Multiple sequence alignment - TraesCS4A01G369200

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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 TraesCS4A01G369200 chr4A 100.000 3767 0 0 1 3767 641450084 641453850 0.000000e+00 6957
1 TraesCS4A01G369200 chr4A 88.086 747 70 11 2014 2751 75214241 75213505 0.000000e+00 869
2 TraesCS4A01G369200 chr4A 85.250 739 63 30 995 1708 75215333 75214616 0.000000e+00 719
3 TraesCS4A01G369200 chr4A 90.291 309 30 0 2016 2324 574870084 574869776 4.530000e-109 405
4 TraesCS4A01G369200 chr4A 92.694 219 16 0 1798 2016 75214542 75214324 2.180000e-82 316
5 TraesCS4A01G369200 chr4A 92.453 212 16 0 1194 1405 574872619 574872408 1.700000e-78 303
6 TraesCS4A01G369200 chr4A 88.182 220 24 2 1798 2016 574870423 574870205 1.040000e-65 261
7 TraesCS4A01G369200 chr5B 89.590 2344 124 44 577 2860 670068563 670066280 0.000000e+00 2867
8 TraesCS4A01G369200 chr5B 95.669 531 20 3 3110 3640 680927892 680927365 0.000000e+00 850
9 TraesCS4A01G369200 chr5B 96.471 510 17 1 3131 3640 10581681 10581173 0.000000e+00 841
10 TraesCS4A01G369200 chr5B 91.000 100 9 0 3041 3140 670065825 670065924 6.560000e-28 135
11 TraesCS4A01G369200 chr5B 96.341 82 2 1 2918 2998 670066282 670066201 2.360000e-27 134
12 TraesCS4A01G369200 chr5B 93.056 72 2 1 3678 3746 670066396 670066325 6.660000e-18 102
13 TraesCS4A01G369200 chr5D 90.491 1977 123 32 837 2799 530826543 530824618 0.000000e+00 2549
14 TraesCS4A01G369200 chr5D 85.861 778 85 12 1 767 530827308 530826545 0.000000e+00 804
15 TraesCS4A01G369200 chr5D 78.370 638 106 19 1 615 443002024 443002652 5.900000e-103 385
16 TraesCS4A01G369200 chr5D 80.224 536 78 18 113 633 35651036 35651558 9.880000e-101 377
17 TraesCS4A01G369200 chr5D 79.923 518 70 19 125 630 443501790 443502285 2.150000e-92 350
18 TraesCS4A01G369200 chr5D 90.650 246 14 6 2897 3140 530824578 530824340 6.070000e-83 318
19 TraesCS4A01G369200 chr5D 91.860 86 5 2 3681 3766 530824662 530824579 6.610000e-23 119
20 TraesCS4A01G369200 chr4D 90.418 741 54 11 2014 2751 393636861 393637587 0.000000e+00 959
21 TraesCS4A01G369200 chr4D 84.327 721 64 32 995 1701 393635783 393636468 0.000000e+00 660
22 TraesCS4A01G369200 chr4D 90.096 313 30 1 2016 2328 28839754 28840065 4.530000e-109 405
23 TraesCS4A01G369200 chr4D 93.665 221 14 0 1796 2016 393636553 393636773 7.800000e-87 331
24 TraesCS4A01G369200 chr4D 91.204 216 19 0 1191 1406 28837074 28837289 1.020000e-75 294
25 TraesCS4A01G369200 chr4D 87.665 227 26 2 1791 2016 28839443 28839668 2.890000e-66 263
26 TraesCS4A01G369200 chr4D 76.835 436 81 13 3 427 318608868 318609294 1.050000e-55 228
27 TraesCS4A01G369200 chr4B 90.431 742 52 14 2014 2751 483334256 483333530 0.000000e+00 959
28 TraesCS4A01G369200 chr4B 85.160 721 73 22 995 1704 483335447 483334750 0.000000e+00 708
29 TraesCS4A01G369200 chr4B 90.291 309 30 0 2016 2324 41012880 41013188 4.530000e-109 405
30 TraesCS4A01G369200 chr4B 93.636 220 14 0 1797 2016 483334558 483334339 2.810000e-86 329
31 TraesCS4A01G369200 chr4B 91.943 211 17 0 1194 1404 41010037 41010247 2.850000e-76 296
32 TraesCS4A01G369200 chr4B 77.374 495 98 8 35 526 40418274 40418757 7.970000e-72 281
33 TraesCS4A01G369200 chr4B 88.636 220 23 2 1798 2016 41012544 41012762 2.230000e-67 267
34 TraesCS4A01G369200 chrUn 96.893 515 14 2 3127 3640 83928409 83928922 0.000000e+00 861
35 TraesCS4A01G369200 chr7D 96.718 518 15 2 3124 3640 137021072 137021588 0.000000e+00 861
36 TraesCS4A01G369200 chr7D 77.394 637 109 19 6 629 628135109 628134495 2.790000e-91 346
37 TraesCS4A01G369200 chr7D 75.538 650 132 19 1 634 469225525 469224887 1.020000e-75 294
38 TraesCS4A01G369200 chr6D 97.065 511 13 2 3131 3640 464466000 464465491 0.000000e+00 859
39 TraesCS4A01G369200 chr6D 96.863 510 16 0 3131 3640 14616166 14615657 0.000000e+00 854
40 TraesCS4A01G369200 chr3A 96.869 511 13 3 3131 3640 716636771 716637279 0.000000e+00 852
41 TraesCS4A01G369200 chr3A 90.135 223 21 1 1182 1404 12815025 12814804 4.760000e-74 289
42 TraesCS4A01G369200 chr1D 96.275 510 19 0 3131 3640 404241850 404241341 0.000000e+00 837
43 TraesCS4A01G369200 chr1D 95.745 517 20 2 3124 3640 487881114 487880600 0.000000e+00 832
44 TraesCS4A01G369200 chr3D 83.125 640 92 5 1 630 90832304 90831671 1.520000e-158 569
45 TraesCS4A01G369200 chr2B 81.782 505 72 15 1205 1708 477529803 477529318 4.530000e-109 405
46 TraesCS4A01G369200 chr2B 77.627 295 64 2 2411 2704 477528063 477527770 1.080000e-40 178
47 TraesCS4A01G369200 chr2A 81.176 510 75 16 1208 1706 540850029 540849530 1.270000e-104 390
48 TraesCS4A01G369200 chr2A 76.108 632 116 19 14 629 713218502 713219114 7.910000e-77 298
49 TraesCS4A01G369200 chr2A 77.736 530 86 21 1498 2016 541776257 541776765 2.850000e-76 296
50 TraesCS4A01G369200 chr2A 75.930 511 98 17 122 628 675088010 675087521 4.860000e-59 239
51 TraesCS4A01G369200 chr2A 77.027 296 64 4 2411 2704 540848333 540848040 2.330000e-37 167
52 TraesCS4A01G369200 chr2D 91.085 258 21 2 2014 2270 403479341 403479597 7.740000e-92 348
53 TraesCS4A01G369200 chr2D 78.005 441 71 11 124 548 575164120 575164550 1.740000e-63 254
54 TraesCS4A01G369200 chr2D 87.019 208 27 0 1499 1706 403347463 403347256 6.290000e-58 235
55 TraesCS4A01G369200 chr3B 76.406 640 114 20 11 629 737705447 737706070 1.020000e-80 311
56 TraesCS4A01G369200 chr5A 76.848 514 99 15 113 618 547667907 547667406 4.790000e-69 272
57 TraesCS4A01G369200 chr5A 77.363 402 71 15 237 630 547660853 547660464 1.760000e-53 220
58 TraesCS4A01G369200 chr1A 76.758 512 86 24 125 629 269590051 269590536 4.830000e-64 255


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 TraesCS4A01G369200 chr4A 641450084 641453850 3766 False 6957.000000 6957 100.000000 1 3767 1 chr4A.!!$F1 3766
1 TraesCS4A01G369200 chr4A 75213505 75215333 1828 True 634.666667 869 88.676667 995 2751 3 chr4A.!!$R1 1756
2 TraesCS4A01G369200 chr4A 574869776 574872619 2843 True 323.000000 405 90.308667 1194 2324 3 chr4A.!!$R2 1130
3 TraesCS4A01G369200 chr5B 670066201 670068563 2362 True 1034.333333 2867 92.995667 577 3746 3 chr5B.!!$R3 3169
4 TraesCS4A01G369200 chr5B 680927365 680927892 527 True 850.000000 850 95.669000 3110 3640 1 chr5B.!!$R2 530
5 TraesCS4A01G369200 chr5B 10581173 10581681 508 True 841.000000 841 96.471000 3131 3640 1 chr5B.!!$R1 509
6 TraesCS4A01G369200 chr5D 530824340 530827308 2968 True 947.500000 2549 89.715500 1 3766 4 chr5D.!!$R1 3765
7 TraesCS4A01G369200 chr5D 443002024 443002652 628 False 385.000000 385 78.370000 1 615 1 chr5D.!!$F2 614
8 TraesCS4A01G369200 chr5D 35651036 35651558 522 False 377.000000 377 80.224000 113 633 1 chr5D.!!$F1 520
9 TraesCS4A01G369200 chr4D 393635783 393637587 1804 False 650.000000 959 89.470000 995 2751 3 chr4D.!!$F3 1756
10 TraesCS4A01G369200 chr4D 28837074 28840065 2991 False 320.666667 405 89.655000 1191 2328 3 chr4D.!!$F2 1137
11 TraesCS4A01G369200 chr4B 483333530 483335447 1917 True 665.333333 959 89.742333 995 2751 3 chr4B.!!$R1 1756
12 TraesCS4A01G369200 chr4B 41010037 41013188 3151 False 322.666667 405 90.290000 1194 2324 3 chr4B.!!$F2 1130
13 TraesCS4A01G369200 chrUn 83928409 83928922 513 False 861.000000 861 96.893000 3127 3640 1 chrUn.!!$F1 513
14 TraesCS4A01G369200 chr7D 137021072 137021588 516 False 861.000000 861 96.718000 3124 3640 1 chr7D.!!$F1 516
15 TraesCS4A01G369200 chr7D 628134495 628135109 614 True 346.000000 346 77.394000 6 629 1 chr7D.!!$R2 623
16 TraesCS4A01G369200 chr7D 469224887 469225525 638 True 294.000000 294 75.538000 1 634 1 chr7D.!!$R1 633
17 TraesCS4A01G369200 chr6D 464465491 464466000 509 True 859.000000 859 97.065000 3131 3640 1 chr6D.!!$R2 509
18 TraesCS4A01G369200 chr6D 14615657 14616166 509 True 854.000000 854 96.863000 3131 3640 1 chr6D.!!$R1 509
19 TraesCS4A01G369200 chr3A 716636771 716637279 508 False 852.000000 852 96.869000 3131 3640 1 chr3A.!!$F1 509
20 TraesCS4A01G369200 chr1D 404241341 404241850 509 True 837.000000 837 96.275000 3131 3640 1 chr1D.!!$R1 509
21 TraesCS4A01G369200 chr1D 487880600 487881114 514 True 832.000000 832 95.745000 3124 3640 1 chr1D.!!$R2 516
22 TraesCS4A01G369200 chr3D 90831671 90832304 633 True 569.000000 569 83.125000 1 630 1 chr3D.!!$R1 629
23 TraesCS4A01G369200 chr2B 477527770 477529803 2033 True 291.500000 405 79.704500 1205 2704 2 chr2B.!!$R1 1499
24 TraesCS4A01G369200 chr2A 713218502 713219114 612 False 298.000000 298 76.108000 14 629 1 chr2A.!!$F2 615
25 TraesCS4A01G369200 chr2A 541776257 541776765 508 False 296.000000 296 77.736000 1498 2016 1 chr2A.!!$F1 518
26 TraesCS4A01G369200 chr2A 540848040 540850029 1989 True 278.500000 390 79.101500 1208 2704 2 chr2A.!!$R2 1496
27 TraesCS4A01G369200 chr3B 737705447 737706070 623 False 311.000000 311 76.406000 11 629 1 chr3B.!!$F1 618
28 TraesCS4A01G369200 chr5A 547667406 547667907 501 True 272.000000 272 76.848000 113 618 1 chr5A.!!$R2 505

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
94 96 0.107214 TTGGTGGATCTCGGCCATTC 60.107 55.0 2.24 0.00 37.81 2.67 F
990 1062 0.168348 CTAGGTCGACTCACACGGTG 59.832 60.0 16.46 6.58 34.45 4.94 F
2300 5507 0.100682 CATCGCGCAGTACTACCAGT 59.899 55.0 8.75 0.00 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1202 1296 0.103208 GATCGACTTCTCCGGCATGT 59.897 55.0 0.00 0.00 0.00 3.21 R
2341 5548 0.108424 AACTGCGAGTCCTCATGAGC 60.108 55.0 17.76 6.31 0.00 4.26 R
3674 7233 0.384669 ATTACTAGCAGACGCCGGTC 59.615 55.0 1.90 0.00 43.76 4.79 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
20 21 2.183679 CTAGTGTTCCTTCTGCCTCCT 58.816 52.381 0.00 0.00 0.00 3.69
63 65 2.354704 CCTCGTCTCATGTGGCCTTAAA 60.355 50.000 3.32 0.00 0.00 1.52
65 67 2.565391 TCGTCTCATGTGGCCTTAAAGA 59.435 45.455 3.32 0.00 0.00 2.52
75 77 2.378547 TGGCCTTAAAGACATGGAGGTT 59.621 45.455 3.32 0.00 0.00 3.50
94 96 0.107214 TTGGTGGATCTCGGCCATTC 60.107 55.000 2.24 0.00 37.81 2.67
200 215 3.713826 TGAAATAAGTTTCTCCCCGCT 57.286 42.857 3.00 0.00 43.30 5.52
208 223 3.635869 TTCTCCCCGCTTAGCCCCT 62.636 63.158 0.00 0.00 0.00 4.79
224 239 1.373435 CCTGTTCCGGTGGTGCTTA 59.627 57.895 0.00 0.00 0.00 3.09
249 264 0.977627 TCATCTGAGGGCGTGTGGAT 60.978 55.000 0.00 0.00 0.00 3.41
325 350 7.093771 GGATTTACATGGATCCAGTCTTTGTTT 60.094 37.037 21.33 7.58 41.21 2.83
331 366 5.630121 TGGATCCAGTCTTTGTTTATGTGT 58.370 37.500 11.44 0.00 0.00 3.72
332 367 5.705441 TGGATCCAGTCTTTGTTTATGTGTC 59.295 40.000 11.44 0.00 0.00 3.67
333 368 5.940470 GGATCCAGTCTTTGTTTATGTGTCT 59.060 40.000 6.95 0.00 0.00 3.41
334 369 7.103641 GGATCCAGTCTTTGTTTATGTGTCTA 58.896 38.462 6.95 0.00 0.00 2.59
335 370 7.770897 GGATCCAGTCTTTGTTTATGTGTCTAT 59.229 37.037 6.95 0.00 0.00 1.98
336 371 9.817809 GATCCAGTCTTTGTTTATGTGTCTATA 57.182 33.333 0.00 0.00 0.00 1.31
337 372 9.823647 ATCCAGTCTTTGTTTATGTGTCTATAG 57.176 33.333 0.00 0.00 0.00 1.31
338 373 8.812972 TCCAGTCTTTGTTTATGTGTCTATAGT 58.187 33.333 0.00 0.00 0.00 2.12
339 374 9.436957 CCAGTCTTTGTTTATGTGTCTATAGTT 57.563 33.333 0.00 0.00 0.00 2.24
350 404 7.682787 ATGTGTCTATAGTTTGGATCCTTCT 57.317 36.000 14.23 10.71 0.00 2.85
366 420 7.656707 GATCCTTCTGATCTAAGCATCTTTC 57.343 40.000 0.00 0.00 45.46 2.62
456 511 7.554835 ACTGTCTATTACAACAAGTTTTGTCCA 59.445 33.333 6.68 0.00 44.59 4.02
505 560 1.598701 GCATCCCTTCGGCTTGCTTT 61.599 55.000 0.00 0.00 35.95 3.51
516 571 2.420022 CGGCTTGCTTTAGTGCTTGTAT 59.580 45.455 0.00 0.00 0.00 2.29
548 604 6.331369 AGGTGTTTTACAAATCTGGATGTG 57.669 37.500 0.00 0.00 32.30 3.21
550 606 6.016276 AGGTGTTTTACAAATCTGGATGTGAC 60.016 38.462 7.66 0.00 30.60 3.67
551 607 6.149633 GTGTTTTACAAATCTGGATGTGACC 58.850 40.000 7.66 0.00 30.60 4.02
664 723 7.768807 TGTTTAACCACAAATATAAGGCAGT 57.231 32.000 0.00 0.00 0.00 4.40
683 742 2.606519 TTCCCCCGTGCTGCTAGT 60.607 61.111 0.00 0.00 0.00 2.57
756 816 4.080015 CCTGACTCTCTCCTTCCTCTTCTA 60.080 50.000 0.00 0.00 0.00 2.10
757 817 5.110814 TGACTCTCTCCTTCCTCTTCTAG 57.889 47.826 0.00 0.00 0.00 2.43
767 827 4.383661 CCTTCCTCTTCTAGCCTTTCCTTC 60.384 50.000 0.00 0.00 0.00 3.46
807 867 1.664333 CCAATGGCAAACGCACCAC 60.664 57.895 0.00 0.00 39.19 4.16
808 868 1.664333 CAATGGCAAACGCACCACC 60.664 57.895 0.00 0.00 39.19 4.61
809 869 3.206211 AATGGCAAACGCACCACCG 62.206 57.895 0.00 0.00 39.19 4.94
813 873 4.954680 CAAACGCACCACCGCACG 62.955 66.667 0.00 0.00 0.00 5.34
917 981 4.024893 ACACCAAAATCGTCGCATCATATC 60.025 41.667 0.00 0.00 0.00 1.63
947 1015 2.751259 TGATTCATCAAGTGCCAGCTTC 59.249 45.455 0.00 0.00 33.08 3.86
982 1050 0.582960 GCGAGTAGCTAGGTCGACTC 59.417 60.000 23.39 13.98 44.04 3.36
983 1051 1.937278 CGAGTAGCTAGGTCGACTCA 58.063 55.000 19.70 2.39 38.21 3.41
984 1052 1.593933 CGAGTAGCTAGGTCGACTCAC 59.406 57.143 19.70 0.00 38.21 3.51
985 1053 2.630158 GAGTAGCTAGGTCGACTCACA 58.370 52.381 16.46 0.00 38.21 3.58
986 1054 2.352342 GAGTAGCTAGGTCGACTCACAC 59.648 54.545 16.46 6.50 38.21 3.82
990 1062 0.168348 CTAGGTCGACTCACACGGTG 59.832 60.000 16.46 6.58 34.45 4.94
992 1064 2.726274 GTCGACTCACACGGTGGT 59.274 61.111 13.48 0.30 33.87 4.16
1093 1167 3.932089 GTCGTCTCTCCCGAGGTATATAC 59.068 52.174 4.14 4.14 37.86 1.47
1254 1348 2.545952 GGCGTACCAGATCATCAACGAT 60.546 50.000 12.84 0.00 35.26 3.73
1406 1500 0.178941 ACCACCGAGTTCCAGGTACT 60.179 55.000 0.00 0.00 39.00 2.73
1413 1507 3.440173 CCGAGTTCCAGGTACTTTACGTA 59.560 47.826 0.00 0.00 34.60 3.57
1414 1508 4.437930 CCGAGTTCCAGGTACTTTACGTAG 60.438 50.000 0.00 0.00 34.60 3.51
1415 1509 4.154918 CGAGTTCCAGGTACTTTACGTAGT 59.845 45.833 0.00 0.00 41.70 2.73
1416 1510 5.635417 AGTTCCAGGTACTTTACGTAGTC 57.365 43.478 0.00 0.00 38.75 2.59
1417 1511 4.460731 AGTTCCAGGTACTTTACGTAGTCC 59.539 45.833 0.00 0.00 38.75 3.85
1449 1667 4.537135 TTTACCAGTCGATCTCTGCTTT 57.463 40.909 8.61 0.70 0.00 3.51
1455 1674 2.094286 AGTCGATCTCTGCTTTGACCTG 60.094 50.000 0.00 0.00 0.00 4.00
1468 1687 1.372683 GACCTGCAGCCTCACAGAA 59.627 57.895 8.66 0.00 35.90 3.02
1471 1690 0.250640 CCTGCAGCCTCACAGAAGTT 60.251 55.000 8.66 0.00 35.90 2.66
1473 1692 0.181114 TGCAGCCTCACAGAAGTTGT 59.819 50.000 0.00 0.00 41.94 3.32
1476 1695 2.099756 GCAGCCTCACAGAAGTTGTTTT 59.900 45.455 0.00 0.00 38.16 2.43
1480 1699 5.743872 CAGCCTCACAGAAGTTGTTTTTAAC 59.256 40.000 0.00 0.00 38.16 2.01
1489 1708 5.771602 AAGTTGTTTTTAACTTTGTGCGG 57.228 34.783 0.00 0.00 45.85 5.69
1491 1710 3.166489 TGTTTTTAACTTTGTGCGGGG 57.834 42.857 0.00 0.00 0.00 5.73
1542 4336 2.125552 CATCTCTTCCACGCGCCA 60.126 61.111 5.73 0.00 0.00 5.69
1587 4381 4.572571 GTGGGCACGGTGGGTTCA 62.573 66.667 10.60 0.00 0.00 3.18
1739 4582 3.242220 CGAATTCATGAAACTGAGAGCCG 60.242 47.826 13.09 2.49 0.00 5.52
1749 4592 1.480137 ACTGAGAGCCGAGAATTCCTG 59.520 52.381 0.65 0.00 0.00 3.86
1770 4613 2.291741 GTCCTTTGAGGTGCAAGTTGAG 59.708 50.000 7.16 0.00 37.87 3.02
1776 4619 5.947228 TTGAGGTGCAAGTTGAGATTTAG 57.053 39.130 7.16 0.00 31.55 1.85
1942 4883 4.708968 GCGGCGATCCTAGGCTCG 62.709 72.222 26.83 26.83 36.91 5.03
2300 5507 0.100682 CATCGCGCAGTACTACCAGT 59.899 55.000 8.75 0.00 0.00 4.00
2311 5518 0.981183 ACTACCAGTTCATCCGCCAA 59.019 50.000 0.00 0.00 0.00 4.52
2351 5558 3.538614 GCTACCGGCTCATGAGGA 58.461 61.111 23.89 0.00 38.06 3.71
2372 5579 3.149196 ACTCGCAGTTCAAACATCCATT 58.851 40.909 0.00 0.00 0.00 3.16
2394 5856 3.070159 TGATCGGGAGGAGATTTGTCATC 59.930 47.826 0.00 0.00 0.00 2.92
2584 6130 0.526662 GTTCGAGGTCTCCGACATGT 59.473 55.000 0.00 0.00 35.61 3.21
2760 6306 3.414700 CCGTCCAACAGCGTCTGC 61.415 66.667 6.74 0.00 43.24 4.26
2799 6350 4.582656 ACGATTAGAGTCTCCAGAATCCAG 59.417 45.833 0.00 0.00 39.73 3.86
2800 6351 4.582656 CGATTAGAGTCTCCAGAATCCAGT 59.417 45.833 0.00 0.00 39.73 4.00
2801 6352 5.278266 CGATTAGAGTCTCCAGAATCCAGTC 60.278 48.000 0.00 0.00 39.73 3.51
2802 6353 2.745968 AGAGTCTCCAGAATCCAGTCC 58.254 52.381 0.44 0.00 39.73 3.85
2803 6354 2.314549 AGAGTCTCCAGAATCCAGTCCT 59.685 50.000 0.44 0.00 39.73 3.85
2804 6355 2.430332 GAGTCTCCAGAATCCAGTCCTG 59.570 54.545 0.00 0.00 33.46 3.86
2831 6389 4.750598 GGAAACTACCGATCTTATCTTGCC 59.249 45.833 0.00 0.00 0.00 4.52
2832 6390 5.453480 GGAAACTACCGATCTTATCTTGCCT 60.453 44.000 0.00 0.00 0.00 4.75
2833 6391 5.615925 AACTACCGATCTTATCTTGCCTT 57.384 39.130 0.00 0.00 0.00 4.35
2836 6394 5.817816 ACTACCGATCTTATCTTGCCTTTTG 59.182 40.000 0.00 0.00 0.00 2.44
2843 6401 7.065803 CGATCTTATCTTGCCTTTTGGAGTAAA 59.934 37.037 0.00 0.00 44.07 2.01
2866 6424 5.896073 AAAAGCTATGATGGTACTAGGCT 57.104 39.130 0.00 0.00 0.00 4.58
2867 6425 4.881019 AAGCTATGATGGTACTAGGCTG 57.119 45.455 0.00 0.00 0.00 4.85
2868 6426 3.850752 AGCTATGATGGTACTAGGCTGT 58.149 45.455 0.00 0.00 0.00 4.40
2869 6427 4.227197 AGCTATGATGGTACTAGGCTGTT 58.773 43.478 0.00 0.00 0.00 3.16
2870 6428 4.656112 AGCTATGATGGTACTAGGCTGTTT 59.344 41.667 0.00 0.00 0.00 2.83
2871 6429 5.131142 AGCTATGATGGTACTAGGCTGTTTT 59.869 40.000 0.00 0.00 0.00 2.43
2872 6430 6.326583 AGCTATGATGGTACTAGGCTGTTTTA 59.673 38.462 0.00 0.00 0.00 1.52
2873 6431 6.647067 GCTATGATGGTACTAGGCTGTTTTAG 59.353 42.308 0.00 0.00 0.00 1.85
2874 6432 5.353394 TGATGGTACTAGGCTGTTTTAGG 57.647 43.478 0.00 0.00 0.00 2.69
2914 6472 6.779860 AGAAGAGGTTGTTTTAGGCAGATTA 58.220 36.000 0.00 0.00 0.00 1.75
2915 6473 7.406104 AGAAGAGGTTGTTTTAGGCAGATTAT 58.594 34.615 0.00 0.00 0.00 1.28
2916 6474 7.554476 AGAAGAGGTTGTTTTAGGCAGATTATC 59.446 37.037 0.00 0.00 0.00 1.75
2926 6484 8.403236 GTTTTAGGCAGATTATCGTAACCAAAT 58.597 33.333 0.00 0.00 0.00 2.32
2950 6508 4.935352 TTGCTGTGGCTTTTATGACTTT 57.065 36.364 0.00 0.00 39.59 2.66
3052 6611 7.552687 TGTTGTGTTCTCTCTCTTGTTTATGTT 59.447 33.333 0.00 0.00 0.00 2.71
3055 6614 7.439356 TGTGTTCTCTCTCTTGTTTATGTTGAG 59.561 37.037 0.00 0.00 0.00 3.02
3090 6649 8.519526 ACTTAAATTGCATTCGGATGAAAGTAA 58.480 29.630 8.22 5.61 34.29 2.24
3239 6798 0.098376 CCACCTAGCGACGACTACAC 59.902 60.000 0.00 0.00 0.00 2.90
3424 6983 2.305927 AGGATTCAACCCGAAGACACAT 59.694 45.455 0.00 0.00 36.95 3.21
3544 7103 3.459063 GAACGAGGGCTAGGCGGT 61.459 66.667 10.58 5.37 0.00 5.68
3654 7213 1.631284 AACGGTTGTTTTTGTTCGGC 58.369 45.000 0.00 0.00 33.53 5.54
3655 7214 0.812549 ACGGTTGTTTTTGTTCGGCT 59.187 45.000 0.00 0.00 0.00 5.52
3656 7215 2.015587 ACGGTTGTTTTTGTTCGGCTA 58.984 42.857 0.00 0.00 0.00 3.93
3657 7216 2.223317 ACGGTTGTTTTTGTTCGGCTAC 60.223 45.455 0.00 0.00 0.00 3.58
3658 7217 2.377880 GGTTGTTTTTGTTCGGCTACG 58.622 47.619 0.00 0.00 42.74 3.51
3669 7228 3.733236 CGGCTACGAACTGAATCCA 57.267 52.632 0.00 0.00 44.60 3.41
3670 7229 2.004583 CGGCTACGAACTGAATCCAA 57.995 50.000 0.00 0.00 44.60 3.53
3671 7230 2.343101 CGGCTACGAACTGAATCCAAA 58.657 47.619 0.00 0.00 44.60 3.28
3672 7231 2.936498 CGGCTACGAACTGAATCCAAAT 59.064 45.455 0.00 0.00 44.60 2.32
3673 7232 3.242413 CGGCTACGAACTGAATCCAAATG 60.242 47.826 0.00 0.00 44.60 2.32
3674 7233 3.065371 GGCTACGAACTGAATCCAAATGG 59.935 47.826 0.00 0.00 0.00 3.16
3683 7242 2.046700 TCCAAATGGACCGGCGTC 60.047 61.111 6.01 3.39 39.78 5.19
3684 7243 2.046314 CCAAATGGACCGGCGTCT 60.046 61.111 6.01 0.00 39.15 4.18
3685 7244 2.398554 CCAAATGGACCGGCGTCTG 61.399 63.158 6.01 0.00 39.15 3.51
3686 7245 2.746277 AAATGGACCGGCGTCTGC 60.746 61.111 6.01 0.00 39.15 4.26
3687 7246 3.254024 AAATGGACCGGCGTCTGCT 62.254 57.895 6.01 0.00 42.25 4.24
3688 7247 1.895020 AAATGGACCGGCGTCTGCTA 61.895 55.000 6.01 0.00 42.25 3.49
3689 7248 2.298158 AATGGACCGGCGTCTGCTAG 62.298 60.000 6.01 0.00 42.25 3.42
3690 7249 3.450115 GGACCGGCGTCTGCTAGT 61.450 66.667 6.01 0.00 42.25 2.57
3691 7250 2.117156 GGACCGGCGTCTGCTAGTA 61.117 63.158 6.01 0.00 42.25 1.82
3692 7251 1.660560 GGACCGGCGTCTGCTAGTAA 61.661 60.000 6.01 0.00 42.25 2.24
3693 7252 0.384669 GACCGGCGTCTGCTAGTAAT 59.615 55.000 6.01 0.00 42.25 1.89
3694 7253 1.605710 GACCGGCGTCTGCTAGTAATA 59.394 52.381 6.01 0.00 42.25 0.98
3695 7254 2.026641 ACCGGCGTCTGCTAGTAATAA 58.973 47.619 6.01 0.00 42.25 1.40
3696 7255 2.034305 ACCGGCGTCTGCTAGTAATAAG 59.966 50.000 6.01 0.00 42.25 1.73
3697 7256 2.052157 CGGCGTCTGCTAGTAATAAGC 58.948 52.381 0.00 0.00 42.25 3.09
3710 7269 9.481340 TGCTAGTAATAAGCAGTGATGATTAAG 57.519 33.333 0.00 0.00 44.78 1.85
3711 7270 9.698309 GCTAGTAATAAGCAGTGATGATTAAGA 57.302 33.333 0.00 0.00 39.83 2.10
3714 7273 9.757227 AGTAATAAGCAGTGATGATTAAGAGTC 57.243 33.333 0.00 0.00 0.00 3.36
3715 7274 9.757227 GTAATAAGCAGTGATGATTAAGAGTCT 57.243 33.333 0.00 0.00 0.00 3.24
3716 7275 8.885494 AATAAGCAGTGATGATTAAGAGTCTC 57.115 34.615 0.00 0.00 0.00 3.36
3717 7276 5.275067 AGCAGTGATGATTAAGAGTCTCC 57.725 43.478 0.00 0.00 0.00 3.71
3718 7277 4.713814 AGCAGTGATGATTAAGAGTCTCCA 59.286 41.667 0.00 0.00 0.00 3.86
3719 7278 5.049167 GCAGTGATGATTAAGAGTCTCCAG 58.951 45.833 0.00 0.00 0.00 3.86
3720 7279 5.163468 GCAGTGATGATTAAGAGTCTCCAGA 60.163 44.000 0.00 0.00 0.00 3.86
3721 7280 6.629068 GCAGTGATGATTAAGAGTCTCCAGAA 60.629 42.308 0.00 0.00 0.00 3.02
3722 7281 7.499292 CAGTGATGATTAAGAGTCTCCAGAAT 58.501 38.462 0.00 0.00 0.00 2.40
3723 7282 7.652909 CAGTGATGATTAAGAGTCTCCAGAATC 59.347 40.741 0.00 10.16 39.24 2.52
3724 7283 6.928492 GTGATGATTAAGAGTCTCCAGAATCC 59.072 42.308 12.85 3.98 39.73 3.01
3725 7284 6.612863 TGATGATTAAGAGTCTCCAGAATCCA 59.387 38.462 12.85 5.72 39.73 3.41
3726 7285 6.874278 TGATTAAGAGTCTCCAGAATCCAA 57.126 37.500 12.85 0.00 39.73 3.53
3727 7286 7.257790 TGATTAAGAGTCTCCAGAATCCAAA 57.742 36.000 12.85 0.00 39.73 3.28
3728 7287 7.865820 TGATTAAGAGTCTCCAGAATCCAAAT 58.134 34.615 12.85 1.75 39.73 2.32
3729 7288 7.772292 TGATTAAGAGTCTCCAGAATCCAAATG 59.228 37.037 12.85 0.00 39.73 2.32
3730 7289 5.768980 AAGAGTCTCCAGAATCCAAATGA 57.231 39.130 0.00 0.00 39.73 2.57
3731 7290 5.972327 AGAGTCTCCAGAATCCAAATGAT 57.028 39.130 0.44 0.00 39.73 2.45
3732 7291 5.682659 AGAGTCTCCAGAATCCAAATGATG 58.317 41.667 0.44 0.00 39.73 3.07
3743 7302 3.513680 CCAAATGATGGTCATGGTGTG 57.486 47.619 0.00 0.00 44.85 3.82
3744 7303 3.090790 CCAAATGATGGTCATGGTGTGA 58.909 45.455 0.00 0.00 44.85 3.58
3745 7304 3.510753 CCAAATGATGGTCATGGTGTGAA 59.489 43.478 0.00 0.00 44.85 3.18
3746 7305 4.381185 CCAAATGATGGTCATGGTGTGAAG 60.381 45.833 0.00 0.00 44.85 3.02
3747 7306 3.726557 ATGATGGTCATGGTGTGAAGT 57.273 42.857 0.00 0.00 38.90 3.01
3748 7307 4.842531 ATGATGGTCATGGTGTGAAGTA 57.157 40.909 0.00 0.00 38.90 2.24
3749 7308 4.632327 TGATGGTCATGGTGTGAAGTAA 57.368 40.909 0.00 0.00 38.90 2.24
3750 7309 4.979335 TGATGGTCATGGTGTGAAGTAAA 58.021 39.130 0.00 0.00 38.90 2.01
3751 7310 5.380900 TGATGGTCATGGTGTGAAGTAAAA 58.619 37.500 0.00 0.00 38.90 1.52
3752 7311 5.473162 TGATGGTCATGGTGTGAAGTAAAAG 59.527 40.000 0.00 0.00 38.90 2.27
3753 7312 3.568007 TGGTCATGGTGTGAAGTAAAAGC 59.432 43.478 0.00 0.00 38.90 3.51
3754 7313 3.821033 GGTCATGGTGTGAAGTAAAAGCT 59.179 43.478 0.00 0.00 38.90 3.74
3755 7314 5.001232 GGTCATGGTGTGAAGTAAAAGCTA 58.999 41.667 0.00 0.00 38.90 3.32
3756 7315 5.648092 GGTCATGGTGTGAAGTAAAAGCTAT 59.352 40.000 0.00 0.00 38.90 2.97
3757 7316 6.403636 GGTCATGGTGTGAAGTAAAAGCTATG 60.404 42.308 0.00 0.00 38.90 2.23
3758 7317 6.371548 GTCATGGTGTGAAGTAAAAGCTATGA 59.628 38.462 0.00 0.00 38.90 2.15
3759 7318 7.066284 GTCATGGTGTGAAGTAAAAGCTATGAT 59.934 37.037 0.00 0.00 38.90 2.45
3760 7319 7.611467 TCATGGTGTGAAGTAAAAGCTATGATT 59.389 33.333 0.00 0.00 32.78 2.57
3761 7320 7.144722 TGGTGTGAAGTAAAAGCTATGATTG 57.855 36.000 0.00 0.00 0.00 2.67
3762 7321 6.714810 TGGTGTGAAGTAAAAGCTATGATTGT 59.285 34.615 0.00 0.00 0.00 2.71
3763 7322 7.880713 TGGTGTGAAGTAAAAGCTATGATTGTA 59.119 33.333 0.00 0.00 0.00 2.41
3764 7323 8.175716 GGTGTGAAGTAAAAGCTATGATTGTAC 58.824 37.037 0.00 0.00 0.00 2.90
3765 7324 8.936864 GTGTGAAGTAAAAGCTATGATTGTACT 58.063 33.333 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 35 3.063084 GAGACGAGGCAGACCGGT 61.063 66.667 6.92 6.92 42.76 5.28
63 65 1.444933 TCCACCAAACCTCCATGTCT 58.555 50.000 0.00 0.00 0.00 3.41
65 67 1.995542 AGATCCACCAAACCTCCATGT 59.004 47.619 0.00 0.00 0.00 3.21
75 77 0.107214 GAATGGCCGAGATCCACCAA 60.107 55.000 0.00 0.00 36.26 3.67
94 96 1.562672 AATGAAGTCCTCCCACCGGG 61.563 60.000 6.32 0.00 46.11 5.73
200 215 2.598787 CCACCGGAACAGGGGCTAA 61.599 63.158 9.46 0.00 31.97 3.09
208 223 0.322098 CCATAAGCACCACCGGAACA 60.322 55.000 9.46 0.00 0.00 3.18
224 239 1.072678 CGCCCTCAGATGATGCCAT 59.927 57.895 0.00 0.00 35.29 4.40
249 264 0.395311 AGATCCGCCGGAGACAAGTA 60.395 55.000 13.12 0.00 34.05 2.24
325 350 8.642432 CAGAAGGATCCAAACTATAGACACATA 58.358 37.037 15.82 0.00 0.00 2.29
350 404 4.191544 CCGTTGGAAAGATGCTTAGATCA 58.808 43.478 0.00 0.00 0.00 2.92
420 474 6.430308 TGTTGTAATAGACAGTCGAGAAGTCT 59.570 38.462 15.84 15.84 44.25 3.24
453 508 2.689073 CTCCCTCTTTGGAGCTGGA 58.311 57.895 0.00 0.00 45.13 3.86
505 560 2.933495 AGCGACGAATACAAGCACTA 57.067 45.000 0.00 0.00 0.00 2.74
516 571 3.367992 TGTAAAACACCTAGCGACGAA 57.632 42.857 0.00 0.00 0.00 3.85
664 723 2.284331 TAGCAGCACGGGGGAAGA 60.284 61.111 0.00 0.00 0.00 2.87
778 838 3.094386 GCCATTGGCCTCGTATTGA 57.906 52.632 17.28 0.00 44.06 2.57
789 849 1.664333 GTGGTGCGTTTGCCATTGG 60.664 57.895 0.00 0.00 41.78 3.16
807 867 2.966309 GAAGTTCTTGGCCGTGCGG 61.966 63.158 6.22 6.22 38.57 5.69
808 868 2.556287 GAAGTTCTTGGCCGTGCG 59.444 61.111 0.00 0.00 0.00 5.34
809 869 1.244019 ATGGAAGTTCTTGGCCGTGC 61.244 55.000 2.25 0.00 0.00 5.34
810 870 0.523072 CATGGAAGTTCTTGGCCGTG 59.477 55.000 2.25 0.00 0.00 4.94
811 871 0.110486 ACATGGAAGTTCTTGGCCGT 59.890 50.000 2.25 0.00 0.00 5.68
812 872 1.247567 AACATGGAAGTTCTTGGCCG 58.752 50.000 2.25 0.00 0.00 6.13
813 873 2.867647 GCAAACATGGAAGTTCTTGGCC 60.868 50.000 0.00 0.00 0.00 5.36
814 874 2.224018 TGCAAACATGGAAGTTCTTGGC 60.224 45.455 2.25 0.00 0.00 4.52
815 875 3.383761 GTGCAAACATGGAAGTTCTTGG 58.616 45.455 2.25 0.00 0.00 3.61
816 876 3.181477 TGGTGCAAACATGGAAGTTCTTG 60.181 43.478 2.25 4.04 0.00 3.02
817 877 3.030291 TGGTGCAAACATGGAAGTTCTT 58.970 40.909 2.25 0.00 0.00 2.52
892 956 0.109781 ATGCGACGATTTTGGTGTGC 60.110 50.000 0.00 0.00 0.00 4.57
917 981 1.708193 TTGATGAATCAGCAGGCGCG 61.708 55.000 0.00 0.00 45.49 6.86
947 1015 2.508891 CGCGTTCTTGGCTCTAGCG 61.509 63.158 0.00 0.00 43.26 4.26
982 1050 3.964875 GGCTGCAACCACCGTGTG 61.965 66.667 0.00 0.00 0.00 3.82
983 1051 3.790416 ATGGCTGCAACCACCGTGT 62.790 57.895 11.90 0.00 44.17 4.49
984 1052 2.985282 ATGGCTGCAACCACCGTG 60.985 61.111 11.90 0.00 44.17 4.94
985 1053 2.985282 CATGGCTGCAACCACCGT 60.985 61.111 11.90 0.00 44.17 4.83
986 1054 3.751246 CCATGGCTGCAACCACCG 61.751 66.667 11.90 5.68 44.17 4.94
990 1062 2.993264 AGCACCATGGCTGCAACC 60.993 61.111 29.08 0.00 43.89 3.77
992 1064 1.676635 GAGAGCACCATGGCTGCAA 60.677 57.895 29.08 0.00 45.99 4.08
1110 1184 3.494332 AGCAAGAAGAAGAACAAGCCAT 58.506 40.909 0.00 0.00 0.00 4.40
1152 1234 3.493699 CCAGCCGGTCGATTATAGGAAAA 60.494 47.826 1.90 0.00 0.00 2.29
1155 1237 1.254026 CCAGCCGGTCGATTATAGGA 58.746 55.000 1.90 0.00 0.00 2.94
1157 1239 1.336887 CCACCAGCCGGTCGATTATAG 60.337 57.143 1.90 0.00 44.71 1.31
1158 1240 0.677288 CCACCAGCCGGTCGATTATA 59.323 55.000 1.90 0.00 44.71 0.98
1159 1241 1.046472 TCCACCAGCCGGTCGATTAT 61.046 55.000 1.90 0.00 44.71 1.28
1202 1296 0.103208 GATCGACTTCTCCGGCATGT 59.897 55.000 0.00 0.00 0.00 3.21
1438 1542 2.105006 TGCAGGTCAAAGCAGAGATC 57.895 50.000 0.00 0.00 35.51 2.75
1449 1667 1.410050 TTCTGTGAGGCTGCAGGTCA 61.410 55.000 17.12 0.00 33.81 4.02
1455 1674 1.312815 AACAACTTCTGTGAGGCTGC 58.687 50.000 0.00 0.00 38.67 5.25
1468 1687 4.177783 CCCGCACAAAGTTAAAAACAACT 58.822 39.130 0.00 0.00 40.49 3.16
1471 1690 2.159085 CCCCCGCACAAAGTTAAAAACA 60.159 45.455 0.00 0.00 0.00 2.83
1473 1692 1.202545 GCCCCCGCACAAAGTTAAAAA 60.203 47.619 0.00 0.00 34.03 1.94
1476 1695 1.152735 TGCCCCCGCACAAAGTTAA 60.153 52.632 0.00 0.00 41.12 2.01
1487 1706 3.451894 GGTTCTGCAATGCCCCCG 61.452 66.667 1.53 0.00 0.00 5.73
1488 1707 3.451894 CGGTTCTGCAATGCCCCC 61.452 66.667 1.53 0.00 0.00 5.40
1489 1708 3.451894 CCGGTTCTGCAATGCCCC 61.452 66.667 1.53 0.00 0.00 5.80
1491 1710 2.568090 CACCGGTTCTGCAATGCC 59.432 61.111 2.97 0.00 0.00 4.40
1542 4336 1.972223 CGTCTCCGACTCACCCAGT 60.972 63.158 0.00 0.00 38.45 4.00
1584 4378 0.535780 GCATGATGGCCTCCGATGAA 60.536 55.000 3.32 0.00 0.00 2.57
1587 4381 1.072678 CAGCATGATGGCCTCCGAT 59.927 57.895 3.32 0.00 39.69 4.18
1739 4582 4.006319 CACCTCAAAGGACAGGAATTCTC 58.994 47.826 5.23 0.00 37.67 2.87
1749 4592 2.291741 CTCAACTTGCACCTCAAAGGAC 59.708 50.000 0.00 0.00 37.67 3.85
1770 4613 7.064253 ACGTACAAGAGCATTACAACCTAAATC 59.936 37.037 0.00 0.00 0.00 2.17
1776 4619 4.565564 CCTACGTACAAGAGCATTACAACC 59.434 45.833 0.00 0.00 0.00 3.77
2300 5507 1.745115 CGAAGCCTTGGCGGATGAA 60.745 57.895 5.95 0.00 33.16 2.57
2337 5544 2.418910 CGAGTCCTCATGAGCCGGT 61.419 63.158 17.76 0.99 0.00 5.28
2339 5546 2.279120 GCGAGTCCTCATGAGCCG 60.279 66.667 17.76 16.50 0.00 5.52
2341 5548 0.108424 AACTGCGAGTCCTCATGAGC 60.108 55.000 17.76 6.31 0.00 4.26
2345 5552 2.224281 TGTTTGAACTGCGAGTCCTCAT 60.224 45.455 0.00 0.00 0.00 2.90
2348 5555 2.417719 GATGTTTGAACTGCGAGTCCT 58.582 47.619 0.00 0.00 0.00 3.85
2349 5556 1.464997 GGATGTTTGAACTGCGAGTCC 59.535 52.381 0.00 0.00 0.00 3.85
2350 5557 2.143122 TGGATGTTTGAACTGCGAGTC 58.857 47.619 0.00 0.00 0.00 3.36
2351 5558 2.254546 TGGATGTTTGAACTGCGAGT 57.745 45.000 0.00 0.00 0.00 4.18
2372 5579 2.466846 TGACAAATCTCCTCCCGATCA 58.533 47.619 0.00 0.00 0.00 2.92
2394 5856 4.214119 CCCTGCATCCATCGTGTAATTAAG 59.786 45.833 0.00 0.00 0.00 1.85
2707 6253 1.390123 GTTCATGACGGTGTCGATGTG 59.610 52.381 0.00 0.00 40.11 3.21
2752 6298 1.207089 TGCTTATTACTGGCAGACGCT 59.793 47.619 23.66 0.12 38.60 5.07
2760 6306 6.504398 TCTAATCGTCACTGCTTATTACTGG 58.496 40.000 0.00 0.00 0.00 4.00
2800 6351 0.178926 TCGGTAGTTTCCCACCAGGA 60.179 55.000 0.00 0.00 45.68 3.86
2801 6352 0.909623 ATCGGTAGTTTCCCACCAGG 59.090 55.000 0.00 0.00 34.25 4.45
2802 6353 1.831736 AGATCGGTAGTTTCCCACCAG 59.168 52.381 0.00 0.00 34.25 4.00
2803 6354 1.946984 AGATCGGTAGTTTCCCACCA 58.053 50.000 0.00 0.00 34.25 4.17
2804 6355 4.344390 AGATAAGATCGGTAGTTTCCCACC 59.656 45.833 0.00 0.00 0.00 4.61
2808 6366 4.750598 GGCAAGATAAGATCGGTAGTTTCC 59.249 45.833 0.00 0.00 0.00 3.13
2819 6377 8.650143 TTTTACTCCAAAAGGCAAGATAAGAT 57.350 30.769 0.00 0.00 32.31 2.40
2843 6401 6.058183 CAGCCTAGTACCATCATAGCTTTTT 58.942 40.000 0.00 0.00 0.00 1.94
2856 6414 3.055312 AGTGCCTAAAACAGCCTAGTACC 60.055 47.826 0.00 0.00 0.00 3.34
2884 6442 6.153680 TGCCTAAAACAACCTCTTCTCAAAAA 59.846 34.615 0.00 0.00 0.00 1.94
2885 6443 5.654650 TGCCTAAAACAACCTCTTCTCAAAA 59.345 36.000 0.00 0.00 0.00 2.44
2886 6444 5.197451 TGCCTAAAACAACCTCTTCTCAAA 58.803 37.500 0.00 0.00 0.00 2.69
2887 6445 4.787551 TGCCTAAAACAACCTCTTCTCAA 58.212 39.130 0.00 0.00 0.00 3.02
2888 6446 4.102524 TCTGCCTAAAACAACCTCTTCTCA 59.897 41.667 0.00 0.00 0.00 3.27
2889 6447 4.642429 TCTGCCTAAAACAACCTCTTCTC 58.358 43.478 0.00 0.00 0.00 2.87
2890 6448 4.706842 TCTGCCTAAAACAACCTCTTCT 57.293 40.909 0.00 0.00 0.00 2.85
2891 6449 5.966742 AATCTGCCTAAAACAACCTCTTC 57.033 39.130 0.00 0.00 0.00 2.87
2892 6450 6.316390 CGATAATCTGCCTAAAACAACCTCTT 59.684 38.462 0.00 0.00 0.00 2.85
2893 6451 5.817816 CGATAATCTGCCTAAAACAACCTCT 59.182 40.000 0.00 0.00 0.00 3.69
2894 6452 5.585047 ACGATAATCTGCCTAAAACAACCTC 59.415 40.000 0.00 0.00 0.00 3.85
2895 6453 5.497474 ACGATAATCTGCCTAAAACAACCT 58.503 37.500 0.00 0.00 0.00 3.50
2914 6472 4.987912 CCACAGCAAAAATTTGGTTACGAT 59.012 37.500 7.79 0.00 45.64 3.73
2915 6473 4.363999 CCACAGCAAAAATTTGGTTACGA 58.636 39.130 7.79 0.00 45.64 3.43
2916 6474 3.059935 GCCACAGCAAAAATTTGGTTACG 60.060 43.478 7.79 1.02 45.64 3.18
2926 6484 5.275067 AGTCATAAAAGCCACAGCAAAAA 57.725 34.783 0.00 0.00 43.56 1.94
2950 6508 1.677942 TCACTGCAATGCAACTGTCA 58.322 45.000 9.92 0.00 38.41 3.58
3022 6581 4.141620 ACAAGAGAGAGAACACAACACCAT 60.142 41.667 0.00 0.00 0.00 3.55
3052 6611 3.002791 CAATTTAAGTGGCTCGCTCTCA 58.997 45.455 0.00 0.00 0.00 3.27
3055 6614 1.468520 TGCAATTTAAGTGGCTCGCTC 59.531 47.619 0.00 0.00 0.00 5.03
3424 6983 2.375110 GTCGTTGTTCGTCTACGTTCA 58.625 47.619 0.00 1.00 43.41 3.18
3532 7091 2.760385 GTCTCACCGCCTAGCCCT 60.760 66.667 0.00 0.00 0.00 5.19
3544 7103 5.104360 CCCTGAAGATGGAATAAAGGTCTCA 60.104 44.000 0.00 0.00 0.00 3.27
3653 7212 3.938963 TCCATTTGGATTCAGTTCGTAGC 59.061 43.478 0.00 0.00 39.78 3.58
3666 7225 2.046700 GACGCCGGTCCATTTGGA 60.047 61.111 1.90 0.00 43.08 3.53
3667 7226 2.046314 AGACGCCGGTCCATTTGG 60.046 61.111 1.90 0.00 44.54 3.28
3668 7227 3.039202 GCAGACGCCGGTCCATTTG 62.039 63.158 1.90 0.00 44.54 2.32
3669 7228 1.895020 TAGCAGACGCCGGTCCATTT 61.895 55.000 1.90 0.00 44.54 2.32
3670 7229 2.298158 CTAGCAGACGCCGGTCCATT 62.298 60.000 1.90 0.00 44.54 3.16
3671 7230 2.758327 TAGCAGACGCCGGTCCAT 60.758 61.111 1.90 0.00 44.54 3.41
3672 7231 2.825075 TACTAGCAGACGCCGGTCCA 62.825 60.000 1.90 0.00 44.54 4.02
3673 7232 1.660560 TTACTAGCAGACGCCGGTCC 61.661 60.000 1.90 0.00 44.54 4.46
3674 7233 0.384669 ATTACTAGCAGACGCCGGTC 59.615 55.000 1.90 0.00 43.76 4.79
3675 7234 1.683943 TATTACTAGCAGACGCCGGT 58.316 50.000 1.90 0.00 39.83 5.28
3676 7235 2.662700 CTTATTACTAGCAGACGCCGG 58.337 52.381 0.00 0.00 39.83 6.13
3677 7236 2.052157 GCTTATTACTAGCAGACGCCG 58.948 52.381 0.00 0.00 39.83 6.46
3678 7237 3.093717 TGCTTATTACTAGCAGACGCC 57.906 47.619 0.00 0.00 43.30 5.68
3684 7243 9.481340 CTTAATCATCACTGCTTATTACTAGCA 57.519 33.333 0.00 0.00 45.78 3.49
3685 7244 9.698309 TCTTAATCATCACTGCTTATTACTAGC 57.302 33.333 0.00 0.00 39.10 3.42
3688 7247 9.757227 GACTCTTAATCATCACTGCTTATTACT 57.243 33.333 0.00 0.00 0.00 2.24
3689 7248 9.757227 AGACTCTTAATCATCACTGCTTATTAC 57.243 33.333 0.00 0.00 0.00 1.89
3690 7249 9.973450 GAGACTCTTAATCATCACTGCTTATTA 57.027 33.333 0.00 0.00 0.00 0.98
3691 7250 7.930865 GGAGACTCTTAATCATCACTGCTTATT 59.069 37.037 1.74 0.00 0.00 1.40
3692 7251 7.070447 TGGAGACTCTTAATCATCACTGCTTAT 59.930 37.037 1.74 0.00 0.00 1.73
3693 7252 6.381133 TGGAGACTCTTAATCATCACTGCTTA 59.619 38.462 1.74 0.00 0.00 3.09
3694 7253 5.188555 TGGAGACTCTTAATCATCACTGCTT 59.811 40.000 1.74 0.00 0.00 3.91
3695 7254 4.713814 TGGAGACTCTTAATCATCACTGCT 59.286 41.667 1.74 0.00 0.00 4.24
3696 7255 5.016051 TGGAGACTCTTAATCATCACTGC 57.984 43.478 1.74 0.00 0.00 4.40
3697 7256 6.462552 TCTGGAGACTCTTAATCATCACTG 57.537 41.667 1.74 0.00 0.00 3.66
3698 7257 7.201992 GGATTCTGGAGACTCTTAATCATCACT 60.202 40.741 18.28 0.00 0.00 3.41
3699 7258 6.928492 GGATTCTGGAGACTCTTAATCATCAC 59.072 42.308 18.28 5.81 0.00 3.06
3700 7259 6.612863 TGGATTCTGGAGACTCTTAATCATCA 59.387 38.462 18.28 10.54 0.00 3.07
3701 7260 7.060383 TGGATTCTGGAGACTCTTAATCATC 57.940 40.000 18.28 8.31 0.00 2.92
3702 7261 7.443302 TTGGATTCTGGAGACTCTTAATCAT 57.557 36.000 18.28 1.80 0.00 2.45
3703 7262 6.874278 TTGGATTCTGGAGACTCTTAATCA 57.126 37.500 18.28 3.81 0.00 2.57
3704 7263 7.989741 TCATTTGGATTCTGGAGACTCTTAATC 59.010 37.037 1.74 8.87 0.00 1.75
3705 7264 7.865820 TCATTTGGATTCTGGAGACTCTTAAT 58.134 34.615 1.74 0.31 0.00 1.40
3706 7265 7.257790 TCATTTGGATTCTGGAGACTCTTAA 57.742 36.000 1.74 0.00 0.00 1.85
3707 7266 6.874278 TCATTTGGATTCTGGAGACTCTTA 57.126 37.500 1.74 0.00 0.00 2.10
3708 7267 5.768980 TCATTTGGATTCTGGAGACTCTT 57.231 39.130 1.74 0.00 0.00 2.85
3709 7268 5.682659 CATCATTTGGATTCTGGAGACTCT 58.317 41.667 1.74 0.00 32.57 3.24
3724 7283 4.219070 ACTTCACACCATGACCATCATTTG 59.781 41.667 0.00 0.00 34.28 2.32
3725 7284 4.410099 ACTTCACACCATGACCATCATTT 58.590 39.130 0.00 0.00 34.28 2.32
3726 7285 4.038271 ACTTCACACCATGACCATCATT 57.962 40.909 0.00 0.00 34.28 2.57
3727 7286 3.726557 ACTTCACACCATGACCATCAT 57.273 42.857 0.00 0.00 37.65 2.45
3728 7287 4.632327 TTACTTCACACCATGACCATCA 57.368 40.909 0.00 0.00 36.92 3.07
3729 7288 5.619981 GCTTTTACTTCACACCATGACCATC 60.620 44.000 0.00 0.00 36.92 3.51
3730 7289 4.218417 GCTTTTACTTCACACCATGACCAT 59.782 41.667 0.00 0.00 36.92 3.55
3731 7290 3.568007 GCTTTTACTTCACACCATGACCA 59.432 43.478 0.00 0.00 36.92 4.02
3732 7291 3.821033 AGCTTTTACTTCACACCATGACC 59.179 43.478 0.00 0.00 36.92 4.02
3733 7292 6.371548 TCATAGCTTTTACTTCACACCATGAC 59.628 38.462 0.00 0.00 36.92 3.06
3734 7293 6.472016 TCATAGCTTTTACTTCACACCATGA 58.528 36.000 0.00 0.00 34.65 3.07
3735 7294 6.741992 TCATAGCTTTTACTTCACACCATG 57.258 37.500 0.00 0.00 0.00 3.66
3736 7295 7.394359 ACAATCATAGCTTTTACTTCACACCAT 59.606 33.333 0.00 0.00 0.00 3.55
3737 7296 6.714810 ACAATCATAGCTTTTACTTCACACCA 59.285 34.615 0.00 0.00 0.00 4.17
3738 7297 7.145932 ACAATCATAGCTTTTACTTCACACC 57.854 36.000 0.00 0.00 0.00 4.16
3739 7298 8.936864 AGTACAATCATAGCTTTTACTTCACAC 58.063 33.333 0.00 0.00 0.00 3.82


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

AutoCloner maintained by Alex Coulton.