Multiple sequence alignment - TraesCS3A01G377100

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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 TraesCS3A01G377100 chr3A 100.000 2776 0 0 1 2776 626072342 626075117 0.000000e+00 5127.0
1 TraesCS3A01G377100 chr3D 93.522 1837 75 17 1 1817 483350998 483352810 0.000000e+00 2693.0
2 TraesCS3A01G377100 chr3D 77.273 242 23 14 2083 2300 483352937 483353170 2.260000e-21 113.0
3 TraesCS3A01G377100 chr3B 92.195 1435 62 20 870 2292 646287837 646289233 0.000000e+00 1984.0
4 TraesCS3A01G377100 chr3B 92.823 418 22 4 1 417 646287060 646287470 1.420000e-167 599.0
5 TraesCS3A01G377100 chr3B 92.377 223 14 3 2556 2775 646338075 646338297 5.770000e-82 315.0
6 TraesCS3A01G377100 chr3B 89.873 237 17 2 405 641 646287402 646287631 5.810000e-77 298.0
7 TraesCS3A01G377100 chr3B 95.302 149 7 0 2278 2426 646290391 646290539 1.290000e-58 237.0
8 TraesCS3A01G377100 chr3B 90.728 151 13 1 655 804 646287678 646287828 1.690000e-47 200.0
9 TraesCS3A01G377100 chr3B 96.875 96 3 0 2424 2519 646337870 646337965 7.960000e-36 161.0
10 TraesCS3A01G377100 chr3B 97.959 49 1 0 2508 2556 646337980 646338028 4.930000e-13 86.1


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 TraesCS3A01G377100 chr3A 626072342 626075117 2775 False 5127.0 5127 100.0000 1 2776 1 chr3A.!!$F1 2775
1 TraesCS3A01G377100 chr3D 483350998 483353170 2172 False 1403.0 2693 85.3975 1 2300 2 chr3D.!!$F1 2299
2 TraesCS3A01G377100 chr3B 646287060 646290539 3479 False 663.6 1984 92.1842 1 2426 5 chr3B.!!$F1 2425

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
196 197 0.036732 TGCAGGATTATGATCGGGGC 59.963 55.0 0.0 0.0 32.84 5.8 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1830 1871 1.063912 CGACAACAGAGCTGCAACAAA 59.936 47.619 1.02 0.0 0.0 2.83 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
193 194 3.667360 TGACATGCAGGATTATGATCGG 58.333 45.455 4.84 0.00 32.84 4.18
195 196 2.290514 ACATGCAGGATTATGATCGGGG 60.291 50.000 4.84 0.00 32.84 5.73
196 197 0.036732 TGCAGGATTATGATCGGGGC 59.963 55.000 0.00 0.00 32.84 5.80
205 206 6.782494 AGGATTATGATCGGGGCTTTTAAAAT 59.218 34.615 0.09 0.00 32.84 1.82
208 209 9.974980 GATTATGATCGGGGCTTTTAAAATTTA 57.025 29.630 0.09 0.00 0.00 1.40
209 210 9.981114 ATTATGATCGGGGCTTTTAAAATTTAG 57.019 29.630 0.09 0.00 0.00 1.85
211 212 7.654022 TGATCGGGGCTTTTAAAATTTAGAT 57.346 32.000 0.09 3.91 0.00 1.98
253 254 3.508840 GCGGTCTGGCAAATCCCG 61.509 66.667 8.81 8.81 41.50 5.14
254 255 3.508840 CGGTCTGGCAAATCCCGC 61.509 66.667 0.00 0.00 0.00 6.13
297 298 2.125106 GCTACCCCTCTTGGCACG 60.125 66.667 0.00 0.00 0.00 5.34
352 353 0.394938 ACTGTCGGCATGTTGTGGTA 59.605 50.000 0.00 0.00 0.00 3.25
365 366 7.445402 GGCATGTTGTGGTATTGTATCTATCTT 59.555 37.037 0.00 0.00 0.00 2.40
455 456 5.874810 GTGGACATAAACTAGATGCACTGAA 59.125 40.000 0.00 0.00 0.00 3.02
456 457 6.036517 GTGGACATAAACTAGATGCACTGAAG 59.963 42.308 0.00 0.00 0.00 3.02
457 458 5.007136 GGACATAAACTAGATGCACTGAAGC 59.993 44.000 0.00 0.00 0.00 3.86
481 482 4.708421 AGAAGCATAGTGGTTTGCATCAAT 59.292 37.500 0.00 0.00 38.31 2.57
496 497 4.022068 TGCATCAATTTGAACCCTGAGAAC 60.022 41.667 2.68 0.00 0.00 3.01
518 519 3.791353 CGTTTGAGAACTTGTGCTTTTCC 59.209 43.478 0.00 0.00 33.51 3.13
557 558 1.875963 GCACTTGCGCCACACTAAT 59.124 52.632 4.18 0.00 0.00 1.73
560 561 1.739466 CACTTGCGCCACACTAATCAT 59.261 47.619 4.18 0.00 0.00 2.45
593 594 2.009774 CGAAAGGTGCCCTACTTGATG 58.990 52.381 0.00 0.00 31.13 3.07
604 605 4.385310 GCCCTACTTGATGGTACCTGAAAT 60.385 45.833 14.36 0.00 0.00 2.17
643 644 4.575973 GGCCGATGCTCCCATGCT 62.576 66.667 0.00 0.00 37.74 3.79
645 646 2.281345 CCGATGCTCCCATGCTCC 60.281 66.667 0.00 0.00 0.00 4.70
646 647 2.281345 CGATGCTCCCATGCTCCC 60.281 66.667 0.00 0.00 0.00 4.30
648 649 1.527844 GATGCTCCCATGCTCCCAC 60.528 63.158 0.00 0.00 0.00 4.61
649 650 3.411114 ATGCTCCCATGCTCCCACG 62.411 63.158 0.00 0.00 0.00 4.94
663 697 0.039978 CCCACGCGAGATACTAGCTG 60.040 60.000 15.93 0.00 30.11 4.24
667 701 0.661780 CGCGAGATACTAGCTGTGCC 60.662 60.000 0.00 0.00 30.11 5.01
1083 1118 4.789697 AGTAGAGGTTGCTACGATGGACG 61.790 52.174 0.00 0.00 44.21 4.79
1359 1394 3.554342 CCGATGGCCTGGAGAGGG 61.554 72.222 3.32 0.00 40.19 4.30
1456 1491 2.728817 GATGGAGTACTCGGCGGG 59.271 66.667 16.56 4.58 0.00 6.13
1714 1749 3.215975 AGACGATCTAGACAACCTAGCC 58.784 50.000 0.00 0.00 43.60 3.93
1739 1774 4.190304 TGTGTGTGAAAAATCGTTCGAG 57.810 40.909 0.80 0.00 0.00 4.04
1768 1809 3.655276 ACAGTACTAGTGAAACGGTGG 57.345 47.619 5.39 0.00 45.86 4.61
1769 1810 2.298163 ACAGTACTAGTGAAACGGTGGG 59.702 50.000 5.39 0.00 45.86 4.61
1770 1811 2.559668 CAGTACTAGTGAAACGGTGGGA 59.440 50.000 5.39 0.00 45.86 4.37
1884 1925 2.548057 TGGTCGTGATCTTTCTTGTTGC 59.452 45.455 0.00 0.00 0.00 4.17
1889 1935 6.188175 GTCGTGATCTTTCTTGTTGCATATC 58.812 40.000 0.00 0.00 0.00 1.63
1925 1971 1.005394 GTGACCCGTGTCCGAATGT 60.005 57.895 0.00 0.00 41.01 2.71
1959 2005 0.107643 TGCGAGTGAAACCACATGGA 59.892 50.000 4.53 0.00 37.80 3.41
1982 2028 8.986847 TGGATAAACTTTTGTGCAATTTATGTG 58.013 29.630 0.00 0.00 27.72 3.21
2009 2055 1.201647 ACACGGTACAATCAGAGACGG 59.798 52.381 0.00 0.00 0.00 4.79
2013 2059 2.099263 CGGTACAATCAGAGACGGTCAT 59.901 50.000 11.27 0.00 0.00 3.06
2017 2063 6.127980 CGGTACAATCAGAGACGGTCATATAT 60.128 42.308 11.27 0.00 0.00 0.86
2019 2065 8.182881 GGTACAATCAGAGACGGTCATATATAC 58.817 40.741 11.27 2.82 0.00 1.47
2020 2066 7.761038 ACAATCAGAGACGGTCATATATACA 57.239 36.000 11.27 0.00 0.00 2.29
2039 2085 4.754372 ACACACATACACTCAAGCAATG 57.246 40.909 0.00 0.00 0.00 2.82
2043 2089 7.102993 ACACACATACACTCAAGCAATGTATA 58.897 34.615 0.00 0.00 37.42 1.47
2044 2090 7.770433 ACACACATACACTCAAGCAATGTATAT 59.230 33.333 0.00 0.00 37.42 0.86
2320 3562 7.013464 CACCCTATTCTACTCTATCGACAGTTT 59.987 40.741 0.00 0.00 0.00 2.66
2327 3569 7.559486 TCTACTCTATCGACAGTTTACACCTA 58.441 38.462 0.00 0.00 0.00 3.08
2331 3573 6.175471 TCTATCGACAGTTTACACCTACTCA 58.825 40.000 0.00 0.00 0.00 3.41
2375 3617 1.284297 CGTTCTCACACATGCTCGCA 61.284 55.000 0.00 0.00 0.00 5.10
2390 3632 2.480555 GCACGCCTGCATACACAC 59.519 61.111 2.56 0.00 43.62 3.82
2426 3668 5.412904 TGTTCAGAAACATACACACACAACA 59.587 36.000 0.00 0.00 40.45 3.33
2427 3669 5.478233 TCAGAAACATACACACACAACAC 57.522 39.130 0.00 0.00 0.00 3.32
2428 3670 4.938226 TCAGAAACATACACACACAACACA 59.062 37.500 0.00 0.00 0.00 3.72
2429 3671 5.064579 TCAGAAACATACACACACAACACAG 59.935 40.000 0.00 0.00 0.00 3.66
2430 3672 5.064579 CAGAAACATACACACACAACACAGA 59.935 40.000 0.00 0.00 0.00 3.41
2431 3673 4.875544 AACATACACACACAACACAGAC 57.124 40.909 0.00 0.00 0.00 3.51
2432 3674 3.867857 ACATACACACACAACACAGACA 58.132 40.909 0.00 0.00 0.00 3.41
2433 3675 3.621268 ACATACACACACAACACAGACAC 59.379 43.478 0.00 0.00 0.00 3.67
2434 3676 2.177394 ACACACACAACACAGACACA 57.823 45.000 0.00 0.00 0.00 3.72
2435 3677 1.804151 ACACACACAACACAGACACAC 59.196 47.619 0.00 0.00 0.00 3.82
2436 3678 1.130373 CACACACAACACAGACACACC 59.870 52.381 0.00 0.00 0.00 4.16
2437 3679 1.003118 ACACACAACACAGACACACCT 59.997 47.619 0.00 0.00 0.00 4.00
2438 3680 1.665679 CACACAACACAGACACACCTC 59.334 52.381 0.00 0.00 0.00 3.85
2439 3681 1.555075 ACACAACACAGACACACCTCT 59.445 47.619 0.00 0.00 0.00 3.69
2440 3682 2.027192 ACACAACACAGACACACCTCTT 60.027 45.455 0.00 0.00 0.00 2.85
2441 3683 2.609459 CACAACACAGACACACCTCTTC 59.391 50.000 0.00 0.00 0.00 2.87
2442 3684 2.213499 CAACACAGACACACCTCTTCC 58.787 52.381 0.00 0.00 0.00 3.46
2443 3685 0.389391 ACACAGACACACCTCTTCCG 59.611 55.000 0.00 0.00 0.00 4.30
2444 3686 0.389391 CACAGACACACCTCTTCCGT 59.611 55.000 0.00 0.00 0.00 4.69
2445 3687 1.120530 ACAGACACACCTCTTCCGTT 58.879 50.000 0.00 0.00 0.00 4.44
2446 3688 2.035449 CACAGACACACCTCTTCCGTTA 59.965 50.000 0.00 0.00 0.00 3.18
2447 3689 2.696707 ACAGACACACCTCTTCCGTTAA 59.303 45.455 0.00 0.00 0.00 2.01
2448 3690 3.243771 ACAGACACACCTCTTCCGTTAAG 60.244 47.826 0.00 0.00 36.45 1.85
2449 3691 2.299297 AGACACACCTCTTCCGTTAAGG 59.701 50.000 0.00 0.00 42.97 2.69
2450 3692 1.346722 ACACACCTCTTCCGTTAAGGG 59.653 52.381 7.93 7.93 41.52 3.95
2451 3693 1.621814 CACACCTCTTCCGTTAAGGGA 59.378 52.381 12.87 12.87 37.99 4.20
2452 3694 2.236395 CACACCTCTTCCGTTAAGGGAT 59.764 50.000 17.25 0.00 37.99 3.85
2453 3695 2.236395 ACACCTCTTCCGTTAAGGGATG 59.764 50.000 17.25 18.31 37.99 3.51
2454 3696 2.500098 CACCTCTTCCGTTAAGGGATGA 59.500 50.000 23.67 23.67 37.99 2.92
2455 3697 3.055385 CACCTCTTCCGTTAAGGGATGAA 60.055 47.826 24.63 9.65 37.99 2.57
2456 3698 3.055312 ACCTCTTCCGTTAAGGGATGAAC 60.055 47.826 24.63 0.00 37.99 3.18
2457 3699 3.532542 CTCTTCCGTTAAGGGATGAACC 58.467 50.000 24.63 0.00 37.99 3.62
2473 3715 7.211966 GGATGAACCCATGAGAAATCATAAG 57.788 40.000 0.00 0.00 32.09 1.73
2474 3716 6.774656 GGATGAACCCATGAGAAATCATAAGT 59.225 38.462 0.00 0.00 32.09 2.24
2475 3717 7.255381 GGATGAACCCATGAGAAATCATAAGTG 60.255 40.741 0.00 0.00 32.09 3.16
2476 3718 5.357878 TGAACCCATGAGAAATCATAAGTGC 59.642 40.000 0.00 0.00 0.00 4.40
2477 3719 5.121380 ACCCATGAGAAATCATAAGTGCT 57.879 39.130 0.00 0.00 0.00 4.40
2478 3720 4.885907 ACCCATGAGAAATCATAAGTGCTG 59.114 41.667 0.00 0.00 0.00 4.41
2479 3721 4.261489 CCCATGAGAAATCATAAGTGCTGC 60.261 45.833 0.00 0.00 0.00 5.25
2480 3722 4.579340 CCATGAGAAATCATAAGTGCTGCT 59.421 41.667 0.00 0.00 0.00 4.24
2481 3723 5.761726 CCATGAGAAATCATAAGTGCTGCTA 59.238 40.000 0.00 0.00 0.00 3.49
2482 3724 6.430308 CCATGAGAAATCATAAGTGCTGCTAT 59.570 38.462 0.00 0.00 0.00 2.97
2483 3725 6.856135 TGAGAAATCATAAGTGCTGCTATG 57.144 37.500 0.00 1.08 0.00 2.23
2484 3726 6.351711 TGAGAAATCATAAGTGCTGCTATGT 58.648 36.000 0.00 0.00 0.00 2.29
2485 3727 6.259387 TGAGAAATCATAAGTGCTGCTATGTG 59.741 38.462 0.00 0.00 0.00 3.21
2486 3728 5.530171 AGAAATCATAAGTGCTGCTATGTGG 59.470 40.000 0.00 0.00 0.00 4.17
2487 3729 3.198409 TCATAAGTGCTGCTATGTGGG 57.802 47.619 0.00 0.00 0.00 4.61
2488 3730 2.505407 TCATAAGTGCTGCTATGTGGGT 59.495 45.455 0.00 0.00 0.00 4.51
2489 3731 3.054434 TCATAAGTGCTGCTATGTGGGTT 60.054 43.478 0.00 0.00 0.00 4.11
2490 3732 1.826385 AAGTGCTGCTATGTGGGTTC 58.174 50.000 0.00 0.00 0.00 3.62
2491 3733 0.987294 AGTGCTGCTATGTGGGTTCT 59.013 50.000 0.00 0.00 0.00 3.01
2492 3734 1.352352 AGTGCTGCTATGTGGGTTCTT 59.648 47.619 0.00 0.00 0.00 2.52
2493 3735 1.470098 GTGCTGCTATGTGGGTTCTTG 59.530 52.381 0.00 0.00 0.00 3.02
2494 3736 1.098050 GCTGCTATGTGGGTTCTTGG 58.902 55.000 0.00 0.00 0.00 3.61
2495 3737 1.755179 CTGCTATGTGGGTTCTTGGG 58.245 55.000 0.00 0.00 0.00 4.12
2496 3738 1.281867 CTGCTATGTGGGTTCTTGGGA 59.718 52.381 0.00 0.00 0.00 4.37
2497 3739 1.281867 TGCTATGTGGGTTCTTGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
2498 3740 2.019156 GCTATGTGGGTTCTTGGGAGC 61.019 57.143 0.00 0.00 0.00 4.70
2499 3741 1.281867 CTATGTGGGTTCTTGGGAGCA 59.718 52.381 0.00 0.00 0.00 4.26
2500 3742 0.706433 ATGTGGGTTCTTGGGAGCAT 59.294 50.000 0.00 0.00 0.00 3.79
2501 3743 0.251297 TGTGGGTTCTTGGGAGCATG 60.251 55.000 0.00 0.00 0.00 4.06
2502 3744 0.251341 GTGGGTTCTTGGGAGCATGT 60.251 55.000 0.00 0.00 0.00 3.21
2503 3745 0.038166 TGGGTTCTTGGGAGCATGTC 59.962 55.000 0.00 0.00 0.00 3.06
2504 3746 0.038166 GGGTTCTTGGGAGCATGTCA 59.962 55.000 0.00 0.00 0.00 3.58
2505 3747 1.547675 GGGTTCTTGGGAGCATGTCAA 60.548 52.381 0.00 0.00 0.00 3.18
2506 3748 1.541588 GGTTCTTGGGAGCATGTCAAC 59.458 52.381 0.00 0.00 0.00 3.18
2507 3749 2.229792 GTTCTTGGGAGCATGTCAACA 58.770 47.619 0.00 0.00 0.00 3.33
2508 3750 2.622942 GTTCTTGGGAGCATGTCAACAA 59.377 45.455 0.00 0.66 0.00 2.83
2509 3751 2.942804 TCTTGGGAGCATGTCAACAAA 58.057 42.857 0.00 0.00 0.00 2.83
2510 3752 3.295093 TCTTGGGAGCATGTCAACAAAA 58.705 40.909 0.00 0.00 0.00 2.44
2511 3753 3.318839 TCTTGGGAGCATGTCAACAAAAG 59.681 43.478 0.00 0.00 0.00 2.27
2512 3754 1.962807 TGGGAGCATGTCAACAAAAGG 59.037 47.619 0.00 0.00 0.00 3.11
2513 3755 1.963515 GGGAGCATGTCAACAAAAGGT 59.036 47.619 0.00 0.00 0.00 3.50
2514 3756 3.153919 GGGAGCATGTCAACAAAAGGTA 58.846 45.455 0.00 0.00 0.00 3.08
2515 3757 3.191371 GGGAGCATGTCAACAAAAGGTAG 59.809 47.826 0.00 0.00 0.00 3.18
2516 3758 3.191371 GGAGCATGTCAACAAAAGGTAGG 59.809 47.826 0.00 0.00 0.00 3.18
2517 3759 3.157087 AGCATGTCAACAAAAGGTAGGG 58.843 45.455 0.00 0.00 0.00 3.53
2518 3760 2.352715 GCATGTCAACAAAAGGTAGGGC 60.353 50.000 0.00 0.00 0.00 5.19
2519 3761 2.738587 TGTCAACAAAAGGTAGGGCA 57.261 45.000 0.00 0.00 0.00 5.36
2520 3762 3.019799 TGTCAACAAAAGGTAGGGCAA 57.980 42.857 0.00 0.00 0.00 4.52
2521 3763 2.691011 TGTCAACAAAAGGTAGGGCAAC 59.309 45.455 0.00 0.00 0.00 4.17
2533 3775 2.867472 GGCAACCGGACATGTTCG 59.133 61.111 20.02 20.02 0.00 3.95
2538 3780 2.264480 CCGGACATGTTCGGCTCA 59.736 61.111 31.79 0.00 39.78 4.26
2539 3781 2.100631 CCGGACATGTTCGGCTCAC 61.101 63.158 31.79 0.00 39.78 3.51
2540 3782 1.079819 CGGACATGTTCGGCTCACT 60.080 57.895 19.23 0.00 0.00 3.41
2541 3783 1.354337 CGGACATGTTCGGCTCACTG 61.354 60.000 19.23 0.00 0.00 3.66
2542 3784 1.639298 GGACATGTTCGGCTCACTGC 61.639 60.000 0.00 0.00 41.94 4.40
2543 3785 1.959899 GACATGTTCGGCTCACTGCG 61.960 60.000 0.00 0.00 44.05 5.18
2544 3786 1.737735 CATGTTCGGCTCACTGCGA 60.738 57.895 0.00 0.00 44.05 5.10
2545 3787 1.086067 CATGTTCGGCTCACTGCGAT 61.086 55.000 0.00 0.00 44.05 4.58
2546 3788 0.459899 ATGTTCGGCTCACTGCGATA 59.540 50.000 0.00 0.00 44.05 2.92
2547 3789 0.179137 TGTTCGGCTCACTGCGATAG 60.179 55.000 0.00 0.00 44.05 2.08
2548 3790 0.100682 GTTCGGCTCACTGCGATAGA 59.899 55.000 0.00 0.00 44.05 1.98
2549 3791 1.032794 TTCGGCTCACTGCGATAGAT 58.967 50.000 0.00 0.00 44.05 1.98
2550 3792 0.312102 TCGGCTCACTGCGATAGATG 59.688 55.000 0.00 0.00 44.05 2.90
2551 3793 0.665670 CGGCTCACTGCGATAGATGG 60.666 60.000 0.00 0.00 44.05 3.51
2552 3794 0.390860 GGCTCACTGCGATAGATGGT 59.609 55.000 0.00 0.00 44.05 3.55
2553 3795 1.495878 GCTCACTGCGATAGATGGTG 58.504 55.000 0.00 0.00 39.76 4.17
2554 3796 1.202463 GCTCACTGCGATAGATGGTGT 60.202 52.381 0.00 0.00 39.76 4.16
2555 3797 2.034685 GCTCACTGCGATAGATGGTGTA 59.965 50.000 0.00 0.00 39.76 2.90
2556 3798 3.490933 GCTCACTGCGATAGATGGTGTAA 60.491 47.826 0.00 0.00 39.76 2.41
2557 3799 4.294232 CTCACTGCGATAGATGGTGTAAG 58.706 47.826 0.00 0.00 39.76 2.34
2558 3800 3.951680 TCACTGCGATAGATGGTGTAAGA 59.048 43.478 0.00 0.00 39.76 2.10
2559 3801 4.584743 TCACTGCGATAGATGGTGTAAGAT 59.415 41.667 0.00 0.00 39.76 2.40
2560 3802 4.920340 CACTGCGATAGATGGTGTAAGATC 59.080 45.833 0.00 0.00 39.76 2.75
2561 3803 4.830046 ACTGCGATAGATGGTGTAAGATCT 59.170 41.667 0.00 0.00 39.76 2.75
2562 3804 5.303078 ACTGCGATAGATGGTGTAAGATCTT 59.697 40.000 13.56 13.56 39.76 2.40
2563 3805 6.490381 ACTGCGATAGATGGTGTAAGATCTTA 59.510 38.462 11.24 11.24 39.76 2.10
2564 3806 7.014326 ACTGCGATAGATGGTGTAAGATCTTAA 59.986 37.037 16.73 1.92 39.76 1.85
2565 3807 7.371159 TGCGATAGATGGTGTAAGATCTTAAG 58.629 38.462 16.73 0.00 39.76 1.85
2566 3808 7.014326 TGCGATAGATGGTGTAAGATCTTAAGT 59.986 37.037 16.73 1.99 39.76 2.24
2567 3809 7.868415 GCGATAGATGGTGTAAGATCTTAAGTT 59.132 37.037 16.73 1.18 39.76 2.66
2572 3814 9.482175 AGATGGTGTAAGATCTTAAGTTAGACT 57.518 33.333 16.73 8.56 0.00 3.24
2605 3847 9.971922 AGTTTGATCAAGTCTTTCCTTTTTATG 57.028 29.630 8.41 0.00 0.00 1.90
2606 3848 9.196552 GTTTGATCAAGTCTTTCCTTTTTATGG 57.803 33.333 8.41 0.00 0.00 2.74
2607 3849 7.466746 TGATCAAGTCTTTCCTTTTTATGGG 57.533 36.000 0.00 0.00 0.00 4.00
2608 3850 7.010160 TGATCAAGTCTTTCCTTTTTATGGGT 58.990 34.615 0.00 0.00 0.00 4.51
2609 3851 8.167392 TGATCAAGTCTTTCCTTTTTATGGGTA 58.833 33.333 0.00 0.00 0.00 3.69
2610 3852 8.950007 ATCAAGTCTTTCCTTTTTATGGGTAA 57.050 30.769 0.00 0.00 0.00 2.85
2611 3853 8.770010 TCAAGTCTTTCCTTTTTATGGGTAAA 57.230 30.769 0.00 0.00 0.00 2.01
2612 3854 9.203163 TCAAGTCTTTCCTTTTTATGGGTAAAA 57.797 29.630 0.00 0.00 37.86 1.52
2613 3855 9.825109 CAAGTCTTTCCTTTTTATGGGTAAAAA 57.175 29.630 6.09 6.09 43.74 1.94
2640 3882 6.464895 CTTGATCAAGCCGATAGAGAAATC 57.535 41.667 21.96 0.00 33.17 2.17
2641 3883 5.798125 TGATCAAGCCGATAGAGAAATCT 57.202 39.130 0.00 0.00 33.17 2.40
2642 3884 5.536260 TGATCAAGCCGATAGAGAAATCTG 58.464 41.667 0.00 0.00 33.17 2.90
2643 3885 3.722147 TCAAGCCGATAGAGAAATCTGC 58.278 45.455 0.00 0.00 36.63 4.26
2644 3886 3.132824 TCAAGCCGATAGAGAAATCTGCA 59.867 43.478 3.64 0.00 38.24 4.41
2645 3887 3.827008 AGCCGATAGAGAAATCTGCAA 57.173 42.857 3.64 0.00 38.24 4.08
2646 3888 4.142609 AGCCGATAGAGAAATCTGCAAA 57.857 40.909 3.64 0.00 38.24 3.68
2647 3889 4.125703 AGCCGATAGAGAAATCTGCAAAG 58.874 43.478 3.64 0.00 38.24 2.77
2648 3890 3.873952 GCCGATAGAGAAATCTGCAAAGT 59.126 43.478 0.00 0.00 36.46 2.66
2649 3891 4.333926 GCCGATAGAGAAATCTGCAAAGTT 59.666 41.667 0.00 0.00 36.46 2.66
2650 3892 5.503194 GCCGATAGAGAAATCTGCAAAGTTC 60.503 44.000 0.00 0.00 36.46 3.01
2651 3893 5.814705 CCGATAGAGAAATCTGCAAAGTTCT 59.185 40.000 1.69 1.69 39.76 3.01
2652 3894 6.980978 CCGATAGAGAAATCTGCAAAGTTCTA 59.019 38.462 2.16 0.00 39.76 2.10
2653 3895 7.655328 CCGATAGAGAAATCTGCAAAGTTCTAT 59.345 37.037 2.16 2.44 39.76 1.98
2654 3896 8.486383 CGATAGAGAAATCTGCAAAGTTCTATG 58.514 37.037 7.57 0.00 39.76 2.23
2655 3897 9.539825 GATAGAGAAATCTGCAAAGTTCTATGA 57.460 33.333 7.57 0.00 30.56 2.15
2660 3902 9.842775 AGAAATCTGCAAAGTTCTATGATATCA 57.157 29.630 8.10 8.10 0.00 2.15
2675 3917 8.655970 TCTATGATATCAAATATTTGTTCGGCG 58.344 33.333 23.95 0.00 39.18 6.46
2676 3918 6.852858 TGATATCAAATATTTGTTCGGCGA 57.147 33.333 23.95 4.99 39.18 5.54
2677 3919 7.252965 TGATATCAAATATTTGTTCGGCGAA 57.747 32.000 23.95 19.83 39.18 4.70
2678 3920 7.870826 TGATATCAAATATTTGTTCGGCGAAT 58.129 30.769 26.42 12.20 39.18 3.34
2679 3921 8.994170 TGATATCAAATATTTGTTCGGCGAATA 58.006 29.630 26.42 20.80 39.18 1.75
2680 3922 9.820229 GATATCAAATATTTGTTCGGCGAATAA 57.180 29.630 26.42 25.51 37.09 1.40
2684 3926 9.820229 TCAAATATTTGTTCGGCGAATAATATC 57.180 29.630 30.84 19.46 37.09 1.63
2685 3927 9.605955 CAAATATTTGTTCGGCGAATAATATCA 57.394 29.630 30.84 21.18 37.09 2.15
2689 3931 7.906611 TTTGTTCGGCGAATAATATCAAATG 57.093 32.000 27.98 0.00 0.00 2.32
2690 3932 6.612247 TGTTCGGCGAATAATATCAAATGT 57.388 33.333 26.42 0.00 0.00 2.71
2691 3933 7.716768 TGTTCGGCGAATAATATCAAATGTA 57.283 32.000 26.42 0.00 0.00 2.29
2692 3934 8.317891 TGTTCGGCGAATAATATCAAATGTAT 57.682 30.769 26.42 0.00 0.00 2.29
2693 3935 9.425577 TGTTCGGCGAATAATATCAAATGTATA 57.574 29.630 26.42 0.00 0.00 1.47
2726 3968 8.404107 TGACGATATACTTCATACTGAATCCA 57.596 34.615 0.00 0.00 35.59 3.41
2727 3969 8.856103 TGACGATATACTTCATACTGAATCCAA 58.144 33.333 0.00 0.00 35.59 3.53
2728 3970 9.862371 GACGATATACTTCATACTGAATCCAAT 57.138 33.333 0.00 0.00 35.59 3.16
2729 3971 9.645059 ACGATATACTTCATACTGAATCCAATG 57.355 33.333 0.00 0.00 35.59 2.82
2730 3972 9.860898 CGATATACTTCATACTGAATCCAATGA 57.139 33.333 0.00 0.00 35.59 2.57
2734 3976 6.688637 CTTCATACTGAATCCAATGAAGCA 57.311 37.500 12.91 0.00 44.76 3.91
2735 3977 7.092137 CTTCATACTGAATCCAATGAAGCAA 57.908 36.000 12.91 0.00 44.76 3.91
2736 3978 7.465353 TTCATACTGAATCCAATGAAGCAAA 57.535 32.000 0.00 0.00 34.34 3.68
2737 3979 7.649533 TCATACTGAATCCAATGAAGCAAAT 57.350 32.000 0.00 0.00 0.00 2.32
2738 3980 8.070034 TCATACTGAATCCAATGAAGCAAATT 57.930 30.769 0.00 0.00 0.00 1.82
2739 3981 8.533657 TCATACTGAATCCAATGAAGCAAATTT 58.466 29.630 0.00 0.00 0.00 1.82
2740 3982 8.600625 CATACTGAATCCAATGAAGCAAATTTG 58.399 33.333 14.03 14.03 0.00 2.32
2741 3983 5.935789 ACTGAATCCAATGAAGCAAATTTGG 59.064 36.000 19.47 1.22 39.98 3.28
2742 3984 5.867330 TGAATCCAATGAAGCAAATTTGGT 58.133 33.333 16.92 16.92 39.67 3.67
2755 3997 7.759489 AGCAAATTTGGTTTATAGACACTGA 57.241 32.000 16.92 0.00 34.89 3.41
2756 3998 8.353423 AGCAAATTTGGTTTATAGACACTGAT 57.647 30.769 16.92 0.00 34.89 2.90
2757 3999 9.461312 AGCAAATTTGGTTTATAGACACTGATA 57.539 29.630 16.92 0.00 34.89 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 3.778360 TATACGCGGCTGGTTCGGC 62.778 63.158 12.47 0.00 34.56 5.54
118 119 1.961277 CAGCGGGTGACAAGTGGAC 60.961 63.158 0.00 0.00 0.00 4.02
177 178 0.036732 GCCCCGATCATAATCCTGCA 59.963 55.000 0.00 0.00 0.00 4.41
193 194 9.529325 AGCGATTAATCTAAATTTTAAAAGCCC 57.471 29.630 13.45 0.00 30.69 5.19
205 206 7.377766 GCCCATCATTAGCGATTAATCTAAA 57.622 36.000 13.45 5.39 29.37 1.85
253 254 1.730612 CGGAAACTCGAAAAGTAGGGC 59.269 52.381 0.00 0.00 37.17 5.19
254 255 2.028748 TCCGGAAACTCGAAAAGTAGGG 60.029 50.000 0.00 0.00 37.17 3.53
320 321 2.429058 ACAGTGCTGCCTGTCTGG 59.571 61.111 15.15 0.00 41.84 3.86
352 353 9.201989 TCCACAAGTACTCAAGATAGATACAAT 57.798 33.333 0.00 0.00 0.00 2.71
365 366 7.770366 TCTAGTTTATGTCCACAAGTACTCA 57.230 36.000 0.00 0.00 0.00 3.41
414 415 6.605471 TGTCCACAAGTACACAAGATAGAT 57.395 37.500 0.00 0.00 0.00 1.98
455 456 1.815003 GCAAACCACTATGCTTCTGCT 59.185 47.619 0.00 0.00 39.46 4.24
456 457 1.541147 TGCAAACCACTATGCTTCTGC 59.459 47.619 0.00 0.00 42.97 4.26
457 458 3.441222 TGATGCAAACCACTATGCTTCTG 59.559 43.478 12.73 0.00 43.36 3.02
458 459 3.689347 TGATGCAAACCACTATGCTTCT 58.311 40.909 12.73 0.00 43.36 2.85
459 460 4.439305 TTGATGCAAACCACTATGCTTC 57.561 40.909 0.00 6.67 43.29 3.86
460 461 5.410355 AATTGATGCAAACCACTATGCTT 57.590 34.783 0.00 0.00 42.97 3.91
481 482 3.611970 TCAAACGTTCTCAGGGTTCAAA 58.388 40.909 0.00 0.00 0.00 2.69
496 497 3.791353 GGAAAAGCACAAGTTCTCAAACG 59.209 43.478 0.00 0.00 40.48 3.60
518 519 2.225068 ACAGTGTCGTTGTCTCAAGG 57.775 50.000 0.00 0.00 0.00 3.61
557 558 3.130516 CCTTTCGTAGTAGTGCAGGATGA 59.869 47.826 0.00 0.00 39.69 2.92
560 561 2.230508 CACCTTTCGTAGTAGTGCAGGA 59.769 50.000 0.00 0.00 0.00 3.86
593 594 1.692411 GCCCATGGATTTCAGGTACC 58.308 55.000 15.22 2.73 0.00 3.34
643 644 0.179026 AGCTAGTATCTCGCGTGGGA 60.179 55.000 5.77 0.00 0.00 4.37
645 646 0.663688 ACAGCTAGTATCTCGCGTGG 59.336 55.000 5.77 0.01 0.00 4.94
646 647 1.747956 CACAGCTAGTATCTCGCGTG 58.252 55.000 5.77 3.13 0.00 5.34
648 649 0.661780 GGCACAGCTAGTATCTCGCG 60.662 60.000 0.00 0.00 0.00 5.87
649 650 0.671251 AGGCACAGCTAGTATCTCGC 59.329 55.000 0.00 0.00 0.00 5.03
650 651 1.678627 ACAGGCACAGCTAGTATCTCG 59.321 52.381 0.00 0.00 0.00 4.04
667 701 1.503542 GCCACGCCTCAAATCACAG 59.496 57.895 0.00 0.00 0.00 3.66
680 714 0.669318 TAACGCTTTCAGAGGCCACG 60.669 55.000 5.01 0.00 0.00 4.94
693 727 1.602165 CGGTCAGAACACTGTAACGCT 60.602 52.381 0.00 0.00 33.82 5.07
753 788 2.169832 TCCGGAGAAGCTTTTGACTG 57.830 50.000 0.00 0.00 0.00 3.51
1456 1491 4.194720 ACACGGCGAGCTCGATCC 62.195 66.667 38.74 28.21 43.02 3.36
1687 1722 1.584175 TGTCTAGATCGTCTCGAGCC 58.416 55.000 7.81 0.00 43.62 4.70
1739 1774 7.148689 CCGTTTCACTAGTACTGTACAATTTCC 60.149 40.741 19.27 0.84 0.00 3.13
1777 1818 9.734620 GCTGCAAAATTGTTCACTATTCATATA 57.265 29.630 0.00 0.00 0.00 0.86
1825 1866 4.937015 ACAACAGAGCTGCAACAAATTTTT 59.063 33.333 1.02 0.00 0.00 1.94
1826 1867 4.506758 ACAACAGAGCTGCAACAAATTTT 58.493 34.783 1.02 0.00 0.00 1.82
1827 1868 4.114794 GACAACAGAGCTGCAACAAATTT 58.885 39.130 1.02 0.00 0.00 1.82
1830 1871 1.063912 CGACAACAGAGCTGCAACAAA 59.936 47.619 1.02 0.00 0.00 2.83
1884 1925 6.257411 CACTTCTACTGCCTCAACAAGATATG 59.743 42.308 0.00 0.00 0.00 1.78
1889 1935 3.743396 GTCACTTCTACTGCCTCAACAAG 59.257 47.826 0.00 0.00 0.00 3.16
1925 1971 3.616821 CACTCGCAACTTATTTCATCGGA 59.383 43.478 0.00 0.00 0.00 4.55
1988 2034 2.421073 CCGTCTCTGATTGTACCGTGTA 59.579 50.000 0.00 0.00 0.00 2.90
2000 2046 6.059484 TGTGTGTATATATGACCGTCTCTGA 58.941 40.000 0.00 0.00 0.00 3.27
2002 2048 7.664318 TGTATGTGTGTATATATGACCGTCTCT 59.336 37.037 0.00 0.00 0.00 3.10
2009 2055 8.916654 GCTTGAGTGTATGTGTGTATATATGAC 58.083 37.037 0.00 0.00 0.00 3.06
2013 2059 9.260002 CATTGCTTGAGTGTATGTGTGTATATA 57.740 33.333 0.00 0.00 0.00 0.86
2017 2063 5.304778 ACATTGCTTGAGTGTATGTGTGTA 58.695 37.500 0.00 0.00 0.00 2.90
2019 2065 4.754372 ACATTGCTTGAGTGTATGTGTG 57.246 40.909 0.00 0.00 0.00 3.82
2020 2066 8.737168 AATATACATTGCTTGAGTGTATGTGT 57.263 30.769 7.33 0.00 38.92 3.72
2086 2132 8.511321 ACAAGAATGCATAATCGTGTCTAAAAA 58.489 29.630 12.43 0.00 33.92 1.94
2087 2133 8.039603 ACAAGAATGCATAATCGTGTCTAAAA 57.960 30.769 12.43 0.00 33.92 1.52
2088 2134 7.609760 ACAAGAATGCATAATCGTGTCTAAA 57.390 32.000 12.43 0.00 33.92 1.85
2089 2135 7.413988 CCAACAAGAATGCATAATCGTGTCTAA 60.414 37.037 16.82 0.00 37.30 2.10
2090 2136 6.037062 CCAACAAGAATGCATAATCGTGTCTA 59.963 38.462 16.82 0.00 37.30 2.59
2091 2137 5.163723 CCAACAAGAATGCATAATCGTGTCT 60.164 40.000 16.82 4.97 37.30 3.41
2092 2138 5.030295 CCAACAAGAATGCATAATCGTGTC 58.970 41.667 16.82 2.83 37.30 3.67
2093 2139 4.699735 TCCAACAAGAATGCATAATCGTGT 59.300 37.500 12.43 12.43 39.42 4.49
2094 2140 5.030295 GTCCAACAAGAATGCATAATCGTG 58.970 41.667 11.34 11.34 0.00 4.35
2095 2141 4.699735 TGTCCAACAAGAATGCATAATCGT 59.300 37.500 0.00 0.00 0.00 3.73
2096 2142 5.233957 TGTCCAACAAGAATGCATAATCG 57.766 39.130 0.00 0.00 0.00 3.34
2097 2143 5.512788 CGTTGTCCAACAAGAATGCATAATC 59.487 40.000 0.00 0.00 39.00 1.75
2327 3569 2.922162 CCTATGGAGGCACCTGAGT 58.078 57.895 1.84 0.00 39.86 3.41
2350 3592 1.945819 GCATGTGTGAGAACGGGTGAT 60.946 52.381 0.00 0.00 0.00 3.06
2352 3594 0.603707 AGCATGTGTGAGAACGGGTG 60.604 55.000 0.00 0.00 0.00 4.61
2375 3617 1.001520 TGTTAGTGTGTATGCAGGCGT 59.998 47.619 0.00 0.00 0.00 5.68
2390 3632 4.211389 GTTTCTGAACATGCGTGTGTTAG 58.789 43.478 13.39 11.20 42.08 2.34
2426 3668 1.120530 AACGGAAGAGGTGTGTCTGT 58.879 50.000 0.00 0.00 32.17 3.41
2427 3669 3.318017 CTTAACGGAAGAGGTGTGTCTG 58.682 50.000 0.00 0.00 37.33 3.51
2428 3670 2.299297 CCTTAACGGAAGAGGTGTGTCT 59.701 50.000 1.18 0.00 37.33 3.41
2429 3671 2.612221 CCCTTAACGGAAGAGGTGTGTC 60.612 54.545 1.18 0.00 37.33 3.67
2430 3672 1.346722 CCCTTAACGGAAGAGGTGTGT 59.653 52.381 1.18 0.00 37.33 3.72
2431 3673 1.621814 TCCCTTAACGGAAGAGGTGTG 59.378 52.381 1.18 0.00 37.33 3.82
2432 3674 2.019807 TCCCTTAACGGAAGAGGTGT 57.980 50.000 1.18 0.00 37.33 4.16
2433 3675 2.500098 TCATCCCTTAACGGAAGAGGTG 59.500 50.000 0.00 0.00 37.33 4.00
2434 3676 2.829023 TCATCCCTTAACGGAAGAGGT 58.171 47.619 0.00 0.00 37.33 3.85
2435 3677 3.532542 GTTCATCCCTTAACGGAAGAGG 58.467 50.000 0.00 1.91 37.33 3.69
2436 3678 3.532542 GGTTCATCCCTTAACGGAAGAG 58.467 50.000 0.00 0.00 37.33 2.85
2437 3679 3.622166 GGTTCATCCCTTAACGGAAGA 57.378 47.619 0.00 0.00 37.33 2.87
2444 3686 7.587979 ATGATTTCTCATGGGTTCATCCCTTAA 60.588 37.037 4.51 0.00 44.17 1.85
2445 3687 6.126097 ATGATTTCTCATGGGTTCATCCCTTA 60.126 38.462 4.51 0.00 44.17 2.69
2446 3688 5.341454 ATGATTTCTCATGGGTTCATCCCTT 60.341 40.000 4.51 0.00 44.17 3.95
2447 3689 4.169461 ATGATTTCTCATGGGTTCATCCCT 59.831 41.667 4.51 0.00 44.17 4.20
2448 3690 4.477249 ATGATTTCTCATGGGTTCATCCC 58.523 43.478 0.00 0.00 44.14 3.85
2449 3691 6.774656 ACTTATGATTTCTCATGGGTTCATCC 59.225 38.462 10.35 0.00 42.19 3.51
2450 3692 7.646314 CACTTATGATTTCTCATGGGTTCATC 58.354 38.462 10.35 3.91 42.19 2.92
2451 3693 6.040166 GCACTTATGATTTCTCATGGGTTCAT 59.960 38.462 11.35 11.35 42.19 2.57
2452 3694 5.357878 GCACTTATGATTTCTCATGGGTTCA 59.642 40.000 0.00 0.00 42.19 3.18
2453 3695 5.591877 AGCACTTATGATTTCTCATGGGTTC 59.408 40.000 0.00 0.00 42.19 3.62
2454 3696 5.359009 CAGCACTTATGATTTCTCATGGGTT 59.641 40.000 0.00 0.00 42.19 4.11
2455 3697 4.885907 CAGCACTTATGATTTCTCATGGGT 59.114 41.667 0.00 0.00 42.19 4.51
2456 3698 4.261489 GCAGCACTTATGATTTCTCATGGG 60.261 45.833 0.00 0.00 42.19 4.00
2457 3699 4.579340 AGCAGCACTTATGATTTCTCATGG 59.421 41.667 0.00 0.00 42.19 3.66
2458 3700 5.752892 AGCAGCACTTATGATTTCTCATG 57.247 39.130 0.00 0.00 42.19 3.07
2459 3701 6.996879 ACATAGCAGCACTTATGATTTCTCAT 59.003 34.615 7.05 0.00 44.39 2.90
2460 3702 6.259387 CACATAGCAGCACTTATGATTTCTCA 59.741 38.462 7.05 0.00 35.41 3.27
2461 3703 6.293298 CCACATAGCAGCACTTATGATTTCTC 60.293 42.308 7.05 0.00 0.00 2.87
2462 3704 5.530171 CCACATAGCAGCACTTATGATTTCT 59.470 40.000 7.05 0.00 0.00 2.52
2463 3705 5.278169 CCCACATAGCAGCACTTATGATTTC 60.278 44.000 7.05 0.00 0.00 2.17
2464 3706 4.581824 CCCACATAGCAGCACTTATGATTT 59.418 41.667 7.05 0.00 0.00 2.17
2465 3707 4.139786 CCCACATAGCAGCACTTATGATT 58.860 43.478 7.05 0.00 0.00 2.57
2466 3708 3.137176 ACCCACATAGCAGCACTTATGAT 59.863 43.478 7.05 0.00 0.00 2.45
2467 3709 2.505407 ACCCACATAGCAGCACTTATGA 59.495 45.455 7.05 0.00 0.00 2.15
2468 3710 2.923121 ACCCACATAGCAGCACTTATG 58.077 47.619 0.00 0.00 0.00 1.90
2469 3711 3.200825 AGAACCCACATAGCAGCACTTAT 59.799 43.478 0.00 0.00 0.00 1.73
2470 3712 2.571653 AGAACCCACATAGCAGCACTTA 59.428 45.455 0.00 0.00 0.00 2.24
2471 3713 1.352352 AGAACCCACATAGCAGCACTT 59.648 47.619 0.00 0.00 0.00 3.16
2472 3714 0.987294 AGAACCCACATAGCAGCACT 59.013 50.000 0.00 0.00 0.00 4.40
2473 3715 1.470098 CAAGAACCCACATAGCAGCAC 59.530 52.381 0.00 0.00 0.00 4.40
2474 3716 1.614051 CCAAGAACCCACATAGCAGCA 60.614 52.381 0.00 0.00 0.00 4.41
2475 3717 1.098050 CCAAGAACCCACATAGCAGC 58.902 55.000 0.00 0.00 0.00 5.25
2476 3718 1.281867 TCCCAAGAACCCACATAGCAG 59.718 52.381 0.00 0.00 0.00 4.24
2477 3719 1.281867 CTCCCAAGAACCCACATAGCA 59.718 52.381 0.00 0.00 0.00 3.49
2478 3720 2.019156 GCTCCCAAGAACCCACATAGC 61.019 57.143 0.00 0.00 0.00 2.97
2479 3721 1.281867 TGCTCCCAAGAACCCACATAG 59.718 52.381 0.00 0.00 0.00 2.23
2480 3722 1.367346 TGCTCCCAAGAACCCACATA 58.633 50.000 0.00 0.00 0.00 2.29
2481 3723 0.706433 ATGCTCCCAAGAACCCACAT 59.294 50.000 0.00 0.00 0.00 3.21
2482 3724 0.251297 CATGCTCCCAAGAACCCACA 60.251 55.000 0.00 0.00 0.00 4.17
2483 3725 0.251341 ACATGCTCCCAAGAACCCAC 60.251 55.000 0.00 0.00 0.00 4.61
2484 3726 0.038166 GACATGCTCCCAAGAACCCA 59.962 55.000 0.00 0.00 0.00 4.51
2485 3727 0.038166 TGACATGCTCCCAAGAACCC 59.962 55.000 0.00 0.00 0.00 4.11
2486 3728 1.541588 GTTGACATGCTCCCAAGAACC 59.458 52.381 0.00 0.00 0.00 3.62
2487 3729 2.229792 TGTTGACATGCTCCCAAGAAC 58.770 47.619 0.00 0.00 0.00 3.01
2488 3730 2.655090 TGTTGACATGCTCCCAAGAA 57.345 45.000 0.00 0.00 0.00 2.52
2489 3731 2.655090 TTGTTGACATGCTCCCAAGA 57.345 45.000 0.00 0.00 0.00 3.02
2490 3732 3.553508 CCTTTTGTTGACATGCTCCCAAG 60.554 47.826 0.00 0.00 0.00 3.61
2491 3733 2.364970 CCTTTTGTTGACATGCTCCCAA 59.635 45.455 0.00 0.00 0.00 4.12
2492 3734 1.962807 CCTTTTGTTGACATGCTCCCA 59.037 47.619 0.00 0.00 0.00 4.37
2493 3735 1.963515 ACCTTTTGTTGACATGCTCCC 59.036 47.619 0.00 0.00 0.00 4.30
2494 3736 3.191371 CCTACCTTTTGTTGACATGCTCC 59.809 47.826 0.00 0.00 0.00 4.70
2495 3737 3.191371 CCCTACCTTTTGTTGACATGCTC 59.809 47.826 0.00 0.00 0.00 4.26
2496 3738 3.157087 CCCTACCTTTTGTTGACATGCT 58.843 45.455 0.00 0.00 0.00 3.79
2497 3739 2.352715 GCCCTACCTTTTGTTGACATGC 60.353 50.000 0.00 0.00 0.00 4.06
2498 3740 2.890311 TGCCCTACCTTTTGTTGACATG 59.110 45.455 0.00 0.00 0.00 3.21
2499 3741 3.237268 TGCCCTACCTTTTGTTGACAT 57.763 42.857 0.00 0.00 0.00 3.06
2500 3742 2.691011 GTTGCCCTACCTTTTGTTGACA 59.309 45.455 0.00 0.00 0.00 3.58
2501 3743 2.035449 GGTTGCCCTACCTTTTGTTGAC 59.965 50.000 0.00 0.00 35.23 3.18
2502 3744 2.312390 GGTTGCCCTACCTTTTGTTGA 58.688 47.619 0.00 0.00 35.23 3.18
2503 3745 1.000717 CGGTTGCCCTACCTTTTGTTG 60.001 52.381 0.00 0.00 35.97 3.33
2504 3746 1.324383 CGGTTGCCCTACCTTTTGTT 58.676 50.000 0.00 0.00 35.97 2.83
2505 3747 0.538746 CCGGTTGCCCTACCTTTTGT 60.539 55.000 0.00 0.00 35.97 2.83
2506 3748 0.250989 TCCGGTTGCCCTACCTTTTG 60.251 55.000 0.00 0.00 35.97 2.44
2507 3749 0.251033 GTCCGGTTGCCCTACCTTTT 60.251 55.000 0.00 0.00 35.97 2.27
2508 3750 1.377612 GTCCGGTTGCCCTACCTTT 59.622 57.895 0.00 0.00 35.97 3.11
2509 3751 1.205460 ATGTCCGGTTGCCCTACCTT 61.205 55.000 0.00 0.00 35.97 3.50
2510 3752 1.615424 ATGTCCGGTTGCCCTACCT 60.615 57.895 0.00 0.00 35.97 3.08
2511 3753 1.451387 CATGTCCGGTTGCCCTACC 60.451 63.158 0.00 0.00 34.72 3.18
2512 3754 0.322187 AACATGTCCGGTTGCCCTAC 60.322 55.000 0.00 0.00 0.00 3.18
2513 3755 0.035820 GAACATGTCCGGTTGCCCTA 60.036 55.000 0.00 0.00 0.00 3.53
2514 3756 1.303317 GAACATGTCCGGTTGCCCT 60.303 57.895 0.00 0.00 0.00 5.19
2515 3757 2.686816 CGAACATGTCCGGTTGCCC 61.687 63.158 0.00 0.00 0.00 5.36
2516 3758 2.686816 CCGAACATGTCCGGTTGCC 61.687 63.158 16.37 0.00 40.78 4.52
2517 3759 2.867472 CCGAACATGTCCGGTTGC 59.133 61.111 16.37 0.00 40.78 4.17
2518 3760 1.635663 GAGCCGAACATGTCCGGTTG 61.636 60.000 25.12 0.00 46.84 3.77
2519 3761 1.375523 GAGCCGAACATGTCCGGTT 60.376 57.895 25.12 19.93 46.84 4.44
2520 3762 2.264794 GAGCCGAACATGTCCGGT 59.735 61.111 25.12 11.69 46.84 5.28
2522 3764 1.079819 AGTGAGCCGAACATGTCCG 60.080 57.895 0.00 0.00 0.00 4.79
2523 3765 1.639298 GCAGTGAGCCGAACATGTCC 61.639 60.000 0.00 0.00 37.23 4.02
2524 3766 1.790387 GCAGTGAGCCGAACATGTC 59.210 57.895 0.00 0.00 37.23 3.06
2525 3767 2.029288 CGCAGTGAGCCGAACATGT 61.029 57.895 0.00 0.00 41.38 3.21
2526 3768 1.086067 ATCGCAGTGAGCCGAACATG 61.086 55.000 0.00 0.00 41.38 3.21
2527 3769 0.459899 TATCGCAGTGAGCCGAACAT 59.540 50.000 0.00 0.00 41.38 2.71
2528 3770 0.179137 CTATCGCAGTGAGCCGAACA 60.179 55.000 0.00 0.00 41.38 3.18
2529 3771 0.100682 TCTATCGCAGTGAGCCGAAC 59.899 55.000 0.00 0.00 41.38 3.95
2530 3772 1.032794 ATCTATCGCAGTGAGCCGAA 58.967 50.000 0.00 0.00 41.38 4.30
2531 3773 0.312102 CATCTATCGCAGTGAGCCGA 59.688 55.000 0.00 0.00 41.38 5.54
2532 3774 0.665670 CCATCTATCGCAGTGAGCCG 60.666 60.000 0.00 0.00 41.38 5.52
2533 3775 0.390860 ACCATCTATCGCAGTGAGCC 59.609 55.000 0.00 0.00 41.38 4.70
2534 3776 1.202463 ACACCATCTATCGCAGTGAGC 60.202 52.381 0.00 0.00 40.87 4.26
2535 3777 2.879002 ACACCATCTATCGCAGTGAG 57.121 50.000 0.00 0.00 32.76 3.51
2536 3778 3.951680 TCTTACACCATCTATCGCAGTGA 59.048 43.478 0.00 0.00 32.76 3.41
2537 3779 4.307443 TCTTACACCATCTATCGCAGTG 57.693 45.455 0.00 0.00 34.61 3.66
2538 3780 4.830046 AGATCTTACACCATCTATCGCAGT 59.170 41.667 0.00 0.00 0.00 4.40
2539 3781 5.384063 AGATCTTACACCATCTATCGCAG 57.616 43.478 0.00 0.00 0.00 5.18
2540 3782 5.791336 AAGATCTTACACCATCTATCGCA 57.209 39.130 6.06 0.00 0.00 5.10
2541 3783 7.371936 ACTTAAGATCTTACACCATCTATCGC 58.628 38.462 14.85 0.00 0.00 4.58
2546 3788 9.482175 AGTCTAACTTAAGATCTTACACCATCT 57.518 33.333 14.85 6.12 0.00 2.90
2579 3821 9.971922 CATAAAAAGGAAAGACTTGATCAAACT 57.028 29.630 9.88 9.04 0.00 2.66
2580 3822 9.196552 CCATAAAAAGGAAAGACTTGATCAAAC 57.803 33.333 9.88 6.87 0.00 2.93
2581 3823 8.367156 CCCATAAAAAGGAAAGACTTGATCAAA 58.633 33.333 9.88 0.00 0.00 2.69
2582 3824 7.508977 ACCCATAAAAAGGAAAGACTTGATCAA 59.491 33.333 8.12 8.12 0.00 2.57
2583 3825 7.010160 ACCCATAAAAAGGAAAGACTTGATCA 58.990 34.615 0.00 0.00 0.00 2.92
2584 3826 7.468141 ACCCATAAAAAGGAAAGACTTGATC 57.532 36.000 0.00 0.00 0.00 2.92
2585 3827 8.950007 TTACCCATAAAAAGGAAAGACTTGAT 57.050 30.769 0.00 0.00 0.00 2.57
2586 3828 8.770010 TTTACCCATAAAAAGGAAAGACTTGA 57.230 30.769 0.00 0.00 0.00 3.02
2587 3829 9.825109 TTTTTACCCATAAAAAGGAAAGACTTG 57.175 29.630 1.74 0.00 42.62 3.16
2617 3859 6.145858 CAGATTTCTCTATCGGCTTGATCAAG 59.854 42.308 27.82 27.82 38.57 3.02
2618 3860 5.987953 CAGATTTCTCTATCGGCTTGATCAA 59.012 40.000 8.12 8.12 38.57 2.57
2619 3861 5.536260 CAGATTTCTCTATCGGCTTGATCA 58.464 41.667 0.00 0.00 38.57 2.92
2620 3862 4.388469 GCAGATTTCTCTATCGGCTTGATC 59.612 45.833 0.00 0.00 40.91 2.92
2621 3863 4.202295 TGCAGATTTCTCTATCGGCTTGAT 60.202 41.667 9.46 0.00 43.36 2.57
2622 3864 3.132824 TGCAGATTTCTCTATCGGCTTGA 59.867 43.478 9.46 0.00 43.36 3.02
2623 3865 3.461061 TGCAGATTTCTCTATCGGCTTG 58.539 45.455 9.46 0.00 43.36 4.01
2624 3866 3.827008 TGCAGATTTCTCTATCGGCTT 57.173 42.857 9.46 0.00 43.36 4.35
2625 3867 3.827008 TTGCAGATTTCTCTATCGGCT 57.173 42.857 9.46 0.00 43.36 5.52
2626 3868 3.873952 ACTTTGCAGATTTCTCTATCGGC 59.126 43.478 0.00 0.00 43.29 5.54
2627 3869 5.814705 AGAACTTTGCAGATTTCTCTATCGG 59.185 40.000 4.24 0.00 0.00 4.18
2628 3870 6.900568 AGAACTTTGCAGATTTCTCTATCG 57.099 37.500 4.24 0.00 0.00 2.92
2629 3871 9.539825 TCATAGAACTTTGCAGATTTCTCTATC 57.460 33.333 12.33 0.00 30.89 2.08
2634 3876 9.842775 TGATATCATAGAACTTTGCAGATTTCT 57.157 29.630 13.32 13.32 32.99 2.52
2649 3891 8.655970 CGCCGAACAAATATTTGATATCATAGA 58.344 33.333 30.18 0.00 40.55 1.98
2650 3892 8.655970 TCGCCGAACAAATATTTGATATCATAG 58.344 33.333 30.18 17.37 40.55 2.23
2651 3893 8.541133 TCGCCGAACAAATATTTGATATCATA 57.459 30.769 30.18 1.78 40.55 2.15
2652 3894 7.433708 TCGCCGAACAAATATTTGATATCAT 57.566 32.000 30.18 7.90 40.55 2.45
2653 3895 6.852858 TCGCCGAACAAATATTTGATATCA 57.147 33.333 30.18 0.00 40.55 2.15
2654 3896 9.820229 TTATTCGCCGAACAAATATTTGATATC 57.180 29.630 30.18 22.13 40.55 1.63
2658 3900 9.820229 GATATTATTCGCCGAACAAATATTTGA 57.180 29.630 30.18 9.37 40.55 2.69
2659 3901 9.605955 TGATATTATTCGCCGAACAAATATTTG 57.394 29.630 23.60 23.60 43.62 2.32
2663 3905 9.605955 CATTTGATATTATTCGCCGAACAAATA 57.394 29.630 17.69 16.33 34.96 1.40
2664 3906 8.134895 ACATTTGATATTATTCGCCGAACAAAT 58.865 29.630 14.34 14.34 36.38 2.32
2665 3907 7.476667 ACATTTGATATTATTCGCCGAACAAA 58.523 30.769 0.00 7.56 0.00 2.83
2666 3908 7.022055 ACATTTGATATTATTCGCCGAACAA 57.978 32.000 0.00 0.00 0.00 2.83
2667 3909 6.612247 ACATTTGATATTATTCGCCGAACA 57.388 33.333 0.00 0.00 0.00 3.18
2714 3956 8.600625 CAAATTTGCTTCATTGGATTCAGTATG 58.399 33.333 5.01 0.00 37.54 2.39
2715 3957 7.767198 CCAAATTTGCTTCATTGGATTCAGTAT 59.233 33.333 12.92 0.00 44.01 2.12
2716 3958 7.098477 CCAAATTTGCTTCATTGGATTCAGTA 58.902 34.615 12.92 0.00 44.01 2.74
2717 3959 5.935789 CCAAATTTGCTTCATTGGATTCAGT 59.064 36.000 12.92 0.00 44.01 3.41
2718 3960 5.935789 ACCAAATTTGCTTCATTGGATTCAG 59.064 36.000 12.92 0.00 44.01 3.02
2719 3961 5.867330 ACCAAATTTGCTTCATTGGATTCA 58.133 33.333 12.92 0.00 44.01 2.57
2720 3962 6.806388 AACCAAATTTGCTTCATTGGATTC 57.194 33.333 12.92 0.00 44.01 2.52
2721 3963 8.866970 ATAAACCAAATTTGCTTCATTGGATT 57.133 26.923 12.92 12.83 44.01 3.01
2722 3964 9.603921 CTATAAACCAAATTTGCTTCATTGGAT 57.396 29.630 12.92 4.50 44.01 3.41
2723 3965 8.811017 TCTATAAACCAAATTTGCTTCATTGGA 58.189 29.630 12.92 2.29 44.01 3.53
2724 3966 8.872845 GTCTATAAACCAAATTTGCTTCATTGG 58.127 33.333 12.92 9.41 46.14 3.16
2725 3967 9.421806 TGTCTATAAACCAAATTTGCTTCATTG 57.578 29.630 12.92 0.00 0.00 2.82
2726 3968 9.423061 GTGTCTATAAACCAAATTTGCTTCATT 57.577 29.630 12.92 5.30 0.00 2.57
2727 3969 8.806146 AGTGTCTATAAACCAAATTTGCTTCAT 58.194 29.630 12.92 0.00 0.00 2.57
2728 3970 8.081633 CAGTGTCTATAAACCAAATTTGCTTCA 58.918 33.333 12.92 0.00 0.00 3.02
2729 3971 8.296713 TCAGTGTCTATAAACCAAATTTGCTTC 58.703 33.333 12.92 0.00 0.00 3.86
2730 3972 8.177119 TCAGTGTCTATAAACCAAATTTGCTT 57.823 30.769 12.92 10.21 0.00 3.91
2731 3973 7.759489 TCAGTGTCTATAAACCAAATTTGCT 57.241 32.000 12.92 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.