Multiple sequence alignment - TraesCS7B01G104000

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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 TraesCS7B01G104000 chr7B 100.000 2790 0 0 1 2790 119318757 119315968 0.000000e+00 5153
1 TraesCS7B01G104000 chr7B 91.429 245 20 1 2544 2788 74741255 74741498 4.450000e-88 335
2 TraesCS7B01G104000 chr7B 91.020 245 22 0 2544 2788 537741057 537741301 5.760000e-87 331
3 TraesCS7B01G104000 chr7B 89.831 59 4 2 1905 1962 119316818 119316761 1.070000e-09 75
4 TraesCS7B01G104000 chr7B 89.831 59 4 2 1940 1997 119316853 119316796 1.070000e-09 75
5 TraesCS7B01G104000 chr7D 94.770 2562 101 8 1 2541 156864964 156862415 0.000000e+00 3958
6 TraesCS7B01G104000 chr7D 88.278 418 45 2 1464 1881 156902369 156901956 5.370000e-137 497
7 TraesCS7B01G104000 chr7A 94.467 1229 54 4 119 1347 159727193 159728407 0.000000e+00 1881
8 TraesCS7B01G104000 chr7A 94.261 575 23 4 1976 2541 159728920 159729493 0.000000e+00 870
9 TraesCS7B01G104000 chr7A 95.402 522 24 0 1402 1923 159728417 159728938 0.000000e+00 832
10 TraesCS7B01G104000 chr5B 95.181 249 12 0 2542 2790 660959297 660959049 7.240000e-106 394
11 TraesCS7B01G104000 chr5B 92.713 247 18 0 2542 2788 613103115 613102869 9.500000e-95 357
12 TraesCS7B01G104000 chr3A 95.181 249 12 0 2542 2790 730332222 730331974 7.240000e-106 394
13 TraesCS7B01G104000 chr1A 93.976 249 15 0 2542 2790 540039737 540039489 7.290000e-101 377
14 TraesCS7B01G104000 chr4B 93.469 245 16 0 2544 2788 5279642 5279398 5.680000e-97 364
15 TraesCS7B01G104000 chr3B 91.736 242 19 1 2547 2788 43379584 43379344 4.450000e-88 335
16 TraesCS7B01G104000 chrUn 91.322 242 21 0 2547 2788 419238699 419238458 5.760000e-87 331
17 TraesCS7B01G104000 chr3D 85.345 116 17 0 2198 2313 592577998 592578113 1.360000e-23 121


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 TraesCS7B01G104000 chr7B 119315968 119318757 2789 True 1767.666667 5153 93.220667 1 2790 3 chr7B.!!$R1 2789
1 TraesCS7B01G104000 chr7D 156862415 156864964 2549 True 3958.000000 3958 94.770000 1 2541 1 chr7D.!!$R1 2540
2 TraesCS7B01G104000 chr7A 159727193 159729493 2300 False 1194.333333 1881 94.710000 119 2541 3 chr7A.!!$F1 2422

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
237 250 0.322816 TTGCTTCTCCTGACATGGCC 60.323 55.0 0.00 0.00 0.00 5.36 F
255 268 0.460987 CCGTGCTTCAGGATGTCCTC 60.461 60.0 0.00 0.00 46.65 3.71 F
598 611 0.533085 GCCCGAGGACTTAAGATGCC 60.533 60.0 10.09 7.52 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1679 1692 0.320946 CCCTCCGGCGTTGAAGTAAA 60.321 55.0 6.01 0.0 0.0 2.01 R
1765 1778 0.665835 GAACATCAAACCGTGCACCA 59.334 50.0 12.15 0.0 0.0 4.17 R
2578 2605 0.032615 CTCTCCTAGCCCCAGTGTCT 60.033 60.0 0.00 0.0 0.0 3.41 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
22 23 2.230664 TGGAACACCTCAACTGGCT 58.769 52.632 0.00 0.00 0.00 4.75
95 96 5.064441 ACTTTTGCCTATGTCAATCTTGC 57.936 39.130 0.00 0.00 0.00 4.01
107 108 5.869579 TGTCAATCTTGCTTCTAGTTTCCT 58.130 37.500 0.00 0.00 0.00 3.36
112 113 8.037758 TCAATCTTGCTTCTAGTTTCCTAAGAG 58.962 37.037 0.00 0.00 0.00 2.85
236 249 1.760192 ATTGCTTCTCCTGACATGGC 58.240 50.000 0.00 0.00 0.00 4.40
237 250 0.322816 TTGCTTCTCCTGACATGGCC 60.323 55.000 0.00 0.00 0.00 5.36
255 268 0.460987 CCGTGCTTCAGGATGTCCTC 60.461 60.000 0.00 0.00 46.65 3.71
314 327 2.483876 TCGGACAAGCACTCTTTCAAG 58.516 47.619 0.00 0.00 0.00 3.02
357 370 8.049117 TGGACATCATGCCCTAATCTAATATTC 58.951 37.037 0.00 0.00 0.00 1.75
425 438 2.503809 CGCGCGGGTTTTCATTGG 60.504 61.111 24.84 0.00 0.00 3.16
483 496 4.520492 ACGGCTGTTGAAGAATTTCAGATT 59.480 37.500 0.00 0.00 43.76 2.40
501 514 7.452880 TCAGATTAAGTTCCCATTTGACAAG 57.547 36.000 0.00 0.00 0.00 3.16
524 537 6.457355 AGCTGCTAGTTGATCATCTCAATAG 58.543 40.000 9.58 2.72 45.36 1.73
545 558 2.352127 GCTGGGTGAAATTTGCTGTCTC 60.352 50.000 0.00 0.00 0.00 3.36
573 586 4.142403 CGGGCAAAGAATCTAGCAATTGAA 60.142 41.667 10.34 0.00 0.00 2.69
598 611 0.533085 GCCCGAGGACTTAAGATGCC 60.533 60.000 10.09 7.52 0.00 4.40
599 612 0.830648 CCCGAGGACTTAAGATGCCA 59.169 55.000 10.09 0.00 0.00 4.92
684 697 1.396301 GAGGCAATTCGTCTCAGCTTG 59.604 52.381 5.09 0.00 46.30 4.01
739 752 1.211190 CCAAGCCTCAAAGCGCTTC 59.789 57.895 25.24 10.61 43.35 3.86
863 876 4.081365 TGACATAAAGGTATCACTTCCGCA 60.081 41.667 0.00 0.00 0.00 5.69
932 945 2.497675 TCATCTCCAAGAACCTCCGAAG 59.502 50.000 0.00 0.00 0.00 3.79
973 986 6.716934 TTATGGTACCTCTTGATCTCAGTC 57.283 41.667 14.36 0.00 0.00 3.51
993 1006 3.495001 GTCAAAGTCTGCAACTAGGACAC 59.505 47.826 17.75 3.48 39.33 3.67
1098 1111 3.876341 TCTGAGTGCATGCATGACATTA 58.124 40.909 30.64 14.81 36.64 1.90
1159 1172 4.890988 TCCCCCTCACATCTATTCACTTA 58.109 43.478 0.00 0.00 0.00 2.24
1167 1180 9.653287 CCTCACATCTATTCACTTAGTTAAACA 57.347 33.333 0.00 0.00 0.00 2.83
1181 1194 8.296713 ACTTAGTTAAACATGCATTTGTAGGTG 58.703 33.333 0.00 0.00 0.00 4.00
1182 1195 6.892658 AGTTAAACATGCATTTGTAGGTGA 57.107 33.333 0.00 0.00 0.00 4.02
1218 1231 3.004734 GGGTGTGACCAAGTTTTCTCATG 59.995 47.826 0.00 0.00 41.02 3.07
1238 1251 5.888161 TCATGTGAAGTATCTACAGCTGAGA 59.112 40.000 23.35 18.38 0.00 3.27
1247 1260 9.757227 AAGTATCTACAGCTGAGATTGTATTTC 57.243 33.333 23.35 8.94 35.30 2.17
1259 1272 6.213397 TGAGATTGTATTTCTCTGGTCAGGAA 59.787 38.462 2.73 0.00 40.26 3.36
1420 1433 4.054671 GTGTTCTCTGTGACTGAAGAAGG 58.945 47.826 0.00 0.00 0.00 3.46
1447 1460 9.013490 CACTGTACAAGAATAAAATGCTAATGC 57.987 33.333 0.00 0.00 40.20 3.56
1453 1466 9.971922 ACAAGAATAAAATGCTAATGCTATTCC 57.028 29.630 0.00 0.00 35.23 3.01
1537 1550 2.579201 CTTCCTCCGTGTCGCCAT 59.421 61.111 0.00 0.00 0.00 4.40
1623 1636 3.311871 GCTCATGTTGCAGATAACTCCAG 59.688 47.826 8.20 0.00 0.00 3.86
1636 1649 3.251509 TCCAGCAGGCTTCAGGCA 61.252 61.111 2.85 0.00 44.01 4.75
1662 1675 5.076182 GGTCATAGATCCAGTCATGAGAGA 58.924 45.833 0.00 0.00 30.40 3.10
1679 1692 7.677319 TCATGAGAGATGTGGATAGGAATATGT 59.323 37.037 0.00 0.00 0.00 2.29
1693 1706 4.331717 AGGAATATGTTTACTTCAACGCCG 59.668 41.667 0.00 0.00 0.00 6.46
1765 1778 1.830587 TTGCCAGGAGAGTCGCACAT 61.831 55.000 0.00 0.00 0.00 3.21
1848 1861 2.289565 GCATTACTGTGTAGGGGCTTC 58.710 52.381 0.00 0.00 0.00 3.86
1868 1881 7.281549 GGGCTTCGTTTTAGGAATAATTCTACA 59.718 37.037 0.00 0.00 0.00 2.74
1869 1882 8.671028 GGCTTCGTTTTAGGAATAATTCTACAA 58.329 33.333 0.00 0.00 0.00 2.41
1876 1889 9.681062 TTTTAGGAATAATTCTACAACCTCCTG 57.319 33.333 0.00 0.00 34.04 3.86
1965 1978 5.034200 TGTGTAGGGGGACATTGTATTAGT 58.966 41.667 0.00 0.00 0.00 2.24
2013 2026 8.807948 ACTTTGCATCTTGTATAAACTATGGT 57.192 30.769 0.00 0.00 0.00 3.55
2014 2027 9.243105 ACTTTGCATCTTGTATAAACTATGGTT 57.757 29.630 0.00 0.00 37.24 3.67
2017 2030 8.800370 TGCATCTTGTATAAACTATGGTTTCA 57.200 30.769 10.79 0.55 43.62 2.69
2212 2230 3.653164 TCTGGTGAGCCATATAGTCCAA 58.347 45.455 0.00 0.00 45.05 3.53
2345 2371 1.217183 AGAATACCCCTCGTCCTGCTA 59.783 52.381 0.00 0.00 0.00 3.49
2470 2497 3.528532 TCGTACTATCAGACGCTTCAGA 58.471 45.455 0.00 0.00 38.93 3.27
2515 2542 4.326826 CATGAGACTGGCTAACCTGAAAA 58.673 43.478 0.00 0.00 38.25 2.29
2541 2568 5.308825 CCAGACAGAAACAGAACTAACCAT 58.691 41.667 0.00 0.00 0.00 3.55
2542 2569 5.180117 CCAGACAGAAACAGAACTAACCATG 59.820 44.000 0.00 0.00 0.00 3.66
2543 2570 4.757149 AGACAGAAACAGAACTAACCATGC 59.243 41.667 0.00 0.00 0.00 4.06
2544 2571 3.821033 ACAGAAACAGAACTAACCATGCC 59.179 43.478 0.00 0.00 0.00 4.40
2545 2572 3.820467 CAGAAACAGAACTAACCATGCCA 59.180 43.478 0.00 0.00 0.00 4.92
2546 2573 4.278170 CAGAAACAGAACTAACCATGCCAA 59.722 41.667 0.00 0.00 0.00 4.52
2547 2574 4.520492 AGAAACAGAACTAACCATGCCAAG 59.480 41.667 0.00 0.00 0.00 3.61
2548 2575 2.795329 ACAGAACTAACCATGCCAAGG 58.205 47.619 0.00 0.00 0.00 3.61
2549 2576 2.094675 CAGAACTAACCATGCCAAGGG 58.905 52.381 0.00 0.00 0.00 3.95
2550 2577 1.710809 AGAACTAACCATGCCAAGGGT 59.289 47.619 0.00 0.00 44.08 4.34
2551 2578 1.818674 GAACTAACCATGCCAAGGGTG 59.181 52.381 0.00 0.00 40.36 4.61
2553 2580 0.684153 CTAACCATGCCAAGGGTGGG 60.684 60.000 0.00 0.00 46.09 4.61
2554 2581 2.161713 TAACCATGCCAAGGGTGGGG 62.162 60.000 0.00 0.00 46.09 4.96
2555 2582 3.671410 CCATGCCAAGGGTGGGGA 61.671 66.667 0.00 0.00 46.09 4.81
2556 2583 2.043652 CATGCCAAGGGTGGGGAG 60.044 66.667 0.00 0.00 46.09 4.30
2557 2584 2.535317 ATGCCAAGGGTGGGGAGT 60.535 61.111 0.00 0.00 46.09 3.85
2558 2585 2.922704 ATGCCAAGGGTGGGGAGTG 61.923 63.158 0.00 0.00 46.09 3.51
2559 2586 3.256960 GCCAAGGGTGGGGAGTGA 61.257 66.667 0.00 0.00 46.09 3.41
2560 2587 2.616458 GCCAAGGGTGGGGAGTGAT 61.616 63.158 0.00 0.00 46.09 3.06
2561 2588 1.609783 CCAAGGGTGGGGAGTGATC 59.390 63.158 0.00 0.00 41.77 2.92
2562 2589 1.207488 CCAAGGGTGGGGAGTGATCA 61.207 60.000 0.00 0.00 41.77 2.92
2563 2590 0.035056 CAAGGGTGGGGAGTGATCAC 60.035 60.000 18.47 18.47 0.00 3.06
2564 2591 0.475632 AAGGGTGGGGAGTGATCACA 60.476 55.000 27.02 3.61 33.45 3.58
2565 2592 1.201429 AGGGTGGGGAGTGATCACAC 61.201 60.000 27.02 20.63 46.24 3.82
2566 2593 1.299976 GGTGGGGAGTGATCACACC 59.700 63.158 28.43 28.43 46.99 4.16
2571 2598 2.377136 GGAGTGATCACACCCACCT 58.623 57.895 26.73 6.15 46.99 4.00
2572 2599 1.568504 GGAGTGATCACACCCACCTA 58.431 55.000 26.73 0.00 46.99 3.08
2573 2600 1.482593 GGAGTGATCACACCCACCTAG 59.517 57.143 26.73 0.00 46.99 3.02
2574 2601 2.180276 GAGTGATCACACCCACCTAGT 58.820 52.381 27.02 2.52 46.99 2.57
2575 2602 2.567615 GAGTGATCACACCCACCTAGTT 59.432 50.000 27.02 1.97 46.99 2.24
2576 2603 2.979678 AGTGATCACACCCACCTAGTTT 59.020 45.455 27.02 0.00 46.99 2.66
2577 2604 3.394606 AGTGATCACACCCACCTAGTTTT 59.605 43.478 27.02 0.00 46.99 2.43
2578 2605 4.595781 AGTGATCACACCCACCTAGTTTTA 59.404 41.667 27.02 0.00 46.99 1.52
2579 2606 4.935808 GTGATCACACCCACCTAGTTTTAG 59.064 45.833 21.07 0.00 40.74 1.85
2580 2607 4.841813 TGATCACACCCACCTAGTTTTAGA 59.158 41.667 0.00 0.00 0.00 2.10
2581 2608 4.612264 TCACACCCACCTAGTTTTAGAC 57.388 45.455 0.00 0.00 0.00 2.59
2582 2609 3.968649 TCACACCCACCTAGTTTTAGACA 59.031 43.478 0.00 0.00 0.00 3.41
2583 2610 4.062991 CACACCCACCTAGTTTTAGACAC 58.937 47.826 0.00 0.00 0.00 3.67
2584 2611 3.971971 ACACCCACCTAGTTTTAGACACT 59.028 43.478 0.00 0.00 0.00 3.55
2585 2612 4.202326 ACACCCACCTAGTTTTAGACACTG 60.202 45.833 0.00 0.00 0.00 3.66
2586 2613 3.326880 ACCCACCTAGTTTTAGACACTGG 59.673 47.826 0.00 0.00 0.00 4.00
2587 2614 3.307480 CCCACCTAGTTTTAGACACTGGG 60.307 52.174 1.20 1.20 46.03 4.45
2588 2615 3.307480 CCACCTAGTTTTAGACACTGGGG 60.307 52.174 7.32 1.14 45.11 4.96
2589 2616 2.305052 ACCTAGTTTTAGACACTGGGGC 59.695 50.000 7.32 0.00 45.11 5.80
2590 2617 2.572104 CCTAGTTTTAGACACTGGGGCT 59.428 50.000 0.00 0.00 38.85 5.19
2591 2618 3.773119 CCTAGTTTTAGACACTGGGGCTA 59.227 47.826 0.00 0.00 38.85 3.93
2592 2619 3.983044 AGTTTTAGACACTGGGGCTAG 57.017 47.619 0.00 0.00 0.00 3.42
2593 2620 2.572104 AGTTTTAGACACTGGGGCTAGG 59.428 50.000 0.00 0.00 0.00 3.02
2594 2621 2.570302 GTTTTAGACACTGGGGCTAGGA 59.430 50.000 0.00 0.00 0.00 2.94
2595 2622 2.160721 TTAGACACTGGGGCTAGGAG 57.839 55.000 0.00 0.00 0.00 3.69
2596 2623 1.305886 TAGACACTGGGGCTAGGAGA 58.694 55.000 0.00 0.00 0.00 3.71
2597 2624 0.032615 AGACACTGGGGCTAGGAGAG 60.033 60.000 0.00 0.00 0.00 3.20
2598 2625 0.324830 GACACTGGGGCTAGGAGAGT 60.325 60.000 0.00 0.00 0.00 3.24
2599 2626 0.117340 ACACTGGGGCTAGGAGAGTT 59.883 55.000 0.00 0.00 0.00 3.01
2600 2627 1.361543 ACACTGGGGCTAGGAGAGTTA 59.638 52.381 0.00 0.00 0.00 2.24
2601 2628 2.225547 ACACTGGGGCTAGGAGAGTTAA 60.226 50.000 0.00 0.00 0.00 2.01
2602 2629 3.041946 CACTGGGGCTAGGAGAGTTAAT 58.958 50.000 0.00 0.00 0.00 1.40
2603 2630 3.456277 CACTGGGGCTAGGAGAGTTAATT 59.544 47.826 0.00 0.00 0.00 1.40
2604 2631 3.456277 ACTGGGGCTAGGAGAGTTAATTG 59.544 47.826 0.00 0.00 0.00 2.32
2605 2632 3.456277 CTGGGGCTAGGAGAGTTAATTGT 59.544 47.826 0.00 0.00 0.00 2.71
2606 2633 3.454812 TGGGGCTAGGAGAGTTAATTGTC 59.545 47.826 0.00 0.00 0.00 3.18
2607 2634 3.181453 GGGGCTAGGAGAGTTAATTGTCC 60.181 52.174 6.07 6.07 0.00 4.02
2608 2635 3.712218 GGGCTAGGAGAGTTAATTGTCCT 59.288 47.826 18.84 18.84 42.32 3.85
2609 2636 4.900054 GGGCTAGGAGAGTTAATTGTCCTA 59.100 45.833 19.03 19.03 40.12 2.94
2610 2637 5.365895 GGGCTAGGAGAGTTAATTGTCCTAA 59.634 44.000 20.12 8.45 40.42 2.69
2611 2638 6.126854 GGGCTAGGAGAGTTAATTGTCCTAAA 60.127 42.308 20.12 6.05 40.42 1.85
2612 2639 7.336396 GGCTAGGAGAGTTAATTGTCCTAAAA 58.664 38.462 20.12 5.46 40.42 1.52
2613 2640 7.993758 GGCTAGGAGAGTTAATTGTCCTAAAAT 59.006 37.037 20.12 2.68 40.42 1.82
2614 2641 8.831550 GCTAGGAGAGTTAATTGTCCTAAAATG 58.168 37.037 20.12 12.16 40.42 2.32
2615 2642 9.892130 CTAGGAGAGTTAATTGTCCTAAAATGT 57.108 33.333 20.12 1.48 40.42 2.71
2617 2644 9.588096 AGGAGAGTTAATTGTCCTAAAATGTTT 57.412 29.630 14.22 0.00 37.67 2.83
2626 2653 9.981114 AATTGTCCTAAAATGTTTAGGTTTGAG 57.019 29.630 20.82 1.52 41.69 3.02
2627 2654 8.754991 TTGTCCTAAAATGTTTAGGTTTGAGA 57.245 30.769 20.82 3.91 41.69 3.27
2628 2655 8.754991 TGTCCTAAAATGTTTAGGTTTGAGAA 57.245 30.769 20.82 3.34 41.69 2.87
2629 2656 9.191479 TGTCCTAAAATGTTTAGGTTTGAGAAA 57.809 29.630 20.82 2.76 41.69 2.52
2632 2659 9.423061 CCTAAAATGTTTAGGTTTGAGAAATGG 57.577 33.333 15.71 0.00 37.38 3.16
2633 2660 9.981114 CTAAAATGTTTAGGTTTGAGAAATGGT 57.019 29.630 0.63 0.00 0.00 3.55
2634 2661 8.661352 AAAATGTTTAGGTTTGAGAAATGGTG 57.339 30.769 0.00 0.00 0.00 4.17
2635 2662 5.782893 TGTTTAGGTTTGAGAAATGGTGG 57.217 39.130 0.00 0.00 0.00 4.61
2636 2663 4.038642 TGTTTAGGTTTGAGAAATGGTGGC 59.961 41.667 0.00 0.00 0.00 5.01
2637 2664 2.683211 AGGTTTGAGAAATGGTGGCT 57.317 45.000 0.00 0.00 0.00 4.75
2638 2665 3.806949 AGGTTTGAGAAATGGTGGCTA 57.193 42.857 0.00 0.00 0.00 3.93
2639 2666 3.690460 AGGTTTGAGAAATGGTGGCTAG 58.310 45.455 0.00 0.00 0.00 3.42
2640 2667 2.164422 GGTTTGAGAAATGGTGGCTAGC 59.836 50.000 6.04 6.04 0.00 3.42
2641 2668 2.128771 TTGAGAAATGGTGGCTAGCC 57.871 50.000 27.71 27.71 0.00 3.93
2642 2669 0.255890 TGAGAAATGGTGGCTAGCCC 59.744 55.000 30.81 20.81 34.56 5.19
2643 2670 0.255890 GAGAAATGGTGGCTAGCCCA 59.744 55.000 30.81 22.08 42.79 5.36
2644 2671 0.257039 AGAAATGGTGGCTAGCCCAG 59.743 55.000 30.81 0.00 46.54 4.45
2660 2687 2.777969 CAGCATGGGTTCTCTCAGC 58.222 57.895 0.00 0.00 0.00 4.26
2661 2688 0.252479 CAGCATGGGTTCTCTCAGCT 59.748 55.000 0.00 0.00 0.00 4.24
2662 2689 0.990374 AGCATGGGTTCTCTCAGCTT 59.010 50.000 0.00 0.00 0.00 3.74
2663 2690 1.093159 GCATGGGTTCTCTCAGCTTG 58.907 55.000 0.00 0.00 0.00 4.01
2664 2691 1.612726 GCATGGGTTCTCTCAGCTTGT 60.613 52.381 0.00 0.00 0.00 3.16
2665 2692 2.787994 CATGGGTTCTCTCAGCTTGTT 58.212 47.619 0.00 0.00 0.00 2.83
2666 2693 2.550830 TGGGTTCTCTCAGCTTGTTC 57.449 50.000 0.00 0.00 0.00 3.18
2667 2694 1.768275 TGGGTTCTCTCAGCTTGTTCA 59.232 47.619 0.00 0.00 0.00 3.18
2668 2695 2.373169 TGGGTTCTCTCAGCTTGTTCAT 59.627 45.455 0.00 0.00 0.00 2.57
2669 2696 2.746362 GGGTTCTCTCAGCTTGTTCATG 59.254 50.000 0.00 0.00 0.00 3.07
2670 2697 3.557898 GGGTTCTCTCAGCTTGTTCATGA 60.558 47.826 0.00 0.00 0.00 3.07
2671 2698 4.260170 GGTTCTCTCAGCTTGTTCATGAT 58.740 43.478 0.00 0.00 0.00 2.45
2672 2699 4.094590 GGTTCTCTCAGCTTGTTCATGATG 59.905 45.833 0.00 0.00 0.00 3.07
2673 2700 4.548451 TCTCTCAGCTTGTTCATGATGT 57.452 40.909 0.00 0.00 0.00 3.06
2674 2701 4.251268 TCTCTCAGCTTGTTCATGATGTG 58.749 43.478 0.00 0.00 0.00 3.21
2675 2702 4.001652 CTCTCAGCTTGTTCATGATGTGT 58.998 43.478 0.00 0.00 0.00 3.72
2676 2703 3.749609 TCTCAGCTTGTTCATGATGTGTG 59.250 43.478 0.00 0.00 0.00 3.82
2677 2704 2.815503 TCAGCTTGTTCATGATGTGTGG 59.184 45.455 0.00 0.00 0.00 4.17
2678 2705 2.815503 CAGCTTGTTCATGATGTGTGGA 59.184 45.455 0.00 0.00 0.00 4.02
2679 2706 2.816087 AGCTTGTTCATGATGTGTGGAC 59.184 45.455 0.00 0.00 0.00 4.02
2680 2707 2.816087 GCTTGTTCATGATGTGTGGACT 59.184 45.455 0.00 0.00 0.00 3.85
2681 2708 4.002982 GCTTGTTCATGATGTGTGGACTA 58.997 43.478 0.00 0.00 0.00 2.59
2682 2709 4.093998 GCTTGTTCATGATGTGTGGACTAG 59.906 45.833 0.00 0.00 0.00 2.57
2683 2710 4.206477 TGTTCATGATGTGTGGACTAGG 57.794 45.455 0.00 0.00 0.00 3.02
2684 2711 2.939103 GTTCATGATGTGTGGACTAGGC 59.061 50.000 0.00 0.00 0.00 3.93
2685 2712 2.187100 TCATGATGTGTGGACTAGGCA 58.813 47.619 0.00 0.00 0.00 4.75
2686 2713 2.773661 TCATGATGTGTGGACTAGGCAT 59.226 45.455 0.00 0.00 0.00 4.40
2687 2714 2.696989 TGATGTGTGGACTAGGCATG 57.303 50.000 0.00 0.00 0.00 4.06
2688 2715 1.210234 TGATGTGTGGACTAGGCATGG 59.790 52.381 0.00 0.00 0.00 3.66
2689 2716 1.210478 GATGTGTGGACTAGGCATGGT 59.790 52.381 0.00 0.00 0.00 3.55
2690 2717 0.324614 TGTGTGGACTAGGCATGGTG 59.675 55.000 0.00 0.00 0.00 4.17
2691 2718 0.613260 GTGTGGACTAGGCATGGTGA 59.387 55.000 0.00 0.00 0.00 4.02
2692 2719 1.210478 GTGTGGACTAGGCATGGTGAT 59.790 52.381 0.00 0.00 0.00 3.06
2693 2720 1.210234 TGTGGACTAGGCATGGTGATG 59.790 52.381 0.00 0.00 0.00 3.07
2704 2731 3.834489 CATGGTGATGCTAGGTCTTCT 57.166 47.619 0.00 0.00 0.00 2.85
2705 2732 4.944619 CATGGTGATGCTAGGTCTTCTA 57.055 45.455 0.00 0.00 0.00 2.10
2706 2733 5.480642 CATGGTGATGCTAGGTCTTCTAT 57.519 43.478 0.00 0.00 0.00 1.98
2707 2734 5.862845 CATGGTGATGCTAGGTCTTCTATT 58.137 41.667 0.00 0.00 0.00 1.73
2708 2735 5.282055 TGGTGATGCTAGGTCTTCTATTG 57.718 43.478 0.00 0.00 0.00 1.90
2709 2736 4.962362 TGGTGATGCTAGGTCTTCTATTGA 59.038 41.667 0.00 0.00 0.00 2.57
2710 2737 5.069648 TGGTGATGCTAGGTCTTCTATTGAG 59.930 44.000 0.00 0.00 0.00 3.02
2711 2738 5.303078 GGTGATGCTAGGTCTTCTATTGAGA 59.697 44.000 0.00 0.00 0.00 3.27
2712 2739 6.183360 GGTGATGCTAGGTCTTCTATTGAGAA 60.183 42.308 0.00 0.00 39.47 2.87
2713 2740 6.699642 GTGATGCTAGGTCTTCTATTGAGAAC 59.300 42.308 0.00 0.00 36.75 3.01
2714 2741 6.609212 TGATGCTAGGTCTTCTATTGAGAACT 59.391 38.462 0.00 0.00 36.75 3.01
2715 2742 6.214191 TGCTAGGTCTTCTATTGAGAACTG 57.786 41.667 2.11 0.00 36.75 3.16
2716 2743 5.127845 TGCTAGGTCTTCTATTGAGAACTGG 59.872 44.000 2.11 0.48 36.75 4.00
2717 2744 5.361285 GCTAGGTCTTCTATTGAGAACTGGA 59.639 44.000 6.71 0.00 36.75 3.86
2718 2745 6.041523 GCTAGGTCTTCTATTGAGAACTGGAT 59.958 42.308 6.71 0.00 36.75 3.41
2719 2746 6.232581 AGGTCTTCTATTGAGAACTGGATG 57.767 41.667 0.00 0.00 36.75 3.51
2720 2747 5.723887 AGGTCTTCTATTGAGAACTGGATGT 59.276 40.000 0.00 0.00 36.75 3.06
2721 2748 5.814705 GGTCTTCTATTGAGAACTGGATGTG 59.185 44.000 0.00 0.00 36.75 3.21
2722 2749 5.293079 GTCTTCTATTGAGAACTGGATGTGC 59.707 44.000 0.00 0.00 36.75 4.57
2723 2750 4.824479 TCTATTGAGAACTGGATGTGCA 57.176 40.909 0.00 0.00 0.00 4.57
2724 2751 5.164620 TCTATTGAGAACTGGATGTGCAA 57.835 39.130 0.00 0.00 0.00 4.08
2725 2752 5.559770 TCTATTGAGAACTGGATGTGCAAA 58.440 37.500 0.00 0.00 0.00 3.68
2726 2753 6.003326 TCTATTGAGAACTGGATGTGCAAAA 58.997 36.000 0.00 0.00 0.00 2.44
2727 2754 3.988379 TGAGAACTGGATGTGCAAAAC 57.012 42.857 0.00 0.00 0.00 2.43
2728 2755 2.622942 TGAGAACTGGATGTGCAAAACC 59.377 45.455 0.00 0.00 0.00 3.27
2729 2756 2.622942 GAGAACTGGATGTGCAAAACCA 59.377 45.455 5.65 5.65 0.00 3.67
2733 2760 2.363306 TGGATGTGCAAAACCAGAGT 57.637 45.000 0.80 0.00 0.00 3.24
2734 2761 2.229792 TGGATGTGCAAAACCAGAGTC 58.770 47.619 0.80 0.00 0.00 3.36
2735 2762 2.158623 TGGATGTGCAAAACCAGAGTCT 60.159 45.455 0.80 0.00 0.00 3.24
2736 2763 2.887152 GGATGTGCAAAACCAGAGTCTT 59.113 45.455 0.00 0.00 0.00 3.01
2737 2764 3.304928 GGATGTGCAAAACCAGAGTCTTG 60.305 47.826 0.00 0.00 0.00 3.02
2738 2765 2.997980 TGTGCAAAACCAGAGTCTTGA 58.002 42.857 0.00 0.00 0.00 3.02
2739 2766 3.351740 TGTGCAAAACCAGAGTCTTGAA 58.648 40.909 0.00 0.00 0.00 2.69
2740 2767 3.378112 TGTGCAAAACCAGAGTCTTGAAG 59.622 43.478 0.00 0.00 0.00 3.02
2741 2768 3.627577 GTGCAAAACCAGAGTCTTGAAGA 59.372 43.478 0.00 0.00 0.00 2.87
2742 2769 4.096382 GTGCAAAACCAGAGTCTTGAAGAA 59.904 41.667 0.00 0.00 0.00 2.52
2743 2770 4.704540 TGCAAAACCAGAGTCTTGAAGAAA 59.295 37.500 0.00 0.00 0.00 2.52
2744 2771 5.184864 TGCAAAACCAGAGTCTTGAAGAAAA 59.815 36.000 0.00 0.00 0.00 2.29
2745 2772 6.127366 TGCAAAACCAGAGTCTTGAAGAAAAT 60.127 34.615 0.00 0.00 0.00 1.82
2746 2773 6.419116 GCAAAACCAGAGTCTTGAAGAAAATC 59.581 38.462 0.00 0.00 0.00 2.17
2747 2774 7.483307 CAAAACCAGAGTCTTGAAGAAAATCA 58.517 34.615 0.00 0.00 0.00 2.57
2748 2775 7.830099 AAACCAGAGTCTTGAAGAAAATCAT 57.170 32.000 0.00 0.00 0.00 2.45
2749 2776 7.830099 AACCAGAGTCTTGAAGAAAATCATT 57.170 32.000 0.00 0.00 0.00 2.57
2750 2777 8.924511 AACCAGAGTCTTGAAGAAAATCATTA 57.075 30.769 0.00 0.00 0.00 1.90
2751 2778 8.924511 ACCAGAGTCTTGAAGAAAATCATTAA 57.075 30.769 0.00 0.00 0.00 1.40
2752 2779 9.354673 ACCAGAGTCTTGAAGAAAATCATTAAA 57.645 29.630 0.00 0.00 0.00 1.52
2753 2780 9.837525 CCAGAGTCTTGAAGAAAATCATTAAAG 57.162 33.333 0.00 0.00 0.00 1.85
2754 2781 9.837525 CAGAGTCTTGAAGAAAATCATTAAAGG 57.162 33.333 0.00 0.00 0.00 3.11
2755 2782 9.579932 AGAGTCTTGAAGAAAATCATTAAAGGT 57.420 29.630 0.00 0.00 0.00 3.50
2757 2784 9.971922 AGTCTTGAAGAAAATCATTAAAGGTTG 57.028 29.630 0.00 0.00 0.00 3.77
2758 2785 9.196552 GTCTTGAAGAAAATCATTAAAGGTTGG 57.803 33.333 0.00 0.00 0.00 3.77
2759 2786 9.142014 TCTTGAAGAAAATCATTAAAGGTTGGA 57.858 29.630 0.00 0.00 0.00 3.53
2760 2787 9.415544 CTTGAAGAAAATCATTAAAGGTTGGAG 57.584 33.333 0.00 0.00 0.00 3.86
2761 2788 8.477419 TGAAGAAAATCATTAAAGGTTGGAGT 57.523 30.769 0.00 0.00 0.00 3.85
2762 2789 9.581289 TGAAGAAAATCATTAAAGGTTGGAGTA 57.419 29.630 0.00 0.00 0.00 2.59
2775 2802 8.521170 AAAGGTTGGAGTATTAATTTAGAGGC 57.479 34.615 0.00 0.00 0.00 4.70
2776 2803 7.453141 AGGTTGGAGTATTAATTTAGAGGCT 57.547 36.000 0.00 0.00 0.00 4.58
2777 2804 7.283329 AGGTTGGAGTATTAATTTAGAGGCTG 58.717 38.462 0.00 0.00 0.00 4.85
2778 2805 6.017026 GGTTGGAGTATTAATTTAGAGGCTGC 60.017 42.308 0.00 0.00 0.00 5.25
2779 2806 5.621193 TGGAGTATTAATTTAGAGGCTGCC 58.379 41.667 11.65 11.65 0.00 4.85
2780 2807 5.131977 TGGAGTATTAATTTAGAGGCTGCCA 59.868 40.000 22.65 0.00 0.00 4.92
2781 2808 6.183361 TGGAGTATTAATTTAGAGGCTGCCAT 60.183 38.462 22.65 11.61 0.00 4.40
2782 2809 6.150140 GGAGTATTAATTTAGAGGCTGCCATG 59.850 42.308 22.65 0.00 0.00 3.66
2783 2810 6.841601 AGTATTAATTTAGAGGCTGCCATGA 58.158 36.000 22.65 2.62 0.00 3.07
2784 2811 7.290061 AGTATTAATTTAGAGGCTGCCATGAA 58.710 34.615 22.65 12.15 0.00 2.57
2785 2812 6.645790 ATTAATTTAGAGGCTGCCATGAAG 57.354 37.500 22.65 0.00 0.00 3.02
2786 2813 3.939740 ATTTAGAGGCTGCCATGAAGA 57.060 42.857 22.65 2.19 0.00 2.87
2787 2814 3.719268 TTTAGAGGCTGCCATGAAGAA 57.281 42.857 22.65 4.87 0.00 2.52
2788 2815 3.719268 TTAGAGGCTGCCATGAAGAAA 57.281 42.857 22.65 2.16 0.00 2.52
2789 2816 2.592102 AGAGGCTGCCATGAAGAAAA 57.408 45.000 22.65 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 3.652869 ACTGAGAAGAAATGGGTGAGGAA 59.347 43.478 0.00 0.00 0.00 3.36
107 108 7.666063 TGGAGAGACAATGATTGATCTCTTA 57.334 36.000 27.40 20.51 42.59 2.10
112 113 7.596494 TGTTTTTGGAGAGACAATGATTGATC 58.404 34.615 12.80 9.29 0.00 2.92
236 249 1.599047 AGGACATCCTGAAGCACGG 59.401 57.895 0.00 0.00 46.55 4.94
314 327 0.877071 CCATGTGTGTCTCCACTTGC 59.123 55.000 0.00 0.00 42.34 4.01
357 370 1.741401 ACACATCGTGGCACCATCG 60.741 57.895 12.86 0.00 37.94 3.84
425 438 4.781071 CTTCAAGACAGCATTGACACTTC 58.219 43.478 0.00 0.00 36.44 3.01
483 496 3.255642 GCAGCTTGTCAAATGGGAACTTA 59.744 43.478 0.00 0.00 0.00 2.24
495 508 3.683365 TGATCAACTAGCAGCTTGTCA 57.317 42.857 10.10 1.24 0.00 3.58
524 537 1.615392 AGACAGCAAATTTCACCCAGC 59.385 47.619 0.00 0.00 0.00 4.85
545 558 1.927174 CTAGATTCTTTGCCCGTGACG 59.073 52.381 0.00 0.00 0.00 4.35
573 586 1.486726 CTTAAGTCCTCGGGCTCCAAT 59.513 52.381 0.00 0.00 0.00 3.16
598 611 0.028770 AACACGTGCCGATGTTTGTG 59.971 50.000 17.22 0.00 35.51 3.33
599 612 0.306533 GAACACGTGCCGATGTTTGT 59.693 50.000 17.22 0.00 39.13 2.83
684 697 4.076394 TGGGTTGTGCTTTAAGTGATACC 58.924 43.478 0.00 0.00 0.00 2.73
725 738 1.656652 TAGATGAAGCGCTTTGAGGC 58.343 50.000 25.84 11.60 0.00 4.70
739 752 4.118410 GAGACATCCACACTGCTTAGATG 58.882 47.826 0.00 0.00 40.12 2.90
848 861 1.202580 GCAGATGCGGAAGTGATACCT 60.203 52.381 0.00 0.00 0.00 3.08
973 986 2.476619 CGTGTCCTAGTTGCAGACTTTG 59.523 50.000 6.82 2.43 39.86 2.77
1020 1033 2.039418 TCGGTAATGGCATGCTCTAGT 58.961 47.619 18.92 6.50 0.00 2.57
1098 1111 1.537202 GTGATCGAGCAGCAAACCTTT 59.463 47.619 2.20 0.00 0.00 3.11
1159 1172 6.892658 TCACCTACAAATGCATGTTTAACT 57.107 33.333 0.00 0.00 34.75 2.24
1167 1180 6.332630 GCAAGTAAATCACCTACAAATGCAT 58.667 36.000 0.00 0.00 31.46 3.96
1181 1194 2.749621 CACACCCTCTGGCAAGTAAATC 59.250 50.000 0.00 0.00 33.59 2.17
1182 1195 2.375174 TCACACCCTCTGGCAAGTAAAT 59.625 45.455 0.00 0.00 33.59 1.40
1218 1231 6.568869 ACAATCTCAGCTGTAGATACTTCAC 58.431 40.000 21.41 0.00 33.32 3.18
1238 1251 8.112183 AGATTTTCCTGACCAGAGAAATACAAT 58.888 33.333 11.58 5.66 32.10 2.71
1259 1272 3.188773 AGAAGCCAAGGAGAGGAGATTT 58.811 45.455 0.00 0.00 0.00 2.17
1420 1433 9.013490 CATTAGCATTTTATTCTTGTACAGTGC 57.987 33.333 0.00 0.00 0.00 4.40
1447 1460 7.655236 CAGAAACTGCATAGATCAGGAATAG 57.345 40.000 0.00 0.00 35.94 1.73
1537 1550 2.501723 GAGCACCCTCTTTAGATGACCA 59.498 50.000 0.00 0.00 35.16 4.02
1582 1595 1.881973 GCTGCAAGTTCAATCTCACCA 59.118 47.619 0.00 0.00 35.30 4.17
1623 1636 1.941999 GACCAATGCCTGAAGCCTGC 61.942 60.000 0.00 0.00 42.71 4.85
1636 1649 5.842874 TCTCATGACTGGATCTATGACCAAT 59.157 40.000 0.00 0.00 35.67 3.16
1679 1692 0.320946 CCCTCCGGCGTTGAAGTAAA 60.321 55.000 6.01 0.00 0.00 2.01
1686 1699 2.125512 CTCTTCCCTCCGGCGTTG 60.126 66.667 6.01 0.00 0.00 4.10
1693 1706 2.630580 CCAGTACATAGCTCTTCCCTCC 59.369 54.545 0.00 0.00 0.00 4.30
1765 1778 0.665835 GAACATCAAACCGTGCACCA 59.334 50.000 12.15 0.00 0.00 4.17
1848 1861 8.610035 GGAGGTTGTAGAATTATTCCTAAAACG 58.390 37.037 0.78 0.00 35.14 3.60
1868 1881 4.941873 GTCAATTAATTCGGACAGGAGGTT 59.058 41.667 11.77 0.00 0.00 3.50
1869 1882 4.514401 GTCAATTAATTCGGACAGGAGGT 58.486 43.478 11.77 0.00 0.00 3.85
1876 1889 4.336532 AACTGCGTCAATTAATTCGGAC 57.663 40.909 10.27 9.16 0.00 4.79
2017 2030 6.697019 GCAAAGGTAATACGATTGCATGAAAT 59.303 34.615 19.77 0.00 44.29 2.17
2134 2152 2.672874 TGTGATAATCGCAGAACAGTGC 59.327 45.455 0.00 0.00 43.58 4.40
2143 2161 3.476552 GATTCCCCTTGTGATAATCGCA 58.523 45.455 0.00 0.00 34.72 5.10
2212 2230 2.122783 TGGCGGCTACAGCTATTTTT 57.877 45.000 11.43 0.00 41.70 1.94
2470 2497 2.017049 GCGGCAATTCTGTCTACCAAT 58.983 47.619 0.00 0.00 0.00 3.16
2515 2542 5.513267 GGTTAGTTCTGTTTCTGTCTGGGAT 60.513 44.000 0.00 0.00 0.00 3.85
2541 2568 3.579302 CACTCCCCACCCTTGGCA 61.579 66.667 0.00 0.00 42.35 4.92
2542 2569 2.558380 GATCACTCCCCACCCTTGGC 62.558 65.000 0.00 0.00 42.35 4.52
2543 2570 1.207488 TGATCACTCCCCACCCTTGG 61.207 60.000 0.00 0.00 43.50 3.61
2544 2571 0.035056 GTGATCACTCCCCACCCTTG 60.035 60.000 18.83 0.00 0.00 3.61
2545 2572 0.475632 TGTGATCACTCCCCACCCTT 60.476 55.000 25.55 0.00 0.00 3.95
2546 2573 1.160870 TGTGATCACTCCCCACCCT 59.839 57.895 25.55 0.00 0.00 4.34
2547 2574 1.299976 GTGTGATCACTCCCCACCC 59.700 63.158 25.55 0.00 40.98 4.61
2548 2575 1.299976 GGTGTGATCACTCCCCACC 59.700 63.158 28.95 21.87 43.41 4.61
2553 2580 1.482593 CTAGGTGGGTGTGATCACTCC 59.517 57.143 30.49 30.49 43.84 3.85
2554 2581 2.180276 ACTAGGTGGGTGTGATCACTC 58.820 52.381 25.55 21.49 44.64 3.51
2555 2582 2.327325 ACTAGGTGGGTGTGATCACT 57.673 50.000 25.55 7.05 43.41 3.41
2556 2583 3.418684 AAACTAGGTGGGTGTGATCAC 57.581 47.619 19.27 19.27 43.19 3.06
2557 2584 4.841813 TCTAAAACTAGGTGGGTGTGATCA 59.158 41.667 0.00 0.00 0.00 2.92
2558 2585 5.176592 GTCTAAAACTAGGTGGGTGTGATC 58.823 45.833 0.00 0.00 0.00 2.92
2559 2586 4.595781 TGTCTAAAACTAGGTGGGTGTGAT 59.404 41.667 0.00 0.00 0.00 3.06
2560 2587 3.968649 TGTCTAAAACTAGGTGGGTGTGA 59.031 43.478 0.00 0.00 0.00 3.58
2561 2588 4.062991 GTGTCTAAAACTAGGTGGGTGTG 58.937 47.826 0.00 0.00 0.00 3.82
2562 2589 3.971971 AGTGTCTAAAACTAGGTGGGTGT 59.028 43.478 0.00 0.00 0.00 4.16
2563 2590 4.315803 CAGTGTCTAAAACTAGGTGGGTG 58.684 47.826 0.00 0.00 0.00 4.61
2564 2591 3.326880 CCAGTGTCTAAAACTAGGTGGGT 59.673 47.826 0.00 0.00 0.00 4.51
2565 2592 3.307480 CCCAGTGTCTAAAACTAGGTGGG 60.307 52.174 0.00 0.00 0.00 4.61
2566 2593 3.307480 CCCCAGTGTCTAAAACTAGGTGG 60.307 52.174 0.00 0.00 0.00 4.61
2567 2594 3.868754 GCCCCAGTGTCTAAAACTAGGTG 60.869 52.174 0.00 0.00 0.00 4.00
2568 2595 2.305052 GCCCCAGTGTCTAAAACTAGGT 59.695 50.000 0.00 0.00 0.00 3.08
2569 2596 2.572104 AGCCCCAGTGTCTAAAACTAGG 59.428 50.000 0.00 0.00 0.00 3.02
2570 2597 3.983044 AGCCCCAGTGTCTAAAACTAG 57.017 47.619 0.00 0.00 0.00 2.57
2571 2598 3.773119 CCTAGCCCCAGTGTCTAAAACTA 59.227 47.826 0.00 0.00 0.00 2.24
2572 2599 2.572104 CCTAGCCCCAGTGTCTAAAACT 59.428 50.000 0.00 0.00 0.00 2.66
2573 2600 2.570302 TCCTAGCCCCAGTGTCTAAAAC 59.430 50.000 0.00 0.00 0.00 2.43
2574 2601 2.838202 CTCCTAGCCCCAGTGTCTAAAA 59.162 50.000 0.00 0.00 0.00 1.52
2575 2602 2.043939 TCTCCTAGCCCCAGTGTCTAAA 59.956 50.000 0.00 0.00 0.00 1.85
2576 2603 1.644337 TCTCCTAGCCCCAGTGTCTAA 59.356 52.381 0.00 0.00 0.00 2.10
2577 2604 1.215673 CTCTCCTAGCCCCAGTGTCTA 59.784 57.143 0.00 0.00 0.00 2.59
2578 2605 0.032615 CTCTCCTAGCCCCAGTGTCT 60.033 60.000 0.00 0.00 0.00 3.41
2579 2606 0.324830 ACTCTCCTAGCCCCAGTGTC 60.325 60.000 0.00 0.00 0.00 3.67
2580 2607 0.117340 AACTCTCCTAGCCCCAGTGT 59.883 55.000 0.00 0.00 0.00 3.55
2581 2608 2.160721 TAACTCTCCTAGCCCCAGTG 57.839 55.000 0.00 0.00 0.00 3.66
2582 2609 2.942604 TTAACTCTCCTAGCCCCAGT 57.057 50.000 0.00 0.00 0.00 4.00
2583 2610 3.456277 ACAATTAACTCTCCTAGCCCCAG 59.544 47.826 0.00 0.00 0.00 4.45
2584 2611 3.454812 GACAATTAACTCTCCTAGCCCCA 59.545 47.826 0.00 0.00 0.00 4.96
2585 2612 3.181453 GGACAATTAACTCTCCTAGCCCC 60.181 52.174 0.00 0.00 0.00 5.80
2586 2613 3.712218 AGGACAATTAACTCTCCTAGCCC 59.288 47.826 0.00 0.00 30.91 5.19
2587 2614 6.481434 TTAGGACAATTAACTCTCCTAGCC 57.519 41.667 4.75 0.00 36.85 3.93
2588 2615 8.831550 CATTTTAGGACAATTAACTCTCCTAGC 58.168 37.037 4.75 0.00 36.85 3.42
2589 2616 9.892130 ACATTTTAGGACAATTAACTCTCCTAG 57.108 33.333 4.75 0.00 36.85 3.02
2591 2618 9.588096 AAACATTTTAGGACAATTAACTCTCCT 57.412 29.630 2.94 2.94 36.99 3.69
2600 2627 9.981114 CTCAAACCTAAACATTTTAGGACAATT 57.019 29.630 25.02 13.91 43.24 2.32
2601 2628 9.362151 TCTCAAACCTAAACATTTTAGGACAAT 57.638 29.630 25.02 9.99 43.24 2.71
2602 2629 8.754991 TCTCAAACCTAAACATTTTAGGACAA 57.245 30.769 25.02 10.68 43.24 3.18
2603 2630 8.754991 TTCTCAAACCTAAACATTTTAGGACA 57.245 30.769 25.02 9.32 43.24 4.02
2606 2633 9.423061 CCATTTCTCAAACCTAAACATTTTAGG 57.577 33.333 19.05 19.05 45.41 2.69
2607 2634 9.981114 ACCATTTCTCAAACCTAAACATTTTAG 57.019 29.630 0.00 0.00 0.00 1.85
2608 2635 9.757227 CACCATTTCTCAAACCTAAACATTTTA 57.243 29.630 0.00 0.00 0.00 1.52
2609 2636 7.714813 CCACCATTTCTCAAACCTAAACATTTT 59.285 33.333 0.00 0.00 0.00 1.82
2610 2637 7.216494 CCACCATTTCTCAAACCTAAACATTT 58.784 34.615 0.00 0.00 0.00 2.32
2611 2638 6.741240 GCCACCATTTCTCAAACCTAAACATT 60.741 38.462 0.00 0.00 0.00 2.71
2612 2639 5.279456 GCCACCATTTCTCAAACCTAAACAT 60.279 40.000 0.00 0.00 0.00 2.71
2613 2640 4.038642 GCCACCATTTCTCAAACCTAAACA 59.961 41.667 0.00 0.00 0.00 2.83
2614 2641 4.280929 AGCCACCATTTCTCAAACCTAAAC 59.719 41.667 0.00 0.00 0.00 2.01
2615 2642 4.479158 AGCCACCATTTCTCAAACCTAAA 58.521 39.130 0.00 0.00 0.00 1.85
2616 2643 4.112634 AGCCACCATTTCTCAAACCTAA 57.887 40.909 0.00 0.00 0.00 2.69
2617 2644 3.806949 AGCCACCATTTCTCAAACCTA 57.193 42.857 0.00 0.00 0.00 3.08
2618 2645 2.683211 AGCCACCATTTCTCAAACCT 57.317 45.000 0.00 0.00 0.00 3.50
2619 2646 2.164422 GCTAGCCACCATTTCTCAAACC 59.836 50.000 2.29 0.00 0.00 3.27
2620 2647 2.164422 GGCTAGCCACCATTTCTCAAAC 59.836 50.000 29.33 0.00 35.81 2.93
2621 2648 2.446435 GGCTAGCCACCATTTCTCAAA 58.554 47.619 29.33 0.00 35.81 2.69
2622 2649 1.340991 GGGCTAGCCACCATTTCTCAA 60.341 52.381 34.09 0.00 37.98 3.02
2623 2650 0.255890 GGGCTAGCCACCATTTCTCA 59.744 55.000 34.09 0.00 37.98 3.27
2624 2651 0.255890 TGGGCTAGCCACCATTTCTC 59.744 55.000 34.09 14.43 37.98 2.87
2625 2652 0.257039 CTGGGCTAGCCACCATTTCT 59.743 55.000 34.09 0.00 35.93 2.52
2626 2653 2.799176 CTGGGCTAGCCACCATTTC 58.201 57.895 34.09 15.90 35.93 2.17
2641 2668 0.747283 GCTGAGAGAACCCATGCTGG 60.747 60.000 0.00 0.00 37.25 4.85
2642 2669 0.252479 AGCTGAGAGAACCCATGCTG 59.748 55.000 0.00 0.00 0.00 4.41
2643 2670 0.990374 AAGCTGAGAGAACCCATGCT 59.010 50.000 0.00 0.00 0.00 3.79
2644 2671 1.093159 CAAGCTGAGAGAACCCATGC 58.907 55.000 0.00 0.00 0.00 4.06
2645 2672 2.486472 ACAAGCTGAGAGAACCCATG 57.514 50.000 0.00 0.00 0.00 3.66
2646 2673 2.373169 TGAACAAGCTGAGAGAACCCAT 59.627 45.455 0.00 0.00 0.00 4.00
2647 2674 1.768275 TGAACAAGCTGAGAGAACCCA 59.232 47.619 0.00 0.00 0.00 4.51
2648 2675 2.550830 TGAACAAGCTGAGAGAACCC 57.449 50.000 0.00 0.00 0.00 4.11
2649 2676 3.668447 TCATGAACAAGCTGAGAGAACC 58.332 45.455 0.00 0.00 0.00 3.62
2650 2677 4.694509 ACATCATGAACAAGCTGAGAGAAC 59.305 41.667 0.00 0.00 0.00 3.01
2651 2678 4.694037 CACATCATGAACAAGCTGAGAGAA 59.306 41.667 0.00 0.00 0.00 2.87
2652 2679 4.251268 CACATCATGAACAAGCTGAGAGA 58.749 43.478 0.00 0.00 0.00 3.10
2653 2680 4.001652 ACACATCATGAACAAGCTGAGAG 58.998 43.478 0.00 0.00 0.00 3.20
2654 2681 3.749609 CACACATCATGAACAAGCTGAGA 59.250 43.478 0.00 0.00 0.00 3.27
2655 2682 3.119955 CCACACATCATGAACAAGCTGAG 60.120 47.826 0.00 0.00 0.00 3.35
2656 2683 2.815503 CCACACATCATGAACAAGCTGA 59.184 45.455 0.00 0.00 0.00 4.26
2657 2684 2.815503 TCCACACATCATGAACAAGCTG 59.184 45.455 0.00 0.00 0.00 4.24
2658 2685 2.816087 GTCCACACATCATGAACAAGCT 59.184 45.455 0.00 0.00 0.00 3.74
2659 2686 2.816087 AGTCCACACATCATGAACAAGC 59.184 45.455 0.00 0.00 0.00 4.01
2660 2687 4.633126 CCTAGTCCACACATCATGAACAAG 59.367 45.833 0.00 0.00 0.00 3.16
2661 2688 4.578871 CCTAGTCCACACATCATGAACAA 58.421 43.478 0.00 0.00 0.00 2.83
2662 2689 3.619733 GCCTAGTCCACACATCATGAACA 60.620 47.826 0.00 0.00 0.00 3.18
2663 2690 2.939103 GCCTAGTCCACACATCATGAAC 59.061 50.000 0.00 0.00 0.00 3.18
2664 2691 2.571202 TGCCTAGTCCACACATCATGAA 59.429 45.455 0.00 0.00 0.00 2.57
2665 2692 2.187100 TGCCTAGTCCACACATCATGA 58.813 47.619 0.00 0.00 0.00 3.07
2666 2693 2.696989 TGCCTAGTCCACACATCATG 57.303 50.000 0.00 0.00 0.00 3.07
2667 2694 2.158711 CCATGCCTAGTCCACACATCAT 60.159 50.000 0.00 0.00 0.00 2.45
2668 2695 1.210234 CCATGCCTAGTCCACACATCA 59.790 52.381 0.00 0.00 0.00 3.07
2669 2696 1.210478 ACCATGCCTAGTCCACACATC 59.790 52.381 0.00 0.00 0.00 3.06
2670 2697 1.065199 CACCATGCCTAGTCCACACAT 60.065 52.381 0.00 0.00 0.00 3.21
2671 2698 0.324614 CACCATGCCTAGTCCACACA 59.675 55.000 0.00 0.00 0.00 3.72
2672 2699 0.613260 TCACCATGCCTAGTCCACAC 59.387 55.000 0.00 0.00 0.00 3.82
2673 2700 1.210234 CATCACCATGCCTAGTCCACA 59.790 52.381 0.00 0.00 0.00 4.17
2674 2701 1.959042 CATCACCATGCCTAGTCCAC 58.041 55.000 0.00 0.00 0.00 4.02
2684 2711 3.834489 AGAAGACCTAGCATCACCATG 57.166 47.619 0.00 0.00 0.00 3.66
2685 2712 5.604231 TCAATAGAAGACCTAGCATCACCAT 59.396 40.000 0.00 0.00 0.00 3.55
2686 2713 4.962362 TCAATAGAAGACCTAGCATCACCA 59.038 41.667 0.00 0.00 0.00 4.17
2687 2714 5.303078 TCTCAATAGAAGACCTAGCATCACC 59.697 44.000 0.00 0.00 0.00 4.02
2688 2715 6.398234 TCTCAATAGAAGACCTAGCATCAC 57.602 41.667 0.00 0.00 0.00 3.06
2689 2716 6.609212 AGTTCTCAATAGAAGACCTAGCATCA 59.391 38.462 0.00 0.00 42.40 3.07
2690 2717 6.922957 CAGTTCTCAATAGAAGACCTAGCATC 59.077 42.308 0.00 0.00 42.40 3.91
2691 2718 6.183360 CCAGTTCTCAATAGAAGACCTAGCAT 60.183 42.308 0.00 0.00 42.40 3.79
2692 2719 5.127845 CCAGTTCTCAATAGAAGACCTAGCA 59.872 44.000 0.00 0.00 42.40 3.49
2693 2720 5.361285 TCCAGTTCTCAATAGAAGACCTAGC 59.639 44.000 0.00 0.00 42.40 3.42
2694 2721 7.069331 ACATCCAGTTCTCAATAGAAGACCTAG 59.931 40.741 0.00 0.00 42.40 3.02
2695 2722 6.897966 ACATCCAGTTCTCAATAGAAGACCTA 59.102 38.462 0.00 0.00 42.40 3.08
2696 2723 5.723887 ACATCCAGTTCTCAATAGAAGACCT 59.276 40.000 0.00 0.00 42.40 3.85
2697 2724 5.814705 CACATCCAGTTCTCAATAGAAGACC 59.185 44.000 0.00 0.00 42.40 3.85
2698 2725 5.293079 GCACATCCAGTTCTCAATAGAAGAC 59.707 44.000 0.00 0.00 42.40 3.01
2699 2726 5.046376 TGCACATCCAGTTCTCAATAGAAGA 60.046 40.000 0.00 0.00 42.40 2.87
2700 2727 5.181009 TGCACATCCAGTTCTCAATAGAAG 58.819 41.667 0.00 0.00 42.40 2.85
2701 2728 5.164620 TGCACATCCAGTTCTCAATAGAA 57.835 39.130 0.00 0.00 39.47 2.10
2702 2729 4.824479 TGCACATCCAGTTCTCAATAGA 57.176 40.909 0.00 0.00 0.00 1.98
2703 2730 5.885230 TTTGCACATCCAGTTCTCAATAG 57.115 39.130 0.00 0.00 0.00 1.73
2704 2731 5.048083 GGTTTTGCACATCCAGTTCTCAATA 60.048 40.000 0.00 0.00 0.00 1.90
2705 2732 4.262164 GGTTTTGCACATCCAGTTCTCAAT 60.262 41.667 0.00 0.00 0.00 2.57
2706 2733 3.068024 GGTTTTGCACATCCAGTTCTCAA 59.932 43.478 0.00 0.00 0.00 3.02
2707 2734 2.622942 GGTTTTGCACATCCAGTTCTCA 59.377 45.455 0.00 0.00 0.00 3.27
2708 2735 2.622942 TGGTTTTGCACATCCAGTTCTC 59.377 45.455 0.00 0.00 0.00 2.87
2709 2736 2.624838 CTGGTTTTGCACATCCAGTTCT 59.375 45.455 18.17 0.00 41.51 3.01
2710 2737 2.622942 TCTGGTTTTGCACATCCAGTTC 59.377 45.455 23.13 0.00 45.18 3.01
2711 2738 2.624838 CTCTGGTTTTGCACATCCAGTT 59.375 45.455 23.13 0.00 45.18 3.16
2712 2739 2.233271 CTCTGGTTTTGCACATCCAGT 58.767 47.619 23.13 0.00 45.18 4.00
2713 2740 2.227388 GACTCTGGTTTTGCACATCCAG 59.773 50.000 19.74 19.74 46.00 3.86
2714 2741 2.158623 AGACTCTGGTTTTGCACATCCA 60.159 45.455 2.76 2.76 0.00 3.41
2715 2742 2.508526 AGACTCTGGTTTTGCACATCC 58.491 47.619 0.00 0.00 0.00 3.51
2716 2743 3.565482 TCAAGACTCTGGTTTTGCACATC 59.435 43.478 0.00 0.00 37.43 3.06
2717 2744 3.554934 TCAAGACTCTGGTTTTGCACAT 58.445 40.909 0.00 0.00 37.43 3.21
2718 2745 2.997980 TCAAGACTCTGGTTTTGCACA 58.002 42.857 0.00 0.00 37.43 4.57
2719 2746 3.627577 TCTTCAAGACTCTGGTTTTGCAC 59.372 43.478 0.00 0.00 37.43 4.57
2720 2747 3.884895 TCTTCAAGACTCTGGTTTTGCA 58.115 40.909 0.00 0.00 37.43 4.08
2721 2748 4.900635 TTCTTCAAGACTCTGGTTTTGC 57.099 40.909 0.00 0.00 37.43 3.68
2722 2749 7.483307 TGATTTTCTTCAAGACTCTGGTTTTG 58.517 34.615 0.00 0.00 38.43 2.44
2723 2750 7.645058 TGATTTTCTTCAAGACTCTGGTTTT 57.355 32.000 0.00 0.00 0.00 2.43
2724 2751 7.830099 ATGATTTTCTTCAAGACTCTGGTTT 57.170 32.000 0.00 0.00 0.00 3.27
2725 2752 7.830099 AATGATTTTCTTCAAGACTCTGGTT 57.170 32.000 0.00 0.00 0.00 3.67
2726 2753 8.924511 TTAATGATTTTCTTCAAGACTCTGGT 57.075 30.769 0.00 0.00 0.00 4.00
2727 2754 9.837525 CTTTAATGATTTTCTTCAAGACTCTGG 57.162 33.333 0.00 0.00 0.00 3.86
2728 2755 9.837525 CCTTTAATGATTTTCTTCAAGACTCTG 57.162 33.333 0.00 0.00 0.00 3.35
2729 2756 9.579932 ACCTTTAATGATTTTCTTCAAGACTCT 57.420 29.630 0.00 0.00 0.00 3.24
2731 2758 9.971922 CAACCTTTAATGATTTTCTTCAAGACT 57.028 29.630 0.00 0.00 0.00 3.24
2732 2759 9.196552 CCAACCTTTAATGATTTTCTTCAAGAC 57.803 33.333 0.00 0.00 0.00 3.01
2733 2760 9.142014 TCCAACCTTTAATGATTTTCTTCAAGA 57.858 29.630 0.00 0.00 0.00 3.02
2734 2761 9.415544 CTCCAACCTTTAATGATTTTCTTCAAG 57.584 33.333 0.00 0.00 0.00 3.02
2735 2762 8.923270 ACTCCAACCTTTAATGATTTTCTTCAA 58.077 29.630 0.00 0.00 0.00 2.69
2736 2763 8.477419 ACTCCAACCTTTAATGATTTTCTTCA 57.523 30.769 0.00 0.00 0.00 3.02
2749 2776 9.623000 GCCTCTAAATTAATACTCCAACCTTTA 57.377 33.333 0.00 0.00 0.00 1.85
2750 2777 8.336987 AGCCTCTAAATTAATACTCCAACCTTT 58.663 33.333 0.00 0.00 0.00 3.11
2751 2778 7.775561 CAGCCTCTAAATTAATACTCCAACCTT 59.224 37.037 0.00 0.00 0.00 3.50
2752 2779 7.283329 CAGCCTCTAAATTAATACTCCAACCT 58.717 38.462 0.00 0.00 0.00 3.50
2753 2780 6.017026 GCAGCCTCTAAATTAATACTCCAACC 60.017 42.308 0.00 0.00 0.00 3.77
2754 2781 6.017026 GGCAGCCTCTAAATTAATACTCCAAC 60.017 42.308 3.29 0.00 0.00 3.77
2755 2782 6.062095 GGCAGCCTCTAAATTAATACTCCAA 58.938 40.000 3.29 0.00 0.00 3.53
2756 2783 5.131977 TGGCAGCCTCTAAATTAATACTCCA 59.868 40.000 14.15 0.00 0.00 3.86
2757 2784 5.621193 TGGCAGCCTCTAAATTAATACTCC 58.379 41.667 14.15 0.00 0.00 3.85
2758 2785 6.936900 TCATGGCAGCCTCTAAATTAATACTC 59.063 38.462 14.15 0.00 0.00 2.59
2759 2786 6.841601 TCATGGCAGCCTCTAAATTAATACT 58.158 36.000 14.15 0.00 0.00 2.12
2760 2787 7.445402 TCTTCATGGCAGCCTCTAAATTAATAC 59.555 37.037 14.15 0.00 0.00 1.89
2761 2788 7.517320 TCTTCATGGCAGCCTCTAAATTAATA 58.483 34.615 14.15 0.00 0.00 0.98
2762 2789 6.367983 TCTTCATGGCAGCCTCTAAATTAAT 58.632 36.000 14.15 0.00 0.00 1.40
2763 2790 5.754782 TCTTCATGGCAGCCTCTAAATTAA 58.245 37.500 14.15 0.00 0.00 1.40
2764 2791 5.372343 TCTTCATGGCAGCCTCTAAATTA 57.628 39.130 14.15 0.00 0.00 1.40
2765 2792 4.240881 TCTTCATGGCAGCCTCTAAATT 57.759 40.909 14.15 0.00 0.00 1.82
2766 2793 3.939740 TCTTCATGGCAGCCTCTAAAT 57.060 42.857 14.15 0.00 0.00 1.40
2767 2794 3.719268 TTCTTCATGGCAGCCTCTAAA 57.281 42.857 14.15 1.07 0.00 1.85
2768 2795 3.719268 TTTCTTCATGGCAGCCTCTAA 57.281 42.857 14.15 2.90 0.00 2.10
2769 2796 3.719268 TTTTCTTCATGGCAGCCTCTA 57.281 42.857 14.15 0.00 0.00 2.43
2770 2797 2.592102 TTTTCTTCATGGCAGCCTCT 57.408 45.000 14.15 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.