Multiple sequence alignment - TraesCS3D01G193600

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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 TraesCS3D01G193600 chr3D 100.000 4747 0 0 1 4747 184369113 184373859 0.000000e+00 8767.0
1 TraesCS3D01G193600 chr3D 100.000 2686 0 0 4968 7653 184374080 184376765 0.000000e+00 4961.0
2 TraesCS3D01G193600 chr3D 100.000 2038 0 0 7936 9973 184377048 184379085 0.000000e+00 3764.0
3 TraesCS3D01G193600 chr3D 97.408 733 19 0 4013 4745 278445279 278446011 0.000000e+00 1249.0
4 TraesCS3D01G193600 chr3D 97.154 738 21 0 4008 4745 278443847 278444584 0.000000e+00 1247.0
5 TraesCS3D01G193600 chr3D 98.485 528 8 0 9249 9776 397784701 397784174 0.000000e+00 931.0
6 TraesCS3D01G193600 chr3D 97.710 524 12 0 9249 9772 181111638 181112161 0.000000e+00 902.0
7 TraesCS3D01G193600 chr3D 91.921 557 39 4 4968 5520 30048393 30047839 0.000000e+00 774.0
8 TraesCS3D01G193600 chr3D 91.577 558 46 1 4971 5528 135264058 135264614 0.000000e+00 769.0
9 TraesCS3D01G193600 chr3D 85.185 243 31 5 8084 8323 565616964 565616724 2.780000e-60 244.0
10 TraesCS3D01G193600 chr3D 96.947 131 4 0 5515 5645 184373348 184373478 4.690000e-53 220.0
11 TraesCS3D01G193600 chr3D 96.947 131 4 0 5515 5645 278444075 278444205 4.690000e-53 220.0
12 TraesCS3D01G193600 chr3D 96.947 131 4 0 5515 5645 278445502 278445632 4.690000e-53 220.0
13 TraesCS3D01G193600 chr3D 76.330 376 51 17 7965 8328 594347075 594347424 6.200000e-37 167.0
14 TraesCS3D01G193600 chr3A 96.090 2813 83 13 408 3205 235370652 235373452 0.000000e+00 4560.0
15 TraesCS3D01G193600 chr3A 93.638 2012 87 28 5644 7647 235374212 235376190 0.000000e+00 2968.0
16 TraesCS3D01G193600 chr3A 91.321 1325 45 21 7937 9252 235376223 235377486 0.000000e+00 1746.0
17 TraesCS3D01G193600 chr3A 95.349 774 24 3 3242 4012 235373453 235374217 0.000000e+00 1219.0
18 TraesCS3D01G193600 chr3A 95.646 735 32 0 4011 4745 9561873 9561139 0.000000e+00 1181.0
19 TraesCS3D01G193600 chr3A 92.870 547 37 2 4968 5513 38023687 38024232 0.000000e+00 793.0
20 TraesCS3D01G193600 chr3A 91.341 358 19 5 5 360 235366985 235367332 7.010000e-131 479.0
21 TraesCS3D01G193600 chr3A 96.575 146 4 1 9828 9973 235380385 235380529 3.600000e-59 241.0
22 TraesCS3D01G193600 chr3A 96.970 132 4 0 5513 5644 331478867 331478998 1.300000e-53 222.0
23 TraesCS3D01G193600 chr3A 95.588 136 6 0 5513 5648 38023156 38023291 1.690000e-52 219.0
24 TraesCS3D01G193600 chr3A 76.370 292 42 14 8039 8328 724889137 724889403 2.260000e-26 132.0
25 TraesCS3D01G193600 chr3A 75.685 292 44 15 8039 8328 724930994 724931260 4.890000e-23 121.0
26 TraesCS3D01G193600 chr3A 85.437 103 15 0 6189 6291 724883402 724883504 3.810000e-19 108.0
27 TraesCS3D01G193600 chr3B 93.652 2489 103 19 1554 4012 262852293 262854756 0.000000e+00 3670.0
28 TraesCS3D01G193600 chr3B 90.754 1352 64 27 7937 9257 262855672 262856993 0.000000e+00 1748.0
29 TraesCS3D01G193600 chr3B 96.354 768 26 2 797 1563 262843253 262844019 0.000000e+00 1262.0
30 TraesCS3D01G193600 chr3B 95.853 651 27 0 5644 6294 262854751 262855401 0.000000e+00 1053.0
31 TraesCS3D01G193600 chr3B 90.000 190 11 2 7447 7630 262855400 262855587 1.290000e-58 239.0
32 TraesCS3D01G193600 chr3B 87.805 205 17 4 557 754 262843057 262843260 6.020000e-57 233.0
33 TraesCS3D01G193600 chr3B 80.620 258 33 12 1 252 262842148 262842394 6.150000e-42 183.0
34 TraesCS3D01G193600 chr3B 97.826 92 2 0 9803 9894 262864329 262864420 1.040000e-34 159.0
35 TraesCS3D01G193600 chr3B 92.857 70 4 1 9889 9957 262877985 262878054 6.370000e-17 100.0
36 TraesCS3D01G193600 chr3B 96.226 53 2 0 3113 3165 262853893 262853945 4.960000e-13 87.9
37 TraesCS3D01G193600 chr3B 100.000 34 0 0 9776 9809 262856977 262857010 8.360000e-06 63.9
38 TraesCS3D01G193600 chr7D 93.508 1109 60 7 6289 7393 305131619 305132719 0.000000e+00 1639.0
39 TraesCS3D01G193600 chr7D 95.652 736 31 1 4010 4745 104506056 104506790 0.000000e+00 1181.0
40 TraesCS3D01G193600 chr7D 95.362 733 34 0 4013 4745 548904816 548904084 0.000000e+00 1166.0
41 TraesCS3D01G193600 chr7D 97.736 530 10 2 9249 9777 13322699 13323227 0.000000e+00 911.0
42 TraesCS3D01G193600 chr7D 94.301 193 10 1 8135 8326 289244712 289244904 2.720000e-75 294.0
43 TraesCS3D01G193600 chr7D 92.697 178 13 0 7449 7626 289244273 289244450 3.570000e-64 257.0
44 TraesCS3D01G193600 chr6D 93.435 1112 62 6 6289 7393 296695652 296696759 0.000000e+00 1639.0
45 TraesCS3D01G193600 chr6D 95.634 733 23 2 4012 4743 235770296 235771020 0.000000e+00 1168.0
46 TraesCS3D01G193600 chr6D 98.488 529 7 1 9249 9776 119965725 119965197 0.000000e+00 931.0
47 TraesCS3D01G193600 chr6D 92.982 57 3 1 7393 7449 115323675 115323620 2.310000e-11 82.4
48 TraesCS3D01G193600 chr6D 92.982 57 3 1 7393 7449 126434301 126434246 2.310000e-11 82.4
49 TraesCS3D01G193600 chr6D 92.982 57 3 1 7393 7449 296696696 296696751 2.310000e-11 82.4
50 TraesCS3D01G193600 chr6D 92.982 57 3 1 7393 7449 401143257 401143202 2.310000e-11 82.4
51 TraesCS3D01G193600 chr2D 93.478 1104 65 3 6290 7393 284549778 284550874 0.000000e+00 1633.0
52 TraesCS3D01G193600 chr2D 97.091 722 21 0 4013 4734 50446206 50446927 0.000000e+00 1218.0
53 TraesCS3D01G193600 chr2D 99.055 529 5 0 9249 9777 203046317 203045789 0.000000e+00 950.0
54 TraesCS3D01G193600 chr2D 96.269 134 5 0 5515 5648 546811563 546811430 4.690000e-53 220.0
55 TraesCS3D01G193600 chr2D 91.447 152 13 0 5513 5664 579950408 579950257 1.020000e-49 209.0
56 TraesCS3D01G193600 chr5A 93.032 1105 77 0 6289 7393 524722811 524723915 0.000000e+00 1615.0
57 TraesCS3D01G193600 chr5A 93.085 1099 76 0 6295 7393 68818884 68817786 0.000000e+00 1609.0
58 TraesCS3D01G193600 chr5A 92.405 553 41 1 4968 5519 338296134 338296686 0.000000e+00 787.0
59 TraesCS3D01G193600 chr2A 92.941 1105 78 0 6289 7393 179281894 179282998 0.000000e+00 1609.0
60 TraesCS3D01G193600 chr2A 92.941 1105 78 0 6289 7393 421218143 421219247 0.000000e+00 1609.0
61 TraesCS3D01G193600 chr2A 92.941 1105 78 0 6289 7393 578391620 578390516 0.000000e+00 1609.0
62 TraesCS3D01G193600 chr2A 92.922 551 36 2 4971 5521 732267528 732266981 0.000000e+00 798.0
63 TraesCS3D01G193600 chr2A 92.168 549 43 0 4971 5519 385646978 385646430 0.000000e+00 776.0
64 TraesCS3D01G193600 chr1D 95.232 734 35 0 4012 4745 402341113 402341846 0.000000e+00 1162.0
65 TraesCS3D01G193600 chr1D 98.110 529 10 0 9249 9777 62578408 62577880 0.000000e+00 922.0
66 TraesCS3D01G193600 chr1D 96.947 131 4 0 5515 5645 402343945 402344075 4.690000e-53 220.0
67 TraesCS3D01G193600 chr1D 92.982 57 3 1 7393 7449 182051052 182050997 2.310000e-11 82.4
68 TraesCS3D01G193600 chr1A 95.694 720 31 0 4012 4731 442609758 442610477 0.000000e+00 1158.0
69 TraesCS3D01G193600 chr5D 97.925 530 9 2 9249 9777 377361712 377361184 0.000000e+00 917.0
70 TraesCS3D01G193600 chr5D 92.973 555 38 1 4968 5521 375395426 375395980 0.000000e+00 808.0
71 TraesCS3D01G193600 chr5D 89.320 103 11 0 6189 6291 221474063 221474165 8.130000e-26 130.0
72 TraesCS3D01G193600 chr6B 97.561 533 12 1 9249 9780 142803291 142803823 0.000000e+00 911.0
73 TraesCS3D01G193600 chr6B 97.538 528 13 0 9249 9776 207153344 207153871 0.000000e+00 904.0
74 TraesCS3D01G193600 chr6B 88.715 319 25 6 8018 8326 82159883 82160200 7.310000e-101 379.0
75 TraesCS3D01G193600 chr6B 81.132 265 35 10 8064 8323 408692786 408693040 2.200000e-46 198.0
76 TraesCS3D01G193600 chr6B 93.204 103 7 0 6189 6291 408692262 408692364 1.730000e-32 152.0
77 TraesCS3D01G193600 chr6B 89.524 105 11 0 6187 6291 82159478 82159582 6.280000e-27 134.0
78 TraesCS3D01G193600 chr7A 93.818 550 34 0 4971 5520 518669932 518670481 0.000000e+00 828.0
79 TraesCS3D01G193600 chr7A 92.266 556 41 2 4968 5521 106239306 106239861 0.000000e+00 787.0
80 TraesCS3D01G193600 chr7A 91.237 194 17 0 7449 7642 330450773 330450580 2.140000e-66 265.0
81 TraesCS3D01G193600 chr7B 92.386 197 11 3 8135 8330 362024755 362024948 2.740000e-70 278.0
82 TraesCS3D01G193600 chr7B 92.188 192 15 0 7449 7640 362024311 362024502 1.280000e-68 272.0
83 TraesCS3D01G193600 chr7B 94.737 57 2 1 7393 7449 445663469 445663414 4.960000e-13 87.9
84 TraesCS3D01G193600 chr4D 92.784 194 11 1 7449 7642 483681327 483681517 2.740000e-70 278.0
85 TraesCS3D01G193600 chr4D 97.015 134 4 0 5515 5648 417675177 417675044 1.010000e-54 226.0
86 TraesCS3D01G193600 chr4D 87.895 190 16 6 7449 7632 499584109 499583921 6.070000e-52 217.0
87 TraesCS3D01G193600 chr4D 78.412 403 35 16 7936 8322 483681586 483681952 2.180000e-51 215.0
88 TraesCS3D01G193600 chr4D 92.982 57 3 1 7393 7449 26252994 26253049 2.310000e-11 82.4
89 TraesCS3D01G193600 chr5B 91.960 199 7 2 7449 7641 325082858 325082663 4.590000e-68 270.0
90 TraesCS3D01G193600 chr5B 93.939 99 6 0 6189 6287 325082964 325082866 6.240000e-32 150.0
91 TraesCS3D01G193600 chr5B 88.350 103 12 0 6189 6291 244004847 244004949 3.780000e-24 124.0
92 TraesCS3D01G193600 chr5B 94.737 57 2 1 7393 7449 474782712 474782767 4.960000e-13 87.9
93 TraesCS3D01G193600 chr4B 86.500 200 20 6 7449 7642 642627595 642627397 7.850000e-51 213.0
94 TraesCS3D01G193600 chr4B 92.982 57 3 1 7393 7449 38792529 38792584 2.310000e-11 82.4
95 TraesCS3D01G193600 chr6A 90.291 103 10 0 6189 6291 374420481 374420583 1.750000e-27 135.0


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 TraesCS3D01G193600 chr3D 184369113 184379085 9972 False 4428.000000 8767 99.236750 1 9973 4 chr3D.!!$F4 9972
1 TraesCS3D01G193600 chr3D 397784174 397784701 527 True 931.000000 931 98.485000 9249 9776 1 chr3D.!!$R2 527
2 TraesCS3D01G193600 chr3D 181111638 181112161 523 False 902.000000 902 97.710000 9249 9772 1 chr3D.!!$F2 523
3 TraesCS3D01G193600 chr3D 30047839 30048393 554 True 774.000000 774 91.921000 4968 5520 1 chr3D.!!$R1 552
4 TraesCS3D01G193600 chr3D 135264058 135264614 556 False 769.000000 769 91.577000 4971 5528 1 chr3D.!!$F1 557
5 TraesCS3D01G193600 chr3D 278443847 278446011 2164 False 734.000000 1249 97.114000 4008 5645 4 chr3D.!!$F5 1637
6 TraesCS3D01G193600 chr3A 235366985 235380529 13544 False 1868.833333 4560 94.052333 5 9973 6 chr3A.!!$F6 9968
7 TraesCS3D01G193600 chr3A 9561139 9561873 734 True 1181.000000 1181 95.646000 4011 4745 1 chr3A.!!$R1 734
8 TraesCS3D01G193600 chr3A 38023156 38024232 1076 False 506.000000 793 94.229000 4968 5648 2 chr3A.!!$F5 680
9 TraesCS3D01G193600 chr3B 262852293 262857010 4717 False 1143.633333 3670 94.414167 1554 9809 6 chr3B.!!$F4 8255
10 TraesCS3D01G193600 chr3B 262842148 262844019 1871 False 559.333333 1262 88.259667 1 1563 3 chr3B.!!$F3 1562
11 TraesCS3D01G193600 chr7D 305131619 305132719 1100 False 1639.000000 1639 93.508000 6289 7393 1 chr7D.!!$F3 1104
12 TraesCS3D01G193600 chr7D 104506056 104506790 734 False 1181.000000 1181 95.652000 4010 4745 1 chr7D.!!$F2 735
13 TraesCS3D01G193600 chr7D 548904084 548904816 732 True 1166.000000 1166 95.362000 4013 4745 1 chr7D.!!$R1 732
14 TraesCS3D01G193600 chr7D 13322699 13323227 528 False 911.000000 911 97.736000 9249 9777 1 chr7D.!!$F1 528
15 TraesCS3D01G193600 chr7D 289244273 289244904 631 False 275.500000 294 93.499000 7449 8326 2 chr7D.!!$F4 877
16 TraesCS3D01G193600 chr6D 235770296 235771020 724 False 1168.000000 1168 95.634000 4012 4743 1 chr6D.!!$F1 731
17 TraesCS3D01G193600 chr6D 119965197 119965725 528 True 931.000000 931 98.488000 9249 9776 1 chr6D.!!$R2 527
18 TraesCS3D01G193600 chr6D 296695652 296696759 1107 False 860.700000 1639 93.208500 6289 7449 2 chr6D.!!$F2 1160
19 TraesCS3D01G193600 chr2D 284549778 284550874 1096 False 1633.000000 1633 93.478000 6290 7393 1 chr2D.!!$F2 1103
20 TraesCS3D01G193600 chr2D 50446206 50446927 721 False 1218.000000 1218 97.091000 4013 4734 1 chr2D.!!$F1 721
21 TraesCS3D01G193600 chr2D 203045789 203046317 528 True 950.000000 950 99.055000 9249 9777 1 chr2D.!!$R1 528
22 TraesCS3D01G193600 chr5A 524722811 524723915 1104 False 1615.000000 1615 93.032000 6289 7393 1 chr5A.!!$F2 1104
23 TraesCS3D01G193600 chr5A 68817786 68818884 1098 True 1609.000000 1609 93.085000 6295 7393 1 chr5A.!!$R1 1098
24 TraesCS3D01G193600 chr5A 338296134 338296686 552 False 787.000000 787 92.405000 4968 5519 1 chr5A.!!$F1 551
25 TraesCS3D01G193600 chr2A 179281894 179282998 1104 False 1609.000000 1609 92.941000 6289 7393 1 chr2A.!!$F1 1104
26 TraesCS3D01G193600 chr2A 421218143 421219247 1104 False 1609.000000 1609 92.941000 6289 7393 1 chr2A.!!$F2 1104
27 TraesCS3D01G193600 chr2A 578390516 578391620 1104 True 1609.000000 1609 92.941000 6289 7393 1 chr2A.!!$R2 1104
28 TraesCS3D01G193600 chr2A 732266981 732267528 547 True 798.000000 798 92.922000 4971 5521 1 chr2A.!!$R3 550
29 TraesCS3D01G193600 chr2A 385646430 385646978 548 True 776.000000 776 92.168000 4971 5519 1 chr2A.!!$R1 548
30 TraesCS3D01G193600 chr1D 62577880 62578408 528 True 922.000000 922 98.110000 9249 9777 1 chr1D.!!$R1 528
31 TraesCS3D01G193600 chr1D 402341113 402344075 2962 False 691.000000 1162 96.089500 4012 5645 2 chr1D.!!$F1 1633
32 TraesCS3D01G193600 chr1A 442609758 442610477 719 False 1158.000000 1158 95.694000 4012 4731 1 chr1A.!!$F1 719
33 TraesCS3D01G193600 chr5D 377361184 377361712 528 True 917.000000 917 97.925000 9249 9777 1 chr5D.!!$R1 528
34 TraesCS3D01G193600 chr5D 375395426 375395980 554 False 808.000000 808 92.973000 4968 5521 1 chr5D.!!$F2 553
35 TraesCS3D01G193600 chr6B 142803291 142803823 532 False 911.000000 911 97.561000 9249 9780 1 chr6B.!!$F1 531
36 TraesCS3D01G193600 chr6B 207153344 207153871 527 False 904.000000 904 97.538000 9249 9776 1 chr6B.!!$F2 527
37 TraesCS3D01G193600 chr6B 82159478 82160200 722 False 256.500000 379 89.119500 6187 8326 2 chr6B.!!$F3 2139
38 TraesCS3D01G193600 chr7A 518669932 518670481 549 False 828.000000 828 93.818000 4971 5520 1 chr7A.!!$F2 549
39 TraesCS3D01G193600 chr7A 106239306 106239861 555 False 787.000000 787 92.266000 4968 5521 1 chr7A.!!$F1 553
40 TraesCS3D01G193600 chr7B 362024311 362024948 637 False 275.000000 278 92.287000 7449 8330 2 chr7B.!!$F1 881
41 TraesCS3D01G193600 chr4D 483681327 483681952 625 False 246.500000 278 85.598000 7449 8322 2 chr4D.!!$F2 873


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
508 3999 1.002069 TGCAGGGATCCAAGACCATT 58.998 50.000 15.23 0.0 0.00 3.16 F
563 4054 1.379527 GGCTTCCTCCACAATTACGG 58.620 55.000 0.00 0.0 0.00 4.02 F
1910 5562 1.215647 GTCGGTGAAGTCGGCTCAT 59.784 57.895 0.00 0.0 0.00 2.90 F
2997 6664 1.792757 ATCCACCTCCTGCTGGCAAA 61.793 55.000 4.42 0.0 0.00 3.68 F
4195 7884 1.555075 TCAGTATTTGCTCGGCTTCCT 59.445 47.619 0.00 0.0 0.00 3.36 F
5184 10554 1.900498 GTTTCCAGGCAGCAGCAGT 60.900 57.895 2.65 0.0 44.61 4.40 F
5623 12097 0.396695 AATCTCCGCCCTAGAACCGA 60.397 55.000 0.00 0.0 0.00 4.69 F
6907 13392 0.387929 ACGAGAGAGTGCCACGAAAA 59.612 50.000 0.00 0.0 0.00 2.29 F
7442 13929 0.323957 ACGGTTTTCACCTCTAGCCC 59.676 55.000 0.00 0.0 41.64 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1673 5325 0.694771 ACTGATTGCCAGCTCCAAGA 59.305 50.000 3.10 0.0 46.81 3.02 R
2300 5960 0.961019 AAACTCGTGCATGTGCCAAT 59.039 45.000 5.68 0.0 41.18 3.16 R
3849 7538 3.447229 TCATCAGCTATCGAACTCAACCA 59.553 43.478 0.00 0.0 0.00 3.67 R
4317 8006 0.327576 AGGGTGGAGATTGTAGGGGG 60.328 60.000 0.00 0.0 0.00 5.40 R
5428 10798 2.515991 CGGTGTGCACAGGTGGTT 60.516 61.111 22.40 0.0 0.00 3.67 R
6339 12813 0.677731 CCACCACATGACATTCCGCT 60.678 55.000 0.00 0.0 0.00 5.52 R
7431 13918 0.264955 TAGGGGAAGGGCTAGAGGTG 59.735 60.000 0.00 0.0 0.00 4.00 R
8034 14585 0.617413 CTCATTGGAGGAGGCTGTGT 59.383 55.000 0.00 0.0 37.51 3.72 R
9246 15873 0.953960 GCGGTCCAAATTCGGTCTGT 60.954 55.000 0.00 0.0 0.00 3.41 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
35 36 6.427853 TGTCATTAGGTATGTGCATATTCTGC 59.572 38.462 0.00 0.00 41.05 4.26
80 82 5.567138 AATGTTTGCGGATTAGAGAAAGG 57.433 39.130 0.00 0.00 0.00 3.11
117 120 6.759356 GTGCAGTGGGTTAAAAATGTAGTTTT 59.241 34.615 0.00 0.00 41.69 2.43
120 123 6.704050 CAGTGGGTTAAAAATGTAGTTTTGGG 59.296 38.462 0.80 0.00 39.86 4.12
180 184 9.474313 AATCAAATTTGTAGGGCTAATGAGTTA 57.526 29.630 17.47 0.00 0.00 2.24
183 187 6.824958 ATTTGTAGGGCTAATGAGTTAGGA 57.175 37.500 0.00 0.00 38.19 2.94
206 210 6.238731 GGATGCTCGTATTGAAATCCATTGAA 60.239 38.462 0.00 0.00 38.74 2.69
210 214 7.488792 TGCTCGTATTGAAATCCATTGAATTTG 59.511 33.333 0.00 0.00 0.00 2.32
276 371 9.118300 ACTCTTAATAAAGCATGGATGAGAAAG 57.882 33.333 0.00 0.00 32.36 2.62
291 386 6.922957 GGATGAGAAAGTATGATCACAGAGAC 59.077 42.308 0.00 0.00 0.00 3.36
302 397 9.619316 GTATGATCACAGAGACTAACATATCAC 57.381 37.037 0.00 0.00 0.00 3.06
345 440 9.696917 GAACAAACATTTGGTTGAAATCTCTAT 57.303 29.630 14.92 0.00 45.19 1.98
372 930 2.110967 CGCTGGCCAACTCCATGAG 61.111 63.158 7.01 0.00 35.22 2.90
385 943 2.679837 CTCCATGAGGGTTGAAATCACG 59.320 50.000 0.00 0.00 38.11 4.35
444 3813 5.507974 TGTTGCGAGAGATAATACACGTAG 58.492 41.667 0.00 0.00 0.00 3.51
508 3999 1.002069 TGCAGGGATCCAAGACCATT 58.998 50.000 15.23 0.00 0.00 3.16
537 4028 2.171209 CTCCATGGTCAGTGTCGGCA 62.171 60.000 12.58 0.00 0.00 5.69
563 4054 1.379527 GGCTTCCTCCACAATTACGG 58.620 55.000 0.00 0.00 0.00 4.02
692 4336 6.030849 CAGGTGTTCTAATCACGAGACTAAG 58.969 44.000 0.00 0.00 36.76 2.18
781 4427 8.716646 TTTTAGTGCTGAGAATCGATTATTCA 57.283 30.769 11.38 15.95 45.58 2.57
1505 5157 7.114953 GCTCTTGCACTAATTTTGTTAGGTTTC 59.885 37.037 0.00 0.00 39.41 2.78
1593 5245 8.339714 TCTTGGTGTAAGAAATTAAACAGAACG 58.660 33.333 0.00 0.00 42.31 3.95
1665 5317 3.342377 TCATTGCTGTCCGGTCAAATA 57.658 42.857 0.00 0.00 0.00 1.40
1673 5325 3.879295 CTGTCCGGTCAAATATGAATGCT 59.121 43.478 0.00 0.00 37.30 3.79
1733 5385 9.664332 TCAGACATTTTTCCAAAGAAATTTTGA 57.336 25.926 0.00 0.00 41.55 2.69
1881 5533 2.027192 GCTACTCTTGGTGGAATGGTGA 60.027 50.000 0.00 0.00 0.00 4.02
1910 5562 1.215647 GTCGGTGAAGTCGGCTCAT 59.784 57.895 0.00 0.00 0.00 2.90
2205 5865 1.978617 AGGTGCAGCAAATTCCCCG 60.979 57.895 19.63 0.00 0.00 5.73
2288 5948 3.054802 ACCTGAGCTGTTTCCTATCAAGG 60.055 47.826 0.00 0.00 45.21 3.61
2313 5973 3.428045 GGAAGAACTATTGGCACATGCAC 60.428 47.826 6.15 0.00 44.36 4.57
2587 6254 3.196254 GGATTTTGATGCCCTGTCATGTT 59.804 43.478 0.00 0.00 0.00 2.71
2688 6355 2.561373 GGCGGCAAAACTTCTCCG 59.439 61.111 3.07 0.00 44.29 4.63
2764 6431 3.303881 TCGGATTGAGCCATCTTATCG 57.696 47.619 0.00 0.00 0.00 2.92
2832 6499 3.438781 TCAACTGTCTTGTTGTTGTGGTC 59.561 43.478 7.17 0.00 45.26 4.02
2997 6664 1.792757 ATCCACCTCCTGCTGGCAAA 61.793 55.000 4.42 0.00 0.00 3.68
3036 6703 6.070653 CCTGTAGTATAACCCACCACAAGTTA 60.071 42.308 0.00 0.00 0.00 2.24
3043 6710 2.307686 ACCCACCACAAGTTATAGGGTG 59.692 50.000 0.00 0.00 45.82 4.61
3047 6714 4.820894 ACCACAAGTTATAGGGTGAGTC 57.179 45.455 0.00 0.00 33.16 3.36
3169 6836 4.268884 GGAGTGCTAAAGCTAATGAAGTCG 59.731 45.833 3.26 0.00 42.66 4.18
3197 6864 9.593134 AATGACAAGTTATTCTCTAGTGATGTC 57.407 33.333 13.34 13.34 35.30 3.06
3218 6885 5.104776 TGTCTGGAGTGCTAAAGCTAATGAT 60.105 40.000 3.26 0.00 42.66 2.45
3281 6948 8.902540 TGCAATATGAAGTAATAACCGAATCT 57.097 30.769 0.00 0.00 0.00 2.40
3325 6992 8.822805 AGTCAGTACCCAAGAGATAAATTAACA 58.177 33.333 0.00 0.00 0.00 2.41
3326 6993 9.614792 GTCAGTACCCAAGAGATAAATTAACAT 57.385 33.333 0.00 0.00 0.00 2.71
3568 7257 8.375506 ACCTGAGTGAGATTAAACAGTTTGATA 58.624 33.333 8.93 0.00 0.00 2.15
3626 7315 4.643387 ACGTTCAGTGGCCAGCCC 62.643 66.667 5.11 0.00 34.56 5.19
3849 7538 8.860088 GCCTCCCATTATTTTTGTTATGATAGT 58.140 33.333 0.00 0.00 0.00 2.12
3863 7552 8.002984 TGTTATGATAGTGGTTGAGTTCGATA 57.997 34.615 0.00 0.00 0.00 2.92
4008 7697 9.689501 ACTTCTAGTGCTTTATCTAGAGTAACT 57.310 33.333 0.00 0.00 41.99 2.24
4195 7884 1.555075 TCAGTATTTGCTCGGCTTCCT 59.445 47.619 0.00 0.00 0.00 3.36
4258 7947 3.068881 CCGCCTCTTCTCCACCAA 58.931 61.111 0.00 0.00 0.00 3.67
4317 8006 2.100087 GACCTCGTCTTCCTCCATCTTC 59.900 54.545 0.00 0.00 0.00 2.87
4465 8154 3.710722 CCGCTGGCCTTCTCCACT 61.711 66.667 3.32 0.00 31.74 4.00
5184 10554 1.900498 GTTTCCAGGCAGCAGCAGT 60.900 57.895 2.65 0.00 44.61 4.40
5424 10794 3.842925 GACGGGCCACTGCTTTCCA 62.843 63.158 4.39 0.00 37.74 3.53
5537 12011 3.068881 CCGCCTCTTCTCCACCAA 58.931 61.111 0.00 0.00 0.00 3.67
5596 12070 2.100087 GACCTCGTCTTCCTCCATCTTC 59.900 54.545 0.00 0.00 0.00 2.87
5623 12097 0.396695 AATCTCCGCCCTAGAACCGA 60.397 55.000 0.00 0.00 0.00 4.69
5760 12234 3.375782 AGAGCAAGTTGATTTGGTTGC 57.624 42.857 7.16 0.00 44.60 4.17
5858 12332 6.627395 ACATCAAACGGTGAAACTTAATCA 57.373 33.333 0.00 0.00 40.50 2.57
6046 12520 5.787380 AGAATGCTTCAGTTTGGATTTTCC 58.213 37.500 0.00 0.00 36.96 3.13
6089 12563 4.407365 CACCCTTTGGAAACTATGGAACT 58.593 43.478 0.00 0.00 33.20 3.01
6208 12682 1.000145 GTAACTTGTAGCTGCTCGGC 59.000 55.000 4.91 0.00 0.00 5.54
6323 12797 4.997395 TGGTGTTCATTGACTTAGAGAAGC 59.003 41.667 0.00 0.00 35.97 3.86
6339 12813 5.632118 AGAGAAGCCCTACGATAAGATACA 58.368 41.667 0.00 0.00 0.00 2.29
6544 13018 2.026822 GGTGATGGATGAGGTCACAAGT 60.027 50.000 7.00 0.00 43.01 3.16
6696 13172 5.575995 GGCTTAGTAGAACTAAAACCGAGTG 59.424 44.000 1.55 0.00 39.89 3.51
6847 13332 3.684305 ACGTGAATCATCGAATCAAAGCA 59.316 39.130 11.02 0.00 0.00 3.91
6890 13375 2.666619 GCTTCTGGCATTCTTTGTGACG 60.667 50.000 0.00 0.00 41.35 4.35
6907 13392 0.387929 ACGAGAGAGTGCCACGAAAA 59.612 50.000 0.00 0.00 0.00 2.29
6931 13416 7.253905 ACTAAAAGGCAAGTTCTATAGGACA 57.746 36.000 13.81 0.00 0.00 4.02
7000 13486 1.603802 AGGCGACATGTTCAACAGTTG 59.396 47.619 6.99 6.99 0.00 3.16
7040 13526 1.352017 TGTTGAGATGGATGTGTGGCT 59.648 47.619 0.00 0.00 0.00 4.75
7120 13606 4.461781 CCAATTGAAGAGAAGCTTGTCCAT 59.538 41.667 19.26 9.40 36.83 3.41
7127 13613 3.055530 AGAGAAGCTTGTCCATCATCGTT 60.056 43.478 19.26 0.00 0.00 3.85
7149 13635 3.213506 TGAGATGGTTTGGGCATATTCG 58.786 45.455 0.00 0.00 0.00 3.34
7168 13655 4.399395 CGCAGGCCTCCAGAAGCA 62.399 66.667 0.00 0.00 0.00 3.91
7394 13881 0.539669 AGCCTACCCCAACTTGTTGC 60.540 55.000 7.89 0.00 0.00 4.17
7395 13882 1.532604 GCCTACCCCAACTTGTTGCC 61.533 60.000 7.89 0.00 0.00 4.52
7397 13884 1.247567 CTACCCCAACTTGTTGCCAG 58.752 55.000 7.89 2.03 0.00 4.85
7398 13885 0.847373 TACCCCAACTTGTTGCCAGA 59.153 50.000 7.89 0.00 0.00 3.86
7400 13887 0.389025 CCCCAACTTGTTGCCAGAAC 59.611 55.000 7.89 0.00 0.00 3.01
7401 13888 0.389025 CCCAACTTGTTGCCAGAACC 59.611 55.000 7.89 0.00 0.00 3.62
7402 13889 1.110442 CCAACTTGTTGCCAGAACCA 58.890 50.000 7.89 0.00 0.00 3.67
7403 13890 1.688197 CCAACTTGTTGCCAGAACCAT 59.312 47.619 7.89 0.00 0.00 3.55
7404 13891 2.546373 CCAACTTGTTGCCAGAACCATG 60.546 50.000 7.89 0.00 0.00 3.66
7405 13892 2.361757 CAACTTGTTGCCAGAACCATGA 59.638 45.455 0.00 0.00 0.00 3.07
7406 13893 2.233271 ACTTGTTGCCAGAACCATGAG 58.767 47.619 0.00 0.00 0.00 2.90
7408 13895 2.363306 TGTTGCCAGAACCATGAGTT 57.637 45.000 0.00 0.00 43.07 3.01
7409 13896 1.955778 TGTTGCCAGAACCATGAGTTG 59.044 47.619 0.00 0.00 39.40 3.16
7418 13905 3.231734 CCATGAGTTGGTTGCGAGA 57.768 52.632 0.00 0.00 40.99 4.04
7420 13907 1.667724 CCATGAGTTGGTTGCGAGATC 59.332 52.381 0.00 0.00 40.99 2.75
7423 13910 3.953712 TGAGTTGGTTGCGAGATCTTA 57.046 42.857 0.00 0.00 0.00 2.10
7424 13911 3.585862 TGAGTTGGTTGCGAGATCTTAC 58.414 45.455 0.00 0.00 0.00 2.34
7425 13912 2.599082 GAGTTGGTTGCGAGATCTTACG 59.401 50.000 0.00 0.00 0.00 3.18
7428 13915 1.274167 TGGTTGCGAGATCTTACGGTT 59.726 47.619 0.00 0.00 0.00 4.44
7429 13916 2.289195 TGGTTGCGAGATCTTACGGTTT 60.289 45.455 0.00 0.00 0.00 3.27
7430 13917 2.740447 GGTTGCGAGATCTTACGGTTTT 59.260 45.455 0.00 0.00 0.00 2.43
7431 13918 3.181523 GGTTGCGAGATCTTACGGTTTTC 60.182 47.826 0.00 0.00 0.00 2.29
7432 13919 3.306917 TGCGAGATCTTACGGTTTTCA 57.693 42.857 0.00 0.00 0.00 2.69
7433 13920 2.991190 TGCGAGATCTTACGGTTTTCAC 59.009 45.455 0.00 0.00 0.00 3.18
7434 13921 2.347755 GCGAGATCTTACGGTTTTCACC 59.652 50.000 0.00 0.00 40.16 4.02
7435 13922 3.846360 CGAGATCTTACGGTTTTCACCT 58.154 45.455 0.00 0.00 41.64 4.00
7436 13923 3.858238 CGAGATCTTACGGTTTTCACCTC 59.142 47.826 0.00 0.00 41.64 3.85
7437 13924 4.380655 CGAGATCTTACGGTTTTCACCTCT 60.381 45.833 0.00 0.00 41.64 3.69
7438 13925 5.163683 CGAGATCTTACGGTTTTCACCTCTA 60.164 44.000 0.00 0.00 41.64 2.43
7439 13926 6.210287 AGATCTTACGGTTTTCACCTCTAG 57.790 41.667 0.00 0.00 41.64 2.43
7440 13927 4.184079 TCTTACGGTTTTCACCTCTAGC 57.816 45.455 0.00 0.00 41.64 3.42
7441 13928 3.056322 TCTTACGGTTTTCACCTCTAGCC 60.056 47.826 0.00 0.00 41.64 3.93
7442 13929 0.323957 ACGGTTTTCACCTCTAGCCC 59.676 55.000 0.00 0.00 41.64 5.19
7443 13930 0.613777 CGGTTTTCACCTCTAGCCCT 59.386 55.000 0.00 0.00 41.64 5.19
7444 13931 1.003233 CGGTTTTCACCTCTAGCCCTT 59.997 52.381 0.00 0.00 41.64 3.95
7445 13932 2.712709 GGTTTTCACCTCTAGCCCTTC 58.287 52.381 0.00 0.00 40.44 3.46
7446 13933 2.618302 GGTTTTCACCTCTAGCCCTTCC 60.618 54.545 0.00 0.00 40.44 3.46
7447 13934 1.286248 TTTCACCTCTAGCCCTTCCC 58.714 55.000 0.00 0.00 0.00 3.97
7522 14021 3.798646 GCAATAAGCAGCAGCAACA 57.201 47.368 3.17 0.00 45.49 3.33
7527 14026 0.524414 TAAGCAGCAGCAACAGCATG 59.476 50.000 3.17 0.00 45.49 4.06
8079 14630 4.862823 CGGGAGGGGAGGGGAGAC 62.863 77.778 0.00 0.00 0.00 3.36
8105 14699 0.404426 GGGCCTGACCTAAAACACCT 59.596 55.000 0.84 0.00 39.10 4.00
8294 14889 2.105993 AGGATTAACTGGCCGATTACCC 59.894 50.000 0.00 3.60 0.00 3.69
8371 14966 5.957842 TGAGGAATTTGCGTTCACTAAAT 57.042 34.783 0.00 0.00 0.00 1.40
8372 14967 5.938322 TGAGGAATTTGCGTTCACTAAATC 58.062 37.500 0.00 0.00 0.00 2.17
8373 14968 5.471797 TGAGGAATTTGCGTTCACTAAATCA 59.528 36.000 0.00 0.00 0.00 2.57
8374 14969 6.150976 TGAGGAATTTGCGTTCACTAAATCAT 59.849 34.615 0.00 0.00 0.00 2.45
8375 14970 7.335673 TGAGGAATTTGCGTTCACTAAATCATA 59.664 33.333 0.00 0.00 0.00 2.15
8376 14971 8.050778 AGGAATTTGCGTTCACTAAATCATAA 57.949 30.769 0.00 0.00 0.00 1.90
8377 14972 8.184192 AGGAATTTGCGTTCACTAAATCATAAG 58.816 33.333 0.00 0.00 0.00 1.73
8483 15078 8.898761 TCACACACTTTCTTTTCTTGCTTATAA 58.101 29.630 0.00 0.00 0.00 0.98
8484 15079 9.173939 CACACACTTTCTTTTCTTGCTTATAAG 57.826 33.333 8.20 8.20 0.00 1.73
8485 15080 8.903820 ACACACTTTCTTTTCTTGCTTATAAGT 58.096 29.630 13.91 0.00 0.00 2.24
8591 15188 6.000219 TCTTGTACGTCAGGGTAGTATATCC 59.000 44.000 0.00 0.00 44.30 2.59
8610 15207 7.716799 ATATCCTAGATCTAGAGGTTGCAAG 57.283 40.000 28.04 10.24 35.21 4.01
8662 15274 6.760298 TGTTAGGTGTGTAATTTCGTGTGTAA 59.240 34.615 0.00 0.00 0.00 2.41
8679 15291 5.766174 GTGTGTAAAGGTGATAAGAAACCCA 59.234 40.000 0.00 0.00 37.13 4.51
8703 15315 3.081804 GGGCAGCTTAGTTAACATGTGT 58.918 45.455 8.61 0.00 0.00 3.72
8707 15319 5.048713 GGCAGCTTAGTTAACATGTGTTCTT 60.049 40.000 8.61 0.00 39.31 2.52
8899 15518 6.467723 ACATGAAGTCGTGTTTTGTCTATC 57.532 37.500 0.00 0.00 43.01 2.08
8981 15600 5.342361 AGGGGAATAGGTAGAGAAGTAGG 57.658 47.826 0.00 0.00 0.00 3.18
9033 15658 3.433274 ACATAGACAAACGAGTGTGCATG 59.567 43.478 0.00 6.37 0.00 4.06
9047 15672 4.821260 AGTGTGCATGTTGTTGTTCAGATA 59.179 37.500 0.00 0.00 0.00 1.98
9086 15713 8.233868 CGGAATAATATTTGTGACAAAGTGACA 58.766 33.333 16.43 1.36 0.00 3.58
9209 15836 7.230747 TCCTCTAATCATGTTTTGTTTCCTCA 58.769 34.615 0.00 0.00 0.00 3.86
9225 15852 6.716628 TGTTTCCTCAGAATCTGCAAGTAATT 59.283 34.615 5.18 0.00 33.76 1.40
9240 15867 6.607689 GCAAGTAATTGCATTGTGTAGTGTA 58.392 36.000 22.11 0.00 46.60 2.90
9241 15868 7.081349 GCAAGTAATTGCATTGTGTAGTGTAA 58.919 34.615 22.11 0.00 46.60 2.41
9242 15869 7.754924 GCAAGTAATTGCATTGTGTAGTGTAAT 59.245 33.333 22.11 0.00 46.60 1.89
9243 15870 9.064804 CAAGTAATTGCATTGTGTAGTGTAATG 57.935 33.333 0.00 0.00 32.26 1.90
9244 15871 7.761409 AGTAATTGCATTGTGTAGTGTAATGG 58.239 34.615 0.00 0.00 32.26 3.16
9245 15872 6.588719 AATTGCATTGTGTAGTGTAATGGT 57.411 33.333 0.00 0.00 32.26 3.55
9246 15873 7.695480 AATTGCATTGTGTAGTGTAATGGTA 57.305 32.000 0.00 0.00 32.26 3.25
9247 15874 6.489127 TTGCATTGTGTAGTGTAATGGTAC 57.511 37.500 0.00 0.00 33.54 3.34
9574 16202 4.097286 TGCTAGGGTATTTCGGCAAAAATC 59.903 41.667 0.00 0.00 31.50 2.17
9814 16442 1.303282 GGTAGGAAGGTTGGCCTGG 59.697 63.158 3.32 0.00 46.33 4.45
9815 16443 1.303282 GTAGGAAGGTTGGCCTGGG 59.697 63.158 3.32 0.00 46.33 4.45
9816 16444 2.612493 TAGGAAGGTTGGCCTGGGC 61.612 63.158 14.23 14.23 46.33 5.36
9818 16446 2.118294 GAAGGTTGGCCTGGGCTT 59.882 61.111 21.72 7.00 46.33 4.35
9819 16447 1.979155 GAAGGTTGGCCTGGGCTTC 60.979 63.158 21.72 12.46 46.33 3.86
9820 16448 3.868200 AAGGTTGGCCTGGGCTTCG 62.868 63.158 21.72 0.00 46.33 3.79
9825 16453 4.176752 GGCCTGGGCTTCGGGTAG 62.177 72.222 13.80 0.00 43.94 3.18
9826 16454 4.858680 GCCTGGGCTTCGGGTAGC 62.859 72.222 4.12 0.00 43.94 3.58
9856 19342 3.036075 TGAGAGCTTGTGTCATGTCAG 57.964 47.619 0.00 0.00 0.00 3.51
9866 19352 5.929697 TGTGTCATGTCAGAGTGAAATTC 57.070 39.130 0.00 0.00 0.00 2.17
9918 19404 6.148811 TGTCGTTGACAAAGAAAGAAAGAAGT 59.851 34.615 5.34 0.00 39.78 3.01
9926 19412 7.475840 ACAAAGAAAGAAAGAAGTAGCAGTTG 58.524 34.615 0.00 0.00 0.00 3.16
9927 19413 6.625873 AAGAAAGAAAGAAGTAGCAGTTGG 57.374 37.500 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 7.658982 CAGAATATGCACATACCTAATGACAGT 59.341 37.037 0.00 0.00 39.07 3.55
97 100 6.584488 ACCCAAAACTACATTTTTAACCCAC 58.416 36.000 0.00 0.00 38.50 4.61
180 184 4.422073 TGGATTTCAATACGAGCATCCT 57.578 40.909 0.00 0.00 36.71 3.24
183 187 6.698008 TTCAATGGATTTCAATACGAGCAT 57.302 33.333 0.00 0.00 0.00 3.79
206 210 2.139917 TGAGAGCGCGTACAAACAAAT 58.860 42.857 8.43 0.00 0.00 2.32
210 214 2.875080 AAATGAGAGCGCGTACAAAC 57.125 45.000 8.43 0.00 0.00 2.93
276 371 9.619316 GTGATATGTTAGTCTCTGTGATCATAC 57.381 37.037 0.00 0.00 0.00 2.39
345 440 1.026182 GTTGGCCAGCGATGACATGA 61.026 55.000 5.11 0.00 0.00 3.07
372 930 5.576447 ATTATTGTCCGTGATTTCAACCC 57.424 39.130 0.00 0.00 0.00 4.11
403 961 4.880696 GCAACAGATATTTCAAGCTCCTCT 59.119 41.667 0.00 0.00 0.00 3.69
418 3785 5.215903 CGTGTATTATCTCTCGCAACAGAT 58.784 41.667 0.00 0.00 33.75 2.90
449 3818 4.321718 GTGGTTAGGAGTGTTAGGGTTTC 58.678 47.826 0.00 0.00 0.00 2.78
537 4028 0.920763 TGTGGAGGAAGCCCATGGAT 60.921 55.000 15.22 0.00 35.91 3.41
563 4054 0.319555 TGAAGTGGTAGCAGACACGC 60.320 55.000 0.00 0.00 42.25 5.34
759 4405 8.893219 AATTGAATAATCGATTCTCAGCACTA 57.107 30.769 15.25 4.25 43.90 2.74
1505 5157 4.342862 TGGACTCTCTCTTGAAAGTTGG 57.657 45.455 0.00 0.00 0.00 3.77
1593 5245 5.048013 CCCAATTTAGAGGTTTGGTTCTGAC 60.048 44.000 0.00 0.00 38.58 3.51
1632 5284 7.255242 CCGGACAGCAATGATAACAAATATTCT 60.255 37.037 0.00 0.00 0.00 2.40
1673 5325 0.694771 ACTGATTGCCAGCTCCAAGA 59.305 50.000 3.10 0.00 46.81 3.02
1881 5533 4.437239 GACTTCACCGACTCATCATCAAT 58.563 43.478 0.00 0.00 0.00 2.57
2288 5948 4.439289 GCATGTGCCAATAGTTCTTCCTTC 60.439 45.833 0.00 0.00 34.31 3.46
2300 5960 0.961019 AAACTCGTGCATGTGCCAAT 59.039 45.000 5.68 0.00 41.18 3.16
2587 6254 0.464036 AGAGACGTGGCTTGTGTCAA 59.536 50.000 0.00 0.00 35.09 3.18
2688 6355 7.309438 GGGCATAATTCCTAAAATCTCCATCAC 60.309 40.741 0.00 0.00 0.00 3.06
2764 6431 4.098960 TCCCACGATCCTACAACAATAGTC 59.901 45.833 0.00 0.00 0.00 2.59
2832 6499 4.498345 GCTAGATCTAGGTGGTCGAACAAG 60.498 50.000 27.21 0.00 33.87 3.16
2897 6564 7.045416 ACATACAAATTTATCGTGGAGCTACA 58.955 34.615 0.00 0.00 0.00 2.74
3134 6801 5.355350 GCTTTAGCACTCCAAACATCACTAT 59.645 40.000 0.00 0.00 41.59 2.12
3169 6836 7.834068 TCACTAGAGAATAACTTGTCATTGC 57.166 36.000 0.00 0.00 0.00 3.56
3197 6864 6.690194 AAATCATTAGCTTTAGCACTCCAG 57.310 37.500 4.33 0.00 45.16 3.86
3281 6948 7.333528 ACTGACTTGCAATTCAACTAAAAGA 57.666 32.000 18.71 0.00 0.00 2.52
3288 6955 3.568007 TGGGTACTGACTTGCAATTCAAC 59.432 43.478 18.71 14.72 0.00 3.18
3325 6992 8.478877 CCTACTCTTAATCAGTTGGTTAGTGAT 58.521 37.037 6.90 0.00 46.60 3.06
3326 6993 7.578955 GCCTACTCTTAATCAGTTGGTTAGTGA 60.579 40.741 13.28 0.00 38.58 3.41
3374 7058 5.983118 CCATACTAGCACGATCAACAATACA 59.017 40.000 0.00 0.00 0.00 2.29
3568 7257 7.770897 GTGAATTTCCCATCAGAGTATAAGTGT 59.229 37.037 0.00 0.00 0.00 3.55
3626 7315 6.528423 CGTAACATCTACTTCCTCTGTTCTTG 59.472 42.308 0.00 0.00 32.66 3.02
3839 7528 7.115095 GCTATCGAACTCAACCACTATCATAAC 59.885 40.741 0.00 0.00 0.00 1.89
3849 7538 3.447229 TCATCAGCTATCGAACTCAACCA 59.553 43.478 0.00 0.00 0.00 3.67
3863 7552 5.470437 CAGTGCAGAATTATCATCATCAGCT 59.530 40.000 0.00 0.00 0.00 4.24
4008 7697 5.995282 CCTAATATGCCGGTCATAACAGAAA 59.005 40.000 18.34 1.54 40.73 2.52
4195 7884 1.688187 GGTCTCCCGGCTCCCTAAA 60.688 63.158 0.00 0.00 0.00 1.85
4291 7980 0.392729 GAGGAAGACGAGGTCGAGGA 60.393 60.000 6.35 0.00 43.02 3.71
4317 8006 0.327576 AGGGTGGAGATTGTAGGGGG 60.328 60.000 0.00 0.00 0.00 5.40
4581 8270 1.000019 AGATCGTTGAGGACCCCGA 60.000 57.895 0.00 0.00 0.00 5.14
5424 10794 2.591715 GTGCACAGGTGGTTCGCT 60.592 61.111 13.17 0.00 0.00 4.93
5428 10798 2.515991 CGGTGTGCACAGGTGGTT 60.516 61.111 22.40 0.00 0.00 3.67
5537 12011 4.148825 CTAGGCGCCGTCCTTGCT 62.149 66.667 23.20 2.71 37.66 3.91
5596 12070 2.819284 GGGCGGAGATTGTAGGGGG 61.819 68.421 0.00 0.00 0.00 5.40
5623 12097 2.832733 GTGTTAGGAGCTAGGGTTCTGT 59.167 50.000 0.00 0.00 0.00 3.41
5735 12209 3.953612 ACCAAATCAACTTGCTCTTCACA 59.046 39.130 0.00 0.00 0.00 3.58
5738 12212 3.737774 GCAACCAAATCAACTTGCTCTTC 59.262 43.478 0.00 0.00 36.81 2.87
5760 12234 3.461061 TCACTCAGCTTTTGTCACTCAG 58.539 45.455 0.00 0.00 0.00 3.35
5974 12448 2.676839 GCATCTCCATCATATTCCGCAG 59.323 50.000 0.00 0.00 0.00 5.18
6046 12520 4.396166 GTGGTTCATCATTGGAAGGTACAG 59.604 45.833 0.00 0.00 0.00 2.74
6089 12563 8.715191 AATACAACTTTGAAAAACATGAAGCA 57.285 26.923 0.00 0.00 0.00 3.91
6208 12682 2.182516 AATCCCTACTCCTCACCTGG 57.817 55.000 0.00 0.00 0.00 4.45
6268 12742 9.232882 AGGTCCTAATTAACCTACCAATGAATA 57.767 33.333 7.02 0.00 44.12 1.75
6323 12797 3.079578 TCCGCTGTATCTTATCGTAGGG 58.920 50.000 0.00 0.00 0.00 3.53
6339 12813 0.677731 CCACCACATGACATTCCGCT 60.678 55.000 0.00 0.00 0.00 5.52
6544 13018 7.126268 CACCATGGGATATCTCCTTGTATATCA 59.874 40.741 18.09 0.00 41.74 2.15
6847 13332 1.153086 GCGCCACTTCATCCATCCT 60.153 57.895 0.00 0.00 0.00 3.24
6890 13375 2.156343 AGTTTTCGTGGCACTCTCTC 57.844 50.000 16.72 3.67 0.00 3.20
6907 13392 7.253905 TGTCCTATAGAACTTGCCTTTTAGT 57.746 36.000 0.00 0.00 0.00 2.24
7040 13526 1.891150 GACTCGGTCCTTCCTTGTGTA 59.109 52.381 0.00 0.00 0.00 2.90
7120 13606 3.081061 CCCAAACCATCTCAAACGATGA 58.919 45.455 2.57 0.00 42.63 2.92
7127 13613 3.631686 CGAATATGCCCAAACCATCTCAA 59.368 43.478 0.00 0.00 0.00 3.02
7168 13655 2.184322 CGTCCGCTATGCACTGGT 59.816 61.111 0.00 0.00 0.00 4.00
7401 13888 2.625737 AGATCTCGCAACCAACTCATG 58.374 47.619 0.00 0.00 0.00 3.07
7402 13889 3.340814 AAGATCTCGCAACCAACTCAT 57.659 42.857 0.00 0.00 0.00 2.90
7403 13890 2.839486 AAGATCTCGCAACCAACTCA 57.161 45.000 0.00 0.00 0.00 3.41
7404 13891 2.599082 CGTAAGATCTCGCAACCAACTC 59.401 50.000 0.00 0.00 43.02 3.01
7405 13892 2.607187 CGTAAGATCTCGCAACCAACT 58.393 47.619 0.00 0.00 43.02 3.16
7406 13893 1.659098 CCGTAAGATCTCGCAACCAAC 59.341 52.381 0.00 0.00 43.02 3.77
7408 13895 0.892755 ACCGTAAGATCTCGCAACCA 59.107 50.000 0.00 0.00 43.02 3.67
7409 13896 2.005971 AACCGTAAGATCTCGCAACC 57.994 50.000 0.00 0.00 43.02 3.77
7410 13897 3.430895 TGAAAACCGTAAGATCTCGCAAC 59.569 43.478 0.00 0.00 43.02 4.17
7411 13898 3.430895 GTGAAAACCGTAAGATCTCGCAA 59.569 43.478 0.00 0.00 43.02 4.85
7413 13900 2.347755 GGTGAAAACCGTAAGATCTCGC 59.652 50.000 0.00 0.00 43.02 5.03
7414 13901 3.846360 AGGTGAAAACCGTAAGATCTCG 58.154 45.455 0.00 0.00 43.02 4.04
7415 13902 5.074584 AGAGGTGAAAACCGTAAGATCTC 57.925 43.478 0.00 0.00 43.02 2.75
7416 13903 5.394333 GCTAGAGGTGAAAACCGTAAGATCT 60.394 44.000 0.00 0.00 43.02 2.75
7418 13905 4.382793 GGCTAGAGGTGAAAACCGTAAGAT 60.383 45.833 0.00 0.00 43.02 2.40
7420 13907 3.259902 GGCTAGAGGTGAAAACCGTAAG 58.740 50.000 0.00 0.00 34.28 2.34
7423 13910 0.323957 GGGCTAGAGGTGAAAACCGT 59.676 55.000 0.00 0.00 34.28 4.83
7424 13911 0.613777 AGGGCTAGAGGTGAAAACCG 59.386 55.000 0.00 0.00 34.28 4.44
7425 13912 2.618302 GGAAGGGCTAGAGGTGAAAACC 60.618 54.545 0.00 0.00 0.00 3.27
7428 13915 1.286248 GGGAAGGGCTAGAGGTGAAA 58.714 55.000 0.00 0.00 0.00 2.69
7429 13916 0.620700 GGGGAAGGGCTAGAGGTGAA 60.621 60.000 0.00 0.00 0.00 3.18
7430 13917 1.003051 GGGGAAGGGCTAGAGGTGA 59.997 63.158 0.00 0.00 0.00 4.02
7431 13918 0.264955 TAGGGGAAGGGCTAGAGGTG 59.735 60.000 0.00 0.00 0.00 4.00
7432 13919 1.256010 ATAGGGGAAGGGCTAGAGGT 58.744 55.000 0.00 0.00 0.00 3.85
7433 13920 3.786213 ATATAGGGGAAGGGCTAGAGG 57.214 52.381 0.00 0.00 0.00 3.69
7434 13921 6.288096 AGATATATAGGGGAAGGGCTAGAG 57.712 45.833 0.00 0.00 0.00 2.43
7435 13922 6.692363 AAGATATATAGGGGAAGGGCTAGA 57.308 41.667 0.00 0.00 0.00 2.43
7436 13923 6.495526 GCTAAGATATATAGGGGAAGGGCTAG 59.504 46.154 0.00 0.00 0.00 3.42
7437 13924 6.164223 AGCTAAGATATATAGGGGAAGGGCTA 59.836 42.308 0.00 0.00 0.00 3.93
7438 13925 5.042218 AGCTAAGATATATAGGGGAAGGGCT 60.042 44.000 0.00 0.00 0.00 5.19
7439 13926 5.220521 AGCTAAGATATATAGGGGAAGGGC 58.779 45.833 0.00 0.00 0.00 5.19
7440 13927 7.363031 TGTAGCTAAGATATATAGGGGAAGGG 58.637 42.308 0.00 0.00 0.00 3.95
7520 14019 3.452264 TCCTGCTCTGTATTACATGCTGT 59.548 43.478 17.13 0.00 31.73 4.40
7521 14020 4.056740 CTCCTGCTCTGTATTACATGCTG 58.943 47.826 17.13 16.21 31.73 4.41
7522 14021 3.494048 GCTCCTGCTCTGTATTACATGCT 60.494 47.826 17.13 0.00 36.03 3.79
7527 14026 3.861840 TGTTGCTCCTGCTCTGTATTAC 58.138 45.455 0.00 0.00 40.48 1.89
7947 14469 2.364317 CCGAGCCTCTTCCTCCCA 60.364 66.667 0.00 0.00 0.00 4.37
7972 14494 1.376466 GCCTGCACTCCTCAAGGAA 59.624 57.895 0.00 0.00 44.91 3.36
8034 14585 0.617413 CTCATTGGAGGAGGCTGTGT 59.383 55.000 0.00 0.00 37.51 3.72
8079 14630 1.573108 TTAGGTCAGGCCCTTCTCAG 58.427 55.000 0.00 0.00 38.26 3.35
8105 14699 3.611358 TCCCTCCTTTACCCCAAAACTA 58.389 45.455 0.00 0.00 0.00 2.24
8154 14749 6.435904 CCGATTAACTGAATAGAGGGAGAGAT 59.564 42.308 0.00 0.00 0.00 2.75
8591 15188 3.244044 GGCCTTGCAACCTCTAGATCTAG 60.244 52.174 21.81 21.81 34.56 2.43
8597 15194 1.474143 GCTAGGCCTTGCAACCTCTAG 60.474 57.143 30.78 10.70 37.50 2.43
8626 15223 5.499139 ACACACCTAACAAAACTGATGTG 57.501 39.130 0.00 0.00 41.49 3.21
8662 15274 3.371595 CCCGATGGGTTTCTTATCACCTT 60.372 47.826 0.00 0.00 38.25 3.50
8679 15291 3.206150 CATGTTAACTAAGCTGCCCGAT 58.794 45.455 7.22 0.00 0.00 4.18
8703 15315 4.163458 CACCCTACCCAGCATAACTAAGAA 59.837 45.833 0.00 0.00 0.00 2.52
8707 15319 3.305720 CTCACCCTACCCAGCATAACTA 58.694 50.000 0.00 0.00 0.00 2.24
8981 15600 7.040686 AGTGTACCACAATTTGATGGAACTTAC 60.041 37.037 18.73 12.91 39.46 2.34
9047 15672 9.314321 CAAATATTATTCCGACTGTACAGAAGT 57.686 33.333 29.30 8.00 0.00 3.01
9225 15852 5.552178 TGTACCATTACACTACACAATGCA 58.448 37.500 0.00 0.00 32.98 3.96
9243 15870 2.353323 GGTCCAAATTCGGTCTGTACC 58.647 52.381 0.00 0.00 42.95 3.34
9244 15871 1.997606 CGGTCCAAATTCGGTCTGTAC 59.002 52.381 0.00 0.00 0.00 2.90
9245 15872 1.673626 GCGGTCCAAATTCGGTCTGTA 60.674 52.381 0.00 0.00 0.00 2.74
9246 15873 0.953960 GCGGTCCAAATTCGGTCTGT 60.954 55.000 0.00 0.00 0.00 3.41
9247 15874 1.644786 GGCGGTCCAAATTCGGTCTG 61.645 60.000 0.00 0.00 0.00 3.51
9409 16036 2.677836 CAATCGGGAATGTTGACGTGAT 59.322 45.455 0.00 0.00 0.00 3.06
9574 16202 3.272334 GAATAGGCGGTGGCGCAG 61.272 66.667 10.83 0.00 41.24 5.18
9815 16443 1.134491 ACAATACAGGCTACCCGAAGC 60.134 52.381 0.00 0.00 41.99 3.86
9816 16444 2.936498 CAACAATACAGGCTACCCGAAG 59.064 50.000 0.00 0.00 35.76 3.79
9818 16446 2.167693 CTCAACAATACAGGCTACCCGA 59.832 50.000 0.00 0.00 35.76 5.14
9819 16447 2.167693 TCTCAACAATACAGGCTACCCG 59.832 50.000 0.00 0.00 35.76 5.28
9820 16448 3.798202 CTCTCAACAATACAGGCTACCC 58.202 50.000 0.00 0.00 0.00 3.69
9822 16450 4.130286 AGCTCTCAACAATACAGGCTAC 57.870 45.455 0.00 0.00 0.00 3.58
9825 16453 3.077359 ACAAGCTCTCAACAATACAGGC 58.923 45.455 0.00 0.00 0.00 4.85
9826 16454 4.067896 ACACAAGCTCTCAACAATACAGG 58.932 43.478 0.00 0.00 0.00 4.00
9856 19342 2.229543 TGCAGGCACATGAATTTCACTC 59.770 45.455 0.00 0.00 0.00 3.51
9866 19352 0.038892 GACAACCTTGCAGGCACATG 60.039 55.000 0.00 0.00 39.63 3.21
9926 19412 1.900498 AAACAGACAGCAGCTGCCC 60.900 57.895 34.39 22.92 43.38 5.36
9927 19413 1.285023 CAAACAGACAGCAGCTGCC 59.715 57.895 34.39 19.70 43.38 4.85



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

AutoCloner maintained by Alex Coulton.