Multiple sequence alignment - TraesCS1D01G067300

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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 TraesCS1D01G067300 chr1D 100.000 3193 0 0 1 3193 49112412 49109220 0.000000e+00 5897.0
1 TraesCS1D01G067300 chr6D 95.184 1931 83 8 1269 3193 443282257 443280331 0.000000e+00 3042.0
2 TraesCS1D01G067300 chr6D 96.184 1284 47 2 1269 2550 443265488 443264205 0.000000e+00 2098.0
3 TraesCS1D01G067300 chr6D 95.821 694 28 1 1 694 300545770 300545078 0.000000e+00 1120.0
4 TraesCS1D01G067300 chr6D 95.376 692 32 0 3 694 403742354 403741663 0.000000e+00 1101.0
5 TraesCS1D01G067300 chr6D 93.640 283 18 0 985 1267 443265814 443265532 1.060000e-114 424.0
6 TraesCS1D01G067300 chr6D 93.262 282 18 1 986 1267 443282581 443282301 6.370000e-112 414.0
7 TraesCS1D01G067300 chr6D 96.667 60 2 0 931 990 443266100 443266041 2.030000e-17 100.0
8 TraesCS1D01G067300 chr6D 96.552 58 2 0 933 990 443282866 443282809 2.620000e-16 97.1
9 TraesCS1D01G067300 chr7D 95.544 1773 69 7 1427 3193 400201424 400199656 0.000000e+00 2828.0
10 TraesCS1D01G067300 chr7D 95.617 1734 66 7 1427 3155 488121204 488119476 0.000000e+00 2772.0
11 TraesCS1D01G067300 chr7D 95.533 694 30 1 1 694 272338891 272339583 0.000000e+00 1109.0
12 TraesCS1D01G067300 chr7D 92.908 282 20 0 986 1267 493949137 493949418 8.240000e-111 411.0
13 TraesCS1D01G067300 chr7D 91.379 290 17 1 986 1267 488121538 488121249 1.070000e-104 390.0
14 TraesCS1D01G067300 chr7D 90.873 252 19 3 2933 3180 84438773 84439024 5.100000e-88 335.0
15 TraesCS1D01G067300 chr7D 91.053 190 9 1 1086 1267 400201658 400201469 1.900000e-62 250.0
16 TraesCS1D01G067300 chr7D 96.610 59 2 0 932 990 488121824 488121766 7.290000e-17 99.0
17 TraesCS1D01G067300 chr4A 93.416 1929 80 16 1269 3193 524273207 524271322 0.000000e+00 2815.0
18 TraesCS1D01G067300 chr4A 91.189 942 76 5 1998 2934 190403307 190404246 0.000000e+00 1273.0
19 TraesCS1D01G067300 chr4A 88.968 281 16 1 986 1266 524273517 524273252 1.840000e-87 333.0
20 TraesCS1D01G067300 chr4A 89.057 265 23 4 2933 3193 190404572 190404834 1.100000e-84 324.0
21 TraesCS1D01G067300 chr4A 92.857 70 3 1 931 998 524273804 524273735 2.030000e-17 100.0
22 TraesCS1D01G067300 chr4A 93.333 60 4 0 931 990 66753822 66753763 4.390000e-14 89.8
23 TraesCS1D01G067300 chrUn 96.405 1057 37 1 1269 2324 101223789 101222733 0.000000e+00 1740.0
24 TraesCS1D01G067300 chrUn 95.631 618 27 0 2576 3193 101222735 101222118 0.000000e+00 992.0
25 TraesCS1D01G067300 chrUn 93.262 282 19 0 986 1267 101224114 101223833 1.770000e-112 416.0
26 TraesCS1D01G067300 chr2D 92.389 946 67 3 1993 2934 439659486 439658542 0.000000e+00 1343.0
27 TraesCS1D01G067300 chr3A 91.410 943 72 7 1998 2934 686266562 686265623 0.000000e+00 1284.0
28 TraesCS1D01G067300 chr3A 90.595 723 63 5 1262 1983 165871076 165870358 0.000000e+00 953.0
29 TraesCS1D01G067300 chr5D 96.974 694 21 0 1 694 408522072 408521379 0.000000e+00 1166.0
30 TraesCS1D01G067300 chr5D 96.542 694 24 0 1 694 311664581 311663888 0.000000e+00 1149.0
31 TraesCS1D01G067300 chr5D 95.965 694 28 0 1 694 56899858 56900551 0.000000e+00 1127.0
32 TraesCS1D01G067300 chr5D 95.396 695 31 1 1 694 462188052 462187358 0.000000e+00 1105.0
33 TraesCS1D01G067300 chr3D 96.104 693 25 2 1 692 175629999 175630690 0.000000e+00 1129.0
34 TraesCS1D01G067300 chr3D 88.929 280 30 1 988 1267 185654845 185655123 8.480000e-91 344.0
35 TraesCS1D01G067300 chr4D 95.677 694 30 0 1 694 370589748 370590441 0.000000e+00 1116.0
36 TraesCS1D01G067300 chr6A 92.571 700 45 5 2497 3193 311853274 311853969 0.000000e+00 998.0
37 TraesCS1D01G067300 chr2A 91.575 724 53 5 1262 1983 568234580 568233863 0.000000e+00 992.0
38 TraesCS1D01G067300 chr5A 90.972 720 59 5 1262 1980 119025446 119026160 0.000000e+00 965.0
39 TraesCS1D01G067300 chr5A 93.333 60 4 0 931 990 105085297 105085238 4.390000e-14 89.8
40 TraesCS1D01G067300 chr7B 90.803 685 58 3 1990 2670 104513951 104514634 0.000000e+00 911.0
41 TraesCS1D01G067300 chr7B 90.494 263 21 2 2933 3193 104515350 104515610 8.480000e-91 344.0
42 TraesCS1D01G067300 chr1A 90.114 263 22 2 2933 3193 244554271 244554011 3.950000e-89 339.0
43 TraesCS1D01G067300 chr4B 86.786 280 31 4 986 1265 247557458 247557185 1.110000e-79 307.0
44 TraesCS1D01G067300 chr4B 83.004 253 32 4 747 990 248365593 248365343 5.360000e-53 219.0
45 TraesCS1D01G067300 chr5B 82.443 262 32 7 734 984 22313685 22313943 1.930000e-52 217.0
46 TraesCS1D01G067300 chr5B 87.013 77 8 2 912 987 443227020 443227095 5.680000e-13 86.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G067300 chr1D 49109220 49112412 3192 True 5897.000000 5897 100.000000 1 3193 1 chr1D.!!$R1 3192
1 TraesCS1D01G067300 chr6D 443280331 443282866 2535 True 1184.366667 3042 94.999333 933 3193 3 chr6D.!!$R4 2260
2 TraesCS1D01G067300 chr6D 300545078 300545770 692 True 1120.000000 1120 95.821000 1 694 1 chr6D.!!$R1 693
3 TraesCS1D01G067300 chr6D 403741663 403742354 691 True 1101.000000 1101 95.376000 3 694 1 chr6D.!!$R2 691
4 TraesCS1D01G067300 chr6D 443264205 443266100 1895 True 874.000000 2098 95.497000 931 2550 3 chr6D.!!$R3 1619
5 TraesCS1D01G067300 chr7D 400199656 400201658 2002 True 1539.000000 2828 93.298500 1086 3193 2 chr7D.!!$R1 2107
6 TraesCS1D01G067300 chr7D 272338891 272339583 692 False 1109.000000 1109 95.533000 1 694 1 chr7D.!!$F2 693
7 TraesCS1D01G067300 chr7D 488119476 488121824 2348 True 1087.000000 2772 94.535333 932 3155 3 chr7D.!!$R2 2223
8 TraesCS1D01G067300 chr4A 524271322 524273804 2482 True 1082.666667 2815 91.747000 931 3193 3 chr4A.!!$R2 2262
9 TraesCS1D01G067300 chr4A 190403307 190404834 1527 False 798.500000 1273 90.123000 1998 3193 2 chr4A.!!$F1 1195
10 TraesCS1D01G067300 chrUn 101222118 101224114 1996 True 1049.333333 1740 95.099333 986 3193 3 chrUn.!!$R1 2207
11 TraesCS1D01G067300 chr2D 439658542 439659486 944 True 1343.000000 1343 92.389000 1993 2934 1 chr2D.!!$R1 941
12 TraesCS1D01G067300 chr3A 686265623 686266562 939 True 1284.000000 1284 91.410000 1998 2934 1 chr3A.!!$R2 936
13 TraesCS1D01G067300 chr3A 165870358 165871076 718 True 953.000000 953 90.595000 1262 1983 1 chr3A.!!$R1 721
14 TraesCS1D01G067300 chr5D 408521379 408522072 693 True 1166.000000 1166 96.974000 1 694 1 chr5D.!!$R2 693
15 TraesCS1D01G067300 chr5D 311663888 311664581 693 True 1149.000000 1149 96.542000 1 694 1 chr5D.!!$R1 693
16 TraesCS1D01G067300 chr5D 56899858 56900551 693 False 1127.000000 1127 95.965000 1 694 1 chr5D.!!$F1 693
17 TraesCS1D01G067300 chr5D 462187358 462188052 694 True 1105.000000 1105 95.396000 1 694 1 chr5D.!!$R3 693
18 TraesCS1D01G067300 chr3D 175629999 175630690 691 False 1129.000000 1129 96.104000 1 692 1 chr3D.!!$F1 691
19 TraesCS1D01G067300 chr4D 370589748 370590441 693 False 1116.000000 1116 95.677000 1 694 1 chr4D.!!$F1 693
20 TraesCS1D01G067300 chr6A 311853274 311853969 695 False 998.000000 998 92.571000 2497 3193 1 chr6A.!!$F1 696
21 TraesCS1D01G067300 chr2A 568233863 568234580 717 True 992.000000 992 91.575000 1262 1983 1 chr2A.!!$R1 721
22 TraesCS1D01G067300 chr5A 119025446 119026160 714 False 965.000000 965 90.972000 1262 1980 1 chr5A.!!$F1 718
23 TraesCS1D01G067300 chr7B 104513951 104515610 1659 False 627.500000 911 90.648500 1990 3193 2 chr7B.!!$F1 1203

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
795 799 0.039035 TAATTGGCCCGCAGTTCCTT 59.961 50.0 0.0 0.0 0.0 3.36 F
881 885 0.105593 AGCCGCAGTCCATATGTCTG 59.894 55.0 16.1 16.1 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2018 2327 0.105039 GGACTCTGCTTCCATACCCG 59.895 60.0 0.0 0.0 32.82 5.28 R
2580 2894 6.012745 ACTCCCAGCAATTTGTAAGAATCTT 58.987 36.0 0.0 0.0 0.00 2.40 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
142 144 7.618019 ATCTTTGACCAGCCTTCTATACATA 57.382 36.000 0.00 0.00 0.00 2.29
291 294 2.621668 GCTTTTAGCCCTGGACATCCTT 60.622 50.000 0.00 0.00 34.48 3.36
378 381 0.742281 ATCAGCACATGACAGGCGTC 60.742 55.000 0.00 3.11 41.91 5.19
423 426 4.278419 AGTCAAATGCCCAGTAAACACTTC 59.722 41.667 0.00 0.00 0.00 3.01
437 440 5.453567 AAACACTTCACTAATCCTTTGCC 57.546 39.130 0.00 0.00 0.00 4.52
543 546 5.299949 GGTCTCATGGAAGCAAACATTTTT 58.700 37.500 0.00 0.00 0.00 1.94
562 565 4.789095 TTTCACTTGAGCGTAACAGAAC 57.211 40.909 0.00 0.00 0.00 3.01
569 572 2.163815 TGAGCGTAACAGAACTCTAGCC 59.836 50.000 0.00 0.00 0.00 3.93
694 698 4.331717 CCTCACATTACGTTACCAACCATC 59.668 45.833 0.00 0.00 0.00 3.51
695 699 5.155278 TCACATTACGTTACCAACCATCT 57.845 39.130 0.00 0.00 0.00 2.90
696 700 5.172934 TCACATTACGTTACCAACCATCTC 58.827 41.667 0.00 0.00 0.00 2.75
697 701 5.046878 TCACATTACGTTACCAACCATCTCT 60.047 40.000 0.00 0.00 0.00 3.10
698 702 5.291128 CACATTACGTTACCAACCATCTCTC 59.709 44.000 0.00 0.00 0.00 3.20
699 703 4.460948 TTACGTTACCAACCATCTCTCC 57.539 45.455 0.00 0.00 0.00 3.71
700 704 1.553704 ACGTTACCAACCATCTCTCCC 59.446 52.381 0.00 0.00 0.00 4.30
701 705 1.553248 CGTTACCAACCATCTCTCCCA 59.447 52.381 0.00 0.00 0.00 4.37
702 706 2.027561 CGTTACCAACCATCTCTCCCAA 60.028 50.000 0.00 0.00 0.00 4.12
703 707 3.558321 CGTTACCAACCATCTCTCCCAAA 60.558 47.826 0.00 0.00 0.00 3.28
704 708 4.600062 GTTACCAACCATCTCTCCCAAAT 58.400 43.478 0.00 0.00 0.00 2.32
705 709 5.628200 CGTTACCAACCATCTCTCCCAAATA 60.628 44.000 0.00 0.00 0.00 1.40
706 710 4.946160 ACCAACCATCTCTCCCAAATAA 57.054 40.909 0.00 0.00 0.00 1.40
707 711 5.472301 ACCAACCATCTCTCCCAAATAAT 57.528 39.130 0.00 0.00 0.00 1.28
708 712 6.590656 ACCAACCATCTCTCCCAAATAATA 57.409 37.500 0.00 0.00 0.00 0.98
709 713 6.980577 ACCAACCATCTCTCCCAAATAATAA 58.019 36.000 0.00 0.00 0.00 1.40
710 714 7.418378 ACCAACCATCTCTCCCAAATAATAAA 58.582 34.615 0.00 0.00 0.00 1.40
711 715 7.561356 ACCAACCATCTCTCCCAAATAATAAAG 59.439 37.037 0.00 0.00 0.00 1.85
712 716 7.428826 CAACCATCTCTCCCAAATAATAAAGC 58.571 38.462 0.00 0.00 0.00 3.51
713 717 6.672593 ACCATCTCTCCCAAATAATAAAGCA 58.327 36.000 0.00 0.00 0.00 3.91
714 718 6.547510 ACCATCTCTCCCAAATAATAAAGCAC 59.452 38.462 0.00 0.00 0.00 4.40
715 719 6.293626 CCATCTCTCCCAAATAATAAAGCACG 60.294 42.308 0.00 0.00 0.00 5.34
716 720 5.123227 TCTCTCCCAAATAATAAAGCACGG 58.877 41.667 0.00 0.00 0.00 4.94
717 721 5.104693 TCTCTCCCAAATAATAAAGCACGGA 60.105 40.000 0.00 0.00 0.00 4.69
718 722 4.879545 TCTCCCAAATAATAAAGCACGGAC 59.120 41.667 0.00 0.00 0.00 4.79
719 723 4.850680 TCCCAAATAATAAAGCACGGACT 58.149 39.130 0.00 0.00 0.00 3.85
720 724 4.638421 TCCCAAATAATAAAGCACGGACTG 59.362 41.667 0.00 0.00 0.00 3.51
721 725 4.638421 CCCAAATAATAAAGCACGGACTGA 59.362 41.667 0.00 0.00 0.00 3.41
722 726 5.220854 CCCAAATAATAAAGCACGGACTGAG 60.221 44.000 0.00 0.00 0.00 3.35
723 727 5.354234 CCAAATAATAAAGCACGGACTGAGT 59.646 40.000 0.00 0.00 0.00 3.41
724 728 6.456988 CCAAATAATAAAGCACGGACTGAGTC 60.457 42.308 3.47 3.47 0.00 3.36
725 729 3.963428 AATAAAGCACGGACTGAGTCT 57.037 42.857 12.92 0.00 32.47 3.24
726 730 3.512033 ATAAAGCACGGACTGAGTCTC 57.488 47.619 12.92 1.90 32.47 3.36
727 731 1.333177 AAAGCACGGACTGAGTCTCT 58.667 50.000 12.92 2.40 32.47 3.10
728 732 0.885196 AAGCACGGACTGAGTCTCTC 59.115 55.000 12.92 0.09 32.47 3.20
729 733 0.250945 AGCACGGACTGAGTCTCTCA 60.251 55.000 12.92 0.00 38.25 3.27
738 742 1.248486 TGAGTCTCTCAGGTTCACCG 58.752 55.000 0.65 0.00 42.08 4.94
739 743 1.249407 GAGTCTCTCAGGTTCACCGT 58.751 55.000 0.00 0.00 42.08 4.83
740 744 1.200484 GAGTCTCTCAGGTTCACCGTC 59.800 57.143 0.00 0.00 42.08 4.79
741 745 0.109689 GTCTCTCAGGTTCACCGTCG 60.110 60.000 0.00 0.00 42.08 5.12
742 746 1.444553 CTCTCAGGTTCACCGTCGC 60.445 63.158 0.00 0.00 42.08 5.19
743 747 2.805353 CTCAGGTTCACCGTCGCG 60.805 66.667 0.00 0.00 42.08 5.87
791 795 4.810191 TTTTTATAATTGGCCCGCAGTT 57.190 36.364 0.00 0.00 0.00 3.16
792 796 4.379339 TTTTATAATTGGCCCGCAGTTC 57.621 40.909 0.00 0.00 0.00 3.01
793 797 1.975660 TATAATTGGCCCGCAGTTCC 58.024 50.000 0.00 0.00 0.00 3.62
794 798 0.258774 ATAATTGGCCCGCAGTTCCT 59.741 50.000 0.00 0.00 0.00 3.36
795 799 0.039035 TAATTGGCCCGCAGTTCCTT 59.961 50.000 0.00 0.00 0.00 3.36
796 800 0.831711 AATTGGCCCGCAGTTCCTTT 60.832 50.000 0.00 0.00 0.00 3.11
797 801 0.831711 ATTGGCCCGCAGTTCCTTTT 60.832 50.000 0.00 0.00 0.00 2.27
798 802 1.045911 TTGGCCCGCAGTTCCTTTTT 61.046 50.000 0.00 0.00 0.00 1.94
799 803 0.178987 TGGCCCGCAGTTCCTTTTTA 60.179 50.000 0.00 0.00 0.00 1.52
800 804 0.963225 GGCCCGCAGTTCCTTTTTAA 59.037 50.000 0.00 0.00 0.00 1.52
801 805 1.067846 GGCCCGCAGTTCCTTTTTAAG 60.068 52.381 0.00 0.00 0.00 1.85
802 806 1.611977 GCCCGCAGTTCCTTTTTAAGT 59.388 47.619 0.00 0.00 0.00 2.24
803 807 2.607038 GCCCGCAGTTCCTTTTTAAGTG 60.607 50.000 0.00 0.00 0.00 3.16
804 808 2.030274 CCCGCAGTTCCTTTTTAAGTGG 60.030 50.000 0.00 0.00 0.00 4.00
805 809 2.607038 CCGCAGTTCCTTTTTAAGTGGC 60.607 50.000 0.00 0.00 0.00 5.01
806 810 2.293399 CGCAGTTCCTTTTTAAGTGGCT 59.707 45.455 0.00 0.00 0.00 4.75
807 811 3.642705 GCAGTTCCTTTTTAAGTGGCTG 58.357 45.455 0.00 0.00 0.00 4.85
808 812 3.317993 GCAGTTCCTTTTTAAGTGGCTGA 59.682 43.478 0.00 0.00 0.00 4.26
809 813 4.793028 GCAGTTCCTTTTTAAGTGGCTGAC 60.793 45.833 0.00 0.00 0.00 3.51
810 814 3.889538 AGTTCCTTTTTAAGTGGCTGACC 59.110 43.478 0.00 0.00 0.00 4.02
811 815 3.586470 TCCTTTTTAAGTGGCTGACCA 57.414 42.857 0.00 0.00 46.51 4.02
821 825 2.957402 TGGCTGACCAGAGAAAATGT 57.043 45.000 0.47 0.00 42.67 2.71
822 826 3.228188 TGGCTGACCAGAGAAAATGTT 57.772 42.857 0.47 0.00 42.67 2.71
823 827 3.565307 TGGCTGACCAGAGAAAATGTTT 58.435 40.909 0.47 0.00 42.67 2.83
824 828 3.569701 TGGCTGACCAGAGAAAATGTTTC 59.430 43.478 0.47 0.00 42.67 2.78
825 829 3.569701 GGCTGACCAGAGAAAATGTTTCA 59.430 43.478 0.47 0.00 35.26 2.69
826 830 4.320788 GGCTGACCAGAGAAAATGTTTCAG 60.321 45.833 0.47 0.00 35.26 3.02
827 831 4.276926 GCTGACCAGAGAAAATGTTTCAGT 59.723 41.667 0.47 0.00 32.42 3.41
828 832 5.221126 GCTGACCAGAGAAAATGTTTCAGTT 60.221 40.000 0.47 0.00 32.42 3.16
829 833 6.681368 GCTGACCAGAGAAAATGTTTCAGTTT 60.681 38.462 0.47 0.00 34.34 2.66
830 834 7.169158 TGACCAGAGAAAATGTTTCAGTTTT 57.831 32.000 3.74 0.00 31.79 2.43
831 835 8.287439 TGACCAGAGAAAATGTTTCAGTTTTA 57.713 30.769 3.74 0.00 31.79 1.52
832 836 8.188139 TGACCAGAGAAAATGTTTCAGTTTTAC 58.812 33.333 3.74 0.00 31.79 2.01
833 837 8.062065 ACCAGAGAAAATGTTTCAGTTTTACA 57.938 30.769 3.74 0.00 31.79 2.41
834 838 8.527810 ACCAGAGAAAATGTTTCAGTTTTACAA 58.472 29.630 3.74 0.00 31.79 2.41
835 839 9.364989 CCAGAGAAAATGTTTCAGTTTTACAAA 57.635 29.630 3.74 0.00 31.79 2.83
842 846 8.926715 AATGTTTCAGTTTTACAAAGAAGACC 57.073 30.769 0.00 0.00 0.00 3.85
843 847 6.859017 TGTTTCAGTTTTACAAAGAAGACCC 58.141 36.000 0.00 0.00 0.00 4.46
844 848 6.661805 TGTTTCAGTTTTACAAAGAAGACCCT 59.338 34.615 0.00 0.00 0.00 4.34
845 849 6.693315 TTCAGTTTTACAAAGAAGACCCTG 57.307 37.500 0.00 0.00 0.00 4.45
846 850 5.751586 TCAGTTTTACAAAGAAGACCCTGT 58.248 37.500 0.00 0.00 0.00 4.00
847 851 6.891388 TCAGTTTTACAAAGAAGACCCTGTA 58.109 36.000 0.00 0.00 0.00 2.74
848 852 6.990349 TCAGTTTTACAAAGAAGACCCTGTAG 59.010 38.462 0.00 0.00 0.00 2.74
849 853 6.766467 CAGTTTTACAAAGAAGACCCTGTAGT 59.234 38.462 0.00 0.00 0.00 2.73
850 854 7.282450 CAGTTTTACAAAGAAGACCCTGTAGTT 59.718 37.037 0.00 0.00 0.00 2.24
851 855 7.832685 AGTTTTACAAAGAAGACCCTGTAGTTT 59.167 33.333 0.00 0.00 0.00 2.66
852 856 7.562454 TTTACAAAGAAGACCCTGTAGTTTG 57.438 36.000 0.00 0.00 0.00 2.93
853 857 5.112129 ACAAAGAAGACCCTGTAGTTTGT 57.888 39.130 0.00 0.00 33.06 2.83
854 858 5.506708 ACAAAGAAGACCCTGTAGTTTGTT 58.493 37.500 0.00 0.00 33.92 2.83
855 859 6.655930 ACAAAGAAGACCCTGTAGTTTGTTA 58.344 36.000 0.00 0.00 33.92 2.41
856 860 7.287810 ACAAAGAAGACCCTGTAGTTTGTTAT 58.712 34.615 0.00 0.00 33.92 1.89
857 861 8.434392 ACAAAGAAGACCCTGTAGTTTGTTATA 58.566 33.333 0.00 0.00 33.92 0.98
858 862 9.449719 CAAAGAAGACCCTGTAGTTTGTTATAT 57.550 33.333 0.00 0.00 0.00 0.86
860 864 9.668497 AAGAAGACCCTGTAGTTTGTTATATTC 57.332 33.333 0.00 0.00 0.00 1.75
861 865 8.822805 AGAAGACCCTGTAGTTTGTTATATTCA 58.177 33.333 0.00 0.00 0.00 2.57
862 866 9.444600 GAAGACCCTGTAGTTTGTTATATTCAA 57.555 33.333 0.00 0.00 0.00 2.69
863 867 9.449719 AAGACCCTGTAGTTTGTTATATTCAAG 57.550 33.333 0.00 0.00 0.00 3.02
864 868 7.553044 AGACCCTGTAGTTTGTTATATTCAAGC 59.447 37.037 0.00 0.00 0.00 4.01
865 869 6.602009 ACCCTGTAGTTTGTTATATTCAAGCC 59.398 38.462 4.50 0.00 0.00 4.35
866 870 6.238374 CCCTGTAGTTTGTTATATTCAAGCCG 60.238 42.308 4.50 0.00 0.00 5.52
867 871 6.114221 TGTAGTTTGTTATATTCAAGCCGC 57.886 37.500 4.50 0.00 0.00 6.53
868 872 5.644206 TGTAGTTTGTTATATTCAAGCCGCA 59.356 36.000 0.00 2.68 0.00 5.69
869 873 5.235305 AGTTTGTTATATTCAAGCCGCAG 57.765 39.130 0.00 0.00 0.00 5.18
870 874 4.700213 AGTTTGTTATATTCAAGCCGCAGT 59.300 37.500 0.00 0.00 0.00 4.40
871 875 4.875544 TTGTTATATTCAAGCCGCAGTC 57.124 40.909 0.00 0.00 0.00 3.51
872 876 3.202906 TGTTATATTCAAGCCGCAGTCC 58.797 45.455 0.00 0.00 0.00 3.85
873 877 3.202906 GTTATATTCAAGCCGCAGTCCA 58.797 45.455 0.00 0.00 0.00 4.02
874 878 2.645838 ATATTCAAGCCGCAGTCCAT 57.354 45.000 0.00 0.00 0.00 3.41
875 879 3.769739 ATATTCAAGCCGCAGTCCATA 57.230 42.857 0.00 0.00 0.00 2.74
876 880 2.645838 ATTCAAGCCGCAGTCCATAT 57.354 45.000 0.00 0.00 0.00 1.78
877 881 1.667236 TTCAAGCCGCAGTCCATATG 58.333 50.000 0.00 0.00 0.00 1.78
878 882 0.541392 TCAAGCCGCAGTCCATATGT 59.459 50.000 1.24 0.00 0.00 2.29
879 883 0.940126 CAAGCCGCAGTCCATATGTC 59.060 55.000 1.24 0.00 0.00 3.06
880 884 0.833287 AAGCCGCAGTCCATATGTCT 59.167 50.000 1.24 0.00 0.00 3.41
881 885 0.105593 AGCCGCAGTCCATATGTCTG 59.894 55.000 16.10 16.10 0.00 3.51
882 886 0.882042 GCCGCAGTCCATATGTCTGG 60.882 60.000 19.62 12.78 37.66 3.86
883 887 0.465705 CCGCAGTCCATATGTCTGGT 59.534 55.000 19.62 0.00 37.57 4.00
884 888 1.134401 CCGCAGTCCATATGTCTGGTT 60.134 52.381 19.62 0.00 37.57 3.67
885 889 2.632377 CGCAGTCCATATGTCTGGTTT 58.368 47.619 19.62 0.00 37.57 3.27
886 890 3.009723 CGCAGTCCATATGTCTGGTTTT 58.990 45.455 19.62 0.00 37.57 2.43
887 891 4.188462 CGCAGTCCATATGTCTGGTTTTA 58.812 43.478 19.62 0.00 37.57 1.52
888 892 4.816385 CGCAGTCCATATGTCTGGTTTTAT 59.184 41.667 19.62 0.00 37.57 1.40
889 893 5.296780 CGCAGTCCATATGTCTGGTTTTATT 59.703 40.000 19.62 0.00 37.57 1.40
890 894 6.481976 CGCAGTCCATATGTCTGGTTTTATTA 59.518 38.462 19.62 0.00 37.57 0.98
891 895 7.011950 CGCAGTCCATATGTCTGGTTTTATTAA 59.988 37.037 19.62 0.00 37.57 1.40
892 896 8.850156 GCAGTCCATATGTCTGGTTTTATTAAT 58.150 33.333 19.62 0.00 37.57 1.40
896 900 9.573166 TCCATATGTCTGGTTTTATTAATCAGG 57.427 33.333 1.24 0.00 37.57 3.86
897 901 8.796475 CCATATGTCTGGTTTTATTAATCAGGG 58.204 37.037 1.24 0.00 0.00 4.45
898 902 9.573166 CATATGTCTGGTTTTATTAATCAGGGA 57.427 33.333 0.00 0.00 0.00 4.20
900 904 7.880160 TGTCTGGTTTTATTAATCAGGGATG 57.120 36.000 0.00 0.00 0.00 3.51
901 905 6.833416 TGTCTGGTTTTATTAATCAGGGATGG 59.167 38.462 0.00 0.00 0.00 3.51
902 906 6.265422 GTCTGGTTTTATTAATCAGGGATGGG 59.735 42.308 0.00 0.00 0.00 4.00
903 907 6.068498 TCTGGTTTTATTAATCAGGGATGGGT 60.068 38.462 0.00 0.00 0.00 4.51
904 908 6.133356 TGGTTTTATTAATCAGGGATGGGTC 58.867 40.000 0.00 0.00 0.00 4.46
905 909 6.133356 GGTTTTATTAATCAGGGATGGGTCA 58.867 40.000 0.00 0.00 0.00 4.02
906 910 6.609616 GGTTTTATTAATCAGGGATGGGTCAA 59.390 38.462 0.00 0.00 0.00 3.18
907 911 7.417456 GGTTTTATTAATCAGGGATGGGTCAAC 60.417 40.741 0.00 0.00 0.00 3.18
908 912 3.275617 TTAATCAGGGATGGGTCAACG 57.724 47.619 0.00 0.00 0.00 4.10
909 913 0.394352 AATCAGGGATGGGTCAACGC 60.394 55.000 0.00 0.00 0.00 4.84
910 914 2.593468 ATCAGGGATGGGTCAACGCG 62.593 60.000 3.53 3.53 0.00 6.01
911 915 4.096003 AGGGATGGGTCAACGCGG 62.096 66.667 12.47 0.00 0.00 6.46
1081 1317 3.916544 CTGAGGCCGCGGATGCTA 61.917 66.667 33.48 9.46 39.65 3.49
1100 1336 2.203728 TCCTACACCCGCACCACT 60.204 61.111 0.00 0.00 0.00 4.00
1102 1338 1.217244 CCTACACCCGCACCACTAC 59.783 63.158 0.00 0.00 0.00 2.73
1103 1339 1.255667 CCTACACCCGCACCACTACT 61.256 60.000 0.00 0.00 0.00 2.57
1210 1469 6.615726 ACTGCTCCTCCTAAATTAGGTCAATA 59.384 38.462 17.76 0.00 46.32 1.90
1212 1471 6.043243 TGCTCCTCCTAAATTAGGTCAATAGG 59.957 42.308 17.76 15.87 46.32 2.57
1224 1483 4.430441 AGGTCAATAGGGTTGACTCTTCT 58.570 43.478 17.36 6.33 45.88 2.85
1284 1585 3.369576 GCTCGGATTTCTTGGTTAGAGGT 60.370 47.826 0.00 0.00 33.51 3.85
1286 1587 5.593010 CTCGGATTTCTTGGTTAGAGGTAG 58.407 45.833 0.00 0.00 33.51 3.18
1465 1767 9.549509 TGTTTGCTAATTTTATGTTCACGATAC 57.450 29.630 0.00 0.00 0.00 2.24
1498 1800 6.542005 GTGTTTTGGAATTTCACAATCCCTTT 59.458 34.615 0.00 0.00 0.00 3.11
1525 1831 8.868522 ATCTCTCTGTTATGATTTTGGTTTCA 57.131 30.769 0.00 0.00 0.00 2.69
1565 1871 1.041447 GCGGGCTGACCTTAGGTAGA 61.041 60.000 2.88 0.00 35.25 2.59
1588 1895 8.613922 AGAAAAATAAATCATGTCCCTTCCAT 57.386 30.769 0.00 0.00 0.00 3.41
1686 1993 7.118825 GGGAACTTTTACTACATGTCCAGTTAC 59.881 40.741 0.00 3.76 0.00 2.50
1687 1994 7.118825 GGAACTTTTACTACATGTCCAGTTACC 59.881 40.741 0.00 3.85 0.00 2.85
1766 2073 3.472652 TGTATGGAGTTCTTGTTGCGTT 58.527 40.909 0.00 0.00 0.00 4.84
2119 2428 4.529219 CATGGAGTGGCGCGGCTA 62.529 66.667 33.23 17.05 0.00 3.93
2134 2443 2.163815 GCGGCTACAACTACTCTGAGAA 59.836 50.000 12.44 0.00 0.00 2.87
2320 2632 5.645067 TCAGATTCCAATGAAACTAGCACTG 59.355 40.000 0.00 0.00 32.42 3.66
2423 2737 9.950680 GATGAATTCGATTGGTATTGTGTAAAT 57.049 29.630 0.04 0.00 0.00 1.40
2545 2859 2.636893 CAGTCTTATCCCTAGGCTGCAT 59.363 50.000 2.05 0.00 38.39 3.96
2688 3129 5.008613 GCTACTTGTGAAGGTGTCAATTTCA 59.991 40.000 0.00 0.00 38.23 2.69
2700 3141 7.844009 AGGTGTCAATTTCAGCATTGATAAAT 58.156 30.769 10.73 0.00 43.47 1.40
2751 3194 8.803235 TCTTTCTGTTAGCTATCTGTACAAGAA 58.197 33.333 0.00 0.00 38.79 2.52
2836 3280 7.989741 TGAAAATTAAAGTTTTTCATGGCTGGA 59.010 29.630 10.12 0.00 44.12 3.86
2987 4085 0.460811 GCTGACGAGGATGCATGACA 60.461 55.000 2.46 0.00 0.00 3.58
2997 4095 5.231702 AGGATGCATGACATTTGGTTTTT 57.768 34.783 2.46 0.00 39.84 1.94
3039 4137 7.229306 GCATATGAACAACCTATCATCTTCCAA 59.771 37.037 6.97 0.00 37.46 3.53
3051 4150 6.956299 ATCATCTTCCAATTTTGCTTTTCG 57.044 33.333 0.00 0.00 0.00 3.46
3178 4281 0.035343 GACCCCCTTTGGCTCTACAC 60.035 60.000 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
225 228 9.621629 TTCTTCTGAGAGTAGGAGAAATACTAG 57.378 37.037 0.00 0.00 38.93 2.57
378 381 2.969262 GTTAGGAGAGGGATCCAGAAGG 59.031 54.545 15.23 0.00 42.26 3.46
423 426 4.942852 TGTTTGTTGGCAAAGGATTAGTG 58.057 39.130 0.00 0.00 44.27 2.74
543 546 3.318275 AGAGTTCTGTTACGCTCAAGTGA 59.682 43.478 0.00 0.00 0.00 3.41
562 565 2.695666 TCCTTCGATCCAAAGGCTAGAG 59.304 50.000 14.17 0.00 42.57 2.43
694 698 5.007724 GTCCGTGCTTTATTATTTGGGAGAG 59.992 44.000 0.00 0.00 0.00 3.20
695 699 4.879545 GTCCGTGCTTTATTATTTGGGAGA 59.120 41.667 0.00 0.00 0.00 3.71
696 700 4.881850 AGTCCGTGCTTTATTATTTGGGAG 59.118 41.667 0.00 0.00 0.00 4.30
697 701 4.638421 CAGTCCGTGCTTTATTATTTGGGA 59.362 41.667 0.00 0.00 0.00 4.37
698 702 4.638421 TCAGTCCGTGCTTTATTATTTGGG 59.362 41.667 0.00 0.00 0.00 4.12
699 703 5.354234 ACTCAGTCCGTGCTTTATTATTTGG 59.646 40.000 0.00 0.00 0.00 3.28
700 704 6.313905 AGACTCAGTCCGTGCTTTATTATTTG 59.686 38.462 0.00 0.00 32.18 2.32
701 705 6.407202 AGACTCAGTCCGTGCTTTATTATTT 58.593 36.000 0.00 0.00 32.18 1.40
702 706 5.978814 AGACTCAGTCCGTGCTTTATTATT 58.021 37.500 0.00 0.00 32.18 1.40
703 707 5.361285 AGAGACTCAGTCCGTGCTTTATTAT 59.639 40.000 0.00 0.00 32.18 1.28
704 708 4.705507 AGAGACTCAGTCCGTGCTTTATTA 59.294 41.667 0.00 0.00 32.18 0.98
705 709 3.511934 AGAGACTCAGTCCGTGCTTTATT 59.488 43.478 0.00 0.00 32.18 1.40
706 710 3.093057 AGAGACTCAGTCCGTGCTTTAT 58.907 45.455 0.00 0.00 32.18 1.40
707 711 2.488545 GAGAGACTCAGTCCGTGCTTTA 59.511 50.000 0.00 0.00 32.18 1.85
708 712 1.271102 GAGAGACTCAGTCCGTGCTTT 59.729 52.381 0.00 0.00 32.18 3.51
709 713 0.885196 GAGAGACTCAGTCCGTGCTT 59.115 55.000 0.00 0.00 32.18 3.91
710 714 0.250945 TGAGAGACTCAGTCCGTGCT 60.251 55.000 0.00 0.00 35.39 4.40
711 715 2.258317 TGAGAGACTCAGTCCGTGC 58.742 57.895 0.00 0.00 35.39 5.34
719 723 1.248486 CGGTGAACCTGAGAGACTCA 58.752 55.000 5.02 0.00 38.25 3.41
720 724 1.200484 GACGGTGAACCTGAGAGACTC 59.800 57.143 0.00 0.00 0.00 3.36
721 725 1.249407 GACGGTGAACCTGAGAGACT 58.751 55.000 0.00 0.00 0.00 3.24
722 726 0.109689 CGACGGTGAACCTGAGAGAC 60.110 60.000 0.00 0.00 0.00 3.36
723 727 1.863662 GCGACGGTGAACCTGAGAGA 61.864 60.000 0.00 0.00 0.00 3.10
724 728 1.444553 GCGACGGTGAACCTGAGAG 60.445 63.158 0.00 0.00 0.00 3.20
725 729 2.649034 GCGACGGTGAACCTGAGA 59.351 61.111 0.00 0.00 0.00 3.27
726 730 2.805353 CGCGACGGTGAACCTGAG 60.805 66.667 0.00 0.00 0.00 3.35
727 731 4.351938 CCGCGACGGTGAACCTGA 62.352 66.667 8.23 0.00 42.73 3.86
770 774 4.382147 GGAACTGCGGGCCAATTATAAAAA 60.382 41.667 4.39 0.00 0.00 1.94
771 775 3.131400 GGAACTGCGGGCCAATTATAAAA 59.869 43.478 4.39 0.00 0.00 1.52
772 776 2.691011 GGAACTGCGGGCCAATTATAAA 59.309 45.455 4.39 0.00 0.00 1.40
773 777 2.092103 AGGAACTGCGGGCCAATTATAA 60.092 45.455 4.39 0.00 37.18 0.98
774 778 1.493022 AGGAACTGCGGGCCAATTATA 59.507 47.619 4.39 0.00 37.18 0.98
775 779 0.258774 AGGAACTGCGGGCCAATTAT 59.741 50.000 4.39 0.00 37.18 1.28
776 780 0.039035 AAGGAACTGCGGGCCAATTA 59.961 50.000 4.39 0.00 40.86 1.40
777 781 0.831711 AAAGGAACTGCGGGCCAATT 60.832 50.000 4.39 0.00 40.86 2.32
778 782 0.831711 AAAAGGAACTGCGGGCCAAT 60.832 50.000 4.39 0.00 40.86 3.16
779 783 1.045911 AAAAAGGAACTGCGGGCCAA 61.046 50.000 4.39 0.00 40.86 4.52
780 784 0.178987 TAAAAAGGAACTGCGGGCCA 60.179 50.000 4.39 0.00 40.86 5.36
781 785 0.963225 TTAAAAAGGAACTGCGGGCC 59.037 50.000 0.00 0.00 40.86 5.80
782 786 1.611977 ACTTAAAAAGGAACTGCGGGC 59.388 47.619 0.00 0.00 40.86 6.13
783 787 2.030274 CCACTTAAAAAGGAACTGCGGG 60.030 50.000 0.00 0.00 40.86 6.13
784 788 2.607038 GCCACTTAAAAAGGAACTGCGG 60.607 50.000 0.00 0.00 40.86 5.69
785 789 2.293399 AGCCACTTAAAAAGGAACTGCG 59.707 45.455 0.00 0.00 40.86 5.18
786 790 3.317993 TCAGCCACTTAAAAAGGAACTGC 59.682 43.478 0.00 0.00 40.86 4.40
787 791 4.261614 GGTCAGCCACTTAAAAAGGAACTG 60.262 45.833 0.00 0.00 34.20 3.16
788 792 3.889538 GGTCAGCCACTTAAAAAGGAACT 59.110 43.478 0.00 0.00 35.27 3.01
789 793 3.634910 TGGTCAGCCACTTAAAAAGGAAC 59.365 43.478 0.00 0.00 40.46 3.62
790 794 3.888930 CTGGTCAGCCACTTAAAAAGGAA 59.111 43.478 0.00 0.00 40.46 3.36
791 795 3.137544 TCTGGTCAGCCACTTAAAAAGGA 59.862 43.478 0.00 0.00 40.46 3.36
792 796 3.486383 TCTGGTCAGCCACTTAAAAAGG 58.514 45.455 0.00 0.00 40.46 3.11
793 797 4.389374 TCTCTGGTCAGCCACTTAAAAAG 58.611 43.478 0.00 0.00 40.46 2.27
794 798 4.431416 TCTCTGGTCAGCCACTTAAAAA 57.569 40.909 0.00 0.00 40.46 1.94
795 799 4.431416 TTCTCTGGTCAGCCACTTAAAA 57.569 40.909 0.00 0.00 40.46 1.52
796 800 4.431416 TTTCTCTGGTCAGCCACTTAAA 57.569 40.909 0.00 0.00 40.46 1.52
797 801 4.431416 TTTTCTCTGGTCAGCCACTTAA 57.569 40.909 0.00 0.00 40.46 1.85
798 802 4.202461 ACATTTTCTCTGGTCAGCCACTTA 60.202 41.667 0.00 0.00 40.46 2.24
799 803 3.152341 CATTTTCTCTGGTCAGCCACTT 58.848 45.455 0.00 0.00 40.46 3.16
800 804 2.107204 ACATTTTCTCTGGTCAGCCACT 59.893 45.455 0.00 0.00 40.46 4.00
801 805 2.508526 ACATTTTCTCTGGTCAGCCAC 58.491 47.619 0.00 0.00 40.46 5.01
802 806 2.957402 ACATTTTCTCTGGTCAGCCA 57.043 45.000 0.00 0.00 43.73 4.75
803 807 3.569701 TGAAACATTTTCTCTGGTCAGCC 59.430 43.478 0.68 0.00 0.00 4.85
804 808 4.276926 ACTGAAACATTTTCTCTGGTCAGC 59.723 41.667 0.00 0.00 35.18 4.26
805 809 6.382869 AACTGAAACATTTTCTCTGGTCAG 57.617 37.500 0.00 0.00 36.61 3.51
806 810 6.773976 AAACTGAAACATTTTCTCTGGTCA 57.226 33.333 0.68 0.00 0.00 4.02
807 811 8.188139 TGTAAAACTGAAACATTTTCTCTGGTC 58.812 33.333 0.68 0.00 30.80 4.02
808 812 8.062065 TGTAAAACTGAAACATTTTCTCTGGT 57.938 30.769 0.68 0.00 30.80 4.00
809 813 8.925161 TTGTAAAACTGAAACATTTTCTCTGG 57.075 30.769 0.68 0.00 30.80 3.86
816 820 9.366216 GGTCTTCTTTGTAAAACTGAAACATTT 57.634 29.630 0.00 0.00 0.00 2.32
817 821 7.979537 GGGTCTTCTTTGTAAAACTGAAACATT 59.020 33.333 0.00 0.00 0.00 2.71
818 822 7.342026 AGGGTCTTCTTTGTAAAACTGAAACAT 59.658 33.333 0.00 0.00 0.00 2.71
819 823 6.661805 AGGGTCTTCTTTGTAAAACTGAAACA 59.338 34.615 0.00 0.00 0.00 2.83
820 824 6.972901 CAGGGTCTTCTTTGTAAAACTGAAAC 59.027 38.462 0.00 0.00 0.00 2.78
821 825 6.661805 ACAGGGTCTTCTTTGTAAAACTGAAA 59.338 34.615 0.00 0.00 0.00 2.69
822 826 6.184789 ACAGGGTCTTCTTTGTAAAACTGAA 58.815 36.000 0.00 0.00 0.00 3.02
823 827 5.751586 ACAGGGTCTTCTTTGTAAAACTGA 58.248 37.500 0.00 0.00 0.00 3.41
824 828 6.766467 ACTACAGGGTCTTCTTTGTAAAACTG 59.234 38.462 0.00 0.00 0.00 3.16
825 829 6.896883 ACTACAGGGTCTTCTTTGTAAAACT 58.103 36.000 0.00 0.00 0.00 2.66
826 830 7.563888 AACTACAGGGTCTTCTTTGTAAAAC 57.436 36.000 0.00 0.00 0.00 2.43
827 831 7.612633 ACAAACTACAGGGTCTTCTTTGTAAAA 59.387 33.333 0.00 0.00 0.00 1.52
828 832 7.114095 ACAAACTACAGGGTCTTCTTTGTAAA 58.886 34.615 0.00 0.00 0.00 2.01
829 833 6.655930 ACAAACTACAGGGTCTTCTTTGTAA 58.344 36.000 0.00 0.00 0.00 2.41
830 834 6.243216 ACAAACTACAGGGTCTTCTTTGTA 57.757 37.500 0.00 0.00 0.00 2.41
831 835 5.112129 ACAAACTACAGGGTCTTCTTTGT 57.888 39.130 0.00 0.00 0.00 2.83
832 836 7.745620 ATAACAAACTACAGGGTCTTCTTTG 57.254 36.000 0.00 0.00 0.00 2.77
834 838 9.668497 GAATATAACAAACTACAGGGTCTTCTT 57.332 33.333 0.00 0.00 0.00 2.52
835 839 8.822805 TGAATATAACAAACTACAGGGTCTTCT 58.177 33.333 0.00 0.00 0.00 2.85
836 840 9.444600 TTGAATATAACAAACTACAGGGTCTTC 57.555 33.333 0.00 0.00 0.00 2.87
837 841 9.449719 CTTGAATATAACAAACTACAGGGTCTT 57.550 33.333 0.00 0.00 0.00 3.01
838 842 7.553044 GCTTGAATATAACAAACTACAGGGTCT 59.447 37.037 0.00 0.00 0.00 3.85
839 843 7.201705 GGCTTGAATATAACAAACTACAGGGTC 60.202 40.741 0.00 0.00 0.00 4.46
840 844 6.602009 GGCTTGAATATAACAAACTACAGGGT 59.398 38.462 0.00 0.00 0.00 4.34
841 845 6.238374 CGGCTTGAATATAACAAACTACAGGG 60.238 42.308 0.00 0.00 0.00 4.45
842 846 6.715464 CGGCTTGAATATAACAAACTACAGG 58.285 40.000 0.00 0.00 0.00 4.00
843 847 6.183360 TGCGGCTTGAATATAACAAACTACAG 60.183 38.462 0.00 0.00 0.00 2.74
844 848 5.644206 TGCGGCTTGAATATAACAAACTACA 59.356 36.000 0.00 0.00 0.00 2.74
845 849 6.114221 TGCGGCTTGAATATAACAAACTAC 57.886 37.500 0.00 0.00 0.00 2.73
846 850 5.878116 ACTGCGGCTTGAATATAACAAACTA 59.122 36.000 0.00 0.00 0.00 2.24
847 851 4.700213 ACTGCGGCTTGAATATAACAAACT 59.300 37.500 0.00 0.00 0.00 2.66
848 852 4.981794 ACTGCGGCTTGAATATAACAAAC 58.018 39.130 0.00 0.00 0.00 2.93
849 853 4.095782 GGACTGCGGCTTGAATATAACAAA 59.904 41.667 0.00 0.00 0.00 2.83
850 854 3.625764 GGACTGCGGCTTGAATATAACAA 59.374 43.478 0.00 0.00 0.00 2.83
851 855 3.202906 GGACTGCGGCTTGAATATAACA 58.797 45.455 0.00 0.00 0.00 2.41
852 856 3.202906 TGGACTGCGGCTTGAATATAAC 58.797 45.455 0.00 0.00 0.00 1.89
853 857 3.552132 TGGACTGCGGCTTGAATATAA 57.448 42.857 0.00 0.00 0.00 0.98
854 858 3.769739 ATGGACTGCGGCTTGAATATA 57.230 42.857 0.00 0.00 0.00 0.86
855 859 2.645838 ATGGACTGCGGCTTGAATAT 57.354 45.000 0.00 0.00 0.00 1.28
856 860 3.181455 ACATATGGACTGCGGCTTGAATA 60.181 43.478 7.80 0.00 0.00 1.75
857 861 2.224606 CATATGGACTGCGGCTTGAAT 58.775 47.619 0.00 0.00 0.00 2.57
858 862 1.065491 ACATATGGACTGCGGCTTGAA 60.065 47.619 7.80 0.00 0.00 2.69
859 863 0.541392 ACATATGGACTGCGGCTTGA 59.459 50.000 7.80 0.00 0.00 3.02
860 864 0.940126 GACATATGGACTGCGGCTTG 59.060 55.000 7.80 0.00 0.00 4.01
861 865 0.833287 AGACATATGGACTGCGGCTT 59.167 50.000 7.80 0.00 0.00 4.35
862 866 0.105593 CAGACATATGGACTGCGGCT 59.894 55.000 15.52 0.00 0.00 5.52
863 867 0.882042 CCAGACATATGGACTGCGGC 60.882 60.000 19.76 0.00 43.57 6.53
864 868 0.465705 ACCAGACATATGGACTGCGG 59.534 55.000 19.76 13.23 43.57 5.69
865 869 2.315925 AACCAGACATATGGACTGCG 57.684 50.000 19.76 16.27 43.57 5.18
866 870 6.699575 AATAAAACCAGACATATGGACTGC 57.300 37.500 19.76 1.67 43.57 4.40
870 874 9.573166 CCTGATTAATAAAACCAGACATATGGA 57.427 33.333 7.80 0.00 43.57 3.41
871 875 8.796475 CCCTGATTAATAAAACCAGACATATGG 58.204 37.037 7.80 0.00 46.47 2.74
872 876 9.573166 TCCCTGATTAATAAAACCAGACATATG 57.427 33.333 0.00 0.00 0.00 1.78
874 878 9.573166 CATCCCTGATTAATAAAACCAGACATA 57.427 33.333 3.33 0.00 0.00 2.29
875 879 7.506938 CCATCCCTGATTAATAAAACCAGACAT 59.493 37.037 3.33 0.00 0.00 3.06
876 880 6.833416 CCATCCCTGATTAATAAAACCAGACA 59.167 38.462 3.33 0.00 0.00 3.41
877 881 6.265422 CCCATCCCTGATTAATAAAACCAGAC 59.735 42.308 3.33 0.00 0.00 3.51
878 882 6.068498 ACCCATCCCTGATTAATAAAACCAGA 60.068 38.462 3.33 0.00 0.00 3.86
879 883 6.136155 ACCCATCCCTGATTAATAAAACCAG 58.864 40.000 0.00 0.00 0.00 4.00
880 884 6.098716 ACCCATCCCTGATTAATAAAACCA 57.901 37.500 0.00 0.00 0.00 3.67
881 885 6.133356 TGACCCATCCCTGATTAATAAAACC 58.867 40.000 0.00 0.00 0.00 3.27
882 886 7.489160 GTTGACCCATCCCTGATTAATAAAAC 58.511 38.462 0.00 0.00 0.00 2.43
883 887 6.320164 CGTTGACCCATCCCTGATTAATAAAA 59.680 38.462 0.00 0.00 0.00 1.52
884 888 5.825679 CGTTGACCCATCCCTGATTAATAAA 59.174 40.000 0.00 0.00 0.00 1.40
885 889 5.373222 CGTTGACCCATCCCTGATTAATAA 58.627 41.667 0.00 0.00 0.00 1.40
886 890 4.745478 GCGTTGACCCATCCCTGATTAATA 60.745 45.833 0.00 0.00 0.00 0.98
887 891 3.820557 CGTTGACCCATCCCTGATTAAT 58.179 45.455 0.00 0.00 0.00 1.40
888 892 2.682563 GCGTTGACCCATCCCTGATTAA 60.683 50.000 0.00 0.00 0.00 1.40
889 893 1.134220 GCGTTGACCCATCCCTGATTA 60.134 52.381 0.00 0.00 0.00 1.75
890 894 0.394352 GCGTTGACCCATCCCTGATT 60.394 55.000 0.00 0.00 0.00 2.57
891 895 1.224592 GCGTTGACCCATCCCTGAT 59.775 57.895 0.00 0.00 0.00 2.90
892 896 2.668632 GCGTTGACCCATCCCTGA 59.331 61.111 0.00 0.00 0.00 3.86
893 897 2.819595 CGCGTTGACCCATCCCTG 60.820 66.667 0.00 0.00 0.00 4.45
894 898 4.096003 CCGCGTTGACCCATCCCT 62.096 66.667 4.92 0.00 0.00 4.20
949 953 4.864334 GCACGGATCTGGCCCCTG 62.864 72.222 6.47 0.00 0.00 4.45
957 961 4.498520 CCTGACGCGCACGGATCT 62.499 66.667 5.73 0.00 46.04 2.75
1030 1266 3.538614 GCCATAGCGACAGGAGGA 58.461 61.111 0.00 0.00 0.00 3.71
1052 1288 4.461119 CCTCAGGGCACTCCACTA 57.539 61.111 0.00 0.00 38.24 2.74
1081 1317 2.203728 TGGTGCGGGTGTAGGAGT 60.204 61.111 0.00 0.00 0.00 3.85
1100 1336 2.650322 AGAGGAGACTGACCTTGGAGTA 59.350 50.000 0.00 0.00 44.43 2.59
1102 1338 2.230130 AGAGGAGACTGACCTTGGAG 57.770 55.000 0.00 0.00 44.43 3.86
1103 1339 2.291670 GGTAGAGGAGACTGACCTTGGA 60.292 54.545 0.00 0.00 44.43 3.53
1204 1463 8.466617 TCTATAGAAGAGTCAACCCTATTGAC 57.533 38.462 11.04 11.04 46.71 3.18
1224 1483 3.960755 CTGACACCACACCATCCTCTATA 59.039 47.826 0.00 0.00 0.00 1.31
1266 1567 4.876679 GCACTACCTCTAACCAAGAAATCC 59.123 45.833 0.00 0.00 32.46 3.01
1267 1568 4.876679 GGCACTACCTCTAACCAAGAAATC 59.123 45.833 0.00 0.00 32.46 2.17
1284 1585 1.702401 TCAAACACCATGAGGGCACTA 59.298 47.619 0.00 0.00 42.05 2.74
1286 1587 0.598065 GTCAAACACCATGAGGGCAC 59.402 55.000 0.00 0.00 42.05 5.01
1606 1913 9.973246 CATGTAACTTTGATGAGTATGTAACAC 57.027 33.333 0.00 0.00 0.00 3.32
1663 1970 6.647895 CGGTAACTGGACATGTAGTAAAAGTT 59.352 38.462 0.00 5.56 33.96 2.66
1686 1993 3.788797 GCGCTCCTTTTATCATGAAACGG 60.789 47.826 0.00 0.00 0.00 4.44
1687 1994 3.181511 TGCGCTCCTTTTATCATGAAACG 60.182 43.478 9.73 0.00 0.00 3.60
1766 2073 7.815840 TTTTACATGGTTGATGACTTGAAGA 57.184 32.000 0.00 0.00 35.80 2.87
1996 2305 3.063704 CCAATGGCGGCTGCTCAA 61.064 61.111 18.85 3.87 42.25 3.02
2018 2327 0.105039 GGACTCTGCTTCCATACCCG 59.895 60.000 0.00 0.00 32.82 5.28
2119 2428 6.257586 AGGAATACCTTCTCAGAGTAGTTGT 58.742 40.000 3.57 0.00 45.36 3.32
2445 2759 7.924541 TGGGATTAGTTAACTCAGTTACCAAT 58.075 34.615 12.39 3.53 0.00 3.16
2567 2881 9.719355 TTTGTAAGAATCTTAGCAACATAGACA 57.281 29.630 2.48 0.00 0.00 3.41
2572 2886 8.526147 AGCAATTTGTAAGAATCTTAGCAACAT 58.474 29.630 2.48 5.56 0.00 2.71
2580 2894 6.012745 ACTCCCAGCAATTTGTAAGAATCTT 58.987 36.000 0.00 0.00 0.00 2.40
2726 3167 8.988064 TTCTTGTACAGATAGCTAACAGAAAG 57.012 34.615 0.00 0.63 0.00 2.62
2987 4085 6.126796 ACCTGATCTTTCCACAAAAACCAAAT 60.127 34.615 0.00 0.00 0.00 2.32
2997 4095 2.885135 ATGCACCTGATCTTTCCACA 57.115 45.000 0.00 0.00 0.00 4.17
3039 4137 5.409214 CCCATTGAATGACGAAAAGCAAAAT 59.591 36.000 6.76 0.00 0.00 1.82
3131 4232 9.495754 GAACAAAGAATCTCATGTGCTAATAAC 57.504 33.333 2.98 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.