 0.00 3.36
199 524 8.143835 CAGAAAGAAGTCCATTTAATTTGGTGT 58.856 33.333 5.20 0.00 35.64 4.16
200 525 7.599998 CCAGAAAGAAGTCCATTTAATTTGGTG 59.400 37.037 5.20 0.00 35.64 4.17
201 526 7.670364 CCAGAAAGAAGTCCATTTAATTTGGT 58.330 34.615 5.20 0.00 35.64 3.67
281 613 6.403200 CGAATCCATGTAACGAGATTTGGTTT 60.403 38.462 0.00 0.00 0.00 3.27
282 614 5.064707 CGAATCCATGTAACGAGATTTGGTT 59.935 40.000 0.00 0.00 0.00 3.67
340 786 0.596577 CGTCCGTCAGAGGAAGTTGA 59.403 55.000 0.00 0.00 42.77 3.18
341 787 0.388649 CCGTCCGTCAGAGGAAGTTG 60.389 60.000 0.00 0.00 42.77 3.16
342 788 1.965219 CCGTCCGTCAGAGGAAGTT 59.035 57.895 0.00 0.00 42.77 2.66
541 1021 0.257328 TGTTGTTGTCTGGAGGCCAA 59.743 50.000 5.01 0.00 30.80 4.52
576 1058 1.338674 TGTGTGTGGGAATAGGCTTCG 60.339 52.381 0.00 0.00 0.00 3.79
589 1071 5.728471 AGGAGACTGAGATTTATGTGTGTG 58.272 41.667 0.00 0.00 41.13 3.82
614 1115 5.733620 AAAACTTATATCGGCGGATAGGA 57.266 39.130 17.66 7.21 38.49 2.94
651 1157 1.271102 AGACCGAAGACTTGCAGAGAC 59.729 52.381 0.00 0.00 0.00 3.36
652 1158 1.621992 AGACCGAAGACTTGCAGAGA 58.378 50.000 0.00 0.00 0.00 3.10
653 1159 2.288457 TGAAGACCGAAGACTTGCAGAG 60.288 50.000 0.00 0.00 0.00 3.35
654 1160 1.686587 TGAAGACCGAAGACTTGCAGA 59.313 47.619 0.00 0.00 0.00 4.26
655 1161 1.795286 GTGAAGACCGAAGACTTGCAG 59.205 52.381 0.00 0.00 0.00 4.41
656 1162 1.540363 GGTGAAGACCGAAGACTTGCA 60.540 52.381 0.00 0.00 30.61 4.08
657 1163 1.149148 GGTGAAGACCGAAGACTTGC 58.851 55.000 0.00 0.00 30.61 4.01
658 1164 2.526304 TGGTGAAGACCGAAGACTTG 57.474 50.000 0.00 0.00 46.62 3.16
659 1165 3.553828 TTTGGTGAAGACCGAAGACTT 57.446 42.857 0.00 0.00 46.62 3.01
664 1170 0.841289 ACCCTTTGGTGAAGACCGAA 59.159 50.000 0.00 0.00 46.62 4.30
665 1171 2.535224 ACCCTTTGGTGAAGACCGA 58.465 52.632 0.00 0.00 46.62 4.69
681 1187 1.609208 ATGTCAAACACAGCCTCACC 58.391 50.000 0.00 0.00 38.85 4.02
685 1191 4.024048 CGTTAGAAATGTCAAACACAGCCT 60.024 41.667 0.00 0.00 38.85 4.58
727 1242 1.808390 GTACGCCGGTGCTTACCTG 60.808 63.158 16.69 0.00 36.50 4.00
877 1415 4.159879 TCCTTTCTTCTCTAGCCCTTTACG 59.840 45.833 0.00 0.00 0.00 3.18
926 1473 1.221635 CCTCTCCTCCTCCTCTCTCA 58.778 60.000 0.00 0.00 0.00 3.27
945 1492 2.087646 CTTAGAGCAAGGCAAAGGTCC 58.912 52.381 0.00 0.00 32.93 4.46
1031 1608 3.329386 TCTTTCAACCGCTCTTCATGAG 58.671 45.455 0.00 0.00 45.33 2.90
1134 1718 9.675464 ATCCAAATAAATGAACAAGCATTCAAT 57.325 25.926 2.66 0.00 41.78 2.57
1164 1752 4.960469 TCCTAACCACTAGTCCTAACCATG 59.040 45.833 0.00 0.00 0.00 3.66
1335 2146 1.854939 TCCAATTCCTGGCTGATCCAT 59.145 47.619 0.00 0.00 45.98 3.41
1376 2189 6.135290 ACACCATGAATTTATTGGATGACG 57.865 37.500 0.00 0.00 34.52 4.35
1442 2290 0.108472 TCTCTCATCTGCAACGCCAG 60.108 55.000 0.00 0.00 0.00 4.85
1584 2468 3.894742 GGCCCTGCCTTATGTAACA 57.105 52.632 0.00 0.00 46.69 2.41
1734 2683 6.154192 GGAGCTAACTAGTTTGGTACCTAGTT 59.846 42.308 21.45 21.45 42.81 2.24
1735 2684 5.655974 GGAGCTAACTAGTTTGGTACCTAGT 59.344 44.000 19.26 9.50 34.50 2.57
1769 2722 5.455612 GGCTACTTGGCTGGGTTTGTATATA 60.456 44.000 0.00 0.00 38.32 0.86
1777 3202 0.539669 GTTGGCTACTTGGCTGGGTT 60.540 55.000 0.00 0.00 42.34 4.11
2056 3491 1.404035 CCGTCGACCAGTGATGTATGA 59.596 52.381 10.58 0.00 0.00 2.15
2115 3565 1.680860 CCATGTTCTGCCTGCTCATGA 60.681 52.381 0.00 0.00 38.35 3.07
2151 3604 6.239217 TGTCATCTGGATTATTAGTGCTGT 57.761 37.500 0.00 0.00 0.00 4.40
2511 4297 4.210331 GCATATGAGTTTCCACATCCCTT 58.790 43.478 6.97 0.00 0.00 3.95
2587 4428 1.822990 CCGTACTTCCTCCACTAGCAA 59.177 52.381 0.00 0.00 0.00 3.91
2674 4515 2.635915 ACATACCTGTTTTCTGACGGGA 59.364 45.455 9.72 0.00 46.98 5.14
2729 4571 3.440173 CGCAGATTCTTTGGTACCATGTT 59.560 43.478 17.17 4.64 0.00 2.71
2781 4623 6.033341 CGAAATTCAAAACACAGGTTCTTCA 58.967 36.000 0.00 0.00 35.82 3.02
2789 4631 2.050691 CGGCCGAAATTCAAAACACAG 58.949 47.619 24.07 0.00 0.00 3.66
2790 4632 1.676529 TCGGCCGAAATTCAAAACACA 59.323 42.857 28.99 0.00 0.00 3.72
2791 4633 2.409152 TCGGCCGAAATTCAAAACAC 57.591 45.000 28.99 0.00 0.00 3.32
2792 4634 3.651803 ATTCGGCCGAAATTCAAAACA 57.348 38.095 41.31 18.01 37.69 2.83
2793 4635 4.432373 CGAAATTCGGCCGAAATTCAAAAC 60.432 41.667 43.90 29.53 41.53 2.43
2794 4636 3.670991 CGAAATTCGGCCGAAATTCAAAA 59.329 39.130 43.90 26.27 41.53 2.44
2795 4637 3.238441 CGAAATTCGGCCGAAATTCAAA 58.762 40.909 43.90 26.91 41.53 2.69
2796 4638 2.857618 CGAAATTCGGCCGAAATTCAA 58.142 42.857 43.90 27.55 41.53 2.69
2797 4639 2.535934 CGAAATTCGGCCGAAATTCA 57.464 45.000 43.90 28.18 41.53 2.57
2808 4650 1.934463 CCGAGATGGCCGAAATTCG 59.066 57.895 8.62 8.62 40.07 3.34
2826 4668 2.271944 AAGTATATTTCGCCCCAGGC 57.728 50.000 0.00 0.00 46.75 4.85
2827 4669 3.146847 GGAAAGTATATTTCGCCCCAGG 58.853 50.000 0.00 0.00 0.00 4.45
2828 4670 3.815401 CTGGAAAGTATATTTCGCCCCAG 59.185 47.826 0.00 0.00 0.00 4.45
2829 4671 3.815809 CTGGAAAGTATATTTCGCCCCA 58.184 45.455 0.00 0.00 0.00 4.96
2830 4672 2.552743 GCTGGAAAGTATATTTCGCCCC 59.447 50.000 0.00 0.00 0.00 5.80
2831 4673 2.223377 CGCTGGAAAGTATATTTCGCCC 59.777 50.000 0.00 0.00 0.00 6.13
2832 4674 3.128349 TCGCTGGAAAGTATATTTCGCC 58.872 45.455 0.00 0.00 0.00 5.54
2833 4675 4.789095 TTCGCTGGAAAGTATATTTCGC 57.211 40.909 0.00 0.00 0.00 4.70
2873 4715 7.977789 ATTTCGGCCAAAATTTGACTAAAAT 57.022 28.000 7.37 3.85 40.32 1.82
2874 4716 7.306866 CGAATTTCGGCCAAAATTTGACTAAAA 60.307 33.333 20.46 1.73 40.31 1.52
2875 4717 6.144724 CGAATTTCGGCCAAAATTTGACTAAA 59.855 34.615 20.46 5.19 40.31 1.85
2876 4718 5.631512 CGAATTTCGGCCAAAATTTGACTAA 59.368 36.000 20.46 0.00 40.31 2.24
2877 4719 5.157781 CGAATTTCGGCCAAAATTTGACTA 58.842 37.500 20.46 0.00 40.31 2.59
2878 4720 3.987220 CGAATTTCGGCCAAAATTTGACT 59.013 39.130 20.46 0.00 40.31 3.41
2879 4721 4.306417 CGAATTTCGGCCAAAATTTGAC 57.694 40.909 20.46 6.21 40.31 3.18
2892 4734 0.305922 GCTGAGATGGCCGAATTTCG 59.694 55.000 11.81 11.81 40.07 3.46
2893 4735 0.665298 GGCTGAGATGGCCGAATTTC 59.335 55.000 0.00 0.00 40.19 2.17
2894 4736 2.799176 GGCTGAGATGGCCGAATTT 58.201 52.632 0.00 0.00 40.19 1.82
2895 4737 4.567318 GGCTGAGATGGCCGAATT 57.433 55.556 0.00 0.00 40.19 2.17
2901 4743 4.891037 GCCCCAGGCTGAGATGGC 62.891 72.222 17.94 17.50 46.69 4.40
2910 4752 0.320050 TGAAATTTTTCGCCCCAGGC 59.680 50.000 0.00 0.00 46.75 4.85
2911 4753 1.342819 TGTGAAATTTTTCGCCCCAGG 59.657 47.619 12.61 0.00 44.75 4.45
2912 4754 2.810439 TGTGAAATTTTTCGCCCCAG 57.190 45.000 12.61 0.00 44.75 4.45
2913 4755 3.198872 GTTTGTGAAATTTTTCGCCCCA 58.801 40.909 12.61 0.00 44.75 4.96
2914 4756 2.546368 GGTTTGTGAAATTTTTCGCCCC 59.454 45.455 12.61 7.41 44.75 5.80
2915 4757 2.546368 GGGTTTGTGAAATTTTTCGCCC 59.454 45.455 12.61 7.63 44.75 6.13
2916 4758 3.198872 TGGGTTTGTGAAATTTTTCGCC 58.801 40.909 12.61 1.16 44.75 5.54
2917 4759 4.866682 TTGGGTTTGTGAAATTTTTCGC 57.133 36.364 9.16 9.16 45.38 4.70
2918 4760 7.467623 TGATTTTGGGTTTGTGAAATTTTTCG 58.532 30.769 0.00 0.00 40.01 3.46
2919 4761 9.631452 TTTGATTTTGGGTTTGTGAAATTTTTC 57.369 25.926 0.00 0.00 37.69 2.29
2920 4762 9.416794 GTTTGATTTTGGGTTTGTGAAATTTTT 57.583 25.926 0.00 0.00 0.00 1.94
2921 4763 8.031864 GGTTTGATTTTGGGTTTGTGAAATTTT 58.968 29.630 0.00 0.00 0.00 1.82
2922 4764 7.395772 AGGTTTGATTTTGGGTTTGTGAAATTT 59.604 29.630 0.00 0.00 0.00 1.82
2923 4765 6.889177 AGGTTTGATTTTGGGTTTGTGAAATT 59.111 30.769 0.00 0.00 0.00 1.82
2924 4766 6.422333 AGGTTTGATTTTGGGTTTGTGAAAT 58.578 32.000 0.00 0.00 0.00 2.17
2925 4767 5.810095 AGGTTTGATTTTGGGTTTGTGAAA 58.190 33.333 0.00 0.00 0.00 2.69
2926 4768 5.428184 AGGTTTGATTTTGGGTTTGTGAA 57.572 34.783 0.00 0.00 0.00 3.18
2927 4769 5.181748 CAAGGTTTGATTTTGGGTTTGTGA 58.818 37.500 0.00 0.00 0.00 3.58
2928 4770 4.201901 GCAAGGTTTGATTTTGGGTTTGTG 60.202 41.667 0.00 0.00 0.00 3.33
2929 4771 3.944650 GCAAGGTTTGATTTTGGGTTTGT 59.055 39.130 0.00 0.00 0.00 2.83
2930 4772 3.002144 CGCAAGGTTTGATTTTGGGTTTG 59.998 43.478 0.00 0.00 32.19 2.93
2931 4773 3.118592 TCGCAAGGTTTGATTTTGGGTTT 60.119 39.130 0.00 0.00 36.50 3.27
2932 4774 2.432510 TCGCAAGGTTTGATTTTGGGTT 59.567 40.909 0.00 0.00 36.50 4.11
2933 4775 2.035632 TCGCAAGGTTTGATTTTGGGT 58.964 42.857 0.00 0.00 36.50 4.51
2934 4776 2.810439 TCGCAAGGTTTGATTTTGGG 57.190 45.000 0.00 0.00 36.46 4.12
2935 4777 3.976169 TCTTCGCAAGGTTTGATTTTGG 58.024 40.909 0.00 0.00 38.47 3.28
2936 4778 5.043248 AGTTCTTCGCAAGGTTTGATTTTG 58.957 37.500 0.00 0.00 38.47 2.44
2937 4779 5.262588 AGTTCTTCGCAAGGTTTGATTTT 57.737 34.783 0.00 0.00 38.47 1.82
2938 4780 4.918810 AGTTCTTCGCAAGGTTTGATTT 57.081 36.364 0.00 0.00 38.47 2.17
2939 4781 6.653320 TGTATAGTTCTTCGCAAGGTTTGATT 59.347 34.615 0.00 0.00 38.47 2.57
2940 4782 6.170506 TGTATAGTTCTTCGCAAGGTTTGAT 58.829 36.000 0.00 0.00 38.47 2.57
2941 4783 5.543714 TGTATAGTTCTTCGCAAGGTTTGA 58.456 37.500 0.00 0.00 38.47 2.69
2942 4784 5.856126 TGTATAGTTCTTCGCAAGGTTTG 57.144 39.130 0.00 0.00 38.47 2.93
2943 4785 5.938125 ACATGTATAGTTCTTCGCAAGGTTT 59.062 36.000 0.00 0.00 38.47 3.27
2944 4786 5.351465 CACATGTATAGTTCTTCGCAAGGTT 59.649 40.000 0.00 0.00 38.47 3.50
2945 4787 4.870426 CACATGTATAGTTCTTCGCAAGGT 59.130 41.667 0.00 0.00 38.47 3.50
2946 4788 4.870426 ACACATGTATAGTTCTTCGCAAGG 59.130 41.667 0.00 0.00 38.47 3.61
2947 4789 6.243551 CAACACATGTATAGTTCTTCGCAAG 58.756 40.000 0.00 0.00 0.00 4.01
2948 4790 5.390461 GCAACACATGTATAGTTCTTCGCAA 60.390 40.000 0.00 0.00 0.00 4.85
2949 4791 4.092821 GCAACACATGTATAGTTCTTCGCA 59.907 41.667 0.00 0.00 0.00 5.10
2950 4792 4.330074 AGCAACACATGTATAGTTCTTCGC 59.670 41.667 0.00 0.00 0.00 4.70
2951 4793 6.408858 AAGCAACACATGTATAGTTCTTCG 57.591 37.500 0.00 0.00 0.00 3.79
2952 4794 6.371548 TGGAAGCAACACATGTATAGTTCTTC 59.628 38.462 18.61 18.61 33.59 2.87
2953 4795 6.237901 TGGAAGCAACACATGTATAGTTCTT 58.762 36.000 0.00 5.24 0.00 2.52
2954 4796 5.804639 TGGAAGCAACACATGTATAGTTCT 58.195 37.500 0.00 0.00 0.00 3.01
2955 4797 6.494893 TTGGAAGCAACACATGTATAGTTC 57.505 37.500 0.00 0.00 0.00 3.01
2956 4798 6.264292 TGTTTGGAAGCAACACATGTATAGTT 59.736 34.615 0.00 0.00 0.00 2.24
2957 4799 5.767665 TGTTTGGAAGCAACACATGTATAGT 59.232 36.000 0.00 0.00 0.00 2.12
2958 4800 6.252967 TGTTTGGAAGCAACACATGTATAG 57.747 37.500 0.00 0.00 0.00 1.31
2972 4814 0.592637 TGCACTGCGATGTTTGGAAG 59.407 50.000 0.00 0.00 0.00 3.46
2991 4833 8.329502 ACAAATAGAGGGAGTGCTAATTAAGTT 58.670 33.333 0.00 0.00 0.00 2.66
3043 4885 3.915437 AGTTTGGTTTGCGGAACATAG 57.085 42.857 0.00 0.00 40.13 2.23
3081 4923 4.887071 ACTTCCTGACATTAAAGCAACACA 59.113 37.500 0.00 0.00 0.00 3.72
3102 4946 4.323477 TGTTAGCCGGCGCCAACT 62.323 61.111 29.22 24.34 37.48 3.16
3152 4996 2.216898 GAGCTTCAACAGTTCAGCACT 58.783 47.619 14.15 0.00 32.96 4.40
3153 4997 1.070309 CGAGCTTCAACAGTTCAGCAC 60.070 52.381 14.15 8.43 32.22 4.40
3195 5040 4.293901 ACAAAAGGGTATCTGGGGTTGTAT 59.706 41.667 0.00 0.00 0.00 2.29
3196 5041 3.658705 ACAAAAGGGTATCTGGGGTTGTA 59.341 43.478 0.00 0.00 0.00 2.41
3197 5042 2.449345 ACAAAAGGGTATCTGGGGTTGT 59.551 45.455 0.00 0.00 0.00 3.32
3198 5043 3.169512 ACAAAAGGGTATCTGGGGTTG 57.830 47.619 0.00 0.00 0.00 3.77
3199 5044 5.342361 TTTACAAAAGGGTATCTGGGGTT 57.658 39.130 0.00 0.00 0.00 4.11
3200 5045 5.342361 TTTTACAAAAGGGTATCTGGGGT 57.658 39.130 0.00 0.00 0.00 4.95
3210 5055 6.127338 GGATCTCCCTGAATTTTACAAAAGGG 60.127 42.308 0.00 0.00 33.31 3.95
3242 5089 5.092554 TCTCGCTGGAAACCAATGTATAA 57.907 39.130 0.00 0.00 30.80 0.98
3245 5092 3.197766 AGATCTCGCTGGAAACCAATGTA 59.802 43.478 0.00 0.00 30.80 2.29
3247 5094 2.636830 AGATCTCGCTGGAAACCAATG 58.363 47.619 0.00 0.00 30.80 2.82
3248 5095 4.487714 TTAGATCTCGCTGGAAACCAAT 57.512 40.909 0.00 0.00 30.80 3.16
3249 5096 3.973206 TTAGATCTCGCTGGAAACCAA 57.027 42.857 0.00 0.00 30.80 3.67
3250 5097 4.487714 AATTAGATCTCGCTGGAAACCA 57.512 40.909 0.00 0.00 0.00 3.67
3251 5098 5.992217 ACATAATTAGATCTCGCTGGAAACC 59.008 40.000 0.00 0.00 0.00 3.27
3253 5100 5.920840 CGACATAATTAGATCTCGCTGGAAA 59.079 40.000 0.00 0.00 0.00 3.13
3254 5101 5.009710 ACGACATAATTAGATCTCGCTGGAA 59.990 40.000 0.00 0.00 0.00 3.53
3294 5141 6.425577 TTGGGCAAACATAAGAATACGTAC 57.574 37.500 0.00 0.00 0.00 3.67
3295 5142 7.450124 TTTTGGGCAAACATAAGAATACGTA 57.550 32.000 0.00 0.00 0.00 3.57
3296 5143 5.968528 TTTGGGCAAACATAAGAATACGT 57.031 34.783 0.00 0.00 0.00 3.57
3297 5144 7.826260 AATTTTGGGCAAACATAAGAATACG 57.174 32.000 0.00 0.00 0.00 3.06
3303 5150 6.873076 TCTTGCTAATTTTGGGCAAACATAAG 59.127 34.615 0.00 0.00 43.79 1.73
3320 5167 6.146184 CGAGAAAAGAGAACACATCTTGCTAA 59.854 38.462 0.00 0.00 38.96 3.09
3326 5174 9.877178 AAATATACGAGAAAAGAGAACACATCT 57.123 29.630 0.00 0.00 42.61 2.90
3385 5233 5.499004 TGATACTGGCTAGTTTTGAACCT 57.501 39.130 8.46 0.00 38.36 3.50
3386 5234 5.705905 ACTTGATACTGGCTAGTTTTGAACC 59.294 40.000 8.46 0.00 38.36 3.62
3387 5235 6.803154 ACTTGATACTGGCTAGTTTTGAAC 57.197 37.500 8.46 0.00 38.36 3.18
3388 5236 6.430000 GGAACTTGATACTGGCTAGTTTTGAA 59.570 38.462 8.46 0.00 38.36 2.69
3389 5237 5.938125 GGAACTTGATACTGGCTAGTTTTGA 59.062 40.000 8.46 0.00 38.36 2.69
3390 5238 5.123979 GGGAACTTGATACTGGCTAGTTTTG 59.876 44.000 8.46 0.00 38.36 2.44
3391 5239 5.254115 GGGAACTTGATACTGGCTAGTTTT 58.746 41.667 8.46 0.00 38.36 2.43
3392 5240 4.324331 GGGGAACTTGATACTGGCTAGTTT 60.324 45.833 8.46 0.00 38.36 2.66
3393 5241 3.200165 GGGGAACTTGATACTGGCTAGTT 59.800 47.826 8.46 0.00 38.36 2.24
3394 5242 2.772515 GGGGAACTTGATACTGGCTAGT 59.227 50.000 8.18 8.18 40.99 2.57
3395 5243 3.041946 AGGGGAACTTGATACTGGCTAG 58.958 50.000 0.00 0.00 0.00 3.42
3396 5244 3.130734 AGGGGAACTTGATACTGGCTA 57.869 47.619 0.00 0.00 0.00 3.93
3397 5245 1.972588 AGGGGAACTTGATACTGGCT 58.027 50.000 0.00 0.00 0.00 4.75
3398 5246 2.026262 TGAAGGGGAACTTGATACTGGC 60.026 50.000 0.00 0.00 40.21 4.85
3399 5247 4.301072 TTGAAGGGGAACTTGATACTGG 57.699 45.455 0.00 0.00 40.21 4.00
3400 5248 6.648879 TTTTTGAAGGGGAACTTGATACTG 57.351 37.500 0.00 0.00 40.21 2.74
3423 5271 4.532314 GTGCCACTTGGTACTAGTACTT 57.468 45.455 27.71 10.93 45.69 2.24
3445 5293 5.127031 ACATGGCGGCTTAATTTAGTTGATT 59.873 36.000 11.43 0.00 0.00 2.57
3468 5316 1.608590 CGGATTTGGGACCATATGCAC 59.391 52.381 12.22 0.00 0.00 4.57
3472 5320 0.250727 CGCCGGATTTGGGACCATAT 60.251 55.000 5.05 0.00 0.00 1.78
3473 5321 1.147376 CGCCGGATTTGGGACCATA 59.853 57.895 5.05 0.00 0.00 2.74
3480 5328 2.106683 GTCTGGACGCCGGATTTGG 61.107 63.158 5.05 0.00 41.38 3.28
3527 5375 4.179599 CTCCCTCCCTCCCTCCCC 62.180 77.778 0.00 0.00 0.00 4.81
3528 5376 4.890306 GCTCCCTCCCTCCCTCCC 62.890 77.778 0.00 0.00 0.00 4.30
3529 5377 2.380571 CTAGCTCCCTCCCTCCCTCC 62.381 70.000 0.00 0.00 0.00 4.30
3530 5378 1.155155 CTAGCTCCCTCCCTCCCTC 59.845 68.421 0.00 0.00 0.00 4.30
3531 5379 3.094751 GCTAGCTCCCTCCCTCCCT 62.095 68.421 7.70 0.00 0.00 4.20
3532 5380 2.525629 GCTAGCTCCCTCCCTCCC 60.526 72.222 7.70 0.00 0.00 4.30
3533 5381 2.915137 CGCTAGCTCCCTCCCTCC 60.915 72.222 13.93 0.00 0.00 4.30
3534 5382 2.915137 CCGCTAGCTCCCTCCCTC 60.915 72.222 13.93 0.00 0.00 4.30
3535 5383 4.548513 CCCGCTAGCTCCCTCCCT 62.549 72.222 13.93 0.00 0.00 4.20
3538 5386 3.811807 TAGGCCCGCTAGCTCCCTC 62.812 68.421 17.55 3.15 0.00 4.30
3539 5387 2.891307 TTTAGGCCCGCTAGCTCCCT 62.891 60.000 13.93 16.41 0.00 4.20
3540 5388 2.440817 TTTAGGCCCGCTAGCTCCC 61.441 63.158 13.93 9.91 0.00 4.30
3541 5389 1.227586 GTTTAGGCCCGCTAGCTCC 60.228 63.158 13.93 10.98 0.00 4.70
3542 5390 0.530870 CTGTTTAGGCCCGCTAGCTC 60.531 60.000 13.93 1.50 0.00 4.09
3543 5391 0.976073 TCTGTTTAGGCCCGCTAGCT 60.976 55.000 13.93 0.00 0.00 3.32
3544 5392 0.107848 TTCTGTTTAGGCCCGCTAGC 60.108 55.000 4.06 4.06 0.00 3.42
3545 5393 1.480954 TCTTCTGTTTAGGCCCGCTAG 59.519 52.381 0.00 0.00 0.00 3.42
3546 5394 1.480954 CTCTTCTGTTTAGGCCCGCTA 59.519 52.381 0.00 0.00 0.00 4.26
3547 5395 0.250513 CTCTTCTGTTTAGGCCCGCT 59.749 55.000 0.00 0.00 0.00 5.52
3548 5396 1.369839 GCTCTTCTGTTTAGGCCCGC 61.370 60.000 0.00 0.00 0.00 6.13
3549 5397 0.036388 TGCTCTTCTGTTTAGGCCCG 60.036 55.000 0.00 0.00 0.00 6.13
3550 5398 1.454201 GTGCTCTTCTGTTTAGGCCC 58.546 55.000 0.00 0.00 0.00 5.80
3551 5399 1.079503 CGTGCTCTTCTGTTTAGGCC 58.920 55.000 0.00 0.00 0.00 5.19
3552 5400 1.797025 ACGTGCTCTTCTGTTTAGGC 58.203 50.000 0.00 0.00 0.00 3.93
3553 5401 2.924290 GCTACGTGCTCTTCTGTTTAGG 59.076 50.000 0.00 0.00 38.95 2.69
3554 5402 2.924290 GGCTACGTGCTCTTCTGTTTAG 59.076 50.000 0.00 0.00 42.39 1.85


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

AutoCloner maintained by Alex Coulton.