Multiple sequence alignment - TraesCS7B01G312000

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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 TraesCS7B01G312000 chr7B 100.000 3675 0 0 1 3675 557258432 557254758 0.000000e+00 6787.0
1 TraesCS7B01G312000 chr7B 88.429 1400 157 4 961 2356 557491646 557490248 0.000000e+00 1683.0
2 TraesCS7B01G312000 chr7B 86.869 1447 169 11 946 2385 528871594 528873026 0.000000e+00 1600.0
3 TraesCS7B01G312000 chr7B 95.848 554 20 2 3122 3675 560801621 560801071 0.000000e+00 893.0
4 TraesCS7B01G312000 chr7B 95.818 550 21 1 3126 3675 720529070 720528523 0.000000e+00 887.0
5 TraesCS7B01G312000 chr7B 95.826 551 18 4 3126 3675 112906285 112905739 0.000000e+00 885.0
6 TraesCS7B01G312000 chr7A 93.501 1554 88 8 874 2423 603331782 603330238 0.000000e+00 2298.0
7 TraesCS7B01G312000 chr7A 87.026 1449 168 10 946 2387 566788194 566789629 0.000000e+00 1616.0
8 TraesCS7B01G312000 chr7A 86.121 1441 189 7 961 2392 603553299 603551861 0.000000e+00 1543.0
9 TraesCS7B01G312000 chr7A 87.715 871 82 15 1 861 603332621 603331766 0.000000e+00 992.0
10 TraesCS7B01G312000 chr7A 88.838 439 25 11 2518 2949 603330195 603329774 5.440000e-143 518.0
11 TraesCS7B01G312000 chr7A 84.663 163 18 4 2965 3120 381242744 381242906 4.910000e-34 156.0
12 TraesCS7B01G312000 chr7A 84.868 152 16 4 2967 3113 27398516 27398665 2.960000e-31 147.0
13 TraesCS7B01G312000 chr7D 94.627 1433 73 2 995 2423 523057029 523055597 0.000000e+00 2217.0
14 TraesCS7B01G312000 chr7D 87.053 1398 176 3 961 2354 523133853 523132457 0.000000e+00 1574.0
15 TraesCS7B01G312000 chr7D 87.108 1404 160 13 946 2341 523128203 523126813 0.000000e+00 1570.0
16 TraesCS7B01G312000 chr7D 86.662 1432 169 12 946 2369 500773698 500775115 0.000000e+00 1567.0
17 TraesCS7B01G312000 chr7D 86.475 1353 158 15 946 2288 113581490 113582827 0.000000e+00 1461.0
18 TraesCS7B01G312000 chr7D 92.094 974 57 10 1 964 523057989 523057026 0.000000e+00 1354.0
19 TraesCS7B01G312000 chr7D 90.575 435 28 5 2518 2949 523055554 523055130 6.890000e-157 564.0
20 TraesCS7B01G312000 chr6B 97.091 550 14 1 3126 3675 439416311 439416858 0.000000e+00 926.0
21 TraesCS7B01G312000 chr6B 96.364 550 18 1 3126 3675 114884393 114884940 0.000000e+00 904.0
22 TraesCS7B01G312000 chr6B 95.811 549 20 2 3127 3675 85117225 85117770 0.000000e+00 883.0
23 TraesCS7B01G312000 chr6B 95.644 551 21 2 3125 3675 633827822 633827275 0.000000e+00 881.0
24 TraesCS7B01G312000 chr6B 82.456 171 20 6 2965 3126 644800972 644800803 1.380000e-29 141.0
25 TraesCS7B01G312000 chr2B 96.250 560 19 1 3116 3675 87799373 87798816 0.000000e+00 917.0
26 TraesCS7B01G312000 chr3B 96.189 551 20 1 3125 3675 48687901 48687352 0.000000e+00 900.0
27 TraesCS7B01G312000 chr3D 80.420 761 106 29 946 1685 603682365 603683103 1.160000e-149 540.0
28 TraesCS7B01G312000 chr5B 76.718 786 118 41 1617 2350 685529070 685528298 9.630000e-101 377.0
29 TraesCS7B01G312000 chr5B 83.505 97 14 2 120 215 700207138 700207233 5.050000e-14 89.8
30 TraesCS7B01G312000 chr5D 84.483 348 50 3 2005 2350 543497457 543497802 1.260000e-89 340.0
31 TraesCS7B01G312000 chr5D 73.707 928 192 35 1014 1894 543496376 543497298 7.660000e-82 315.0
32 TraesCS7B01G312000 chr5D 77.539 512 75 26 3 511 111592458 111592932 4.680000e-69 272.0
33 TraesCS7B01G312000 chr4D 76.339 448 82 15 7 439 495527897 495527459 6.180000e-53 219.0
34 TraesCS7B01G312000 chr4D 82.209 163 23 5 336 494 488510445 488510285 6.400000e-28 135.0
35 TraesCS7B01G312000 chr2D 86.928 153 13 3 2967 3113 511918623 511918774 8.160000e-37 165.0
36 TraesCS7B01G312000 chr2D 83.537 164 17 6 2968 3123 555946392 555946553 1.060000e-30 145.0
37 TraesCS7B01G312000 chr1D 85.811 148 18 3 2966 3113 106848883 106848739 1.770000e-33 154.0
38 TraesCS7B01G312000 chr3A 85.034 147 20 1 2967 3113 621323072 621322928 8.220000e-32 148.0
39 TraesCS7B01G312000 chr6A 84.516 155 17 4 2967 3114 85268215 85268061 2.960000e-31 147.0
40 TraesCS7B01G312000 chr1A 85.034 147 16 4 2966 3112 532966095 532966235 1.060000e-30 145.0
41 TraesCS7B01G312000 chr4B 82.677 127 18 2 386 511 451820822 451820699 3.880000e-20 110.0
42 TraesCS7B01G312000 chr5A 78.916 166 27 6 336 494 670272974 670272810 5.020000e-19 106.0


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 TraesCS7B01G312000 chr7B 557254758 557258432 3674 True 6787.000000 6787 100.000 1 3675 1 chr7B.!!$R2 3674
1 TraesCS7B01G312000 chr7B 557490248 557491646 1398 True 1683.000000 1683 88.429 961 2356 1 chr7B.!!$R3 1395
2 TraesCS7B01G312000 chr7B 528871594 528873026 1432 False 1600.000000 1600 86.869 946 2385 1 chr7B.!!$F1 1439
3 TraesCS7B01G312000 chr7B 560801071 560801621 550 True 893.000000 893 95.848 3122 3675 1 chr7B.!!$R4 553
4 TraesCS7B01G312000 chr7B 720528523 720529070 547 True 887.000000 887 95.818 3126 3675 1 chr7B.!!$R5 549
5 TraesCS7B01G312000 chr7B 112905739 112906285 546 True 885.000000 885 95.826 3126 3675 1 chr7B.!!$R1 549
6 TraesCS7B01G312000 chr7A 566788194 566789629 1435 False 1616.000000 1616 87.026 946 2387 1 chr7A.!!$F3 1441
7 TraesCS7B01G312000 chr7A 603551861 603553299 1438 True 1543.000000 1543 86.121 961 2392 1 chr7A.!!$R1 1431
8 TraesCS7B01G312000 chr7A 603329774 603332621 2847 True 1269.333333 2298 90.018 1 2949 3 chr7A.!!$R2 2948
9 TraesCS7B01G312000 chr7D 523132457 523133853 1396 True 1574.000000 1574 87.053 961 2354 1 chr7D.!!$R2 1393
10 TraesCS7B01G312000 chr7D 523126813 523128203 1390 True 1570.000000 1570 87.108 946 2341 1 chr7D.!!$R1 1395
11 TraesCS7B01G312000 chr7D 500773698 500775115 1417 False 1567.000000 1567 86.662 946 2369 1 chr7D.!!$F2 1423
12 TraesCS7B01G312000 chr7D 113581490 113582827 1337 False 1461.000000 1461 86.475 946 2288 1 chr7D.!!$F1 1342
13 TraesCS7B01G312000 chr7D 523055130 523057989 2859 True 1378.333333 2217 92.432 1 2949 3 chr7D.!!$R3 2948
14 TraesCS7B01G312000 chr6B 439416311 439416858 547 False 926.000000 926 97.091 3126 3675 1 chr6B.!!$F3 549
15 TraesCS7B01G312000 chr6B 114884393 114884940 547 False 904.000000 904 96.364 3126 3675 1 chr6B.!!$F2 549
16 TraesCS7B01G312000 chr6B 85117225 85117770 545 False 883.000000 883 95.811 3127 3675 1 chr6B.!!$F1 548
17 TraesCS7B01G312000 chr6B 633827275 633827822 547 True 881.000000 881 95.644 3125 3675 1 chr6B.!!$R1 550
18 TraesCS7B01G312000 chr2B 87798816 87799373 557 True 917.000000 917 96.250 3116 3675 1 chr2B.!!$R1 559
19 TraesCS7B01G312000 chr3B 48687352 48687901 549 True 900.000000 900 96.189 3125 3675 1 chr3B.!!$R1 550
20 TraesCS7B01G312000 chr3D 603682365 603683103 738 False 540.000000 540 80.420 946 1685 1 chr3D.!!$F1 739
21 TraesCS7B01G312000 chr5B 685528298 685529070 772 True 377.000000 377 76.718 1617 2350 1 chr5B.!!$R1 733
22 TraesCS7B01G312000 chr5D 543496376 543497802 1426 False 327.500000 340 79.095 1014 2350 2 chr5D.!!$F2 1336

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
43 44 0.038618 GAGGTTTGCGGCGGAAAATT 60.039 50.0 27.61 18.21 0.00 1.82 F
131 135 0.107459 GATGACAAGGCTGGACCCTC 60.107 60.0 0.00 0.00 40.58 4.30 F
865 873 0.109132 CATTCTTGCCGTGCCTTTCC 60.109 55.0 0.00 0.00 0.00 3.13 F
992 1007 0.389948 CGAGTTGGACTACCTGCCAC 60.390 60.0 0.00 0.00 37.04 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1425 1473 0.872021 CTCGACGAGCTTGGGCATAC 60.872 60.000 12.67 0.0 41.7 2.39 R
1842 1916 1.006102 AGGAACTCGGTGAACTGCG 60.006 57.895 0.00 0.0 0.0 5.18 R
2519 2654 0.332293 TGAGGAAGCATGGATGGCAA 59.668 50.000 0.00 0.0 0.0 4.52 R
2877 3013 0.298707 CGTCGGATTCTGCATGTTCG 59.701 55.000 0.00 0.0 0.0 3.95 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
43 44 0.038618 GAGGTTTGCGGCGGAAAATT 60.039 50.000 27.61 18.21 0.00 1.82
55 56 2.331194 CGGAAAATTCGTACCTCGTGT 58.669 47.619 0.00 0.00 40.80 4.49
114 118 2.885388 ACAAGGAGATGGAGGAGGAT 57.115 50.000 0.00 0.00 0.00 3.24
126 130 0.252881 AGGAGGATGACAAGGCTGGA 60.253 55.000 0.00 0.00 0.00 3.86
131 135 0.107459 GATGACAAGGCTGGACCCTC 60.107 60.000 0.00 0.00 40.58 4.30
215 219 0.323542 ATCGACTGGGACGACCTCTT 60.324 55.000 3.44 0.00 42.37 2.85
257 261 9.333497 AGTAGTTTTTGTTTTTGTTTCGTAGTC 57.667 29.630 0.00 0.00 0.00 2.59
274 278 7.046862 TCGTAGTCGAAGTATCATTCTATCG 57.953 40.000 0.00 0.00 43.34 2.92
350 355 7.475771 TGTTTGAAATTTGCAATGTTCCTAC 57.524 32.000 16.03 14.04 0.00 3.18
352 357 4.233789 TGAAATTTGCAATGTTCCTACGC 58.766 39.130 16.03 0.00 0.00 4.42
378 383 2.710377 TGTCCAATACACATCACCTGC 58.290 47.619 0.00 0.00 31.43 4.85
379 384 1.665679 GTCCAATACACATCACCTGCG 59.334 52.381 0.00 0.00 0.00 5.18
417 422 5.451798 GCCCTATTTTACATCATGTGTTGGG 60.452 44.000 0.00 5.21 42.29 4.12
446 451 6.757237 ACATGTTTGAGGTGATGCAAAATTA 58.243 32.000 0.00 0.00 35.95 1.40
520 525 4.284490 GGTGGAGATGCTCTTATGGTGATA 59.716 45.833 0.00 0.00 0.00 2.15
559 564 6.017211 ACCATAATGATGATGGACCAGAAA 57.983 37.500 15.87 0.00 45.89 2.52
567 572 3.955471 TGATGGACCAGAAAATGACCTC 58.045 45.455 0.00 0.00 0.00 3.85
590 595 7.372451 TCGTAAAAATCATGGTTTTCTCGAT 57.628 32.000 25.46 12.49 34.53 3.59
643 648 6.406849 GGAGGCAATGCAATATTTACCTTTGA 60.407 38.462 7.79 0.00 0.00 2.69
749 756 5.044558 TCAAGTAAATGTTTCGGTTTTGGC 58.955 37.500 0.00 0.00 0.00 4.52
799 806 4.295141 TCAGTATTTTGGTACAGGGTGG 57.705 45.455 0.00 0.00 42.39 4.61
800 807 3.009695 TCAGTATTTTGGTACAGGGTGGG 59.990 47.826 0.00 0.00 42.39 4.61
805 812 3.399952 TTTGGTACAGGGTGGGAAAAA 57.600 42.857 0.00 0.00 42.39 1.94
865 873 0.109132 CATTCTTGCCGTGCCTTTCC 60.109 55.000 0.00 0.00 0.00 3.13
868 876 1.002624 CTTGCCGTGCCTTTCCCTA 60.003 57.895 0.00 0.00 0.00 3.53
901 914 0.928229 GCCGTGCCGATACAACTAAG 59.072 55.000 0.00 0.00 0.00 2.18
913 926 3.402628 ACAACTAAGGAACAGCGACAT 57.597 42.857 0.00 0.00 0.00 3.06
914 927 3.067106 ACAACTAAGGAACAGCGACATG 58.933 45.455 0.00 0.00 0.00 3.21
983 998 3.506067 CCCTTAAATTTGCGAGTTGGACT 59.494 43.478 0.00 0.00 0.00 3.85
992 1007 0.389948 CGAGTTGGACTACCTGCCAC 60.390 60.000 0.00 0.00 37.04 5.01
1001 1017 2.257409 CTACCTGCCACTTCCCGCAT 62.257 60.000 0.00 0.00 33.78 4.73
1177 1205 3.845259 CCGGGCCTACGCTTGCTA 61.845 66.667 0.84 0.00 34.44 3.49
1286 1323 2.684843 GCCCTGCTCTTGTCGCTTG 61.685 63.158 0.00 0.00 0.00 4.01
1290 1327 0.788995 CTGCTCTTGTCGCTTGTCTG 59.211 55.000 0.00 0.00 0.00 3.51
1414 1462 3.449227 AGCGCGTGCAGCTACCTA 61.449 61.111 24.79 0.00 44.05 3.08
1425 1473 3.347411 GCTACCTAGCGTTCCTGTG 57.653 57.895 0.00 0.00 39.82 3.66
1456 1504 3.501548 GTCGAGCTCGGCGAGACT 61.502 66.667 38.56 31.51 38.59 3.24
1480 1528 3.231736 ACTGCGGACGACCTGGTT 61.232 61.111 0.00 0.00 0.00 3.67
1482 1530 2.027625 CTGCGGACGACCTGGTTTC 61.028 63.158 0.00 0.44 0.00 2.78
1951 2052 2.410687 CGCTCTCCTCCGAGAAGCA 61.411 63.158 14.08 0.00 44.62 3.91
2191 2322 2.716017 GGACGTCTGCCAGAGAGGG 61.716 68.421 16.46 0.00 40.35 4.30
2212 2343 1.674651 CGTGGAGAGGACGGTGAGA 60.675 63.158 0.00 0.00 33.08 3.27
2350 2481 2.036414 AGGGAGCTCAGCGTCAGA 59.964 61.111 17.19 0.00 0.00 3.27
2372 2507 3.397527 TCCTCCTCAAGCCCAGAATTAT 58.602 45.455 0.00 0.00 0.00 1.28
2387 2522 6.152661 CCCAGAATTATTGGAAACTAGCACAA 59.847 38.462 9.50 0.00 37.96 3.33
2416 2551 6.272318 CAGAGGTCTCTCATTTACATCTCAC 58.728 44.000 0.00 0.00 42.34 3.51
2423 2558 9.116067 GTCTCTCATTTACATCTCACTACTACT 57.884 37.037 0.00 0.00 0.00 2.57
2456 2591 1.523934 GACACGTGGTCCTGTAAAACG 59.476 52.381 21.57 0.00 40.83 3.60
2458 2593 2.203401 CACGTGGTCCTGTAAAACGAA 58.797 47.619 7.95 0.00 37.66 3.85
2470 2605 7.375017 GTCCTGTAAAACGAACACATTGTTTAG 59.625 37.037 0.00 0.00 41.28 1.85
2476 2611 6.870971 AACGAACACATTGTTTAGTGGTAT 57.129 33.333 0.00 0.00 41.28 2.73
2477 2612 6.476243 ACGAACACATTGTTTAGTGGTATC 57.524 37.500 0.00 0.00 41.28 2.24
2479 2614 6.367969 ACGAACACATTGTTTAGTGGTATCTC 59.632 38.462 0.00 0.00 41.28 2.75
2480 2615 6.183360 CGAACACATTGTTTAGTGGTATCTCC 60.183 42.308 0.00 0.00 41.28 3.71
2481 2616 6.121776 ACACATTGTTTAGTGGTATCTCCA 57.878 37.500 0.00 0.00 45.01 3.86
2482 2617 7.001674 AACACATTGTTTAGTGGTATCTCCAA 58.998 34.615 0.00 0.00 42.24 3.53
2483 2618 7.504238 AACACATTGTTTAGTGGTATCTCCAAA 59.496 33.333 0.00 0.00 42.24 3.28
2494 2629 6.126863 TGGTATCTCCAAATCTTGAGTTGT 57.873 37.500 9.44 0.00 44.12 3.32
2495 2630 5.939883 TGGTATCTCCAAATCTTGAGTTGTG 59.060 40.000 9.44 3.39 44.12 3.33
2496 2631 5.940470 GGTATCTCCAAATCTTGAGTTGTGT 59.060 40.000 9.44 0.00 35.97 3.72
2497 2632 7.103641 GGTATCTCCAAATCTTGAGTTGTGTA 58.896 38.462 9.44 0.00 35.97 2.90
2498 2633 7.278868 GGTATCTCCAAATCTTGAGTTGTGTAG 59.721 40.741 9.44 4.99 35.97 2.74
2499 2634 6.419484 TCTCCAAATCTTGAGTTGTGTAGA 57.581 37.500 9.44 6.79 0.00 2.59
2500 2635 6.223852 TCTCCAAATCTTGAGTTGTGTAGAC 58.776 40.000 9.44 0.00 0.00 2.59
2501 2636 5.305585 TCCAAATCTTGAGTTGTGTAGACC 58.694 41.667 9.44 0.00 0.00 3.85
2502 2637 4.152402 CCAAATCTTGAGTTGTGTAGACCG 59.848 45.833 9.44 0.00 0.00 4.79
2503 2638 4.866508 AATCTTGAGTTGTGTAGACCGA 57.133 40.909 0.00 0.00 0.00 4.69
2504 2639 5.407407 AATCTTGAGTTGTGTAGACCGAT 57.593 39.130 0.00 0.00 0.00 4.18
2505 2640 4.436242 TCTTGAGTTGTGTAGACCGATC 57.564 45.455 0.00 0.00 0.00 3.69
2506 2641 3.824443 TCTTGAGTTGTGTAGACCGATCA 59.176 43.478 0.00 0.00 0.00 2.92
2507 2642 4.462834 TCTTGAGTTGTGTAGACCGATCAT 59.537 41.667 0.00 0.00 0.00 2.45
2508 2643 4.110036 TGAGTTGTGTAGACCGATCATG 57.890 45.455 0.00 0.00 0.00 3.07
2509 2644 3.509967 TGAGTTGTGTAGACCGATCATGT 59.490 43.478 0.00 0.00 0.00 3.21
2510 2645 4.021456 TGAGTTGTGTAGACCGATCATGTT 60.021 41.667 0.00 0.00 0.00 2.71
2511 2646 4.894784 AGTTGTGTAGACCGATCATGTTT 58.105 39.130 0.00 0.00 0.00 2.83
2512 2647 5.305585 AGTTGTGTAGACCGATCATGTTTT 58.694 37.500 0.00 0.00 0.00 2.43
2513 2648 5.763204 AGTTGTGTAGACCGATCATGTTTTT 59.237 36.000 0.00 0.00 0.00 1.94
2514 2649 5.605564 TGTGTAGACCGATCATGTTTTTG 57.394 39.130 0.00 0.00 0.00 2.44
2515 2650 5.060506 TGTGTAGACCGATCATGTTTTTGT 58.939 37.500 0.00 0.00 0.00 2.83
2516 2651 5.529430 TGTGTAGACCGATCATGTTTTTGTT 59.471 36.000 0.00 0.00 0.00 2.83
2517 2652 6.706716 TGTGTAGACCGATCATGTTTTTGTTA 59.293 34.615 0.00 0.00 0.00 2.41
2518 2653 7.389330 TGTGTAGACCGATCATGTTTTTGTTAT 59.611 33.333 0.00 0.00 0.00 1.89
2519 2654 8.234546 GTGTAGACCGATCATGTTTTTGTTATT 58.765 33.333 0.00 0.00 0.00 1.40
2520 2655 8.788806 TGTAGACCGATCATGTTTTTGTTATTT 58.211 29.630 0.00 0.00 0.00 1.40
2521 2656 9.061610 GTAGACCGATCATGTTTTTGTTATTTG 57.938 33.333 0.00 0.00 0.00 2.32
2522 2657 6.586082 AGACCGATCATGTTTTTGTTATTTGC 59.414 34.615 0.00 0.00 0.00 3.68
2523 2658 5.637387 ACCGATCATGTTTTTGTTATTTGCC 59.363 36.000 0.00 0.00 0.00 4.52
2524 2659 5.636965 CCGATCATGTTTTTGTTATTTGCCA 59.363 36.000 0.00 0.00 0.00 4.92
2565 2700 0.110486 GGTCTGGTGGACATGGTGTT 59.890 55.000 0.00 0.00 46.16 3.32
2566 2701 1.238439 GTCTGGTGGACATGGTGTTG 58.762 55.000 0.00 0.00 43.94 3.33
2567 2702 0.110295 TCTGGTGGACATGGTGTTGG 59.890 55.000 0.00 0.00 0.00 3.77
2568 2703 0.110295 CTGGTGGACATGGTGTTGGA 59.890 55.000 0.00 0.00 0.00 3.53
2569 2704 0.179004 TGGTGGACATGGTGTTGGAC 60.179 55.000 0.00 0.00 0.00 4.02
2570 2705 0.110486 GGTGGACATGGTGTTGGACT 59.890 55.000 0.00 0.00 0.00 3.85
2611 2746 4.503714 TTATTTCTCTCCCCATCACCAC 57.496 45.455 0.00 0.00 0.00 4.16
2614 2749 1.616327 CTCTCCCCATCACCACCCA 60.616 63.158 0.00 0.00 0.00 4.51
2616 2751 1.925455 CTCCCCATCACCACCCACT 60.925 63.158 0.00 0.00 0.00 4.00
2685 2820 8.731591 ATGATCAAGAATAAAATATTGCCCCT 57.268 30.769 0.00 0.00 0.00 4.79
2702 2837 1.618343 CCCTTTGATTTTCAACCCGCT 59.382 47.619 0.00 0.00 35.89 5.52
2724 2859 2.167075 GGGGAATCATGGCAAAACAGAG 59.833 50.000 0.00 0.00 0.00 3.35
2759 2894 5.796424 AACATGATTTCCTTCAAGTTGCT 57.204 34.783 0.00 0.00 36.49 3.91
2769 2904 6.500684 TCCTTCAAGTTGCTTTCATACATC 57.499 37.500 0.00 0.00 0.00 3.06
2855 2991 3.891049 AGGGATTTTGTACTGCCTGATC 58.109 45.455 0.00 0.00 31.20 2.92
2877 3013 4.997395 TCACTTTTGAATCACTGTAGGAGC 59.003 41.667 0.00 0.00 0.00 4.70
2927 3069 9.575868 ACCTGATTCTAGATATTTCGAAGTAGA 57.424 33.333 6.53 3.60 0.00 2.59
2964 3106 7.939782 AGATGATCATCTATCTATAAGGCACG 58.060 38.462 32.26 0.00 45.69 5.34
2965 3107 7.559533 AGATGATCATCTATCTATAAGGCACGT 59.440 37.037 32.26 6.40 45.69 4.49
2966 3108 7.089770 TGATCATCTATCTATAAGGCACGTC 57.910 40.000 0.00 0.00 35.45 4.34
2967 3109 6.887002 TGATCATCTATCTATAAGGCACGTCT 59.113 38.462 0.00 0.00 35.45 4.18
2968 3110 8.047310 TGATCATCTATCTATAAGGCACGTCTA 58.953 37.037 0.00 0.00 35.45 2.59
2969 3111 7.851387 TCATCTATCTATAAGGCACGTCTAG 57.149 40.000 0.00 0.00 0.00 2.43
2970 3112 7.395617 TCATCTATCTATAAGGCACGTCTAGT 58.604 38.462 0.00 0.00 0.00 2.57
2971 3113 7.883833 TCATCTATCTATAAGGCACGTCTAGTT 59.116 37.037 0.00 0.00 0.00 2.24
2972 3114 9.163899 CATCTATCTATAAGGCACGTCTAGTTA 57.836 37.037 0.00 0.00 0.00 2.24
2973 3115 9.908747 ATCTATCTATAAGGCACGTCTAGTTAT 57.091 33.333 0.00 0.00 0.00 1.89
2974 3116 9.736414 TCTATCTATAAGGCACGTCTAGTTATT 57.264 33.333 0.00 0.00 0.00 1.40
2975 3117 9.991388 CTATCTATAAGGCACGTCTAGTTATTC 57.009 37.037 0.00 0.00 0.00 1.75
2976 3118 8.638629 ATCTATAAGGCACGTCTAGTTATTCT 57.361 34.615 0.00 0.00 0.00 2.40
2977 3119 9.736414 ATCTATAAGGCACGTCTAGTTATTCTA 57.264 33.333 0.00 0.00 0.00 2.10
2978 3120 8.997323 TCTATAAGGCACGTCTAGTTATTCTAC 58.003 37.037 0.00 0.00 0.00 2.59
2979 3121 4.548991 AGGCACGTCTAGTTATTCTACG 57.451 45.455 0.00 0.00 0.00 3.51
2980 3122 3.944015 AGGCACGTCTAGTTATTCTACGT 59.056 43.478 0.00 0.00 33.63 3.57
2981 3123 4.034975 AGGCACGTCTAGTTATTCTACGTC 59.965 45.833 0.00 0.00 31.92 4.34
2982 3124 4.278058 GCACGTCTAGTTATTCTACGTCC 58.722 47.826 0.00 0.00 31.92 4.79
2983 3125 4.201851 GCACGTCTAGTTATTCTACGTCCA 60.202 45.833 0.00 0.00 31.92 4.02
2984 3126 5.674569 GCACGTCTAGTTATTCTACGTCCAA 60.675 44.000 0.00 0.00 31.92 3.53
2985 3127 5.964168 CACGTCTAGTTATTCTACGTCCAAG 59.036 44.000 0.00 0.00 31.92 3.61
2986 3128 5.645497 ACGTCTAGTTATTCTACGTCCAAGT 59.355 40.000 0.00 0.00 29.49 3.16
2987 3129 5.964168 CGTCTAGTTATTCTACGTCCAAGTG 59.036 44.000 0.00 0.00 0.00 3.16
2988 3130 6.183360 CGTCTAGTTATTCTACGTCCAAGTGA 60.183 42.308 0.00 0.00 0.00 3.41
2989 3131 6.966066 GTCTAGTTATTCTACGTCCAAGTGAC 59.034 42.308 0.00 0.00 40.81 3.67
2990 3132 5.979288 AGTTATTCTACGTCCAAGTGACT 57.021 39.130 0.00 0.00 42.13 3.41
2991 3133 5.952033 AGTTATTCTACGTCCAAGTGACTC 58.048 41.667 0.00 0.00 42.13 3.36
2992 3134 5.475909 AGTTATTCTACGTCCAAGTGACTCA 59.524 40.000 0.00 0.00 42.13 3.41
2993 3135 4.866508 ATTCTACGTCCAAGTGACTCAA 57.133 40.909 0.00 0.00 42.13 3.02
2994 3136 4.866508 TTCTACGTCCAAGTGACTCAAT 57.133 40.909 0.00 0.00 42.13 2.57
2995 3137 4.436242 TCTACGTCCAAGTGACTCAATC 57.564 45.455 0.00 0.00 42.13 2.67
2996 3138 3.824443 TCTACGTCCAAGTGACTCAATCA 59.176 43.478 0.00 0.00 42.13 2.57
2997 3139 3.469008 ACGTCCAAGTGACTCAATCAA 57.531 42.857 0.00 0.00 42.13 2.57
2998 3140 3.804036 ACGTCCAAGTGACTCAATCAAA 58.196 40.909 0.00 0.00 42.13 2.69
2999 3141 3.560068 ACGTCCAAGTGACTCAATCAAAC 59.440 43.478 0.00 0.00 42.13 2.93
3000 3142 3.559655 CGTCCAAGTGACTCAATCAAACA 59.440 43.478 0.00 0.00 42.13 2.83
3001 3143 4.035091 CGTCCAAGTGACTCAATCAAACAA 59.965 41.667 0.00 0.00 42.13 2.83
3002 3144 5.514279 GTCCAAGTGACTCAATCAAACAAG 58.486 41.667 0.00 0.00 39.72 3.16
3003 3145 5.296780 GTCCAAGTGACTCAATCAAACAAGA 59.703 40.000 0.00 0.00 39.72 3.02
3004 3146 5.885352 TCCAAGTGACTCAATCAAACAAGAA 59.115 36.000 0.00 0.00 39.72 2.52
3005 3147 6.376864 TCCAAGTGACTCAATCAAACAAGAAA 59.623 34.615 0.00 0.00 39.72 2.52
3006 3148 6.473455 CCAAGTGACTCAATCAAACAAGAAAC 59.527 38.462 0.00 0.00 39.72 2.78
3007 3149 6.757897 AGTGACTCAATCAAACAAGAAACA 57.242 33.333 0.00 0.00 39.72 2.83
3008 3150 7.156876 AGTGACTCAATCAAACAAGAAACAA 57.843 32.000 0.00 0.00 39.72 2.83
3009 3151 7.601856 AGTGACTCAATCAAACAAGAAACAAA 58.398 30.769 0.00 0.00 39.72 2.83
3010 3152 8.087750 AGTGACTCAATCAAACAAGAAACAAAA 58.912 29.630 0.00 0.00 39.72 2.44
3011 3153 8.707839 GTGACTCAATCAAACAAGAAACAAAAA 58.292 29.630 0.00 0.00 39.72 1.94
3012 3154 8.924691 TGACTCAATCAAACAAGAAACAAAAAG 58.075 29.630 0.00 0.00 33.02 2.27
3013 3155 9.139174 GACTCAATCAAACAAGAAACAAAAAGA 57.861 29.630 0.00 0.00 0.00 2.52
3014 3156 8.925700 ACTCAATCAAACAAGAAACAAAAAGAC 58.074 29.630 0.00 0.00 0.00 3.01
3015 3157 8.824159 TCAATCAAACAAGAAACAAAAAGACA 57.176 26.923 0.00 0.00 0.00 3.41
3016 3158 9.265901 TCAATCAAACAAGAAACAAAAAGACAA 57.734 25.926 0.00 0.00 0.00 3.18
3017 3159 9.875675 CAATCAAACAAGAAACAAAAAGACAAA 57.124 25.926 0.00 0.00 0.00 2.83
3020 3162 9.319143 TCAAACAAGAAACAAAAAGACAAAAGA 57.681 25.926 0.00 0.00 0.00 2.52
3021 3163 9.928236 CAAACAAGAAACAAAAAGACAAAAGAA 57.072 25.926 0.00 0.00 0.00 2.52
3027 3169 9.822185 AGAAACAAAAAGACAAAAGAATATGCT 57.178 25.926 0.00 0.00 0.00 3.79
3030 3172 7.854534 ACAAAAAGACAAAAGAATATGCTTGC 58.145 30.769 0.00 0.00 0.00 4.01
3031 3173 7.495279 ACAAAAAGACAAAAGAATATGCTTGCA 59.505 29.630 0.00 0.00 0.00 4.08
3032 3174 7.412137 AAAAGACAAAAGAATATGCTTGCAC 57.588 32.000 0.00 0.00 0.00 4.57
3033 3175 5.710513 AGACAAAAGAATATGCTTGCACA 57.289 34.783 0.00 0.00 0.00 4.57
3034 3176 6.088016 AGACAAAAGAATATGCTTGCACAA 57.912 33.333 0.00 0.00 0.00 3.33
3035 3177 6.514947 AGACAAAAGAATATGCTTGCACAAA 58.485 32.000 0.00 0.00 0.00 2.83
3036 3178 7.156673 AGACAAAAGAATATGCTTGCACAAAT 58.843 30.769 0.00 0.00 0.00 2.32
3037 3179 7.330208 AGACAAAAGAATATGCTTGCACAAATC 59.670 33.333 0.00 0.00 0.00 2.17
3038 3180 7.156673 ACAAAAGAATATGCTTGCACAAATCT 58.843 30.769 0.00 0.00 0.00 2.40
3039 3181 8.306038 ACAAAAGAATATGCTTGCACAAATCTA 58.694 29.630 0.00 0.00 0.00 1.98
3040 3182 9.309516 CAAAAGAATATGCTTGCACAAATCTAT 57.690 29.630 0.00 0.00 0.00 1.98
3041 3183 8.867112 AAAGAATATGCTTGCACAAATCTATG 57.133 30.769 0.00 0.00 0.00 2.23
3042 3184 6.444633 AGAATATGCTTGCACAAATCTATGC 58.555 36.000 0.00 0.00 42.40 3.14
3079 3221 6.441093 CATACAACTTGGATGTGCAATACT 57.559 37.500 5.87 0.00 34.01 2.12
3080 3222 6.855836 CATACAACTTGGATGTGCAATACTT 58.144 36.000 5.87 0.00 34.01 2.24
3081 3223 7.984391 CATACAACTTGGATGTGCAATACTTA 58.016 34.615 5.87 0.00 34.01 2.24
3082 3224 6.500684 ACAACTTGGATGTGCAATACTTAG 57.499 37.500 0.00 0.00 0.00 2.18
3083 3225 6.237901 ACAACTTGGATGTGCAATACTTAGA 58.762 36.000 0.00 0.00 0.00 2.10
3084 3226 6.372659 ACAACTTGGATGTGCAATACTTAGAG 59.627 38.462 0.00 0.00 0.00 2.43
3085 3227 4.878397 ACTTGGATGTGCAATACTTAGAGC 59.122 41.667 0.00 0.00 0.00 4.09
3086 3228 4.486125 TGGATGTGCAATACTTAGAGCA 57.514 40.909 0.00 0.00 34.10 4.26
3094 3236 6.715347 TGCAATACTTAGAGCACATCTAGA 57.285 37.500 0.00 0.00 41.57 2.43
3095 3237 7.295322 TGCAATACTTAGAGCACATCTAGAT 57.705 36.000 0.00 0.00 41.57 1.98
3096 3238 7.150640 TGCAATACTTAGAGCACATCTAGATG 58.849 38.462 27.63 27.63 41.57 2.90
3200 3342 2.351276 GTGGCATGGACGGGAACT 59.649 61.111 0.00 0.00 0.00 3.01
3374 3516 1.685765 CATCGTCCCCCACCTCTCA 60.686 63.158 0.00 0.00 0.00 3.27
3390 3532 0.981943 CTCAAACCCCTACCTCCGTT 59.018 55.000 0.00 0.00 0.00 4.44
3431 3573 1.300963 GGCAACCAGAGCAGATCCA 59.699 57.895 0.00 0.00 0.00 3.41
3437 3579 1.061812 ACCAGAGCAGATCCATAGGGT 60.062 52.381 0.00 0.00 34.93 4.34
3629 3775 1.626825 GGGGCAACACCAGTAGTTCTA 59.373 52.381 0.00 0.00 42.05 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 3.057736 GCATAGAACTCGTATTCCGCCTA 60.058 47.826 0.00 0.00 36.19 3.93
114 118 2.583441 CGAGGGTCCAGCCTTGTCA 61.583 63.158 0.00 0.00 37.43 3.58
147 151 2.933495 TCACCGAGTCCAAACTATCG 57.067 50.000 0.00 0.00 35.28 2.92
186 190 2.418910 CCAGTCGATGTCGGAGCCT 61.419 63.158 2.25 0.00 40.29 4.58
215 219 3.211865 ACTACTGCCGAATACTCATCGA 58.788 45.455 0.00 0.00 42.76 3.59
228 232 6.128769 ACGAAACAAAAACAAAAACTACTGCC 60.129 34.615 0.00 0.00 0.00 4.85
257 261 7.808672 AGTAGTTCCGATAGAATGATACTTCG 58.191 38.462 0.00 0.00 36.69 3.79
274 278 9.791820 GTCTGATAGAAACTTAAGAGTAGTTCC 57.208 37.037 10.09 0.00 34.88 3.62
378 383 1.039233 AGGGCATCATTTTGCTCCCG 61.039 55.000 0.00 0.00 44.52 5.14
379 384 2.071778 TAGGGCATCATTTTGCTCCC 57.928 50.000 0.00 0.00 44.52 4.30
417 422 3.319755 CATCACCTCAAACATGTTTGCC 58.680 45.455 35.90 0.00 46.92 4.52
559 564 6.834168 AACCATGATTTTTACGAGGTCATT 57.166 33.333 0.00 0.00 0.00 2.57
567 572 7.007367 CACATCGAGAAAACCATGATTTTTACG 59.993 37.037 14.61 14.61 31.90 3.18
617 622 4.808042 AGGTAAATATTGCATTGCCTCCT 58.192 39.130 6.12 0.10 37.06 3.69
734 739 3.810310 TTTCAGCCAAAACCGAAACAT 57.190 38.095 0.00 0.00 0.00 2.71
749 756 9.170734 TCCACTGAATCTCTGATTTTATTTCAG 57.829 33.333 7.91 7.91 41.61 3.02
806 813 7.795047 ACCATGGAAAAGAAAGTTCAATCTTT 58.205 30.769 21.47 0.00 45.30 2.52
807 814 7.365497 ACCATGGAAAAGAAAGTTCAATCTT 57.635 32.000 21.47 0.00 37.49 2.40
842 850 2.128771 AGGCACGGCAAGAATGTTAT 57.871 45.000 0.00 0.00 0.00 1.89
901 914 2.100631 CCGGACATGTCGCTGTTCC 61.101 63.158 19.33 3.62 0.00 3.62
913 926 0.747852 TAATAGCATGCGTCCGGACA 59.252 50.000 32.80 16.34 0.00 4.02
914 927 1.000607 TCTAATAGCATGCGTCCGGAC 60.001 52.381 25.28 25.28 0.00 4.79
963 978 5.411669 AGGTAGTCCAACTCGCAAATTTAAG 59.588 40.000 0.00 0.00 35.89 1.85
983 998 0.978667 TATGCGGGAAGTGGCAGGTA 60.979 55.000 0.00 0.00 43.27 3.08
992 1007 1.446907 GCATCCATCTATGCGGGAAG 58.553 55.000 0.00 0.00 42.57 3.46
1001 1017 2.421314 CACCGCGGCATCCATCTA 59.579 61.111 28.58 0.00 0.00 1.98
1095 1114 1.153329 AACGTGACTTGGACGCCAA 60.153 52.632 10.28 10.28 41.69 4.52
1096 1115 1.593209 GAACGTGACTTGGACGCCA 60.593 57.895 0.00 0.00 40.56 5.69
1177 1205 4.880426 AGGCCGTCGGGGATGGAT 62.880 66.667 14.38 0.00 40.94 3.41
1286 1323 2.783275 CGCATCAGCAGCACAGAC 59.217 61.111 0.00 0.00 42.27 3.51
1290 1327 4.175489 CTGGCGCATCAGCAGCAC 62.175 66.667 10.83 0.00 42.27 4.40
1414 1462 1.078426 GGGCATACACAGGAACGCT 60.078 57.895 0.00 0.00 0.00 5.07
1425 1473 0.872021 CTCGACGAGCTTGGGCATAC 60.872 60.000 12.67 0.00 41.70 2.39
1456 1504 2.599281 TCGTCCGCAGTGAAGGGA 60.599 61.111 0.00 0.00 0.00 4.20
1561 1624 3.963733 CTTGAGCACCAAGGGATCA 57.036 52.632 10.06 0.00 46.54 2.92
1804 1878 2.435693 GCTCCCCAGGCTCACGTAT 61.436 63.158 0.00 0.00 0.00 3.06
1842 1916 1.006102 AGGAACTCGGTGAACTGCG 60.006 57.895 0.00 0.00 0.00 5.18
1879 1953 2.732619 CCAGAGGAAGGCGTACCCC 61.733 68.421 0.00 0.00 36.11 4.95
2191 2322 2.675772 ACCGTCCTCTCCACGACC 60.676 66.667 0.00 0.00 39.75 4.79
2212 2343 2.769621 TCGGATGCCATGGCCTCT 60.770 61.111 32.59 19.90 41.09 3.69
2350 2481 1.904440 ATTCTGGGCTTGAGGAGGAT 58.096 50.000 0.00 0.00 0.00 3.24
2387 2522 1.570803 AATGAGAGACCTCTGCAGCT 58.429 50.000 9.47 0.00 40.61 4.24
2395 2530 7.122715 AGTAGTGAGATGTAAATGAGAGACCT 58.877 38.462 0.00 0.00 0.00 3.85
2397 2532 9.116067 AGTAGTAGTGAGATGTAAATGAGAGAC 57.884 37.037 0.00 0.00 0.00 3.36
2433 2568 0.594602 TTACAGGACCACGTGTCTCG 59.405 55.000 15.65 0.92 43.89 4.04
2434 2569 2.798847 GTTTTACAGGACCACGTGTCTC 59.201 50.000 15.65 8.32 43.89 3.36
2441 2576 2.937799 TGTGTTCGTTTTACAGGACCAC 59.062 45.455 0.00 0.00 34.25 4.16
2443 2578 4.035909 ACAATGTGTTCGTTTTACAGGACC 59.964 41.667 0.00 0.00 0.00 4.46
2456 2591 6.653320 TGGAGATACCACTAAACAATGTGTTC 59.347 38.462 0.00 0.00 44.64 3.18
2458 2593 6.121776 TGGAGATACCACTAAACAATGTGT 57.878 37.500 0.00 0.00 44.64 3.72
2476 2611 6.223852 GTCTACACAACTCAAGATTTGGAGA 58.776 40.000 0.00 2.77 35.17 3.71
2477 2612 5.409826 GGTCTACACAACTCAAGATTTGGAG 59.590 44.000 5.36 0.00 37.18 3.86
2479 2614 4.152402 CGGTCTACACAACTCAAGATTTGG 59.848 45.833 5.36 0.00 0.00 3.28
2480 2615 4.988540 TCGGTCTACACAACTCAAGATTTG 59.011 41.667 0.00 0.00 0.00 2.32
2481 2616 5.209818 TCGGTCTACACAACTCAAGATTT 57.790 39.130 0.00 0.00 0.00 2.17
2482 2617 4.866508 TCGGTCTACACAACTCAAGATT 57.133 40.909 0.00 0.00 0.00 2.40
2483 2618 4.462834 TGATCGGTCTACACAACTCAAGAT 59.537 41.667 0.00 0.00 0.00 2.40
2484 2619 3.824443 TGATCGGTCTACACAACTCAAGA 59.176 43.478 0.00 0.00 0.00 3.02
2485 2620 4.174411 TGATCGGTCTACACAACTCAAG 57.826 45.455 0.00 0.00 0.00 3.02
2486 2621 4.021456 ACATGATCGGTCTACACAACTCAA 60.021 41.667 0.00 0.00 0.00 3.02
2487 2622 3.509967 ACATGATCGGTCTACACAACTCA 59.490 43.478 0.00 0.00 0.00 3.41
2488 2623 4.111375 ACATGATCGGTCTACACAACTC 57.889 45.455 0.00 0.00 0.00 3.01
2489 2624 4.537135 AACATGATCGGTCTACACAACT 57.463 40.909 0.00 0.00 0.00 3.16
2490 2625 5.607119 AAAACATGATCGGTCTACACAAC 57.393 39.130 0.00 0.00 0.00 3.32
2491 2626 5.529430 ACAAAAACATGATCGGTCTACACAA 59.471 36.000 0.00 0.00 0.00 3.33
2492 2627 5.060506 ACAAAAACATGATCGGTCTACACA 58.939 37.500 0.00 0.00 0.00 3.72
2493 2628 5.607119 ACAAAAACATGATCGGTCTACAC 57.393 39.130 0.00 0.00 0.00 2.90
2494 2629 7.915293 ATAACAAAAACATGATCGGTCTACA 57.085 32.000 0.00 0.00 0.00 2.74
2495 2630 9.061610 CAAATAACAAAAACATGATCGGTCTAC 57.938 33.333 0.00 0.00 0.00 2.59
2496 2631 7.753132 GCAAATAACAAAAACATGATCGGTCTA 59.247 33.333 0.00 0.00 0.00 2.59
2497 2632 6.586082 GCAAATAACAAAAACATGATCGGTCT 59.414 34.615 0.00 0.00 0.00 3.85
2498 2633 6.183360 GGCAAATAACAAAAACATGATCGGTC 60.183 38.462 0.00 0.00 0.00 4.79
2499 2634 5.637387 GGCAAATAACAAAAACATGATCGGT 59.363 36.000 0.00 0.00 0.00 4.69
2500 2635 5.636965 TGGCAAATAACAAAAACATGATCGG 59.363 36.000 0.00 0.00 0.00 4.18
2501 2636 6.702972 TGGCAAATAACAAAAACATGATCG 57.297 33.333 0.00 0.00 0.00 3.69
2502 2637 7.333921 TGGATGGCAAATAACAAAAACATGATC 59.666 33.333 0.00 0.00 0.00 2.92
2503 2638 7.166851 TGGATGGCAAATAACAAAAACATGAT 58.833 30.769 0.00 0.00 0.00 2.45
2504 2639 6.528321 TGGATGGCAAATAACAAAAACATGA 58.472 32.000 0.00 0.00 0.00 3.07
2505 2640 6.798315 TGGATGGCAAATAACAAAAACATG 57.202 33.333 0.00 0.00 0.00 3.21
2506 2641 6.127952 GCATGGATGGCAAATAACAAAAACAT 60.128 34.615 0.00 0.00 0.00 2.71
2507 2642 5.180868 GCATGGATGGCAAATAACAAAAACA 59.819 36.000 0.00 0.00 0.00 2.83
2508 2643 5.412286 AGCATGGATGGCAAATAACAAAAAC 59.588 36.000 0.00 0.00 0.00 2.43
2509 2644 5.558818 AGCATGGATGGCAAATAACAAAAA 58.441 33.333 0.00 0.00 0.00 1.94
2510 2645 5.163281 AGCATGGATGGCAAATAACAAAA 57.837 34.783 0.00 0.00 0.00 2.44
2511 2646 4.822685 AGCATGGATGGCAAATAACAAA 57.177 36.364 0.00 0.00 0.00 2.83
2512 2647 4.382901 GGAAGCATGGATGGCAAATAACAA 60.383 41.667 0.00 0.00 0.00 2.83
2513 2648 3.132646 GGAAGCATGGATGGCAAATAACA 59.867 43.478 0.00 0.00 0.00 2.41
2514 2649 3.385755 AGGAAGCATGGATGGCAAATAAC 59.614 43.478 0.00 0.00 0.00 1.89
2515 2650 3.638160 GAGGAAGCATGGATGGCAAATAA 59.362 43.478 0.00 0.00 0.00 1.40
2516 2651 3.225104 GAGGAAGCATGGATGGCAAATA 58.775 45.455 0.00 0.00 0.00 1.40
2517 2652 2.037144 GAGGAAGCATGGATGGCAAAT 58.963 47.619 0.00 0.00 0.00 2.32
2518 2653 1.272592 TGAGGAAGCATGGATGGCAAA 60.273 47.619 0.00 0.00 0.00 3.68
2519 2654 0.332293 TGAGGAAGCATGGATGGCAA 59.668 50.000 0.00 0.00 0.00 4.52
2520 2655 0.554305 ATGAGGAAGCATGGATGGCA 59.446 50.000 0.00 0.00 0.00 4.92
2521 2656 0.959553 CATGAGGAAGCATGGATGGC 59.040 55.000 0.00 0.00 41.45 4.40
2565 2700 9.645128 AATAATAATTGTGATGATCCAAGTCCA 57.355 29.630 1.12 0.00 0.00 4.02
2611 2746 3.282885 GGAAAGAATAAGAGCCAGTGGG 58.717 50.000 12.15 0.00 37.18 4.61
2614 2749 5.441718 TCATGGAAAGAATAAGAGCCAGT 57.558 39.130 0.00 0.00 0.00 4.00
2616 2751 4.949856 GGTTCATGGAAAGAATAAGAGCCA 59.050 41.667 0.00 0.00 0.00 4.75
2685 2820 1.342819 CCCAGCGGGTTGAAAATCAAA 59.657 47.619 1.11 0.00 38.22 2.69
2702 2837 1.901159 CTGTTTTGCCATGATTCCCCA 59.099 47.619 0.00 0.00 0.00 4.96
2724 2859 5.405269 GGAAATCATGTTACCTGTTTGCAAC 59.595 40.000 0.00 0.00 0.00 4.17
2759 2894 5.069318 TCACTTTGGCTGTGATGTATGAAA 58.931 37.500 4.89 0.00 39.23 2.69
2788 2923 4.244862 GGCTTATGCTTTAGCTTTTGCAA 58.755 39.130 10.01 0.00 43.20 4.08
2855 2991 4.143030 CGCTCCTACAGTGATTCAAAAGTG 60.143 45.833 0.00 0.00 34.07 3.16
2877 3013 0.298707 CGTCGGATTCTGCATGTTCG 59.701 55.000 0.00 0.00 0.00 3.95
2946 3088 7.618502 ACTAGACGTGCCTTATAGATAGATG 57.381 40.000 0.00 0.00 0.00 2.90
2949 3091 9.991388 GAATAACTAGACGTGCCTTATAGATAG 57.009 37.037 0.00 0.00 0.00 2.08
2950 3092 9.736414 AGAATAACTAGACGTGCCTTATAGATA 57.264 33.333 0.00 0.00 0.00 1.98
2951 3093 8.638629 AGAATAACTAGACGTGCCTTATAGAT 57.361 34.615 0.00 0.00 0.00 1.98
2952 3094 8.997323 GTAGAATAACTAGACGTGCCTTATAGA 58.003 37.037 0.00 0.00 0.00 1.98
2953 3095 7.956403 CGTAGAATAACTAGACGTGCCTTATAG 59.044 40.741 0.00 0.00 0.00 1.31
2954 3096 7.442364 ACGTAGAATAACTAGACGTGCCTTATA 59.558 37.037 0.00 0.00 40.69 0.98
2955 3097 6.261826 ACGTAGAATAACTAGACGTGCCTTAT 59.738 38.462 0.00 0.00 40.69 1.73
2956 3098 5.586243 ACGTAGAATAACTAGACGTGCCTTA 59.414 40.000 0.00 0.00 40.69 2.69
2957 3099 4.397417 ACGTAGAATAACTAGACGTGCCTT 59.603 41.667 0.00 0.00 40.69 4.35
2958 3100 3.944015 ACGTAGAATAACTAGACGTGCCT 59.056 43.478 0.00 0.00 40.69 4.75
2959 3101 4.278058 GACGTAGAATAACTAGACGTGCC 58.722 47.826 8.09 0.00 41.76 5.01
2960 3102 4.201851 TGGACGTAGAATAACTAGACGTGC 60.202 45.833 13.23 13.23 45.35 5.34
2961 3103 5.475273 TGGACGTAGAATAACTAGACGTG 57.525 43.478 8.09 0.00 41.76 4.49
2962 3104 5.645497 ACTTGGACGTAGAATAACTAGACGT 59.355 40.000 0.00 0.00 43.52 4.34
2963 3105 5.964168 CACTTGGACGTAGAATAACTAGACG 59.036 44.000 0.00 0.00 36.85 4.18
2964 3106 6.966066 GTCACTTGGACGTAGAATAACTAGAC 59.034 42.308 0.00 0.00 36.65 2.59
2965 3107 7.081526 GTCACTTGGACGTAGAATAACTAGA 57.918 40.000 0.00 0.00 36.65 2.43
2980 3122 5.436175 TCTTGTTTGATTGAGTCACTTGGA 58.564 37.500 0.00 0.00 36.32 3.53
2981 3123 5.756195 TCTTGTTTGATTGAGTCACTTGG 57.244 39.130 0.00 0.00 36.32 3.61
2982 3124 7.028962 TGTTTCTTGTTTGATTGAGTCACTTG 58.971 34.615 0.00 0.00 36.32 3.16
2983 3125 7.156876 TGTTTCTTGTTTGATTGAGTCACTT 57.843 32.000 0.00 0.00 36.32 3.16
2984 3126 6.757897 TGTTTCTTGTTTGATTGAGTCACT 57.242 33.333 0.00 0.00 36.32 3.41
2985 3127 7.810766 TTTGTTTCTTGTTTGATTGAGTCAC 57.189 32.000 0.00 0.00 36.32 3.67
2986 3128 8.824159 TTTTTGTTTCTTGTTTGATTGAGTCA 57.176 26.923 0.00 0.00 34.25 3.41
2987 3129 9.139174 TCTTTTTGTTTCTTGTTTGATTGAGTC 57.861 29.630 0.00 0.00 0.00 3.36
2988 3130 8.925700 GTCTTTTTGTTTCTTGTTTGATTGAGT 58.074 29.630 0.00 0.00 0.00 3.41
2989 3131 8.924691 TGTCTTTTTGTTTCTTGTTTGATTGAG 58.075 29.630 0.00 0.00 0.00 3.02
2990 3132 8.824159 TGTCTTTTTGTTTCTTGTTTGATTGA 57.176 26.923 0.00 0.00 0.00 2.57
2991 3133 9.875675 TTTGTCTTTTTGTTTCTTGTTTGATTG 57.124 25.926 0.00 0.00 0.00 2.67
2994 3136 9.319143 TCTTTTGTCTTTTTGTTTCTTGTTTGA 57.681 25.926 0.00 0.00 0.00 2.69
2995 3137 9.928236 TTCTTTTGTCTTTTTGTTTCTTGTTTG 57.072 25.926 0.00 0.00 0.00 2.93
3001 3143 9.822185 AGCATATTCTTTTGTCTTTTTGTTTCT 57.178 25.926 0.00 0.00 0.00 2.52
3004 3146 8.337532 GCAAGCATATTCTTTTGTCTTTTTGTT 58.662 29.630 0.00 0.00 0.00 2.83
3005 3147 7.495279 TGCAAGCATATTCTTTTGTCTTTTTGT 59.505 29.630 0.00 0.00 0.00 2.83
3006 3148 7.795272 GTGCAAGCATATTCTTTTGTCTTTTTG 59.205 33.333 0.00 0.00 0.00 2.44
3007 3149 7.495279 TGTGCAAGCATATTCTTTTGTCTTTTT 59.505 29.630 0.00 0.00 0.00 1.94
3008 3150 6.985645 TGTGCAAGCATATTCTTTTGTCTTTT 59.014 30.769 0.00 0.00 0.00 2.27
3009 3151 6.514947 TGTGCAAGCATATTCTTTTGTCTTT 58.485 32.000 0.00 0.00 0.00 2.52
3010 3152 6.088016 TGTGCAAGCATATTCTTTTGTCTT 57.912 33.333 0.00 0.00 0.00 3.01
3011 3153 5.710513 TGTGCAAGCATATTCTTTTGTCT 57.289 34.783 0.00 0.00 0.00 3.41
3012 3154 6.768029 TTTGTGCAAGCATATTCTTTTGTC 57.232 33.333 0.00 0.00 0.00 3.18
3013 3155 7.156673 AGATTTGTGCAAGCATATTCTTTTGT 58.843 30.769 0.00 0.00 0.00 2.83
3014 3156 7.591006 AGATTTGTGCAAGCATATTCTTTTG 57.409 32.000 0.00 0.00 0.00 2.44
3015 3157 9.309516 CATAGATTTGTGCAAGCATATTCTTTT 57.690 29.630 0.00 0.00 0.00 2.27
3016 3158 7.437267 GCATAGATTTGTGCAAGCATATTCTTT 59.563 33.333 0.00 0.00 40.73 2.52
3017 3159 6.921857 GCATAGATTTGTGCAAGCATATTCTT 59.078 34.615 0.00 0.00 40.73 2.52
3018 3160 6.040054 TGCATAGATTTGTGCAAGCATATTCT 59.960 34.615 5.14 4.33 46.58 2.40
3019 3161 6.210796 TGCATAGATTTGTGCAAGCATATTC 58.789 36.000 5.14 0.00 46.58 1.75
3020 3162 6.151663 TGCATAGATTTGTGCAAGCATATT 57.848 33.333 5.14 0.00 46.58 1.28
3021 3163 5.777850 TGCATAGATTTGTGCAAGCATAT 57.222 34.783 5.14 0.00 46.58 1.78
3046 3188 9.859427 CACATCCAAGTTGTATGTCATTAATTT 57.141 29.630 10.84 0.00 31.60 1.82
3047 3189 7.975616 GCACATCCAAGTTGTATGTCATTAATT 59.024 33.333 10.84 0.00 31.60 1.40
3048 3190 7.122501 TGCACATCCAAGTTGTATGTCATTAAT 59.877 33.333 10.84 0.00 31.60 1.40
3049 3191 6.432472 TGCACATCCAAGTTGTATGTCATTAA 59.568 34.615 10.84 0.00 31.60 1.40
3050 3192 5.942826 TGCACATCCAAGTTGTATGTCATTA 59.057 36.000 10.84 0.00 31.60 1.90
3051 3193 4.766373 TGCACATCCAAGTTGTATGTCATT 59.234 37.500 10.84 0.00 31.60 2.57
3052 3194 4.334552 TGCACATCCAAGTTGTATGTCAT 58.665 39.130 10.84 0.00 31.60 3.06
3053 3195 3.749226 TGCACATCCAAGTTGTATGTCA 58.251 40.909 10.84 9.47 31.60 3.58
3054 3196 4.764679 TTGCACATCCAAGTTGTATGTC 57.235 40.909 10.84 7.36 31.60 3.06
3055 3197 5.945784 AGTATTGCACATCCAAGTTGTATGT 59.054 36.000 8.17 8.17 34.22 2.29
3056 3198 6.441093 AGTATTGCACATCCAAGTTGTATG 57.559 37.500 6.87 6.87 0.00 2.39
3057 3199 8.046708 TCTAAGTATTGCACATCCAAGTTGTAT 58.953 33.333 1.45 0.00 0.00 2.29
3058 3200 7.390823 TCTAAGTATTGCACATCCAAGTTGTA 58.609 34.615 1.45 0.00 0.00 2.41
3059 3201 6.237901 TCTAAGTATTGCACATCCAAGTTGT 58.762 36.000 1.45 0.00 0.00 3.32
3060 3202 6.676456 GCTCTAAGTATTGCACATCCAAGTTG 60.676 42.308 0.00 0.00 0.00 3.16
3061 3203 5.355350 GCTCTAAGTATTGCACATCCAAGTT 59.645 40.000 0.00 0.00 0.00 2.66
3062 3204 4.878397 GCTCTAAGTATTGCACATCCAAGT 59.122 41.667 0.00 0.00 0.00 3.16
3063 3205 4.877823 TGCTCTAAGTATTGCACATCCAAG 59.122 41.667 0.00 0.00 0.00 3.61
3064 3206 4.842574 TGCTCTAAGTATTGCACATCCAA 58.157 39.130 0.00 0.00 0.00 3.53
3065 3207 4.486125 TGCTCTAAGTATTGCACATCCA 57.514 40.909 0.00 0.00 0.00 3.41
3071 3213 6.715347 TCTAGATGTGCTCTAAGTATTGCA 57.285 37.500 0.00 0.00 36.02 4.08
3072 3214 7.579589 CATCTAGATGTGCTCTAAGTATTGC 57.420 40.000 22.42 0.00 36.02 3.56
3102 3244 9.288576 CCCTTGATATAATCATCAGTTTTGCTA 57.711 33.333 0.00 0.00 39.39 3.49
3103 3245 7.781693 ACCCTTGATATAATCATCAGTTTTGCT 59.218 33.333 0.00 0.00 39.39 3.91
3104 3246 7.945134 ACCCTTGATATAATCATCAGTTTTGC 58.055 34.615 0.00 0.00 39.39 3.68
3105 3247 8.571336 GGACCCTTGATATAATCATCAGTTTTG 58.429 37.037 0.00 0.00 39.39 2.44
3106 3248 7.445402 CGGACCCTTGATATAATCATCAGTTTT 59.555 37.037 0.00 0.00 39.39 2.43
3107 3249 6.936900 CGGACCCTTGATATAATCATCAGTTT 59.063 38.462 0.00 0.00 39.39 2.66
3108 3250 6.270000 TCGGACCCTTGATATAATCATCAGTT 59.730 38.462 0.00 0.00 39.39 3.16
3109 3251 5.780282 TCGGACCCTTGATATAATCATCAGT 59.220 40.000 0.00 0.00 39.39 3.41
3110 3252 6.286240 TCGGACCCTTGATATAATCATCAG 57.714 41.667 0.00 0.00 39.39 2.90
3111 3253 6.680148 TTCGGACCCTTGATATAATCATCA 57.320 37.500 0.00 0.00 39.39 3.07
3112 3254 9.099454 GTTATTCGGACCCTTGATATAATCATC 57.901 37.037 0.00 0.00 39.39 2.92
3113 3255 8.826765 AGTTATTCGGACCCTTGATATAATCAT 58.173 33.333 0.00 0.00 39.39 2.45
3114 3256 8.094548 CAGTTATTCGGACCCTTGATATAATCA 58.905 37.037 0.00 0.00 37.55 2.57
3115 3257 7.064728 GCAGTTATTCGGACCCTTGATATAATC 59.935 40.741 0.00 0.00 0.00 1.75
3116 3258 6.879458 GCAGTTATTCGGACCCTTGATATAAT 59.121 38.462 0.00 0.00 0.00 1.28
3117 3259 6.228258 GCAGTTATTCGGACCCTTGATATAA 58.772 40.000 0.00 0.00 0.00 0.98
3118 3260 5.279809 GGCAGTTATTCGGACCCTTGATATA 60.280 44.000 0.00 0.00 0.00 0.86
3119 3261 4.505039 GGCAGTTATTCGGACCCTTGATAT 60.505 45.833 0.00 0.00 0.00 1.63
3120 3262 3.181458 GGCAGTTATTCGGACCCTTGATA 60.181 47.826 0.00 0.00 0.00 2.15
3374 3516 1.377612 GCAACGGAGGTAGGGGTTT 59.622 57.895 0.00 0.00 0.00 3.27
3390 3532 3.249189 AACCAGAGAAGGCCGGCA 61.249 61.111 30.85 0.00 0.00 5.69
3437 3579 0.395311 TGTGGTTTGCGGTGGGTTTA 60.395 50.000 0.00 0.00 0.00 2.01
3608 3754 0.608308 GAACTACTGGTGTTGCCCCC 60.608 60.000 0.00 0.00 36.04 5.40
3609 3755 0.400594 AGAACTACTGGTGTTGCCCC 59.599 55.000 0.00 0.00 36.04 5.80
3610 3756 3.007614 TCTTAGAACTACTGGTGTTGCCC 59.992 47.826 0.00 0.00 36.04 5.36
3629 3775 7.036220 CGTAGATCACAAAACTACTGGATCTT 58.964 38.462 7.20 0.00 41.11 2.40


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

AutoCloner maintained by Alex Coulton.