Multiple sequence alignment - TraesCS3D01G351100

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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 TraesCS3D01G351100 chr3D 100.000 4138 0 0 1 4138 462232554 462236691 0.000000e+00 7642.0
1 TraesCS3D01G351100 chr3B 87.688 1665 131 35 1 1607 613801487 613803135 0.000000e+00 1871.0
2 TraesCS3D01G351100 chr3B 85.257 1031 91 28 2678 3672 613804380 613805385 0.000000e+00 1005.0
3 TraesCS3D01G351100 chr3B 86.957 782 63 26 1606 2365 613803226 613803990 0.000000e+00 843.0
4 TraesCS3D01G351100 chr3B 86.977 430 49 6 3711 4138 613805383 613805807 1.040000e-130 477.0
5 TraesCS3D01G351100 chr3B 86.631 187 23 2 2371 2555 613804076 613804262 5.420000e-49 206.0
6 TraesCS3D01G351100 chr3A 92.141 738 54 3 1 737 605167834 605168568 0.000000e+00 1038.0
7 TraesCS3D01G351100 chr3A 87.019 701 53 19 1606 2278 605169565 605170255 0.000000e+00 756.0
8 TraesCS3D01G351100 chr3A 85.100 698 57 29 735 1408 605168598 605169272 0.000000e+00 669.0
9 TraesCS3D01G351100 chr3A 85.540 657 56 9 3209 3862 605171172 605171792 0.000000e+00 651.0
10 TraesCS3D01G351100 chr3A 85.045 448 54 9 2739 3176 605170732 605171176 1.060000e-120 444.0
11 TraesCS3D01G351100 chr3A 90.950 221 19 1 3919 4138 605171962 605172182 3.130000e-76 296.0
12 TraesCS3D01G351100 chr3A 81.509 265 29 9 2379 2638 605170378 605170627 2.520000e-47 200.0
13 TraesCS3D01G351100 chr1D 96.923 65 2 0 1150 1214 382725853 382725789 4.370000e-20 110.0
14 TraesCS3D01G351100 chr1B 98.387 62 1 0 1153 1214 512636952 512636891 4.370000e-20 110.0
15 TraesCS3D01G351100 chr1B 96.552 58 2 0 1302 1359 512636777 512636720 3.400000e-16 97.1
16 TraesCS3D01G351100 chr1A 98.387 62 1 0 1153 1214 482780061 482780000 4.370000e-20 110.0
17 TraesCS3D01G351100 chr1A 98.276 58 1 0 1302 1359 482779883 482779826 7.320000e-18 102.0


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 TraesCS3D01G351100 chr3D 462232554 462236691 4137 False 7642.000000 7642 100.000000 1 4138 1 chr3D.!!$F1 4137
1 TraesCS3D01G351100 chr3B 613801487 613805807 4320 False 880.400000 1871 86.702000 1 4138 5 chr3B.!!$F1 4137
2 TraesCS3D01G351100 chr3A 605167834 605172182 4348 False 579.142857 1038 86.757714 1 4138 7 chr3A.!!$F1 4137

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
796 846 0.874175 TCCGAACTCTGTTGCGTGTG 60.874 55.0 0.0 0.0 0.0 3.82 F
1225 1318 0.446222 CCAAGGTACGTTTGCCGATG 59.554 55.0 0.0 0.0 40.7 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2627 2963 1.002900 ACCGTTGACGTCAAGCAAATG 60.003 47.619 30.38 14.61 36.39 2.32 R
3193 3584 0.105039 CCCATGCCTAGTCGAGTTCC 59.895 60.000 0.00 0.00 0.00 3.62 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
274 275 1.008767 GGGATCGTCATCGTCCGAC 60.009 63.158 0.00 0.00 37.77 4.79
328 330 3.474570 ATGTCGAGGGCCAGCCTC 61.475 66.667 6.18 0.37 36.10 4.70
513 522 1.153086 GTCTGCCGGCTGATGGATT 60.153 57.895 34.54 0.00 0.00 3.01
682 691 2.124570 CTGGCCGAGGTTGGGATG 60.125 66.667 0.00 0.00 0.00 3.51
688 697 1.450312 CGAGGTTGGGATGCAGGTC 60.450 63.158 0.00 0.00 0.00 3.85
694 710 1.203441 TTGGGATGCAGGTCTCAGCT 61.203 55.000 0.00 0.00 28.66 4.24
701 717 1.739562 CAGGTCTCAGCTGTTCGCC 60.740 63.158 14.67 11.79 38.80 5.54
741 789 2.004583 TCGATTTGGACACCACGATC 57.995 50.000 0.00 0.00 30.78 3.69
796 846 0.874175 TCCGAACTCTGTTGCGTGTG 60.874 55.000 0.00 0.00 0.00 3.82
834 895 3.340034 CAAATAAGGCCCACGTAGAACA 58.660 45.455 0.00 0.00 0.00 3.18
863 924 3.080647 CCATACGGGCCAGAAAGTC 57.919 57.895 10.86 0.00 0.00 3.01
1061 1154 1.858091 GTGTCCATGCTCAGGTATCG 58.142 55.000 0.00 0.00 0.00 2.92
1076 1169 2.287909 GGTATCGAGCGCTGATCTTCTT 60.288 50.000 18.48 0.00 0.00 2.52
1086 1179 2.417924 GCTGATCTTCTTTCTCCGCTCA 60.418 50.000 0.00 0.00 0.00 4.26
1220 1313 1.205820 GTCGCCAAGGTACGTTTGC 59.794 57.895 12.88 12.88 0.00 3.68
1225 1318 0.446222 CCAAGGTACGTTTGCCGATG 59.554 55.000 0.00 0.00 40.70 3.84
1269 1362 0.528924 CGGACCGGAATCTGTGTGTA 59.471 55.000 9.46 0.00 0.00 2.90
1300 1394 1.888512 CCCTTTCTGGTGATTGGTGTG 59.111 52.381 0.00 0.00 0.00 3.82
1364 1458 2.222819 GCTCGGCAAAGATGTAAACTCG 60.223 50.000 0.00 0.00 0.00 4.18
1374 1468 7.572353 GCAAAGATGTAAACTCGACACCATTTA 60.572 37.037 0.00 0.00 0.00 1.40
1416 1510 8.614469 TTTTTGACCTGAAAACACTTCATTTT 57.386 26.923 0.00 0.00 31.96 1.82
1446 1540 2.857186 TGGAGCTATGTGTCTGCAAA 57.143 45.000 0.00 0.00 0.00 3.68
1457 1551 3.189080 TGTGTCTGCAAACATGATGTAGC 59.811 43.478 13.84 13.84 33.75 3.58
1463 1557 4.331108 TGCAAACATGATGTAGCCAACTA 58.669 39.130 16.81 0.00 32.65 2.24
1489 1583 9.257651 ACACACACAGTTTAGAACTAGTTAATC 57.742 33.333 8.42 0.00 40.46 1.75
1490 1584 9.256477 CACACACAGTTTAGAACTAGTTAATCA 57.744 33.333 8.42 0.00 40.46 2.57
1491 1585 9.477484 ACACACAGTTTAGAACTAGTTAATCAG 57.523 33.333 8.42 0.00 40.46 2.90
1503 1597 9.982651 GAACTAGTTAATCAGCAGGAATATGTA 57.017 33.333 8.42 0.00 0.00 2.29
1505 1599 9.765795 ACTAGTTAATCAGCAGGAATATGTAAC 57.234 33.333 0.00 0.00 0.00 2.50
1512 1606 9.950496 AATCAGCAGGAATATGTAACTAATAGG 57.050 33.333 0.00 0.00 0.00 2.57
1513 1607 8.721133 TCAGCAGGAATATGTAACTAATAGGA 57.279 34.615 0.00 0.00 0.00 2.94
1514 1608 9.326489 TCAGCAGGAATATGTAACTAATAGGAT 57.674 33.333 0.00 0.00 0.00 3.24
1516 1610 9.554053 AGCAGGAATATGTAACTAATAGGATCT 57.446 33.333 0.00 0.00 0.00 2.75
1538 1632 2.380084 TCCGAGGTGTTAGCATTCAC 57.620 50.000 0.00 0.00 0.00 3.18
1539 1633 1.621317 TCCGAGGTGTTAGCATTCACA 59.379 47.619 7.30 0.00 36.43 3.58
1540 1634 2.236146 TCCGAGGTGTTAGCATTCACAT 59.764 45.455 7.30 0.86 36.43 3.21
1541 1635 3.449377 TCCGAGGTGTTAGCATTCACATA 59.551 43.478 7.30 0.00 36.43 2.29
1542 1636 3.555956 CCGAGGTGTTAGCATTCACATAC 59.444 47.826 7.30 0.00 36.43 2.39
1543 1637 4.433615 CGAGGTGTTAGCATTCACATACT 58.566 43.478 7.30 0.00 36.43 2.12
1547 1641 7.145932 AGGTGTTAGCATTCACATACTTTTC 57.854 36.000 7.30 0.00 36.43 2.29
1548 1642 6.942576 AGGTGTTAGCATTCACATACTTTTCT 59.057 34.615 7.30 0.00 36.43 2.52
1551 1645 9.151471 GTGTTAGCATTCACATACTTTTCTAGA 57.849 33.333 0.00 0.00 35.04 2.43
1567 1661 8.861086 ACTTTTCTAGACACTTAGAATCAGACA 58.139 33.333 0.00 0.00 38.92 3.41
1580 1674 9.838339 CTTAGAATCAGACATTATACCTTTGGT 57.162 33.333 0.00 0.00 40.16 3.67
1610 1831 8.500753 TCATCGTAAGGCTTACATGTTATTTT 57.499 30.769 30.67 7.05 35.89 1.82
1612 1833 7.908827 TCGTAAGGCTTACATGTTATTTTCA 57.091 32.000 30.67 0.00 35.89 2.69
1620 1841 7.274250 GGCTTACATGTTATTTTCAAGCAGAAG 59.726 37.037 22.22 9.35 38.87 2.85
1628 1850 9.033481 TGTTATTTTCAAGCAGAAGAATTGTTG 57.967 29.630 0.00 0.00 37.57 3.33
1727 1949 3.070018 AGTCTGTGTTTCAGCATAGTGC 58.930 45.455 0.00 0.00 45.46 4.40
1734 1956 3.007940 TGTTTCAGCATAGTGCCTAGTGT 59.992 43.478 0.00 0.00 46.52 3.55
1735 1957 2.967599 TCAGCATAGTGCCTAGTGTG 57.032 50.000 0.00 0.00 46.52 3.82
1737 1959 3.361786 TCAGCATAGTGCCTAGTGTGTA 58.638 45.455 0.00 0.00 46.52 2.90
1747 1970 7.145932 AGTGCCTAGTGTGTATCAATTTTTC 57.854 36.000 0.00 0.00 0.00 2.29
1796 2019 4.519906 AAATCCCTTCGATACATTGGGT 57.480 40.909 0.00 0.00 38.95 4.51
1799 2022 2.574369 TCCCTTCGATACATTGGGTGTT 59.426 45.455 0.00 0.00 42.29 3.32
1802 2026 3.871594 CCTTCGATACATTGGGTGTTCTC 59.128 47.826 0.00 0.00 42.29 2.87
1810 2034 7.388776 CGATACATTGGGTGTTCTCATTATCAT 59.611 37.037 0.00 0.00 42.29 2.45
1812 2036 7.722949 ACATTGGGTGTTCTCATTATCATTT 57.277 32.000 0.00 0.00 38.01 2.32
1813 2037 8.137745 ACATTGGGTGTTCTCATTATCATTTT 57.862 30.769 0.00 0.00 38.01 1.82
1873 2114 4.471904 TTCTGTTCTTCCATATGCGACT 57.528 40.909 0.00 0.00 0.00 4.18
1909 2150 6.318648 TGTTATCTACCCAAGATGTTGCATTC 59.681 38.462 0.00 0.00 44.95 2.67
1915 2156 3.936453 CCCAAGATGTTGCATTCATTTGG 59.064 43.478 21.71 21.71 35.64 3.28
1971 2212 5.981174 TCATGTGCTCTTGTTATCTGATCA 58.019 37.500 0.00 0.00 0.00 2.92
1976 2221 6.537660 TGTGCTCTTGTTATCTGATCAAGATG 59.462 38.462 17.20 13.50 45.64 2.90
2193 2442 6.743575 AGTTTGATCTAATACAACTGGCAC 57.256 37.500 0.00 0.00 0.00 5.01
2218 2467 7.014326 ACTCCCTTTGATTTACTTTTCAACCTC 59.986 37.037 0.00 0.00 31.87 3.85
2222 2471 5.356882 TGATTTACTTTTCAACCTCGCTG 57.643 39.130 0.00 0.00 0.00 5.18
2247 2496 4.989875 ACTCCTGCATGCTTAGGATTAT 57.010 40.909 23.11 11.82 41.96 1.28
2252 2501 8.605947 ACTCCTGCATGCTTAGGATTATTATTA 58.394 33.333 23.11 2.54 41.96 0.98
2282 2531 9.847224 TCAAAGAAAAGTAACCTTCTAGTTGAT 57.153 29.630 0.00 0.00 29.63 2.57
2283 2532 9.884465 CAAAGAAAAGTAACCTTCTAGTTGATG 57.116 33.333 0.00 0.00 31.61 3.07
2285 2534 9.847224 AAGAAAAGTAACCTTCTAGTTGATGAA 57.153 29.630 0.00 0.00 31.61 2.57
2287 2536 9.490379 GAAAAGTAACCTTCTAGTTGATGAAGA 57.510 33.333 0.00 0.00 41.38 2.87
2292 2541 5.729510 ACCTTCTAGTTGATGAAGAAGAGC 58.270 41.667 11.81 0.00 45.94 4.09
2294 2543 6.665680 ACCTTCTAGTTGATGAAGAAGAGCTA 59.334 38.462 11.81 0.00 45.94 3.32
2303 2552 5.538053 TGATGAAGAAGAGCTATGTAGGGAG 59.462 44.000 0.00 0.00 0.00 4.30
2326 2575 6.969043 AGGGATATGTTGTAAATGTCCTCAA 58.031 36.000 0.00 0.00 36.03 3.02
2334 2583 8.684386 TGTTGTAAATGTCCTCAAATCTGTAA 57.316 30.769 0.00 0.00 0.00 2.41
2353 2603 8.862325 TCTGTAAGAGCCATTATTTCTGAAAA 57.138 30.769 6.95 0.00 38.67 2.29
2383 2714 6.651225 AGACACTAAGGCTAGACAATTGTTTC 59.349 38.462 13.36 0.37 29.36 2.78
2387 2718 8.017946 CACTAAGGCTAGACAATTGTTTCTTTC 58.982 37.037 13.36 0.00 0.00 2.62
2400 2731 2.561478 TTCTTTCGAAACAGGGGAGG 57.439 50.000 6.47 0.00 0.00 4.30
2413 2744 5.937492 ACAGGGGAGGATATCATTTTCAT 57.063 39.130 4.83 0.00 0.00 2.57
2414 2745 7.406620 AACAGGGGAGGATATCATTTTCATA 57.593 36.000 4.83 0.00 0.00 2.15
2416 2747 6.183347 CAGGGGAGGATATCATTTTCATACC 58.817 44.000 4.83 0.00 0.00 2.73
2417 2748 5.857283 AGGGGAGGATATCATTTTCATACCA 59.143 40.000 4.83 0.00 27.82 3.25
2431 2762 9.072294 CATTTTCATACCAAACCTAACGATTTC 57.928 33.333 0.00 0.00 0.00 2.17
2440 2771 9.471084 ACCAAACCTAACGATTTCTTTTTATTG 57.529 29.630 0.00 0.00 0.00 1.90
2467 2803 8.410673 TTTTATATTCTAGAGATCGAGCAGGT 57.589 34.615 2.38 0.00 0.00 4.00
2506 2842 3.057736 TGCGAACTAGGATACGAATAGGC 60.058 47.826 0.00 0.00 46.39 3.93
2512 2848 1.893137 AGGATACGAATAGGCGATGCA 59.107 47.619 0.00 0.00 46.39 3.96
2567 2903 9.565090 CTTTGTTCATATATCCTCTCATTTCCA 57.435 33.333 0.00 0.00 0.00 3.53
2568 2904 8.908786 TTGTTCATATATCCTCTCATTTCCAC 57.091 34.615 0.00 0.00 0.00 4.02
2569 2905 8.267620 TGTTCATATATCCTCTCATTTCCACT 57.732 34.615 0.00 0.00 0.00 4.00
2570 2906 8.152898 TGTTCATATATCCTCTCATTTCCACTG 58.847 37.037 0.00 0.00 0.00 3.66
2571 2907 7.250032 TCATATATCCTCTCATTTCCACTGG 57.750 40.000 0.00 0.00 0.00 4.00
2572 2908 4.989875 ATATCCTCTCATTTCCACTGGG 57.010 45.455 0.00 0.00 0.00 4.45
2573 2909 2.044793 TCCTCTCATTTCCACTGGGT 57.955 50.000 0.00 0.00 34.93 4.51
2574 2910 1.630369 TCCTCTCATTTCCACTGGGTG 59.370 52.381 0.00 0.00 34.93 4.61
2575 2911 1.630369 CCTCTCATTTCCACTGGGTGA 59.370 52.381 0.00 0.00 35.23 4.02
2577 2913 3.455910 CCTCTCATTTCCACTGGGTGATA 59.544 47.826 0.00 0.00 35.23 2.15
2578 2914 4.444022 CCTCTCATTTCCACTGGGTGATAG 60.444 50.000 0.00 1.05 35.23 2.08
2579 2915 4.104086 TCTCATTTCCACTGGGTGATAGT 58.896 43.478 0.00 0.00 35.23 2.12
2580 2916 5.277250 TCTCATTTCCACTGGGTGATAGTA 58.723 41.667 0.00 0.00 35.23 1.82
2581 2917 5.363868 TCTCATTTCCACTGGGTGATAGTAG 59.636 44.000 0.00 0.00 35.23 2.57
2582 2918 3.906720 TTTCCACTGGGTGATAGTAGC 57.093 47.619 0.00 0.00 35.23 3.58
2583 2919 2.848678 TCCACTGGGTGATAGTAGCT 57.151 50.000 0.00 0.00 35.23 3.32
2584 2920 3.965470 TCCACTGGGTGATAGTAGCTA 57.035 47.619 0.00 0.00 35.23 3.32
2585 2921 3.563223 TCCACTGGGTGATAGTAGCTAC 58.437 50.000 16.43 16.43 35.23 3.58
2586 2922 3.204606 TCCACTGGGTGATAGTAGCTACT 59.795 47.826 28.50 28.50 36.67 2.57
2587 2923 3.570550 CCACTGGGTGATAGTAGCTACTC 59.429 52.174 29.28 16.88 35.25 2.59
2588 2924 4.465886 CACTGGGTGATAGTAGCTACTCT 58.534 47.826 29.28 20.19 35.25 3.24
2589 2925 5.456330 CCACTGGGTGATAGTAGCTACTCTA 60.456 48.000 29.28 14.16 35.25 2.43
2590 2926 6.242396 CACTGGGTGATAGTAGCTACTCTAT 58.758 44.000 29.28 18.38 35.25 1.98
2591 2927 6.150307 CACTGGGTGATAGTAGCTACTCTATG 59.850 46.154 29.28 14.21 35.25 2.23
2624 2960 8.023706 CCTTTTATTTCTACTTGACTTTGCCTC 58.976 37.037 0.00 0.00 0.00 4.70
2627 2963 3.045601 TCTACTTGACTTTGCCTCTGC 57.954 47.619 0.00 0.00 38.26 4.26
2638 2974 0.599558 TGCCTCTGCATTTGCTTGAC 59.400 50.000 3.94 0.00 44.23 3.18
2641 2977 1.135859 CCTCTGCATTTGCTTGACGTC 60.136 52.381 9.11 9.11 42.66 4.34
2642 2978 1.532437 CTCTGCATTTGCTTGACGTCA 59.468 47.619 15.76 15.76 42.66 4.35
2643 2979 1.946081 TCTGCATTTGCTTGACGTCAA 59.054 42.857 28.07 28.07 42.66 3.18
2644 2980 2.046313 CTGCATTTGCTTGACGTCAAC 58.954 47.619 26.53 21.55 42.66 3.18
2645 2981 1.044725 GCATTTGCTTGACGTCAACG 58.955 50.000 26.53 21.40 40.89 4.10
2646 2982 1.673760 CATTTGCTTGACGTCAACGG 58.326 50.000 26.53 18.60 44.95 4.44
2647 2983 1.002900 CATTTGCTTGACGTCAACGGT 60.003 47.619 26.53 8.70 44.95 4.83
2648 2984 0.653636 TTTGCTTGACGTCAACGGTC 59.346 50.000 26.53 15.45 44.95 4.79
2649 2985 0.460459 TTGCTTGACGTCAACGGTCA 60.460 50.000 26.53 17.59 44.95 4.02
2653 2989 2.700694 CTTGACGTCAACGGTCAAAAC 58.299 47.619 26.53 0.00 44.95 2.43
2666 3002 2.033424 GGTCAAAACTCTGACTGGTTGC 59.967 50.000 3.94 0.00 44.33 4.17
2667 3003 2.945668 GTCAAAACTCTGACTGGTTGCT 59.054 45.455 0.00 0.00 42.11 3.91
2668 3004 3.002759 GTCAAAACTCTGACTGGTTGCTC 59.997 47.826 0.00 0.00 42.11 4.26
2669 3005 3.118261 TCAAAACTCTGACTGGTTGCTCT 60.118 43.478 0.00 0.00 0.00 4.09
2670 3006 4.100963 TCAAAACTCTGACTGGTTGCTCTA 59.899 41.667 0.00 0.00 0.00 2.43
2671 3007 3.669251 AACTCTGACTGGTTGCTCTAC 57.331 47.619 0.00 0.00 0.00 2.59
2673 3009 3.169099 ACTCTGACTGGTTGCTCTACAT 58.831 45.455 0.00 0.00 0.00 2.29
2676 3057 3.771479 TCTGACTGGTTGCTCTACATCAT 59.229 43.478 0.00 0.00 0.00 2.45
2685 3066 6.209192 TGGTTGCTCTACATCATGAATGTTTT 59.791 34.615 13.57 0.00 46.73 2.43
2694 3075 7.894376 ACATCATGAATGTTTTCAAATCCAC 57.106 32.000 0.00 0.00 46.73 4.02
2696 3077 5.468592 TCATGAATGTTTTCAAATCCACGG 58.531 37.500 0.00 0.00 44.70 4.94
2702 3083 8.961634 TGAATGTTTTCAAATCCACGGATTATA 58.038 29.630 11.67 0.86 43.26 0.98
2731 3112 9.529325 TTACTATGCTCAGACAATGTAATGTAC 57.471 33.333 0.00 0.00 32.57 2.90
2732 3113 5.973651 ATGCTCAGACAATGTAATGTACG 57.026 39.130 0.00 0.00 32.57 3.67
2735 3116 5.347635 TGCTCAGACAATGTAATGTACGTTC 59.652 40.000 2.93 0.00 35.82 3.95
2745 3126 5.038683 TGTAATGTACGTTCGAAGGCTATG 58.961 41.667 17.29 0.00 0.00 2.23
2747 3128 3.416119 TGTACGTTCGAAGGCTATGAG 57.584 47.619 17.29 0.00 0.00 2.90
2748 3129 2.751259 TGTACGTTCGAAGGCTATGAGT 59.249 45.455 17.29 0.00 0.00 3.41
2762 3143 4.637534 GGCTATGAGTTGATGAAGAAAGCA 59.362 41.667 0.00 0.00 0.00 3.91
2766 3148 3.742882 TGAGTTGATGAAGAAAGCAGTCG 59.257 43.478 0.00 0.00 0.00 4.18
2771 3153 2.613026 TGAAGAAAGCAGTCGGTTCA 57.387 45.000 0.00 0.00 30.88 3.18
2773 3155 1.801178 GAAGAAAGCAGTCGGTTCAGG 59.199 52.381 0.00 0.00 30.88 3.86
2793 3175 7.349412 TCAGGAATAGGTCTAGAGCTTTTAC 57.651 40.000 28.17 25.03 40.09 2.01
2796 3178 6.898521 AGGAATAGGTCTAGAGCTTTTACTGT 59.101 38.462 28.50 13.50 38.82 3.55
2800 3182 5.785243 AGGTCTAGAGCTTTTACTGTCAAC 58.215 41.667 18.72 0.00 35.28 3.18
2801 3183 4.621886 GGTCTAGAGCTTTTACTGTCAACG 59.378 45.833 14.73 0.00 0.00 4.10
2806 3193 8.086522 TCTAGAGCTTTTACTGTCAACGTAATT 58.913 33.333 0.00 0.00 0.00 1.40
2809 3196 8.403236 AGAGCTTTTACTGTCAACGTAATTTTT 58.597 29.630 0.00 0.00 0.00 1.94
2835 3222 6.015519 TGCTATGTTTTAGCAAACTTGACCAT 60.016 34.615 4.90 0.00 46.29 3.55
2837 3224 4.942852 TGTTTTAGCAAACTTGACCATGG 58.057 39.130 11.19 11.19 42.61 3.66
2851 3241 1.392589 CCATGGTTGGCACTATCACC 58.607 55.000 2.57 0.00 35.85 4.02
2852 3242 1.340893 CCATGGTTGGCACTATCACCA 60.341 52.381 10.22 10.22 35.85 4.17
2905 3296 4.154918 CCATAACTGGTTGTCTTCAGCTTC 59.845 45.833 0.00 0.00 37.79 3.86
2908 3299 2.149578 CTGGTTGTCTTCAGCTTCTGG 58.850 52.381 0.00 0.00 31.51 3.86
2940 3331 2.076863 GTGGATCAACAGGACTTTCCG 58.923 52.381 0.00 0.00 42.75 4.30
2970 3361 8.327832 GCTTTTGCATATGTTGTATCTAACAC 57.672 34.615 4.29 0.00 43.10 3.32
2972 3363 5.651172 TGCATATGTTGTATCTAACACGC 57.349 39.130 4.29 0.00 42.74 5.34
3005 3396 3.053455 GTTTGTGGACAGAGAGAACGAG 58.947 50.000 0.00 0.00 0.00 4.18
3011 3402 1.309499 ACAGAGAGAACGAGCTCCGG 61.309 60.000 8.47 0.00 43.93 5.14
3080 3471 3.628646 ATGGGCCAAGTCTCGTGCC 62.629 63.158 11.89 0.00 43.26 5.01
3089 3480 1.891919 GTCTCGTGCCAGCCAACAA 60.892 57.895 0.00 0.00 0.00 2.83
3101 3492 3.439540 CAACAATGGGCGGGACCG 61.440 66.667 6.35 6.35 40.62 4.79
3111 3502 1.004679 GCGGGACCGAAAGTTACCA 60.005 57.895 15.99 0.00 42.83 3.25
3122 3513 3.190535 CGAAAGTTACCATGAACCCCAAG 59.809 47.826 0.00 0.00 0.00 3.61
3173 3564 5.276270 CACTGTGTTTCTTTCTGGTGAATG 58.724 41.667 0.00 0.00 31.56 2.67
3175 3566 5.297776 ACTGTGTTTCTTTCTGGTGAATGAG 59.702 40.000 0.00 0.00 37.56 2.90
3187 3578 7.854557 TCTGGTGAATGAGAGTATTCATTTG 57.145 36.000 4.70 0.05 45.30 2.32
3188 3579 7.397221 TCTGGTGAATGAGAGTATTCATTTGT 58.603 34.615 4.70 0.00 45.30 2.83
3191 3582 8.298854 TGGTGAATGAGAGTATTCATTTGTTTG 58.701 33.333 4.70 0.00 45.30 2.93
3192 3583 8.299570 GGTGAATGAGAGTATTCATTTGTTTGT 58.700 33.333 4.70 0.00 45.30 2.83
3193 3584 9.121517 GTGAATGAGAGTATTCATTTGTTTGTG 57.878 33.333 4.70 0.00 45.30 3.33
3195 3586 8.408043 AATGAGAGTATTCATTTGTTTGTGGA 57.592 30.769 0.00 0.00 43.41 4.02
3196 3587 7.815840 TGAGAGTATTCATTTGTTTGTGGAA 57.184 32.000 0.00 0.00 0.00 3.53
3197 3588 7.648142 TGAGAGTATTCATTTGTTTGTGGAAC 58.352 34.615 0.00 0.00 38.78 3.62
3198 3589 7.502226 TGAGAGTATTCATTTGTTTGTGGAACT 59.498 33.333 0.00 0.00 39.08 3.01
3199 3590 7.875971 AGAGTATTCATTTGTTTGTGGAACTC 58.124 34.615 0.00 0.00 39.08 3.01
3200 3591 6.668323 AGTATTCATTTGTTTGTGGAACTCG 58.332 36.000 0.00 0.00 39.08 4.18
3201 3592 5.766150 ATTCATTTGTTTGTGGAACTCGA 57.234 34.783 0.00 0.00 39.08 4.04
3202 3593 4.545823 TCATTTGTTTGTGGAACTCGAC 57.454 40.909 0.00 0.00 39.08 4.20
3203 3594 4.196193 TCATTTGTTTGTGGAACTCGACT 58.804 39.130 0.00 0.00 39.08 4.18
3205 3596 5.465390 TCATTTGTTTGTGGAACTCGACTAG 59.535 40.000 0.00 0.00 39.08 2.57
3207 3598 2.067013 GTTTGTGGAACTCGACTAGGC 58.933 52.381 0.00 0.00 38.04 3.93
3208 3599 1.334160 TTGTGGAACTCGACTAGGCA 58.666 50.000 0.00 0.00 38.04 4.75
3209 3600 1.557099 TGTGGAACTCGACTAGGCAT 58.443 50.000 0.00 0.00 38.04 4.40
3210 3601 1.204704 TGTGGAACTCGACTAGGCATG 59.795 52.381 0.00 0.00 38.04 4.06
3211 3602 0.824109 TGGAACTCGACTAGGCATGG 59.176 55.000 0.00 0.00 0.00 3.66
3288 3681 4.608948 ACTTAGATTTGCTATCCCTCCG 57.391 45.455 0.00 0.00 0.00 4.63
3290 3683 1.807814 AGATTTGCTATCCCTCCGGT 58.192 50.000 0.00 0.00 0.00 5.28
3310 3703 6.071896 TCCGGTGAATACAGAGATGTATGATC 60.072 42.308 0.00 0.00 35.40 2.92
3347 3740 0.673333 TGGTATGGCGCAAGTGTCAG 60.673 55.000 10.83 0.00 41.68 3.51
3348 3741 0.673644 GGTATGGCGCAAGTGTCAGT 60.674 55.000 10.83 0.00 41.68 3.41
3352 3745 0.320050 TGGCGCAAGTGTCAGTGATA 59.680 50.000 10.83 0.00 41.68 2.15
3379 3785 6.509418 TGGTTTTTCCTATTGCTGATGTAC 57.491 37.500 0.00 0.00 37.07 2.90
3380 3786 6.007076 TGGTTTTTCCTATTGCTGATGTACA 58.993 36.000 0.00 0.00 37.07 2.90
3408 3815 2.886523 TGTTTGAAGAATCACCTGGCAG 59.113 45.455 7.75 7.75 34.61 4.85
3524 3944 4.083271 GCTAGTGGAGTGCTTTTGTTTAGG 60.083 45.833 0.00 0.00 0.00 2.69
3525 3945 4.164843 AGTGGAGTGCTTTTGTTTAGGA 57.835 40.909 0.00 0.00 0.00 2.94
3571 3991 9.158233 CATACAAAATGGAAAATTTGCTGATCT 57.842 29.630 0.00 0.00 39.55 2.75
3646 4066 4.022935 CGCATTGTACCATTTGATGCCTAT 60.023 41.667 0.00 0.00 39.83 2.57
3647 4067 5.181056 CGCATTGTACCATTTGATGCCTATA 59.819 40.000 0.00 0.00 39.83 1.31
3692 4112 4.019681 TCCATTCTATGAACCAAACGACCT 60.020 41.667 0.00 0.00 0.00 3.85
3701 4121 5.475719 TGAACCAAACGACCTACATAGAAG 58.524 41.667 0.00 0.00 0.00 2.85
3704 4124 5.721232 ACCAAACGACCTACATAGAAGAAG 58.279 41.667 0.00 0.00 0.00 2.85
3710 4130 9.503399 AAACGACCTACATAGAAGAAGAAAAAT 57.497 29.630 0.00 0.00 0.00 1.82
3712 4132 7.764901 ACGACCTACATAGAAGAAGAAAAATCC 59.235 37.037 0.00 0.00 0.00 3.01
3735 4155 8.852671 TCCAACCATCCAAATCCTATAAAATT 57.147 30.769 0.00 0.00 0.00 1.82
3736 4156 9.944079 TCCAACCATCCAAATCCTATAAAATTA 57.056 29.630 0.00 0.00 0.00 1.40
3788 4208 3.503363 ACAAGTGGAGATTGACGTACGTA 59.497 43.478 22.87 7.19 0.00 3.57
3804 4224 7.042590 TGACGTACGTACTTGTCATTTCAAAAT 60.043 33.333 22.87 0.00 36.50 1.82
3818 4238 9.410556 GTCATTTCAAAATATGCAGTAACAAGT 57.589 29.630 0.00 0.00 0.00 3.16
3865 4286 8.321353 TCTCTGTATTTTACACATCACTTGGAT 58.679 33.333 0.00 0.00 33.68 3.41
3870 4291 6.509418 TTTTACACATCACTTGGATAAGCC 57.491 37.500 0.00 0.00 37.43 4.35
3880 4416 4.608948 CTTGGATAAGCCTAGTCCGATT 57.391 45.455 0.00 0.00 35.15 3.34
3881 4417 4.561105 CTTGGATAAGCCTAGTCCGATTC 58.439 47.826 0.00 0.00 35.15 2.52
3894 4430 3.572255 AGTCCGATTCTTCTGCTATCTCC 59.428 47.826 0.00 0.00 0.00 3.71
3895 4431 2.894126 TCCGATTCTTCTGCTATCTCCC 59.106 50.000 0.00 0.00 0.00 4.30
3898 4434 3.365868 CGATTCTTCTGCTATCTCCCTCG 60.366 52.174 0.00 0.00 0.00 4.63
3900 4436 0.316841 CTTCTGCTATCTCCCTCGGC 59.683 60.000 0.00 0.00 0.00 5.54
3901 4437 0.397114 TTCTGCTATCTCCCTCGGCA 60.397 55.000 0.00 0.00 0.00 5.69
3902 4438 1.664873 CTGCTATCTCCCTCGGCAG 59.335 63.158 0.00 0.00 43.03 4.85
3903 4439 1.075970 TGCTATCTCCCTCGGCAGT 60.076 57.895 0.00 0.00 0.00 4.40
3904 4440 1.109920 TGCTATCTCCCTCGGCAGTC 61.110 60.000 0.00 0.00 0.00 3.51
3908 4444 0.692419 ATCTCCCTCGGCAGTCCATT 60.692 55.000 0.00 0.00 0.00 3.16
3909 4445 0.909610 TCTCCCTCGGCAGTCCATTT 60.910 55.000 0.00 0.00 0.00 2.32
3910 4446 0.035056 CTCCCTCGGCAGTCCATTTT 60.035 55.000 0.00 0.00 0.00 1.82
3911 4447 0.035439 TCCCTCGGCAGTCCATTTTC 60.035 55.000 0.00 0.00 0.00 2.29
3912 4448 1.032114 CCCTCGGCAGTCCATTTTCC 61.032 60.000 0.00 0.00 0.00 3.13
3915 4451 2.052104 CGGCAGTCCATTTTCCCCC 61.052 63.158 0.00 0.00 0.00 5.40
3916 4452 2.052104 GGCAGTCCATTTTCCCCCG 61.052 63.158 0.00 0.00 0.00 5.73
3917 4453 2.710902 GCAGTCCATTTTCCCCCGC 61.711 63.158 0.00 0.00 0.00 6.13
3938 4475 2.124151 CCCGGGCAAATCTCCCTG 60.124 66.667 8.08 0.00 41.69 4.45
3941 4478 1.678635 CGGGCAAATCTCCCTGCAA 60.679 57.895 0.00 0.00 41.69 4.08
3955 4493 2.203972 CTGCAACAATCCCTGCACCG 62.204 60.000 0.00 0.00 43.44 4.94
4111 4649 4.400109 GCGTGACCTGCTCGACGA 62.400 66.667 0.00 0.00 35.64 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.642488 TGACCAGGGGTACGGCCA 62.642 66.667 2.24 0.00 35.25 5.36
86 87 3.059982 CCTGGACGACTGGCTTCA 58.940 61.111 0.00 0.00 0.00 3.02
120 121 4.994744 TCGACGTCGAGTACCTCA 57.005 55.556 34.97 12.17 44.22 3.86
189 190 3.027170 TTCGTCTACGCCGTCGACC 62.027 63.158 15.13 0.00 39.60 4.79
328 330 4.785453 GCCTGGAAGCACTCCCCG 62.785 72.222 0.00 0.00 44.69 5.73
357 359 4.662961 CCAGCGTGCTGTCGACCA 62.663 66.667 19.58 1.13 42.15 4.02
497 506 1.442526 GACAATCCATCAGCCGGCAG 61.443 60.000 31.54 22.82 0.00 4.85
532 541 2.124403 CCCAGCCTGATCTGCCAC 60.124 66.667 0.00 0.00 32.87 5.01
680 689 0.390866 CGAACAGCTGAGACCTGCAT 60.391 55.000 23.35 0.00 39.38 3.96
682 691 2.386660 GCGAACAGCTGAGACCTGC 61.387 63.158 23.35 11.20 44.04 4.85
694 710 1.371267 CTCGTTCTCGTGGCGAACA 60.371 57.895 0.00 0.00 40.50 3.18
701 717 3.759527 TGATCTTACCTCGTTCTCGTG 57.240 47.619 0.00 0.00 38.33 4.35
816 877 2.303600 TGTTGTTCTACGTGGGCCTTAT 59.696 45.455 4.53 0.00 0.00 1.73
834 895 0.750182 CCCGTATGGCCCGAAATGTT 60.750 55.000 0.00 0.00 0.00 2.71
860 921 0.322546 GGAAATGTTGCCCTCCGACT 60.323 55.000 0.00 0.00 0.00 4.18
862 923 4.734652 GGAAATGTTGCCCTCCGA 57.265 55.556 0.00 0.00 0.00 4.55
863 924 3.187058 CGGAAATGTTGCCCTCCG 58.813 61.111 0.00 0.00 44.31 4.63
995 1088 2.877691 GGAACTTGCCCATGTCGC 59.122 61.111 0.00 0.00 0.00 5.19
998 1091 1.526575 CTTGCGGAACTTGCCCATGT 61.527 55.000 0.00 0.00 0.00 3.21
1061 1154 2.200899 GGAGAAAGAAGATCAGCGCTC 58.799 52.381 7.13 0.00 0.00 5.03
1064 1157 0.926846 GCGGAGAAAGAAGATCAGCG 59.073 55.000 0.00 0.00 0.00 5.18
1086 1179 2.103094 AGCACATATACATCACAGCGGT 59.897 45.455 0.00 0.00 0.00 5.68
1225 1318 2.791868 AAACACCCACCGCAAAGCC 61.792 57.895 0.00 0.00 0.00 4.35
1269 1362 4.104102 TCACCAGAAAGGGTCAGTACAAAT 59.896 41.667 0.00 0.00 43.89 2.32
1300 1394 2.435059 GCACCTCCTTCGCCTGAC 60.435 66.667 0.00 0.00 0.00 3.51
1364 1458 2.026636 TGGGCACTAGGTAAATGGTGTC 60.027 50.000 0.00 0.00 35.72 3.67
1374 1468 2.061509 AAAAACGTTGGGCACTAGGT 57.938 45.000 0.00 0.00 0.00 3.08
1395 1489 6.522625 TGAAAATGAAGTGTTTTCAGGTCA 57.477 33.333 9.27 0.00 45.49 4.02
1407 1501 6.406624 GCTCCATGGATCAATGAAAATGAAGT 60.407 38.462 16.63 0.00 0.00 3.01
1416 1510 4.103627 ACACATAGCTCCATGGATCAATGA 59.896 41.667 25.59 8.83 0.00 2.57
1457 1551 5.815740 AGTTCTAAACTGTGTGTGTAGTTGG 59.184 40.000 0.00 0.00 41.01 3.77
1463 1557 9.257651 GATTAACTAGTTCTAAACTGTGTGTGT 57.742 33.333 12.39 0.00 42.84 3.72
1488 1582 8.721133 TCCTATTAGTTACATATTCCTGCTGA 57.279 34.615 0.00 0.00 0.00 4.26
1489 1583 9.593134 GATCCTATTAGTTACATATTCCTGCTG 57.407 37.037 0.00 0.00 0.00 4.41
1490 1584 9.554053 AGATCCTATTAGTTACATATTCCTGCT 57.446 33.333 0.00 0.00 0.00 4.24
1491 1585 9.593134 CAGATCCTATTAGTTACATATTCCTGC 57.407 37.037 0.00 0.00 0.00 4.85
1499 1593 7.039644 CCTCGGAACAGATCCTATTAGTTACAT 60.040 40.741 0.00 0.00 46.98 2.29
1503 1597 5.069251 CACCTCGGAACAGATCCTATTAGTT 59.931 44.000 0.00 0.00 46.98 2.24
1505 1599 4.585162 ACACCTCGGAACAGATCCTATTAG 59.415 45.833 0.00 0.00 46.98 1.73
1507 1601 3.375699 ACACCTCGGAACAGATCCTATT 58.624 45.455 0.00 0.00 46.98 1.73
1510 1604 1.645710 AACACCTCGGAACAGATCCT 58.354 50.000 0.00 0.00 46.98 3.24
1512 1606 2.094182 TGCTAACACCTCGGAACAGATC 60.094 50.000 0.00 0.00 0.00 2.75
1513 1607 1.899814 TGCTAACACCTCGGAACAGAT 59.100 47.619 0.00 0.00 0.00 2.90
1514 1608 1.334160 TGCTAACACCTCGGAACAGA 58.666 50.000 0.00 0.00 0.00 3.41
1516 1610 2.037902 TGAATGCTAACACCTCGGAACA 59.962 45.455 0.00 0.00 0.00 3.18
1521 1615 4.433615 AGTATGTGAATGCTAACACCTCG 58.566 43.478 0.00 0.00 36.35 4.63
1523 1617 6.942576 AGAAAAGTATGTGAATGCTAACACCT 59.057 34.615 0.00 0.00 36.35 4.00
1524 1618 7.145932 AGAAAAGTATGTGAATGCTAACACC 57.854 36.000 0.00 0.00 36.35 4.16
1525 1619 9.151471 TCTAGAAAAGTATGTGAATGCTAACAC 57.849 33.333 0.00 0.00 37.51 3.32
1527 1621 9.151471 TGTCTAGAAAAGTATGTGAATGCTAAC 57.849 33.333 0.00 0.00 0.00 2.34
1541 1635 8.861086 TGTCTGATTCTAAGTGTCTAGAAAAGT 58.139 33.333 0.00 0.00 40.42 2.66
1542 1636 9.868277 ATGTCTGATTCTAAGTGTCTAGAAAAG 57.132 33.333 0.00 0.45 40.42 2.27
1573 1667 6.231211 AGCCTTACGATGATATAACCAAAGG 58.769 40.000 0.00 0.00 35.22 3.11
1582 1676 9.944376 AATAACATGTAAGCCTTACGATGATAT 57.056 29.630 22.51 18.88 38.98 1.63
1583 1677 9.772973 AAATAACATGTAAGCCTTACGATGATA 57.227 29.630 22.51 18.00 38.98 2.15
1584 1678 8.677148 AAATAACATGTAAGCCTTACGATGAT 57.323 30.769 22.51 16.98 38.98 2.45
1590 1686 8.026607 TGCTTGAAAATAACATGTAAGCCTTAC 58.973 33.333 19.43 7.68 38.52 2.34
1592 1688 6.991938 TGCTTGAAAATAACATGTAAGCCTT 58.008 32.000 19.43 3.12 38.52 4.35
1610 1831 6.319658 AGACTTTCAACAATTCTTCTGCTTGA 59.680 34.615 0.00 0.00 0.00 3.02
1612 1833 6.545298 AGAGACTTTCAACAATTCTTCTGCTT 59.455 34.615 0.00 0.00 0.00 3.91
1620 1841 7.664082 TCTGATGAGAGACTTTCAACAATTC 57.336 36.000 7.27 0.00 28.79 2.17
1711 1933 3.372206 CACTAGGCACTATGCTGAAACAC 59.628 47.826 0.13 0.00 44.28 3.32
1713 1935 3.372206 CACACTAGGCACTATGCTGAAAC 59.628 47.826 0.13 0.00 44.28 2.78
1727 1949 6.404734 GCAGGGAAAAATTGATACACACTAGG 60.405 42.308 0.00 0.00 0.00 3.02
1747 1970 9.820725 TGATCAAATAATGAATTTTTAGCAGGG 57.179 29.630 0.00 0.00 42.54 4.45
1767 1990 7.880160 ATGTATCGAAGGGATTTTTGATCAA 57.120 32.000 3.38 3.38 36.55 2.57
1768 1991 7.201812 CCAATGTATCGAAGGGATTTTTGATCA 60.202 37.037 0.00 0.00 36.55 2.92
1770 1993 6.040842 CCCAATGTATCGAAGGGATTTTTGAT 59.959 38.462 0.00 0.00 42.25 2.57
1771 1994 5.359576 CCCAATGTATCGAAGGGATTTTTGA 59.640 40.000 0.00 0.00 42.25 2.69
1776 1999 3.202151 ACACCCAATGTATCGAAGGGATT 59.798 43.478 2.29 0.00 40.88 3.01
1812 2036 7.143514 ACTTACGTTCTACCAACAACAAAAA 57.856 32.000 0.00 0.00 0.00 1.94
1813 2037 6.740411 ACTTACGTTCTACCAACAACAAAA 57.260 33.333 0.00 0.00 0.00 2.44
1817 2041 5.050567 CAGGAACTTACGTTCTACCAACAAC 60.051 44.000 11.43 0.00 46.84 3.32
1826 2050 9.886132 AAATATAACATCAGGAACTTACGTTCT 57.114 29.630 11.43 0.00 46.84 3.01
1845 2069 9.554395 TCGCATATGGAAGAACAGAAAATATAA 57.446 29.630 4.56 0.00 0.00 0.98
1847 2071 7.716998 AGTCGCATATGGAAGAACAGAAAATAT 59.283 33.333 4.56 0.00 0.00 1.28
1849 2073 5.882557 AGTCGCATATGGAAGAACAGAAAAT 59.117 36.000 4.56 0.00 0.00 1.82
1850 2074 5.245531 AGTCGCATATGGAAGAACAGAAAA 58.754 37.500 4.56 0.00 0.00 2.29
1852 2076 4.471904 AGTCGCATATGGAAGAACAGAA 57.528 40.909 4.56 0.00 0.00 3.02
1854 2078 4.183865 TGAAGTCGCATATGGAAGAACAG 58.816 43.478 4.56 0.00 0.00 3.16
1856 2080 4.494855 GCTTGAAGTCGCATATGGAAGAAC 60.495 45.833 4.56 0.00 0.00 3.01
1857 2081 3.623060 GCTTGAAGTCGCATATGGAAGAA 59.377 43.478 4.56 0.00 0.00 2.52
1859 2083 2.289002 GGCTTGAAGTCGCATATGGAAG 59.711 50.000 4.56 0.00 0.00 3.46
1873 2114 4.534500 TGGGTAGATAACAAGAGGCTTGAA 59.466 41.667 13.56 2.52 0.00 2.69
1909 2150 8.567285 AAACCTGAAGATAAGACTACCAAATG 57.433 34.615 0.00 0.00 0.00 2.32
2193 2442 7.290110 AGGTTGAAAAGTAAATCAAAGGGAG 57.710 36.000 0.00 0.00 37.31 4.30
2218 2467 1.150567 GCATGCAGGAGTACTCAGCG 61.151 60.000 23.91 15.07 35.72 5.18
2222 2471 2.695666 TCCTAAGCATGCAGGAGTACTC 59.304 50.000 20.03 14.87 35.99 2.59
2255 2504 9.675464 TCAACTAGAAGGTTACTTTTCTTTGAA 57.325 29.630 0.00 0.00 36.97 2.69
2259 2508 9.847224 TTCATCAACTAGAAGGTTACTTTTCTT 57.153 29.630 0.00 0.00 36.97 2.52
2265 2514 8.423906 TCTTCTTCATCAACTAGAAGGTTACT 57.576 34.615 10.24 0.00 43.14 2.24
2274 2523 8.081633 CCTACATAGCTCTTCTTCATCAACTAG 58.918 40.741 0.00 0.00 0.00 2.57
2275 2524 7.014711 CCCTACATAGCTCTTCTTCATCAACTA 59.985 40.741 0.00 0.00 0.00 2.24
2276 2525 6.183360 CCCTACATAGCTCTTCTTCATCAACT 60.183 42.308 0.00 0.00 0.00 3.16
2277 2526 5.988561 CCCTACATAGCTCTTCTTCATCAAC 59.011 44.000 0.00 0.00 0.00 3.18
2279 2528 5.458595 TCCCTACATAGCTCTTCTTCATCA 58.541 41.667 0.00 0.00 0.00 3.07
2282 2531 4.219115 CCTCCCTACATAGCTCTTCTTCA 58.781 47.826 0.00 0.00 0.00 3.02
2283 2532 3.576550 CCCTCCCTACATAGCTCTTCTTC 59.423 52.174 0.00 0.00 0.00 2.87
2285 2534 2.792370 TCCCTCCCTACATAGCTCTTCT 59.208 50.000 0.00 0.00 0.00 2.85
2287 2536 3.933239 ATCCCTCCCTACATAGCTCTT 57.067 47.619 0.00 0.00 0.00 2.85
2292 2541 7.792364 TTACAACATATCCCTCCCTACATAG 57.208 40.000 0.00 0.00 0.00 2.23
2294 2543 7.073725 ACATTTACAACATATCCCTCCCTACAT 59.926 37.037 0.00 0.00 0.00 2.29
2303 2552 7.639113 TTTGAGGACATTTACAACATATCCC 57.361 36.000 0.00 0.00 0.00 3.85
2326 2575 9.466497 TTTCAGAAATAATGGCTCTTACAGATT 57.534 29.630 0.00 0.00 0.00 2.40
2359 2609 6.651225 AGAAACAATTGTCTAGCCTTAGTGTC 59.349 38.462 12.39 0.00 0.00 3.67
2362 2612 7.095187 CGAAAGAAACAATTGTCTAGCCTTAGT 60.095 37.037 12.39 0.00 0.00 2.24
2363 2613 7.117812 TCGAAAGAAACAATTGTCTAGCCTTAG 59.882 37.037 12.39 8.67 37.03 2.18
2364 2614 6.932400 TCGAAAGAAACAATTGTCTAGCCTTA 59.068 34.615 12.39 0.00 37.03 2.69
2365 2615 5.763204 TCGAAAGAAACAATTGTCTAGCCTT 59.237 36.000 12.39 8.05 37.03 4.35
2366 2616 5.305585 TCGAAAGAAACAATTGTCTAGCCT 58.694 37.500 12.39 2.30 37.03 4.58
2367 2617 5.607119 TCGAAAGAAACAATTGTCTAGCC 57.393 39.130 12.39 0.00 37.03 3.93
2383 2714 2.789409 ATCCTCCCCTGTTTCGAAAG 57.211 50.000 11.66 0.00 0.00 2.62
2387 2718 4.357918 AATGATATCCTCCCCTGTTTCG 57.642 45.455 0.00 0.00 0.00 3.46
2395 2726 7.039714 GGTTTGGTATGAAAATGATATCCTCCC 60.040 40.741 0.00 0.00 0.00 4.30
2396 2727 7.725844 AGGTTTGGTATGAAAATGATATCCTCC 59.274 37.037 0.00 0.00 0.00 4.30
2400 2731 9.878599 CGTTAGGTTTGGTATGAAAATGATATC 57.121 33.333 0.00 0.00 0.00 1.63
2414 2745 9.471084 CAATAAAAAGAAATCGTTAGGTTTGGT 57.529 29.630 0.00 0.00 0.00 3.67
2439 2770 9.684448 CTGCTCGATCTCTAGAATATAAAAACA 57.316 33.333 0.00 0.00 0.00 2.83
2440 2771 9.134734 CCTGCTCGATCTCTAGAATATAAAAAC 57.865 37.037 0.00 0.00 0.00 2.43
2450 2786 1.490910 TCCACCTGCTCGATCTCTAGA 59.509 52.381 0.00 0.00 0.00 2.43
2467 2803 6.170506 AGTTCGCAAAAGTCTTGTATATCCA 58.829 36.000 0.00 0.00 0.00 3.41
2506 2842 2.011741 ATGCCATTGGTGCTGCATCG 62.012 55.000 5.27 0.00 40.21 3.84
2567 2903 4.799715 AGAGTAGCTACTATCACCCAGT 57.200 45.455 26.11 0.13 36.50 4.00
2568 2904 6.242396 ACATAGAGTAGCTACTATCACCCAG 58.758 44.000 26.11 12.71 36.50 4.45
2569 2905 6.202202 ACATAGAGTAGCTACTATCACCCA 57.798 41.667 26.11 8.34 36.50 4.51
2570 2906 7.396418 AGTACATAGAGTAGCTACTATCACCC 58.604 42.308 26.11 12.62 36.50 4.61
2571 2907 8.095792 TGAGTACATAGAGTAGCTACTATCACC 58.904 40.741 26.11 13.34 36.50 4.02
2572 2908 8.928733 GTGAGTACATAGAGTAGCTACTATCAC 58.071 40.741 26.11 19.24 36.50 3.06
2573 2909 8.095792 GGTGAGTACATAGAGTAGCTACTATCA 58.904 40.741 26.11 14.19 36.50 2.15
2574 2910 8.316214 AGGTGAGTACATAGAGTAGCTACTATC 58.684 40.741 26.11 15.00 36.50 2.08
2575 2911 8.209802 AGGTGAGTACATAGAGTAGCTACTAT 57.790 38.462 26.11 24.73 36.50 2.12
2577 2913 6.503560 AGGTGAGTACATAGAGTAGCTACT 57.496 41.667 26.35 26.35 39.71 2.57
2578 2914 7.571080 AAAGGTGAGTACATAGAGTAGCTAC 57.429 40.000 16.43 16.43 32.19 3.58
2579 2915 9.863650 ATAAAAGGTGAGTACATAGAGTAGCTA 57.136 33.333 0.00 0.00 32.19 3.32
2580 2916 8.770010 ATAAAAGGTGAGTACATAGAGTAGCT 57.230 34.615 0.00 0.00 32.19 3.32
2581 2917 9.819267 AAATAAAAGGTGAGTACATAGAGTAGC 57.181 33.333 0.00 0.00 32.19 3.58
2590 2926 9.485206 GTCAAGTAGAAATAAAAGGTGAGTACA 57.515 33.333 0.00 0.00 0.00 2.90
2591 2927 9.708092 AGTCAAGTAGAAATAAAAGGTGAGTAC 57.292 33.333 0.00 0.00 0.00 2.73
2624 2960 2.046313 GTTGACGTCAAGCAAATGCAG 58.954 47.619 30.38 0.00 45.16 4.41
2627 2963 1.002900 ACCGTTGACGTCAAGCAAATG 60.003 47.619 30.38 14.61 36.39 2.32
2628 2964 1.263217 GACCGTTGACGTCAAGCAAAT 59.737 47.619 30.38 14.62 36.39 2.32
2638 2974 2.034001 GTCAGAGTTTTGACCGTTGACG 60.034 50.000 0.00 0.00 41.24 4.35
2641 2977 2.287915 CCAGTCAGAGTTTTGACCGTTG 59.712 50.000 2.76 0.00 46.81 4.10
2642 2978 2.093128 ACCAGTCAGAGTTTTGACCGTT 60.093 45.455 2.76 0.00 46.81 4.44
2643 2979 1.485066 ACCAGTCAGAGTTTTGACCGT 59.515 47.619 2.76 0.00 46.81 4.83
2644 2980 2.240493 ACCAGTCAGAGTTTTGACCG 57.760 50.000 2.76 0.00 46.81 4.79
2645 2981 2.033424 GCAACCAGTCAGAGTTTTGACC 59.967 50.000 2.76 0.00 46.81 4.02
2646 2982 2.945668 AGCAACCAGTCAGAGTTTTGAC 59.054 45.455 0.00 0.00 46.14 3.18
2647 2983 3.118261 AGAGCAACCAGTCAGAGTTTTGA 60.118 43.478 1.74 0.00 0.00 2.69
2648 2984 3.209410 AGAGCAACCAGTCAGAGTTTTG 58.791 45.455 0.00 0.00 0.00 2.44
2649 2985 3.567478 AGAGCAACCAGTCAGAGTTTT 57.433 42.857 0.00 0.00 0.00 2.43
2653 2989 3.194329 TGATGTAGAGCAACCAGTCAGAG 59.806 47.826 0.00 0.00 0.00 3.35
2671 3007 6.035220 CCGTGGATTTGAAAACATTCATGATG 59.965 38.462 0.00 0.00 41.71 3.07
2673 3009 5.242615 TCCGTGGATTTGAAAACATTCATGA 59.757 36.000 0.00 0.00 0.00 3.07
2676 3057 5.720371 ATCCGTGGATTTGAAAACATTCA 57.280 34.783 0.00 0.00 0.00 2.57
2709 3090 6.569780 ACGTACATTACATTGTCTGAGCATA 58.430 36.000 0.00 0.00 0.00 3.14
2714 3095 5.701855 TCGAACGTACATTACATTGTCTGA 58.298 37.500 0.00 0.00 0.00 3.27
2724 3105 5.066893 ACTCATAGCCTTCGAACGTACATTA 59.933 40.000 0.00 0.00 0.00 1.90
2731 3112 2.876091 TCAACTCATAGCCTTCGAACG 58.124 47.619 0.00 0.00 0.00 3.95
2732 3113 4.433615 TCATCAACTCATAGCCTTCGAAC 58.566 43.478 0.00 0.00 0.00 3.95
2735 3116 4.686972 TCTTCATCAACTCATAGCCTTCG 58.313 43.478 0.00 0.00 0.00 3.79
2745 3126 3.124297 CCGACTGCTTTCTTCATCAACTC 59.876 47.826 0.00 0.00 0.00 3.01
2747 3128 2.808543 ACCGACTGCTTTCTTCATCAAC 59.191 45.455 0.00 0.00 0.00 3.18
2748 3129 3.126001 ACCGACTGCTTTCTTCATCAA 57.874 42.857 0.00 0.00 0.00 2.57
2762 3143 3.103080 AGACCTATTCCTGAACCGACT 57.897 47.619 0.00 0.00 0.00 4.18
2766 3148 4.219919 AGCTCTAGACCTATTCCTGAACC 58.780 47.826 0.00 0.00 0.00 3.62
2771 3153 6.898521 ACAGTAAAAGCTCTAGACCTATTCCT 59.101 38.462 0.00 0.00 0.00 3.36
2773 3155 7.773149 TGACAGTAAAAGCTCTAGACCTATTC 58.227 38.462 0.00 0.00 0.00 1.75
2814 3201 5.070313 ACCATGGTCAAGTTTGCTAAAACAT 59.930 36.000 13.00 0.00 46.80 2.71
2835 3222 2.666272 TTTGGTGATAGTGCCAACCA 57.334 45.000 0.00 0.00 43.59 3.67
2858 3248 4.953781 TCTGGAAATTTCAGGGAGGAAT 57.046 40.909 19.49 0.00 33.36 3.01
2861 3251 3.511540 GGTTTCTGGAAATTTCAGGGAGG 59.488 47.826 19.49 3.42 33.36 4.30
2940 3331 2.273557 CAACATATGCAAAAGCTGGGC 58.726 47.619 1.58 0.00 0.00 5.36
3011 3402 2.919494 CGTTGCAGGTTTGGCCTCC 61.919 63.158 3.32 4.01 46.96 4.30
3089 3480 1.555477 TAACTTTCGGTCCCGCCCAT 61.555 55.000 0.00 0.00 39.59 4.00
3095 3486 2.745821 GTTCATGGTAACTTTCGGTCCC 59.254 50.000 0.00 0.00 37.61 4.46
3101 3492 4.149598 ACTTGGGGTTCATGGTAACTTTC 58.850 43.478 0.00 0.00 37.61 2.62
3111 3502 1.272147 GCCTTCTGACTTGGGGTTCAT 60.272 52.381 0.00 0.00 0.00 2.57
3122 3513 3.456280 CTGCTCTCATAAGCCTTCTGAC 58.544 50.000 0.00 0.00 41.77 3.51
3173 3564 7.875971 AGTTCCACAAACAAATGAATACTCTC 58.124 34.615 0.00 0.00 40.56 3.20
3175 3566 6.797033 CGAGTTCCACAAACAAATGAATACTC 59.203 38.462 0.00 0.00 40.56 2.59
3187 3578 2.067013 GCCTAGTCGAGTTCCACAAAC 58.933 52.381 0.00 0.00 38.21 2.93
3188 3579 1.689813 TGCCTAGTCGAGTTCCACAAA 59.310 47.619 0.00 0.00 0.00 2.83
3191 3582 1.471676 CCATGCCTAGTCGAGTTCCAC 60.472 57.143 0.00 0.00 0.00 4.02
3192 3583 0.824109 CCATGCCTAGTCGAGTTCCA 59.176 55.000 0.00 0.00 0.00 3.53
3193 3584 0.105039 CCCATGCCTAGTCGAGTTCC 59.895 60.000 0.00 0.00 0.00 3.62
3195 3586 1.972660 GCCCCATGCCTAGTCGAGTT 61.973 60.000 0.00 0.00 0.00 3.01
3196 3587 2.435693 GCCCCATGCCTAGTCGAGT 61.436 63.158 0.00 0.00 0.00 4.18
3197 3588 1.690219 AAGCCCCATGCCTAGTCGAG 61.690 60.000 0.00 0.00 42.71 4.04
3198 3589 1.689233 AAGCCCCATGCCTAGTCGA 60.689 57.895 0.00 0.00 42.71 4.20
3199 3590 1.524621 CAAGCCCCATGCCTAGTCG 60.525 63.158 0.00 0.00 42.71 4.18
3200 3591 0.464554 GACAAGCCCCATGCCTAGTC 60.465 60.000 0.00 0.00 42.71 2.59
3201 3592 1.207488 TGACAAGCCCCATGCCTAGT 61.207 55.000 0.00 0.00 42.71 2.57
3202 3593 0.749454 GTGACAAGCCCCATGCCTAG 60.749 60.000 0.00 0.00 42.71 3.02
3203 3594 1.302949 GTGACAAGCCCCATGCCTA 59.697 57.895 0.00 0.00 42.71 3.93
3205 3596 3.443045 CGTGACAAGCCCCATGCC 61.443 66.667 0.00 0.00 42.71 4.40
3207 3598 2.672651 TGCGTGACAAGCCCCATG 60.673 61.111 10.95 0.00 0.00 3.66
3208 3599 2.360350 CTGCGTGACAAGCCCCAT 60.360 61.111 10.95 0.00 0.00 4.00
3209 3600 4.641645 CCTGCGTGACAAGCCCCA 62.642 66.667 10.95 0.00 0.00 4.96
3210 3601 4.329545 TCCTGCGTGACAAGCCCC 62.330 66.667 10.95 0.00 0.00 5.80
3211 3602 2.743928 CTCCTGCGTGACAAGCCC 60.744 66.667 10.95 0.00 0.00 5.19
3221 3612 1.135575 GCTGACAAAAATCCTCCTGCG 60.136 52.381 0.00 0.00 0.00 5.18
3288 3681 6.914259 TCGATCATACATCTCTGTATTCACC 58.086 40.000 0.00 0.00 44.42 4.02
3290 3683 8.031277 CCATTCGATCATACATCTCTGTATTCA 58.969 37.037 0.00 0.00 44.42 2.57
3310 3703 2.901840 CCACCGCATCCCCATTCG 60.902 66.667 0.00 0.00 0.00 3.34
3347 3740 7.489113 CAGCAATAGGAAAAACCAACATATCAC 59.511 37.037 0.00 0.00 42.04 3.06
3348 3741 7.395772 TCAGCAATAGGAAAAACCAACATATCA 59.604 33.333 0.00 0.00 42.04 2.15
3352 3745 6.014327 ACATCAGCAATAGGAAAAACCAACAT 60.014 34.615 0.00 0.00 42.04 2.71
3379 3785 7.117236 CCAGGTGATTCTTCAAACATTTCATTG 59.883 37.037 0.00 0.00 32.48 2.82
3380 3786 7.156673 CCAGGTGATTCTTCAAACATTTCATT 58.843 34.615 0.00 0.00 32.48 2.57
3408 3815 2.686235 CATGAGATCCAGGCTCGAATC 58.314 52.381 0.00 0.00 35.15 2.52
3524 3944 3.264947 GGGAAAAGAAGGCATTTGCATC 58.735 45.455 4.74 2.48 44.36 3.91
3525 3945 2.638855 TGGGAAAAGAAGGCATTTGCAT 59.361 40.909 4.74 0.00 44.36 3.96
3576 3996 8.983789 TCCACCATAACAGAAATATGTACAGTA 58.016 33.333 0.33 0.00 31.70 2.74
3577 3997 7.857456 TCCACCATAACAGAAATATGTACAGT 58.143 34.615 0.33 0.00 31.70 3.55
3578 3998 8.731275 TTCCACCATAACAGAAATATGTACAG 57.269 34.615 0.33 0.00 31.70 2.74
3579 3999 9.693739 AATTCCACCATAACAGAAATATGTACA 57.306 29.630 0.00 0.00 31.70 2.90
3580 4000 9.950680 CAATTCCACCATAACAGAAATATGTAC 57.049 33.333 0.00 0.00 31.70 2.90
3596 4016 5.080337 TGTTAAATGGTAGCAATTCCACCA 58.920 37.500 0.00 5.11 45.96 4.17
3660 4080 9.919416 TTTGGTTCATAGAATGGAATCATTAGA 57.081 29.630 0.00 0.00 43.08 2.10
3692 4112 9.753674 ATGGTTGGATTTTTCTTCTTCTATGTA 57.246 29.630 0.00 0.00 0.00 2.29
3701 4121 6.595326 GGATTTGGATGGTTGGATTTTTCTTC 59.405 38.462 0.00 0.00 0.00 2.87
3704 4124 6.053632 AGGATTTGGATGGTTGGATTTTTC 57.946 37.500 0.00 0.00 0.00 2.29
3710 4130 8.852671 AATTTTATAGGATTTGGATGGTTGGA 57.147 30.769 0.00 0.00 0.00 3.53
3735 4155 8.400947 GCTCAAGTGCTTATCTGATTCAAAATA 58.599 33.333 0.00 0.00 0.00 1.40
3736 4156 7.122353 AGCTCAAGTGCTTATCTGATTCAAAAT 59.878 33.333 0.00 0.00 40.93 1.82
3737 4157 6.432162 AGCTCAAGTGCTTATCTGATTCAAAA 59.568 34.615 0.00 0.00 40.93 2.44
3747 4167 3.254060 TGTTCGAGCTCAAGTGCTTATC 58.746 45.455 15.40 0.00 44.17 1.75
3788 4208 9.410556 GTTACTGCATATTTTGAAATGACAAGT 57.589 29.630 0.00 2.07 0.00 3.16
3818 4238 7.335924 CAGAGACGGGGTTTGAAAATTATAGAA 59.664 37.037 0.00 0.00 0.00 2.10
3865 4286 3.068307 GCAGAAGAATCGGACTAGGCTTA 59.932 47.826 0.00 0.00 0.00 3.09
3868 4289 1.410882 AGCAGAAGAATCGGACTAGGC 59.589 52.381 0.00 0.00 0.00 3.93
3870 4291 5.106317 GGAGATAGCAGAAGAATCGGACTAG 60.106 48.000 0.00 0.00 0.00 2.57
3878 4414 2.896685 CCGAGGGAGATAGCAGAAGAAT 59.103 50.000 0.00 0.00 0.00 2.40
3879 4415 2.311463 CCGAGGGAGATAGCAGAAGAA 58.689 52.381 0.00 0.00 0.00 2.52
3880 4416 1.988293 CCGAGGGAGATAGCAGAAGA 58.012 55.000 0.00 0.00 0.00 2.87
3881 4417 0.316841 GCCGAGGGAGATAGCAGAAG 59.683 60.000 0.00 0.00 0.00 2.85
3894 4430 1.032114 GGGAAAATGGACTGCCGAGG 61.032 60.000 0.00 0.00 36.79 4.63
3895 4431 1.032114 GGGGAAAATGGACTGCCGAG 61.032 60.000 0.00 0.00 36.79 4.63
3898 4434 2.052104 CGGGGGAAAATGGACTGCC 61.052 63.158 0.00 0.00 0.00 4.85
3900 4436 2.052104 GGCGGGGGAAAATGGACTG 61.052 63.158 0.00 0.00 0.00 3.51
3901 4437 2.359011 GGCGGGGGAAAATGGACT 59.641 61.111 0.00 0.00 0.00 3.85
3902 4438 2.036572 TGGCGGGGGAAAATGGAC 59.963 61.111 0.00 0.00 0.00 4.02
3903 4439 2.036572 GTGGCGGGGGAAAATGGA 59.963 61.111 0.00 0.00 0.00 3.41
3904 4440 3.074369 GGTGGCGGGGGAAAATGG 61.074 66.667 0.00 0.00 0.00 3.16
3917 4453 2.440247 GAGATTTGCCCGGGGTGG 60.440 66.667 25.28 0.00 37.55 4.61
3938 4475 2.568090 CGGTGCAGGGATTGTTGC 59.432 61.111 0.00 0.00 40.67 4.17
3941 4478 3.545124 TTCGCGGTGCAGGGATTGT 62.545 57.895 6.13 0.00 33.07 2.71
4098 4636 1.696832 GGCATTTCGTCGAGCAGGTC 61.697 60.000 7.20 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.