Multiple sequence alignment - TraesCS5D01G334300

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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 TraesCS5D01G334300 chr5D 100.000 3160 0 0 1 3160 423972169 423975328 0.000000e+00 5836.0
1 TraesCS5D01G334300 chr5D 78.161 696 127 19 1078 1756 520909988 520910675 1.360000e-113 420.0
2 TraesCS5D01G334300 chr5D 75.000 684 122 31 1084 1756 424033306 424033951 1.440000e-68 270.0
3 TraesCS5D01G334300 chr5A 90.146 1786 103 32 703 2460 537615487 537617227 0.000000e+00 2255.0
4 TraesCS5D01G334300 chr5A 90.708 678 28 17 2498 3160 537617219 537617876 0.000000e+00 870.0
5 TraesCS5D01G334300 chr5A 86.380 558 30 21 147 693 537614982 537615504 4.570000e-158 568.0
6 TraesCS5D01G334300 chr5A 76.620 710 128 24 1078 1756 649441448 649442150 1.080000e-94 357.0
7 TraesCS5D01G334300 chr5A 74.779 678 128 28 1084 1756 537626134 537626773 6.720000e-67 265.0
8 TraesCS5D01G334300 chr5B 87.570 1794 105 63 709 2460 511852099 511853816 0.000000e+00 1969.0
9 TraesCS5D01G334300 chr5B 88.817 465 28 9 2498 2959 511853808 511854251 1.660000e-152 549.0
10 TraesCS5D01G334300 chr5B 83.000 400 42 12 2 401 511851488 511851861 3.900000e-89 339.0
11 TraesCS5D01G334300 chr5B 91.566 249 13 5 441 687 511851868 511852110 1.400000e-88 337.0
12 TraesCS5D01G334300 chr5B 74.963 679 125 28 1084 1756 512212667 512213306 1.440000e-68 270.0
13 TraesCS5D01G334300 chr5B 81.699 306 38 13 1463 1756 656926196 656926495 4.070000e-59 239.0
14 TraesCS5D01G334300 chr5B 92.000 50 3 1 1241 1290 474968796 474968748 5.660000e-08 69.4
15 TraesCS5D01G334300 chr5B 96.970 33 1 0 1323 1355 703301777 703301745 4.400000e-04 56.5
16 TraesCS5D01G334300 chr4B 74.174 666 126 35 1115 1763 474378599 474379235 5.270000e-58 235.0
17 TraesCS5D01G334300 chr7D 72.504 611 131 24 1113 1718 262285922 262286500 2.520000e-36 163.0
18 TraesCS5D01G334300 chrUn 92.000 50 3 1 1241 1290 279044456 279044408 5.660000e-08 69.4
19 TraesCS5D01G334300 chr6D 93.182 44 3 0 1385 1428 84207062 84207105 7.320000e-07 65.8
20 TraesCS5D01G334300 chr6B 93.182 44 3 0 1385 1428 159952205 159952248 7.320000e-07 65.8
21 TraesCS5D01G334300 chr6A 93.182 44 3 0 1385 1428 101429011 101429054 7.320000e-07 65.8
22 TraesCS5D01G334300 chr2B 96.970 33 1 0 1323 1355 118043278 118043246 4.400000e-04 56.5
23 TraesCS5D01G334300 chr2A 96.970 33 1 0 1323 1355 86435239 86435271 4.400000e-04 56.5


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 TraesCS5D01G334300 chr5D 423972169 423975328 3159 False 5836.0 5836 100.00000 1 3160 1 chr5D.!!$F1 3159
1 TraesCS5D01G334300 chr5D 520909988 520910675 687 False 420.0 420 78.16100 1078 1756 1 chr5D.!!$F3 678
2 TraesCS5D01G334300 chr5D 424033306 424033951 645 False 270.0 270 75.00000 1084 1756 1 chr5D.!!$F2 672
3 TraesCS5D01G334300 chr5A 537614982 537617876 2894 False 1231.0 2255 89.07800 147 3160 3 chr5A.!!$F3 3013
4 TraesCS5D01G334300 chr5A 649441448 649442150 702 False 357.0 357 76.62000 1078 1756 1 chr5A.!!$F2 678
5 TraesCS5D01G334300 chr5A 537626134 537626773 639 False 265.0 265 74.77900 1084 1756 1 chr5A.!!$F1 672
6 TraesCS5D01G334300 chr5B 511851488 511854251 2763 False 798.5 1969 87.73825 2 2959 4 chr5B.!!$F3 2957
7 TraesCS5D01G334300 chr5B 512212667 512213306 639 False 270.0 270 74.96300 1084 1756 1 chr5B.!!$F1 672
8 TraesCS5D01G334300 chr4B 474378599 474379235 636 False 235.0 235 74.17400 1115 1763 1 chr4B.!!$F1 648

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
816 856 0.035056 CTCCATGTCCAAGTCCACCC 60.035 60.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2274 2422 0.030369 GTGAGGTGATACTACGGCCG 59.97 60.0 26.86 26.86 0.0 6.13 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
29 30 4.002267 TCGATGCTGTAAATTTTGCTCG 57.998 40.909 0.00 9.88 0.00 5.03
118 135 2.816411 TGGAGATGTTCTTACGGAGGT 58.184 47.619 0.00 0.00 0.00 3.85
119 136 2.496070 TGGAGATGTTCTTACGGAGGTG 59.504 50.000 0.00 0.00 0.00 4.00
120 137 2.159085 GGAGATGTTCTTACGGAGGTGG 60.159 54.545 0.00 0.00 0.00 4.61
121 138 1.831736 AGATGTTCTTACGGAGGTGGG 59.168 52.381 0.00 0.00 0.00 4.61
122 139 1.829222 GATGTTCTTACGGAGGTGGGA 59.171 52.381 0.00 0.00 0.00 4.37
123 140 1.946984 TGTTCTTACGGAGGTGGGAT 58.053 50.000 0.00 0.00 0.00 3.85
124 141 1.829222 TGTTCTTACGGAGGTGGGATC 59.171 52.381 0.00 0.00 0.00 3.36
125 142 1.829222 GTTCTTACGGAGGTGGGATCA 59.171 52.381 0.00 0.00 0.00 2.92
126 143 2.235402 GTTCTTACGGAGGTGGGATCAA 59.765 50.000 0.00 0.00 0.00 2.57
127 144 2.108168 TCTTACGGAGGTGGGATCAAG 58.892 52.381 0.00 0.00 0.00 3.02
128 145 0.539986 TTACGGAGGTGGGATCAAGC 59.460 55.000 0.00 0.00 0.00 4.01
129 146 1.672854 TACGGAGGTGGGATCAAGCG 61.673 60.000 0.00 0.00 0.00 4.68
130 147 2.721167 CGGAGGTGGGATCAAGCGA 61.721 63.158 0.00 0.00 0.00 4.93
131 148 1.144936 GGAGGTGGGATCAAGCGAG 59.855 63.158 0.00 0.00 0.00 5.03
132 149 1.522580 GAGGTGGGATCAAGCGAGC 60.523 63.158 0.00 0.00 0.00 5.03
133 150 2.892425 GGTGGGATCAAGCGAGCG 60.892 66.667 0.00 0.00 0.00 5.03
134 151 2.184322 GTGGGATCAAGCGAGCGA 59.816 61.111 0.00 0.00 0.00 4.93
135 152 2.167861 GTGGGATCAAGCGAGCGAC 61.168 63.158 0.00 0.00 0.00 5.19
136 153 2.351244 TGGGATCAAGCGAGCGACT 61.351 57.895 0.00 0.00 0.00 4.18
137 154 1.880340 GGGATCAAGCGAGCGACTG 60.880 63.158 0.00 0.00 0.00 3.51
138 155 1.880340 GGATCAAGCGAGCGACTGG 60.880 63.158 0.00 0.00 0.00 4.00
139 156 1.139734 GATCAAGCGAGCGACTGGA 59.860 57.895 0.00 0.00 0.00 3.86
140 157 0.869454 GATCAAGCGAGCGACTGGAG 60.869 60.000 0.00 0.00 0.00 3.86
141 158 2.897641 ATCAAGCGAGCGACTGGAGC 62.898 60.000 0.00 0.00 0.00 4.70
142 159 4.785512 AAGCGAGCGACTGGAGCG 62.786 66.667 0.00 0.00 40.04 5.03
148 165 4.560856 GCGACTGGAGCGAGCGAT 62.561 66.667 0.00 0.00 0.00 4.58
149 166 2.352915 CGACTGGAGCGAGCGATC 60.353 66.667 0.00 0.00 0.00 3.69
150 167 2.801421 GACTGGAGCGAGCGATCA 59.199 61.111 10.40 0.00 31.28 2.92
151 168 1.299014 GACTGGAGCGAGCGATCAG 60.299 63.158 10.40 7.96 31.28 2.90
152 169 2.027314 CTGGAGCGAGCGATCAGG 59.973 66.667 10.40 0.00 31.28 3.86
153 170 2.755876 TGGAGCGAGCGATCAGGT 60.756 61.111 10.40 0.00 31.28 4.00
157 174 0.371645 GAGCGAGCGATCAGGTTTTG 59.628 55.000 0.00 0.00 0.00 2.44
188 205 4.303603 ATGATGATGCACGCGCGC 62.304 61.111 32.58 23.91 42.97 6.86
375 400 3.423154 GGCTCCGCTGAAACCACG 61.423 66.667 0.00 0.00 0.00 4.94
377 402 3.777925 CTCCGCTGAAACCACGCG 61.778 66.667 3.53 3.53 45.86 6.01
383 408 2.202946 TGAAACCACGCGAGCACA 60.203 55.556 15.93 2.00 0.00 4.57
388 413 3.648982 CCACGCGAGCACAGCAAA 61.649 61.111 15.93 0.00 34.19 3.68
404 429 1.268234 GCAAAATGCAGCTAGCTACCG 60.268 52.381 18.86 6.55 44.26 4.02
405 430 1.017387 AAAATGCAGCTAGCTACCGC 58.983 50.000 18.86 17.47 45.94 5.68
440 466 0.103026 CACCGAGATTCGCCTCATGA 59.897 55.000 0.00 0.00 38.82 3.07
441 467 1.043816 ACCGAGATTCGCCTCATGAT 58.956 50.000 0.00 0.00 38.82 2.45
442 468 1.269988 ACCGAGATTCGCCTCATGATG 60.270 52.381 0.00 0.00 38.82 3.07
447 473 1.467734 GATTCGCCTCATGATGCATCC 59.532 52.381 23.67 6.29 0.00 3.51
460 486 1.115326 TGCATCCCTCGTGATCCGAT 61.115 55.000 6.73 0.00 46.23 4.18
491 523 0.947244 CATAACTTGATCAGCCCGGC 59.053 55.000 0.00 0.00 0.00 6.13
507 539 3.734902 GCCCGGCTCATCAAATTAACAAG 60.735 47.826 0.71 0.00 0.00 3.16
527 559 5.122396 ACAAGTCATCATTTTAGTCGCTTCC 59.878 40.000 0.00 0.00 0.00 3.46
528 560 5.091261 AGTCATCATTTTAGTCGCTTCCT 57.909 39.130 0.00 0.00 0.00 3.36
529 561 5.491982 AGTCATCATTTTAGTCGCTTCCTT 58.508 37.500 0.00 0.00 0.00 3.36
530 562 5.352569 AGTCATCATTTTAGTCGCTTCCTTG 59.647 40.000 0.00 0.00 0.00 3.61
607 639 4.685169 AAACCGCAAGTAATCATGAGTG 57.315 40.909 5.80 0.00 0.00 3.51
625 659 4.466015 TGAGTGATCACTTAGCATGTGGTA 59.534 41.667 28.46 0.00 42.66 3.25
679 713 2.898738 CACTGCCCGATGCTCTCT 59.101 61.111 0.00 0.00 42.00 3.10
680 714 1.227205 CACTGCCCGATGCTCTCTC 60.227 63.158 0.00 0.00 42.00 3.20
681 715 1.381056 ACTGCCCGATGCTCTCTCT 60.381 57.895 0.00 0.00 42.00 3.10
682 716 1.363443 CTGCCCGATGCTCTCTCTC 59.637 63.158 0.00 0.00 42.00 3.20
683 717 1.076412 TGCCCGATGCTCTCTCTCT 60.076 57.895 0.00 0.00 42.00 3.10
684 718 1.106351 TGCCCGATGCTCTCTCTCTC 61.106 60.000 0.00 0.00 42.00 3.20
685 719 0.823356 GCCCGATGCTCTCTCTCTCT 60.823 60.000 0.00 0.00 36.87 3.10
686 720 1.238439 CCCGATGCTCTCTCTCTCTC 58.762 60.000 0.00 0.00 0.00 3.20
687 721 1.202806 CCCGATGCTCTCTCTCTCTCT 60.203 57.143 0.00 0.00 0.00 3.10
688 722 2.146342 CCGATGCTCTCTCTCTCTCTC 58.854 57.143 0.00 0.00 0.00 3.20
689 723 2.224378 CCGATGCTCTCTCTCTCTCTCT 60.224 54.545 0.00 0.00 0.00 3.10
690 724 3.062763 CGATGCTCTCTCTCTCTCTCTC 58.937 54.545 0.00 0.00 0.00 3.20
691 725 3.244009 CGATGCTCTCTCTCTCTCTCTCT 60.244 52.174 0.00 0.00 0.00 3.10
692 726 3.827008 TGCTCTCTCTCTCTCTCTCTC 57.173 52.381 0.00 0.00 0.00 3.20
693 727 3.378512 TGCTCTCTCTCTCTCTCTCTCT 58.621 50.000 0.00 0.00 0.00 3.10
694 728 3.386078 TGCTCTCTCTCTCTCTCTCTCTC 59.614 52.174 0.00 0.00 0.00 3.20
695 729 3.640967 GCTCTCTCTCTCTCTCTCTCTCT 59.359 52.174 0.00 0.00 0.00 3.10
696 730 4.261994 GCTCTCTCTCTCTCTCTCTCTCTC 60.262 54.167 0.00 0.00 0.00 3.20
697 731 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
698 732 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
699 733 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
700 734 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
701 735 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
702 736 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
703 737 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
704 738 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
705 739 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
706 740 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
707 741 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
708 742 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
709 743 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
710 744 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
711 745 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
712 746 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
713 747 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
802 842 1.826024 GTCCATCACGAGCCTCCAT 59.174 57.895 0.00 0.00 0.00 3.41
816 856 0.035056 CTCCATGTCCAAGTCCACCC 60.035 60.000 0.00 0.00 0.00 4.61
822 862 1.128188 GTCCAAGTCCACCCCTGTCT 61.128 60.000 0.00 0.00 0.00 3.41
855 899 5.221283 ACGCTAGCTCTCTTCTTATAAACCC 60.221 44.000 13.93 0.00 0.00 4.11
860 904 2.101917 TCTCTTCTTATAAACCCGCCGG 59.898 50.000 0.00 0.00 0.00 6.13
949 995 1.748647 ATTCATCGCGCAACCGTACG 61.749 55.000 8.75 8.69 36.67 3.67
950 996 3.176578 CATCGCGCAACCGTACGT 61.177 61.111 15.21 0.00 36.67 3.57
952 998 1.869132 ATCGCGCAACCGTACGTAC 60.869 57.895 15.90 15.90 36.67 3.67
953 999 2.257286 ATCGCGCAACCGTACGTACT 62.257 55.000 22.55 2.79 36.67 2.73
954 1000 2.491271 CGCGCAACCGTACGTACTC 61.491 63.158 22.55 6.47 36.67 2.59
955 1001 1.154150 GCGCAACCGTACGTACTCT 60.154 57.895 22.55 5.24 36.67 3.24
956 1002 0.096976 GCGCAACCGTACGTACTCTA 59.903 55.000 22.55 0.00 36.67 2.43
957 1003 1.853646 GCGCAACCGTACGTACTCTAG 60.854 57.143 22.55 11.45 36.67 2.43
959 1005 1.399791 GCAACCGTACGTACTCTAGCT 59.600 52.381 22.55 0.00 0.00 3.32
960 1006 2.609459 GCAACCGTACGTACTCTAGCTA 59.391 50.000 22.55 0.00 0.00 3.32
962 1008 3.810310 ACCGTACGTACTCTAGCTACT 57.190 47.619 22.55 0.00 0.00 2.57
963 1009 3.712187 ACCGTACGTACTCTAGCTACTC 58.288 50.000 22.55 0.00 0.00 2.59
964 1010 3.131223 ACCGTACGTACTCTAGCTACTCA 59.869 47.826 22.55 0.00 0.00 3.41
970 1016 3.184783 CGTACTCTAGCTACTCATCACCG 59.815 52.174 0.00 0.00 0.00 4.94
974 1020 2.105993 TCTAGCTACTCATCACCGCCTA 59.894 50.000 0.00 0.00 0.00 3.93
980 1026 3.185246 ACTCATCACCGCCTAATCAAG 57.815 47.619 0.00 0.00 0.00 3.02
981 1027 1.869767 CTCATCACCGCCTAATCAAGC 59.130 52.381 0.00 0.00 0.00 4.01
1717 1830 1.770110 ACCTCCACCTTCACCTGCA 60.770 57.895 0.00 0.00 0.00 4.41
1774 1887 1.152963 GCCGCCATGTCCAGGTAAT 60.153 57.895 0.00 0.00 0.00 1.89
1777 1890 1.308998 CGCCATGTCCAGGTAATTCC 58.691 55.000 0.00 0.00 0.00 3.01
1784 1897 5.513788 CCATGTCCAGGTAATTCCTCCATAG 60.514 48.000 0.00 0.00 46.24 2.23
1811 1925 0.521867 GTGCTGTGCATGCATACGTG 60.522 55.000 25.64 10.71 41.91 4.49
1846 1983 1.533129 GCAAAACCTTGTCACGTCCAC 60.533 52.381 0.00 0.00 34.79 4.02
1849 1986 0.463116 AACCTTGTCACGTCCACCAC 60.463 55.000 0.00 0.00 0.00 4.16
1850 1987 1.145156 CCTTGTCACGTCCACCACA 59.855 57.895 0.00 0.00 0.00 4.17
1851 1988 0.250295 CCTTGTCACGTCCACCACAT 60.250 55.000 0.00 0.00 0.00 3.21
1877 2016 5.106869 TGCGTACTAACTAATGTTTGGCTTG 60.107 40.000 0.00 0.00 37.59 4.01
1881 2020 2.490115 TAACTAATGTTTGGCTTGGCCG 59.510 45.455 0.00 0.00 43.52 6.13
1883 2022 5.870571 TAACTAATGTTTGGCTTGGCCGTC 61.871 45.833 0.00 0.00 43.52 4.79
1899 2038 1.060713 CGTCCGTCTGTGATTGTGAC 58.939 55.000 0.00 0.00 0.00 3.67
1922 2061 1.154263 CCTCAAGTCGTCCGTCGTC 60.154 63.158 0.00 0.00 40.80 4.20
1924 2063 0.725118 CTCAAGTCGTCCGTCGTCAC 60.725 60.000 0.00 0.00 40.80 3.67
1985 2133 3.155167 GTCTCCTACCTGGGCCGG 61.155 72.222 5.01 5.01 36.20 6.13
2091 2239 3.782244 CCTTCGCAGTCGCAGCAC 61.782 66.667 0.00 0.00 38.40 4.40
2155 2303 2.811317 GCCGCTTCTGTCTCCGTG 60.811 66.667 0.00 0.00 0.00 4.94
2161 2309 0.179124 CTTCTGTCTCCGTGCTAGCC 60.179 60.000 13.29 2.49 0.00 3.93
2274 2422 2.035442 GCAGTTTGACCTCGCCTCC 61.035 63.158 0.00 0.00 0.00 4.30
2286 2434 2.649614 GCCTCCGGCCGTAGTATC 59.350 66.667 26.12 5.25 44.06 2.24
2288 2436 1.658673 CCTCCGGCCGTAGTATCAC 59.341 63.158 26.12 0.00 0.00 3.06
2320 2469 7.817641 TGTATAGATTATTGTAGCGAGTCTGG 58.182 38.462 0.00 0.00 0.00 3.86
2398 2552 4.272100 GCAACCAGCTTGGCATTG 57.728 55.556 0.00 0.00 42.67 2.82
2399 2553 1.368579 GCAACCAGCTTGGCATTGT 59.631 52.632 0.00 0.00 42.67 2.71
2400 2554 0.602562 GCAACCAGCTTGGCATTGTA 59.397 50.000 0.00 0.00 42.67 2.41
2401 2555 1.669795 GCAACCAGCTTGGCATTGTAC 60.670 52.381 0.00 0.00 42.67 2.90
2432 2586 9.488762 TTTTTACTAGGAGTATCAGATTGGAGA 57.511 33.333 0.00 0.00 36.25 3.71
2438 2592 6.070656 AGGAGTATCAGATTGGAGAAGAGAG 58.929 44.000 0.00 0.00 36.25 3.20
2468 2622 4.082523 CAGGTGGGCGTGGTCGAT 62.083 66.667 0.00 0.00 39.71 3.59
2469 2623 4.082523 AGGTGGGCGTGGTCGATG 62.083 66.667 0.00 0.00 39.71 3.84
2475 2629 4.856801 GCGTGGTCGATGGGGCAT 62.857 66.667 0.00 0.00 39.71 4.40
2476 2630 2.896854 CGTGGTCGATGGGGCATG 60.897 66.667 0.00 0.00 39.71 4.06
2477 2631 2.516930 GTGGTCGATGGGGCATGG 60.517 66.667 0.00 0.00 0.00 3.66
2478 2632 3.807839 TGGTCGATGGGGCATGGG 61.808 66.667 0.00 0.00 0.00 4.00
2479 2633 4.586235 GGTCGATGGGGCATGGGG 62.586 72.222 0.00 0.00 0.00 4.96
2490 2644 2.358125 CATGGGGCGACGTGTGAA 60.358 61.111 0.00 0.00 0.00 3.18
2491 2645 1.745115 CATGGGGCGACGTGTGAAT 60.745 57.895 0.00 0.00 0.00 2.57
2492 2646 0.461163 CATGGGGCGACGTGTGAATA 60.461 55.000 0.00 0.00 0.00 1.75
2493 2647 0.468226 ATGGGGCGACGTGTGAATAT 59.532 50.000 0.00 0.00 0.00 1.28
2494 2648 1.112950 TGGGGCGACGTGTGAATATA 58.887 50.000 0.00 0.00 0.00 0.86
2495 2649 1.689813 TGGGGCGACGTGTGAATATAT 59.310 47.619 0.00 0.00 0.00 0.86
2496 2650 2.066262 GGGGCGACGTGTGAATATATG 58.934 52.381 0.00 0.00 0.00 1.78
2497 2651 1.459592 GGGCGACGTGTGAATATATGC 59.540 52.381 0.00 0.00 0.00 3.14
2498 2652 2.131972 GGCGACGTGTGAATATATGCA 58.868 47.619 0.00 0.00 0.00 3.96
2499 2653 2.155732 GGCGACGTGTGAATATATGCAG 59.844 50.000 0.00 0.00 0.00 4.41
2500 2654 2.155732 GCGACGTGTGAATATATGCAGG 59.844 50.000 0.00 0.00 0.00 4.85
2501 2655 3.381045 CGACGTGTGAATATATGCAGGT 58.619 45.455 0.00 2.44 33.47 4.00
2502 2656 3.182372 CGACGTGTGAATATATGCAGGTG 59.818 47.826 0.00 1.56 31.38 4.00
2503 2657 3.466836 ACGTGTGAATATATGCAGGTGG 58.533 45.455 0.00 0.00 0.00 4.61
2504 2658 2.807967 CGTGTGAATATATGCAGGTGGG 59.192 50.000 0.00 0.00 0.00 4.61
2547 2705 1.520342 GTCGACCATGAGCTCTGCC 60.520 63.158 16.19 4.90 0.00 4.85
2599 2757 1.032657 CCCCATCTCGAGACAGACGT 61.033 60.000 19.30 0.00 0.00 4.34
2600 2758 0.099613 CCCATCTCGAGACAGACGTG 59.900 60.000 19.30 10.89 0.00 4.49
2601 2759 1.087501 CCATCTCGAGACAGACGTGA 58.912 55.000 19.30 0.00 37.58 4.35
2602 2760 1.202087 CCATCTCGAGACAGACGTGAC 60.202 57.143 19.30 0.00 36.42 3.67
2603 2761 1.464997 CATCTCGAGACAGACGTGACA 59.535 52.381 19.30 0.00 36.42 3.58
2641 2804 2.410322 ATCAGTGCAAAGGTGGCCGA 62.410 55.000 0.00 0.00 0.00 5.54
2650 2813 3.670377 GGTGGCCGACCTTGTTGC 61.670 66.667 14.93 0.00 42.25 4.17
2668 2836 1.071605 GCTTACTGCTTGTCCGTCAG 58.928 55.000 0.00 0.00 38.95 3.51
2669 2837 1.714794 CTTACTGCTTGTCCGTCAGG 58.285 55.000 0.00 0.00 39.46 3.86
2670 2838 1.000955 CTTACTGCTTGTCCGTCAGGT 59.999 52.381 0.00 0.00 39.05 4.00
2671 2839 0.601558 TACTGCTTGTCCGTCAGGTC 59.398 55.000 0.00 0.00 39.05 3.85
2672 2840 1.367471 CTGCTTGTCCGTCAGGTCA 59.633 57.895 0.00 0.00 39.05 4.02
2673 2841 0.668706 CTGCTTGTCCGTCAGGTCAG 60.669 60.000 0.00 0.00 36.93 3.51
2674 2842 1.374758 GCTTGTCCGTCAGGTCAGG 60.375 63.158 0.00 0.00 36.93 3.86
2675 2843 2.050269 CTTGTCCGTCAGGTCAGGT 58.950 57.895 0.00 0.00 36.93 4.00
2676 2844 0.038159 CTTGTCCGTCAGGTCAGGTC 60.038 60.000 0.00 0.00 36.93 3.85
2677 2845 0.757561 TTGTCCGTCAGGTCAGGTCA 60.758 55.000 0.00 0.00 36.93 4.02
2734 2902 2.429058 CAGCTGCACTGTGGGAGT 59.571 61.111 10.21 0.00 41.86 3.85
2763 2931 1.755179 GCATGTGTCTACTTGCCCAT 58.245 50.000 6.95 0.00 46.52 4.00
2765 2933 3.278574 GCATGTGTCTACTTGCCCATAA 58.721 45.455 6.95 0.00 46.52 1.90
2766 2934 3.694072 GCATGTGTCTACTTGCCCATAAA 59.306 43.478 6.95 0.00 46.52 1.40
2768 2936 5.677091 GCATGTGTCTACTTGCCCATAAAAG 60.677 44.000 6.95 0.00 46.52 2.27
2784 2955 2.736670 AAAGCCATATGTGTCCTCCC 57.263 50.000 1.24 0.00 0.00 4.30
2839 3010 1.480205 CAAAGTTGCAAGTTGCTCCG 58.520 50.000 27.17 7.50 45.31 4.63
2870 3042 4.806330 TCGTACGCATCTTCTTCTTCTTT 58.194 39.130 11.24 0.00 0.00 2.52
2872 3044 5.118664 TCGTACGCATCTTCTTCTTCTTTTG 59.881 40.000 11.24 0.00 0.00 2.44
2873 3045 5.118664 CGTACGCATCTTCTTCTTCTTTTGA 59.881 40.000 0.52 0.00 0.00 2.69
2875 3047 6.175712 ACGCATCTTCTTCTTCTTTTGATC 57.824 37.500 0.00 0.00 0.00 2.92
2876 3048 5.936956 ACGCATCTTCTTCTTCTTTTGATCT 59.063 36.000 0.00 0.00 0.00 2.75
2992 3168 2.094659 CGCTACCTCCACAGCAACG 61.095 63.158 0.00 0.00 37.66 4.10
3001 3177 3.242739 CCTCCACAGCAACGTTATAATGC 60.243 47.826 0.00 0.00 40.34 3.56
3002 3178 3.339141 TCCACAGCAACGTTATAATGCA 58.661 40.909 11.43 0.00 42.45 3.96
3003 3179 3.944650 TCCACAGCAACGTTATAATGCAT 59.055 39.130 11.43 0.00 42.45 3.96
3004 3180 5.119694 TCCACAGCAACGTTATAATGCATA 58.880 37.500 11.43 0.00 42.45 3.14
3007 3183 6.429624 CACAGCAACGTTATAATGCATACAT 58.570 36.000 11.43 0.00 42.45 2.29
3011 3187 7.693536 CAGCAACGTTATAATGCATACATATGG 59.306 37.037 11.43 0.00 42.45 2.74
3034 3210 2.985957 CCATGTGGCCCCTTTTATTG 57.014 50.000 0.00 0.00 0.00 1.90
3145 3324 1.888512 ACCACCATTACTTGCTTGCTG 59.111 47.619 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.717233 ATTTACAGCATCGAAATTGCCA 57.283 36.364 5.88 0.00 41.06 4.92
14 15 4.159377 TGGCTTCGAGCAAAATTTACAG 57.841 40.909 8.71 0.00 44.75 2.74
18 19 3.733443 AGTTGGCTTCGAGCAAAATTT 57.267 38.095 8.71 0.00 44.75 1.82
80 81 9.432982 ACATCTCCAATAGATACTCTCTCTTTT 57.567 33.333 0.00 0.00 43.42 2.27
84 100 8.635765 AGAACATCTCCAATAGATACTCTCTC 57.364 38.462 0.00 0.00 43.42 3.20
105 121 1.829222 TGATCCCACCTCCGTAAGAAC 59.171 52.381 0.00 0.00 43.02 3.01
118 135 2.184322 GTCGCTCGCTTGATCCCA 59.816 61.111 0.00 0.00 0.00 4.37
119 136 1.880340 CAGTCGCTCGCTTGATCCC 60.880 63.158 0.00 0.00 0.00 3.85
120 137 1.880340 CCAGTCGCTCGCTTGATCC 60.880 63.158 0.00 0.00 0.00 3.36
121 138 0.869454 CTCCAGTCGCTCGCTTGATC 60.869 60.000 0.00 0.00 0.00 2.92
122 139 1.140589 CTCCAGTCGCTCGCTTGAT 59.859 57.895 0.00 0.00 0.00 2.57
123 140 2.568612 CTCCAGTCGCTCGCTTGA 59.431 61.111 0.00 0.00 0.00 3.02
124 141 3.184683 GCTCCAGTCGCTCGCTTG 61.185 66.667 0.00 0.00 0.00 4.01
125 142 4.785512 CGCTCCAGTCGCTCGCTT 62.786 66.667 0.00 0.00 0.00 4.68
131 148 4.560856 ATCGCTCGCTCCAGTCGC 62.561 66.667 0.00 0.00 0.00 5.19
132 149 2.352915 GATCGCTCGCTCCAGTCG 60.353 66.667 0.00 0.00 0.00 4.18
133 150 1.299014 CTGATCGCTCGCTCCAGTC 60.299 63.158 0.00 0.00 0.00 3.51
134 151 2.780094 CCTGATCGCTCGCTCCAGT 61.780 63.158 0.00 0.00 0.00 4.00
135 152 2.027314 CCTGATCGCTCGCTCCAG 59.973 66.667 0.00 0.00 0.00 3.86
136 153 1.888436 AAACCTGATCGCTCGCTCCA 61.888 55.000 0.00 0.00 0.00 3.86
137 154 0.741221 AAAACCTGATCGCTCGCTCC 60.741 55.000 0.00 0.00 0.00 4.70
138 155 0.371645 CAAAACCTGATCGCTCGCTC 59.628 55.000 0.00 0.00 0.00 5.03
139 156 1.021390 CCAAAACCTGATCGCTCGCT 61.021 55.000 0.00 0.00 0.00 4.93
140 157 1.019278 TCCAAAACCTGATCGCTCGC 61.019 55.000 0.00 0.00 0.00 5.03
141 158 1.128692 GTTCCAAAACCTGATCGCTCG 59.871 52.381 0.00 0.00 0.00 5.03
142 159 2.902065 GTTCCAAAACCTGATCGCTC 57.098 50.000 0.00 0.00 0.00 5.03
152 169 1.243902 TGGATGCTCGGTTCCAAAAC 58.756 50.000 0.00 0.00 39.05 2.43
153 170 1.818060 CATGGATGCTCGGTTCCAAAA 59.182 47.619 0.00 0.00 44.83 2.44
157 174 1.202687 TCATCATGGATGCTCGGTTCC 60.203 52.381 1.37 0.00 39.63 3.62
188 205 2.035961 CCCGTGACCTGTATCTGTATGG 59.964 54.545 0.00 0.00 0.00 2.74
234 253 1.867919 CGTGCGTCCTTCCTCTCAGT 61.868 60.000 0.00 0.00 0.00 3.41
235 254 1.153939 CGTGCGTCCTTCCTCTCAG 60.154 63.158 0.00 0.00 0.00 3.35
236 255 2.962569 CGTGCGTCCTTCCTCTCA 59.037 61.111 0.00 0.00 0.00 3.27
237 256 2.507324 GCGTGCGTCCTTCCTCTC 60.507 66.667 0.00 0.00 0.00 3.20
238 257 3.303135 TGCGTGCGTCCTTCCTCT 61.303 61.111 0.00 0.00 0.00 3.69
239 258 3.112709 GTGCGTGCGTCCTTCCTC 61.113 66.667 0.00 0.00 0.00 3.71
264 283 1.144936 GGCCGGAGAATCTCACTGG 59.855 63.158 5.05 11.20 36.70 4.00
364 389 3.345808 TGCTCGCGTGGTTTCAGC 61.346 61.111 5.77 6.36 0.00 4.26
375 400 1.342082 CTGCATTTTGCTGTGCTCGC 61.342 55.000 0.75 0.00 45.31 5.03
377 402 0.038526 AGCTGCATTTTGCTGTGCTC 60.039 50.000 1.02 0.00 45.31 4.26
378 403 1.201647 CTAGCTGCATTTTGCTGTGCT 59.798 47.619 8.34 15.16 45.31 4.40
383 408 2.019984 GGTAGCTAGCTGCATTTTGCT 58.980 47.619 30.27 3.49 45.31 3.91
388 413 1.592669 CGCGGTAGCTAGCTGCATT 60.593 57.895 30.27 6.90 45.94 3.56
412 438 2.938539 GAATCTCGGTGGACGGCTCG 62.939 65.000 0.00 0.00 44.45 5.03
507 539 5.351465 TCAAGGAAGCGACTAAAATGATGAC 59.649 40.000 0.00 0.00 0.00 3.06
527 559 1.334419 CGTCTTTGCAGTGGCTTCAAG 60.334 52.381 0.00 0.00 41.91 3.02
528 560 0.662619 CGTCTTTGCAGTGGCTTCAA 59.337 50.000 0.00 0.00 41.91 2.69
529 561 0.463654 ACGTCTTTGCAGTGGCTTCA 60.464 50.000 0.00 0.00 41.91 3.02
530 562 1.194772 GTACGTCTTTGCAGTGGCTTC 59.805 52.381 0.00 0.00 41.91 3.86
607 639 4.034510 GTGCTTACCACATGCTAAGTGATC 59.965 45.833 0.00 0.00 44.06 2.92
625 659 1.891150 CCTGCCAGATTCTTTGTGCTT 59.109 47.619 0.00 0.00 0.00 3.91
679 713 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
680 714 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
681 715 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
682 716 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
683 717 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
684 718 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
685 719 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
686 720 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
687 721 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
688 722 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
689 723 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
690 724 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
691 725 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
692 726 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
693 727 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
694 728 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
695 729 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
696 730 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
697 731 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
698 732 4.892345 TGAGAGAGAGAGAGAGAGAGAGAG 59.108 50.000 0.00 0.00 0.00 3.20
699 733 4.871822 TGAGAGAGAGAGAGAGAGAGAGA 58.128 47.826 0.00 0.00 0.00 3.10
700 734 5.511031 CCATGAGAGAGAGAGAGAGAGAGAG 60.511 52.000 0.00 0.00 0.00 3.20
701 735 4.346127 CCATGAGAGAGAGAGAGAGAGAGA 59.654 50.000 0.00 0.00 0.00 3.10
702 736 4.639334 CCATGAGAGAGAGAGAGAGAGAG 58.361 52.174 0.00 0.00 0.00 3.20
703 737 3.181451 GCCATGAGAGAGAGAGAGAGAGA 60.181 52.174 0.00 0.00 0.00 3.10
704 738 3.144506 GCCATGAGAGAGAGAGAGAGAG 58.855 54.545 0.00 0.00 0.00 3.20
705 739 2.485302 CGCCATGAGAGAGAGAGAGAGA 60.485 54.545 0.00 0.00 0.00 3.10
706 740 1.875514 CGCCATGAGAGAGAGAGAGAG 59.124 57.143 0.00 0.00 0.00 3.20
707 741 1.965935 CGCCATGAGAGAGAGAGAGA 58.034 55.000 0.00 0.00 0.00 3.10
708 742 0.311790 GCGCCATGAGAGAGAGAGAG 59.688 60.000 0.00 0.00 0.00 3.20
709 743 0.394899 TGCGCCATGAGAGAGAGAGA 60.395 55.000 4.18 0.00 0.00 3.10
710 744 0.248990 GTGCGCCATGAGAGAGAGAG 60.249 60.000 4.18 0.00 0.00 3.20
711 745 0.967380 TGTGCGCCATGAGAGAGAGA 60.967 55.000 4.18 0.00 0.00 3.10
712 746 0.528033 CTGTGCGCCATGAGAGAGAG 60.528 60.000 4.18 0.00 0.00 3.20
713 747 0.967380 TCTGTGCGCCATGAGAGAGA 60.967 55.000 4.18 0.00 0.00 3.10
802 842 1.385347 ACAGGGGTGGACTTGGACA 60.385 57.895 0.00 0.00 0.00 4.02
816 856 2.487428 CGTGAGAGCGGAGACAGG 59.513 66.667 0.00 0.00 0.00 4.00
822 862 2.438614 AGCTAGCGTGAGAGCGGA 60.439 61.111 9.55 0.00 43.72 5.54
949 995 3.058777 GCGGTGATGAGTAGCTAGAGTAC 60.059 52.174 0.00 0.00 0.00 2.73
950 996 3.139850 GCGGTGATGAGTAGCTAGAGTA 58.860 50.000 0.00 0.00 0.00 2.59
952 998 1.268352 GGCGGTGATGAGTAGCTAGAG 59.732 57.143 0.00 0.00 0.00 2.43
953 999 1.133761 AGGCGGTGATGAGTAGCTAGA 60.134 52.381 0.00 0.00 0.00 2.43
954 1000 1.323412 AGGCGGTGATGAGTAGCTAG 58.677 55.000 0.00 0.00 0.00 3.42
955 1001 2.651382 TAGGCGGTGATGAGTAGCTA 57.349 50.000 0.00 0.00 0.00 3.32
956 1002 1.776662 TTAGGCGGTGATGAGTAGCT 58.223 50.000 0.00 0.00 0.00 3.32
957 1003 2.035961 TGATTAGGCGGTGATGAGTAGC 59.964 50.000 0.00 0.00 0.00 3.58
959 1005 3.492656 GCTTGATTAGGCGGTGATGAGTA 60.493 47.826 0.00 0.00 0.00 2.59
960 1006 2.743183 GCTTGATTAGGCGGTGATGAGT 60.743 50.000 0.00 0.00 0.00 3.41
962 1008 1.486310 AGCTTGATTAGGCGGTGATGA 59.514 47.619 0.00 0.00 0.00 2.92
963 1009 1.869767 GAGCTTGATTAGGCGGTGATG 59.130 52.381 0.00 0.00 0.00 3.07
964 1010 1.539065 CGAGCTTGATTAGGCGGTGAT 60.539 52.381 0.00 0.00 0.00 3.06
970 1016 2.247437 CCGGCGAGCTTGATTAGGC 61.247 63.158 9.30 0.00 0.00 3.93
1774 1887 2.158957 GCACGAATGGTCTATGGAGGAA 60.159 50.000 0.00 0.00 0.00 3.36
1777 1890 2.159043 ACAGCACGAATGGTCTATGGAG 60.159 50.000 0.00 0.00 33.06 3.86
1784 1897 0.179181 CATGCACAGCACGAATGGTC 60.179 55.000 0.00 0.00 43.04 4.02
1825 1939 0.736053 GGACGTGACAAGGTTTTGCA 59.264 50.000 0.00 0.00 37.85 4.08
1846 1983 6.417191 ACATTAGTTAGTACGCAAATGTGG 57.583 37.500 11.60 0.00 36.52 4.17
1849 1986 6.250527 GCCAAACATTAGTTAGTACGCAAATG 59.749 38.462 7.47 7.47 36.84 2.32
1850 1987 6.150474 AGCCAAACATTAGTTAGTACGCAAAT 59.850 34.615 0.00 0.00 36.84 2.32
1851 1988 5.470777 AGCCAAACATTAGTTAGTACGCAAA 59.529 36.000 0.00 0.00 36.84 3.68
1877 2016 2.100631 CAATCACAGACGGACGGCC 61.101 63.158 0.00 0.00 0.00 6.13
1881 2020 1.429463 GGTCACAATCACAGACGGAC 58.571 55.000 0.00 0.00 33.18 4.79
1883 2022 0.034756 TGGGTCACAATCACAGACGG 59.965 55.000 0.00 0.00 33.18 4.79
1884 2023 1.432514 CTGGGTCACAATCACAGACG 58.567 55.000 0.00 0.00 38.46 4.18
1885 2024 1.160137 GCTGGGTCACAATCACAGAC 58.840 55.000 0.00 0.00 38.46 3.51
1886 2025 0.036732 GGCTGGGTCACAATCACAGA 59.963 55.000 0.00 0.00 38.46 3.41
1887 2026 0.037303 AGGCTGGGTCACAATCACAG 59.963 55.000 0.00 0.00 39.11 3.66
1899 2038 2.266055 GGACGACTTGAGGCTGGG 59.734 66.667 0.00 0.00 0.00 4.45
2168 2316 4.318021 GGCATGCATGGCGCTACG 62.318 66.667 33.91 4.73 43.58 3.51
2234 2382 1.890979 CTCCATCCGCACATGGCTC 60.891 63.158 6.09 0.00 42.97 4.70
2245 2393 2.044946 AAACTGCCGGCTCCATCC 60.045 61.111 29.70 0.00 0.00 3.51
2256 2404 2.035442 GGAGGCGAGGTCAAACTGC 61.035 63.158 0.00 0.00 0.00 4.40
2274 2422 0.030369 GTGAGGTGATACTACGGCCG 59.970 60.000 26.86 26.86 0.00 6.13
2285 2433 7.914427 ACAATAATCTATACAGGTGAGGTGA 57.086 36.000 0.00 0.00 0.00 4.02
2286 2434 7.815068 GCTACAATAATCTATACAGGTGAGGTG 59.185 40.741 0.00 0.00 0.00 4.00
2288 2436 7.030165 CGCTACAATAATCTATACAGGTGAGG 58.970 42.308 0.00 0.00 0.00 3.86
2320 2469 1.422388 GCCTTGCTTGCTTGCTAAAC 58.578 50.000 3.47 0.00 0.00 2.01
2415 2569 5.243730 CCTCTCTTCTCCAATCTGATACTCC 59.756 48.000 0.00 0.00 0.00 3.85
2416 2570 5.243730 CCCTCTCTTCTCCAATCTGATACTC 59.756 48.000 0.00 0.00 0.00 2.59
2417 2571 5.147032 CCCTCTCTTCTCCAATCTGATACT 58.853 45.833 0.00 0.00 0.00 2.12
2432 2586 1.274416 TGGCCTATGTTCCCCTCTCTT 60.274 52.381 3.32 0.00 0.00 2.85
2438 2592 1.227383 CACCTGGCCTATGTTCCCC 59.773 63.158 3.32 0.00 0.00 4.81
2459 2613 2.896854 CATGCCCCATCGACCACG 60.897 66.667 0.00 0.00 41.26 4.94
2460 2614 2.516930 CCATGCCCCATCGACCAC 60.517 66.667 0.00 0.00 0.00 4.16
2461 2615 3.807839 CCCATGCCCCATCGACCA 61.808 66.667 0.00 0.00 0.00 4.02
2462 2616 4.586235 CCCCATGCCCCATCGACC 62.586 72.222 0.00 0.00 0.00 4.79
2473 2627 0.461163 TATTCACACGTCGCCCCATG 60.461 55.000 0.00 0.00 0.00 3.66
2474 2628 0.468226 ATATTCACACGTCGCCCCAT 59.532 50.000 0.00 0.00 0.00 4.00
2475 2629 1.112950 TATATTCACACGTCGCCCCA 58.887 50.000 0.00 0.00 0.00 4.96
2476 2630 2.066262 CATATATTCACACGTCGCCCC 58.934 52.381 0.00 0.00 0.00 5.80
2477 2631 1.459592 GCATATATTCACACGTCGCCC 59.540 52.381 0.00 0.00 0.00 6.13
2478 2632 2.131972 TGCATATATTCACACGTCGCC 58.868 47.619 0.00 0.00 0.00 5.54
2479 2633 2.155732 CCTGCATATATTCACACGTCGC 59.844 50.000 0.00 0.00 0.00 5.19
2480 2634 3.182372 CACCTGCATATATTCACACGTCG 59.818 47.826 0.00 0.00 0.00 5.12
2481 2635 3.494626 CCACCTGCATATATTCACACGTC 59.505 47.826 0.00 0.00 0.00 4.34
2482 2636 3.466836 CCACCTGCATATATTCACACGT 58.533 45.455 0.00 0.00 0.00 4.49
2483 2637 2.807967 CCCACCTGCATATATTCACACG 59.192 50.000 0.00 0.00 0.00 4.49
2484 2638 2.554032 GCCCACCTGCATATATTCACAC 59.446 50.000 0.00 0.00 0.00 3.82
2485 2639 2.488891 GGCCCACCTGCATATATTCACA 60.489 50.000 0.00 0.00 0.00 3.58
2486 2640 2.162681 GGCCCACCTGCATATATTCAC 58.837 52.381 0.00 0.00 0.00 3.18
2487 2641 1.271325 CGGCCCACCTGCATATATTCA 60.271 52.381 0.00 0.00 0.00 2.57
2488 2642 1.453155 CGGCCCACCTGCATATATTC 58.547 55.000 0.00 0.00 0.00 1.75
2489 2643 0.038166 CCGGCCCACCTGCATATATT 59.962 55.000 0.00 0.00 0.00 1.28
2490 2644 1.133809 ACCGGCCCACCTGCATATAT 61.134 55.000 0.00 0.00 0.00 0.86
2491 2645 1.768482 ACCGGCCCACCTGCATATA 60.768 57.895 0.00 0.00 0.00 0.86
2492 2646 3.096495 ACCGGCCCACCTGCATAT 61.096 61.111 0.00 0.00 0.00 1.78
2493 2647 4.108299 CACCGGCCCACCTGCATA 62.108 66.667 0.00 0.00 0.00 3.14
2504 2658 3.704231 ATGTGATGGAGGCACCGGC 62.704 63.158 0.00 0.00 42.61 6.13
2515 2669 1.935873 GGTCGACCATGTGATGTGATG 59.064 52.381 29.75 0.00 35.64 3.07
2516 2670 1.554617 TGGTCGACCATGTGATGTGAT 59.445 47.619 33.23 0.00 42.01 3.06
2517 2671 0.972883 TGGTCGACCATGTGATGTGA 59.027 50.000 33.23 6.51 42.01 3.58
2518 2672 3.531073 TGGTCGACCATGTGATGTG 57.469 52.632 33.23 0.00 42.01 3.21
2599 2757 0.968393 TCGTGACCCCGATCATGTCA 60.968 55.000 5.18 5.18 37.00 3.58
2600 2758 0.249073 CTCGTGACCCCGATCATGTC 60.249 60.000 0.00 0.00 37.00 3.06
2601 2759 1.676678 CCTCGTGACCCCGATCATGT 61.677 60.000 0.00 0.00 37.00 3.21
2602 2760 1.068083 CCTCGTGACCCCGATCATG 59.932 63.158 0.00 0.00 36.08 3.07
2603 2761 2.134287 CCCTCGTGACCCCGATCAT 61.134 63.158 0.00 0.00 36.08 2.45
2650 2813 1.000955 ACCTGACGGACAAGCAGTAAG 59.999 52.381 0.00 0.00 0.00 2.34
2668 2836 0.832135 TGACCTGACCTGACCTGACC 60.832 60.000 0.00 0.00 0.00 4.02
2669 2837 0.605589 CTGACCTGACCTGACCTGAC 59.394 60.000 0.00 0.00 0.00 3.51
2670 2838 0.542938 CCTGACCTGACCTGACCTGA 60.543 60.000 0.00 0.00 0.00 3.86
2671 2839 0.833834 ACCTGACCTGACCTGACCTG 60.834 60.000 0.00 0.00 0.00 4.00
2672 2840 0.833834 CACCTGACCTGACCTGACCT 60.834 60.000 0.00 0.00 0.00 3.85
2673 2841 1.674057 CACCTGACCTGACCTGACC 59.326 63.158 0.00 0.00 0.00 4.02
2674 2842 1.122019 ACCACCTGACCTGACCTGAC 61.122 60.000 0.00 0.00 0.00 3.51
2675 2843 1.121407 CACCACCTGACCTGACCTGA 61.121 60.000 0.00 0.00 0.00 3.86
2676 2844 1.372683 CACCACCTGACCTGACCTG 59.627 63.158 0.00 0.00 0.00 4.00
2677 2845 2.520536 GCACCACCTGACCTGACCT 61.521 63.158 0.00 0.00 0.00 3.85
2734 2902 0.599991 AGACACATGCGCGACTGAAA 60.600 50.000 12.10 0.00 0.00 2.69
2760 2928 4.520492 GGAGGACACATATGGCTTTTATGG 59.480 45.833 7.80 1.38 32.54 2.74
2761 2929 4.520492 GGGAGGACACATATGGCTTTTATG 59.480 45.833 7.80 0.00 32.54 1.90
2763 2931 3.433031 CGGGAGGACACATATGGCTTTTA 60.433 47.826 7.80 0.00 32.54 1.52
2765 2933 1.134098 CGGGAGGACACATATGGCTTT 60.134 52.381 7.80 0.00 32.54 3.51
2766 2934 0.469917 CGGGAGGACACATATGGCTT 59.530 55.000 7.80 0.00 32.54 4.35
2768 2936 4.779475 CGGGAGGACACATATGGC 57.221 61.111 7.80 0.00 0.00 4.40
2784 2955 4.335315 CCAGAATCTATCTAGCTAGAGCCG 59.665 50.000 26.64 17.17 37.89 5.52
2870 3042 8.690203 TCTTGGATTACAAAACAGAAGATCAA 57.310 30.769 0.00 0.00 38.91 2.57
2872 3044 8.401709 GGATCTTGGATTACAAAACAGAAGATC 58.598 37.037 0.00 0.00 41.70 2.75
2873 3045 8.112183 AGGATCTTGGATTACAAAACAGAAGAT 58.888 33.333 0.00 0.00 38.91 2.40
2875 3047 7.693969 AGGATCTTGGATTACAAAACAGAAG 57.306 36.000 0.00 0.00 38.91 2.85
2992 3168 5.301805 GGCCCCCATATGTATGCATTATAAC 59.698 44.000 3.54 0.00 36.58 1.89
3001 3177 2.449464 CACATGGCCCCCATATGTATG 58.551 52.381 0.00 0.00 43.15 2.39
3002 3178 1.358787 CCACATGGCCCCCATATGTAT 59.641 52.381 0.00 0.00 43.15 2.29
3003 3179 0.776810 CCACATGGCCCCCATATGTA 59.223 55.000 0.00 0.00 43.15 2.29
3004 3180 1.543184 CCACATGGCCCCCATATGT 59.457 57.895 0.00 0.00 43.15 2.29
3045 3221 3.883631 TTCATGCATGCGCTATAACAG 57.116 42.857 22.25 0.00 39.64 3.16
3046 3222 4.629251 TTTTCATGCATGCGCTATAACA 57.371 36.364 22.25 0.08 39.64 2.41
3054 3233 2.990774 GCTTGATTTTCATGCATGCG 57.009 45.000 22.25 0.00 44.16 4.73
3126 3305 2.642139 CAGCAAGCAAGTAATGGTGG 57.358 50.000 0.00 0.00 40.33 4.61


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

AutoCloner maintained by Alex Coulton.