Multiple sequence alignment - TraesCS3D01G370600

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3D01G370600 chr3D 100.000 5654 0 0 1 5654 484339887 484345540 0.000000e+00 10442
1 TraesCS3D01G370600 chr3A 90.054 2423 157 44 1 2362 627269579 627271978 0.000000e+00 3062
2 TraesCS3D01G370600 chr3A 89.504 1210 61 32 3319 4494 627273222 627274399 0.000000e+00 1471
3 TraesCS3D01G370600 chr3A 94.008 968 15 7 2359 3319 627272234 627273165 0.000000e+00 1426
4 TraesCS3D01G370600 chr3A 87.203 1180 64 29 4492 5635 627274434 627275562 0.000000e+00 1262
5 TraesCS3D01G370600 chr3B 87.291 2038 162 44 1 2014 647169837 647171801 0.000000e+00 2239
6 TraesCS3D01G370600 chr3B 85.178 985 106 26 2347 3316 647171984 647172943 0.000000e+00 974
7 TraesCS3D01G370600 chr3B 81.695 885 76 39 4071 4928 647176376 647177201 0.000000e+00 658
8 TraesCS3D01G370600 chr3B 84.649 684 49 28 4987 5654 647177200 647177843 1.030000e-176 630
9 TraesCS3D01G370600 chr3B 88.788 330 27 7 1022 1351 290615134 290615453 4.110000e-106 396
10 TraesCS3D01G370600 chr3B 86.552 290 22 6 3356 3629 647173017 647173305 2.560000e-78 303
11 TraesCS3D01G370600 chr4D 95.652 299 13 0 1 299 444177399 444177697 1.100000e-131 481
12 TraesCS3D01G370600 chr1A 94.822 309 14 2 1 309 468599087 468598781 1.100000e-131 481
13 TraesCS3D01G370600 chr1A 94.771 306 15 1 1 306 400975237 400974933 5.130000e-130 475
14 TraesCS3D01G370600 chr1D 95.318 299 14 0 1 299 321640780 321641078 5.130000e-130 475
15 TraesCS3D01G370600 chr1D 95.318 299 14 0 1 299 321704840 321704542 5.130000e-130 475
16 TraesCS3D01G370600 chr1D 94.498 309 15 2 1 309 369925818 369925512 5.130000e-130 475
17 TraesCS3D01G370600 chr1B 95.318 299 14 0 1 299 434409194 434409492 5.130000e-130 475
18 TraesCS3D01G370600 chr5D 90.909 330 20 6 1022 1351 79988055 79988374 8.700000e-118 435
19 TraesCS3D01G370600 chr6A 90.060 332 23 6 1021 1351 251475484 251475162 6.770000e-114 422
20 TraesCS3D01G370600 chr6A 88.485 330 28 7 1022 1351 252021073 252021392 1.910000e-104 390
21 TraesCS3D01G370600 chr6D 90.074 272 22 3 1080 1351 294698274 294698008 1.170000e-91 348
22 TraesCS3D01G370600 chr7B 89.455 275 24 3 1077 1351 601441486 601441755 5.420000e-90 342
23 TraesCS3D01G370600 chr4B 88.652 282 26 6 1071 1351 397269108 397268832 7.020000e-89 339


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 TraesCS3D01G370600 chr3D 484339887 484345540 5653 False 10442.00 10442 100.00000 1 5654 1 chr3D.!!$F1 5653
1 TraesCS3D01G370600 chr3A 627269579 627275562 5983 False 1805.25 3062 90.19225 1 5635 4 chr3A.!!$F1 5634
2 TraesCS3D01G370600 chr3B 647169837 647177843 8006 False 960.80 2239 85.07300 1 5654 5 chr3B.!!$F2 5653

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
912 951 0.321564 CCCGCTGTCATTGACTTGGA 60.322 55.000 17.26 0.00 33.15 3.53 F
1323 1363 0.103755 CTCAGATCTGCTTGCCGCTA 59.896 55.000 18.36 0.00 40.11 4.26 F
1416 1456 0.173708 GTCAGTCTTCTGCTACGGGG 59.826 60.000 0.00 0.00 41.10 5.73 F
2750 3100 1.497286 TCTTTGGTGGCTTGGTAACCT 59.503 47.619 0.00 0.00 34.90 3.50 F
3728 6408 0.257039 GAATCACTGCCCATGGGACT 59.743 55.000 36.00 12.38 37.50 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2316 2399 1.378531 ACTGCATGACAACAACGTGT 58.621 45.000 0.00 0.00 0.00 4.49 R
3020 3377 1.448893 GGAACGCCGCACCTGATTA 60.449 57.895 0.00 0.00 0.00 1.75 R
3354 3774 5.474578 TGATATCTCCAGTACAAGATGGC 57.525 43.478 12.94 7.37 36.47 4.40 R
3962 7094 0.112218 TGCCTTAAGAGCCCTTGCAA 59.888 50.000 3.36 0.00 41.13 4.08 R
5160 8401 0.182775 AAGCTCGGGGTGTTGTTCTT 59.817 50.000 0.00 0.00 0.00 2.52 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 93 3.207669 CTGATCCGCAAGCTGCCC 61.208 66.667 0.00 0.00 41.12 5.36
377 378 1.717032 TCAGAGCTTGGTGGTGTAGT 58.283 50.000 0.00 0.00 0.00 2.73
392 394 5.529800 GTGGTGTAGTTAACATGTTCCTGTT 59.470 40.000 15.85 0.55 41.10 3.16
399 401 2.550830 ACATGTTCCTGTTCGCTCTT 57.449 45.000 0.00 0.00 0.00 2.85
468 470 7.226128 TCAATGAAGAGTGCAGTTATCATCATC 59.774 37.037 18.06 0.29 32.03 2.92
509 511 3.887777 TTTTTCTGTGCGACGTGTG 57.112 47.368 0.00 0.00 0.00 3.82
510 512 1.080298 TTTTTCTGTGCGACGTGTGT 58.920 45.000 0.00 0.00 0.00 3.72
553 573 2.602217 CGTTGTCTAGCTTGTTTGTGCC 60.602 50.000 0.00 0.00 0.00 5.01
564 584 0.593128 GTTTGTGCCGTGAAGCAGAT 59.407 50.000 0.00 0.00 45.14 2.90
570 603 1.712081 CCGTGAAGCAGATGAAGCG 59.288 57.895 0.00 0.00 37.01 4.68
580 613 7.374491 GTGAAGCAGATGAAGCGTAATAATTTC 59.626 37.037 0.00 0.00 37.01 2.17
581 614 7.280876 TGAAGCAGATGAAGCGTAATAATTTCT 59.719 33.333 0.00 0.00 37.01 2.52
586 619 9.208022 CAGATGAAGCGTAATAATTTCTATCCA 57.792 33.333 0.00 0.00 0.00 3.41
588 621 9.979270 GATGAAGCGTAATAATTTCTATCCATG 57.021 33.333 0.00 0.00 0.00 3.66
619 653 0.732571 CCGTCATTGGATTGTTCCCG 59.267 55.000 0.00 0.00 41.83 5.14
621 655 2.623535 CGTCATTGGATTGTTCCCGTA 58.376 47.619 0.00 0.00 41.83 4.02
633 670 3.581755 TGTTCCCGTATTCTTTCACTCG 58.418 45.455 0.00 0.00 0.00 4.18
635 672 4.240096 GTTCCCGTATTCTTTCACTCGAA 58.760 43.478 0.00 0.00 0.00 3.71
638 675 4.868171 TCCCGTATTCTTTCACTCGAATTG 59.132 41.667 0.00 0.00 32.53 2.32
658 695 6.859715 ATTGATTTTTCGATCTTTCGCTTG 57.140 33.333 0.00 0.00 45.10 4.01
659 696 4.722194 TGATTTTTCGATCTTTCGCTTGG 58.278 39.130 0.00 0.00 45.10 3.61
672 709 1.202879 TCGCTTGGGTTTTCTGATGGT 60.203 47.619 0.00 0.00 0.00 3.55
709 746 1.201343 GAAGAACAGTATCGCCGCTC 58.799 55.000 0.00 0.00 0.00 5.03
740 778 2.205074 GTCATGGATAAGCTCACCGTG 58.795 52.381 15.43 15.43 40.72 4.94
741 779 2.107366 TCATGGATAAGCTCACCGTGA 58.893 47.619 18.42 18.42 44.22 4.35
745 783 3.270027 TGGATAAGCTCACCGTGATTTG 58.730 45.455 0.62 0.00 0.00 2.32
747 785 3.531538 GATAAGCTCACCGTGATTTGGA 58.468 45.455 0.62 0.00 0.00 3.53
748 786 2.270352 AAGCTCACCGTGATTTGGAA 57.730 45.000 0.62 0.00 0.00 3.53
749 787 2.496899 AGCTCACCGTGATTTGGAAT 57.503 45.000 0.62 0.00 0.00 3.01
750 788 2.795329 AGCTCACCGTGATTTGGAATT 58.205 42.857 0.62 0.00 0.00 2.17
751 789 2.489329 AGCTCACCGTGATTTGGAATTG 59.511 45.455 0.62 0.00 0.00 2.32
753 791 3.825308 CTCACCGTGATTTGGAATTGTG 58.175 45.455 0.62 0.00 0.00 3.33
755 793 3.634448 TCACCGTGATTTGGAATTGTGTT 59.366 39.130 0.00 0.00 0.00 3.32
756 794 3.735240 CACCGTGATTTGGAATTGTGTTG 59.265 43.478 0.00 0.00 0.00 3.33
758 796 4.142049 ACCGTGATTTGGAATTGTGTTGTT 60.142 37.500 0.00 0.00 0.00 2.83
759 797 4.808364 CCGTGATTTGGAATTGTGTTGTTT 59.192 37.500 0.00 0.00 0.00 2.83
760 798 5.051106 CCGTGATTTGGAATTGTGTTGTTTC 60.051 40.000 0.00 0.00 0.00 2.78
761 799 5.051106 CGTGATTTGGAATTGTGTTGTTTCC 60.051 40.000 0.00 0.00 39.50 3.13
767 805 8.655651 TTTGGAATTGTGTTGTTTCCTATTTC 57.344 30.769 0.00 0.00 39.72 2.17
815 853 2.427410 GTGCTCCGCGTTTGCTTG 60.427 61.111 4.92 0.00 39.65 4.01
827 865 0.459489 TTTGCTTGTTTGCCGCTTCT 59.541 45.000 0.00 0.00 0.00 2.85
833 872 1.007387 GTTTGCCGCTTCTGTTGGG 60.007 57.895 0.00 0.00 0.00 4.12
834 873 2.855514 TTTGCCGCTTCTGTTGGGC 61.856 57.895 0.00 0.00 45.76 5.36
837 876 3.423154 CCGCTTCTGTTGGGCGTC 61.423 66.667 0.00 0.00 46.23 5.19
867 906 8.281212 GAAGGAATCCAATAGTAGCTGAAAAA 57.719 34.615 0.61 0.00 0.00 1.94
881 920 2.677573 GAAAAACAACGCTGGCCGCT 62.678 55.000 15.78 2.80 41.76 5.52
882 921 1.448922 AAAAACAACGCTGGCCGCTA 61.449 50.000 15.78 0.00 41.76 4.26
884 923 2.125202 AAACAACGCTGGCCGCTAAC 62.125 55.000 15.78 0.00 41.76 2.34
885 924 3.047280 CAACGCTGGCCGCTAACA 61.047 61.111 15.78 0.00 41.76 2.41
886 925 2.281208 AACGCTGGCCGCTAACAA 60.281 55.556 15.78 0.00 41.76 2.83
887 926 2.613506 AACGCTGGCCGCTAACAAC 61.614 57.895 15.78 0.00 41.76 3.32
888 927 3.799755 CGCTGGCCGCTAACAACC 61.800 66.667 15.78 0.00 36.13 3.77
911 950 1.926511 GCCCGCTGTCATTGACTTGG 61.927 60.000 17.26 14.61 33.15 3.61
912 951 0.321564 CCCGCTGTCATTGACTTGGA 60.322 55.000 17.26 0.00 33.15 3.53
928 967 3.300765 GAGACGTCGTGGGGGTGT 61.301 66.667 10.46 0.00 0.00 4.16
951 990 2.093447 ACCGAATCCAGCAAAGTAGGAG 60.093 50.000 0.00 0.00 34.40 3.69
962 1001 2.123382 GTAGGAGACGGGAGGGGG 60.123 72.222 0.00 0.00 0.00 5.40
1007 1047 1.405526 CGATCTCACGTCCAAACCCAT 60.406 52.381 0.00 0.00 0.00 4.00
1052 1092 2.257067 GCGGATCTAGCGAGCCTC 59.743 66.667 0.00 0.00 43.59 4.70
1053 1093 2.558821 CGGATCTAGCGAGCCTCG 59.441 66.667 10.36 10.36 43.59 4.63
1054 1094 2.958576 GGATCTAGCGAGCCTCGG 59.041 66.667 16.95 0.00 42.48 4.63
1323 1363 0.103755 CTCAGATCTGCTTGCCGCTA 59.896 55.000 18.36 0.00 40.11 4.26
1324 1364 0.755079 TCAGATCTGCTTGCCGCTAT 59.245 50.000 18.36 0.00 40.11 2.97
1395 1435 2.029380 GGTTTGGACTGATTTTTCCGGG 60.029 50.000 0.00 0.00 34.24 5.73
1410 1450 2.286523 CGGGGGTCAGTCTTCTGCT 61.287 63.158 0.00 0.00 41.10 4.24
1416 1456 0.173708 GTCAGTCTTCTGCTACGGGG 59.826 60.000 0.00 0.00 41.10 5.73
1446 1486 4.227864 AGTTTGATTCCTAGAGCAAGGG 57.772 45.455 0.00 0.00 37.24 3.95
1482 1522 2.093973 CCGGTGATCTCTGCAAAGTAGT 60.094 50.000 0.00 0.00 0.00 2.73
1494 1534 3.835978 TGCAAAGTAGTCTGTAGCCCTAA 59.164 43.478 0.00 0.00 0.00 2.69
1526 1566 2.107366 TCCGATGTGCTGTAGGATTCA 58.893 47.619 0.00 0.00 0.00 2.57
1532 1572 4.882842 TGTGCTGTAGGATTCACACTTA 57.117 40.909 0.00 0.00 34.87 2.24
1729 1771 3.613299 GCTAGTGCTCCTTCTCGTTTTAC 59.387 47.826 0.00 0.00 36.03 2.01
1744 1786 5.565695 TCGTTTTACTGACTTTGAGCAAAC 58.434 37.500 0.00 0.00 0.00 2.93
1770 1812 9.454585 CTCATTTTCGCATATGTAATTGTGAAT 57.545 29.630 4.29 0.00 40.77 2.57
1774 1816 9.715123 TTTTCGCATATGTAATTGTGAATACAG 57.285 29.630 4.29 0.00 40.77 2.74
1775 1817 7.420184 TCGCATATGTAATTGTGAATACAGG 57.580 36.000 4.29 0.00 38.23 4.00
1787 1829 6.421377 TGTGAATACAGGATCATTCAAACG 57.579 37.500 7.54 0.00 41.50 3.60
1961 2004 5.353938 TGTATTTCGTGATTGGCCTAGTAC 58.646 41.667 3.32 0.00 0.00 2.73
1976 2019 5.713389 GGCCTAGTACCAATTTTTACCAACT 59.287 40.000 0.00 0.00 0.00 3.16
2033 2099 9.451002 CTTATTCTGATGAATGCTTCCAGATAT 57.549 33.333 0.00 0.00 42.34 1.63
2134 2217 2.688958 CTCCCGCTAGGCTGGTATATAC 59.311 54.545 4.14 4.14 34.54 1.47
2181 2264 5.237048 TGCTTTGGCATTATTGAAAAGGAC 58.763 37.500 11.80 0.00 44.28 3.85
2219 2302 3.274288 GAGCTACAAGGAAACATCTGGG 58.726 50.000 0.00 0.00 0.00 4.45
2316 2399 8.523658 GTGTAAGTCAGGAGATGCATACATATA 58.476 37.037 0.00 0.00 36.35 0.86
2500 2850 3.118956 AGTTCCATAGAGCAGTTCTTCCG 60.119 47.826 0.00 0.00 37.36 4.30
2531 2881 5.472137 TGTTTTTGGGTGATACTTAGCTGTC 59.528 40.000 0.00 0.00 0.00 3.51
2533 2883 2.453521 TGGGTGATACTTAGCTGTCGT 58.546 47.619 0.00 0.00 0.00 4.34
2737 3087 8.353423 ACATAATGCTCTATGTTTTCTTTGGT 57.647 30.769 5.68 0.00 39.02 3.67
2739 3089 5.649782 ATGCTCTATGTTTTCTTTGGTGG 57.350 39.130 0.00 0.00 0.00 4.61
2740 3090 3.255642 TGCTCTATGTTTTCTTTGGTGGC 59.744 43.478 0.00 0.00 0.00 5.01
2742 3092 4.021981 GCTCTATGTTTTCTTTGGTGGCTT 60.022 41.667 0.00 0.00 0.00 4.35
2744 3094 2.977772 TGTTTTCTTTGGTGGCTTGG 57.022 45.000 0.00 0.00 0.00 3.61
2745 3095 2.183679 TGTTTTCTTTGGTGGCTTGGT 58.816 42.857 0.00 0.00 0.00 3.67
2747 3097 3.769844 TGTTTTCTTTGGTGGCTTGGTAA 59.230 39.130 0.00 0.00 0.00 2.85
2749 3099 1.989706 TCTTTGGTGGCTTGGTAACC 58.010 50.000 0.00 0.00 34.38 2.85
2750 3100 1.497286 TCTTTGGTGGCTTGGTAACCT 59.503 47.619 0.00 0.00 34.90 3.50
2751 3101 1.886542 CTTTGGTGGCTTGGTAACCTC 59.113 52.381 0.00 0.00 34.90 3.85
2754 3104 1.906574 TGGTGGCTTGGTAACCTCTAG 59.093 52.381 0.00 0.00 34.90 2.43
2960 3317 5.014755 TGGGGTGGCTTCTAATTTTCTAAGA 59.985 40.000 0.00 0.00 0.00 2.10
2993 3350 7.672240 TGTATCTTGTGGTTGTATGTCTGTTA 58.328 34.615 0.00 0.00 0.00 2.41
3030 3387 7.607250 AGTAGCTATGTATTCTAATCAGGTGC 58.393 38.462 0.00 0.00 0.00 5.01
3031 3388 5.473931 AGCTATGTATTCTAATCAGGTGCG 58.526 41.667 0.00 0.00 0.00 5.34
3032 3389 4.627467 GCTATGTATTCTAATCAGGTGCGG 59.373 45.833 0.00 0.00 0.00 5.69
3033 3390 2.833794 TGTATTCTAATCAGGTGCGGC 58.166 47.619 0.00 0.00 0.00 6.53
3330 3750 4.159557 TGATTTTTCTAGGCCAGCCTTTT 58.840 39.130 17.94 0.00 45.70 2.27
3354 3774 6.351711 TCCTGTAAAGATGATCTTCACCATG 58.648 40.000 8.32 3.56 35.27 3.66
3662 4112 2.288395 GCACATTGTTTTACTGCAGGCT 60.288 45.455 19.93 0.00 0.00 4.58
3663 4113 3.799917 GCACATTGTTTTACTGCAGGCTT 60.800 43.478 19.93 0.00 0.00 4.35
3665 4115 5.156355 CACATTGTTTTACTGCAGGCTTAG 58.844 41.667 19.93 1.16 0.00 2.18
3710 6384 9.754382 AGATTGTAAAGTTTACTTGTCTAACGA 57.246 29.630 22.87 0.40 36.12 3.85
3727 6407 1.097547 CGAATCACTGCCCATGGGAC 61.098 60.000 36.00 24.66 37.50 4.46
3728 6408 0.257039 GAATCACTGCCCATGGGACT 59.743 55.000 36.00 12.38 37.50 3.85
3735 6415 1.414181 CTGCCCATGGGACTACTGTAG 59.586 57.143 36.00 13.13 37.50 2.74
3736 6416 1.273609 TGCCCATGGGACTACTGTAGT 60.274 52.381 36.00 19.79 42.86 2.73
3738 6418 1.762957 CCCATGGGACTACTGTAGTGG 59.237 57.143 28.27 17.37 39.59 4.00
3739 6419 2.625883 CCCATGGGACTACTGTAGTGGA 60.626 54.545 28.27 8.61 39.59 4.02
3740 6420 2.431057 CCATGGGACTACTGTAGTGGAC 59.569 54.545 24.15 13.90 39.59 4.02
3791 6472 6.886459 GTGATGCTAATATAATGATGTGGGGT 59.114 38.462 0.00 0.00 0.00 4.95
3794 6475 7.523293 TGCTAATATAATGATGTGGGGTTTG 57.477 36.000 0.00 0.00 0.00 2.93
3799 6480 8.421249 AATATAATGATGTGGGGTTTGGTATG 57.579 34.615 0.00 0.00 0.00 2.39
3838 6519 8.902540 TGTTATATTACATCATTCACTCACCC 57.097 34.615 0.00 0.00 0.00 4.61
3883 6564 2.082231 CTGCTCTAATGCTGCACTTGT 58.918 47.619 3.57 0.00 32.91 3.16
3884 6565 1.808343 TGCTCTAATGCTGCACTTGTG 59.192 47.619 3.57 0.00 0.00 3.33
3945 7077 4.202141 TGTCCAGTTTCCAGAATGCTTTTG 60.202 41.667 0.00 0.00 31.97 2.44
3948 7080 4.301628 CAGTTTCCAGAATGCTTTTGGTC 58.698 43.478 10.91 6.12 33.65 4.02
3955 7087 4.154918 CCAGAATGCTTTTGGTCAGAGTAC 59.845 45.833 0.00 0.00 31.97 2.73
3956 7088 4.999950 CAGAATGCTTTTGGTCAGAGTACT 59.000 41.667 0.00 0.00 0.00 2.73
3957 7089 6.166279 CAGAATGCTTTTGGTCAGAGTACTA 58.834 40.000 0.00 0.00 0.00 1.82
3958 7090 6.091441 CAGAATGCTTTTGGTCAGAGTACTAC 59.909 42.308 0.00 0.00 0.00 2.73
3959 7091 4.948341 TGCTTTTGGTCAGAGTACTACA 57.052 40.909 0.00 0.00 0.00 2.74
3960 7092 5.483685 TGCTTTTGGTCAGAGTACTACAT 57.516 39.130 0.00 0.00 0.00 2.29
3961 7093 6.599356 TGCTTTTGGTCAGAGTACTACATA 57.401 37.500 0.00 0.00 0.00 2.29
3962 7094 7.182817 TGCTTTTGGTCAGAGTACTACATAT 57.817 36.000 0.00 0.00 0.00 1.78
3963 7095 7.620880 TGCTTTTGGTCAGAGTACTACATATT 58.379 34.615 0.00 0.00 0.00 1.28
3964 7096 7.549134 TGCTTTTGGTCAGAGTACTACATATTG 59.451 37.037 0.00 0.00 0.00 1.90
3965 7097 7.466050 GCTTTTGGTCAGAGTACTACATATTGC 60.466 40.741 0.00 0.00 0.00 3.56
4022 7166 4.351111 ACATAACCAGGTCCTGTTCTTCTT 59.649 41.667 17.85 2.12 0.00 2.52
4032 7176 4.936411 GTCCTGTTCTTCTTAGGCTTTACC 59.064 45.833 0.00 0.00 39.61 2.85
4034 7178 3.933332 CTGTTCTTCTTAGGCTTTACCGG 59.067 47.826 0.00 0.00 46.52 5.28
4035 7179 3.268330 GTTCTTCTTAGGCTTTACCGGG 58.732 50.000 6.32 0.00 46.52 5.73
4055 7199 5.334879 CCGGGTTTTCAGTCATAAAACAGAG 60.335 44.000 12.05 4.36 44.76 3.35
4056 7200 5.238650 CGGGTTTTCAGTCATAAAACAGAGT 59.761 40.000 12.05 0.00 44.76 3.24
4057 7201 6.438763 GGGTTTTCAGTCATAAAACAGAGTG 58.561 40.000 12.05 0.00 44.76 3.51
4068 7215 8.770828 GTCATAAAACAGAGTGCTTGTAACTTA 58.229 33.333 0.00 0.00 0.00 2.24
4106 7253 9.840427 GATTTTGGTGTTATGGATATATTTCGG 57.160 33.333 0.00 0.00 0.00 4.30
4107 7254 8.754991 TTTTGGTGTTATGGATATATTTCGGT 57.245 30.769 0.00 0.00 0.00 4.69
4108 7255 7.737972 TTGGTGTTATGGATATATTTCGGTG 57.262 36.000 0.00 0.00 0.00 4.94
4109 7256 5.703592 TGGTGTTATGGATATATTTCGGTGC 59.296 40.000 0.00 0.00 0.00 5.01
4110 7257 5.938125 GGTGTTATGGATATATTTCGGTGCT 59.062 40.000 0.00 0.00 0.00 4.40
4160 7312 3.475566 TGCTGATAGATGTTACCCTGC 57.524 47.619 0.00 0.00 0.00 4.85
4230 7382 8.923683 GTTGTACTATACTCTGAAGTTTGAACC 58.076 37.037 0.00 0.00 36.92 3.62
4239 7391 3.815401 CTGAAGTTTGAACCGTGATCCTT 59.185 43.478 0.00 0.00 0.00 3.36
4297 7449 2.766263 TCCGACAAAGATGCTGATACCT 59.234 45.455 0.00 0.00 0.00 3.08
4329 7481 6.535540 TGCTCCTTGTACCTTTAATTACACA 58.464 36.000 0.00 0.00 0.00 3.72
4333 7485 7.172342 TCCTTGTACCTTTAATTACACATGCT 58.828 34.615 0.00 0.00 0.00 3.79
4430 7582 2.253603 GATTGCTCATGAAAACGTGCC 58.746 47.619 0.00 0.00 0.00 5.01
4434 7594 1.922135 CTCATGAAAACGTGCCGGGG 61.922 60.000 2.18 0.00 0.00 5.73
4472 7632 3.252215 TGTTATTCTTTGGTGACGCCTTG 59.748 43.478 6.60 0.00 38.35 3.61
4517 7714 3.517602 CAATGGCCAACATCATTGTCTG 58.482 45.455 10.96 0.00 42.90 3.51
4524 7721 1.028330 ACATCATTGTCTGCCCTGCG 61.028 55.000 0.00 0.00 0.00 5.18
4535 7732 1.141019 GCCCTGCGTAGATTGTCGA 59.859 57.895 0.53 0.00 0.00 4.20
4590 7795 5.270853 CGTTGCTGCCCTTAATTTATGTAC 58.729 41.667 0.00 0.00 0.00 2.90
4591 7796 5.065988 CGTTGCTGCCCTTAATTTATGTACT 59.934 40.000 0.00 0.00 0.00 2.73
4592 7797 6.404293 CGTTGCTGCCCTTAATTTATGTACTT 60.404 38.462 0.00 0.00 0.00 2.24
4593 7798 7.320399 GTTGCTGCCCTTAATTTATGTACTTT 58.680 34.615 0.00 0.00 0.00 2.66
4594 7799 7.475137 TGCTGCCCTTAATTTATGTACTTTT 57.525 32.000 0.00 0.00 0.00 2.27
4615 7820 6.909550 TTTTGTTGGAATACTGGTTGCTAT 57.090 33.333 0.00 0.00 0.00 2.97
4632 7837 9.311916 TGGTTGCTATTCATAATTTATGTTTGC 57.688 29.630 14.48 14.63 37.45 3.68
4650 7855 6.990798 TGTTTGCAATATGATTGAAGGTTGA 58.009 32.000 0.00 0.00 0.00 3.18
4652 7857 7.546316 TGTTTGCAATATGATTGAAGGTTGATG 59.454 33.333 0.00 0.00 0.00 3.07
4664 7869 5.185454 TGAAGGTTGATGGTACTATGCTTG 58.815 41.667 0.00 0.00 0.00 4.01
4829 8061 5.523916 GGCACGTTATCTCTGTTGACATTAT 59.476 40.000 0.00 0.00 0.00 1.28
4831 8063 6.901887 GCACGTTATCTCTGTTGACATTATTG 59.098 38.462 0.00 0.00 0.00 1.90
4833 8065 7.064609 CACGTTATCTCTGTTGACATTATTGGT 59.935 37.037 0.00 0.00 0.00 3.67
4835 8067 7.277760 CGTTATCTCTGTTGACATTATTGGTCA 59.722 37.037 0.00 0.00 43.12 4.02
4871 8103 0.166814 CAAGTTTGCGCTAGTGGCTC 59.833 55.000 9.73 0.00 39.13 4.70
4874 8106 0.108329 GTTTGCGCTAGTGGCTCCTA 60.108 55.000 9.73 0.00 39.13 2.94
4888 8120 2.342179 GCTCCTACAAGTCTTGACTGC 58.658 52.381 19.53 11.12 0.00 4.40
4952 8184 2.149973 AAAAGCAGCTATTCCCCTGG 57.850 50.000 0.00 0.00 0.00 4.45
5012 8244 1.657804 GGCTGGGCCTGGTATATACT 58.342 55.000 12.70 0.00 46.69 2.12
5013 8245 1.555533 GGCTGGGCCTGGTATATACTC 59.444 57.143 12.70 3.99 46.69 2.59
5014 8246 1.555533 GCTGGGCCTGGTATATACTCC 59.444 57.143 12.70 8.60 0.00 3.85
5053 8290 6.893020 AAAGGTACTCCAGGATATTCACTT 57.107 37.500 0.00 0.00 38.49 3.16
5130 8370 2.422832 CCATCAAGCAAAGCTCCTCTTC 59.577 50.000 0.00 0.00 38.25 2.87
5132 8372 3.430042 TCAAGCAAAGCTCCTCTTCAT 57.570 42.857 0.00 0.00 38.25 2.57
5134 8374 3.755378 TCAAGCAAAGCTCCTCTTCATTC 59.245 43.478 0.00 0.00 38.25 2.67
5135 8375 3.717452 AGCAAAGCTCCTCTTCATTCT 57.283 42.857 0.00 0.00 30.62 2.40
5138 8378 4.458642 AGCAAAGCTCCTCTTCATTCTTTC 59.541 41.667 0.00 0.00 30.62 2.62
5157 8398 6.985117 TCTTTCTGAATGCAATAACAGCTTT 58.015 32.000 0.00 0.00 33.14 3.51
5158 8399 8.109705 TCTTTCTGAATGCAATAACAGCTTTA 57.890 30.769 0.00 0.00 33.14 1.85
5159 8400 8.023128 TCTTTCTGAATGCAATAACAGCTTTAC 58.977 33.333 0.00 0.00 33.14 2.01
5160 8401 6.816134 TCTGAATGCAATAACAGCTTTACA 57.184 33.333 0.00 0.00 33.14 2.41
5161 8402 7.213216 TCTGAATGCAATAACAGCTTTACAA 57.787 32.000 0.00 0.00 33.14 2.41
5162 8403 7.307694 TCTGAATGCAATAACAGCTTTACAAG 58.692 34.615 0.00 0.00 33.14 3.16
5163 8404 7.174772 TCTGAATGCAATAACAGCTTTACAAGA 59.825 33.333 0.00 0.00 33.14 3.02
5164 8405 7.656412 TGAATGCAATAACAGCTTTACAAGAA 58.344 30.769 0.00 0.00 30.66 2.52
5174 8415 2.287368 GCTTTACAAGAACAACACCCCG 60.287 50.000 0.00 0.00 0.00 5.73
5271 8520 2.563179 AGCTAAACATCGTCACTGTCCT 59.437 45.455 0.00 0.00 0.00 3.85
5276 8525 0.037882 CATCGTCACTGTCCTGCTGT 60.038 55.000 0.00 0.00 0.00 4.40
5585 8841 2.202837 GCCGTACTACTTGGGCGG 60.203 66.667 0.00 0.00 44.60 6.13
5586 8842 2.202837 CCGTACTACTTGGGCGGC 60.203 66.667 0.00 0.00 35.90 6.53
5587 8843 2.574929 CGTACTACTTGGGCGGCA 59.425 61.111 12.47 0.00 0.00 5.69
5588 8844 1.143183 CGTACTACTTGGGCGGCAT 59.857 57.895 12.47 0.00 0.00 4.40
5589 8845 0.386476 CGTACTACTTGGGCGGCATA 59.614 55.000 12.47 0.00 0.00 3.14
5590 8846 1.602165 CGTACTACTTGGGCGGCATAG 60.602 57.143 12.47 9.73 0.00 2.23
5597 8853 2.234908 ACTTGGGCGGCATAGATAGATC 59.765 50.000 12.47 0.00 0.00 2.75
5599 8855 0.528684 GGGCGGCATAGATAGATCGC 60.529 60.000 12.47 0.00 42.02 4.58
5612 8868 1.139734 GATCGCTCGCTCACTTCCA 59.860 57.895 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 111 1.139734 GAAGTCCTGCGCGATCTCA 59.860 57.895 12.10 0.00 0.00 3.27
377 378 4.002906 AGAGCGAACAGGAACATGTTAA 57.997 40.909 11.95 0.00 43.32 2.01
392 394 1.487482 CAAGACAACGACAAGAGCGA 58.513 50.000 0.00 0.00 0.00 4.93
399 401 3.052455 ACATATGGCAAGACAACGACA 57.948 42.857 7.80 0.00 0.00 4.35
495 497 2.521771 GCAACACACGTCGCACAGA 61.522 57.895 0.00 0.00 0.00 3.41
496 498 2.035617 AAGCAACACACGTCGCACAG 62.036 55.000 0.00 0.00 0.00 3.66
497 499 1.640210 AAAGCAACACACGTCGCACA 61.640 50.000 0.00 0.00 0.00 4.57
498 500 0.923911 GAAAGCAACACACGTCGCAC 60.924 55.000 0.00 0.00 0.00 5.34
499 501 1.087202 AGAAAGCAACACACGTCGCA 61.087 50.000 0.00 0.00 0.00 5.10
500 502 0.027586 AAGAAAGCAACACACGTCGC 59.972 50.000 0.00 0.00 0.00 5.19
502 504 2.825086 ACAAGAAAGCAACACACGTC 57.175 45.000 0.00 0.00 0.00 4.34
503 505 2.747446 AGAACAAGAAAGCAACACACGT 59.253 40.909 0.00 0.00 0.00 4.49
504 506 3.405170 AGAACAAGAAAGCAACACACG 57.595 42.857 0.00 0.00 0.00 4.49
505 507 4.732784 TGAAGAACAAGAAAGCAACACAC 58.267 39.130 0.00 0.00 0.00 3.82
507 509 4.986622 ACTGAAGAACAAGAAAGCAACAC 58.013 39.130 0.00 0.00 0.00 3.32
508 510 5.643379 AACTGAAGAACAAGAAAGCAACA 57.357 34.783 0.00 0.00 0.00 3.33
509 511 5.228012 CGAAACTGAAGAACAAGAAAGCAAC 59.772 40.000 0.00 0.00 0.00 4.17
510 512 5.106317 ACGAAACTGAAGAACAAGAAAGCAA 60.106 36.000 0.00 0.00 0.00 3.91
553 573 1.629013 TACGCTTCATCTGCTTCACG 58.371 50.000 0.00 0.00 0.00 4.35
564 584 8.154203 TCCATGGATAGAAATTATTACGCTTCA 58.846 33.333 11.44 0.00 0.00 3.02
580 613 4.467795 ACGGGATGTCTAATCCATGGATAG 59.532 45.833 27.54 21.80 39.93 2.08
581 614 4.425772 ACGGGATGTCTAATCCATGGATA 58.574 43.478 27.54 12.13 39.93 2.59
595 628 2.806945 ACAATCCAATGACGGGATGT 57.193 45.000 0.00 0.00 44.30 3.06
649 686 3.568538 CATCAGAAAACCCAAGCGAAAG 58.431 45.455 0.00 0.00 0.00 2.62
653 690 1.068333 CACCATCAGAAAACCCAAGCG 60.068 52.381 0.00 0.00 0.00 4.68
654 691 1.337167 GCACCATCAGAAAACCCAAGC 60.337 52.381 0.00 0.00 0.00 4.01
658 695 0.244721 GCAGCACCATCAGAAAACCC 59.755 55.000 0.00 0.00 0.00 4.11
659 696 1.068055 CAGCAGCACCATCAGAAAACC 60.068 52.381 0.00 0.00 0.00 3.27
672 709 0.906775 TCATCTCCATCACAGCAGCA 59.093 50.000 0.00 0.00 0.00 4.41
733 771 3.218453 ACACAATTCCAAATCACGGTGA 58.782 40.909 14.01 14.01 0.00 4.02
740 778 8.831715 AATAGGAAACAACACAATTCCAAATC 57.168 30.769 6.55 0.00 44.08 2.17
741 779 9.271828 GAAATAGGAAACAACACAATTCCAAAT 57.728 29.630 6.55 0.00 44.08 2.32
745 783 7.598869 GGAAGAAATAGGAAACAACACAATTCC 59.401 37.037 0.00 0.00 42.38 3.01
747 785 7.441836 GGGAAGAAATAGGAAACAACACAATT 58.558 34.615 0.00 0.00 0.00 2.32
748 786 6.014584 GGGGAAGAAATAGGAAACAACACAAT 60.015 38.462 0.00 0.00 0.00 2.71
749 787 5.303333 GGGGAAGAAATAGGAAACAACACAA 59.697 40.000 0.00 0.00 0.00 3.33
750 788 4.830600 GGGGAAGAAATAGGAAACAACACA 59.169 41.667 0.00 0.00 0.00 3.72
751 789 4.830600 TGGGGAAGAAATAGGAAACAACAC 59.169 41.667 0.00 0.00 0.00 3.32
753 791 5.321927 TCTGGGGAAGAAATAGGAAACAAC 58.678 41.667 0.00 0.00 29.54 3.32
755 793 5.796502 ATCTGGGGAAGAAATAGGAAACA 57.203 39.130 0.00 0.00 38.79 2.83
756 794 7.039011 ACAAAATCTGGGGAAGAAATAGGAAAC 60.039 37.037 0.00 0.00 38.79 2.78
758 796 6.561294 ACAAAATCTGGGGAAGAAATAGGAA 58.439 36.000 0.00 0.00 38.79 3.36
759 797 6.152638 ACAAAATCTGGGGAAGAAATAGGA 57.847 37.500 0.00 0.00 38.79 2.94
760 798 6.857437 AACAAAATCTGGGGAAGAAATAGG 57.143 37.500 0.00 0.00 38.79 2.57
761 799 7.603784 CCAAAACAAAATCTGGGGAAGAAATAG 59.396 37.037 0.00 0.00 38.79 1.73
767 805 4.953940 TCCAAAACAAAATCTGGGGAAG 57.046 40.909 0.00 0.00 0.00 3.46
813 851 0.102120 CCAACAGAAGCGGCAAACAA 59.898 50.000 1.45 0.00 0.00 2.83
815 853 1.007387 CCCAACAGAAGCGGCAAAC 60.007 57.895 1.45 0.00 0.00 2.93
833 872 3.262686 GATTCCTTCCGCCGACGC 61.263 66.667 0.00 0.00 38.22 5.19
834 873 2.585247 GGATTCCTTCCGCCGACG 60.585 66.667 0.00 0.00 33.93 5.12
881 920 3.253838 AGCGGGCCAGGGTTGTTA 61.254 61.111 4.39 0.00 0.00 2.41
882 921 4.974721 CAGCGGGCCAGGGTTGTT 62.975 66.667 4.39 0.00 0.00 2.83
887 926 4.431131 AATGACAGCGGGCCAGGG 62.431 66.667 4.39 0.00 0.00 4.45
888 927 3.136123 CAATGACAGCGGGCCAGG 61.136 66.667 4.39 0.00 0.00 4.45
911 950 3.300765 ACACCCCCACGACGTCTC 61.301 66.667 14.70 0.00 0.00 3.36
912 951 3.612681 CACACCCCCACGACGTCT 61.613 66.667 14.70 0.00 0.00 4.18
928 967 2.354704 CCTACTTTGCTGGATTCGGTCA 60.355 50.000 0.00 0.00 0.00 4.02
994 1033 0.034477 GGATGGATGGGTTTGGACGT 60.034 55.000 0.00 0.00 0.00 4.34
1007 1047 4.041762 GGCGGTGGGTTGGATGGA 62.042 66.667 0.00 0.00 0.00 3.41
1050 1090 4.637489 CATCTCCGCTCCGCCGAG 62.637 72.222 0.00 0.00 39.33 4.63
1052 1092 4.207281 TTCATCTCCGCTCCGCCG 62.207 66.667 0.00 0.00 0.00 6.46
1053 1093 2.093537 ATCTTCATCTCCGCTCCGCC 62.094 60.000 0.00 0.00 0.00 6.13
1054 1094 0.665972 GATCTTCATCTCCGCTCCGC 60.666 60.000 0.00 0.00 0.00 5.54
1277 1317 1.668151 GTCACCTTCGTGCTGGACC 60.668 63.158 0.00 0.00 40.04 4.46
1293 1333 2.444895 ATCTGAGGAGGGGCGGTC 60.445 66.667 0.00 0.00 0.00 4.79
1323 1363 7.894364 TCACAAAGTAAACTAGACCTAGAGGAT 59.106 37.037 10.74 0.00 38.94 3.24
1324 1364 7.236529 TCACAAAGTAAACTAGACCTAGAGGA 58.763 38.462 10.74 0.00 38.94 3.71
1395 1435 0.173708 CCGTAGCAGAAGACTGACCC 59.826 60.000 0.00 0.00 46.03 4.46
1410 1450 1.252904 AAACTACTGCGAGCCCCGTA 61.253 55.000 0.00 0.00 41.15 4.02
1416 1456 2.622436 AGGAATCAAACTACTGCGAGC 58.378 47.619 0.00 0.00 0.00 5.03
1446 1486 2.180204 CCGGAATCACCCATGTCGC 61.180 63.158 0.00 0.00 34.64 5.19
1448 1488 0.251916 TCACCGGAATCACCCATGTC 59.748 55.000 9.46 0.00 34.64 3.06
1494 1534 0.615331 ACATCGGATGAACTGCCAGT 59.385 50.000 23.98 0.00 0.00 4.00
1648 1689 5.007528 GGGTTTAAATTACGCCGTAAGCATA 59.992 40.000 15.55 5.62 44.04 3.14
1744 1786 8.839947 TTCACAATTACATATGCGAAAATGAG 57.160 30.769 1.58 0.00 0.00 2.90
1770 1812 4.759693 ACAAAGCGTTTGAATGATCCTGTA 59.240 37.500 14.58 0.00 43.26 2.74
1774 1816 3.163594 CGACAAAGCGTTTGAATGATCC 58.836 45.455 14.58 0.00 43.26 3.36
1775 1817 3.810373 ACGACAAAGCGTTTGAATGATC 58.190 40.909 14.58 0.00 42.71 2.92
1787 1829 3.065019 TCTGCAAAGAAACGACAAAGC 57.935 42.857 0.00 0.00 0.00 3.51
1961 2004 4.057432 CCTGCACAGTTGGTAAAAATTGG 58.943 43.478 0.00 0.00 0.00 3.16
1976 2019 1.833630 AGGAAGATCGAATCCTGCACA 59.166 47.619 14.81 0.00 44.38 4.57
2134 2217 5.416952 ACTTCTCTAATGTTGAGGGCAATTG 59.583 40.000 0.00 0.00 36.22 2.32
2181 2264 1.379977 TCCGCCACTCACTAGGGAG 60.380 63.158 20.82 20.82 40.79 4.30
2207 2290 3.140814 GCCCGCCCAGATGTTTCC 61.141 66.667 0.00 0.00 0.00 3.13
2286 2369 2.675348 GCATCTCCTGACTTACACAAGC 59.325 50.000 0.00 0.00 34.94 4.01
2316 2399 1.378531 ACTGCATGACAACAACGTGT 58.621 45.000 0.00 0.00 0.00 4.49
2349 2433 5.941948 AGCAAAGACTGTACATGGTTTAC 57.058 39.130 0.00 0.00 0.00 2.01
2389 2732 1.942657 ACGCATGAATGTATGTCAGGC 59.057 47.619 0.00 1.21 46.51 4.85
2433 2783 7.654520 CAGAAAATATTTGCATGACCCCAATAG 59.345 37.037 8.91 0.00 0.00 1.73
2500 2850 7.974482 AAGTATCACCCAAAAACACTACTAC 57.026 36.000 0.00 0.00 0.00 2.73
2670 3020 3.189287 CACAAGCATACAGAACCTTCCAC 59.811 47.826 0.00 0.00 0.00 4.02
2734 3084 1.906574 CTAGAGGTTACCAAGCCACCA 59.093 52.381 3.51 0.00 32.43 4.17
2735 3085 2.093606 GTCTAGAGGTTACCAAGCCACC 60.094 54.545 3.51 0.00 0.00 4.61
2737 3087 2.832129 CAGTCTAGAGGTTACCAAGCCA 59.168 50.000 3.51 0.00 0.00 4.75
2739 3089 2.832733 ACCAGTCTAGAGGTTACCAAGC 59.167 50.000 3.51 0.00 33.39 4.01
2740 3090 4.345854 AGACCAGTCTAGAGGTTACCAAG 58.654 47.826 3.51 0.00 38.50 3.61
2742 3092 5.728937 ATAGACCAGTCTAGAGGTTACCA 57.271 43.478 12.72 0.00 44.47 3.25
2744 3094 8.795513 GGATAAATAGACCAGTCTAGAGGTTAC 58.204 40.741 12.72 0.00 44.47 2.50
2745 3095 8.734763 AGGATAAATAGACCAGTCTAGAGGTTA 58.265 37.037 12.72 8.73 44.47 2.85
2747 3097 7.169287 AGGATAAATAGACCAGTCTAGAGGT 57.831 40.000 12.72 3.37 44.47 3.85
2780 3130 6.070538 CCTCCCTCTCATTTTCTCTTTCTGTA 60.071 42.308 0.00 0.00 0.00 2.74
2848 3198 5.724328 ACACGATACAATGGATATAGCAGG 58.276 41.667 0.00 0.00 0.00 4.85
2960 3317 3.456380 ACCACAAGATACAGCCCATTT 57.544 42.857 0.00 0.00 0.00 2.32
3020 3377 1.448893 GGAACGCCGCACCTGATTA 60.449 57.895 0.00 0.00 0.00 1.75
3330 3750 6.351711 CATGGTGAAGATCATCTTTACAGGA 58.648 40.000 20.66 7.31 42.62 3.86
3354 3774 5.474578 TGATATCTCCAGTACAAGATGGC 57.525 43.478 12.94 7.37 36.47 4.40
3663 4113 9.710900 CAATCTAATGGAGTATATGCACAACTA 57.289 33.333 0.00 0.00 28.84 2.24
3665 4115 8.383318 ACAATCTAATGGAGTATATGCACAAC 57.617 34.615 0.00 0.00 28.84 3.32
3707 6381 1.077501 CCCATGGGCAGTGATTCGT 60.078 57.895 20.41 0.00 0.00 3.85
3708 6382 1.097547 GTCCCATGGGCAGTGATTCG 61.098 60.000 27.41 0.00 34.68 3.34
3710 6384 1.212935 GTAGTCCCATGGGCAGTGATT 59.787 52.381 27.41 7.81 34.68 2.57
3735 6415 8.844244 AGCAGATGAATAGAAATAAATGTCCAC 58.156 33.333 0.00 0.00 0.00 4.02
3736 6416 8.985315 AGCAGATGAATAGAAATAAATGTCCA 57.015 30.769 0.00 0.00 0.00 4.02
3782 6463 5.690865 TCTTATCATACCAAACCCCACATC 58.309 41.667 0.00 0.00 0.00 3.06
3817 6498 9.071276 GAAATGGGTGAGTGAATGATGTAATAT 57.929 33.333 0.00 0.00 0.00 1.28
3818 6499 8.274322 AGAAATGGGTGAGTGAATGATGTAATA 58.726 33.333 0.00 0.00 0.00 0.98
3838 6519 4.433186 TGGGCATTGTCGTAAAGAAATG 57.567 40.909 0.00 0.00 34.00 2.32
3918 7050 1.967319 TTCTGGAAACTGGACAGCAC 58.033 50.000 0.00 0.00 32.42 4.40
3945 7077 5.986135 CCTTGCAATATGTAGTACTCTGACC 59.014 44.000 0.00 0.00 0.00 4.02
3948 7080 4.752101 GCCCTTGCAATATGTAGTACTCTG 59.248 45.833 0.00 0.00 37.47 3.35
3955 7087 5.471456 CCTTAAGAGCCCTTGCAATATGTAG 59.529 44.000 3.36 0.00 41.13 2.74
3956 7088 5.376625 CCTTAAGAGCCCTTGCAATATGTA 58.623 41.667 3.36 0.00 41.13 2.29
3957 7089 4.210331 CCTTAAGAGCCCTTGCAATATGT 58.790 43.478 3.36 0.00 41.13 2.29
3958 7090 3.005155 GCCTTAAGAGCCCTTGCAATATG 59.995 47.826 3.36 0.00 41.13 1.78
3959 7091 3.225940 GCCTTAAGAGCCCTTGCAATAT 58.774 45.455 3.36 0.00 41.13 1.28
3960 7092 2.025416 TGCCTTAAGAGCCCTTGCAATA 60.025 45.455 3.36 0.00 41.13 1.90
3961 7093 1.272648 TGCCTTAAGAGCCCTTGCAAT 60.273 47.619 3.36 0.00 41.13 3.56
3962 7094 0.112218 TGCCTTAAGAGCCCTTGCAA 59.888 50.000 3.36 0.00 41.13 4.08
3963 7095 0.609131 GTGCCTTAAGAGCCCTTGCA 60.609 55.000 3.36 0.00 41.13 4.08
3964 7096 0.322906 AGTGCCTTAAGAGCCCTTGC 60.323 55.000 3.36 0.00 33.94 4.01
3965 7097 2.206576 AAGTGCCTTAAGAGCCCTTG 57.793 50.000 3.36 0.00 33.94 3.61
3985 7129 8.721133 ACCTGGTTATGTAAAAAGAAAAGGAT 57.279 30.769 0.00 0.00 0.00 3.24
3986 7130 7.231925 GGACCTGGTTATGTAAAAAGAAAAGGA 59.768 37.037 0.00 0.00 0.00 3.36
3987 7131 7.232737 AGGACCTGGTTATGTAAAAAGAAAAGG 59.767 37.037 0.00 0.00 0.00 3.11
4022 7166 2.372837 ACTGAAAACCCGGTAAAGCCTA 59.627 45.455 0.00 0.00 34.25 3.93
4032 7176 5.238650 ACTCTGTTTTATGACTGAAAACCCG 59.761 40.000 8.15 1.50 43.21 5.28
4034 7178 5.915196 GCACTCTGTTTTATGACTGAAAACC 59.085 40.000 8.15 0.00 43.21 3.27
4035 7179 6.729187 AGCACTCTGTTTTATGACTGAAAAC 58.271 36.000 4.45 4.45 43.83 2.43
4055 7199 8.289618 TCATGATTTTCAGTAAGTTACAAGCAC 58.710 33.333 15.28 1.85 0.00 4.40
4056 7200 8.389779 TCATGATTTTCAGTAAGTTACAAGCA 57.610 30.769 15.28 9.50 0.00 3.91
4057 7201 9.846248 AATCATGATTTTCAGTAAGTTACAAGC 57.154 29.630 15.36 4.29 0.00 4.01
4068 7215 9.426837 CATAACACCAAAATCATGATTTTCAGT 57.573 29.630 33.48 29.44 46.01 3.41
4086 7233 5.938125 AGCACCGAAATATATCCATAACACC 59.062 40.000 0.00 0.00 0.00 4.16
4098 7245 8.519526 TGAAATAAGACAAAAGCACCGAAATAT 58.480 29.630 0.00 0.00 0.00 1.28
4099 7246 7.877003 TGAAATAAGACAAAAGCACCGAAATA 58.123 30.769 0.00 0.00 0.00 1.40
4100 7247 6.744112 TGAAATAAGACAAAAGCACCGAAAT 58.256 32.000 0.00 0.00 0.00 2.17
4103 7250 4.819630 ACTGAAATAAGACAAAAGCACCGA 59.180 37.500 0.00 0.00 0.00 4.69
4104 7251 5.108385 ACTGAAATAAGACAAAAGCACCG 57.892 39.130 0.00 0.00 0.00 4.94
4105 7252 8.296713 TGATAACTGAAATAAGACAAAAGCACC 58.703 33.333 0.00 0.00 0.00 5.01
4106 7253 9.118236 GTGATAACTGAAATAAGACAAAAGCAC 57.882 33.333 0.00 0.00 0.00 4.40
4107 7254 9.066892 AGTGATAACTGAAATAAGACAAAAGCA 57.933 29.630 0.00 0.00 0.00 3.91
4136 7283 5.300286 GCAGGGTAACATCTATCAGCAAAAT 59.700 40.000 0.00 0.00 39.74 1.82
4140 7287 2.104792 GGCAGGGTAACATCTATCAGCA 59.895 50.000 0.00 0.00 39.74 4.41
4141 7288 2.551071 GGGCAGGGTAACATCTATCAGC 60.551 54.545 0.00 0.00 39.74 4.26
4160 7312 4.761739 TGCTTGTAGAACATCTGAAAAGGG 59.238 41.667 0.00 0.00 0.00 3.95
4217 7369 3.403038 AGGATCACGGTTCAAACTTCAG 58.597 45.455 0.00 0.00 0.00 3.02
4230 7382 4.937620 TCCAAGAAAGATTGAAGGATCACG 59.062 41.667 0.00 0.00 34.61 4.35
4239 7391 3.690460 GGAGCCTTCCAAGAAAGATTGA 58.310 45.455 0.00 0.00 43.45 2.57
4297 7449 5.435686 AAGGTACAAGGAGCATGTATGAA 57.564 39.130 0.00 0.00 35.84 2.57
4329 7481 7.530426 AAAAAGTGTCCTGAGAATTAAGCAT 57.470 32.000 0.00 0.00 0.00 3.79
4333 7485 8.437575 AGGAGTAAAAAGTGTCCTGAGAATTAA 58.562 33.333 0.00 0.00 38.05 1.40
4380 7532 4.989797 ACGGTACAACACAACGATATTCAA 59.010 37.500 0.00 0.00 0.00 2.69
4381 7533 4.558178 ACGGTACAACACAACGATATTCA 58.442 39.130 0.00 0.00 0.00 2.57
4430 7582 4.766375 ACAGATTTACAGTATTGACCCCG 58.234 43.478 0.00 0.00 0.00 5.73
4472 7632 6.538742 TGCTAAGTGATGTTAGTTGCTATTCC 59.461 38.462 0.00 0.00 33.24 3.01
4517 7714 0.872021 CTCGACAATCTACGCAGGGC 60.872 60.000 0.00 0.00 0.00 5.19
4524 7721 6.260050 AGAACTGAGAGATCTCGACAATCTAC 59.740 42.308 23.00 15.08 45.72 2.59
4535 7732 7.363705 CCAACATACTTGAGAACTGAGAGATCT 60.364 40.741 0.00 0.00 29.40 2.75
4590 7795 5.600696 AGCAACCAGTATTCCAACAAAAAG 58.399 37.500 0.00 0.00 0.00 2.27
4591 7796 5.606348 AGCAACCAGTATTCCAACAAAAA 57.394 34.783 0.00 0.00 0.00 1.94
4592 7797 6.909550 ATAGCAACCAGTATTCCAACAAAA 57.090 33.333 0.00 0.00 0.00 2.44
4593 7798 6.491745 TGAATAGCAACCAGTATTCCAACAAA 59.508 34.615 0.00 0.00 35.57 2.83
4594 7799 6.007076 TGAATAGCAACCAGTATTCCAACAA 58.993 36.000 0.00 0.00 35.57 2.83
4630 7835 5.657745 ACCATCAACCTTCAATCATATTGCA 59.342 36.000 0.00 0.00 0.00 4.08
4631 7836 6.152932 ACCATCAACCTTCAATCATATTGC 57.847 37.500 0.00 0.00 0.00 3.56
4632 7837 8.455903 AGTACCATCAACCTTCAATCATATTG 57.544 34.615 0.00 0.00 0.00 1.90
4634 7839 9.730705 CATAGTACCATCAACCTTCAATCATAT 57.269 33.333 0.00 0.00 0.00 1.78
4635 7840 7.661437 GCATAGTACCATCAACCTTCAATCATA 59.339 37.037 0.00 0.00 0.00 2.15
4636 7841 6.488006 GCATAGTACCATCAACCTTCAATCAT 59.512 38.462 0.00 0.00 0.00 2.45
4646 7851 4.635765 TCAAGCAAGCATAGTACCATCAAC 59.364 41.667 0.00 0.00 0.00 3.18
4650 7855 6.780457 AAAATCAAGCAAGCATAGTACCAT 57.220 33.333 0.00 0.00 0.00 3.55
4652 7857 9.665264 GTAATAAAATCAAGCAAGCATAGTACC 57.335 33.333 0.00 0.00 0.00 3.34
4723 7928 0.665835 TGTTGACCATTTGACACGGC 59.334 50.000 0.00 0.00 0.00 5.68
4761 7976 1.097232 TTGCATCCAGGAAATCAGCG 58.903 50.000 0.00 0.00 0.00 5.18
4829 8061 4.699637 ACACTGTCGATAACTTTGACCAA 58.300 39.130 0.00 0.00 37.88 3.67
4831 8063 4.304110 TGACACTGTCGATAACTTTGACC 58.696 43.478 4.71 0.00 37.88 4.02
4833 8065 5.597806 ACTTGACACTGTCGATAACTTTGA 58.402 37.500 4.71 0.00 34.95 2.69
4835 8067 6.715464 CAAACTTGACACTGTCGATAACTTT 58.285 36.000 4.71 0.00 34.95 2.66
4871 8103 2.224281 TGGTGCAGTCAAGACTTGTAGG 60.224 50.000 14.75 6.71 40.20 3.18
4874 8106 1.668419 GTGGTGCAGTCAAGACTTGT 58.332 50.000 14.75 0.00 40.20 3.16
4888 8120 0.233590 TCGAATGCGTTTTCGTGGTG 59.766 50.000 17.30 0.00 46.50 4.17
4952 8184 2.512515 CCTCAACGCTAGCCTGGC 60.513 66.667 11.65 11.65 0.00 4.85
4998 8230 1.907255 GGTGGGAGTATATACCAGGCC 59.093 57.143 9.32 0.00 34.39 5.19
5075 8312 2.030540 GCGTACGTGGAATATCCTAGCA 60.031 50.000 17.90 0.00 37.46 3.49
5103 8343 1.969085 CTTTGCTTGATGGCCTGCA 59.031 52.632 3.32 4.02 0.00 4.41
5132 8372 6.579666 AGCTGTTATTGCATTCAGAAAGAA 57.420 33.333 10.58 0.00 41.28 2.52
5134 8374 7.809331 TGTAAAGCTGTTATTGCATTCAGAAAG 59.191 33.333 10.58 0.00 0.00 2.62
5135 8375 7.656412 TGTAAAGCTGTTATTGCATTCAGAAA 58.344 30.769 10.58 0.00 0.00 2.52
5138 8378 7.307694 TCTTGTAAAGCTGTTATTGCATTCAG 58.692 34.615 0.00 0.00 45.70 3.02
5157 8398 1.541670 GCTCGGGGTGTTGTTCTTGTA 60.542 52.381 0.00 0.00 0.00 2.41
5158 8399 0.818040 GCTCGGGGTGTTGTTCTTGT 60.818 55.000 0.00 0.00 0.00 3.16
5159 8400 0.535102 AGCTCGGGGTGTTGTTCTTG 60.535 55.000 0.00 0.00 0.00 3.02
5160 8401 0.182775 AAGCTCGGGGTGTTGTTCTT 59.817 50.000 0.00 0.00 0.00 2.52
5161 8402 0.182775 AAAGCTCGGGGTGTTGTTCT 59.817 50.000 0.00 0.00 0.00 3.01
5162 8403 0.310854 CAAAGCTCGGGGTGTTGTTC 59.689 55.000 0.00 0.00 0.00 3.18
5163 8404 1.734388 GCAAAGCTCGGGGTGTTGTT 61.734 55.000 9.88 0.00 0.00 2.83
5164 8405 2.193536 GCAAAGCTCGGGGTGTTGT 61.194 57.895 9.88 0.00 0.00 3.32
5174 8415 0.661483 GTTCGCACCAAGCAAAGCTC 60.661 55.000 0.00 0.00 46.13 4.09
5209 8458 3.343421 GGCGAGACGGTTTTGCGT 61.343 61.111 4.96 0.00 0.00 5.24
5416 8672 1.665916 CTATCCGCGATGGCTGGTG 60.666 63.158 8.23 0.00 37.80 4.17
5484 8740 1.301293 GGAGAAAGTGAGGCTGGGG 59.699 63.158 0.00 0.00 0.00 4.96
5584 8840 1.403679 AGCGAGCGATCTATCTATGCC 59.596 52.381 0.00 0.00 0.00 4.40
5585 8841 2.096657 TGAGCGAGCGATCTATCTATGC 59.903 50.000 9.60 0.00 0.00 3.14
5586 8842 3.373748 AGTGAGCGAGCGATCTATCTATG 59.626 47.826 9.60 0.00 0.00 2.23
5587 8843 3.605634 AGTGAGCGAGCGATCTATCTAT 58.394 45.455 9.60 0.00 0.00 1.98
5588 8844 3.046968 AGTGAGCGAGCGATCTATCTA 57.953 47.619 9.60 0.00 0.00 1.98
5589 8845 1.890876 AGTGAGCGAGCGATCTATCT 58.109 50.000 9.60 3.14 0.00 1.98
5590 8846 2.580589 GAAGTGAGCGAGCGATCTATC 58.419 52.381 9.60 0.00 0.00 2.08
5597 8853 2.507992 CCTGGAAGTGAGCGAGCG 60.508 66.667 0.00 0.00 0.00 5.03
5599 8855 2.125350 GCCCTGGAAGTGAGCGAG 60.125 66.667 0.00 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.