Multiple sequence alignment - TraesCS2A01G405600

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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 TraesCS2A01G405600 chr2A 100.000 4252 0 0 1 4252 661445724 661449975 0.000000e+00 7853.0
1 TraesCS2A01G405600 chr2A 88.641 898 53 22 2491 3342 661395402 661396296 0.000000e+00 1048.0
2 TraesCS2A01G405600 chr2A 83.111 1202 127 45 859 2020 661151209 661152374 0.000000e+00 1026.0
3 TraesCS2A01G405600 chr2A 82.892 1134 135 28 2491 3606 661152495 661153587 0.000000e+00 965.0
4 TraesCS2A01G405600 chr2A 85.544 837 76 21 1161 1976 661394536 661395348 0.000000e+00 833.0
5 TraesCS2A01G405600 chr2A 85.172 580 68 9 2513 3078 661082678 661083253 2.850000e-161 579.0
6 TraesCS2A01G405600 chr2A 90.954 409 29 7 2085 2490 748770499 748770096 1.040000e-150 544.0
7 TraesCS2A01G405600 chr2A 90.529 359 29 3 3409 3762 661403477 661403835 1.790000e-128 470.0
8 TraesCS2A01G405600 chr2A 85.442 419 49 5 3779 4195 661405042 661405450 3.930000e-115 425.0
9 TraesCS2A01G405600 chr2A 79.592 490 69 14 3134 3596 661083307 661083792 5.300000e-84 322.0
10 TraesCS2A01G405600 chr2A 86.096 187 13 6 773 950 661149031 661149213 5.610000e-44 189.0
11 TraesCS2A01G405600 chr2D 95.035 1571 61 8 517 2084 517085714 517087270 0.000000e+00 2453.0
12 TraesCS2A01G405600 chr2D 93.548 1302 41 9 2491 3765 517087261 517088546 0.000000e+00 1899.0
13 TraesCS2A01G405600 chr2D 82.331 1330 135 53 741 2020 516924152 516925431 0.000000e+00 1062.0
14 TraesCS2A01G405600 chr2D 83.569 1132 142 21 2491 3606 516925551 516926654 0.000000e+00 1020.0
15 TraesCS2A01G405600 chr2D 81.737 1117 154 27 2513 3595 516863240 516864340 0.000000e+00 887.0
16 TraesCS2A01G405600 chr2D 86.790 757 70 16 1161 1909 517037468 517038202 0.000000e+00 817.0
17 TraesCS2A01G405600 chr2D 87.558 643 56 10 3336 3972 517045911 517046535 0.000000e+00 723.0
18 TraesCS2A01G405600 chr2D 92.667 450 28 2 2491 2935 517038284 517038733 0.000000e+00 643.0
19 TraesCS2A01G405600 chr2D 88.462 520 53 7 1 516 585349778 585349262 4.670000e-174 621.0
20 TraesCS2A01G405600 chr2D 92.365 406 24 3 3797 4198 517088540 517088942 4.770000e-159 571.0
21 TraesCS2A01G405600 chr2D 90.534 412 28 10 2085 2491 66134215 66133810 6.260000e-148 534.0
22 TraesCS2A01G405600 chr2D 86.283 452 25 12 2928 3342 517045421 517045872 1.390000e-124 457.0
23 TraesCS2A01G405600 chr2D 81.235 421 62 10 517 936 516872404 516872808 1.470000e-84 324.0
24 TraesCS2A01G405600 chr2D 89.362 94 4 4 1997 2084 517038200 517038293 3.470000e-21 113.0
25 TraesCS2A01G405600 chr2D 78.448 116 21 4 420 534 15592463 15592351 5.900000e-09 73.1
26 TraesCS2A01G405600 chr2D 86.792 53 5 1 897 947 516856636 516856688 1.650000e-04 58.4
27 TraesCS2A01G405600 chr2B 83.805 1130 123 26 2492 3603 608668091 608669178 0.000000e+00 1018.0
28 TraesCS2A01G405600 chr2B 87.708 903 60 16 2491 3342 608802810 608803712 0.000000e+00 1005.0
29 TraesCS2A01G405600 chr2B 82.609 1196 118 50 859 2015 608666791 608667935 0.000000e+00 974.0
30 TraesCS2A01G405600 chr2B 81.501 1119 154 32 2513 3596 608540838 608541938 0.000000e+00 870.0
31 TraesCS2A01G405600 chr2B 86.243 756 73 17 1161 1909 608801994 608802725 0.000000e+00 791.0
32 TraesCS2A01G405600 chr2B 91.463 410 26 8 2085 2491 391525938 391525535 4.800000e-154 555.0
33 TraesCS2A01G405600 chr2B 90.675 311 24 2 3363 3670 608803770 608804078 3.960000e-110 409.0
34 TraesCS2A01G405600 chr2B 89.753 283 21 5 3659 3935 608804173 608804453 5.230000e-94 355.0
35 TraesCS2A01G405600 chr2B 95.238 63 2 1 4190 4252 257923641 257923702 9.730000e-17 99.0
36 TraesCS2A01G405600 chr2B 86.598 97 4 4 1997 2084 608802723 608802819 9.730000e-17 99.0
37 TraesCS2A01G405600 chr5A 90.595 521 41 7 1 517 698950605 698951121 0.000000e+00 684.0
38 TraesCS2A01G405600 chr5A 90.843 415 26 7 2085 2490 126098068 126098479 2.890000e-151 545.0
39 TraesCS2A01G405600 chr5A 87.805 82 6 4 4173 4252 240225639 240225718 4.530000e-15 93.5
40 TraesCS2A01G405600 chr7B 88.868 521 52 6 1 518 664563353 664563870 1.670000e-178 636.0
41 TraesCS2A01G405600 chr6B 88.588 517 58 1 1 517 714815025 714814510 1.000000e-175 627.0
42 TraesCS2A01G405600 chr6B 90.164 427 29 10 2081 2501 156218841 156218422 1.040000e-150 544.0
43 TraesCS2A01G405600 chr6B 89.647 425 29 11 2081 2493 5678796 5679217 1.050000e-145 527.0
44 TraesCS2A01G405600 chr3D 88.350 515 50 9 8 517 470899807 470899298 1.010000e-170 610.0
45 TraesCS2A01G405600 chr3D 95.238 63 2 1 4190 4252 84562605 84562666 9.730000e-17 99.0
46 TraesCS2A01G405600 chr4D 87.743 514 51 11 8 516 416699003 416698497 1.320000e-164 590.0
47 TraesCS2A01G405600 chr4D 92.010 413 25 5 2084 2490 334160741 334160331 1.330000e-159 573.0
48 TraesCS2A01G405600 chr7D 88.024 501 48 11 1 493 54231251 54231747 2.200000e-162 582.0
49 TraesCS2A01G405600 chr7D 91.346 416 25 9 2084 2492 89076139 89075728 3.710000e-155 558.0
50 TraesCS2A01G405600 chr7D 87.805 82 8 2 4173 4252 565069400 565069319 1.260000e-15 95.3
51 TraesCS2A01G405600 chr7D 85.714 91 10 1 4165 4252 135442120 135442210 4.530000e-15 93.5
52 TraesCS2A01G405600 chr5D 86.998 523 60 8 1 517 540106402 540105882 2.200000e-162 582.0
53 TraesCS2A01G405600 chr1D 87.165 522 53 13 1 515 8851967 8852481 7.930000e-162 580.0
54 TraesCS2A01G405600 chr1D 90.268 411 30 9 2085 2490 195738160 195737755 2.910000e-146 529.0
55 TraesCS2A01G405600 chr1D 85.427 199 24 5 328 524 12818605 12818800 7.210000e-48 202.0
56 TraesCS2A01G405600 chr4A 80.124 322 31 16 1667 1976 541336410 541336110 4.310000e-50 209.0
57 TraesCS2A01G405600 chr1B 95.385 65 3 0 4188 4252 625574974 625574910 2.090000e-18 104.0
58 TraesCS2A01G405600 chr5B 91.667 72 5 1 4179 4250 703263391 703263461 9.730000e-17 99.0
59 TraesCS2A01G405600 chr5B 91.429 70 6 0 4182 4251 29363446 29363377 3.500000e-16 97.1
60 TraesCS2A01G405600 chr3A 93.939 66 3 1 4188 4252 209610977 209610912 9.730000e-17 99.0


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 TraesCS2A01G405600 chr2A 661445724 661449975 4251 False 7853.000000 7853 100.000000 1 4252 1 chr2A.!!$F1 4251
1 TraesCS2A01G405600 chr2A 661394536 661396296 1760 False 940.500000 1048 87.092500 1161 3342 2 chr2A.!!$F4 2181
2 TraesCS2A01G405600 chr2A 661149031 661153587 4556 False 726.666667 1026 84.033000 773 3606 3 chr2A.!!$F3 2833
3 TraesCS2A01G405600 chr2A 661082678 661083792 1114 False 450.500000 579 82.382000 2513 3596 2 chr2A.!!$F2 1083
4 TraesCS2A01G405600 chr2A 661403477 661405450 1973 False 447.500000 470 87.985500 3409 4195 2 chr2A.!!$F5 786
5 TraesCS2A01G405600 chr2D 517085714 517088942 3228 False 1641.000000 2453 93.649333 517 4198 3 chr2D.!!$F7 3681
6 TraesCS2A01G405600 chr2D 516924152 516926654 2502 False 1041.000000 1062 82.950000 741 3606 2 chr2D.!!$F4 2865
7 TraesCS2A01G405600 chr2D 516863240 516864340 1100 False 887.000000 887 81.737000 2513 3595 1 chr2D.!!$F2 1082
8 TraesCS2A01G405600 chr2D 585349262 585349778 516 True 621.000000 621 88.462000 1 516 1 chr2D.!!$R3 515
9 TraesCS2A01G405600 chr2D 517045421 517046535 1114 False 590.000000 723 86.920500 2928 3972 2 chr2D.!!$F6 1044
10 TraesCS2A01G405600 chr2D 517037468 517038733 1265 False 524.333333 817 89.606333 1161 2935 3 chr2D.!!$F5 1774
11 TraesCS2A01G405600 chr2B 608666791 608669178 2387 False 996.000000 1018 83.207000 859 3603 2 chr2B.!!$F3 2744
12 TraesCS2A01G405600 chr2B 608540838 608541938 1100 False 870.000000 870 81.501000 2513 3596 1 chr2B.!!$F2 1083
13 TraesCS2A01G405600 chr2B 608801994 608804453 2459 False 531.800000 1005 88.195400 1161 3935 5 chr2B.!!$F4 2774
14 TraesCS2A01G405600 chr5A 698950605 698951121 516 False 684.000000 684 90.595000 1 517 1 chr5A.!!$F3 516
15 TraesCS2A01G405600 chr7B 664563353 664563870 517 False 636.000000 636 88.868000 1 518 1 chr7B.!!$F1 517
16 TraesCS2A01G405600 chr6B 714814510 714815025 515 True 627.000000 627 88.588000 1 517 1 chr6B.!!$R2 516
17 TraesCS2A01G405600 chr3D 470899298 470899807 509 True 610.000000 610 88.350000 8 517 1 chr3D.!!$R1 509
18 TraesCS2A01G405600 chr4D 416698497 416699003 506 True 590.000000 590 87.743000 8 516 1 chr4D.!!$R2 508
19 TraesCS2A01G405600 chr5D 540105882 540106402 520 True 582.000000 582 86.998000 1 517 1 chr5D.!!$R1 516
20 TraesCS2A01G405600 chr1D 8851967 8852481 514 False 580.000000 580 87.165000 1 515 1 chr1D.!!$F1 514

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
436 445 0.245539 CACGAACCGGGACATGTACT 59.754 55.0 8.27 0.0 28.17 2.73 F
1843 4033 0.316196 GCGATCAATGCAACCGCTAC 60.316 55.0 12.12 0.0 42.24 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2077 4374 0.174845 CAAATCCGCCTCCGACACTA 59.825 55.0 0.00 0.0 36.29 2.74 R
3318 5751 0.526662 ACTAGCTGCTCCACACGTAC 59.473 55.0 4.91 0.0 0.00 3.67 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
150 151 3.356290 CAAATCTCGGGGAAAATGGAGT 58.644 45.455 0.00 0.00 0.00 3.85
158 159 1.550524 GGGAAAATGGAGTTTGGAGGC 59.449 52.381 0.00 0.00 0.00 4.70
198 199 1.067071 GCTTAACTAGTGTGGCTCGGT 60.067 52.381 0.00 0.00 0.00 4.69
213 214 2.609459 GCTCGGTCATTTCATCGAACAT 59.391 45.455 0.00 0.00 0.00 2.71
310 316 4.519437 CTCTGCTGCGGCGATGGA 62.519 66.667 12.98 7.51 42.25 3.41
311 317 4.081185 TCTGCTGCGGCGATGGAA 62.081 61.111 12.98 0.00 42.25 3.53
324 330 5.164233 CGGCGATGGAATATATATAGGCAG 58.836 45.833 0.00 0.00 0.00 4.85
341 347 1.247567 CAGCTCATTTGTCCCGGTTT 58.752 50.000 0.00 0.00 0.00 3.27
377 383 1.420138 ACAAATGGGTCCAGACGAACT 59.580 47.619 0.00 0.00 0.00 3.01
430 439 2.567497 GGACTCACGAACCGGGACA 61.567 63.158 6.32 0.00 32.99 4.02
431 440 1.590147 GACTCACGAACCGGGACAT 59.410 57.895 6.32 0.00 32.99 3.06
432 441 0.736325 GACTCACGAACCGGGACATG 60.736 60.000 6.32 0.00 32.99 3.21
434 443 0.528924 CTCACGAACCGGGACATGTA 59.471 55.000 6.32 0.00 32.99 2.29
436 445 0.245539 CACGAACCGGGACATGTACT 59.754 55.000 8.27 0.00 28.17 2.73
444 454 1.507140 GGGACATGTACTCCCATGGA 58.493 55.000 15.22 0.00 46.30 3.41
449 459 1.002430 CATGTACTCCCATGGATCCCG 59.998 57.143 15.22 0.00 38.83 5.14
454 464 2.111043 CCCATGGATCCCGGTTCG 59.889 66.667 15.22 0.00 0.00 3.95
458 468 0.810031 CATGGATCCCGGTTCGTGAC 60.810 60.000 9.90 0.00 0.00 3.67
459 469 0.976073 ATGGATCCCGGTTCGTGACT 60.976 55.000 9.90 0.00 0.00 3.41
518 528 6.869206 AAGCCCTGTTTTCTACTAGTGATA 57.131 37.500 5.39 0.00 0.00 2.15
527 537 8.627403 TGTTTTCTACTAGTGATAATACTCCCG 58.373 37.037 5.39 0.00 32.19 5.14
538 548 1.492764 ATACTCCCGGTACAACCAGG 58.507 55.000 0.00 0.00 38.47 4.45
539 549 1.259840 TACTCCCGGTACAACCAGGC 61.260 60.000 0.00 0.00 35.73 4.85
558 568 7.189794 ACCAGGCTACTAAGATATAGGCATTA 58.810 38.462 7.47 0.00 44.33 1.90
585 595 4.563184 GTGCACCGAAATTGTTTACACAAA 59.437 37.500 5.22 0.00 46.17 2.83
587 597 4.026393 GCACCGAAATTGTTTACACAAACC 60.026 41.667 0.00 0.00 46.17 3.27
588 598 4.205385 CACCGAAATTGTTTACACAAACCG 59.795 41.667 0.00 3.30 46.17 4.44
589 599 3.731717 CCGAAATTGTTTACACAAACCGG 59.268 43.478 0.00 0.00 46.17 5.28
591 601 5.505324 CCGAAATTGTTTACACAAACCGGTA 60.505 40.000 8.00 0.00 46.17 4.02
592 602 5.396070 CGAAATTGTTTACACAAACCGGTAC 59.604 40.000 8.00 0.00 46.17 3.34
608 619 5.362263 ACCGGTACAACGATTAAGCATTAT 58.638 37.500 4.49 0.00 35.47 1.28
615 626 6.821482 ACAACGATTAAGCATTATATCTGCG 58.179 36.000 0.00 0.00 44.38 5.18
625 636 2.394545 TATATCTGCGTGGTCGAACG 57.605 50.000 5.29 5.29 46.30 3.95
634 645 2.032204 GCGTGGTCGAACGTATATCTCT 60.032 50.000 10.99 0.00 45.32 3.10
701 712 4.331166 TTCGGCGCGAGAACACGA 62.331 61.111 12.10 6.31 37.14 4.35
721 732 3.576118 CGATGAAGGATCCATCTGGTACT 59.424 47.826 17.46 0.00 38.53 2.73
748 759 5.660864 TGGGTGTTGACAGATACATGATCTA 59.339 40.000 0.00 0.00 43.52 1.98
758 769 6.206243 ACAGATACATGATCTAGCAAAATGCC 59.794 38.462 0.00 0.00 43.25 4.40
775 786 1.580942 CCATGTGGCTTCAACACCG 59.419 57.895 0.00 0.00 38.05 4.94
779 790 1.034838 TGTGGCTTCAACACCGCTTT 61.035 50.000 0.00 0.00 38.05 3.51
853 871 4.315264 AAAAGGTGCCGCCCCCAT 62.315 61.111 0.00 0.00 38.26 4.00
1074 3225 5.660417 ACACACTCTATGGTCAGATTCATCT 59.340 40.000 0.00 0.00 37.72 2.90
1169 3326 4.027864 GCGTGAGACGTGCTTACTAATTAC 60.028 45.833 0.00 0.00 44.73 1.89
1386 3567 2.348971 TCTCGATCGATATAGCTCACGC 59.651 50.000 19.78 0.00 0.00 5.34
1421 3603 3.859961 CGGATGTGTGTTGACTATCTGTC 59.140 47.826 0.00 0.00 45.54 3.51
1732 3922 2.751436 GCATGGAGCGGGCAGAAA 60.751 61.111 0.00 0.00 0.00 2.52
1829 4019 2.509336 CGTGGTGGTGGAGCGATC 60.509 66.667 0.00 0.00 0.00 3.69
1843 4033 0.316196 GCGATCAATGCAACCGCTAC 60.316 55.000 12.12 0.00 42.24 3.58
1901 4091 7.527457 AGAACGAAAATCTTTTAATTCCTCCG 58.473 34.615 0.00 0.00 30.33 4.63
1922 4112 3.853671 CGTGCATTTGTGCCTTTAGATTC 59.146 43.478 0.00 0.00 0.00 2.52
1927 4117 6.935771 TGCATTTGTGCCTTTAGATTCATTTT 59.064 30.769 0.00 0.00 0.00 1.82
1946 4140 7.800767 TCATTTTTCAAATCTTCGTCTGAGAG 58.199 34.615 0.00 0.00 0.00 3.20
1948 4142 7.786178 TTTTTCAAATCTTCGTCTGAGAGAA 57.214 32.000 0.00 0.00 0.00 2.87
1949 4143 7.786178 TTTTCAAATCTTCGTCTGAGAGAAA 57.214 32.000 0.00 0.00 0.00 2.52
1950 4144 7.413475 TTTCAAATCTTCGTCTGAGAGAAAG 57.587 36.000 0.00 0.00 0.00 2.62
1951 4145 6.090483 TCAAATCTTCGTCTGAGAGAAAGT 57.910 37.500 4.31 0.00 0.00 2.66
2068 4365 3.971871 CGACGGTTAGTACAAACGTGTAA 59.028 43.478 20.54 0.00 41.89 2.41
2070 4367 5.386323 CGACGGTTAGTACAAACGTGTAAAG 60.386 44.000 20.54 7.54 41.89 1.85
2071 4368 4.209080 ACGGTTAGTACAAACGTGTAAAGC 59.791 41.667 16.64 0.00 41.89 3.51
2072 4369 4.208873 CGGTTAGTACAAACGTGTAAAGCA 59.791 41.667 0.00 0.00 41.89 3.91
2073 4370 5.276773 CGGTTAGTACAAACGTGTAAAGCAA 60.277 40.000 0.00 0.00 41.89 3.91
2074 4371 6.131389 GGTTAGTACAAACGTGTAAAGCAAG 58.869 40.000 0.00 0.00 41.89 4.01
2075 4372 6.238184 GGTTAGTACAAACGTGTAAAGCAAGT 60.238 38.462 0.00 0.00 41.89 3.16
2076 4373 7.042791 GGTTAGTACAAACGTGTAAAGCAAGTA 60.043 37.037 0.00 0.00 41.89 2.24
2077 4374 8.490355 GTTAGTACAAACGTGTAAAGCAAGTAT 58.510 33.333 0.00 0.00 41.89 2.12
2078 4375 9.689976 TTAGTACAAACGTGTAAAGCAAGTATA 57.310 29.630 0.00 0.00 41.89 1.47
2079 4376 8.236084 AGTACAAACGTGTAAAGCAAGTATAG 57.764 34.615 0.00 0.00 41.89 1.31
2080 4377 7.869429 AGTACAAACGTGTAAAGCAAGTATAGT 59.131 33.333 0.00 0.00 41.89 2.12
2081 4378 6.884187 ACAAACGTGTAAAGCAAGTATAGTG 58.116 36.000 0.00 0.00 38.82 2.74
2082 4379 6.480981 ACAAACGTGTAAAGCAAGTATAGTGT 59.519 34.615 0.00 0.00 38.82 3.55
2083 4380 6.701432 AACGTGTAAAGCAAGTATAGTGTC 57.299 37.500 0.00 0.00 38.82 3.67
2084 4381 4.855388 ACGTGTAAAGCAAGTATAGTGTCG 59.145 41.667 0.00 0.00 38.01 4.35
2085 4382 4.264614 CGTGTAAAGCAAGTATAGTGTCGG 59.735 45.833 0.00 0.00 0.00 4.79
2086 4383 5.404946 GTGTAAAGCAAGTATAGTGTCGGA 58.595 41.667 0.00 0.00 0.00 4.55
2087 4384 5.515626 GTGTAAAGCAAGTATAGTGTCGGAG 59.484 44.000 0.00 0.00 0.00 4.63
2088 4385 3.802948 AAGCAAGTATAGTGTCGGAGG 57.197 47.619 0.00 0.00 0.00 4.30
2089 4386 1.409427 AGCAAGTATAGTGTCGGAGGC 59.591 52.381 0.00 0.00 0.00 4.70
2090 4387 1.864435 GCAAGTATAGTGTCGGAGGCG 60.864 57.143 0.00 0.00 28.88 5.52
2091 4388 1.030457 AAGTATAGTGTCGGAGGCGG 58.970 55.000 0.00 0.00 28.88 6.13
2092 4389 0.182061 AGTATAGTGTCGGAGGCGGA 59.818 55.000 0.00 0.00 28.88 5.54
2093 4390 1.202903 AGTATAGTGTCGGAGGCGGAT 60.203 52.381 0.00 0.00 28.88 4.18
2094 4391 1.612463 GTATAGTGTCGGAGGCGGATT 59.388 52.381 0.00 0.00 28.88 3.01
2095 4392 1.120530 ATAGTGTCGGAGGCGGATTT 58.879 50.000 0.00 0.00 28.88 2.17
2096 4393 0.174845 TAGTGTCGGAGGCGGATTTG 59.825 55.000 0.00 0.00 28.88 2.32
2097 4394 1.375523 GTGTCGGAGGCGGATTTGT 60.376 57.895 0.00 0.00 28.88 2.83
2098 4395 1.375396 TGTCGGAGGCGGATTTGTG 60.375 57.895 0.00 0.00 28.88 3.33
2099 4396 2.106683 GTCGGAGGCGGATTTGTGG 61.107 63.158 0.00 0.00 0.00 4.17
2100 4397 2.046314 CGGAGGCGGATTTGTGGT 60.046 61.111 0.00 0.00 0.00 4.16
2101 4398 1.674322 CGGAGGCGGATTTGTGGTT 60.674 57.895 0.00 0.00 0.00 3.67
2102 4399 1.241315 CGGAGGCGGATTTGTGGTTT 61.241 55.000 0.00 0.00 0.00 3.27
2103 4400 1.828979 GGAGGCGGATTTGTGGTTTA 58.171 50.000 0.00 0.00 0.00 2.01
2104 4401 2.375146 GGAGGCGGATTTGTGGTTTAT 58.625 47.619 0.00 0.00 0.00 1.40
2105 4402 2.099098 GGAGGCGGATTTGTGGTTTATG 59.901 50.000 0.00 0.00 0.00 1.90
2106 4403 2.099098 GAGGCGGATTTGTGGTTTATGG 59.901 50.000 0.00 0.00 0.00 2.74
2107 4404 1.136110 GGCGGATTTGTGGTTTATGGG 59.864 52.381 0.00 0.00 0.00 4.00
2108 4405 1.136110 GCGGATTTGTGGTTTATGGGG 59.864 52.381 0.00 0.00 0.00 4.96
2109 4406 2.729194 CGGATTTGTGGTTTATGGGGA 58.271 47.619 0.00 0.00 0.00 4.81
2110 4407 2.425668 CGGATTTGTGGTTTATGGGGAC 59.574 50.000 0.00 0.00 0.00 4.46
2123 4420 2.634639 TGGGGACACCTACACACTAT 57.365 50.000 0.00 0.00 41.11 2.12
2124 4421 3.761685 TGGGGACACCTACACACTATA 57.238 47.619 0.00 0.00 41.11 1.31
2125 4422 4.274794 TGGGGACACCTACACACTATAT 57.725 45.455 0.00 0.00 41.11 0.86
2126 4423 3.964688 TGGGGACACCTACACACTATATG 59.035 47.826 0.00 0.00 41.11 1.78
2127 4424 4.220724 GGGGACACCTACACACTATATGA 58.779 47.826 0.00 0.00 36.80 2.15
2128 4425 4.281182 GGGGACACCTACACACTATATGAG 59.719 50.000 0.00 0.00 36.80 2.90
2129 4426 5.138276 GGGACACCTACACACTATATGAGA 58.862 45.833 0.00 0.00 0.00 3.27
2130 4427 5.597182 GGGACACCTACACACTATATGAGAA 59.403 44.000 0.00 0.00 0.00 2.87
2131 4428 6.097839 GGGACACCTACACACTATATGAGAAA 59.902 42.308 0.00 0.00 0.00 2.52
2132 4429 7.364408 GGGACACCTACACACTATATGAGAAAA 60.364 40.741 0.00 0.00 0.00 2.29
2133 4430 8.038944 GGACACCTACACACTATATGAGAAAAA 58.961 37.037 0.00 0.00 0.00 1.94
2168 4465 8.839310 TTCAACAAAAAGTCAAAAATTCCTGA 57.161 26.923 0.00 0.00 0.00 3.86
2169 4466 8.839310 TCAACAAAAAGTCAAAAATTCCTGAA 57.161 26.923 0.00 0.00 0.00 3.02
2170 4467 9.277783 TCAACAAAAAGTCAAAAATTCCTGAAA 57.722 25.926 0.00 0.00 0.00 2.69
2171 4468 9.890352 CAACAAAAAGTCAAAAATTCCTGAAAA 57.110 25.926 0.00 0.00 0.00 2.29
2210 4507 8.418597 AACTTGACCTTCTATTGTACTAGTGA 57.581 34.615 5.39 0.00 0.00 3.41
2211 4508 8.057536 ACTTGACCTTCTATTGTACTAGTGAG 57.942 38.462 5.39 0.00 0.00 3.51
2212 4509 7.889073 ACTTGACCTTCTATTGTACTAGTGAGA 59.111 37.037 5.39 0.00 0.00 3.27
2213 4510 8.645814 TTGACCTTCTATTGTACTAGTGAGAA 57.354 34.615 5.39 5.87 0.00 2.87
2214 4511 8.645814 TGACCTTCTATTGTACTAGTGAGAAA 57.354 34.615 5.39 0.00 0.00 2.52
2215 4512 9.085645 TGACCTTCTATTGTACTAGTGAGAAAA 57.914 33.333 5.39 0.00 0.00 2.29
2216 4513 9.924650 GACCTTCTATTGTACTAGTGAGAAAAA 57.075 33.333 5.39 0.00 0.00 1.94
2249 4546 9.739276 AAAAAGAAAATTTTCCCTTTGACTTCT 57.261 25.926 24.01 8.07 37.92 2.85
2250 4547 9.739276 AAAAGAAAATTTTCCCTTTGACTTCTT 57.261 25.926 24.01 7.29 37.92 2.52
2251 4548 9.739276 AAAGAAAATTTTCCCTTTGACTTCTTT 57.261 25.926 24.01 12.21 37.92 2.52
2252 4549 9.739276 AAGAAAATTTTCCCTTTGACTTCTTTT 57.261 25.926 24.01 6.83 37.92 2.27
2253 4550 9.383519 AGAAAATTTTCCCTTTGACTTCTTTTC 57.616 29.630 24.01 0.00 37.92 2.29
2254 4551 9.161629 GAAAATTTTCCCTTTGACTTCTTTTCA 57.838 29.630 18.43 0.00 32.16 2.69
2255 4552 9.513906 AAAATTTTCCCTTTGACTTCTTTTCAA 57.486 25.926 0.00 0.00 0.00 2.69
2256 4553 9.513906 AAATTTTCCCTTTGACTTCTTTTCAAA 57.486 25.926 0.00 0.00 39.99 2.69
2257 4554 9.513906 AATTTTCCCTTTGACTTCTTTTCAAAA 57.486 25.926 0.00 0.00 41.32 2.44
2258 4555 8.910351 TTTTCCCTTTGACTTCTTTTCAAAAA 57.090 26.923 0.00 0.00 41.32 1.94
2293 4590 9.906660 TTTTTGGCTAAAATAGTGTGAATAGTG 57.093 29.630 8.93 0.00 35.82 2.74
2294 4591 8.856153 TTTGGCTAAAATAGTGTGAATAGTGA 57.144 30.769 0.00 0.00 0.00 3.41
2295 4592 7.843490 TGGCTAAAATAGTGTGAATAGTGAC 57.157 36.000 0.00 0.00 0.00 3.67
2296 4593 6.821665 TGGCTAAAATAGTGTGAATAGTGACC 59.178 38.462 0.00 0.00 0.00 4.02
2297 4594 7.048512 GGCTAAAATAGTGTGAATAGTGACCT 58.951 38.462 0.00 0.00 0.00 3.85
2298 4595 8.202137 GGCTAAAATAGTGTGAATAGTGACCTA 58.798 37.037 0.00 0.00 0.00 3.08
2299 4596 9.765795 GCTAAAATAGTGTGAATAGTGACCTAT 57.234 33.333 0.00 0.00 35.33 2.57
2306 4603 8.478775 AGTGTGAATAGTGACCTATAATAGCA 57.521 34.615 0.00 0.00 32.57 3.49
2307 4604 8.924303 AGTGTGAATAGTGACCTATAATAGCAA 58.076 33.333 0.00 0.00 32.57 3.91
2308 4605 9.542462 GTGTGAATAGTGACCTATAATAGCAAA 57.458 33.333 0.00 0.00 32.57 3.68
2342 4639 4.799564 TTTTTGCTGTGAGGTCAACTTT 57.200 36.364 0.00 0.00 0.00 2.66
2343 4640 4.799564 TTTTGCTGTGAGGTCAACTTTT 57.200 36.364 0.00 0.00 0.00 2.27
2344 4641 3.781079 TTGCTGTGAGGTCAACTTTTG 57.219 42.857 0.00 0.00 0.00 2.44
2345 4642 2.722094 TGCTGTGAGGTCAACTTTTGT 58.278 42.857 0.00 0.00 0.00 2.83
2346 4643 3.088532 TGCTGTGAGGTCAACTTTTGTT 58.911 40.909 0.00 0.00 44.66 2.83
2347 4644 3.509575 TGCTGTGAGGTCAACTTTTGTTT 59.490 39.130 0.00 0.00 41.35 2.83
2348 4645 4.021544 TGCTGTGAGGTCAACTTTTGTTTT 60.022 37.500 0.00 0.00 41.35 2.43
2349 4646 4.929211 GCTGTGAGGTCAACTTTTGTTTTT 59.071 37.500 0.00 0.00 41.35 1.94
2464 4761 9.686683 AAAAATCCTCATATAGGGTGCATATAC 57.313 33.333 0.00 0.00 46.55 1.47
2465 4762 7.995052 AATCCTCATATAGGGTGCATATACA 57.005 36.000 0.00 0.00 46.55 2.29
2466 4763 7.995052 ATCCTCATATAGGGTGCATATACAA 57.005 36.000 0.00 0.00 46.55 2.41
2467 4764 7.182817 TCCTCATATAGGGTGCATATACAAC 57.817 40.000 0.00 0.00 46.55 3.32
2475 4772 3.616219 GGTGCATATACAACCAGGAACA 58.384 45.455 0.00 0.00 0.00 3.18
2476 4773 3.377172 GGTGCATATACAACCAGGAACAC 59.623 47.826 0.00 0.00 0.00 3.32
2477 4774 4.006989 GTGCATATACAACCAGGAACACA 58.993 43.478 0.00 0.00 0.00 3.72
2478 4775 4.457603 GTGCATATACAACCAGGAACACAA 59.542 41.667 0.00 0.00 0.00 3.33
2479 4776 4.699735 TGCATATACAACCAGGAACACAAG 59.300 41.667 0.00 0.00 0.00 3.16
2480 4777 4.700213 GCATATACAACCAGGAACACAAGT 59.300 41.667 0.00 0.00 0.00 3.16
2481 4778 5.391950 GCATATACAACCAGGAACACAAGTG 60.392 44.000 0.00 0.00 0.00 3.16
2483 4780 3.637911 ACAACCAGGAACACAAGTGTA 57.362 42.857 6.24 0.00 44.13 2.90
2484 4781 4.164843 ACAACCAGGAACACAAGTGTAT 57.835 40.909 6.24 0.00 44.13 2.29
2485 4782 4.532834 ACAACCAGGAACACAAGTGTATT 58.467 39.130 6.24 0.00 44.13 1.89
2486 4783 4.953579 ACAACCAGGAACACAAGTGTATTT 59.046 37.500 6.24 0.00 44.13 1.40
2487 4784 5.067283 ACAACCAGGAACACAAGTGTATTTC 59.933 40.000 6.24 0.83 44.13 2.17
2488 4785 4.142038 ACCAGGAACACAAGTGTATTTCC 58.858 43.478 12.48 12.48 44.13 3.13
2489 4786 3.506067 CCAGGAACACAAGTGTATTTCCC 59.494 47.826 15.43 8.77 44.13 3.97
2550 4852 3.242413 GCATGTAACCTCATTGCGTACTG 60.242 47.826 0.00 0.00 0.00 2.74
2614 4919 4.056125 CCGACGTGGAGCTGAGCA 62.056 66.667 7.39 0.00 42.00 4.26
2635 4940 1.906990 ATTCAGCAGCAAGAACAGCT 58.093 45.000 0.00 0.00 44.62 4.24
2649 4954 2.251409 ACAGCTCGCAGATGCATATT 57.749 45.000 0.00 0.00 42.21 1.28
3048 5416 4.553330 ACGTCCACTTCATCAATACCTT 57.447 40.909 0.00 0.00 0.00 3.50
3081 5451 0.973632 ATCAAGACGTGGCAGGTACA 59.026 50.000 13.47 0.00 0.00 2.90
3082 5452 0.317160 TCAAGACGTGGCAGGTACAG 59.683 55.000 13.47 5.98 0.00 2.74
3125 5518 1.160137 CTGAAACCGGCCTTCTCTTG 58.840 55.000 15.73 3.22 0.00 3.02
3132 5525 1.339151 CCGGCCTTCTCTTGCTAACTT 60.339 52.381 0.00 0.00 0.00 2.66
3318 5751 7.387673 TGTTCATTAACTGTTGGACTATCTGTG 59.612 37.037 2.69 0.00 36.51 3.66
3338 5794 0.526211 TACGTGTGGAGCAGCTAGTG 59.474 55.000 0.00 0.00 0.00 2.74
3369 5872 0.537188 GCGTCTTCTTCTGGGGATCA 59.463 55.000 0.00 0.00 0.00 2.92
3459 5962 4.395583 GACGGCCGTCGAGTTCGT 62.396 66.667 39.77 11.15 42.43 3.85
3533 6039 0.177373 ATTTCCGTACGGAGAAGCCC 59.823 55.000 33.67 0.00 46.06 5.19
3614 6120 8.154856 TCCCTTGCCTTAGATAATGTATGTAAC 58.845 37.037 0.00 0.00 0.00 2.50
3678 6290 1.467734 GCAGTGCATTTGGAGAGAGTG 59.532 52.381 11.09 0.00 0.00 3.51
3790 7608 5.592054 TCTTCGCAAGGAATATGTCTACAG 58.408 41.667 0.00 0.00 33.26 2.74
3800 7618 7.283329 AGGAATATGTCTACAGCCCTTAAAAG 58.717 38.462 0.00 0.00 0.00 2.27
3884 7702 5.066634 TGCTAGAAAAACACGATCCACAAAA 59.933 36.000 0.00 0.00 0.00 2.44
3980 7805 4.142469 GGCAAGGCTACGACAAATAACAAT 60.142 41.667 0.00 0.00 0.00 2.71
4104 7929 7.605309 AGAACGGAAATAACTAGTTAAGGGTTG 59.395 37.037 18.88 10.11 0.00 3.77
4122 7947 1.422531 TGCCCCTTTGCAAAAGTCAT 58.577 45.000 13.84 0.00 38.56 3.06
4123 7948 1.344114 TGCCCCTTTGCAAAAGTCATC 59.656 47.619 13.84 1.65 38.56 2.92
4170 7995 0.665298 GCGCATCTGGGAATTTCTCC 59.335 55.000 0.30 0.00 44.54 3.71
4183 8008 6.183361 TGGGAATTTCTCCTTTTCAGTAGACA 60.183 38.462 0.00 0.00 44.68 3.41
4185 8010 6.710744 GGAATTTCTCCTTTTCAGTAGACACA 59.289 38.462 0.00 0.00 41.61 3.72
4205 8030 9.307121 AGACACATTTATTCAATACTCTCTTCG 57.693 33.333 0.00 0.00 0.00 3.79
4206 8031 9.088512 GACACATTTATTCAATACTCTCTTCGT 57.911 33.333 0.00 0.00 0.00 3.85
4207 8032 9.088512 ACACATTTATTCAATACTCTCTTCGTC 57.911 33.333 0.00 0.00 0.00 4.20
4208 8033 8.543774 CACATTTATTCAATACTCTCTTCGTCC 58.456 37.037 0.00 0.00 0.00 4.79
4209 8034 7.435488 ACATTTATTCAATACTCTCTTCGTCCG 59.565 37.037 0.00 0.00 0.00 4.79
4210 8035 6.688637 TTATTCAATACTCTCTTCGTCCGA 57.311 37.500 0.00 0.00 0.00 4.55
4211 8036 5.578005 ATTCAATACTCTCTTCGTCCGAA 57.422 39.130 1.81 1.81 0.00 4.30
4212 8037 5.381174 TTCAATACTCTCTTCGTCCGAAA 57.619 39.130 3.52 0.00 33.34 3.46
4213 8038 5.381174 TCAATACTCTCTTCGTCCGAAAA 57.619 39.130 3.52 0.00 33.34 2.29
4214 8039 5.962433 TCAATACTCTCTTCGTCCGAAAAT 58.038 37.500 3.52 0.00 33.34 1.82
4215 8040 7.092137 TCAATACTCTCTTCGTCCGAAAATA 57.908 36.000 3.52 0.00 33.34 1.40
4216 8041 6.971184 TCAATACTCTCTTCGTCCGAAAATAC 59.029 38.462 3.52 0.00 33.34 1.89
4217 8042 6.696441 ATACTCTCTTCGTCCGAAAATACT 57.304 37.500 3.52 0.00 33.34 2.12
4218 8043 5.388408 ACTCTCTTCGTCCGAAAATACTT 57.612 39.130 3.52 0.00 33.34 2.24
4219 8044 5.162075 ACTCTCTTCGTCCGAAAATACTTG 58.838 41.667 3.52 0.00 33.34 3.16
4220 8045 5.130292 TCTCTTCGTCCGAAAATACTTGT 57.870 39.130 3.52 0.00 33.34 3.16
4221 8046 5.159209 TCTCTTCGTCCGAAAATACTTGTC 58.841 41.667 3.52 0.00 33.34 3.18
4222 8047 4.873817 TCTTCGTCCGAAAATACTTGTCA 58.126 39.130 3.52 0.00 33.34 3.58
4223 8048 5.475719 TCTTCGTCCGAAAATACTTGTCAT 58.524 37.500 3.52 0.00 33.34 3.06
4224 8049 5.575606 TCTTCGTCCGAAAATACTTGTCATC 59.424 40.000 3.52 0.00 33.34 2.92
4225 8050 4.811908 TCGTCCGAAAATACTTGTCATCA 58.188 39.130 0.00 0.00 0.00 3.07
4226 8051 5.231702 TCGTCCGAAAATACTTGTCATCAA 58.768 37.500 0.00 0.00 0.00 2.57
4227 8052 5.697178 TCGTCCGAAAATACTTGTCATCAAA 59.303 36.000 0.00 0.00 32.87 2.69
4228 8053 6.203145 TCGTCCGAAAATACTTGTCATCAAAA 59.797 34.615 0.00 0.00 32.87 2.44
4229 8054 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
4230 8055 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
4231 8056 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
4232 8057 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
4233 8058 7.975616 CCGAAAATACTTGTCATCAAAATGGAT 59.024 33.333 0.00 0.00 33.42 3.41
4241 8066 8.096414 ACTTGTCATCAAAATGGATAAAAAGGG 58.904 33.333 0.00 0.00 33.42 3.95
4242 8067 7.789202 TGTCATCAAAATGGATAAAAAGGGA 57.211 32.000 0.00 0.00 33.42 4.20
4243 8068 8.378115 TGTCATCAAAATGGATAAAAAGGGAT 57.622 30.769 0.00 0.00 33.42 3.85
4244 8069 8.259411 TGTCATCAAAATGGATAAAAAGGGATG 58.741 33.333 0.00 0.00 33.42 3.51
4245 8070 8.260114 GTCATCAAAATGGATAAAAAGGGATGT 58.740 33.333 0.00 0.00 33.42 3.06
4246 8071 9.486123 TCATCAAAATGGATAAAAAGGGATGTA 57.514 29.630 0.00 0.00 33.42 2.29
4249 8074 9.713684 TCAAAATGGATAAAAAGGGATGTATCT 57.286 29.630 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 4.796231 GCCGTCGATCGCCTGTGT 62.796 66.667 11.09 0.00 38.35 3.72
150 151 2.047274 CGAAGCTCGGCCTCCAAA 60.047 61.111 0.00 0.00 36.00 3.28
158 159 0.811915 TTTCTCCTCTCGAAGCTCGG 59.188 55.000 5.87 0.00 40.88 4.63
198 199 5.220719 GCACATGAGATGTTCGATGAAATGA 60.221 40.000 0.00 0.00 42.70 2.57
213 214 2.697229 CTCACCTCCTATGCACATGAGA 59.303 50.000 0.00 0.00 35.22 3.27
310 316 7.995488 GGGACAAATGAGCTGCCTATATATATT 59.005 37.037 0.00 0.00 0.00 1.28
311 317 7.512992 GGGACAAATGAGCTGCCTATATATAT 58.487 38.462 0.00 0.00 0.00 0.86
324 330 0.958822 ACAAACCGGGACAAATGAGC 59.041 50.000 6.32 0.00 0.00 4.26
341 347 2.136298 TTGTCTTGGTTTCAGCCACA 57.864 45.000 0.00 0.00 38.42 4.17
354 360 1.697432 TCGTCTGGACCCATTTGTCTT 59.303 47.619 0.00 0.00 35.54 3.01
355 361 1.348064 TCGTCTGGACCCATTTGTCT 58.652 50.000 0.00 0.00 35.54 3.41
377 383 1.303236 CTCGTGGGCATTGGTTCCA 60.303 57.895 0.00 0.00 0.00 3.53
414 423 1.292223 CATGTCCCGGTTCGTGAGT 59.708 57.895 0.00 0.00 0.00 3.41
430 439 1.352083 CGGGATCCATGGGAGTACAT 58.648 55.000 15.23 0.00 34.05 2.29
431 440 0.762842 CCGGGATCCATGGGAGTACA 60.763 60.000 15.23 0.00 34.05 2.90
432 441 0.763223 ACCGGGATCCATGGGAGTAC 60.763 60.000 22.37 0.00 34.05 2.73
434 443 1.307866 AACCGGGATCCATGGGAGT 60.308 57.895 22.37 7.99 34.05 3.85
436 445 2.439960 CGAACCGGGATCCATGGGA 61.440 63.158 22.37 0.00 35.55 4.37
444 454 0.037605 GTTCAGTCACGAACCGGGAT 60.038 55.000 6.32 0.00 42.67 3.85
454 464 3.512680 CCATTAGTCTCGGTTCAGTCAC 58.487 50.000 0.00 0.00 0.00 3.67
458 468 1.482593 AGCCCATTAGTCTCGGTTCAG 59.517 52.381 0.00 0.00 0.00 3.02
459 469 1.568504 AGCCCATTAGTCTCGGTTCA 58.431 50.000 0.00 0.00 0.00 3.18
466 476 1.428869 CCTGGCTAGCCCATTAGTCT 58.571 55.000 30.81 0.00 44.33 3.24
527 537 6.667558 ATATCTTAGTAGCCTGGTTGTACC 57.332 41.667 0.00 0.00 39.22 3.34
558 568 5.289917 GTGTAAACAATTTCGGTGCACTTTT 59.710 36.000 17.98 6.22 0.00 2.27
584 594 3.042871 TGCTTAATCGTTGTACCGGTT 57.957 42.857 15.04 0.00 35.02 4.44
585 595 2.747396 TGCTTAATCGTTGTACCGGT 57.253 45.000 13.98 13.98 0.00 5.28
587 597 8.373256 CAGATATAATGCTTAATCGTTGTACCG 58.627 37.037 0.00 0.00 0.00 4.02
588 598 8.169268 GCAGATATAATGCTTAATCGTTGTACC 58.831 37.037 5.36 0.00 40.59 3.34
589 599 7.893236 CGCAGATATAATGCTTAATCGTTGTAC 59.107 37.037 9.91 0.00 41.61 2.90
591 601 6.423905 ACGCAGATATAATGCTTAATCGTTGT 59.576 34.615 9.91 0.00 41.61 3.32
592 602 6.733725 CACGCAGATATAATGCTTAATCGTTG 59.266 38.462 9.91 0.00 41.61 4.10
608 619 1.085893 TACGTTCGACCACGCAGATA 58.914 50.000 9.46 0.00 44.37 1.98
615 626 6.882458 AAAAAGAGATATACGTTCGACCAC 57.118 37.500 0.00 0.00 0.00 4.16
671 682 1.332377 GCGCCGAAGAAATGAAGATCG 60.332 52.381 0.00 0.00 0.00 3.69
701 712 3.649981 CCAGTACCAGATGGATCCTTCAT 59.350 47.826 25.15 14.58 39.02 2.57
721 732 2.050918 TGTATCTGTCAACACCCACCA 58.949 47.619 0.00 0.00 0.00 4.17
758 769 1.081242 GCGGTGTTGAAGCCACATG 60.081 57.895 0.00 0.00 34.46 3.21
775 786 2.224018 TGGTGTTGAAGATTGCCAAAGC 60.224 45.455 0.00 0.00 40.48 3.51
779 790 3.196469 TGTTTTGGTGTTGAAGATTGCCA 59.804 39.130 0.00 0.00 0.00 4.92
834 852 4.986708 GGGGGCGGCACCTTTTCA 62.987 66.667 25.50 0.00 39.10 2.69
853 871 2.025418 GCCGGAGAAGCGTCGAAAA 61.025 57.895 5.05 0.00 0.00 2.29
876 894 7.695055 TGTTTTCCTGTGGGGGTATATATATG 58.305 38.462 5.44 0.00 35.33 1.78
1094 3245 4.378356 CCAGCACGTACGTACTAGTTGTTA 60.378 45.833 22.34 0.00 0.00 2.41
1095 3246 3.558505 CAGCACGTACGTACTAGTTGTT 58.441 45.455 22.34 9.85 0.00 2.83
1096 3247 2.095567 CCAGCACGTACGTACTAGTTGT 60.096 50.000 22.34 10.38 0.00 3.32
1169 3326 1.164662 CCGATGATGCCCTGCAAGAG 61.165 60.000 0.00 0.00 43.62 2.85
1306 3472 1.954146 CTTGGTGTCGTCCGTGGTG 60.954 63.158 0.00 0.00 0.00 4.17
1386 3567 1.949133 CATCCGGCCGTCACGTATG 60.949 63.158 26.12 13.04 0.00 2.39
1587 3772 1.480137 AGAGCAGATCAGGAAAGACGG 59.520 52.381 0.00 0.00 0.00 4.79
1732 3922 6.240002 GGACCTGGTAGAACATCATCCAATAT 60.240 42.308 0.00 0.00 0.00 1.28
1843 4033 1.374758 GAGTTGGGCTCTCACACCG 60.375 63.158 0.00 0.00 40.98 4.94
1922 4112 7.800767 TCTCTCAGACGAAGATTTGAAAAATG 58.199 34.615 0.00 0.00 0.00 2.32
1927 4117 6.422100 CACTTTCTCTCAGACGAAGATTTGAA 59.578 38.462 0.00 0.00 0.00 2.69
1980 4174 5.393962 AGTGAAAACTGATAAATGCTTCGC 58.606 37.500 0.00 0.00 0.00 4.70
2068 4365 2.159085 GCCTCCGACACTATACTTGCTT 60.159 50.000 0.00 0.00 0.00 3.91
2070 4367 1.854227 GCCTCCGACACTATACTTGC 58.146 55.000 0.00 0.00 0.00 4.01
2071 4368 1.269102 CCGCCTCCGACACTATACTTG 60.269 57.143 0.00 0.00 36.29 3.16
2072 4369 1.030457 CCGCCTCCGACACTATACTT 58.970 55.000 0.00 0.00 36.29 2.24
2073 4370 0.182061 TCCGCCTCCGACACTATACT 59.818 55.000 0.00 0.00 36.29 2.12
2074 4371 1.245732 ATCCGCCTCCGACACTATAC 58.754 55.000 0.00 0.00 36.29 1.47
2075 4372 1.991121 AATCCGCCTCCGACACTATA 58.009 50.000 0.00 0.00 36.29 1.31
2076 4373 1.120530 AAATCCGCCTCCGACACTAT 58.879 50.000 0.00 0.00 36.29 2.12
2077 4374 0.174845 CAAATCCGCCTCCGACACTA 59.825 55.000 0.00 0.00 36.29 2.74
2078 4375 1.079127 CAAATCCGCCTCCGACACT 60.079 57.895 0.00 0.00 36.29 3.55
2079 4376 1.375523 ACAAATCCGCCTCCGACAC 60.376 57.895 0.00 0.00 36.29 3.67
2080 4377 1.375396 CACAAATCCGCCTCCGACA 60.375 57.895 0.00 0.00 36.29 4.35
2081 4378 2.106683 CCACAAATCCGCCTCCGAC 61.107 63.158 0.00 0.00 36.29 4.79
2082 4379 2.119484 AACCACAAATCCGCCTCCGA 62.119 55.000 0.00 0.00 36.29 4.55
2083 4380 1.241315 AAACCACAAATCCGCCTCCG 61.241 55.000 0.00 0.00 0.00 4.63
2084 4381 1.828979 TAAACCACAAATCCGCCTCC 58.171 50.000 0.00 0.00 0.00 4.30
2085 4382 2.099098 CCATAAACCACAAATCCGCCTC 59.901 50.000 0.00 0.00 0.00 4.70
2086 4383 2.099405 CCATAAACCACAAATCCGCCT 58.901 47.619 0.00 0.00 0.00 5.52
2087 4384 1.136110 CCCATAAACCACAAATCCGCC 59.864 52.381 0.00 0.00 0.00 6.13
2088 4385 1.136110 CCCCATAAACCACAAATCCGC 59.864 52.381 0.00 0.00 0.00 5.54
2089 4386 2.425668 GTCCCCATAAACCACAAATCCG 59.574 50.000 0.00 0.00 0.00 4.18
2090 4387 3.194755 GTGTCCCCATAAACCACAAATCC 59.805 47.826 0.00 0.00 0.00 3.01
2091 4388 3.194755 GGTGTCCCCATAAACCACAAATC 59.805 47.826 0.00 0.00 32.69 2.17
2092 4389 3.169908 GGTGTCCCCATAAACCACAAAT 58.830 45.455 0.00 0.00 32.69 2.32
2093 4390 2.178106 AGGTGTCCCCATAAACCACAAA 59.822 45.455 0.00 0.00 35.01 2.83
2094 4391 1.783979 AGGTGTCCCCATAAACCACAA 59.216 47.619 0.00 0.00 35.01 3.33
2095 4392 1.451449 AGGTGTCCCCATAAACCACA 58.549 50.000 0.00 0.00 35.01 4.17
2096 4393 2.306512 TGTAGGTGTCCCCATAAACCAC 59.693 50.000 0.00 0.00 35.01 4.16
2097 4394 2.306512 GTGTAGGTGTCCCCATAAACCA 59.693 50.000 0.00 0.00 35.01 3.67
2098 4395 2.306512 TGTGTAGGTGTCCCCATAAACC 59.693 50.000 0.00 0.00 34.66 3.27
2099 4396 3.008704 AGTGTGTAGGTGTCCCCATAAAC 59.991 47.826 0.00 0.00 34.66 2.01
2100 4397 3.253220 AGTGTGTAGGTGTCCCCATAAA 58.747 45.455 0.00 0.00 34.66 1.40
2101 4398 2.910544 AGTGTGTAGGTGTCCCCATAA 58.089 47.619 0.00 0.00 34.66 1.90
2102 4399 2.634639 AGTGTGTAGGTGTCCCCATA 57.365 50.000 0.00 0.00 34.66 2.74
2103 4400 2.634639 TAGTGTGTAGGTGTCCCCAT 57.365 50.000 0.00 0.00 34.66 4.00
2104 4401 2.634639 ATAGTGTGTAGGTGTCCCCA 57.365 50.000 0.00 0.00 34.66 4.96
2105 4402 4.220724 TCATATAGTGTGTAGGTGTCCCC 58.779 47.826 0.00 0.00 0.00 4.81
2106 4403 5.138276 TCTCATATAGTGTGTAGGTGTCCC 58.862 45.833 0.00 0.00 0.00 4.46
2107 4404 6.710597 TTCTCATATAGTGTGTAGGTGTCC 57.289 41.667 0.00 0.00 0.00 4.02
2108 4405 8.997621 TTTTTCTCATATAGTGTGTAGGTGTC 57.002 34.615 0.00 0.00 0.00 3.67
2142 4439 9.447157 TCAGGAATTTTTGACTTTTTGTTGAAT 57.553 25.926 0.00 0.00 0.00 2.57
2143 4440 8.839310 TCAGGAATTTTTGACTTTTTGTTGAA 57.161 26.923 0.00 0.00 0.00 2.69
2144 4441 8.839310 TTCAGGAATTTTTGACTTTTTGTTGA 57.161 26.923 0.00 0.00 0.00 3.18
2145 4442 9.890352 TTTTCAGGAATTTTTGACTTTTTGTTG 57.110 25.926 0.00 0.00 0.00 3.33
2184 4481 8.867097 TCACTAGTACAATAGAAGGTCAAGTTT 58.133 33.333 0.00 0.00 0.00 2.66
2185 4482 8.418597 TCACTAGTACAATAGAAGGTCAAGTT 57.581 34.615 0.00 0.00 0.00 2.66
2186 4483 7.889073 TCTCACTAGTACAATAGAAGGTCAAGT 59.111 37.037 0.00 0.00 0.00 3.16
2187 4484 8.282455 TCTCACTAGTACAATAGAAGGTCAAG 57.718 38.462 0.00 0.00 0.00 3.02
2188 4485 8.645814 TTCTCACTAGTACAATAGAAGGTCAA 57.354 34.615 0.00 0.00 0.00 3.18
2189 4486 8.645814 TTTCTCACTAGTACAATAGAAGGTCA 57.354 34.615 0.00 0.00 0.00 4.02
2190 4487 9.924650 TTTTTCTCACTAGTACAATAGAAGGTC 57.075 33.333 0.00 0.00 0.00 3.85
2223 4520 9.739276 AGAAGTCAAAGGGAAAATTTTCTTTTT 57.261 25.926 25.86 21.78 37.35 1.94
2224 4521 9.739276 AAGAAGTCAAAGGGAAAATTTTCTTTT 57.261 25.926 25.86 22.05 37.35 2.27
2225 4522 9.739276 AAAGAAGTCAAAGGGAAAATTTTCTTT 57.261 25.926 25.86 17.89 37.46 2.52
2226 4523 9.739276 AAAAGAAGTCAAAGGGAAAATTTTCTT 57.261 25.926 25.86 13.61 37.35 2.52
2227 4524 9.383519 GAAAAGAAGTCAAAGGGAAAATTTTCT 57.616 29.630 25.86 8.60 37.35 2.52
2228 4525 9.161629 TGAAAAGAAGTCAAAGGGAAAATTTTC 57.838 29.630 20.51 20.51 34.90 2.29
2229 4526 9.513906 TTGAAAAGAAGTCAAAGGGAAAATTTT 57.486 25.926 2.28 2.28 32.13 1.82
2230 4527 9.513906 TTTGAAAAGAAGTCAAAGGGAAAATTT 57.486 25.926 0.00 0.00 39.46 1.82
2231 4528 9.513906 TTTTGAAAAGAAGTCAAAGGGAAAATT 57.486 25.926 0.47 0.00 43.76 1.82
2232 4529 9.513906 TTTTTGAAAAGAAGTCAAAGGGAAAAT 57.486 25.926 0.47 0.00 43.76 1.82
2233 4530 8.910351 TTTTTGAAAAGAAGTCAAAGGGAAAA 57.090 26.923 0.47 0.00 43.76 2.29
2267 4564 9.906660 CACTATTCACACTATTTTAGCCAAAAA 57.093 29.630 0.00 0.00 41.21 1.94
2268 4565 9.290988 TCACTATTCACACTATTTTAGCCAAAA 57.709 29.630 0.00 0.00 38.00 2.44
2269 4566 8.726988 GTCACTATTCACACTATTTTAGCCAAA 58.273 33.333 0.00 0.00 0.00 3.28
2270 4567 7.335924 GGTCACTATTCACACTATTTTAGCCAA 59.664 37.037 0.00 0.00 0.00 4.52
2271 4568 6.821665 GGTCACTATTCACACTATTTTAGCCA 59.178 38.462 0.00 0.00 0.00 4.75
2272 4569 7.048512 AGGTCACTATTCACACTATTTTAGCC 58.951 38.462 0.00 0.00 0.00 3.93
2273 4570 9.765795 ATAGGTCACTATTCACACTATTTTAGC 57.234 33.333 0.00 0.00 36.51 3.09
2280 4577 9.582648 TGCTATTATAGGTCACTATTCACACTA 57.417 33.333 1.12 0.00 40.35 2.74
2281 4578 8.478775 TGCTATTATAGGTCACTATTCACACT 57.521 34.615 1.12 0.00 40.35 3.55
2282 4579 9.542462 TTTGCTATTATAGGTCACTATTCACAC 57.458 33.333 1.12 0.00 40.35 3.82
2321 4618 4.799564 AAAGTTGACCTCACAGCAAAAA 57.200 36.364 0.00 0.00 0.00 1.94
2322 4619 4.021544 ACAAAAGTTGACCTCACAGCAAAA 60.022 37.500 0.00 0.00 0.00 2.44
2323 4620 3.509575 ACAAAAGTTGACCTCACAGCAAA 59.490 39.130 0.00 0.00 0.00 3.68
2324 4621 3.088532 ACAAAAGTTGACCTCACAGCAA 58.911 40.909 0.00 0.00 0.00 3.91
2325 4622 2.722094 ACAAAAGTTGACCTCACAGCA 58.278 42.857 0.00 0.00 0.00 4.41
2326 4623 3.782889 AACAAAAGTTGACCTCACAGC 57.217 42.857 0.00 0.00 0.00 4.40
2444 4741 6.070251 TGGTTGTATATGCACCCTATATGAGG 60.070 42.308 8.77 0.00 46.25 3.86
2445 4742 6.946340 TGGTTGTATATGCACCCTATATGAG 58.054 40.000 8.77 0.00 0.00 2.90
2446 4743 6.070251 CCTGGTTGTATATGCACCCTATATGA 60.070 42.308 8.77 0.00 0.00 2.15
2447 4744 6.070251 TCCTGGTTGTATATGCACCCTATATG 60.070 42.308 8.77 0.00 0.00 1.78
2448 4745 6.029431 TCCTGGTTGTATATGCACCCTATAT 58.971 40.000 8.77 0.00 0.00 0.86
2449 4746 5.407936 TCCTGGTTGTATATGCACCCTATA 58.592 41.667 8.77 0.00 0.00 1.31
2450 4747 4.239495 TCCTGGTTGTATATGCACCCTAT 58.761 43.478 8.77 0.00 0.00 2.57
2451 4748 3.659841 TCCTGGTTGTATATGCACCCTA 58.340 45.455 8.77 0.00 0.00 3.53
2452 4749 2.487775 TCCTGGTTGTATATGCACCCT 58.512 47.619 8.77 0.00 0.00 4.34
2453 4750 2.949644 GTTCCTGGTTGTATATGCACCC 59.050 50.000 0.12 0.12 0.00 4.61
2454 4751 3.377172 GTGTTCCTGGTTGTATATGCACC 59.623 47.826 0.00 0.00 0.00 5.01
2455 4752 4.006989 TGTGTTCCTGGTTGTATATGCAC 58.993 43.478 0.00 0.00 0.00 4.57
2456 4753 4.293662 TGTGTTCCTGGTTGTATATGCA 57.706 40.909 0.00 0.00 0.00 3.96
2457 4754 4.700213 ACTTGTGTTCCTGGTTGTATATGC 59.300 41.667 0.00 0.00 0.00 3.14
2458 4755 5.705441 ACACTTGTGTTCCTGGTTGTATATG 59.295 40.000 0.00 0.00 0.00 1.78
2459 4756 5.876357 ACACTTGTGTTCCTGGTTGTATAT 58.124 37.500 0.00 0.00 0.00 0.86
2460 4757 5.298989 ACACTTGTGTTCCTGGTTGTATA 57.701 39.130 0.00 0.00 0.00 1.47
2461 4758 4.164843 ACACTTGTGTTCCTGGTTGTAT 57.835 40.909 0.00 0.00 0.00 2.29
2462 4759 3.637911 ACACTTGTGTTCCTGGTTGTA 57.362 42.857 0.00 0.00 0.00 2.41
2463 4760 2.507407 ACACTTGTGTTCCTGGTTGT 57.493 45.000 0.00 0.00 0.00 3.32
2464 4761 5.507315 GGAAATACACTTGTGTTCCTGGTTG 60.507 44.000 11.80 0.00 38.98 3.77
2465 4762 4.583073 GGAAATACACTTGTGTTCCTGGTT 59.417 41.667 11.80 0.00 38.98 3.67
2466 4763 4.142038 GGAAATACACTTGTGTTCCTGGT 58.858 43.478 11.80 0.00 38.98 4.00
2467 4764 3.506067 GGGAAATACACTTGTGTTCCTGG 59.494 47.826 17.42 0.00 40.49 4.45
2468 4765 3.188460 CGGGAAATACACTTGTGTTCCTG 59.812 47.826 17.42 15.75 40.49 3.86
2469 4766 3.181448 ACGGGAAATACACTTGTGTTCCT 60.181 43.478 17.42 3.19 40.49 3.36
2470 4767 3.143728 ACGGGAAATACACTTGTGTTCC 58.856 45.455 11.80 12.10 40.20 3.62
2471 4768 6.815142 ACTATACGGGAAATACACTTGTGTTC 59.185 38.462 11.80 3.90 0.00 3.18
2472 4769 6.592607 CACTATACGGGAAATACACTTGTGTT 59.407 38.462 11.80 0.00 0.00 3.32
2473 4770 6.103997 CACTATACGGGAAATACACTTGTGT 58.896 40.000 11.30 11.30 0.00 3.72
2474 4771 6.103997 ACACTATACGGGAAATACACTTGTG 58.896 40.000 0.00 0.00 0.00 3.33
2475 4772 6.154021 AGACACTATACGGGAAATACACTTGT 59.846 38.462 0.00 0.00 0.00 3.16
2476 4773 6.570692 AGACACTATACGGGAAATACACTTG 58.429 40.000 0.00 0.00 0.00 3.16
2477 4774 6.786967 AGACACTATACGGGAAATACACTT 57.213 37.500 0.00 0.00 0.00 3.16
2478 4775 7.285566 TCTAGACACTATACGGGAAATACACT 58.714 38.462 0.00 0.00 0.00 3.55
2479 4776 7.502120 TCTAGACACTATACGGGAAATACAC 57.498 40.000 0.00 0.00 0.00 2.90
2480 4777 9.797642 TTATCTAGACACTATACGGGAAATACA 57.202 33.333 0.00 0.00 0.00 2.29
2485 4782 8.954350 GCTAATTATCTAGACACTATACGGGAA 58.046 37.037 0.00 0.00 0.00 3.97
2486 4783 8.105197 TGCTAATTATCTAGACACTATACGGGA 58.895 37.037 0.00 0.00 0.00 5.14
2487 4784 8.277490 TGCTAATTATCTAGACACTATACGGG 57.723 38.462 0.00 0.00 0.00 5.28
2614 4919 2.626743 AGCTGTTCTTGCTGCTGAATTT 59.373 40.909 0.00 0.00 41.12 1.82
2649 4954 4.383861 CTGCTCTGGCTGACGGCA 62.384 66.667 8.86 7.81 44.01 5.69
2884 5193 0.545646 GCAGATGGAAGAAGCCTCCT 59.454 55.000 0.00 0.00 0.00 3.69
3048 5416 2.027745 GTCTTGATCCTTGCTCCACTCA 60.028 50.000 0.00 0.00 0.00 3.41
3081 5451 2.290323 GGTTTCATGGCACCTCAGTACT 60.290 50.000 6.91 0.00 0.00 2.73
3082 5452 2.084546 GGTTTCATGGCACCTCAGTAC 58.915 52.381 6.91 0.00 0.00 2.73
3125 5518 2.934553 GTGTAATCACCCGGAAGTTAGC 59.065 50.000 0.73 0.00 38.51 3.09
3132 5525 2.635915 AGAAACAGTGTAATCACCCGGA 59.364 45.455 0.73 0.00 44.83 5.14
3251 5680 1.982938 GACGTGGTAGGGGTCTGCT 60.983 63.158 0.00 0.00 0.00 4.24
3318 5751 0.526662 ACTAGCTGCTCCACACGTAC 59.473 55.000 4.91 0.00 0.00 3.67
3338 5794 3.813529 AGAAGACGCACAAACATTAGC 57.186 42.857 0.00 0.00 0.00 3.09
3473 5976 2.177531 GATGTTGGTGCAGCTGCG 59.822 61.111 32.11 0.00 45.83 5.18
3627 6133 6.603201 CCTGGGCTGGGTATTATTACATTATG 59.397 42.308 0.00 0.00 0.00 1.90
3678 6290 1.227674 GGAGATGGCATCACCGGAC 60.228 63.158 27.93 11.85 43.94 4.79
3762 7580 6.115446 AGACATATTCCTTGCGAAGATTCAA 58.885 36.000 0.00 0.00 29.79 2.69
3767 7585 5.592054 CTGTAGACATATTCCTTGCGAAGA 58.408 41.667 0.00 0.00 32.78 2.87
3790 7608 2.993220 CCGATTTGCAACTTTTAAGGGC 59.007 45.455 0.00 0.00 0.00 5.19
3800 7618 2.030805 AGAAGTTCAGCCGATTTGCAAC 60.031 45.455 0.00 0.00 0.00 4.17
3961 7786 6.653320 TCTTTCATTGTTATTTGTCGTAGCCT 59.347 34.615 0.00 0.00 0.00 4.58
3980 7805 1.208052 CTCGGGCCTGATTCTCTTTCA 59.792 52.381 16.52 0.00 0.00 2.69
4020 7845 4.941873 TCGCTCACTTAGTAAGTCTCATCA 59.058 41.667 12.75 0.00 40.46 3.07
4083 7908 6.446781 GGCAACCCTTAACTAGTTATTTCC 57.553 41.667 15.92 7.70 0.00 3.13
4104 7929 1.338105 GGATGACTTTTGCAAAGGGGC 60.338 52.381 23.33 17.15 0.00 5.80
4108 7933 1.969923 TGGGGGATGACTTTTGCAAAG 59.030 47.619 12.41 9.23 0.00 2.77
4183 8008 7.435488 CGGACGAAGAGAGTATTGAATAAATGT 59.565 37.037 0.00 0.00 0.00 2.71
4185 8010 7.713750 TCGGACGAAGAGAGTATTGAATAAAT 58.286 34.615 0.00 0.00 0.00 1.40
4198 8023 5.130292 ACAAGTATTTTCGGACGAAGAGA 57.870 39.130 7.25 0.00 35.38 3.10
4199 8024 4.921515 TGACAAGTATTTTCGGACGAAGAG 59.078 41.667 7.25 0.00 35.38 2.85
4200 8025 4.873817 TGACAAGTATTTTCGGACGAAGA 58.126 39.130 7.25 3.70 35.38 2.87
4201 8026 5.347635 TGATGACAAGTATTTTCGGACGAAG 59.652 40.000 7.25 0.00 35.38 3.79
4202 8027 5.231702 TGATGACAAGTATTTTCGGACGAA 58.768 37.500 2.62 2.62 0.00 3.85
4203 8028 4.811908 TGATGACAAGTATTTTCGGACGA 58.188 39.130 0.00 0.00 0.00 4.20
4204 8029 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
4205 8030 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
4206 8031 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
4207 8032 7.312154 TCCATTTTGATGACAAGTATTTTCGG 58.688 34.615 0.00 0.00 37.32 4.30
4208 8033 8.915871 ATCCATTTTGATGACAAGTATTTTCG 57.084 30.769 0.00 0.00 37.32 3.46
4215 8040 8.096414 CCCTTTTTATCCATTTTGATGACAAGT 58.904 33.333 0.00 0.00 37.32 3.16
4216 8041 8.313292 TCCCTTTTTATCCATTTTGATGACAAG 58.687 33.333 0.00 0.00 37.32 3.16
4217 8042 8.200024 TCCCTTTTTATCCATTTTGATGACAA 57.800 30.769 0.00 0.00 0.00 3.18
4218 8043 7.789202 TCCCTTTTTATCCATTTTGATGACA 57.211 32.000 0.00 0.00 0.00 3.58
4219 8044 8.260114 ACATCCCTTTTTATCCATTTTGATGAC 58.740 33.333 0.00 0.00 32.39 3.06
4220 8045 8.378115 ACATCCCTTTTTATCCATTTTGATGA 57.622 30.769 0.00 0.00 32.39 2.92
4223 8048 9.713684 AGATACATCCCTTTTTATCCATTTTGA 57.286 29.630 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.