Multiple sequence alignment - TraesCS3D01G332300

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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 TraesCS3D01G332300 chr3D 100.000 5128 0 0 1 5128 444677244 444672117 0.000000e+00 9470.0
1 TraesCS3D01G332300 chr3D 95.098 102 2 2 534 632 336826076 336826177 1.910000e-34 158.0
2 TraesCS3D01G332300 chr3A 94.084 1758 71 18 1863 3604 585476680 585474940 0.000000e+00 2639.0
3 TraesCS3D01G332300 chr3A 94.907 1296 54 6 3609 4899 585474775 585473487 0.000000e+00 2017.0
4 TraesCS3D01G332300 chr3A 97.137 489 13 1 1379 1867 585477219 585476732 0.000000e+00 824.0
5 TraesCS3D01G332300 chr3A 83.333 672 43 30 704 1355 585478225 585477603 1.610000e-154 556.0
6 TraesCS3D01G332300 chr3A 89.526 401 19 9 1 378 585479204 585478804 2.150000e-133 486.0
7 TraesCS3D01G332300 chr3A 92.661 109 7 1 534 641 678509033 678508925 6.870000e-34 156.0
8 TraesCS3D01G332300 chr3A 100.000 34 0 0 5095 5128 585473489 585473456 4.290000e-06 63.9
9 TraesCS3D01G332300 chr3B 89.411 1001 72 11 3424 4420 582464093 582463123 0.000000e+00 1230.0
10 TraesCS3D01G332300 chr3B 91.527 897 40 16 1383 2272 582466352 582465485 0.000000e+00 1203.0
11 TraesCS3D01G332300 chr3B 90.113 708 41 12 683 1375 582467349 582466656 0.000000e+00 893.0
12 TraesCS3D01G332300 chr3B 91.319 576 21 12 2314 2884 582465486 582464935 0.000000e+00 760.0
13 TraesCS3D01G332300 chr3B 91.848 552 30 3 2889 3425 582464805 582464254 0.000000e+00 756.0
14 TraesCS3D01G332300 chr3B 84.919 431 27 17 1 417 582467931 582467525 8.000000e-108 401.0
15 TraesCS3D01G332300 chr4B 84.746 354 36 5 4789 5128 142684443 142684792 6.360000e-89 339.0
16 TraesCS3D01G332300 chr4B 87.805 246 22 6 4543 4787 142683791 142684029 1.090000e-71 281.0
17 TraesCS3D01G332300 chr7A 96.000 100 4 0 534 633 445605691 445605790 4.110000e-36 163.0
18 TraesCS3D01G332300 chr7A 96.907 97 3 0 534 630 701288403 701288499 4.110000e-36 163.0
19 TraesCS3D01G332300 chr2A 96.040 101 2 1 534 632 81461686 81461586 4.110000e-36 163.0
20 TraesCS3D01G332300 chr2A 95.960 99 4 0 534 632 32775195 32775097 1.480000e-35 161.0
21 TraesCS3D01G332300 chr1D 75.783 351 70 6 4789 5125 468835246 468835595 4.110000e-36 163.0
22 TraesCS3D01G332300 chr1A 95.960 99 4 0 534 632 407652279 407652377 1.480000e-35 161.0
23 TraesCS3D01G332300 chr1A 94.949 99 5 0 534 632 10585606 10585704 6.870000e-34 156.0
24 TraesCS3D01G332300 chr1B 94.118 102 6 0 534 635 160502066 160502167 6.870000e-34 156.0
25 TraesCS3D01G332300 chr6D 82.759 116 20 0 5013 5128 445999426 445999541 2.530000e-18 104.0


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 TraesCS3D01G332300 chr3D 444672117 444677244 5127 True 9470.000000 9470 100.000000 1 5128 1 chr3D.!!$R1 5127
1 TraesCS3D01G332300 chr3A 585473456 585479204 5748 True 1097.650000 2639 93.164500 1 5128 6 chr3A.!!$R2 5127
2 TraesCS3D01G332300 chr3B 582463123 582467931 4808 True 873.833333 1230 89.856167 1 4420 6 chr3B.!!$R1 4419
3 TraesCS3D01G332300 chr4B 142683791 142684792 1001 False 310.000000 339 86.275500 4543 5128 2 chr4B.!!$F1 585

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
457 896 0.170561 GTGTACTCACCGAGACGCAT 59.829 55.0 0.00 0.00 38.51 4.73 F
1146 1604 0.038067 TGTATGGTTGCGCGTACTGT 60.038 50.0 8.43 2.65 0.00 3.55 F
1667 2514 0.829182 CTGGTGCTCTTTTTGCCCCT 60.829 55.0 0.00 0.00 0.00 4.79 F
2735 3644 0.857935 GCGCAGTCATCTGATACAGC 59.142 55.0 0.30 0.00 43.76 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1375 1847 0.536460 ACAACAAGCGTAACAGGGGG 60.536 55.000 0.0 0.0 0.00 5.40 R
2573 3482 1.381056 TGCCCTTGCAACCTGTGTT 60.381 52.632 0.0 0.0 46.66 3.32 R
2884 3801 1.471287 GGGAAACAATACTTGGCGTCC 59.529 52.381 0.0 0.0 34.12 4.79 R
4479 5859 0.320771 CCATACGCCCTAGCATGTCC 60.321 60.000 0.0 0.0 39.83 4.02 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
63 64 2.260844 ATCATACACCAATCAGCCGG 57.739 50.000 0.00 0.00 0.00 6.13
144 153 0.395173 AAACAAGTGACCAAGCCCGT 60.395 50.000 0.00 0.00 0.00 5.28
186 204 3.957497 GACCAGGGCATCTATCGATCTAT 59.043 47.826 0.00 0.00 0.00 1.98
204 228 4.883083 TCTATCTACCAATCAATCCACGC 58.117 43.478 0.00 0.00 0.00 5.34
236 260 0.742990 GCCATTCCGGTCGATCACAA 60.743 55.000 0.00 0.00 36.97 3.33
264 288 1.410850 CCAGCGTCCCATACCCAGAT 61.411 60.000 0.00 0.00 0.00 2.90
298 326 3.252974 AGCACGAAATTACTCTCCCAG 57.747 47.619 0.00 0.00 0.00 4.45
304 332 0.253630 AATTACTCTCCCAGCCCCCA 60.254 55.000 0.00 0.00 0.00 4.96
316 344 3.120086 GCCCCCACTATGGCGATGT 62.120 63.158 0.00 0.00 38.00 3.06
324 352 1.202651 ACTATGGCGATGTGCTAACCC 60.203 52.381 0.00 0.00 45.43 4.11
343 371 3.091545 CCCTGCATCACCATTACAGTTT 58.908 45.455 0.00 0.00 0.00 2.66
345 373 4.096382 CCCTGCATCACCATTACAGTTTAC 59.904 45.833 0.00 0.00 0.00 2.01
347 375 5.163723 CCTGCATCACCATTACAGTTTACAG 60.164 44.000 0.00 0.00 0.00 2.74
348 376 4.155826 TGCATCACCATTACAGTTTACAGC 59.844 41.667 0.00 0.00 0.00 4.40
349 377 4.438744 GCATCACCATTACAGTTTACAGCC 60.439 45.833 0.00 0.00 0.00 4.85
351 379 3.329520 TCACCATTACAGTTTACAGCCCT 59.670 43.478 0.00 0.00 0.00 5.19
385 724 3.697045 TCTCTACAGGCTTAGCTTCAGTC 59.303 47.826 3.59 0.00 0.00 3.51
417 756 0.673333 ATGACACGCAGGAAATCGCA 60.673 50.000 0.00 0.00 0.00 5.10
418 757 0.882484 TGACACGCAGGAAATCGCAA 60.882 50.000 0.00 0.00 0.00 4.85
434 873 4.668576 TCGCAATTCTGAAGCTACTTTG 57.331 40.909 0.00 0.00 0.00 2.77
442 881 3.323691 TCTGAAGCTACTTTGGCAGTGTA 59.676 43.478 0.00 0.00 35.97 2.90
457 896 0.170561 GTGTACTCACCGAGACGCAT 59.829 55.000 0.00 0.00 38.51 4.73
465 904 1.590238 CACCGAGACGCATCTGAAATC 59.410 52.381 0.00 0.00 34.34 2.17
477 916 3.340814 TCTGAAATCCAGGCTCTGTTC 57.659 47.619 0.00 1.07 43.12 3.18
493 932 0.935196 GTTCGCGTTTCTGAAGGTGT 59.065 50.000 5.77 0.00 33.94 4.16
502 941 2.869233 TCTGAAGGTGTTTTTGCAGC 57.131 45.000 0.00 0.00 37.16 5.25
507 946 2.989422 AGGTGTTTTTGCAGCGTATC 57.011 45.000 0.00 0.00 41.28 2.24
512 951 2.359214 TGTTTTTGCAGCGTATCCACAA 59.641 40.909 0.00 0.00 0.00 3.33
526 965 2.238521 TCCACAATTTCTGAAGGTGGC 58.761 47.619 22.57 0.00 46.62 5.01
527 966 1.962807 CCACAATTTCTGAAGGTGGCA 59.037 47.619 18.53 0.00 42.11 4.92
528 967 2.364970 CCACAATTTCTGAAGGTGGCAA 59.635 45.455 18.53 0.00 42.11 4.52
530 969 4.503643 CCACAATTTCTGAAGGTGGCAATT 60.504 41.667 18.53 1.60 42.11 2.32
531 970 5.058490 CACAATTTCTGAAGGTGGCAATTT 58.942 37.500 0.00 0.00 0.00 1.82
532 971 5.178067 CACAATTTCTGAAGGTGGCAATTTC 59.822 40.000 0.00 0.00 0.00 2.17
533 972 4.541973 ATTTCTGAAGGTGGCAATTTCC 57.458 40.909 9.05 0.00 0.00 3.13
534 973 1.533625 TCTGAAGGTGGCAATTTCCG 58.466 50.000 9.05 4.25 0.00 4.30
535 974 1.073125 TCTGAAGGTGGCAATTTCCGA 59.927 47.619 9.05 6.16 0.00 4.55
536 975 1.470098 CTGAAGGTGGCAATTTCCGAG 59.530 52.381 9.05 0.00 0.00 4.63
537 976 1.073125 TGAAGGTGGCAATTTCCGAGA 59.927 47.619 9.05 0.00 0.00 4.04
538 977 1.740025 GAAGGTGGCAATTTCCGAGAG 59.260 52.381 0.00 0.00 0.00 3.20
539 978 0.693049 AGGTGGCAATTTCCGAGAGT 59.307 50.000 0.00 0.00 0.00 3.24
540 979 1.906574 AGGTGGCAATTTCCGAGAGTA 59.093 47.619 0.00 0.00 0.00 2.59
541 980 2.304761 AGGTGGCAATTTCCGAGAGTAA 59.695 45.455 0.00 0.00 0.00 2.24
542 981 3.054361 AGGTGGCAATTTCCGAGAGTAAT 60.054 43.478 0.00 0.00 0.00 1.89
543 982 3.312697 GGTGGCAATTTCCGAGAGTAATC 59.687 47.826 0.00 0.00 0.00 1.75
544 983 4.192317 GTGGCAATTTCCGAGAGTAATCT 58.808 43.478 0.00 0.00 0.00 2.40
545 984 4.034510 GTGGCAATTTCCGAGAGTAATCTG 59.965 45.833 0.00 0.00 0.00 2.90
546 985 4.192317 GGCAATTTCCGAGAGTAATCTGT 58.808 43.478 0.00 0.00 0.00 3.41
547 986 4.636206 GGCAATTTCCGAGAGTAATCTGTT 59.364 41.667 0.00 0.00 0.00 3.16
548 987 5.447818 GGCAATTTCCGAGAGTAATCTGTTG 60.448 44.000 0.00 0.00 0.00 3.33
549 988 5.122396 GCAATTTCCGAGAGTAATCTGTTGT 59.878 40.000 0.00 0.00 0.00 3.32
550 989 6.312918 GCAATTTCCGAGAGTAATCTGTTGTA 59.687 38.462 0.00 0.00 0.00 2.41
551 990 7.148474 GCAATTTCCGAGAGTAATCTGTTGTAA 60.148 37.037 0.00 0.00 0.00 2.41
552 991 8.883731 CAATTTCCGAGAGTAATCTGTTGTAAT 58.116 33.333 0.00 0.00 0.00 1.89
553 992 9.449719 AATTTCCGAGAGTAATCTGTTGTAATT 57.550 29.630 0.00 0.00 0.00 1.40
554 993 8.475331 TTTCCGAGAGTAATCTGTTGTAATTC 57.525 34.615 0.00 0.00 0.00 2.17
555 994 6.263344 TCCGAGAGTAATCTGTTGTAATTCG 58.737 40.000 0.00 0.00 0.00 3.34
556 995 5.459107 CCGAGAGTAATCTGTTGTAATTCGG 59.541 44.000 0.00 0.00 37.05 4.30
557 996 5.051641 CGAGAGTAATCTGTTGTAATTCGGC 60.052 44.000 0.00 0.00 0.00 5.54
558 997 5.978814 AGAGTAATCTGTTGTAATTCGGCT 58.021 37.500 0.00 0.00 0.00 5.52
559 998 6.407202 AGAGTAATCTGTTGTAATTCGGCTT 58.593 36.000 0.00 0.00 0.00 4.35
560 999 6.879458 AGAGTAATCTGTTGTAATTCGGCTTT 59.121 34.615 0.00 0.00 0.00 3.51
561 1000 7.390718 AGAGTAATCTGTTGTAATTCGGCTTTT 59.609 33.333 0.00 0.00 0.00 2.27
562 1001 7.882179 AGTAATCTGTTGTAATTCGGCTTTTT 58.118 30.769 0.00 0.00 0.00 1.94
563 1002 7.807907 AGTAATCTGTTGTAATTCGGCTTTTTG 59.192 33.333 0.00 0.00 0.00 2.44
564 1003 4.865776 TCTGTTGTAATTCGGCTTTTTGG 58.134 39.130 0.00 0.00 0.00 3.28
565 1004 3.385577 TGTTGTAATTCGGCTTTTTGGC 58.614 40.909 0.00 0.00 37.94 4.52
575 1014 2.620251 GCTTTTTGGCCAAAACCTCT 57.380 45.000 37.24 0.00 39.70 3.69
576 1015 3.744238 GCTTTTTGGCCAAAACCTCTA 57.256 42.857 37.24 23.69 39.70 2.43
577 1016 4.066646 GCTTTTTGGCCAAAACCTCTAA 57.933 40.909 37.24 23.04 39.70 2.10
578 1017 4.447290 GCTTTTTGGCCAAAACCTCTAAA 58.553 39.130 37.24 22.39 39.70 1.85
579 1018 4.272504 GCTTTTTGGCCAAAACCTCTAAAC 59.727 41.667 37.24 17.23 39.70 2.01
580 1019 4.409718 TTTTGGCCAAAACCTCTAAACC 57.590 40.909 34.56 0.00 35.57 3.27
581 1020 3.322191 TTGGCCAAAACCTCTAAACCT 57.678 42.857 17.98 0.00 0.00 3.50
582 1021 3.322191 TGGCCAAAACCTCTAAACCTT 57.678 42.857 0.61 0.00 0.00 3.50
583 1022 3.227614 TGGCCAAAACCTCTAAACCTTC 58.772 45.455 0.61 0.00 0.00 3.46
584 1023 3.117284 TGGCCAAAACCTCTAAACCTTCT 60.117 43.478 0.61 0.00 0.00 2.85
585 1024 3.895656 GGCCAAAACCTCTAAACCTTCTT 59.104 43.478 0.00 0.00 0.00 2.52
586 1025 4.022242 GGCCAAAACCTCTAAACCTTCTTC 60.022 45.833 0.00 0.00 0.00 2.87
587 1026 4.827835 GCCAAAACCTCTAAACCTTCTTCT 59.172 41.667 0.00 0.00 0.00 2.85
588 1027 5.302059 GCCAAAACCTCTAAACCTTCTTCTT 59.698 40.000 0.00 0.00 0.00 2.52
589 1028 6.489022 GCCAAAACCTCTAAACCTTCTTCTTA 59.511 38.462 0.00 0.00 0.00 2.10
590 1029 7.013942 GCCAAAACCTCTAAACCTTCTTCTTAA 59.986 37.037 0.00 0.00 0.00 1.85
591 1030 9.078990 CCAAAACCTCTAAACCTTCTTCTTAAT 57.921 33.333 0.00 0.00 0.00 1.40
593 1032 9.862149 AAAACCTCTAAACCTTCTTCTTAATCA 57.138 29.630 0.00 0.00 0.00 2.57
594 1033 9.862149 AAACCTCTAAACCTTCTTCTTAATCAA 57.138 29.630 0.00 0.00 0.00 2.57
596 1035 9.454859 ACCTCTAAACCTTCTTCTTAATCAATG 57.545 33.333 0.00 0.00 0.00 2.82
597 1036 9.672673 CCTCTAAACCTTCTTCTTAATCAATGA 57.327 33.333 0.00 0.00 0.00 2.57
602 1041 9.971922 AAACCTTCTTCTTAATCAATGAAAGTG 57.028 29.630 0.00 0.00 0.00 3.16
603 1042 8.115490 ACCTTCTTCTTAATCAATGAAAGTGG 57.885 34.615 0.00 0.00 29.44 4.00
604 1043 7.031975 CCTTCTTCTTAATCAATGAAAGTGGC 58.968 38.462 0.00 0.00 29.44 5.01
605 1044 7.309377 CCTTCTTCTTAATCAATGAAAGTGGCA 60.309 37.037 0.00 0.00 29.44 4.92
606 1045 7.523293 TCTTCTTAATCAATGAAAGTGGCAA 57.477 32.000 0.00 0.00 29.44 4.52
607 1046 7.950512 TCTTCTTAATCAATGAAAGTGGCAAA 58.049 30.769 0.00 0.00 29.44 3.68
608 1047 8.587608 TCTTCTTAATCAATGAAAGTGGCAAAT 58.412 29.630 0.00 0.00 29.44 2.32
609 1048 8.761575 TTCTTAATCAATGAAAGTGGCAAATC 57.238 30.769 0.00 0.00 29.44 2.17
610 1049 8.125978 TCTTAATCAATGAAAGTGGCAAATCT 57.874 30.769 0.00 0.00 29.44 2.40
611 1050 8.587608 TCTTAATCAATGAAAGTGGCAAATCTT 58.412 29.630 0.00 0.00 29.44 2.40
612 1051 9.211485 CTTAATCAATGAAAGTGGCAAATCTTT 57.789 29.630 1.63 1.63 36.72 2.52
613 1052 9.558396 TTAATCAATGAAAGTGGCAAATCTTTT 57.442 25.926 3.47 0.00 34.60 2.27
614 1053 6.847956 TCAATGAAAGTGGCAAATCTTTTG 57.152 33.333 3.47 0.00 34.60 2.44
615 1054 5.236911 TCAATGAAAGTGGCAAATCTTTTGC 59.763 36.000 14.88 14.88 44.22 3.68
626 1065 6.370433 GCAAATCTTTTGCCCAGTTAAAAA 57.630 33.333 12.74 0.00 39.38 1.94
650 1089 6.908870 AAAAACAATTTCTGAAGGTGCTTC 57.091 33.333 0.00 0.00 40.54 3.86
651 1090 5.859205 AAACAATTTCTGAAGGTGCTTCT 57.141 34.783 0.00 0.00 40.73 2.85
652 1091 4.843220 ACAATTTCTGAAGGTGCTTCTG 57.157 40.909 0.00 0.00 40.73 3.02
653 1092 3.005155 ACAATTTCTGAAGGTGCTTCTGC 59.995 43.478 0.00 0.00 40.73 4.26
664 1103 2.154854 TGCTTCTGCAGTGTAGTCAC 57.845 50.000 14.67 0.00 45.31 3.67
665 1104 1.270305 TGCTTCTGCAGTGTAGTCACC 60.270 52.381 14.67 0.00 45.31 4.02
666 1105 1.702886 CTTCTGCAGTGTAGTCACCG 58.297 55.000 14.67 0.00 44.83 4.94
667 1106 1.269723 CTTCTGCAGTGTAGTCACCGA 59.730 52.381 14.67 0.00 44.83 4.69
668 1107 0.881796 TCTGCAGTGTAGTCACCGAG 59.118 55.000 14.67 0.00 44.83 4.63
669 1108 0.881796 CTGCAGTGTAGTCACCGAGA 59.118 55.000 5.25 0.00 44.83 4.04
670 1109 1.269723 CTGCAGTGTAGTCACCGAGAA 59.730 52.381 5.25 0.00 44.83 2.87
671 1110 1.269723 TGCAGTGTAGTCACCGAGAAG 59.730 52.381 0.00 0.00 44.83 2.85
672 1111 1.540267 GCAGTGTAGTCACCGAGAAGA 59.460 52.381 0.00 0.00 44.83 2.87
673 1112 2.414824 GCAGTGTAGTCACCGAGAAGAG 60.415 54.545 0.00 0.00 44.83 2.85
674 1113 3.075148 CAGTGTAGTCACCGAGAAGAGA 58.925 50.000 0.00 0.00 44.83 3.10
675 1114 3.502595 CAGTGTAGTCACCGAGAAGAGAA 59.497 47.826 0.00 0.00 44.83 2.87
676 1115 3.754323 AGTGTAGTCACCGAGAAGAGAAG 59.246 47.826 0.00 0.00 44.83 2.85
677 1116 3.752222 GTGTAGTCACCGAGAAGAGAAGA 59.248 47.826 0.00 0.00 38.51 2.87
678 1117 4.004314 TGTAGTCACCGAGAAGAGAAGAG 58.996 47.826 0.00 0.00 0.00 2.85
681 1120 2.165437 GTCACCGAGAAGAGAAGAGCAT 59.835 50.000 0.00 0.00 0.00 3.79
712 1151 4.709397 TCAGACCCTGTTTGTGTTTTGAAT 59.291 37.500 0.00 0.00 32.61 2.57
816 1256 1.010419 CGGTGGTTTCCGTCTTACCG 61.010 60.000 0.00 0.00 44.77 4.02
852 1292 4.798682 CACCTACCCCCGCTCCCT 62.799 72.222 0.00 0.00 0.00 4.20
888 1333 3.681593 CCCCGTCTTCTAATTCCAAACA 58.318 45.455 0.00 0.00 0.00 2.83
937 1382 2.600470 GAGGCACCCAACCAACCC 60.600 66.667 0.00 0.00 0.00 4.11
938 1383 4.233558 AGGCACCCAACCAACCCC 62.234 66.667 0.00 0.00 0.00 4.95
1143 1601 2.195096 TGTATGTATGGTTGCGCGTAC 58.805 47.619 8.43 6.46 0.00 3.67
1146 1604 0.038067 TGTATGGTTGCGCGTACTGT 60.038 50.000 8.43 2.65 0.00 3.55
1159 1617 3.181525 CGCGTACTGTTGTGCATATTTCA 60.182 43.478 0.00 0.00 0.00 2.69
1161 1619 4.142902 GCGTACTGTTGTGCATATTTCAGT 60.143 41.667 15.95 15.95 39.11 3.41
1201 1659 1.065926 TGAGATGCCTGTGATTTCGCT 60.066 47.619 0.00 0.00 0.00 4.93
1215 1673 2.309528 TTCGCTTGCGATCTGGTATT 57.690 45.000 18.40 0.00 0.00 1.89
1222 1680 2.107366 TGCGATCTGGTATTCTGGTGA 58.893 47.619 0.00 0.00 0.00 4.02
1267 1725 4.135153 TTCTCGCTGAGAGGCCGC 62.135 66.667 8.56 0.00 46.82 6.53
1314 1779 5.291971 ACTGTGAAAATTGCTGAATTGGTC 58.708 37.500 0.00 0.00 31.83 4.02
1355 1827 1.963338 GTGACAGACACTGCCTGCC 60.963 63.158 0.00 0.00 45.13 4.85
1359 1831 3.325753 AGACACTGCCTGCCTCCC 61.326 66.667 0.00 0.00 0.00 4.30
1667 2514 0.829182 CTGGTGCTCTTTTTGCCCCT 60.829 55.000 0.00 0.00 0.00 4.79
1927 2830 6.544928 TTATTCAGAGGTCAAGATGCTACA 57.455 37.500 0.00 0.00 0.00 2.74
1978 2881 7.151308 CACCTACTACATTGGATTCTGATCTC 58.849 42.308 0.00 0.00 32.66 2.75
2095 2998 5.237344 GTGTGTTCAGCTGTAGTTTCTTCAT 59.763 40.000 14.67 0.00 0.00 2.57
2493 3397 5.684550 ACTCCGATGTTCCAAGTAAAAAC 57.315 39.130 0.00 0.00 0.00 2.43
2505 3414 7.589574 TCCAAGTAAAAACAAAGTTCAAAGC 57.410 32.000 0.00 0.00 0.00 3.51
2735 3644 0.857935 GCGCAGTCATCTGATACAGC 59.142 55.000 0.30 0.00 43.76 4.40
2805 3714 7.288852 AGACCAGAGTTACTGTGAGCATATATT 59.711 37.037 11.24 0.00 44.40 1.28
2839 3749 9.609346 TGCTAGAACTTTATAAGGTTGTTATCC 57.391 33.333 16.81 2.71 0.00 2.59
2840 3750 9.609346 GCTAGAACTTTATAAGGTTGTTATCCA 57.391 33.333 16.81 0.00 0.00 3.41
2914 3954 4.788679 AGTATTGTTTCCCCTTATTCCCG 58.211 43.478 0.00 0.00 0.00 5.14
3148 4192 2.843730 TGCCAGCTAAGGGATGTTCTTA 59.156 45.455 0.00 0.00 0.00 2.10
3259 4303 2.304180 CCTGGCCGAAGAATATCCTGAT 59.696 50.000 0.00 0.00 0.00 2.90
3281 4325 2.280183 CGCTTCAAGATCTTCTACGTGC 59.720 50.000 4.57 4.00 0.00 5.34
3488 4705 0.036952 ACATCGGACAGGCTGTTGAG 60.037 55.000 22.98 15.55 0.00 3.02
3506 4723 3.407698 TGAGCGTTGAACACATGGTAAT 58.592 40.909 0.00 0.00 0.00 1.89
3511 4728 4.647964 CGTTGAACACATGGTAATGTAGC 58.352 43.478 0.00 0.00 45.50 3.58
3523 4740 4.082733 TGGTAATGTAGCGCTGCTAGATAG 60.083 45.833 25.90 0.00 42.88 2.08
3769 5146 6.037172 GTCACGACTTCCATTGCACTATAAAT 59.963 38.462 0.00 0.00 0.00 1.40
3933 5310 4.036734 TCAAGTGTTCATTCCTTGCAAGTC 59.963 41.667 24.35 6.90 36.41 3.01
3934 5311 3.554934 AGTGTTCATTCCTTGCAAGTCA 58.445 40.909 24.35 11.21 0.00 3.41
3957 5334 4.561213 ACAACTTTGTTTACAAGAAAGCGC 59.439 37.500 0.00 0.00 43.38 5.92
4013 5390 1.640069 CGTCTCCGAGATAACGCGA 59.360 57.895 15.93 0.00 41.48 5.87
4014 5391 0.653897 CGTCTCCGAGATAACGCGAC 60.654 60.000 15.93 0.65 41.48 5.19
4129 5506 4.081420 GGAGATGCAGTTCCAGTTCTAAGA 60.081 45.833 13.01 0.00 33.55 2.10
4130 5507 4.826556 AGATGCAGTTCCAGTTCTAAGAC 58.173 43.478 0.00 0.00 0.00 3.01
4178 5555 2.638480 TGCCCTACATTATCCAGCAC 57.362 50.000 0.00 0.00 0.00 4.40
4228 5605 7.320443 TCTTACAGAAGCGATGCATTTTTAT 57.680 32.000 0.00 0.00 32.21 1.40
4369 5746 4.083537 CCAACATTCGACCGAAAGAAATCA 60.084 41.667 13.23 0.00 37.69 2.57
4370 5747 4.663636 ACATTCGACCGAAAGAAATCAC 57.336 40.909 13.23 0.00 37.69 3.06
4445 5825 0.688487 CCCCCAACGAACAAGTAGGA 59.312 55.000 0.00 0.00 0.00 2.94
4480 5860 3.856508 CGTAGCTCGTGGTGTTGG 58.143 61.111 0.00 0.00 34.52 3.77
4504 5884 1.893137 TGCTAGGGCGTATGGTATCTG 59.107 52.381 0.00 0.00 42.25 2.90
4509 5889 1.411246 GGGCGTATGGTATCTGTGTGA 59.589 52.381 0.00 0.00 0.00 3.58
4510 5890 2.545952 GGGCGTATGGTATCTGTGTGAG 60.546 54.545 0.00 0.00 0.00 3.51
4518 5898 4.325972 TGGTATCTGTGTGAGTACGTACA 58.674 43.478 26.55 6.64 0.00 2.90
4523 5903 6.997239 ATCTGTGTGAGTACGTACATAGAA 57.003 37.500 26.55 14.41 44.45 2.10
4610 5990 4.187694 AGGATCAATTGAAGCTCGAACTC 58.812 43.478 13.09 1.81 0.00 3.01
4905 6699 1.202687 TGGCTAATGAGATGGGCTTCG 60.203 52.381 0.00 0.00 0.00 3.79
4909 6703 2.787473 AATGAGATGGGCTTCGACAA 57.213 45.000 0.00 0.00 0.00 3.18
4916 6710 5.041191 AGATGGGCTTCGACAAGATTATT 57.959 39.130 0.00 0.00 0.00 1.40
4917 6711 4.818546 AGATGGGCTTCGACAAGATTATTG 59.181 41.667 0.00 0.00 0.00 1.90
4918 6712 2.682856 TGGGCTTCGACAAGATTATTGC 59.317 45.455 0.00 0.00 0.00 3.56
4920 6714 3.242870 GGGCTTCGACAAGATTATTGCTG 60.243 47.826 0.00 0.00 0.00 4.41
4965 6772 4.207955 GGAGGAGGTTTTTCTTCAACAGT 58.792 43.478 0.00 0.00 0.00 3.55
4970 6777 5.278022 GGAGGTTTTTCTTCAACAGTAGCTG 60.278 44.000 0.00 0.00 37.52 4.24
4972 6779 4.036852 GGTTTTTCTTCAACAGTAGCTGCT 59.963 41.667 7.57 7.57 34.37 4.24
4973 6780 5.208503 GTTTTTCTTCAACAGTAGCTGCTC 58.791 41.667 4.91 0.00 34.37 4.26
4974 6781 4.342862 TTTCTTCAACAGTAGCTGCTCT 57.657 40.909 4.91 0.07 34.37 4.09
5036 6844 7.817478 TCAGTAGATTAGAATTTTCGTCTTGCA 59.183 33.333 0.00 0.00 0.00 4.08
5047 6855 0.947244 CGTCTTGCAATAGGGATGCC 59.053 55.000 0.00 0.00 43.16 4.40
5053 6861 2.318908 TGCAATAGGGATGCCAATTCC 58.681 47.619 5.86 0.00 43.16 3.01
5062 6870 1.887344 ATGCCAATTCCGTTGCCCAC 61.887 55.000 0.00 0.00 36.46 4.61
5063 6871 2.569354 GCCAATTCCGTTGCCCACA 61.569 57.895 0.00 0.00 36.46 4.17
5066 6874 0.673437 CAATTCCGTTGCCCACAGTT 59.327 50.000 0.00 0.00 0.00 3.16
5079 6887 1.134371 CCACAGTTTAGCTAGGGAGGC 60.134 57.143 0.00 0.00 0.00 4.70
5080 6888 0.824759 ACAGTTTAGCTAGGGAGGCG 59.175 55.000 0.00 0.00 34.52 5.52
5086 6894 0.409876 TAGCTAGGGAGGCGGATCAT 59.590 55.000 0.00 0.00 34.52 2.45
5092 6900 0.250338 GGGAGGCGGATCATAACCAC 60.250 60.000 0.00 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
144 153 4.545610 GTCAGTTTTTCAATTGGCATCGA 58.454 39.130 5.42 0.00 0.00 3.59
186 204 2.419990 CCAGCGTGGATTGATTGGTAGA 60.420 50.000 0.00 0.00 40.96 2.59
204 228 0.110104 GAATGGCTCCCTCATCCCAG 59.890 60.000 0.00 0.00 0.00 4.45
264 288 1.336755 TCGTGCTAGCATCAATCGCTA 59.663 47.619 22.51 1.31 40.96 4.26
304 332 1.202651 GGGTTAGCACATCGCCATAGT 60.203 52.381 0.00 0.00 44.04 2.12
324 352 5.674569 GCTGTAAACTGTAATGGTGATGCAG 60.675 44.000 0.00 0.00 0.00 4.41
351 379 5.869579 AGCCTGTAGAGAAACTCATTTTGA 58.130 37.500 0.00 0.00 32.06 2.69
385 724 1.583856 CGTGTCATTCGAGAATCACGG 59.416 52.381 21.84 10.78 41.37 4.94
417 756 4.217118 CACTGCCAAAGTAGCTTCAGAATT 59.783 41.667 0.00 0.00 36.83 2.17
418 757 3.755378 CACTGCCAAAGTAGCTTCAGAAT 59.245 43.478 0.00 0.00 36.83 2.40
442 881 0.960861 TCAGATGCGTCTCGGTGAGT 60.961 55.000 5.16 0.00 30.42 3.41
457 896 2.354103 CGAACAGAGCCTGGATTTCAGA 60.354 50.000 0.00 0.00 46.18 3.27
465 904 1.901650 GAAACGCGAACAGAGCCTGG 61.902 60.000 15.93 0.00 35.51 4.45
477 916 2.468532 AAAACACCTTCAGAAACGCG 57.531 45.000 3.53 3.53 0.00 6.01
502 941 5.221891 CACCTTCAGAAATTGTGGATACG 57.778 43.478 0.00 0.00 42.51 3.06
512 951 3.056607 CGGAAATTGCCACCTTCAGAAAT 60.057 43.478 2.58 0.00 0.00 2.17
525 964 5.122396 ACAACAGATTACTCTCGGAAATTGC 59.878 40.000 0.00 0.00 0.00 3.56
526 965 6.727824 ACAACAGATTACTCTCGGAAATTG 57.272 37.500 0.00 0.00 0.00 2.32
527 966 9.449719 AATTACAACAGATTACTCTCGGAAATT 57.550 29.630 0.00 0.00 0.00 1.82
528 967 9.099454 GAATTACAACAGATTACTCTCGGAAAT 57.901 33.333 0.00 0.00 0.00 2.17
530 969 6.750501 CGAATTACAACAGATTACTCTCGGAA 59.249 38.462 0.00 0.00 0.00 4.30
531 970 6.263344 CGAATTACAACAGATTACTCTCGGA 58.737 40.000 0.00 0.00 0.00 4.55
532 971 5.459107 CCGAATTACAACAGATTACTCTCGG 59.541 44.000 0.00 0.00 0.00 4.63
533 972 5.051641 GCCGAATTACAACAGATTACTCTCG 60.052 44.000 0.00 0.00 0.00 4.04
534 973 6.043411 AGCCGAATTACAACAGATTACTCTC 58.957 40.000 0.00 0.00 0.00 3.20
535 974 5.978814 AGCCGAATTACAACAGATTACTCT 58.021 37.500 0.00 0.00 0.00 3.24
536 975 6.663944 AAGCCGAATTACAACAGATTACTC 57.336 37.500 0.00 0.00 0.00 2.59
537 976 7.448748 AAAAGCCGAATTACAACAGATTACT 57.551 32.000 0.00 0.00 0.00 2.24
538 977 7.061789 CCAAAAAGCCGAATTACAACAGATTAC 59.938 37.037 0.00 0.00 0.00 1.89
539 978 7.087639 CCAAAAAGCCGAATTACAACAGATTA 58.912 34.615 0.00 0.00 0.00 1.75
540 979 5.925969 CCAAAAAGCCGAATTACAACAGATT 59.074 36.000 0.00 0.00 0.00 2.40
541 980 5.469479 CCAAAAAGCCGAATTACAACAGAT 58.531 37.500 0.00 0.00 0.00 2.90
542 981 4.794655 GCCAAAAAGCCGAATTACAACAGA 60.795 41.667 0.00 0.00 0.00 3.41
543 982 3.428534 GCCAAAAAGCCGAATTACAACAG 59.571 43.478 0.00 0.00 0.00 3.16
544 983 3.385577 GCCAAAAAGCCGAATTACAACA 58.614 40.909 0.00 0.00 0.00 3.33
545 984 2.734606 GGCCAAAAAGCCGAATTACAAC 59.265 45.455 0.00 0.00 44.57 3.32
546 985 3.033368 GGCCAAAAAGCCGAATTACAA 57.967 42.857 0.00 0.00 44.57 2.41
547 986 2.734276 GGCCAAAAAGCCGAATTACA 57.266 45.000 0.00 0.00 44.57 2.41
557 996 4.814234 GGTTTAGAGGTTTTGGCCAAAAAG 59.186 41.667 38.37 0.00 41.37 2.27
558 997 4.471747 AGGTTTAGAGGTTTTGGCCAAAAA 59.528 37.500 38.37 23.54 41.37 1.94
559 998 4.034410 AGGTTTAGAGGTTTTGGCCAAAA 58.966 39.130 34.56 34.56 37.90 2.44
560 999 3.648739 AGGTTTAGAGGTTTTGGCCAAA 58.351 40.909 27.13 27.13 0.00 3.28
561 1000 3.322191 AGGTTTAGAGGTTTTGGCCAA 57.678 42.857 16.05 16.05 0.00 4.52
562 1001 3.117284 AGAAGGTTTAGAGGTTTTGGCCA 60.117 43.478 0.00 0.00 0.00 5.36
563 1002 3.497332 AGAAGGTTTAGAGGTTTTGGCC 58.503 45.455 0.00 0.00 0.00 5.36
564 1003 4.827835 AGAAGAAGGTTTAGAGGTTTTGGC 59.172 41.667 0.00 0.00 0.00 4.52
565 1004 6.961360 AAGAAGAAGGTTTAGAGGTTTTGG 57.039 37.500 0.00 0.00 0.00 3.28
567 1006 9.862149 TGATTAAGAAGAAGGTTTAGAGGTTTT 57.138 29.630 0.00 0.00 0.00 2.43
568 1007 9.862149 TTGATTAAGAAGAAGGTTTAGAGGTTT 57.138 29.630 0.00 0.00 0.00 3.27
570 1009 9.454859 CATTGATTAAGAAGAAGGTTTAGAGGT 57.545 33.333 0.00 0.00 0.00 3.85
571 1010 9.672673 TCATTGATTAAGAAGAAGGTTTAGAGG 57.327 33.333 0.00 0.00 0.00 3.69
576 1015 9.971922 CACTTTCATTGATTAAGAAGAAGGTTT 57.028 29.630 5.34 0.00 0.00 3.27
577 1016 8.579863 CCACTTTCATTGATTAAGAAGAAGGTT 58.420 33.333 5.34 0.00 0.00 3.50
578 1017 7.309438 GCCACTTTCATTGATTAAGAAGAAGGT 60.309 37.037 5.34 0.00 0.00 3.50
579 1018 7.031975 GCCACTTTCATTGATTAAGAAGAAGG 58.968 38.462 5.34 6.19 0.00 3.46
580 1019 7.596494 TGCCACTTTCATTGATTAAGAAGAAG 58.404 34.615 5.34 0.00 0.00 2.85
581 1020 7.523293 TGCCACTTTCATTGATTAAGAAGAA 57.477 32.000 5.34 0.00 0.00 2.52
582 1021 7.523293 TTGCCACTTTCATTGATTAAGAAGA 57.477 32.000 5.34 0.00 0.00 2.87
583 1022 8.767478 ATTTGCCACTTTCATTGATTAAGAAG 57.233 30.769 5.34 0.39 0.00 2.85
584 1023 8.587608 AGATTTGCCACTTTCATTGATTAAGAA 58.412 29.630 5.34 0.00 0.00 2.52
585 1024 8.125978 AGATTTGCCACTTTCATTGATTAAGA 57.874 30.769 5.34 0.00 0.00 2.10
586 1025 8.767478 AAGATTTGCCACTTTCATTGATTAAG 57.233 30.769 0.00 0.00 0.00 1.85
587 1026 9.558396 AAAAGATTTGCCACTTTCATTGATTAA 57.442 25.926 0.00 0.00 35.66 1.40
588 1027 8.991026 CAAAAGATTTGCCACTTTCATTGATTA 58.009 29.630 0.00 0.00 35.66 1.75
589 1028 7.520937 GCAAAAGATTTGCCACTTTCATTGATT 60.521 33.333 15.12 0.00 39.38 2.57
590 1029 6.072893 GCAAAAGATTTGCCACTTTCATTGAT 60.073 34.615 15.12 0.00 39.38 2.57
591 1030 5.236911 GCAAAAGATTTGCCACTTTCATTGA 59.763 36.000 15.12 0.00 39.38 2.57
592 1031 5.445845 GCAAAAGATTTGCCACTTTCATTG 58.554 37.500 15.12 0.00 39.38 2.82
593 1032 5.678132 GCAAAAGATTTGCCACTTTCATT 57.322 34.783 15.12 0.00 39.38 2.57
603 1042 6.370433 TTTTTAACTGGGCAAAAGATTTGC 57.630 33.333 17.18 17.18 44.22 3.68
627 1066 6.536224 CAGAAGCACCTTCAGAAATTGTTTTT 59.464 34.615 7.62 0.00 42.37 1.94
628 1067 6.044682 CAGAAGCACCTTCAGAAATTGTTTT 58.955 36.000 7.62 0.00 42.37 2.43
629 1068 5.594926 CAGAAGCACCTTCAGAAATTGTTT 58.405 37.500 7.62 0.00 42.37 2.83
630 1069 4.500375 GCAGAAGCACCTTCAGAAATTGTT 60.500 41.667 7.62 0.00 42.37 2.83
631 1070 3.005155 GCAGAAGCACCTTCAGAAATTGT 59.995 43.478 7.62 0.00 42.37 2.71
632 1071 3.572584 GCAGAAGCACCTTCAGAAATTG 58.427 45.455 7.62 0.00 42.37 2.32
633 1072 3.930634 GCAGAAGCACCTTCAGAAATT 57.069 42.857 7.62 0.00 42.37 1.82
646 1085 1.433534 GGTGACTACACTGCAGAAGC 58.566 55.000 23.35 10.81 45.32 3.86
647 1086 1.702886 CGGTGACTACACTGCAGAAG 58.297 55.000 23.35 16.35 44.70 2.85
648 1087 3.886044 CGGTGACTACACTGCAGAA 57.114 52.632 23.35 4.27 44.70 3.02
654 1093 3.420300 TCTCTTCTCGGTGACTACACT 57.580 47.619 0.00 0.00 45.32 3.55
655 1094 3.752222 TCTTCTCTTCTCGGTGACTACAC 59.248 47.826 0.00 0.00 45.27 2.90
656 1095 4.004314 CTCTTCTCTTCTCGGTGACTACA 58.996 47.826 0.00 0.00 0.00 2.74
657 1096 3.181504 GCTCTTCTCTTCTCGGTGACTAC 60.182 52.174 0.00 0.00 0.00 2.73
658 1097 3.011119 GCTCTTCTCTTCTCGGTGACTA 58.989 50.000 0.00 0.00 0.00 2.59
659 1098 1.816224 GCTCTTCTCTTCTCGGTGACT 59.184 52.381 0.00 0.00 0.00 3.41
660 1099 1.542030 TGCTCTTCTCTTCTCGGTGAC 59.458 52.381 0.00 0.00 0.00 3.67
661 1100 1.911057 TGCTCTTCTCTTCTCGGTGA 58.089 50.000 0.00 0.00 0.00 4.02
662 1101 2.426738 AGATGCTCTTCTCTTCTCGGTG 59.573 50.000 0.00 0.00 0.00 4.94
663 1102 2.426738 CAGATGCTCTTCTCTTCTCGGT 59.573 50.000 0.00 0.00 0.00 4.69
664 1103 2.687425 TCAGATGCTCTTCTCTTCTCGG 59.313 50.000 0.00 0.00 0.00 4.63
665 1104 4.368874 TTCAGATGCTCTTCTCTTCTCG 57.631 45.455 0.00 0.00 0.00 4.04
666 1105 6.817641 TGAATTTCAGATGCTCTTCTCTTCTC 59.182 38.462 0.00 0.00 0.00 2.87
667 1106 6.709281 TGAATTTCAGATGCTCTTCTCTTCT 58.291 36.000 0.00 0.00 0.00 2.85
668 1107 6.981762 TGAATTTCAGATGCTCTTCTCTTC 57.018 37.500 0.00 0.00 0.00 2.87
695 1134 4.201802 GCCACAATTCAAAACACAAACAGG 60.202 41.667 0.00 0.00 0.00 4.00
701 1140 2.223688 CCTCGCCACAATTCAAAACACA 60.224 45.455 0.00 0.00 0.00 3.72
702 1141 2.393764 CCTCGCCACAATTCAAAACAC 58.606 47.619 0.00 0.00 0.00 3.32
703 1142 1.339610 CCCTCGCCACAATTCAAAACA 59.660 47.619 0.00 0.00 0.00 2.83
712 1151 2.199652 CCTTTTGCCCTCGCCACAA 61.200 57.895 0.00 0.00 0.00 3.33
770 1210 4.394712 GGTGAGACCTGTGGGCGG 62.395 72.222 0.00 0.00 34.73 6.13
888 1333 2.472695 TTGGTGCGAGATTTAGCTGT 57.527 45.000 0.00 0.00 0.00 4.40
945 1390 4.838486 CTCGCGACGCTGTCCCTC 62.838 72.222 19.02 0.00 0.00 4.30
951 1396 4.838486 GTCTCCCTCGCGACGCTG 62.838 72.222 19.02 11.58 0.00 5.18
1143 1601 8.759641 GTCTATCTACTGAAATATGCACAACAG 58.240 37.037 0.00 0.00 0.00 3.16
1146 1604 6.420903 GCGTCTATCTACTGAAATATGCACAA 59.579 38.462 0.00 0.00 0.00 3.33
1159 1617 5.465051 CATGTAAGCATGCGTCTATCTACT 58.535 41.667 10.11 0.00 44.87 2.57
1201 1659 2.499693 TCACCAGAATACCAGATCGCAA 59.500 45.455 0.00 0.00 0.00 4.85
1215 1673 2.367202 GGGATTCCGGCTCACCAGA 61.367 63.158 0.00 0.00 34.57 3.86
1375 1847 0.536460 ACAACAAGCGTAACAGGGGG 60.536 55.000 0.00 0.00 0.00 5.40
1376 1848 0.591170 CACAACAAGCGTAACAGGGG 59.409 55.000 0.00 0.00 0.00 4.79
1482 2329 1.002087 AGATTCGACAGAACCACCCAC 59.998 52.381 0.00 0.00 39.48 4.61
1647 2494 2.732289 GGGCAAAAAGAGCACCAGA 58.268 52.632 0.00 0.00 0.00 3.86
1667 2514 1.811778 AGGATCCAAGCAGCCTGATA 58.188 50.000 15.82 0.00 0.00 2.15
1927 2830 4.917906 AGGCTTGATTACTTCTTCACCT 57.082 40.909 0.00 0.00 0.00 4.00
1978 2881 7.812669 ACCTTTATAACAAGCTGAAAATTTCCG 59.187 33.333 3.00 0.00 0.00 4.30
2109 3012 9.243105 CTGAATTTTGGGGAAGAGAAAGTATTA 57.757 33.333 0.00 0.00 0.00 0.98
2111 3014 7.470192 TCTGAATTTTGGGGAAGAGAAAGTAT 58.530 34.615 0.00 0.00 0.00 2.12
2112 3015 6.848069 TCTGAATTTTGGGGAAGAGAAAGTA 58.152 36.000 0.00 0.00 0.00 2.24
2113 3016 5.705400 TCTGAATTTTGGGGAAGAGAAAGT 58.295 37.500 0.00 0.00 0.00 2.66
2114 3017 6.210185 ACATCTGAATTTTGGGGAAGAGAAAG 59.790 38.462 0.00 0.00 0.00 2.62
2116 3019 5.644188 ACATCTGAATTTTGGGGAAGAGAA 58.356 37.500 0.00 0.00 0.00 2.87
2117 3020 5.261040 ACATCTGAATTTTGGGGAAGAGA 57.739 39.130 0.00 0.00 0.00 3.10
2120 3023 4.402474 GGGTACATCTGAATTTTGGGGAAG 59.598 45.833 0.00 0.00 0.00 3.46
2246 3149 7.995488 AGCAGCTATTTCTTATGAACCTAACAT 59.005 33.333 0.00 0.00 31.02 2.71
2287 3190 5.356426 GCTAAACCAGAGCAAAAGGAAAAA 58.644 37.500 0.00 0.00 39.84 1.94
2288 3191 4.202212 GGCTAAACCAGAGCAAAAGGAAAA 60.202 41.667 0.00 0.00 41.98 2.29
2493 3397 7.533426 ACTGCAATATAGAGCTTTGAACTTTG 58.467 34.615 0.00 0.00 0.00 2.77
2505 3414 7.601508 TGTAGCATCATTGACTGCAATATAGAG 59.398 37.037 17.48 0.00 42.66 2.43
2573 3482 1.381056 TGCCCTTGCAACCTGTGTT 60.381 52.632 0.00 0.00 46.66 3.32
2574 3483 2.278404 TGCCCTTGCAACCTGTGT 59.722 55.556 0.00 0.00 46.66 3.72
2717 3626 2.214387 TGCTGTATCAGATGACTGCG 57.786 50.000 0.66 0.00 43.17 5.18
2805 3714 9.953565 ACCTTATAAAGTTCTAGCAAATGTGTA 57.046 29.630 0.00 0.00 0.00 2.90
2814 3723 9.609346 TGGATAACAACCTTATAAAGTTCTAGC 57.391 33.333 0.00 0.00 0.00 3.42
2839 3749 8.235226 ACAACTATACGGAATAGATACATCGTG 58.765 37.037 12.46 0.00 40.16 4.35
2840 3750 8.332996 ACAACTATACGGAATAGATACATCGT 57.667 34.615 12.46 0.00 40.16 3.73
2882 3799 2.554893 GGAAACAATACTTGGCGTCCAA 59.445 45.455 10.28 10.28 41.69 3.53
2883 3800 2.156098 GGAAACAATACTTGGCGTCCA 58.844 47.619 0.00 0.00 32.45 4.02
2884 3801 1.471287 GGGAAACAATACTTGGCGTCC 59.529 52.381 0.00 0.00 34.12 4.79
2887 3927 1.834188 AGGGGAAACAATACTTGGCG 58.166 50.000 0.00 0.00 34.12 5.69
3129 4169 7.009179 TCATATAAGAACATCCCTTAGCTGG 57.991 40.000 0.00 0.00 30.61 4.85
3130 4170 7.551974 CCATCATATAAGAACATCCCTTAGCTG 59.448 40.741 0.00 0.00 30.61 4.24
3148 4192 3.413846 AGTGAAGCGCATCCATCATAT 57.586 42.857 11.47 0.00 0.00 1.78
3259 4303 3.759418 CACGTAGAAGATCTTGAAGCGA 58.241 45.455 14.00 0.00 0.00 4.93
3324 4368 5.731278 CAGTGTACTGATTTGATATGCACG 58.269 41.667 6.15 0.00 46.59 5.34
3455 4672 3.876914 GTCCGATGTTATTGCCATGAGAA 59.123 43.478 0.00 0.00 0.00 2.87
3461 4678 2.016604 GCCTGTCCGATGTTATTGCCA 61.017 52.381 0.00 0.00 0.00 4.92
3488 4705 3.552604 ACATTACCATGTGTTCAACGC 57.447 42.857 0.00 0.00 42.46 4.84
3506 4723 2.543861 GCAACTATCTAGCAGCGCTACA 60.544 50.000 10.99 0.00 40.44 2.74
3636 5013 7.078228 GCGGATTTATTTCAGAACATGGTATC 58.922 38.462 0.00 0.00 0.00 2.24
3769 5146 6.624204 CAGTATGAGATTCTGTTGCAAATGCA 60.624 38.462 0.00 3.51 45.48 3.96
3933 5310 5.498542 GCGCTTTCTTGTAAACAAAGTTGTG 60.499 40.000 0.00 0.00 41.31 3.33
3934 5311 4.561213 GCGCTTTCTTGTAAACAAAGTTGT 59.439 37.500 0.00 0.00 44.72 3.32
3957 5334 0.951558 CCTGGAAAACGACCACTTGG 59.048 55.000 0.00 0.00 42.17 3.61
4129 5506 4.504858 CTTATTTTGCTGTACTCCGGAGT 58.495 43.478 37.59 37.59 45.02 3.85
4130 5507 3.309954 GCTTATTTTGCTGTACTCCGGAG 59.690 47.826 30.11 30.11 0.00 4.63
4159 5536 1.202639 CGTGCTGGATAATGTAGGGCA 60.203 52.381 0.00 0.00 0.00 5.36
4389 5766 5.635417 TTTACCAATGATTGATGTTCGCA 57.365 34.783 6.76 0.00 0.00 5.10
4426 5806 0.688487 TCCTACTTGTTCGTTGGGGG 59.312 55.000 0.00 0.00 31.84 5.40
4427 5807 2.356135 CATCCTACTTGTTCGTTGGGG 58.644 52.381 0.00 0.00 31.84 4.96
4437 5817 2.237143 TCAGAAGGCACCATCCTACTTG 59.763 50.000 0.00 0.00 34.82 3.16
4445 5825 1.378250 GCAGCTCAGAAGGCACCAT 60.378 57.895 0.00 0.00 0.00 3.55
4479 5859 0.320771 CCATACGCCCTAGCATGTCC 60.321 60.000 0.00 0.00 39.83 4.02
4480 5860 0.393077 ACCATACGCCCTAGCATGTC 59.607 55.000 0.00 0.00 39.83 3.06
4504 5884 8.456904 TTTGATTTCTATGTACGTACTCACAC 57.543 34.615 25.12 1.88 0.00 3.82
4509 5889 9.136952 GTTGTCTTTGATTTCTATGTACGTACT 57.863 33.333 25.12 13.70 0.00 2.73
4510 5890 8.918658 TGTTGTCTTTGATTTCTATGTACGTAC 58.081 33.333 18.90 18.90 0.00 3.67
4610 5990 2.936498 CTGTAGCCCATAGTGTTTTCCG 59.064 50.000 0.00 0.00 0.00 4.30
4654 6036 5.430886 AGCAGAGTTTTCCAAGCAATTTTT 58.569 33.333 0.00 0.00 0.00 1.94
4655 6037 5.027293 AGCAGAGTTTTCCAAGCAATTTT 57.973 34.783 0.00 0.00 0.00 1.82
4656 6038 4.677673 AGCAGAGTTTTCCAAGCAATTT 57.322 36.364 0.00 0.00 0.00 1.82
4731 6113 2.176889 GGCACCTAGGACACAGACTTA 58.823 52.381 17.98 0.00 0.00 2.24
4905 6699 7.065563 ACAATCAGACTCAGCAATAATCTTGTC 59.934 37.037 0.00 0.00 0.00 3.18
4909 6703 6.887013 AGACAATCAGACTCAGCAATAATCT 58.113 36.000 0.00 0.00 0.00 2.40
4916 6710 3.306571 CCTCAAGACAATCAGACTCAGCA 60.307 47.826 0.00 0.00 0.00 4.41
4917 6711 3.260740 CCTCAAGACAATCAGACTCAGC 58.739 50.000 0.00 0.00 0.00 4.26
4918 6712 3.260740 GCCTCAAGACAATCAGACTCAG 58.739 50.000 0.00 0.00 0.00 3.35
4920 6714 2.027745 TGGCCTCAAGACAATCAGACTC 60.028 50.000 3.32 0.00 0.00 3.36
4965 6772 8.657387 AATATCCTCAAAGTATAGAGCAGCTA 57.343 34.615 0.00 0.00 0.00 3.32
5018 6825 6.882140 TCCCTATTGCAAGACGAAAATTCTAA 59.118 34.615 4.94 0.00 0.00 2.10
5023 6830 4.202050 GCATCCCTATTGCAAGACGAAAAT 60.202 41.667 4.94 0.00 39.90 1.82
5028 6836 0.947244 GGCATCCCTATTGCAAGACG 59.053 55.000 4.94 0.00 41.95 4.18
5031 6839 3.243975 GGAATTGGCATCCCTATTGCAAG 60.244 47.826 4.94 0.00 41.71 4.01
5036 6844 2.958355 CAACGGAATTGGCATCCCTATT 59.042 45.455 1.61 0.00 38.91 1.73
5040 6848 1.141665 GCAACGGAATTGGCATCCC 59.858 57.895 1.61 0.00 38.88 3.85
5047 6855 0.673437 AACTGTGGGCAACGGAATTG 59.327 50.000 8.12 0.00 41.69 2.32
5053 6861 1.732259 CTAGCTAAACTGTGGGCAACG 59.268 52.381 0.00 0.00 37.60 4.10
5062 6870 0.105039 CCGCCTCCCTAGCTAAACTG 59.895 60.000 0.00 0.00 0.00 3.16
5063 6871 0.032416 TCCGCCTCCCTAGCTAAACT 60.032 55.000 0.00 0.00 0.00 2.66
5066 6874 0.187606 TGATCCGCCTCCCTAGCTAA 59.812 55.000 0.00 0.00 0.00 3.09
5079 6887 4.439974 CCCAAACATTGTGGTTATGATCCG 60.440 45.833 0.00 0.00 34.01 4.18
5080 6888 4.466015 ACCCAAACATTGTGGTTATGATCC 59.534 41.667 0.00 0.00 32.56 3.36
5086 6894 4.895889 TCATCAACCCAAACATTGTGGTTA 59.104 37.500 9.09 1.51 40.13 2.85


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

AutoCloner maintained by Alex Coulton.