Multiple sequence alignment - TraesCS7A01G122800

Loading Multiple Alignment...

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 TraesCS7A01G122800 chr7A 100.000 3374 0 0 1 3374 79336145 79332772 0.000000e+00 6231
1 TraesCS7A01G122800 chr7B 91.218 2175 130 34 259 2379 20722465 20720298 0.000000e+00 2902
2 TraesCS7A01G122800 chr7B 83.817 241 26 7 2416 2656 20718639 20718412 2.040000e-52 217
3 TraesCS7A01G122800 chrUn 89.775 1467 89 28 59 1489 399559206 399557765 0.000000e+00 1821
4 TraesCS7A01G122800 chrUn 91.140 1298 63 20 226 1489 416667063 416665784 0.000000e+00 1712
5 TraesCS7A01G122800 chrUn 97.208 1003 21 1 1491 2493 452897074 452896079 0.000000e+00 1690
6 TraesCS7A01G122800 chrUn 93.007 1001 40 11 518 1489 452459059 452460058 0.000000e+00 1434
7 TraesCS7A01G122800 chrUn 86.441 354 13 6 2495 2831 298661687 298662022 4.140000e-94 355
8 TraesCS7A01G122800 chr4B 85.558 1641 191 30 760 2378 138275810 138277426 0.000000e+00 1676
9 TraesCS7A01G122800 chr4B 86.392 1286 161 12 1102 2379 137702449 137703728 0.000000e+00 1393
10 TraesCS7A01G122800 chr4A 87.403 1286 147 13 1102 2378 480557713 480556434 0.000000e+00 1463
11 TraesCS7A01G122800 chr4A 87.188 1280 149 13 1108 2378 479624696 479623423 0.000000e+00 1441
12 TraesCS7A01G122800 chr4A 86.781 1286 157 10 1102 2379 479903500 479902220 0.000000e+00 1421
13 TraesCS7A01G122800 chr4A 86.381 1285 162 10 1102 2378 479431021 479429742 0.000000e+00 1391
14 TraesCS7A01G122800 chr4A 86.148 1285 150 14 1102 2378 481064735 481063471 0.000000e+00 1362
15 TraesCS7A01G122800 chr4A 86.412 471 44 13 714 1178 479903952 479903496 6.500000e-137 497
16 TraesCS7A01G122800 chr4A 85.845 438 42 13 747 1178 480558132 480557709 6.640000e-122 448
17 TraesCS7A01G122800 chr4A 85.616 438 43 13 747 1178 479431440 479431017 3.090000e-120 442
18 TraesCS7A01G122800 chr4A 84.770 348 33 13 714 1055 479647487 479647154 6.980000e-87 331
19 TraesCS7A01G122800 chr4D 87.160 1285 152 11 1102 2378 96712153 96713432 0.000000e+00 1447
20 TraesCS7A01G122800 chr4D 86.304 1285 148 14 1102 2378 96892512 96893776 0.000000e+00 1373
21 TraesCS7A01G122800 chr4D 86.567 469 42 12 714 1178 96711706 96712157 6.500000e-137 497
22 TraesCS7A01G122800 chr2D 92.857 504 28 3 2875 3373 468753464 468752964 0.000000e+00 725
23 TraesCS7A01G122800 chr2D 91.816 501 31 5 2879 3373 585125499 585125003 0.000000e+00 689
24 TraesCS7A01G122800 chr6D 92.368 511 29 5 2868 3373 456226246 456225741 0.000000e+00 719
25 TraesCS7A01G122800 chr6D 90.533 507 38 5 2874 3374 445310726 445311228 0.000000e+00 662
26 TraesCS7A01G122800 chr5D 92.200 500 31 4 2877 3370 77743053 77743550 0.000000e+00 701
27 TraesCS7A01G122800 chr5B 91.485 505 32 5 2875 3373 548523432 548523931 0.000000e+00 684
28 TraesCS7A01G122800 chr2B 91.417 501 35 3 2879 3373 61368170 61368668 0.000000e+00 680
29 TraesCS7A01G122800 chr7D 91.107 506 33 8 2875 3373 574788701 574788201 0.000000e+00 675
30 TraesCS7A01G122800 chr3D 90.403 521 38 8 2861 3373 579031172 579030656 0.000000e+00 675


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 TraesCS7A01G122800 chr7A 79332772 79336145 3373 True 6231.0 6231 100.0000 1 3374 1 chr7A.!!$R1 3373
1 TraesCS7A01G122800 chr7B 20718412 20722465 4053 True 1559.5 2902 87.5175 259 2656 2 chr7B.!!$R1 2397
2 TraesCS7A01G122800 chrUn 399557765 399559206 1441 True 1821.0 1821 89.7750 59 1489 1 chrUn.!!$R1 1430
3 TraesCS7A01G122800 chrUn 416665784 416667063 1279 True 1712.0 1712 91.1400 226 1489 1 chrUn.!!$R2 1263
4 TraesCS7A01G122800 chrUn 452896079 452897074 995 True 1690.0 1690 97.2080 1491 2493 1 chrUn.!!$R3 1002
5 TraesCS7A01G122800 chrUn 452459059 452460058 999 False 1434.0 1434 93.0070 518 1489 1 chrUn.!!$F2 971
6 TraesCS7A01G122800 chr4B 138275810 138277426 1616 False 1676.0 1676 85.5580 760 2378 1 chr4B.!!$F2 1618
7 TraesCS7A01G122800 chr4B 137702449 137703728 1279 False 1393.0 1393 86.3920 1102 2379 1 chr4B.!!$F1 1277
8 TraesCS7A01G122800 chr4A 479623423 479624696 1273 True 1441.0 1441 87.1880 1108 2378 1 chr4A.!!$R1 1270
9 TraesCS7A01G122800 chr4A 481063471 481064735 1264 True 1362.0 1362 86.1480 1102 2378 1 chr4A.!!$R3 1276
10 TraesCS7A01G122800 chr4A 479902220 479903952 1732 True 959.0 1421 86.5965 714 2379 2 chr4A.!!$R5 1665
11 TraesCS7A01G122800 chr4A 480556434 480558132 1698 True 955.5 1463 86.6240 747 2378 2 chr4A.!!$R6 1631
12 TraesCS7A01G122800 chr4A 479429742 479431440 1698 True 916.5 1391 85.9985 747 2378 2 chr4A.!!$R4 1631
13 TraesCS7A01G122800 chr4D 96892512 96893776 1264 False 1373.0 1373 86.3040 1102 2378 1 chr4D.!!$F1 1276
14 TraesCS7A01G122800 chr4D 96711706 96713432 1726 False 972.0 1447 86.8635 714 2378 2 chr4D.!!$F2 1664
15 TraesCS7A01G122800 chr2D 468752964 468753464 500 True 725.0 725 92.8570 2875 3373 1 chr2D.!!$R1 498
16 TraesCS7A01G122800 chr6D 456225741 456226246 505 True 719.0 719 92.3680 2868 3373 1 chr6D.!!$R1 505
17 TraesCS7A01G122800 chr6D 445310726 445311228 502 False 662.0 662 90.5330 2874 3374 1 chr6D.!!$F1 500
18 TraesCS7A01G122800 chr7D 574788201 574788701 500 True 675.0 675 91.1070 2875 3373 1 chr7D.!!$R1 498
19 TraesCS7A01G122800 chr3D 579030656 579031172 516 True 675.0 675 90.4030 2861 3373 1 chr3D.!!$R1 512

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
450 491 0.976641 AAGATCCTTGTGACGGCTGA 59.023 50.0 0.0 0.0 0.0 4.26 F
1620 1858 0.390472 CGGACTCAGGCTCCAAACTC 60.390 60.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2225 2469 0.036671 CCGGGGATTCGGCTTATACC 60.037 60.0 0.00 0.0 43.71 2.73 R
2780 4646 0.107945 AGCGGTGCTCCTTGAGAATC 60.108 55.0 2.85 0.0 30.62 2.52 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
47 48 9.442047 ACCAAAAATGTAGAATGAAAACACAAA 57.558 25.926 0.00 0.00 0.00 2.83
54 55 9.868277 ATGTAGAATGAAAACACAAAAGAAACA 57.132 25.926 0.00 0.00 0.00 2.83
55 56 9.698309 TGTAGAATGAAAACACAAAAGAAACAA 57.302 25.926 0.00 0.00 0.00 2.83
58 59 8.720562 AGAATGAAAACACAAAAGAAACAAAGG 58.279 29.630 0.00 0.00 0.00 3.11
59 60 8.614469 AATGAAAACACAAAAGAAACAAAGGA 57.386 26.923 0.00 0.00 0.00 3.36
60 61 8.614469 ATGAAAACACAAAAGAAACAAAGGAA 57.386 26.923 0.00 0.00 0.00 3.36
61 62 8.438676 TGAAAACACAAAAGAAACAAAGGAAA 57.561 26.923 0.00 0.00 0.00 3.13
62 63 8.893727 TGAAAACACAAAAGAAACAAAGGAAAA 58.106 25.926 0.00 0.00 0.00 2.29
63 64 9.891828 GAAAACACAAAAGAAACAAAGGAAAAT 57.108 25.926 0.00 0.00 0.00 1.82
64 65 9.676195 AAAACACAAAAGAAACAAAGGAAAATG 57.324 25.926 0.00 0.00 0.00 2.32
65 66 8.614469 AACACAAAAGAAACAAAGGAAAATGA 57.386 26.923 0.00 0.00 0.00 2.57
66 67 8.614469 ACACAAAAGAAACAAAGGAAAATGAA 57.386 26.923 0.00 0.00 0.00 2.57
67 68 9.061435 ACACAAAAGAAACAAAGGAAAATGAAA 57.939 25.926 0.00 0.00 0.00 2.69
68 69 9.890352 CACAAAAGAAACAAAGGAAAATGAAAA 57.110 25.926 0.00 0.00 0.00 2.29
138 150 8.907222 ATAAACAAGTGCAAAAGAATGGAAAT 57.093 26.923 0.00 0.00 0.00 2.17
139 151 6.607735 AACAAGTGCAAAAGAATGGAAATG 57.392 33.333 0.00 0.00 0.00 2.32
140 152 4.512571 ACAAGTGCAAAAGAATGGAAATGC 59.487 37.500 0.00 0.00 0.00 3.56
141 153 4.339872 AGTGCAAAAGAATGGAAATGCA 57.660 36.364 0.00 0.00 41.08 3.96
149 161 6.849588 AAAGAATGGAAATGCAGTGAAAAC 57.150 33.333 0.00 0.00 0.00 2.43
162 174 4.670221 GCAGTGAAAACCGATAAGAGCAAG 60.670 45.833 0.00 0.00 0.00 4.01
166 178 2.604046 AACCGATAAGAGCAAGCGAT 57.396 45.000 0.00 0.00 0.00 4.58
168 180 1.137086 ACCGATAAGAGCAAGCGATGT 59.863 47.619 0.00 0.00 0.00 3.06
170 182 2.463876 CGATAAGAGCAAGCGATGTGA 58.536 47.619 0.00 0.00 0.00 3.58
178 190 5.634896 AGAGCAAGCGATGTGAATAAAAAG 58.365 37.500 0.00 0.00 0.00 2.27
179 191 5.412594 AGAGCAAGCGATGTGAATAAAAAGA 59.587 36.000 0.00 0.00 0.00 2.52
182 194 6.922957 AGCAAGCGATGTGAATAAAAAGAAAA 59.077 30.769 0.00 0.00 0.00 2.29
184 196 7.737311 GCAAGCGATGTGAATAAAAAGAAAAAG 59.263 33.333 0.00 0.00 0.00 2.27
192 204 9.296400 TGTGAATAAAAAGAAAAAGAGAAACCG 57.704 29.630 0.00 0.00 0.00 4.44
209 221 9.346005 AGAGAAACCGAAGAAACCTAATAAAAA 57.654 29.630 0.00 0.00 0.00 1.94
396 412 6.707599 AAACGAAGAAGGAATAGAAAGACG 57.292 37.500 0.00 0.00 0.00 4.18
408 424 6.128363 GGAATAGAAAGACGAATGAAAACCGT 60.128 38.462 0.00 0.00 39.41 4.83
419 435 6.142817 CGAATGAAAACCGTGAAGAGAAAAT 58.857 36.000 0.00 0.00 0.00 1.82
438 479 3.914426 ATACCTTTGCGTCAAGATCCT 57.086 42.857 0.00 0.00 0.00 3.24
444 485 1.795768 TGCGTCAAGATCCTTGTGAC 58.204 50.000 6.59 6.43 38.62 3.67
450 491 0.976641 AAGATCCTTGTGACGGCTGA 59.023 50.000 0.00 0.00 0.00 4.26
451 492 1.198713 AGATCCTTGTGACGGCTGAT 58.801 50.000 0.00 0.00 0.00 2.90
456 497 2.094182 TCCTTGTGACGGCTGATAAGAC 60.094 50.000 0.00 0.00 0.00 3.01
475 516 5.880054 AGACGTTCATTTGGGTTTATCTG 57.120 39.130 0.00 0.00 0.00 2.90
510 552 7.520590 CGTTCGTCGTATAATATTTCCGAAAAC 59.479 37.037 0.00 6.83 35.23 2.43
538 580 3.355626 AAATGAATCGATCTCTCGCGA 57.644 42.857 9.26 9.26 44.65 5.87
571 613 2.051345 CGGGTGCAAAACAGACGC 60.051 61.111 0.00 0.00 0.00 5.19
591 633 2.183811 CTCCGCTCACCTCTGCAG 59.816 66.667 7.63 7.63 0.00 4.41
602 644 2.050077 TCTGCAGACGCGACACAG 60.050 61.111 15.93 18.52 42.97 3.66
603 645 3.771491 CTGCAGACGCGACACAGC 61.771 66.667 15.93 13.35 42.97 4.40
679 750 1.474077 GCTGCCAATTACTCCTGGTTG 59.526 52.381 0.00 0.00 34.97 3.77
866 953 1.140852 TCACAGGTGAGGTTGGACTTG 59.859 52.381 0.00 0.00 34.14 3.16
1047 1141 4.157289 AGGATAGTGAGCTTTGCACATTTG 59.843 41.667 6.78 0.00 38.70 2.32
1149 1387 5.105917 GGAAACTGAAACTGTGGTGAGAAAA 60.106 40.000 0.00 0.00 0.00 2.29
1272 1510 2.240493 ATACCAGCCTATGCAACGAC 57.760 50.000 0.00 0.00 41.13 4.34
1620 1858 0.390472 CGGACTCAGGCTCCAAACTC 60.390 60.000 0.00 0.00 0.00 3.01
1857 2095 2.779755 TGTATGCATTCACGGGAACT 57.220 45.000 0.00 0.00 35.46 3.01
1870 2108 4.224147 TCACGGGAACTGGAAGAATTGATA 59.776 41.667 0.00 0.00 40.47 2.15
1910 2148 2.358939 ACCGTCACGAGGAACATAAC 57.641 50.000 0.00 0.00 0.00 1.89
2225 2469 6.669278 CAGATGATGAGCAACATAATTGGAG 58.331 40.000 0.00 0.00 39.56 3.86
2294 2538 7.822334 TGATGACAGTACGGAAGAAATTGTATT 59.178 33.333 0.00 0.00 0.00 1.89
2297 2541 6.469410 ACAGTACGGAAGAAATTGTATTCCA 58.531 36.000 13.87 0.00 42.20 3.53
2398 2795 8.714906 AGGTAGTAACATGGCAAGTCTATTAAT 58.285 33.333 0.00 0.00 0.00 1.40
2499 4365 2.159170 GCGTCTAAGGAGCTTGATGAGT 60.159 50.000 0.00 0.00 0.00 3.41
2500 4366 3.677424 GCGTCTAAGGAGCTTGATGAGTT 60.677 47.826 0.00 0.00 0.00 3.01
2511 4377 8.049117 AGGAGCTTGATGAGTTTGATATTTGTA 58.951 33.333 0.00 0.00 0.00 2.41
2512 4378 8.844244 GGAGCTTGATGAGTTTGATATTTGTAT 58.156 33.333 0.00 0.00 0.00 2.29
2585 4451 8.027189 TGTACTTGCACTATTAGATATAAGGCG 58.973 37.037 0.00 0.00 0.00 5.52
2587 4453 7.667557 ACTTGCACTATTAGATATAAGGCGAA 58.332 34.615 0.00 0.00 0.00 4.70
2588 4454 7.599245 ACTTGCACTATTAGATATAAGGCGAAC 59.401 37.037 0.00 0.00 0.00 3.95
2591 4457 8.799367 TGCACTATTAGATATAAGGCGAACTTA 58.201 33.333 0.00 3.03 45.24 2.24
2650 4516 5.129634 TGGTTCAGAATCAGTACTGCAAAA 58.870 37.500 18.45 0.79 34.57 2.44
2656 4522 7.542890 TCAGAATCAGTACTGCAAAACAAAAA 58.457 30.769 18.45 0.00 34.57 1.94
2657 4523 8.196771 TCAGAATCAGTACTGCAAAACAAAAAT 58.803 29.630 18.45 0.00 34.57 1.82
2658 4524 8.819974 CAGAATCAGTACTGCAAAACAAAAATT 58.180 29.630 18.45 8.24 0.00 1.82
2659 4525 9.382275 AGAATCAGTACTGCAAAACAAAAATTT 57.618 25.926 18.45 0.00 0.00 1.82
2660 4526 9.424659 GAATCAGTACTGCAAAACAAAAATTTG 57.575 29.630 18.45 4.40 43.62 2.32
2669 4535 6.051646 CAAAACAAAAATTTGCTCCTCAGG 57.948 37.500 5.82 0.00 41.79 3.86
2670 4536 5.357742 AAACAAAAATTTGCTCCTCAGGT 57.642 34.783 5.82 0.00 41.79 4.00
2671 4537 4.590850 ACAAAAATTTGCTCCTCAGGTC 57.409 40.909 5.82 0.00 41.79 3.85
2672 4538 3.960102 ACAAAAATTTGCTCCTCAGGTCA 59.040 39.130 5.82 0.00 41.79 4.02
2673 4539 4.202151 ACAAAAATTTGCTCCTCAGGTCAC 60.202 41.667 5.82 0.00 41.79 3.67
2674 4540 2.206576 AATTTGCTCCTCAGGTCACC 57.793 50.000 0.00 0.00 0.00 4.02
2675 4541 1.366319 ATTTGCTCCTCAGGTCACCT 58.634 50.000 0.00 0.00 0.00 4.00
2684 4550 3.402186 CAGGTCACCTGCACTTTGA 57.598 52.632 12.03 0.00 45.13 2.69
2685 4551 1.901591 CAGGTCACCTGCACTTTGAT 58.098 50.000 12.03 0.00 45.13 2.57
2686 4552 1.538512 CAGGTCACCTGCACTTTGATG 59.461 52.381 12.03 0.00 45.13 3.07
2687 4553 0.242017 GGTCACCTGCACTTTGATGC 59.758 55.000 0.00 0.00 46.32 3.91
2696 4562 1.599542 GCACTTTGATGCGGATAGACC 59.400 52.381 0.00 0.00 35.50 3.85
2697 4563 2.905075 CACTTTGATGCGGATAGACCA 58.095 47.619 0.00 0.00 38.90 4.02
2698 4564 2.609459 CACTTTGATGCGGATAGACCAC 59.391 50.000 0.00 0.00 38.90 4.16
2699 4565 2.213499 CTTTGATGCGGATAGACCACC 58.787 52.381 0.00 0.00 38.90 4.61
2700 4566 1.199615 TTGATGCGGATAGACCACCA 58.800 50.000 0.00 0.00 38.90 4.17
2701 4567 1.199615 TGATGCGGATAGACCACCAA 58.800 50.000 0.00 0.00 38.90 3.67
2702 4568 1.557371 TGATGCGGATAGACCACCAAA 59.443 47.619 0.00 0.00 38.90 3.28
2703 4569 1.940613 GATGCGGATAGACCACCAAAC 59.059 52.381 0.00 0.00 38.90 2.93
2704 4570 0.981183 TGCGGATAGACCACCAAACT 59.019 50.000 0.00 0.00 38.90 2.66
2705 4571 1.066430 TGCGGATAGACCACCAAACTC 60.066 52.381 0.00 0.00 38.90 3.01
2706 4572 1.066430 GCGGATAGACCACCAAACTCA 60.066 52.381 0.00 0.00 38.90 3.41
2707 4573 2.614481 GCGGATAGACCACCAAACTCAA 60.614 50.000 0.00 0.00 38.90 3.02
2708 4574 3.670625 CGGATAGACCACCAAACTCAAA 58.329 45.455 0.00 0.00 38.90 2.69
2709 4575 3.684788 CGGATAGACCACCAAACTCAAAG 59.315 47.826 0.00 0.00 38.90 2.77
2710 4576 4.562757 CGGATAGACCACCAAACTCAAAGA 60.563 45.833 0.00 0.00 38.90 2.52
2711 4577 5.313712 GGATAGACCACCAAACTCAAAGAA 58.686 41.667 0.00 0.00 38.79 2.52
2712 4578 5.768164 GGATAGACCACCAAACTCAAAGAAA 59.232 40.000 0.00 0.00 38.79 2.52
2713 4579 4.983671 AGACCACCAAACTCAAAGAAAC 57.016 40.909 0.00 0.00 0.00 2.78
2714 4580 4.340617 AGACCACCAAACTCAAAGAAACA 58.659 39.130 0.00 0.00 0.00 2.83
2715 4581 4.157840 AGACCACCAAACTCAAAGAAACAC 59.842 41.667 0.00 0.00 0.00 3.32
2716 4582 3.119637 ACCACCAAACTCAAAGAAACACG 60.120 43.478 0.00 0.00 0.00 4.49
2717 4583 3.434637 CACCAAACTCAAAGAAACACGG 58.565 45.455 0.00 0.00 0.00 4.94
2718 4584 2.425668 ACCAAACTCAAAGAAACACGGG 59.574 45.455 0.00 0.00 0.00 5.28
2719 4585 2.459934 CAAACTCAAAGAAACACGGGC 58.540 47.619 0.00 0.00 0.00 6.13
2720 4586 1.757682 AACTCAAAGAAACACGGGCA 58.242 45.000 0.00 0.00 0.00 5.36
2721 4587 1.757682 ACTCAAAGAAACACGGGCAA 58.242 45.000 0.00 0.00 0.00 4.52
2722 4588 2.306847 ACTCAAAGAAACACGGGCAAT 58.693 42.857 0.00 0.00 0.00 3.56
2723 4589 2.693074 ACTCAAAGAAACACGGGCAATT 59.307 40.909 0.00 0.00 0.00 2.32
2724 4590 3.132111 ACTCAAAGAAACACGGGCAATTT 59.868 39.130 0.00 0.00 0.00 1.82
2725 4591 4.119136 CTCAAAGAAACACGGGCAATTTT 58.881 39.130 0.00 0.00 0.00 1.82
2726 4592 5.163499 ACTCAAAGAAACACGGGCAATTTTA 60.163 36.000 0.00 0.00 0.00 1.52
2727 4593 5.285651 TCAAAGAAACACGGGCAATTTTAG 58.714 37.500 0.00 0.00 0.00 1.85
2728 4594 4.929819 AAGAAACACGGGCAATTTTAGT 57.070 36.364 0.00 0.00 0.00 2.24
2729 4595 4.929819 AGAAACACGGGCAATTTTAGTT 57.070 36.364 0.00 0.00 0.00 2.24
2730 4596 5.270893 AGAAACACGGGCAATTTTAGTTT 57.729 34.783 0.00 0.00 0.00 2.66
2731 4597 5.666462 AGAAACACGGGCAATTTTAGTTTT 58.334 33.333 0.00 0.00 0.00 2.43
2732 4598 5.751509 AGAAACACGGGCAATTTTAGTTTTC 59.248 36.000 0.00 0.00 0.00 2.29
2733 4599 4.657436 ACACGGGCAATTTTAGTTTTCA 57.343 36.364 0.00 0.00 0.00 2.69
2734 4600 5.208463 ACACGGGCAATTTTAGTTTTCAT 57.792 34.783 0.00 0.00 0.00 2.57
2735 4601 6.334102 ACACGGGCAATTTTAGTTTTCATA 57.666 33.333 0.00 0.00 0.00 2.15
2736 4602 6.930731 ACACGGGCAATTTTAGTTTTCATAT 58.069 32.000 0.00 0.00 0.00 1.78
2737 4603 7.382898 ACACGGGCAATTTTAGTTTTCATATT 58.617 30.769 0.00 0.00 0.00 1.28
2738 4604 8.524487 ACACGGGCAATTTTAGTTTTCATATTA 58.476 29.630 0.00 0.00 0.00 0.98
2739 4605 9.528018 CACGGGCAATTTTAGTTTTCATATTAT 57.472 29.630 0.00 0.00 0.00 1.28
2757 4623 9.440773 TCATATTATAATTTGATTCGCTGAGCT 57.559 29.630 12.84 0.00 0.00 4.09
2766 4632 9.807649 AATTTGATTCGCTGAGCTATTTATTTT 57.192 25.926 1.78 0.00 0.00 1.82
2767 4633 8.619146 TTTGATTCGCTGAGCTATTTATTTTG 57.381 30.769 1.78 0.00 0.00 2.44
2768 4634 7.320443 TGATTCGCTGAGCTATTTATTTTGT 57.680 32.000 1.78 0.00 0.00 2.83
2769 4635 7.761409 TGATTCGCTGAGCTATTTATTTTGTT 58.239 30.769 1.78 0.00 0.00 2.83
2770 4636 7.697710 TGATTCGCTGAGCTATTTATTTTGTTG 59.302 33.333 1.78 0.00 0.00 3.33
2771 4637 6.494893 TCGCTGAGCTATTTATTTTGTTGT 57.505 33.333 1.78 0.00 0.00 3.32
2772 4638 6.314018 TCGCTGAGCTATTTATTTTGTTGTG 58.686 36.000 1.78 0.00 0.00 3.33
2773 4639 5.003778 CGCTGAGCTATTTATTTTGTTGTGC 59.996 40.000 1.78 0.00 0.00 4.57
2774 4640 5.289434 GCTGAGCTATTTATTTTGTTGTGCC 59.711 40.000 0.00 0.00 0.00 5.01
2775 4641 5.398169 TGAGCTATTTATTTTGTTGTGCCG 58.602 37.500 0.00 0.00 0.00 5.69
2776 4642 4.173256 AGCTATTTATTTTGTTGTGCCGC 58.827 39.130 0.00 0.00 0.00 6.53
2777 4643 3.923461 GCTATTTATTTTGTTGTGCCGCA 59.077 39.130 0.00 0.00 0.00 5.69
2778 4644 4.566360 GCTATTTATTTTGTTGTGCCGCAT 59.434 37.500 0.00 0.00 0.00 4.73
2779 4645 5.063312 GCTATTTATTTTGTTGTGCCGCATT 59.937 36.000 0.00 0.00 0.00 3.56
2780 4646 4.722203 TTTATTTTGTTGTGCCGCATTG 57.278 36.364 0.00 0.00 0.00 2.82
2781 4647 2.522836 ATTTTGTTGTGCCGCATTGA 57.477 40.000 0.00 0.00 0.00 2.57
2782 4648 2.522836 TTTTGTTGTGCCGCATTGAT 57.477 40.000 0.00 0.00 0.00 2.57
2783 4649 2.522836 TTTGTTGTGCCGCATTGATT 57.477 40.000 0.00 0.00 0.00 2.57
2784 4650 2.063156 TTGTTGTGCCGCATTGATTC 57.937 45.000 0.00 0.00 0.00 2.52
2785 4651 1.246649 TGTTGTGCCGCATTGATTCT 58.753 45.000 0.00 0.00 0.00 2.40
2786 4652 1.199789 TGTTGTGCCGCATTGATTCTC 59.800 47.619 0.00 0.00 0.00 2.87
2787 4653 1.199789 GTTGTGCCGCATTGATTCTCA 59.800 47.619 0.00 0.00 0.00 3.27
2788 4654 1.532523 TGTGCCGCATTGATTCTCAA 58.467 45.000 0.00 0.00 41.09 3.02
2789 4655 1.469703 TGTGCCGCATTGATTCTCAAG 59.530 47.619 0.00 0.00 40.05 3.02
2790 4656 1.097232 TGCCGCATTGATTCTCAAGG 58.903 50.000 0.00 0.00 40.05 3.61
2791 4657 1.339920 TGCCGCATTGATTCTCAAGGA 60.340 47.619 5.77 0.00 40.25 3.36
2792 4658 1.332997 GCCGCATTGATTCTCAAGGAG 59.667 52.381 5.77 2.48 40.25 3.69
2793 4659 1.332997 CCGCATTGATTCTCAAGGAGC 59.667 52.381 5.77 4.30 40.25 4.70
2794 4660 2.011947 CGCATTGATTCTCAAGGAGCA 58.988 47.619 5.77 0.00 40.25 4.26
2795 4661 2.223203 CGCATTGATTCTCAAGGAGCAC 60.223 50.000 5.77 0.00 40.25 4.40
2796 4662 2.098770 GCATTGATTCTCAAGGAGCACC 59.901 50.000 5.77 0.00 40.25 5.01
2797 4663 2.099141 TTGATTCTCAAGGAGCACCG 57.901 50.000 0.00 0.00 41.83 4.94
2798 4664 0.391661 TGATTCTCAAGGAGCACCGC 60.392 55.000 0.00 0.00 41.83 5.68
2799 4665 0.107945 GATTCTCAAGGAGCACCGCT 60.108 55.000 0.00 0.00 43.88 5.52
2800 4666 0.326264 ATTCTCAAGGAGCACCGCTT 59.674 50.000 0.00 0.00 39.88 4.68
2801 4667 0.603707 TTCTCAAGGAGCACCGCTTG 60.604 55.000 0.00 0.00 39.88 4.01
2809 4675 2.339712 GCACCGCTTGCCAACATT 59.660 55.556 0.00 0.00 46.63 2.71
2810 4676 1.300853 GCACCGCTTGCCAACATTT 60.301 52.632 0.00 0.00 46.63 2.32
2811 4677 1.284297 GCACCGCTTGCCAACATTTC 61.284 55.000 0.00 0.00 46.63 2.17
2812 4678 0.667184 CACCGCTTGCCAACATTTCC 60.667 55.000 0.00 0.00 0.00 3.13
2813 4679 0.827507 ACCGCTTGCCAACATTTCCT 60.828 50.000 0.00 0.00 0.00 3.36
2814 4680 0.318120 CCGCTTGCCAACATTTCCTT 59.682 50.000 0.00 0.00 0.00 3.36
2815 4681 1.543802 CCGCTTGCCAACATTTCCTTA 59.456 47.619 0.00 0.00 0.00 2.69
2816 4682 2.595386 CGCTTGCCAACATTTCCTTAC 58.405 47.619 0.00 0.00 0.00 2.34
2817 4683 2.030363 CGCTTGCCAACATTTCCTTACA 60.030 45.455 0.00 0.00 0.00 2.41
2818 4684 3.367292 CGCTTGCCAACATTTCCTTACAT 60.367 43.478 0.00 0.00 0.00 2.29
2819 4685 4.142491 CGCTTGCCAACATTTCCTTACATA 60.142 41.667 0.00 0.00 0.00 2.29
2820 4686 5.102313 GCTTGCCAACATTTCCTTACATAC 58.898 41.667 0.00 0.00 0.00 2.39
2821 4687 5.105756 GCTTGCCAACATTTCCTTACATACT 60.106 40.000 0.00 0.00 0.00 2.12
2822 4688 6.572314 GCTTGCCAACATTTCCTTACATACTT 60.572 38.462 0.00 0.00 0.00 2.24
2823 4689 6.509418 TGCCAACATTTCCTTACATACTTC 57.491 37.500 0.00 0.00 0.00 3.01
2824 4690 5.417580 TGCCAACATTTCCTTACATACTTCC 59.582 40.000 0.00 0.00 0.00 3.46
2825 4691 5.417580 GCCAACATTTCCTTACATACTTCCA 59.582 40.000 0.00 0.00 0.00 3.53
2826 4692 6.096846 GCCAACATTTCCTTACATACTTCCAT 59.903 38.462 0.00 0.00 0.00 3.41
2827 4693 7.363793 GCCAACATTTCCTTACATACTTCCATT 60.364 37.037 0.00 0.00 0.00 3.16
2828 4694 8.531146 CCAACATTTCCTTACATACTTCCATTT 58.469 33.333 0.00 0.00 0.00 2.32
2829 4695 9.927668 CAACATTTCCTTACATACTTCCATTTT 57.072 29.630 0.00 0.00 0.00 1.82
2835 4701 9.457436 TTCCTTACATACTTCCATTTTAGGAAC 57.543 33.333 0.00 0.00 42.56 3.62
2836 4702 8.050930 TCCTTACATACTTCCATTTTAGGAACC 58.949 37.037 0.00 0.00 42.56 3.62
2837 4703 7.832187 CCTTACATACTTCCATTTTAGGAACCA 59.168 37.037 0.00 0.00 42.56 3.67
2838 4704 8.570068 TTACATACTTCCATTTTAGGAACCAC 57.430 34.615 0.00 0.00 42.56 4.16
2839 4705 5.949952 ACATACTTCCATTTTAGGAACCACC 59.050 40.000 0.00 0.00 42.56 4.61
2840 4706 4.463050 ACTTCCATTTTAGGAACCACCA 57.537 40.909 0.00 0.00 42.56 4.17
2841 4707 4.149598 ACTTCCATTTTAGGAACCACCAC 58.850 43.478 0.00 0.00 42.56 4.16
2842 4708 3.163616 TCCATTTTAGGAACCACCACC 57.836 47.619 0.00 0.00 42.04 4.61
2843 4709 2.176045 CCATTTTAGGAACCACCACCC 58.824 52.381 0.00 0.00 42.04 4.61
2844 4710 2.225267 CCATTTTAGGAACCACCACCCT 60.225 50.000 0.00 0.00 42.04 4.34
2845 4711 3.506398 CATTTTAGGAACCACCACCCTT 58.494 45.455 0.00 0.00 42.04 3.95
2846 4712 2.668144 TTTAGGAACCACCACCCTTG 57.332 50.000 0.00 0.00 42.04 3.61
2847 4713 1.525175 TTAGGAACCACCACCCTTGT 58.475 50.000 0.00 0.00 42.04 3.16
2848 4714 1.525175 TAGGAACCACCACCCTTGTT 58.475 50.000 0.00 0.00 42.04 2.83
2849 4715 0.634465 AGGAACCACCACCCTTGTTT 59.366 50.000 0.00 0.00 42.04 2.83
2850 4716 1.007842 AGGAACCACCACCCTTGTTTT 59.992 47.619 0.00 0.00 42.04 2.43
2851 4717 1.834896 GGAACCACCACCCTTGTTTTT 59.165 47.619 0.00 0.00 38.79 1.94
2892 4758 7.668469 ACTTTATTTGACGAAATAGGGTTTCCT 59.332 33.333 0.00 0.00 46.96 3.36
2907 4773 4.204799 GGTTTCCTCCCGCTTTGTATTAT 58.795 43.478 0.00 0.00 0.00 1.28
3020 4891 0.601576 CGACACCGGTGGATCAACAA 60.602 55.000 36.47 0.00 34.19 2.83
3134 5007 1.007271 GGGATGCGACGATGACGAT 60.007 57.895 0.00 0.00 42.66 3.73
3177 5050 1.405256 GGTACACGACGAGGAGAGAGA 60.405 57.143 0.00 0.00 0.00 3.10
3216 5089 2.750350 CAGGAAGGTTCGGTGGCT 59.250 61.111 0.00 0.00 0.00 4.75
3265 5138 1.068588 CTCGGCCGACATGGATTTCTA 59.931 52.381 27.28 0.00 42.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 9.442047 TTTGTGTTTTCATTCTACATTTTTGGT 57.558 25.926 0.00 0.00 0.00 3.67
28 29 9.868277 TGTTTCTTTTGTGTTTTCATTCTACAT 57.132 25.926 0.00 0.00 0.00 2.29
29 30 9.698309 TTGTTTCTTTTGTGTTTTCATTCTACA 57.302 25.926 0.00 0.00 0.00 2.74
32 33 8.720562 CCTTTGTTTCTTTTGTGTTTTCATTCT 58.279 29.630 0.00 0.00 0.00 2.40
33 34 8.716909 TCCTTTGTTTCTTTTGTGTTTTCATTC 58.283 29.630 0.00 0.00 0.00 2.67
34 35 8.614469 TCCTTTGTTTCTTTTGTGTTTTCATT 57.386 26.923 0.00 0.00 0.00 2.57
35 36 8.614469 TTCCTTTGTTTCTTTTGTGTTTTCAT 57.386 26.923 0.00 0.00 0.00 2.57
36 37 8.438676 TTTCCTTTGTTTCTTTTGTGTTTTCA 57.561 26.923 0.00 0.00 0.00 2.69
37 38 9.891828 ATTTTCCTTTGTTTCTTTTGTGTTTTC 57.108 25.926 0.00 0.00 0.00 2.29
38 39 9.676195 CATTTTCCTTTGTTTCTTTTGTGTTTT 57.324 25.926 0.00 0.00 0.00 2.43
39 40 9.061435 TCATTTTCCTTTGTTTCTTTTGTGTTT 57.939 25.926 0.00 0.00 0.00 2.83
40 41 8.614469 TCATTTTCCTTTGTTTCTTTTGTGTT 57.386 26.923 0.00 0.00 0.00 3.32
41 42 8.614469 TTCATTTTCCTTTGTTTCTTTTGTGT 57.386 26.923 0.00 0.00 0.00 3.72
42 43 9.890352 TTTTCATTTTCCTTTGTTTCTTTTGTG 57.110 25.926 0.00 0.00 0.00 3.33
109 110 7.768120 TCCATTCTTTTGCACTTGTTTATTTGT 59.232 29.630 0.00 0.00 0.00 2.83
110 111 8.140677 TCCATTCTTTTGCACTTGTTTATTTG 57.859 30.769 0.00 0.00 0.00 2.32
114 115 7.254727 GCATTTCCATTCTTTTGCACTTGTTTA 60.255 33.333 0.00 0.00 0.00 2.01
118 130 4.512198 TGCATTTCCATTCTTTTGCACTTG 59.488 37.500 0.00 0.00 35.36 3.16
138 150 2.742053 GCTCTTATCGGTTTTCACTGCA 59.258 45.455 0.00 0.00 0.00 4.41
139 151 2.742053 TGCTCTTATCGGTTTTCACTGC 59.258 45.455 0.00 0.00 0.00 4.40
140 152 4.670221 GCTTGCTCTTATCGGTTTTCACTG 60.670 45.833 0.00 0.00 0.00 3.66
141 153 3.437049 GCTTGCTCTTATCGGTTTTCACT 59.563 43.478 0.00 0.00 0.00 3.41
149 161 1.524355 CACATCGCTTGCTCTTATCGG 59.476 52.381 0.00 0.00 0.00 4.18
162 174 8.728088 TCTCTTTTTCTTTTTATTCACATCGC 57.272 30.769 0.00 0.00 0.00 4.58
166 178 9.296400 CGGTTTCTCTTTTTCTTTTTATTCACA 57.704 29.630 0.00 0.00 0.00 3.58
178 190 6.132791 AGGTTTCTTCGGTTTCTCTTTTTC 57.867 37.500 0.00 0.00 0.00 2.29
179 191 7.634671 TTAGGTTTCTTCGGTTTCTCTTTTT 57.365 32.000 0.00 0.00 0.00 1.94
182 194 8.913487 TTTATTAGGTTTCTTCGGTTTCTCTT 57.087 30.769 0.00 0.00 0.00 2.85
238 250 6.490040 TCTTTGATTTTCTCGGTTTCCATTCT 59.510 34.615 0.00 0.00 0.00 2.40
396 412 7.537649 GGTATTTTCTCTTCACGGTTTTCATTC 59.462 37.037 0.00 0.00 0.00 2.67
408 424 5.060506 TGACGCAAAGGTATTTTCTCTTCA 58.939 37.500 0.00 0.00 0.00 3.02
419 435 3.244422 ACAAGGATCTTGACGCAAAGGTA 60.244 43.478 13.74 0.00 0.00 3.08
438 479 1.271379 ACGTCTTATCAGCCGTCACAA 59.729 47.619 0.00 0.00 0.00 3.33
444 485 3.242413 CCAAATGAACGTCTTATCAGCCG 60.242 47.826 0.00 0.00 0.00 5.52
450 491 7.415206 GCAGATAAACCCAAATGAACGTCTTAT 60.415 37.037 0.00 0.00 0.00 1.73
451 492 6.128117 GCAGATAAACCCAAATGAACGTCTTA 60.128 38.462 0.00 0.00 0.00 2.10
456 497 4.414852 CAGCAGATAAACCCAAATGAACG 58.585 43.478 0.00 0.00 0.00 3.95
475 516 2.844146 CGACGAACGTTCACCAGC 59.156 61.111 26.71 10.22 37.22 4.85
510 552 9.470490 GCGAGAGATCGATTCATTTTTAATATG 57.530 33.333 0.00 0.00 34.64 1.78
531 573 2.202479 CGTGTGCTCATCGCGAGA 60.202 61.111 16.66 11.33 45.45 4.04
557 599 2.130073 GAGGGGCGTCTGTTTTGCAC 62.130 60.000 0.00 0.00 0.00 4.57
558 600 1.896660 GAGGGGCGTCTGTTTTGCA 60.897 57.895 0.00 0.00 0.00 4.08
571 613 3.465403 CAGAGGTGAGCGGAGGGG 61.465 72.222 0.00 0.00 0.00 4.79
866 953 5.011125 TGCACTTATATAGAGAAGCCTGTCC 59.989 44.000 0.00 0.00 0.00 4.02
963 1057 1.618837 CTCGGTCTTGTGGGAGAAGAA 59.381 52.381 0.00 0.00 31.27 2.52
1272 1510 0.517316 GCCGTTTGTACAGCTCAAGG 59.483 55.000 0.00 0.00 0.00 3.61
1620 1858 5.385509 AGGTTAACATTTTGGGATCAACG 57.614 39.130 8.10 0.00 31.78 4.10
1857 2095 8.950210 GTGAGATCAAAAGTATCAATTCTTCCA 58.050 33.333 0.00 0.00 0.00 3.53
1870 2108 1.707427 AGGGCCAGTGAGATCAAAAGT 59.293 47.619 6.18 0.00 0.00 2.66
1983 2227 3.401033 TCAATCTTTCTGCGGACTTGA 57.599 42.857 0.00 0.00 0.00 3.02
2225 2469 0.036671 CCGGGGATTCGGCTTATACC 60.037 60.000 0.00 0.00 43.71 2.73
2398 2795 5.070001 GCTCCTTGGTGGCAAATACATATA 58.930 41.667 0.00 0.00 35.26 0.86
2411 2808 2.486472 AACTCATCAGCTCCTTGGTG 57.514 50.000 0.00 0.00 44.85 4.17
2459 4325 9.921637 TTAGACGCAATGACATATGTGAATATA 57.078 29.630 14.43 0.00 0.00 0.86
2539 4405 8.472007 AGTACACTTCATTATTCCCACAAAAA 57.528 30.769 0.00 0.00 0.00 1.94
2540 4406 8.356657 CAAGTACACTTCATTATTCCCACAAAA 58.643 33.333 0.00 0.00 33.11 2.44
2541 4407 7.523052 GCAAGTACACTTCATTATTCCCACAAA 60.523 37.037 0.00 0.00 33.11 2.83
2542 4408 6.072175 GCAAGTACACTTCATTATTCCCACAA 60.072 38.462 0.00 0.00 33.11 3.33
2543 4409 5.414454 GCAAGTACACTTCATTATTCCCACA 59.586 40.000 0.00 0.00 33.11 4.17
2544 4410 5.414454 TGCAAGTACACTTCATTATTCCCAC 59.586 40.000 0.00 0.00 33.11 4.61
2545 4411 5.414454 GTGCAAGTACACTTCATTATTCCCA 59.586 40.000 0.00 0.00 37.58 4.37
2558 4424 9.141400 GCCTTATATCTAATAGTGCAAGTACAC 57.859 37.037 0.00 0.00 41.02 2.90
2580 4446 9.678941 CTCTTTTATTTTCTTTAAGTTCGCCTT 57.321 29.630 0.00 0.00 37.17 4.35
2650 4516 3.960102 TGACCTGAGGAGCAAATTTTTGT 59.040 39.130 4.99 0.00 40.24 2.83
2656 4522 1.366319 AGGTGACCTGAGGAGCAAAT 58.634 50.000 4.99 0.00 29.57 2.32
2657 4523 2.854253 AGGTGACCTGAGGAGCAAA 58.146 52.632 4.99 0.00 29.57 3.68
2658 4524 4.648007 AGGTGACCTGAGGAGCAA 57.352 55.556 4.99 0.00 29.57 3.91
2667 4533 1.901591 CATCAAAGTGCAGGTGACCT 58.098 50.000 0.00 0.00 0.00 3.85
2668 4534 0.242017 GCATCAAAGTGCAGGTGACC 59.758 55.000 0.00 0.00 44.43 4.02
2669 4535 0.110056 CGCATCAAAGTGCAGGTGAC 60.110 55.000 0.00 0.00 45.30 3.67
2670 4536 1.236616 CCGCATCAAAGTGCAGGTGA 61.237 55.000 0.00 0.00 45.30 4.02
2671 4537 1.210931 CCGCATCAAAGTGCAGGTG 59.789 57.895 0.00 0.00 45.30 4.00
2672 4538 0.322816 ATCCGCATCAAAGTGCAGGT 60.323 50.000 0.00 0.00 45.30 4.00
2673 4539 1.600957 CTATCCGCATCAAAGTGCAGG 59.399 52.381 0.00 2.28 45.30 4.85
2674 4540 2.286294 GTCTATCCGCATCAAAGTGCAG 59.714 50.000 0.00 0.00 45.30 4.41
2675 4541 2.279741 GTCTATCCGCATCAAAGTGCA 58.720 47.619 0.00 0.00 45.30 4.57
2676 4542 1.599542 GGTCTATCCGCATCAAAGTGC 59.400 52.381 0.00 0.00 41.65 4.40
2677 4543 2.609459 GTGGTCTATCCGCATCAAAGTG 59.391 50.000 0.00 0.00 45.32 3.16
2678 4544 2.906354 GTGGTCTATCCGCATCAAAGT 58.094 47.619 0.00 0.00 45.32 2.66
2686 4552 1.066430 TGAGTTTGGTGGTCTATCCGC 60.066 52.381 0.00 0.00 45.27 5.54
2687 4553 3.328382 TTGAGTTTGGTGGTCTATCCG 57.672 47.619 0.00 0.00 39.52 4.18
2688 4554 4.906618 TCTTTGAGTTTGGTGGTCTATCC 58.093 43.478 0.00 0.00 0.00 2.59
2689 4555 6.262273 TGTTTCTTTGAGTTTGGTGGTCTATC 59.738 38.462 0.00 0.00 0.00 2.08
2690 4556 6.039382 GTGTTTCTTTGAGTTTGGTGGTCTAT 59.961 38.462 0.00 0.00 0.00 1.98
2691 4557 5.355910 GTGTTTCTTTGAGTTTGGTGGTCTA 59.644 40.000 0.00 0.00 0.00 2.59
2692 4558 4.157840 GTGTTTCTTTGAGTTTGGTGGTCT 59.842 41.667 0.00 0.00 0.00 3.85
2693 4559 4.421058 GTGTTTCTTTGAGTTTGGTGGTC 58.579 43.478 0.00 0.00 0.00 4.02
2694 4560 3.119637 CGTGTTTCTTTGAGTTTGGTGGT 60.120 43.478 0.00 0.00 0.00 4.16
2695 4561 3.434637 CGTGTTTCTTTGAGTTTGGTGG 58.565 45.455 0.00 0.00 0.00 4.61
2696 4562 3.434637 CCGTGTTTCTTTGAGTTTGGTG 58.565 45.455 0.00 0.00 0.00 4.17
2697 4563 2.425668 CCCGTGTTTCTTTGAGTTTGGT 59.574 45.455 0.00 0.00 0.00 3.67
2698 4564 2.798145 GCCCGTGTTTCTTTGAGTTTGG 60.798 50.000 0.00 0.00 0.00 3.28
2699 4565 2.159310 TGCCCGTGTTTCTTTGAGTTTG 60.159 45.455 0.00 0.00 0.00 2.93
2700 4566 2.096248 TGCCCGTGTTTCTTTGAGTTT 58.904 42.857 0.00 0.00 0.00 2.66
2701 4567 1.757682 TGCCCGTGTTTCTTTGAGTT 58.242 45.000 0.00 0.00 0.00 3.01
2702 4568 1.757682 TTGCCCGTGTTTCTTTGAGT 58.242 45.000 0.00 0.00 0.00 3.41
2703 4569 3.369546 AATTGCCCGTGTTTCTTTGAG 57.630 42.857 0.00 0.00 0.00 3.02
2704 4570 3.810310 AAATTGCCCGTGTTTCTTTGA 57.190 38.095 0.00 0.00 0.00 2.69
2705 4571 5.047188 ACTAAAATTGCCCGTGTTTCTTTG 58.953 37.500 0.00 0.00 0.00 2.77
2706 4572 5.270893 ACTAAAATTGCCCGTGTTTCTTT 57.729 34.783 0.00 0.00 0.00 2.52
2707 4573 4.929819 ACTAAAATTGCCCGTGTTTCTT 57.070 36.364 0.00 0.00 0.00 2.52
2708 4574 4.929819 AACTAAAATTGCCCGTGTTTCT 57.070 36.364 0.00 0.00 0.00 2.52
2709 4575 5.520649 TGAAAACTAAAATTGCCCGTGTTTC 59.479 36.000 0.00 0.00 0.00 2.78
2710 4576 5.420409 TGAAAACTAAAATTGCCCGTGTTT 58.580 33.333 0.00 0.00 0.00 2.83
2711 4577 5.012328 TGAAAACTAAAATTGCCCGTGTT 57.988 34.783 0.00 0.00 0.00 3.32
2712 4578 4.657436 TGAAAACTAAAATTGCCCGTGT 57.343 36.364 0.00 0.00 0.00 4.49
2713 4579 7.826260 AATATGAAAACTAAAATTGCCCGTG 57.174 32.000 0.00 0.00 0.00 4.94
2731 4597 9.440773 AGCTCAGCGAATCAAATTATAATATGA 57.559 29.630 0.00 0.00 0.00 2.15
2740 4606 9.807649 AAAATAAATAGCTCAGCGAATCAAATT 57.192 25.926 0.00 0.00 0.00 1.82
2741 4607 9.241317 CAAAATAAATAGCTCAGCGAATCAAAT 57.759 29.630 0.00 0.00 0.00 2.32
2742 4608 8.243426 ACAAAATAAATAGCTCAGCGAATCAAA 58.757 29.630 0.00 0.00 0.00 2.69
2743 4609 7.761409 ACAAAATAAATAGCTCAGCGAATCAA 58.239 30.769 0.00 0.00 0.00 2.57
2744 4610 7.320443 ACAAAATAAATAGCTCAGCGAATCA 57.680 32.000 0.00 0.00 0.00 2.57
2745 4611 7.698130 ACAACAAAATAAATAGCTCAGCGAATC 59.302 33.333 0.00 0.00 0.00 2.52
2746 4612 7.485913 CACAACAAAATAAATAGCTCAGCGAAT 59.514 33.333 0.00 0.00 0.00 3.34
2747 4613 6.801377 CACAACAAAATAAATAGCTCAGCGAA 59.199 34.615 0.00 0.00 0.00 4.70
2748 4614 6.314018 CACAACAAAATAAATAGCTCAGCGA 58.686 36.000 0.00 0.00 0.00 4.93
2749 4615 5.003778 GCACAACAAAATAAATAGCTCAGCG 59.996 40.000 0.00 0.00 0.00 5.18
2750 4616 5.289434 GGCACAACAAAATAAATAGCTCAGC 59.711 40.000 0.00 0.00 0.00 4.26
2751 4617 5.512788 CGGCACAACAAAATAAATAGCTCAG 59.487 40.000 0.00 0.00 0.00 3.35
2752 4618 5.398169 CGGCACAACAAAATAAATAGCTCA 58.602 37.500 0.00 0.00 0.00 4.26
2753 4619 4.265320 GCGGCACAACAAAATAAATAGCTC 59.735 41.667 0.00 0.00 0.00 4.09
2754 4620 4.173256 GCGGCACAACAAAATAAATAGCT 58.827 39.130 0.00 0.00 0.00 3.32
2755 4621 3.923461 TGCGGCACAACAAAATAAATAGC 59.077 39.130 0.00 0.00 0.00 2.97
2756 4622 6.309980 TCAATGCGGCACAACAAAATAAATAG 59.690 34.615 4.03 0.00 0.00 1.73
2757 4623 6.159293 TCAATGCGGCACAACAAAATAAATA 58.841 32.000 4.03 0.00 0.00 1.40
2758 4624 4.993584 TCAATGCGGCACAACAAAATAAAT 59.006 33.333 4.03 0.00 0.00 1.40
2759 4625 4.371786 TCAATGCGGCACAACAAAATAAA 58.628 34.783 4.03 0.00 0.00 1.40
2760 4626 3.982475 TCAATGCGGCACAACAAAATAA 58.018 36.364 4.03 0.00 0.00 1.40
2761 4627 3.650070 TCAATGCGGCACAACAAAATA 57.350 38.095 4.03 0.00 0.00 1.40
2762 4628 2.522836 TCAATGCGGCACAACAAAAT 57.477 40.000 4.03 0.00 0.00 1.82
2763 4629 2.522836 ATCAATGCGGCACAACAAAA 57.477 40.000 4.03 0.00 0.00 2.44
2764 4630 2.035704 AGAATCAATGCGGCACAACAAA 59.964 40.909 4.03 0.00 0.00 2.83
2765 4631 1.612950 AGAATCAATGCGGCACAACAA 59.387 42.857 4.03 0.00 0.00 2.83
2766 4632 1.199789 GAGAATCAATGCGGCACAACA 59.800 47.619 4.03 0.00 33.17 3.33
2767 4633 1.199789 TGAGAATCAATGCGGCACAAC 59.800 47.619 4.03 0.00 45.97 3.32
2768 4634 1.532523 TGAGAATCAATGCGGCACAA 58.467 45.000 4.03 0.00 45.97 3.33
2769 4635 3.246403 TGAGAATCAATGCGGCACA 57.754 47.368 4.03 0.00 45.97 4.57
2777 4643 5.512446 AGCGGTGCTCCTTGAGAATCAAT 62.512 47.826 2.85 0.00 45.75 2.57
2778 4644 4.258430 AGCGGTGCTCCTTGAGAATCAA 62.258 50.000 2.85 0.00 44.98 2.57
2779 4645 2.782999 AGCGGTGCTCCTTGAGAATCA 61.783 52.381 2.85 0.00 37.71 2.57
2780 4646 0.107945 AGCGGTGCTCCTTGAGAATC 60.108 55.000 2.85 0.00 30.62 2.52
2781 4647 0.326264 AAGCGGTGCTCCTTGAGAAT 59.674 50.000 2.85 0.00 38.25 2.40
2782 4648 0.603707 CAAGCGGTGCTCCTTGAGAA 60.604 55.000 2.85 0.00 40.59 2.87
2783 4649 1.004560 CAAGCGGTGCTCCTTGAGA 60.005 57.895 2.85 0.00 40.59 3.27
2784 4650 3.571119 CAAGCGGTGCTCCTTGAG 58.429 61.111 2.85 0.00 40.59 3.02
2793 4659 0.667184 GGAAATGTTGGCAAGCGGTG 60.667 55.000 0.00 0.00 0.00 4.94
2794 4660 0.827507 AGGAAATGTTGGCAAGCGGT 60.828 50.000 0.00 0.00 0.00 5.68
2795 4661 0.318120 AAGGAAATGTTGGCAAGCGG 59.682 50.000 0.00 0.00 0.00 5.52
2796 4662 2.030363 TGTAAGGAAATGTTGGCAAGCG 60.030 45.455 0.00 0.00 0.00 4.68
2797 4663 3.658757 TGTAAGGAAATGTTGGCAAGC 57.341 42.857 0.00 0.00 0.00 4.01
2798 4664 6.515272 AGTATGTAAGGAAATGTTGGCAAG 57.485 37.500 0.00 0.00 0.00 4.01
2799 4665 6.071616 GGAAGTATGTAAGGAAATGTTGGCAA 60.072 38.462 0.00 0.00 0.00 4.52
2800 4666 5.417580 GGAAGTATGTAAGGAAATGTTGGCA 59.582 40.000 0.00 0.00 0.00 4.92
2801 4667 5.417580 TGGAAGTATGTAAGGAAATGTTGGC 59.582 40.000 0.00 0.00 0.00 4.52
2802 4668 7.645058 ATGGAAGTATGTAAGGAAATGTTGG 57.355 36.000 0.00 0.00 0.00 3.77
2803 4669 9.927668 AAAATGGAAGTATGTAAGGAAATGTTG 57.072 29.630 0.00 0.00 0.00 3.33
2809 4675 9.457436 GTTCCTAAAATGGAAGTATGTAAGGAA 57.543 33.333 0.00 0.00 45.62 3.36
2810 4676 8.050930 GGTTCCTAAAATGGAAGTATGTAAGGA 58.949 37.037 0.00 0.00 45.62 3.36
2811 4677 7.832187 TGGTTCCTAAAATGGAAGTATGTAAGG 59.168 37.037 0.00 0.00 45.62 2.69
2812 4678 8.674607 GTGGTTCCTAAAATGGAAGTATGTAAG 58.325 37.037 0.00 0.00 45.62 2.34
2813 4679 7.612633 GGTGGTTCCTAAAATGGAAGTATGTAA 59.387 37.037 0.00 0.00 45.62 2.41
2814 4680 7.114095 GGTGGTTCCTAAAATGGAAGTATGTA 58.886 38.462 0.00 0.00 45.62 2.29
2815 4681 5.949952 GGTGGTTCCTAAAATGGAAGTATGT 59.050 40.000 0.00 0.00 45.62 2.29
2816 4682 5.949354 TGGTGGTTCCTAAAATGGAAGTATG 59.051 40.000 0.00 0.00 45.62 2.39
2817 4683 5.949952 GTGGTGGTTCCTAAAATGGAAGTAT 59.050 40.000 0.00 0.00 45.62 2.12
2818 4684 5.318630 GTGGTGGTTCCTAAAATGGAAGTA 58.681 41.667 0.00 0.00 45.62 2.24
2819 4685 4.149598 GTGGTGGTTCCTAAAATGGAAGT 58.850 43.478 0.00 0.00 45.62 3.01
2820 4686 3.509967 GGTGGTGGTTCCTAAAATGGAAG 59.490 47.826 0.00 0.00 45.62 3.46
2821 4687 3.502356 GGTGGTGGTTCCTAAAATGGAA 58.498 45.455 0.00 0.00 43.16 3.53
2822 4688 2.225167 GGGTGGTGGTTCCTAAAATGGA 60.225 50.000 0.00 0.00 37.07 3.41
2823 4689 2.176045 GGGTGGTGGTTCCTAAAATGG 58.824 52.381 0.00 0.00 37.07 3.16
2824 4690 3.169512 AGGGTGGTGGTTCCTAAAATG 57.830 47.619 0.00 0.00 37.07 2.32
2825 4691 3.116900 ACAAGGGTGGTGGTTCCTAAAAT 60.117 43.478 0.00 0.00 37.07 1.82
2826 4692 2.245287 ACAAGGGTGGTGGTTCCTAAAA 59.755 45.455 0.00 0.00 37.07 1.52
2827 4693 1.854280 ACAAGGGTGGTGGTTCCTAAA 59.146 47.619 0.00 0.00 37.07 1.85
2828 4694 1.525175 ACAAGGGTGGTGGTTCCTAA 58.475 50.000 0.00 0.00 37.07 2.69
2829 4695 1.525175 AACAAGGGTGGTGGTTCCTA 58.475 50.000 0.00 0.00 37.07 2.94
2830 4696 0.634465 AAACAAGGGTGGTGGTTCCT 59.366 50.000 0.00 0.00 37.07 3.36
2831 4697 1.491668 AAAACAAGGGTGGTGGTTCC 58.508 50.000 0.00 0.00 0.00 3.62
2853 4719 9.483916 TCGTCAAATAAAGTCTATTTTCTGTCA 57.516 29.630 0.00 0.00 0.00 3.58
2861 4727 9.901172 ACCCTATTTCGTCAAATAAAGTCTATT 57.099 29.630 0.00 0.00 34.64 1.73
2862 4728 9.901172 AACCCTATTTCGTCAAATAAAGTCTAT 57.099 29.630 0.00 0.00 34.64 1.98
2863 4729 9.729281 AAACCCTATTTCGTCAAATAAAGTCTA 57.271 29.630 0.00 0.00 34.64 2.59
2864 4730 8.631480 AAACCCTATTTCGTCAAATAAAGTCT 57.369 30.769 0.00 0.00 34.64 3.24
2865 4731 7.966753 GGAAACCCTATTTCGTCAAATAAAGTC 59.033 37.037 0.00 0.00 34.64 3.01
2866 4732 7.668469 AGGAAACCCTATTTCGTCAAATAAAGT 59.332 33.333 0.00 0.00 34.64 2.66
2867 4733 8.051901 AGGAAACCCTATTTCGTCAAATAAAG 57.948 34.615 0.00 0.00 34.64 1.85
2868 4734 7.121611 GGAGGAAACCCTATTTCGTCAAATAAA 59.878 37.037 18.47 0.00 42.07 1.40
2869 4735 6.600427 GGAGGAAACCCTATTTCGTCAAATAA 59.400 38.462 18.47 0.00 42.07 1.40
2870 4736 6.117488 GGAGGAAACCCTATTTCGTCAAATA 58.883 40.000 18.47 0.00 42.07 1.40
2871 4737 4.948004 GGAGGAAACCCTATTTCGTCAAAT 59.052 41.667 18.47 0.00 42.07 2.32
2872 4738 4.329392 GGAGGAAACCCTATTTCGTCAAA 58.671 43.478 18.47 0.00 42.07 2.69
2907 4773 5.106475 GGTTGTATCGGTGATGTTTGCTTTA 60.106 40.000 0.00 0.00 0.00 1.85
2955 4826 1.064946 CGTTTCTTTTGGGCGTGCA 59.935 52.632 0.00 0.00 0.00 4.57
3134 5007 2.123338 AAACCCTTGGCAGCAGCA 60.123 55.556 2.65 0.00 44.61 4.41
3162 5035 1.455248 CCTTTCTCTCTCCTCGTCGT 58.545 55.000 0.00 0.00 0.00 4.34
3177 5050 2.653087 GGCGTCGGAGGTACCCTTT 61.653 63.158 8.74 0.00 31.76 3.11
3256 5129 2.171870 GGTTGGGATCGGTAGAAATCCA 59.828 50.000 3.97 0.00 42.78 3.41
3265 5138 0.840722 AGGTGAAGGTTGGGATCGGT 60.841 55.000 0.00 0.00 0.00 4.69


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

AutoCloner maintained by Alex Coulton.