Multiple sequence alignment - TraesCS2D01G027600

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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 TraesCS2D01G027600 chr2D 100.000 4524 0 0 1 4524 11463479 11458956 0.000000e+00 8355.0
1 TraesCS2D01G027600 chr2D 89.372 828 61 13 2406 3219 11433064 11432250 0.000000e+00 1016.0
2 TraesCS2D01G027600 chr2D 85.378 595 76 7 971 1564 11522923 11522339 1.390000e-169 606.0
3 TraesCS2D01G027600 chr2D 78.223 923 149 40 2635 3531 11783621 11784517 1.110000e-150 544.0
4 TraesCS2D01G027600 chr2D 76.577 888 186 15 2657 3531 11628180 11627302 6.850000e-128 468.0
5 TraesCS2D01G027600 chr2D 91.489 329 27 1 3206 3534 11431751 11431424 6.900000e-123 451.0
6 TraesCS2D01G027600 chr2D 92.715 302 17 5 2494 2795 11423165 11422869 8.990000e-117 431.0
7 TraesCS2D01G027600 chr2D 84.915 411 45 7 466 865 235597423 235597827 2.540000e-107 399.0
8 TraesCS2D01G027600 chr2D 81.288 326 23 18 3539 3852 11422867 11422568 3.520000e-56 230.0
9 TraesCS2D01G027600 chrUn 92.297 2090 122 17 2134 4190 276512855 276510772 0.000000e+00 2931.0
10 TraesCS2D01G027600 chrUn 96.556 726 22 3 1412 2135 276513926 276513202 0.000000e+00 1199.0
11 TraesCS2D01G027600 chrUn 94.426 305 0 4 865 1167 270144958 270145247 1.920000e-123 453.0
12 TraesCS2D01G027600 chrUn 80.791 531 88 10 2601 3126 331371228 331370707 1.960000e-108 403.0
13 TraesCS2D01G027600 chrUn 94.444 198 11 0 4327 4524 276510780 276510583 5.690000e-79 305.0
14 TraesCS2D01G027600 chrUn 90.854 164 10 5 2114 2274 81477800 81477639 9.860000e-52 215.0
15 TraesCS2D01G027600 chr2A 92.046 1823 107 16 2134 3924 12035669 12033853 0.000000e+00 2529.0
16 TraesCS2D01G027600 chr2A 96.556 726 22 3 1412 2135 12036740 12036016 0.000000e+00 1199.0
17 TraesCS2D01G027600 chr2A 89.412 595 57 5 2627 3219 12026518 12025928 0.000000e+00 745.0
18 TraesCS2D01G027600 chr2A 84.848 594 77 9 973 1564 12141638 12141056 1.810000e-163 586.0
19 TraesCS2D01G027600 chr2A 89.103 468 43 6 3237 3701 12023066 12022604 3.920000e-160 575.0
20 TraesCS2D01G027600 chr2A 81.805 709 108 14 2829 3525 12290330 12289631 3.920000e-160 575.0
21 TraesCS2D01G027600 chr2A 84.291 592 81 8 974 1564 12131626 12131046 6.570000e-158 568.0
22 TraesCS2D01G027600 chr2A 92.401 329 25 0 3206 3534 12025535 12025207 1.910000e-128 470.0
23 TraesCS2D01G027600 chr2A 94.426 305 0 4 865 1167 12037957 12037668 1.920000e-123 453.0
24 TraesCS2D01G027600 chr2A 82.308 520 74 13 1013 1529 12291432 12290928 6.950000e-118 435.0
25 TraesCS2D01G027600 chr2A 81.696 519 76 15 1013 1529 12249910 12249409 9.050000e-112 414.0
26 TraesCS2D01G027600 chr2A 94.798 173 7 1 2406 2576 12026698 12026526 7.460000e-68 268.0
27 TraesCS2D01G027600 chr7D 97.238 869 23 1 1 868 309153710 309154578 0.000000e+00 1471.0
28 TraesCS2D01G027600 chr7D 87.156 545 33 23 3282 3821 430993670 430993158 6.520000e-163 584.0
29 TraesCS2D01G027600 chr7D 83.403 476 61 8 402 865 5278757 5279226 4.180000e-115 425.0
30 TraesCS2D01G027600 chr7D 91.358 162 12 2 2115 2274 566026736 566026575 2.120000e-53 220.0
31 TraesCS2D01G027600 chr7D 83.333 102 13 3 4335 4434 504829150 504829051 1.730000e-14 91.6
32 TraesCS2D01G027600 chr6D 96.770 867 24 2 1 864 17302848 17303713 0.000000e+00 1443.0
33 TraesCS2D01G027600 chr2B 86.808 1228 114 28 2337 3531 17836997 17835785 0.000000e+00 1327.0
34 TraesCS2D01G027600 chr2B 87.145 809 53 25 980 1788 17838158 17837401 0.000000e+00 870.0
35 TraesCS2D01G027600 chr2B 84.014 882 93 16 6 865 784910890 784910035 0.000000e+00 804.0
36 TraesCS2D01G027600 chr2B 85.690 594 77 6 971 1563 17899658 17899072 1.790000e-173 619.0
37 TraesCS2D01G027600 chr2B 82.270 705 100 18 2834 3525 18176189 18176881 1.810000e-163 586.0
38 TraesCS2D01G027600 chr2B 90.649 385 25 5 3284 3658 17827075 17826692 6.760000e-138 501.0
39 TraesCS2D01G027600 chr2B 83.301 521 73 12 1013 1529 18175070 18175580 6.850000e-128 468.0
40 TraesCS2D01G027600 chr2B 93.262 282 10 4 3678 3954 17869060 17868783 1.520000e-109 407.0
41 TraesCS2D01G027600 chr2B 84.595 383 29 9 2454 2825 17827452 17827089 2.000000e-93 353.0
42 TraesCS2D01G027600 chr2B 85.926 270 28 5 11 279 462936483 462936223 3.450000e-71 279.0
43 TraesCS2D01G027600 chr2B 92.350 183 12 1 1863 2045 17837399 17837219 4.490000e-65 259.0
44 TraesCS2D01G027600 chr2B 93.130 131 9 0 4320 4450 17868784 17868654 4.620000e-45 193.0
45 TraesCS2D01G027600 chr2B 91.892 74 6 0 4449 4522 17868495 17868422 2.230000e-18 104.0
46 TraesCS2D01G027600 chr6A 93.529 850 45 6 29 876 490390562 490389721 0.000000e+00 1256.0
47 TraesCS2D01G027600 chr1B 92.000 875 54 3 1 864 12573474 12572605 0.000000e+00 1214.0
48 TraesCS2D01G027600 chr7B 85.528 767 81 17 121 868 351006551 351005796 0.000000e+00 774.0
49 TraesCS2D01G027600 chr5D 86.296 540 56 16 3285 3821 526715211 526714687 5.080000e-159 571.0
50 TraesCS2D01G027600 chr4A 87.448 478 46 6 402 867 600385842 600386317 5.150000e-149 538.0
51 TraesCS2D01G027600 chr3D 83.208 530 62 17 1000 1529 564919126 564919628 1.150000e-125 460.0
52 TraesCS2D01G027600 chr3D 89.820 167 13 3 2111 2275 563861158 563861322 1.280000e-50 211.0
53 TraesCS2D01G027600 chr3B 82.863 531 62 18 1000 1529 752439355 752439857 2.480000e-122 449.0
54 TraesCS2D01G027600 chr1A 81.888 519 72 14 1013 1529 12355217 12355715 7.000000e-113 418.0
55 TraesCS2D01G027600 chr6B 85.159 283 27 8 1 279 234684318 234684589 4.460000e-70 276.0
56 TraesCS2D01G027600 chr4D 91.463 164 12 2 2114 2275 75266910 75266747 1.640000e-54 224.0
57 TraesCS2D01G027600 chr5B 90.854 164 13 2 2113 2274 194184983 194185146 7.620000e-53 219.0
58 TraesCS2D01G027600 chr5A 90.854 164 13 2 2115 2276 653299601 653299438 7.620000e-53 219.0
59 TraesCS2D01G027600 chr5A 90.303 165 13 2 2113 2274 371028324 371028488 3.550000e-51 213.0
60 TraesCS2D01G027600 chr7A 81.754 285 25 13 6 280 445220197 445220464 3.550000e-51 213.0
61 TraesCS2D01G027600 chr7A 82.353 102 14 3 4335 4434 572491504 572491405 8.060000e-13 86.1


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 TraesCS2D01G027600 chr2D 11458956 11463479 4523 True 8355.000000 8355 100.000000 1 4524 1 chr2D.!!$R1 4523
1 TraesCS2D01G027600 chr2D 11431424 11433064 1640 True 733.500000 1016 90.430500 2406 3534 2 chr2D.!!$R5 1128
2 TraesCS2D01G027600 chr2D 11522339 11522923 584 True 606.000000 606 85.378000 971 1564 1 chr2D.!!$R2 593
3 TraesCS2D01G027600 chr2D 11783621 11784517 896 False 544.000000 544 78.223000 2635 3531 1 chr2D.!!$F1 896
4 TraesCS2D01G027600 chr2D 11627302 11628180 878 True 468.000000 468 76.577000 2657 3531 1 chr2D.!!$R3 874
5 TraesCS2D01G027600 chr2D 11422568 11423165 597 True 330.500000 431 87.001500 2494 3852 2 chr2D.!!$R4 1358
6 TraesCS2D01G027600 chrUn 276510583 276513926 3343 True 1478.333333 2931 94.432333 1412 4524 3 chrUn.!!$R3 3112
7 TraesCS2D01G027600 chrUn 331370707 331371228 521 True 403.000000 403 80.791000 2601 3126 1 chrUn.!!$R2 525
8 TraesCS2D01G027600 chr2A 12033853 12037957 4104 True 1393.666667 2529 94.342667 865 3924 3 chr2A.!!$R5 3059
9 TraesCS2D01G027600 chr2A 12141056 12141638 582 True 586.000000 586 84.848000 973 1564 1 chr2A.!!$R2 591
10 TraesCS2D01G027600 chr2A 12131046 12131626 580 True 568.000000 568 84.291000 974 1564 1 chr2A.!!$R1 590
11 TraesCS2D01G027600 chr2A 12022604 12026698 4094 True 514.500000 745 91.428500 2406 3701 4 chr2A.!!$R4 1295
12 TraesCS2D01G027600 chr2A 12289631 12291432 1801 True 505.000000 575 82.056500 1013 3525 2 chr2A.!!$R6 2512
13 TraesCS2D01G027600 chr2A 12249409 12249910 501 True 414.000000 414 81.696000 1013 1529 1 chr2A.!!$R3 516
14 TraesCS2D01G027600 chr7D 309153710 309154578 868 False 1471.000000 1471 97.238000 1 868 1 chr7D.!!$F2 867
15 TraesCS2D01G027600 chr7D 430993158 430993670 512 True 584.000000 584 87.156000 3282 3821 1 chr7D.!!$R1 539
16 TraesCS2D01G027600 chr6D 17302848 17303713 865 False 1443.000000 1443 96.770000 1 864 1 chr6D.!!$F1 863
17 TraesCS2D01G027600 chr2B 17835785 17838158 2373 True 818.666667 1327 88.767667 980 3531 3 chr2B.!!$R5 2551
18 TraesCS2D01G027600 chr2B 784910035 784910890 855 True 804.000000 804 84.014000 6 865 1 chr2B.!!$R3 859
19 TraesCS2D01G027600 chr2B 17899072 17899658 586 True 619.000000 619 85.690000 971 1563 1 chr2B.!!$R1 592
20 TraesCS2D01G027600 chr2B 18175070 18176881 1811 False 527.000000 586 82.785500 1013 3525 2 chr2B.!!$F1 2512
21 TraesCS2D01G027600 chr2B 17826692 17827452 760 True 427.000000 501 87.622000 2454 3658 2 chr2B.!!$R4 1204
22 TraesCS2D01G027600 chr2B 17868422 17869060 638 True 234.666667 407 92.761333 3678 4522 3 chr2B.!!$R6 844
23 TraesCS2D01G027600 chr6A 490389721 490390562 841 True 1256.000000 1256 93.529000 29 876 1 chr6A.!!$R1 847
24 TraesCS2D01G027600 chr1B 12572605 12573474 869 True 1214.000000 1214 92.000000 1 864 1 chr1B.!!$R1 863
25 TraesCS2D01G027600 chr7B 351005796 351006551 755 True 774.000000 774 85.528000 121 868 1 chr7B.!!$R1 747
26 TraesCS2D01G027600 chr5D 526714687 526715211 524 True 571.000000 571 86.296000 3285 3821 1 chr5D.!!$R1 536
27 TraesCS2D01G027600 chr3D 564919126 564919628 502 False 460.000000 460 83.208000 1000 1529 1 chr3D.!!$F2 529
28 TraesCS2D01G027600 chr3B 752439355 752439857 502 False 449.000000 449 82.863000 1000 1529 1 chr3B.!!$F1 529

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
531 575 1.669779 GCACATGGCATGAGAGAGAAC 59.330 52.381 32.74 8.2 43.97 3.01 F
1174 1270 1.002134 CCATCCCAAGAACTGCCGT 60.002 57.895 0.00 0.0 0.00 5.68 F
1791 2581 0.251165 AAATCCCCACGAACCACCAG 60.251 55.000 0.00 0.0 0.00 4.00 F
1795 2585 0.889186 CCCCACGAACCACCAGAAAG 60.889 60.000 0.00 0.0 0.00 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1770 2560 0.250989 GGTGGTTCGTGGGGATTTGA 60.251 55.000 0.00 0.0 0.00 2.69 R
2392 3689 0.958822 ATTCCCACCACGAAAAGCAC 59.041 50.000 0.00 0.0 0.00 4.40 R
2902 4386 1.269012 AGAGCTTCTGAGAGCAGCTT 58.731 50.000 9.79 0.0 44.12 3.74 R
3525 5529 2.147150 GACAGAAAGCCTCCTTCACAC 58.853 52.381 0.00 0.0 0.00 3.82 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
53 54 4.279671 TGAAGCAAAACAAATCACCGGTAT 59.720 37.500 6.87 0.00 0.00 2.73
174 194 8.816640 AATAAGAAAACAGTGGTAGCAAAATG 57.183 30.769 0.00 0.00 0.00 2.32
435 479 4.027572 TGAACGGCAAGAAAAGAAACAG 57.972 40.909 0.00 0.00 0.00 3.16
531 575 1.669779 GCACATGGCATGAGAGAGAAC 59.330 52.381 32.74 8.20 43.97 3.01
614 663 4.460731 GGAAGCAGAGAAGGCAGTAAAAAT 59.539 41.667 0.00 0.00 0.00 1.82
620 669 5.182760 CAGAGAAGGCAGTAAAAATGAGCTT 59.817 40.000 0.00 0.00 0.00 3.74
1174 1270 1.002134 CCATCCCAAGAACTGCCGT 60.002 57.895 0.00 0.00 0.00 5.68
1216 1955 2.755876 TGATCGACCTCAGCGGCT 60.756 61.111 0.00 0.00 35.61 5.52
1218 1957 2.441164 ATCGACCTCAGCGGCTCT 60.441 61.111 0.00 0.00 35.61 4.09
1286 2025 1.056660 GGGTTCTTCCAGGTGACAGA 58.943 55.000 0.00 0.00 38.11 3.41
1618 2407 2.388310 GAGTGCTCTCCTGGTTAACC 57.612 55.000 18.27 18.27 34.87 2.85
1744 2533 9.421806 TGCTTATGCCAATAATTAATTATGCAC 57.578 29.630 24.45 16.62 35.70 4.57
1770 2560 7.117285 TGAGTGTGCTTGAGAGAATATGTAT 57.883 36.000 0.00 0.00 0.00 2.29
1781 2571 7.453393 TGAGAGAATATGTATCAAATCCCCAC 58.547 38.462 0.00 0.00 0.00 4.61
1791 2581 0.251165 AAATCCCCACGAACCACCAG 60.251 55.000 0.00 0.00 0.00 4.00
1795 2585 0.889186 CCCCACGAACCACCAGAAAG 60.889 60.000 0.00 0.00 0.00 2.62
1799 2589 1.971695 CGAACCACCAGAAAGGGCC 60.972 63.158 0.00 0.00 43.89 5.80
1827 2617 6.127535 TGCCCCGCTTTATACATATAGTCTAC 60.128 42.308 0.00 0.00 0.00 2.59
2064 2880 4.435554 CGATGCTCAATTGAATTTGTAGCG 59.564 41.667 9.88 8.05 34.92 4.26
2123 2940 9.975218 ACATGTAAACAAATTTATACTCCCTCT 57.025 29.630 0.00 0.00 32.91 3.69
2172 3337 5.766670 AGATTCCAATACGGACTACATACGA 59.233 40.000 0.00 0.00 46.36 3.43
2179 3345 3.916761 ACGGACTACATACGAAGCAAAA 58.083 40.909 0.00 0.00 0.00 2.44
2180 3346 4.501071 ACGGACTACATACGAAGCAAAAT 58.499 39.130 0.00 0.00 0.00 1.82
2183 3349 4.873827 GGACTACATACGAAGCAAAATGGA 59.126 41.667 0.00 0.00 0.00 3.41
2190 3356 7.047891 ACATACGAAGCAAAATGGAGAATCTA 58.952 34.615 0.00 0.00 33.73 1.98
2195 3361 6.456181 CGAAGCAAAATGGAGAATCTACACTC 60.456 42.308 0.00 0.00 33.73 3.51
2207 3373 7.741554 AGAATCTACACTCCAAAATAGGTCT 57.258 36.000 0.00 0.00 0.00 3.85
2241 3407 8.304596 TCCATATGTAGTCCGTATTGAAATCTC 58.695 37.037 1.24 0.00 0.00 2.75
2401 3698 1.061131 CTGATGGTAGCGTGCTTTTCG 59.939 52.381 0.00 0.00 0.00 3.46
2413 3710 1.243902 GCTTTTCGTGGTGGGAATGA 58.756 50.000 0.00 0.00 0.00 2.57
2902 4386 5.332743 AGAATTTGGGGAGCACTTTATTCA 58.667 37.500 0.00 0.00 0.00 2.57
3096 4580 2.524394 GGCGGCCTCCAGATCCTA 60.524 66.667 12.87 0.00 0.00 2.94
3197 4685 5.125100 TGTGAACATTCCAAGCAGAATTC 57.875 39.130 0.00 0.00 34.19 2.17
3219 4707 0.537143 TGTTCAAGGCGAGCATTGGT 60.537 50.000 20.00 0.00 38.15 3.67
3220 4708 0.598065 GTTCAAGGCGAGCATTGGTT 59.402 50.000 20.00 0.00 38.15 3.67
3234 5237 2.519377 TTGGTTAGTCACTCGTGGTG 57.481 50.000 0.00 5.25 46.60 4.17
3254 5257 4.215613 GGTGGTGTGGAACTGATAGTTTTC 59.784 45.833 0.00 0.00 38.80 2.29
3316 5319 2.193248 GAGCATAGGGTGGTGGCC 59.807 66.667 0.00 0.00 39.00 5.36
3394 5397 1.001597 GCCTCTACGAGAATGTACGGG 60.002 57.143 0.00 0.00 0.00 5.28
3525 5529 3.664107 TCTCTGATTTCCGGTTGTGAAG 58.336 45.455 0.00 0.00 0.00 3.02
3536 5540 2.222027 GGTTGTGAAGTGTGAAGGAGG 58.778 52.381 0.00 0.00 0.00 4.30
3537 7979 1.604278 GTTGTGAAGTGTGAAGGAGGC 59.396 52.381 0.00 0.00 0.00 4.70
3541 7983 2.550180 GTGAAGTGTGAAGGAGGCTTTC 59.450 50.000 0.00 0.00 0.00 2.62
3625 8079 8.128582 CAGTTTGTAATGCTAAAGAAGTGACAA 58.871 33.333 0.00 0.00 0.00 3.18
3660 8119 8.712363 CAGTACAAGTGCCATCATATTGTATAC 58.288 37.037 0.00 0.00 38.41 1.47
3662 8121 9.219603 GTACAAGTGCCATCATATTGTATACAT 57.780 33.333 6.36 0.01 38.41 2.29
3663 8122 8.102800 ACAAGTGCCATCATATTGTATACATG 57.897 34.615 6.36 2.41 34.96 3.21
3666 8125 6.656270 AGTGCCATCATATTGTATACATGTGG 59.344 38.462 9.11 12.40 0.00 4.17
3667 8126 6.430925 GTGCCATCATATTGTATACATGTGGT 59.569 38.462 9.11 0.00 0.00 4.16
3668 8127 7.606073 GTGCCATCATATTGTATACATGTGGTA 59.394 37.037 9.11 9.08 36.16 3.25
3669 8128 7.606073 TGCCATCATATTGTATACATGTGGTAC 59.394 37.037 9.11 11.84 34.07 3.34
3671 8130 9.671279 CCATCATATTGTATACATGTGGTACAT 57.329 33.333 19.98 14.50 44.52 2.29
3721 8207 7.594015 GGTACAGGAGTGATTATATTGTGTACG 59.406 40.741 0.00 0.00 38.95 3.67
3727 8213 6.636705 AGTGATTATATTGTGTACGTGTGGT 58.363 36.000 0.00 0.00 0.00 4.16
3821 8307 8.630917 CATGAAATTCTCCTCAATTATGCTTCT 58.369 33.333 0.00 0.00 0.00 2.85
3822 8308 9.857656 ATGAAATTCTCCTCAATTATGCTTCTA 57.142 29.630 0.00 0.00 0.00 2.10
3823 8309 9.685276 TGAAATTCTCCTCAATTATGCTTCTAA 57.315 29.630 0.00 0.00 0.00 2.10
3826 8312 8.632906 ATTCTCCTCAATTATGCTTCTAATGG 57.367 34.615 0.00 0.00 0.00 3.16
3929 8418 3.127533 GATGGTGGCGTGGCTCAC 61.128 66.667 0.00 0.00 0.00 3.51
3966 8455 4.999950 GGATCTATTGACAGTTATGCCCAG 59.000 45.833 0.00 0.00 0.00 4.45
3996 8485 7.308782 ACTCACGGTCATGATTTTCTTAATC 57.691 36.000 0.00 0.00 0.00 1.75
4019 8508 2.431057 ACCTCCGCGTTAGATTCTTGAT 59.569 45.455 4.92 0.00 0.00 2.57
4107 8596 3.855524 GCCACAAAACACTTGGTATTCCG 60.856 47.826 0.00 0.00 36.30 4.30
4112 8601 0.322187 ACACTTGGTATTCCGGTGGC 60.322 55.000 0.00 0.00 41.09 5.01
4136 8625 1.302993 ACCGTTGGTTCAATCCCCG 60.303 57.895 0.00 0.00 27.29 5.73
4176 8665 1.318158 CCCATTGCACTGAGGCCTTC 61.318 60.000 6.77 0.10 0.00 3.46
4180 8669 0.111061 TTGCACTGAGGCCTTCATGT 59.889 50.000 6.77 0.30 34.68 3.21
4206 8695 4.695217 TTTAAATGACGATTGTGGGAGC 57.305 40.909 0.00 0.00 0.00 4.70
4207 8696 2.198827 AAATGACGATTGTGGGAGCA 57.801 45.000 0.00 0.00 0.00 4.26
4208 8697 1.742761 AATGACGATTGTGGGAGCAG 58.257 50.000 0.00 0.00 0.00 4.24
4209 8698 0.615331 ATGACGATTGTGGGAGCAGT 59.385 50.000 0.00 0.00 0.00 4.40
4210 8699 1.262417 TGACGATTGTGGGAGCAGTA 58.738 50.000 0.00 0.00 0.00 2.74
4211 8700 1.067142 TGACGATTGTGGGAGCAGTAC 60.067 52.381 0.00 0.00 0.00 2.73
4212 8701 0.249398 ACGATTGTGGGAGCAGTACC 59.751 55.000 0.00 0.00 0.00 3.34
4213 8702 0.537188 CGATTGTGGGAGCAGTACCT 59.463 55.000 0.00 0.00 0.00 3.08
4214 8703 1.066143 CGATTGTGGGAGCAGTACCTT 60.066 52.381 0.00 0.00 0.00 3.50
4215 8704 2.615493 CGATTGTGGGAGCAGTACCTTT 60.615 50.000 0.00 0.00 0.00 3.11
4216 8705 3.421844 GATTGTGGGAGCAGTACCTTTT 58.578 45.455 0.00 0.00 0.00 2.27
4217 8706 3.306472 TTGTGGGAGCAGTACCTTTTT 57.694 42.857 0.00 0.00 0.00 1.94
4218 8707 4.440826 TTGTGGGAGCAGTACCTTTTTA 57.559 40.909 0.00 0.00 0.00 1.52
4219 8708 3.746940 TGTGGGAGCAGTACCTTTTTAC 58.253 45.455 0.00 0.00 0.00 2.01
4220 8709 3.136809 TGTGGGAGCAGTACCTTTTTACA 59.863 43.478 0.00 0.00 0.00 2.41
4221 8710 4.202524 TGTGGGAGCAGTACCTTTTTACAT 60.203 41.667 0.00 0.00 0.00 2.29
4222 8711 4.765339 GTGGGAGCAGTACCTTTTTACATT 59.235 41.667 0.00 0.00 0.00 2.71
4223 8712 4.764823 TGGGAGCAGTACCTTTTTACATTG 59.235 41.667 0.00 0.00 0.00 2.82
4224 8713 4.157840 GGGAGCAGTACCTTTTTACATTGG 59.842 45.833 0.00 0.00 0.00 3.16
4225 8714 5.007682 GGAGCAGTACCTTTTTACATTGGA 58.992 41.667 0.00 0.00 0.00 3.53
4226 8715 5.123979 GGAGCAGTACCTTTTTACATTGGAG 59.876 44.000 0.00 0.00 0.00 3.86
4227 8716 5.010282 AGCAGTACCTTTTTACATTGGAGG 58.990 41.667 0.00 0.00 0.00 4.30
4228 8717 4.380550 GCAGTACCTTTTTACATTGGAGGC 60.381 45.833 0.00 0.00 0.00 4.70
4229 8718 4.007659 AGTACCTTTTTACATTGGAGGCG 58.992 43.478 0.00 0.00 0.00 5.52
4230 8719 2.167662 ACCTTTTTACATTGGAGGCGG 58.832 47.619 0.00 0.00 0.00 6.13
4231 8720 2.167662 CCTTTTTACATTGGAGGCGGT 58.832 47.619 0.00 0.00 0.00 5.68
4232 8721 2.094752 CCTTTTTACATTGGAGGCGGTG 60.095 50.000 0.00 0.00 0.00 4.94
4233 8722 1.540267 TTTTACATTGGAGGCGGTGG 58.460 50.000 0.00 0.00 0.00 4.61
4234 8723 0.322997 TTTACATTGGAGGCGGTGGG 60.323 55.000 0.00 0.00 0.00 4.61
4235 8724 2.830186 TTACATTGGAGGCGGTGGGC 62.830 60.000 0.00 0.00 42.51 5.36
4243 8732 2.909965 GGCGGTGGGCTCACAAAA 60.910 61.111 20.52 0.00 45.32 2.44
4244 8733 2.494530 GGCGGTGGGCTCACAAAAA 61.495 57.895 20.52 0.00 45.32 1.94
4245 8734 1.007387 GCGGTGGGCTCACAAAAAG 60.007 57.895 20.52 5.07 45.32 2.27
4246 8735 1.007387 CGGTGGGCTCACAAAAAGC 60.007 57.895 20.52 0.00 45.32 3.51
4251 8740 4.198087 GCTCACAAAAAGCCCCCT 57.802 55.556 0.00 0.00 33.53 4.79
4252 8741 1.667722 GCTCACAAAAAGCCCCCTG 59.332 57.895 0.00 0.00 33.53 4.45
4253 8742 1.115326 GCTCACAAAAAGCCCCCTGT 61.115 55.000 0.00 0.00 33.53 4.00
4254 8743 1.821666 GCTCACAAAAAGCCCCCTGTA 60.822 52.381 0.00 0.00 33.53 2.74
4255 8744 2.593026 CTCACAAAAAGCCCCCTGTAA 58.407 47.619 0.00 0.00 0.00 2.41
4256 8745 2.962421 CTCACAAAAAGCCCCCTGTAAA 59.038 45.455 0.00 0.00 0.00 2.01
4257 8746 3.375699 TCACAAAAAGCCCCCTGTAAAA 58.624 40.909 0.00 0.00 0.00 1.52
4258 8747 3.970640 TCACAAAAAGCCCCCTGTAAAAT 59.029 39.130 0.00 0.00 0.00 1.82
4259 8748 4.410555 TCACAAAAAGCCCCCTGTAAAATT 59.589 37.500 0.00 0.00 0.00 1.82
4260 8749 5.104318 TCACAAAAAGCCCCCTGTAAAATTT 60.104 36.000 0.00 0.00 0.00 1.82
4261 8750 5.008514 CACAAAAAGCCCCCTGTAAAATTTG 59.991 40.000 0.00 0.00 0.00 2.32
4262 8751 5.104318 ACAAAAAGCCCCCTGTAAAATTTGA 60.104 36.000 0.00 0.00 0.00 2.69
4263 8752 5.841267 AAAAGCCCCCTGTAAAATTTGAT 57.159 34.783 0.00 0.00 0.00 2.57
4264 8753 5.420725 AAAGCCCCCTGTAAAATTTGATC 57.579 39.130 0.00 0.00 0.00 2.92
4265 8754 3.374764 AGCCCCCTGTAAAATTTGATCC 58.625 45.455 0.00 0.00 0.00 3.36
4266 8755 3.103742 GCCCCCTGTAAAATTTGATCCA 58.896 45.455 0.00 0.00 0.00 3.41
4267 8756 3.517500 GCCCCCTGTAAAATTTGATCCAA 59.482 43.478 0.00 0.00 0.00 3.53
4268 8757 4.164030 GCCCCCTGTAAAATTTGATCCAAT 59.836 41.667 0.00 0.00 0.00 3.16
4269 8758 5.339118 GCCCCCTGTAAAATTTGATCCAATT 60.339 40.000 0.00 0.00 0.00 2.32
4270 8759 6.114767 CCCCCTGTAAAATTTGATCCAATTG 58.885 40.000 5.58 0.00 0.00 2.32
4271 8760 5.585844 CCCCTGTAAAATTTGATCCAATTGC 59.414 40.000 5.58 1.53 0.00 3.56
4272 8761 5.291614 CCCTGTAAAATTTGATCCAATTGCG 59.708 40.000 5.58 0.00 0.00 4.85
4273 8762 6.098679 CCTGTAAAATTTGATCCAATTGCGA 58.901 36.000 5.58 0.00 0.00 5.10
4274 8763 6.254157 CCTGTAAAATTTGATCCAATTGCGAG 59.746 38.462 5.58 1.33 0.00 5.03
4275 8764 6.098679 TGTAAAATTTGATCCAATTGCGAGG 58.901 36.000 5.58 0.00 0.00 4.63
4276 8765 3.806625 AATTTGATCCAATTGCGAGGG 57.193 42.857 4.05 0.00 0.00 4.30
4277 8766 2.505650 TTTGATCCAATTGCGAGGGA 57.494 45.000 0.00 0.00 34.70 4.20
4278 8767 2.734755 TTGATCCAATTGCGAGGGAT 57.265 45.000 9.21 9.21 43.92 3.85
4280 8769 1.151668 GATCCAATTGCGAGGGATCG 58.848 55.000 17.32 0.00 45.34 3.69
4281 8770 0.758734 ATCCAATTGCGAGGGATCGA 59.241 50.000 0.00 0.00 36.74 3.59
4282 8771 0.539518 TCCAATTGCGAGGGATCGAA 59.460 50.000 0.00 0.00 34.64 3.71
4283 8772 0.940126 CCAATTGCGAGGGATCGAAG 59.060 55.000 0.00 0.00 34.64 3.79
4284 8773 0.940126 CAATTGCGAGGGATCGAAGG 59.060 55.000 1.17 0.00 34.64 3.46
4285 8774 0.541863 AATTGCGAGGGATCGAAGGT 59.458 50.000 1.17 0.00 34.64 3.50
4286 8775 1.410004 ATTGCGAGGGATCGAAGGTA 58.590 50.000 1.17 0.00 34.64 3.08
4287 8776 0.458669 TTGCGAGGGATCGAAGGTAC 59.541 55.000 1.17 0.00 34.64 3.34
4288 8777 0.681887 TGCGAGGGATCGAAGGTACA 60.682 55.000 1.17 0.00 34.64 2.90
4289 8778 0.248949 GCGAGGGATCGAAGGTACAC 60.249 60.000 1.17 0.00 34.64 2.90
4290 8779 0.384669 CGAGGGATCGAAGGTACACC 59.615 60.000 0.00 0.00 34.64 4.16
4291 8780 1.481871 GAGGGATCGAAGGTACACCA 58.518 55.000 0.38 0.00 38.89 4.17
4292 8781 1.829222 GAGGGATCGAAGGTACACCAA 59.171 52.381 0.38 0.00 38.89 3.67
4293 8782 1.553704 AGGGATCGAAGGTACACCAAC 59.446 52.381 0.38 0.00 38.89 3.77
4294 8783 1.276989 GGGATCGAAGGTACACCAACA 59.723 52.381 0.38 0.00 38.89 3.33
4295 8784 2.093128 GGGATCGAAGGTACACCAACAT 60.093 50.000 0.38 0.00 38.89 2.71
4296 8785 2.936498 GGATCGAAGGTACACCAACATG 59.064 50.000 0.38 0.00 38.89 3.21
4297 8786 2.465860 TCGAAGGTACACCAACATGG 57.534 50.000 0.38 0.00 45.02 3.66
4298 8787 0.802494 CGAAGGTACACCAACATGGC 59.198 55.000 0.38 0.00 42.67 4.40
4299 8788 1.880221 CGAAGGTACACCAACATGGCA 60.880 52.381 0.38 0.00 42.67 4.92
4300 8789 1.812571 GAAGGTACACCAACATGGCAG 59.187 52.381 0.38 0.00 42.67 4.85
4301 8790 0.609131 AGGTACACCAACATGGCAGC 60.609 55.000 0.38 0.00 42.67 5.25
4302 8791 1.595093 GGTACACCAACATGGCAGCC 61.595 60.000 3.66 3.66 42.67 4.85
4303 8792 0.893270 GTACACCAACATGGCAGCCA 60.893 55.000 18.99 18.99 42.67 4.75
4304 8793 0.893270 TACACCAACATGGCAGCCAC 60.893 55.000 19.10 0.00 42.67 5.01
4305 8794 1.904865 CACCAACATGGCAGCCACT 60.905 57.895 19.10 0.98 42.67 4.00
4306 8795 1.152483 ACCAACATGGCAGCCACTT 60.152 52.632 19.10 8.46 42.67 3.16
4307 8796 0.760189 ACCAACATGGCAGCCACTTT 60.760 50.000 19.10 10.15 42.67 2.66
4308 8797 0.393820 CCAACATGGCAGCCACTTTT 59.606 50.000 19.10 7.27 35.80 2.27
4309 8798 1.606224 CCAACATGGCAGCCACTTTTC 60.606 52.381 19.10 0.00 35.80 2.29
4310 8799 1.342174 CAACATGGCAGCCACTTTTCT 59.658 47.619 19.10 0.00 35.80 2.52
4311 8800 1.251251 ACATGGCAGCCACTTTTCTC 58.749 50.000 19.10 0.00 35.80 2.87
4312 8801 1.202976 ACATGGCAGCCACTTTTCTCT 60.203 47.619 19.10 0.00 35.80 3.10
4313 8802 2.040278 ACATGGCAGCCACTTTTCTCTA 59.960 45.455 19.10 0.00 35.80 2.43
4314 8803 2.185004 TGGCAGCCACTTTTCTCTAC 57.815 50.000 11.22 0.00 0.00 2.59
4315 8804 1.699634 TGGCAGCCACTTTTCTCTACT 59.300 47.619 11.22 0.00 0.00 2.57
4316 8805 2.289694 TGGCAGCCACTTTTCTCTACTC 60.290 50.000 11.22 0.00 0.00 2.59
4317 8806 2.027653 GGCAGCCACTTTTCTCTACTCT 60.028 50.000 6.55 0.00 0.00 3.24
4318 8807 3.258228 GCAGCCACTTTTCTCTACTCTC 58.742 50.000 0.00 0.00 0.00 3.20
4319 8808 3.506810 CAGCCACTTTTCTCTACTCTCG 58.493 50.000 0.00 0.00 0.00 4.04
4320 8809 3.191581 CAGCCACTTTTCTCTACTCTCGA 59.808 47.826 0.00 0.00 0.00 4.04
4321 8810 3.827302 AGCCACTTTTCTCTACTCTCGAA 59.173 43.478 0.00 0.00 0.00 3.71
4322 8811 4.464597 AGCCACTTTTCTCTACTCTCGAAT 59.535 41.667 0.00 0.00 0.00 3.34
4323 8812 4.801516 GCCACTTTTCTCTACTCTCGAATC 59.198 45.833 0.00 0.00 0.00 2.52
4324 8813 5.031578 CCACTTTTCTCTACTCTCGAATCG 58.968 45.833 0.00 0.00 0.00 3.34
4325 8814 5.031578 CACTTTTCTCTACTCTCGAATCGG 58.968 45.833 1.76 0.00 0.00 4.18
4326 8815 4.701171 ACTTTTCTCTACTCTCGAATCGGT 59.299 41.667 1.76 0.00 0.00 4.69
4327 8816 5.183522 ACTTTTCTCTACTCTCGAATCGGTT 59.816 40.000 1.76 0.00 0.00 4.44
4328 8817 5.640189 TTTCTCTACTCTCGAATCGGTTT 57.360 39.130 1.76 0.00 0.00 3.27
4329 8818 5.640189 TTCTCTACTCTCGAATCGGTTTT 57.360 39.130 1.76 0.00 0.00 2.43
4330 8819 5.232610 TCTCTACTCTCGAATCGGTTTTC 57.767 43.478 1.76 0.00 0.00 2.29
4331 8820 4.942483 TCTCTACTCTCGAATCGGTTTTCT 59.058 41.667 1.76 0.00 0.00 2.52
4378 8867 2.777832 AGTTCAATCACCTCCTCAGC 57.222 50.000 0.00 0.00 0.00 4.26
4416 8905 9.369904 GTGTGCAATCATTTTAAGTTAATGGAT 57.630 29.630 0.00 0.00 34.51 3.41
4483 9132 6.541934 TTAGAGATGGATGGCATCTATCAG 57.458 41.667 38.48 0.00 46.20 2.90
4485 9134 3.518705 GAGATGGATGGCATCTATCAGGT 59.481 47.826 38.48 26.32 46.20 4.00
4491 9140 5.426509 TGGATGGCATCTATCAGGTTATAGG 59.573 44.000 25.48 0.00 31.50 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 2.104111 AGCCGGCAACACATATAGCTAA 59.896 45.455 31.54 0.00 0.00 3.09
174 194 6.377780 ACAACTTCCATTTTTGTTTTGCAAC 58.622 32.000 0.00 0.00 36.72 4.17
312 355 1.202405 AGCGTTTGGTTTTGCTGGAAG 60.202 47.619 0.00 0.00 36.09 3.46
435 479 1.747924 GCTCTTGGGAAAGGAGATTGC 59.252 52.381 0.00 0.00 0.00 3.56
546 593 1.489649 CATGAGAGGGGTCAGCTCATT 59.510 52.381 0.00 0.00 44.55 2.57
548 597 0.979709 CCATGAGAGGGGTCAGCTCA 60.980 60.000 0.00 0.00 42.25 4.26
614 663 4.860802 TCTCCCCATCAATTTAAGCTCA 57.139 40.909 0.00 0.00 0.00 4.26
620 669 6.160282 TCTCCAGAAATCTCCCCATCAATTTA 59.840 38.462 0.00 0.00 0.00 1.40
750 815 3.715648 ATCTCTATCCCCACCACTTCT 57.284 47.619 0.00 0.00 0.00 2.85
842 915 1.929169 GGAAACGCTTGTATACGGTCC 59.071 52.381 0.00 0.00 32.71 4.46
926 1001 5.535029 ACTATGGACCTTCTACCAATGGTA 58.465 41.667 12.12 12.12 39.69 3.25
927 1002 4.371681 ACTATGGACCTTCTACCAATGGT 58.628 43.478 10.81 10.81 39.69 3.55
928 1003 4.408921 TGACTATGGACCTTCTACCAATGG 59.591 45.833 0.00 0.00 39.69 3.16
929 1004 5.614324 TGACTATGGACCTTCTACCAATG 57.386 43.478 0.00 0.00 39.69 2.82
930 1005 6.636454 TTTGACTATGGACCTTCTACCAAT 57.364 37.500 0.00 0.00 39.69 3.16
931 1006 5.570844 GCTTTGACTATGGACCTTCTACCAA 60.571 44.000 0.00 0.00 39.69 3.67
932 1007 4.081087 GCTTTGACTATGGACCTTCTACCA 60.081 45.833 0.00 0.00 40.57 3.25
933 1008 4.162509 AGCTTTGACTATGGACCTTCTACC 59.837 45.833 0.00 0.00 0.00 3.18
934 1009 5.346181 AGCTTTGACTATGGACCTTCTAC 57.654 43.478 0.00 0.00 0.00 2.59
935 1010 5.483937 TCAAGCTTTGACTATGGACCTTCTA 59.516 40.000 0.00 0.00 34.08 2.10
936 1011 4.287067 TCAAGCTTTGACTATGGACCTTCT 59.713 41.667 0.00 0.00 34.08 2.85
937 1012 4.579869 TCAAGCTTTGACTATGGACCTTC 58.420 43.478 0.00 0.00 34.08 3.46
1533 2322 2.606519 TCAGGTAAGCTGCGGGGT 60.607 61.111 0.00 0.00 0.00 4.95
1608 2397 1.834188 AAATCAGGCGGTTAACCAGG 58.166 50.000 24.14 10.11 35.14 4.45
1618 2407 4.361451 AGCTCAATTTGTAAATCAGGCG 57.639 40.909 0.00 0.00 0.00 5.52
1744 2533 5.873712 ACATATTCTCTCAAGCACACTCAAG 59.126 40.000 0.00 0.00 0.00 3.02
1770 2560 0.250989 GGTGGTTCGTGGGGATTTGA 60.251 55.000 0.00 0.00 0.00 2.69
1781 2571 1.971695 GGCCCTTTCTGGTGGTTCG 60.972 63.158 0.00 0.00 0.00 3.95
1799 2589 5.938125 ACTATATGTATAAAGCGGGGCAAAG 59.062 40.000 0.00 0.00 0.00 2.77
1827 2617 5.384063 TGTATTGTGGTTGTGGCTTTATG 57.616 39.130 0.00 0.00 0.00 1.90
1945 2735 7.758495 TGAGAAGTTGAGGTAAAACTTTCAAC 58.242 34.615 14.46 14.46 45.50 3.18
2158 3323 3.581024 TTTGCTTCGTATGTAGTCCGT 57.419 42.857 0.00 0.00 0.00 4.69
2172 3337 5.649831 GGAGTGTAGATTCTCCATTTTGCTT 59.350 40.000 6.37 0.00 46.59 3.91
2183 3349 7.741554 AGACCTATTTTGGAGTGTAGATTCT 57.258 36.000 0.00 0.00 0.00 2.40
2221 3387 9.582431 CTTTTAGAGATTTCAATACGGACTACA 57.418 33.333 0.00 0.00 0.00 2.74
2223 3389 9.798994 GACTTTTAGAGATTTCAATACGGACTA 57.201 33.333 0.00 0.00 0.00 2.59
2331 3604 2.036556 AAACTGCGTCATTTGCTTCG 57.963 45.000 0.00 0.00 0.00 3.79
2332 3605 2.472488 CCAAAACTGCGTCATTTGCTTC 59.528 45.455 0.00 0.00 33.72 3.86
2334 3607 1.680735 TCCAAAACTGCGTCATTTGCT 59.319 42.857 0.00 0.00 33.72 3.91
2335 3608 2.132740 TCCAAAACTGCGTCATTTGC 57.867 45.000 0.00 0.00 33.72 3.68
2392 3689 0.958822 ATTCCCACCACGAAAAGCAC 59.041 50.000 0.00 0.00 0.00 4.40
2401 3698 1.995376 ACTGGTTTCATTCCCACCAC 58.005 50.000 0.00 0.00 35.57 4.16
2413 3710 7.651704 GCATTAACAGAACATGTAAACTGGTTT 59.348 33.333 22.38 14.90 43.00 3.27
2576 3897 4.855340 TGGGATCTATTTGTGGGAAGAAC 58.145 43.478 0.00 0.00 0.00 3.01
2821 4265 6.175471 TGTGAATCAACATGTTAGAGCTGAT 58.825 36.000 11.53 6.70 0.00 2.90
2902 4386 1.269012 AGAGCTTCTGAGAGCAGCTT 58.731 50.000 9.79 0.00 44.12 3.74
3096 4580 3.512154 TACCCACCGGTCCTCGTGT 62.512 63.158 2.59 0.00 43.29 4.49
3197 4685 2.322161 CAATGCTCGCCTTGAACAAAG 58.678 47.619 1.35 0.00 35.47 2.77
3234 5237 5.763204 TGAAGAAAACTATCAGTTCCACACC 59.237 40.000 0.00 0.00 37.47 4.16
3254 5257 5.474532 TGGAGATCAACTGGACATTTTGAAG 59.525 40.000 0.00 0.00 33.13 3.02
3394 5397 2.178890 CAGCAGCTCCTTGATCGGC 61.179 63.158 0.00 0.00 0.00 5.54
3457 5461 7.382488 CCGATGGAGTAGTAATGTTTGATGTAG 59.618 40.741 0.00 0.00 0.00 2.74
3525 5529 2.147150 GACAGAAAGCCTCCTTCACAC 58.853 52.381 0.00 0.00 0.00 3.82
3536 5540 5.283457 AGTATACCATCAGGACAGAAAGC 57.717 43.478 0.00 0.00 38.69 3.51
3537 7979 9.521841 TCTATAGTATACCATCAGGACAGAAAG 57.478 37.037 0.00 0.00 38.69 2.62
3571 8013 7.552687 TCAACTTATCAATGTTCCAGGTACATC 59.447 37.037 11.89 0.00 35.26 3.06
3662 8121 8.264347 ACACAATATAATCACTCATGTACCACA 58.736 33.333 0.00 0.00 0.00 4.17
3663 8122 8.662781 ACACAATATAATCACTCATGTACCAC 57.337 34.615 0.00 0.00 0.00 4.16
3668 8127 9.836864 ACATGTACACAATATAATCACTCATGT 57.163 29.630 0.00 0.00 37.00 3.21
3671 8130 8.264347 ACCACATGTACACAATATAATCACTCA 58.736 33.333 0.00 0.00 0.00 3.41
3672 8131 8.662781 ACCACATGTACACAATATAATCACTC 57.337 34.615 0.00 0.00 0.00 3.51
3721 8207 2.240493 AGTGCACTTCTGTACCACAC 57.760 50.000 15.25 0.00 33.66 3.82
3727 8213 4.377021 CACCAAACTAGTGCACTTCTGTA 58.623 43.478 27.06 5.23 0.00 2.74
3821 8307 5.381757 ACACTCTGTTTTTACAGGCCATTA 58.618 37.500 5.01 0.00 38.23 1.90
3822 8308 4.215109 ACACTCTGTTTTTACAGGCCATT 58.785 39.130 5.01 0.00 38.23 3.16
3823 8309 3.832527 ACACTCTGTTTTTACAGGCCAT 58.167 40.909 5.01 0.00 38.23 4.40
3825 8311 3.630312 TCAACACTCTGTTTTTACAGGCC 59.370 43.478 0.00 0.00 38.77 5.19
3826 8312 4.893424 TCAACACTCTGTTTTTACAGGC 57.107 40.909 5.55 0.00 38.77 4.85
3906 8395 1.600636 CCACGCCACCATCAACAGT 60.601 57.895 0.00 0.00 0.00 3.55
3966 8455 2.871182 TCATGACCGTGAGTAGATGC 57.129 50.000 0.00 0.00 0.00 3.91
3996 8485 2.295253 AGAATCTAACGCGGAGGTTG 57.705 50.000 12.47 0.00 0.00 3.77
4124 8613 0.902531 TCACTCTCGGGGATTGAACC 59.097 55.000 0.00 0.00 31.98 3.62
4136 8625 1.079750 GGGCTCAACGGTCACTCTC 60.080 63.158 0.00 0.00 0.00 3.20
4161 8650 0.111061 ACATGAAGGCCTCAGTGCAA 59.889 50.000 5.23 0.00 37.52 4.08
4188 8677 2.086869 CTGCTCCCACAATCGTCATTT 58.913 47.619 0.00 0.00 0.00 2.32
4189 8678 1.003580 ACTGCTCCCACAATCGTCATT 59.996 47.619 0.00 0.00 0.00 2.57
4190 8679 0.615331 ACTGCTCCCACAATCGTCAT 59.385 50.000 0.00 0.00 0.00 3.06
4191 8680 1.067142 GTACTGCTCCCACAATCGTCA 60.067 52.381 0.00 0.00 0.00 4.35
4192 8681 1.641577 GTACTGCTCCCACAATCGTC 58.358 55.000 0.00 0.00 0.00 4.20
4193 8682 0.249398 GGTACTGCTCCCACAATCGT 59.751 55.000 0.00 0.00 0.00 3.73
4194 8683 0.537188 AGGTACTGCTCCCACAATCG 59.463 55.000 0.00 0.00 37.18 3.34
4195 8684 2.789409 AAGGTACTGCTCCCACAATC 57.211 50.000 0.00 0.00 40.86 2.67
4196 8685 3.525800 AAAAGGTACTGCTCCCACAAT 57.474 42.857 0.00 0.00 40.86 2.71
4197 8686 3.306472 AAAAAGGTACTGCTCCCACAA 57.694 42.857 0.00 0.00 40.86 3.33
4198 8687 3.136809 TGTAAAAAGGTACTGCTCCCACA 59.863 43.478 0.00 0.00 40.86 4.17
4199 8688 3.746940 TGTAAAAAGGTACTGCTCCCAC 58.253 45.455 0.00 0.00 40.86 4.61
4200 8689 4.650972 ATGTAAAAAGGTACTGCTCCCA 57.349 40.909 0.00 0.00 40.86 4.37
4201 8690 4.157840 CCAATGTAAAAAGGTACTGCTCCC 59.842 45.833 0.00 0.00 40.86 4.30
4202 8691 5.007682 TCCAATGTAAAAAGGTACTGCTCC 58.992 41.667 0.00 0.00 40.86 4.70
4203 8692 5.123979 CCTCCAATGTAAAAAGGTACTGCTC 59.876 44.000 0.00 0.00 40.86 4.26
4204 8693 5.010282 CCTCCAATGTAAAAAGGTACTGCT 58.990 41.667 0.00 0.00 40.86 4.24
4205 8694 4.380550 GCCTCCAATGTAAAAAGGTACTGC 60.381 45.833 0.00 0.00 40.86 4.40
4206 8695 4.142687 CGCCTCCAATGTAAAAAGGTACTG 60.143 45.833 0.00 0.00 40.86 2.74
4208 8697 3.128068 CCGCCTCCAATGTAAAAAGGTAC 59.872 47.826 0.00 0.00 0.00 3.34
4209 8698 3.244981 ACCGCCTCCAATGTAAAAAGGTA 60.245 43.478 0.00 0.00 0.00 3.08
4210 8699 2.167662 CCGCCTCCAATGTAAAAAGGT 58.832 47.619 0.00 0.00 0.00 3.50
4211 8700 2.094752 CACCGCCTCCAATGTAAAAAGG 60.095 50.000 0.00 0.00 0.00 3.11
4212 8701 2.094752 CCACCGCCTCCAATGTAAAAAG 60.095 50.000 0.00 0.00 0.00 2.27
4213 8702 1.889829 CCACCGCCTCCAATGTAAAAA 59.110 47.619 0.00 0.00 0.00 1.94
4214 8703 1.540267 CCACCGCCTCCAATGTAAAA 58.460 50.000 0.00 0.00 0.00 1.52
4215 8704 0.322997 CCCACCGCCTCCAATGTAAA 60.323 55.000 0.00 0.00 0.00 2.01
4216 8705 1.301623 CCCACCGCCTCCAATGTAA 59.698 57.895 0.00 0.00 0.00 2.41
4217 8706 2.994699 CCCACCGCCTCCAATGTA 59.005 61.111 0.00 0.00 0.00 2.29
4218 8707 4.740822 GCCCACCGCCTCCAATGT 62.741 66.667 0.00 0.00 0.00 2.71
4219 8708 4.431131 AGCCCACCGCCTCCAATG 62.431 66.667 0.00 0.00 38.78 2.82
4220 8709 4.115199 GAGCCCACCGCCTCCAAT 62.115 66.667 0.00 0.00 38.78 3.16
4224 8713 3.842925 TTTGTGAGCCCACCGCCTC 62.843 63.158 0.00 0.00 42.53 4.70
4225 8714 2.920076 TTTTTGTGAGCCCACCGCCT 62.920 55.000 0.00 0.00 42.53 5.52
4226 8715 2.420466 CTTTTTGTGAGCCCACCGCC 62.420 60.000 0.00 0.00 42.53 6.13
4227 8716 1.007387 CTTTTTGTGAGCCCACCGC 60.007 57.895 0.00 0.00 42.53 5.68
4228 8717 1.007387 GCTTTTTGTGAGCCCACCG 60.007 57.895 0.00 0.00 42.53 4.94
4234 8723 1.115326 ACAGGGGGCTTTTTGTGAGC 61.115 55.000 0.00 0.00 39.41 4.26
4235 8724 2.286365 TACAGGGGGCTTTTTGTGAG 57.714 50.000 0.00 0.00 0.00 3.51
4236 8725 2.757894 TTACAGGGGGCTTTTTGTGA 57.242 45.000 0.00 0.00 0.00 3.58
4237 8726 3.828875 TTTTACAGGGGGCTTTTTGTG 57.171 42.857 0.00 0.00 0.00 3.33
4238 8727 5.104318 TCAAATTTTACAGGGGGCTTTTTGT 60.104 36.000 0.00 0.00 0.00 2.83
4239 8728 5.372373 TCAAATTTTACAGGGGGCTTTTTG 58.628 37.500 0.00 0.00 0.00 2.44
4240 8729 5.638530 TCAAATTTTACAGGGGGCTTTTT 57.361 34.783 0.00 0.00 0.00 1.94
4241 8730 5.280470 GGATCAAATTTTACAGGGGGCTTTT 60.280 40.000 0.00 0.00 0.00 2.27
4242 8731 4.225042 GGATCAAATTTTACAGGGGGCTTT 59.775 41.667 0.00 0.00 0.00 3.51
4243 8732 3.774766 GGATCAAATTTTACAGGGGGCTT 59.225 43.478 0.00 0.00 0.00 4.35
4244 8733 3.245948 TGGATCAAATTTTACAGGGGGCT 60.246 43.478 0.00 0.00 0.00 5.19
4245 8734 3.103742 TGGATCAAATTTTACAGGGGGC 58.896 45.455 0.00 0.00 0.00 5.80
4246 8735 5.955961 ATTGGATCAAATTTTACAGGGGG 57.044 39.130 0.00 0.00 0.00 5.40
4247 8736 5.585844 GCAATTGGATCAAATTTTACAGGGG 59.414 40.000 5.25 0.00 0.00 4.79
4248 8737 5.291614 CGCAATTGGATCAAATTTTACAGGG 59.708 40.000 5.25 0.00 0.00 4.45
4249 8738 6.098679 TCGCAATTGGATCAAATTTTACAGG 58.901 36.000 5.25 0.00 0.00 4.00
4250 8739 6.254157 CCTCGCAATTGGATCAAATTTTACAG 59.746 38.462 5.25 0.60 0.00 2.74
4251 8740 6.098679 CCTCGCAATTGGATCAAATTTTACA 58.901 36.000 5.25 0.00 0.00 2.41
4252 8741 5.519927 CCCTCGCAATTGGATCAAATTTTAC 59.480 40.000 5.25 0.00 0.00 2.01
4253 8742 5.420421 TCCCTCGCAATTGGATCAAATTTTA 59.580 36.000 5.25 0.00 0.00 1.52
4254 8743 4.222588 TCCCTCGCAATTGGATCAAATTTT 59.777 37.500 5.25 0.00 0.00 1.82
4255 8744 3.768757 TCCCTCGCAATTGGATCAAATTT 59.231 39.130 5.25 0.00 0.00 1.82
4256 8745 3.364549 TCCCTCGCAATTGGATCAAATT 58.635 40.909 7.72 1.92 0.00 1.82
4257 8746 3.017048 TCCCTCGCAATTGGATCAAAT 57.983 42.857 7.72 0.00 0.00 2.32
4258 8747 2.505650 TCCCTCGCAATTGGATCAAA 57.494 45.000 7.72 0.00 0.00 2.69
4259 8748 2.734755 ATCCCTCGCAATTGGATCAA 57.265 45.000 7.72 0.00 33.61 2.57
4262 8751 0.758734 TCGATCCCTCGCAATTGGAT 59.241 50.000 7.72 0.37 44.65 3.41
4263 8752 0.539518 TTCGATCCCTCGCAATTGGA 59.460 50.000 7.72 2.15 44.65 3.53
4264 8753 0.940126 CTTCGATCCCTCGCAATTGG 59.060 55.000 7.72 0.00 44.65 3.16
4265 8754 0.940126 CCTTCGATCCCTCGCAATTG 59.060 55.000 0.00 0.00 44.65 2.32
4266 8755 0.541863 ACCTTCGATCCCTCGCAATT 59.458 50.000 0.00 0.00 44.65 2.32
4267 8756 1.068741 GTACCTTCGATCCCTCGCAAT 59.931 52.381 0.00 0.00 44.65 3.56
4268 8757 0.458669 GTACCTTCGATCCCTCGCAA 59.541 55.000 0.00 0.00 44.65 4.85
4269 8758 0.681887 TGTACCTTCGATCCCTCGCA 60.682 55.000 0.00 0.00 44.65 5.10
4270 8759 0.248949 GTGTACCTTCGATCCCTCGC 60.249 60.000 0.00 0.00 44.65 5.03
4271 8760 0.384669 GGTGTACCTTCGATCCCTCG 59.615 60.000 0.00 0.00 46.41 4.63
4272 8761 1.481871 TGGTGTACCTTCGATCCCTC 58.518 55.000 2.32 0.00 36.82 4.30
4273 8762 1.553704 GTTGGTGTACCTTCGATCCCT 59.446 52.381 2.32 0.00 36.82 4.20
4274 8763 1.276989 TGTTGGTGTACCTTCGATCCC 59.723 52.381 2.32 0.00 36.82 3.85
4275 8764 2.754946 TGTTGGTGTACCTTCGATCC 57.245 50.000 2.32 0.00 36.82 3.36
4276 8765 2.936498 CCATGTTGGTGTACCTTCGATC 59.064 50.000 2.32 0.00 36.82 3.69
4277 8766 2.939640 GCCATGTTGGTGTACCTTCGAT 60.940 50.000 2.32 0.00 40.46 3.59
4278 8767 1.609580 GCCATGTTGGTGTACCTTCGA 60.610 52.381 2.32 0.00 40.46 3.71
4279 8768 0.802494 GCCATGTTGGTGTACCTTCG 59.198 55.000 2.32 0.00 40.46 3.79
4280 8769 1.812571 CTGCCATGTTGGTGTACCTTC 59.187 52.381 2.32 0.00 40.46 3.46
4281 8770 1.909700 CTGCCATGTTGGTGTACCTT 58.090 50.000 2.32 0.00 40.46 3.50
4282 8771 0.609131 GCTGCCATGTTGGTGTACCT 60.609 55.000 2.32 0.00 40.46 3.08
4283 8772 1.595093 GGCTGCCATGTTGGTGTACC 61.595 60.000 15.17 0.00 40.46 3.34
4284 8773 0.893270 TGGCTGCCATGTTGGTGTAC 60.893 55.000 19.30 0.00 40.46 2.90
4285 8774 0.893270 GTGGCTGCCATGTTGGTGTA 60.893 55.000 26.22 0.00 40.46 2.90
4286 8775 2.198150 TGGCTGCCATGTTGGTGT 59.802 55.556 19.30 0.00 40.46 4.16
4287 8776 1.466025 AAGTGGCTGCCATGTTGGTG 61.466 55.000 26.22 0.00 40.46 4.17
4288 8777 0.760189 AAAGTGGCTGCCATGTTGGT 60.760 50.000 26.22 4.98 40.46 3.67
4289 8778 0.393820 AAAAGTGGCTGCCATGTTGG 59.606 50.000 26.22 0.00 41.55 3.77
4290 8779 1.342174 AGAAAAGTGGCTGCCATGTTG 59.658 47.619 26.22 0.00 35.28 3.33
4291 8780 1.615392 GAGAAAAGTGGCTGCCATGTT 59.385 47.619 26.22 18.15 35.28 2.71
4292 8781 1.202976 AGAGAAAAGTGGCTGCCATGT 60.203 47.619 26.22 12.79 35.28 3.21
4293 8782 1.542492 AGAGAAAAGTGGCTGCCATG 58.458 50.000 26.22 0.00 35.28 3.66
4294 8783 2.307098 AGTAGAGAAAAGTGGCTGCCAT 59.693 45.455 26.22 8.69 35.28 4.40
4295 8784 1.699634 AGTAGAGAAAAGTGGCTGCCA 59.300 47.619 19.30 19.30 0.00 4.92
4296 8785 2.027653 AGAGTAGAGAAAAGTGGCTGCC 60.028 50.000 12.87 12.87 0.00 4.85
4297 8786 3.258228 GAGAGTAGAGAAAAGTGGCTGC 58.742 50.000 0.00 0.00 0.00 5.25
4298 8787 3.191581 TCGAGAGTAGAGAAAAGTGGCTG 59.808 47.826 0.00 0.00 0.00 4.85
4299 8788 3.422796 TCGAGAGTAGAGAAAAGTGGCT 58.577 45.455 0.00 0.00 0.00 4.75
4300 8789 3.851976 TCGAGAGTAGAGAAAAGTGGC 57.148 47.619 0.00 0.00 0.00 5.01
4301 8790 5.031578 CGATTCGAGAGTAGAGAAAAGTGG 58.968 45.833 0.00 0.00 0.00 4.00
4302 8791 5.031578 CCGATTCGAGAGTAGAGAAAAGTG 58.968 45.833 7.83 0.00 0.00 3.16
4303 8792 4.701171 ACCGATTCGAGAGTAGAGAAAAGT 59.299 41.667 7.83 0.00 0.00 2.66
4304 8793 5.238006 ACCGATTCGAGAGTAGAGAAAAG 57.762 43.478 7.83 0.00 0.00 2.27
4305 8794 5.640189 AACCGATTCGAGAGTAGAGAAAA 57.360 39.130 7.83 0.00 0.00 2.29
4306 8795 5.640189 AAACCGATTCGAGAGTAGAGAAA 57.360 39.130 7.83 0.00 0.00 2.52
4307 8796 5.415077 AGAAAACCGATTCGAGAGTAGAGAA 59.585 40.000 7.83 0.00 34.46 2.87
4308 8797 4.942483 AGAAAACCGATTCGAGAGTAGAGA 59.058 41.667 7.83 0.00 34.46 3.10
4309 8798 5.238006 AGAAAACCGATTCGAGAGTAGAG 57.762 43.478 7.83 0.00 34.46 2.43
4310 8799 5.640189 AAGAAAACCGATTCGAGAGTAGA 57.360 39.130 7.83 0.00 34.46 2.59
4311 8800 7.701078 TGATTAAGAAAACCGATTCGAGAGTAG 59.299 37.037 7.83 0.00 34.46 2.57
4312 8801 7.487189 GTGATTAAGAAAACCGATTCGAGAGTA 59.513 37.037 7.83 0.00 34.46 2.59
4313 8802 6.310711 GTGATTAAGAAAACCGATTCGAGAGT 59.689 38.462 7.83 0.00 34.46 3.24
4314 8803 6.310467 TGTGATTAAGAAAACCGATTCGAGAG 59.690 38.462 7.83 0.00 34.46 3.20
4315 8804 6.160684 TGTGATTAAGAAAACCGATTCGAGA 58.839 36.000 7.83 0.00 34.46 4.04
4316 8805 6.403333 TGTGATTAAGAAAACCGATTCGAG 57.597 37.500 7.83 0.23 34.46 4.04
4317 8806 6.978343 ATGTGATTAAGAAAACCGATTCGA 57.022 33.333 7.83 0.00 34.46 3.71
4318 8807 8.995906 GTTTATGTGATTAAGAAAACCGATTCG 58.004 33.333 0.00 0.00 34.46 3.34
4319 8808 9.834628 TGTTTATGTGATTAAGAAAACCGATTC 57.165 29.630 0.00 0.00 0.00 2.52
4321 8810 9.840427 CTTGTTTATGTGATTAAGAAAACCGAT 57.160 29.630 0.00 0.00 0.00 4.18
4322 8811 8.842280 ACTTGTTTATGTGATTAAGAAAACCGA 58.158 29.630 0.00 0.00 0.00 4.69
4323 8812 9.458374 AACTTGTTTATGTGATTAAGAAAACCG 57.542 29.630 0.00 0.00 0.00 4.44
4360 8849 2.777832 AGCTGAGGAGGTGATTGAAC 57.222 50.000 0.00 0.00 0.00 3.18
4378 8867 1.317613 TTGCACACTTTAGGCCACAG 58.682 50.000 5.01 0.00 0.00 3.66
4416 8905 3.755905 TCTCAAGTGAAATGCGCCATTAA 59.244 39.130 4.18 0.00 32.43 1.40
4483 9132 4.104261 AGTTTATGGCTGGTCCCTATAACC 59.896 45.833 0.00 0.00 37.31 2.85
4485 9134 7.642094 ATTAGTTTATGGCTGGTCCCTATAA 57.358 36.000 0.00 0.00 0.00 0.98
4491 9140 4.532834 TCCAATTAGTTTATGGCTGGTCC 58.467 43.478 0.00 0.00 34.13 4.46


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

AutoCloner maintained by Alex Coulton.