Multiple sequence alignment - TraesCS5D01G257000

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


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

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5D01G257000 chr5D 100.000 7239 0 0 1 7239 363175699 363182937 0.000000e+00 13369.0
1 TraesCS5D01G257000 chr5D 94.428 2782 126 8 3751 6530 363341571 363344325 0.000000e+00 4252.0
2 TraesCS5D01G257000 chr5D 86.942 1815 170 39 4757 6523 363978799 363980594 0.000000e+00 1977.0
3 TraesCS5D01G257000 chr5D 92.723 1333 43 21 1770 3079 363339715 363341016 0.000000e+00 1875.0
4 TraesCS5D01G257000 chr5D 95.624 1074 21 11 1770 2826 363975751 363976815 0.000000e+00 1700.0
5 TraesCS5D01G257000 chr5D 94.167 960 37 11 710 1659 363338761 363339711 0.000000e+00 1445.0
6 TraesCS5D01G257000 chr5D 92.872 968 42 11 710 1659 363974789 363975747 0.000000e+00 1380.0
7 TraesCS5D01G257000 chr5D 98.739 714 9 0 6526 7239 371281096 371281809 0.000000e+00 1269.0
8 TraesCS5D01G257000 chr5D 86.704 722 71 7 2 704 363338000 363338715 0.000000e+00 778.0
9 TraesCS5D01G257000 chr5D 86.846 707 79 10 3 704 363974053 363974750 0.000000e+00 778.0
10 TraesCS5D01G257000 chr5D 88.629 642 46 13 3037 3664 363340945 363341573 0.000000e+00 756.0
11 TraesCS5D01G257000 chr5D 89.216 102 8 3 3904 4004 363977533 363977632 2.740000e-24 124.0
12 TraesCS5D01G257000 chr5B 94.818 2007 102 2 4244 6249 429729338 429731343 0.000000e+00 3129.0
13 TraesCS5D01G257000 chr5B 87.936 1691 146 32 1 1668 429818415 429820070 0.000000e+00 1940.0
14 TraesCS5D01G257000 chr5B 93.617 1081 36 21 1767 2826 429820130 429821198 0.000000e+00 1583.0
15 TraesCS5D01G257000 chr5B 94.933 967 40 5 710 1668 429726086 429727051 0.000000e+00 1506.0
16 TraesCS5D01G257000 chr5B 90.229 1136 99 10 5400 6529 429823751 429824880 0.000000e+00 1472.0
17 TraesCS5D01G257000 chr5B 88.529 1203 99 11 4243 5407 429822272 429823473 0.000000e+00 1421.0
18 TraesCS5D01G257000 chr5B 88.056 1147 112 16 5400 6529 429887585 429888723 0.000000e+00 1336.0
19 TraesCS5D01G257000 chr5B 87.940 1136 95 19 4246 5371 429886266 429887369 0.000000e+00 1301.0
20 TraesCS5D01G257000 chr5B 97.911 718 15 0 6522 7239 277632882 277633599 0.000000e+00 1243.0
21 TraesCS5D01G257000 chr5B 93.420 851 19 17 1767 2597 429727115 429727948 0.000000e+00 1227.0
22 TraesCS5D01G257000 chr5B 97.047 508 13 2 2027 2533 429883151 429883657 0.000000e+00 854.0
23 TraesCS5D01G257000 chr5B 83.538 978 86 32 710 1668 429881911 429882832 0.000000e+00 845.0
24 TraesCS5D01G257000 chr5B 87.281 629 77 2 1 627 429725155 429725782 0.000000e+00 715.0
25 TraesCS5D01G257000 chr5B 92.800 250 18 0 6281 6530 429731340 429731589 5.340000e-96 363.0
26 TraesCS5D01G257000 chr5B 81.864 397 46 15 3097 3468 429728340 429728735 1.960000e-80 311.0
27 TraesCS5D01G257000 chr5B 88.987 227 17 7 3995 4218 429822056 429822277 2.570000e-69 274.0
28 TraesCS5D01G257000 chr5B 90.909 198 9 5 4040 4237 429728902 429729090 2.590000e-64 257.0
29 TraesCS5D01G257000 chr5B 86.758 219 18 6 489 704 429725837 429726047 4.370000e-57 233.0
30 TraesCS5D01G257000 chr5B 88.265 196 17 2 4008 4202 429886079 429886269 5.650000e-56 230.0
31 TraesCS5D01G257000 chr5B 92.073 164 8 1 1835 1993 429882991 429883154 7.310000e-55 226.0
32 TraesCS5D01G257000 chr5B 87.255 102 11 2 3907 4008 429821924 429822023 1.650000e-21 115.0
33 TraesCS5D01G257000 chr5B 74.457 368 39 28 381 704 429881515 429881871 2.760000e-19 108.0
34 TraesCS5D01G257000 chr5B 95.122 41 2 0 1700 1740 564486554 564486594 1.690000e-06 65.8
35 TraesCS5D01G257000 chr5A 94.786 1074 32 12 1767 2826 464634301 464635364 0.000000e+00 1652.0
36 TraesCS5D01G257000 chr5A 91.792 1133 87 5 5400 6530 464637883 464639011 0.000000e+00 1572.0
37 TraesCS5D01G257000 chr5A 89.933 1202 78 22 4242 5411 464636429 464637619 0.000000e+00 1509.0
38 TraesCS5D01G257000 chr5A 91.931 979 37 18 710 1668 464633285 464634241 0.000000e+00 1332.0
39 TraesCS5D01G257000 chr5A 85.232 711 74 12 1 704 464632560 464633246 0.000000e+00 702.0
40 TraesCS5D01G257000 chr5A 90.086 232 16 6 3995 4224 464636218 464636444 1.970000e-75 294.0
41 TraesCS5D01G257000 chr5A 86.364 110 8 5 3904 4008 464636078 464636185 5.940000e-21 113.0
42 TraesCS5D01G257000 chr5A 90.196 51 2 2 1700 1750 538327091 538327138 6.060000e-06 63.9
43 TraesCS5D01G257000 chr5A 100.000 31 0 0 1667 1697 464634270 464634300 2.820000e-04 58.4
44 TraesCS5D01G257000 chr6D 99.020 714 7 0 6526 7239 72032922 72033635 0.000000e+00 1280.0
45 TraesCS5D01G257000 chr1D 98.331 719 11 1 6521 7239 107614140 107613423 0.000000e+00 1260.0
46 TraesCS5D01G257000 chr3B 97.762 715 15 1 6526 7239 245965689 245966403 0.000000e+00 1230.0
47 TraesCS5D01G257000 chr7D 97.759 714 15 1 6526 7239 95086382 95085670 0.000000e+00 1229.0
48 TraesCS5D01G257000 chr6A 97.626 716 16 1 6524 7239 610915749 610916463 0.000000e+00 1227.0
49 TraesCS5D01G257000 chr2A 97.339 714 19 0 6526 7239 642737057 642736344 0.000000e+00 1214.0
50 TraesCS5D01G257000 chr7A 97.075 718 21 0 6522 7239 652168105 652168822 0.000000e+00 1210.0
51 TraesCS5D01G257000 chr7A 95.122 41 2 0 1700 1740 236464866 236464906 1.690000e-06 65.8
52 TraesCS5D01G257000 chr6B 82.489 474 81 2 2044 2516 179464122 179464594 1.450000e-111 414.0
53 TraesCS5D01G257000 chr6B 95.122 41 2 0 1700 1740 234869378 234869338 1.690000e-06 65.8
54 TraesCS5D01G257000 chrUn 77.377 305 56 13 2042 2339 22056738 22056440 1.250000e-37 169.0
55 TraesCS5D01G257000 chrUn 100.000 33 0 0 1706 1738 416475930 416475898 2.180000e-05 62.1
56 TraesCS5D01G257000 chr2D 77.181 298 60 8 2046 2339 474750280 474749987 4.490000e-37 167.0
57 TraesCS5D01G257000 chr2D 97.436 39 1 0 1700 1738 17163438 17163476 4.690000e-07 67.6
58 TraesCS5D01G257000 chr4B 94.340 53 3 0 4326 4378 644707689 644707741 1.670000e-11 82.4
59 TraesCS5D01G257000 chr2B 100.000 39 0 0 1700 1738 764914690 764914728 1.010000e-08 73.1
60 TraesCS5D01G257000 chr3D 97.436 39 1 0 1700 1738 351116946 351116984 4.690000e-07 67.6
61 TraesCS5D01G257000 chr3A 95.122 41 2 0 1700 1740 572464725 572464765 1.690000e-06 65.8


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 TraesCS5D01G257000 chr5D 363175699 363182937 7238 False 13369.000000 13369 100.000000 1 7239 1 chr5D.!!$F1 7238
1 TraesCS5D01G257000 chr5D 363338000 363344325 6325 False 1821.200000 4252 91.330200 2 6530 5 chr5D.!!$F3 6528
2 TraesCS5D01G257000 chr5D 371281096 371281809 713 False 1269.000000 1269 98.739000 6526 7239 1 chr5D.!!$F2 713
3 TraesCS5D01G257000 chr5D 363974053 363980594 6541 False 1191.800000 1977 90.300000 3 6523 5 chr5D.!!$F4 6520
4 TraesCS5D01G257000 chr5B 277632882 277633599 717 False 1243.000000 1243 97.911000 6522 7239 1 chr5B.!!$F1 717
5 TraesCS5D01G257000 chr5B 429818415 429824880 6465 False 1134.166667 1940 89.425500 1 6529 6 chr5B.!!$F4 6528
6 TraesCS5D01G257000 chr5B 429725155 429731589 6434 False 967.625000 3129 90.347875 1 6530 8 chr5B.!!$F3 6529
7 TraesCS5D01G257000 chr5B 429881515 429888723 7208 False 700.000000 1336 87.339429 381 6529 7 chr5B.!!$F5 6148
8 TraesCS5D01G257000 chr5A 464632560 464639011 6451 False 904.050000 1652 91.265500 1 6530 8 chr5A.!!$F2 6529
9 TraesCS5D01G257000 chr6D 72032922 72033635 713 False 1280.000000 1280 99.020000 6526 7239 1 chr6D.!!$F1 713
10 TraesCS5D01G257000 chr1D 107613423 107614140 717 True 1260.000000 1260 98.331000 6521 7239 1 chr1D.!!$R1 718
11 TraesCS5D01G257000 chr3B 245965689 245966403 714 False 1230.000000 1230 97.762000 6526 7239 1 chr3B.!!$F1 713
12 TraesCS5D01G257000 chr7D 95085670 95086382 712 True 1229.000000 1229 97.759000 6526 7239 1 chr7D.!!$R1 713
13 TraesCS5D01G257000 chr6A 610915749 610916463 714 False 1227.000000 1227 97.626000 6524 7239 1 chr6A.!!$F1 715
14 TraesCS5D01G257000 chr2A 642736344 642737057 713 True 1214.000000 1214 97.339000 6526 7239 1 chr2A.!!$R1 713
15 TraesCS5D01G257000 chr7A 652168105 652168822 717 False 1210.000000 1210 97.075000 6522 7239 1 chr7A.!!$F2 717

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
637 692 0.108138 GAACCAGAGCCGCACATAGT 60.108 55.000 0.00 0.00 0.00 2.12 F
1655 1991 0.524392 CTTCGCTACTCAGACAGCCG 60.524 60.000 0.00 0.00 34.15 5.52 F
1708 2091 0.184451 TTAGTATCCGCTCCCTCCGT 59.816 55.000 0.00 0.00 0.00 4.69 F
1709 2092 0.250640 TAGTATCCGCTCCCTCCGTC 60.251 60.000 0.00 0.00 0.00 4.79 F
2637 3412 0.318784 GGACATGATCGCGACCCTAC 60.319 60.000 12.93 1.37 0.00 3.18 F
3484 4323 0.531532 CCTAGCATTGTGAGAGGGCG 60.532 60.000 0.00 0.00 0.00 6.13 F
3915 6509 0.028242 CGACTAGGAGCACTGCTACG 59.972 60.000 7.65 0.00 45.59 3.51 F
3926 6520 0.109689 ACTGCTACGCGACTGAAGAC 60.110 55.000 15.93 0.00 0.00 3.01 F
4116 6760 0.250038 TTCAGTGGTGACAGCTGAGC 60.250 55.000 23.35 12.52 43.93 4.26 F
4809 8165 1.003233 GGGAAGAAGATGACCACCGTT 59.997 52.381 0.00 0.00 0.00 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1697 2080 0.962489 ATTATGAGACGGAGGGAGCG 59.038 55.000 0.00 0.00 0.00 5.03 R
3472 4311 0.323302 TGTTATGCGCCCTCTCACAA 59.677 50.000 4.18 0.00 0.00 3.33 R
3502 4341 3.447944 TGCATTATGGTGTACGTCTGGTA 59.552 43.478 0.00 0.00 0.00 3.25 R
3604 4443 6.097356 CAGAACGGTAAGTACTAAATCAGCA 58.903 40.000 0.00 0.00 0.00 4.41 R
3896 6477 0.028242 CGTAGCAGTGCTCCTAGTCG 59.972 60.000 23.64 13.48 40.44 4.18 R
4848 8204 0.182299 TCACCTTGTCCATGTGTGCA 59.818 50.000 0.00 0.00 0.00 4.57 R
4851 8207 0.884704 GCGTCACCTTGTCCATGTGT 60.885 55.000 0.00 0.00 0.00 3.72 R
4988 8356 0.921256 CCACCTCCCCTCCCTGAAAT 60.921 60.000 0.00 0.00 0.00 2.17 R
5293 8678 1.349688 AGGAAGGCACCAACGAACATA 59.650 47.619 0.00 0.00 0.00 2.29 R
6697 10698 0.978146 CCTCCGGTCCTTCTCCATGT 60.978 60.000 0.00 0.00 0.00 3.21 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
22 23 2.205074 GAAGTATCTGTCCATGTGCCG 58.795 52.381 0.00 0.00 0.00 5.69
23 24 1.485124 AGTATCTGTCCATGTGCCGA 58.515 50.000 0.00 0.00 0.00 5.54
38 39 3.900892 CGATACGGACCAGCGCCT 61.901 66.667 2.29 0.00 0.00 5.52
51 52 1.137404 GCGCCTTGTAGCCACAATG 59.863 57.895 0.00 0.00 43.58 2.82
120 121 2.819154 CGCCGCACATCCATGACA 60.819 61.111 0.00 0.00 0.00 3.58
137 138 2.074576 GACAAGAAACCCTAACCTCGC 58.925 52.381 0.00 0.00 0.00 5.03
138 139 1.076332 CAAGAAACCCTAACCTCGCG 58.924 55.000 0.00 0.00 0.00 5.87
155 156 1.141881 CGGTCCCAAGGAGATGACG 59.858 63.158 0.00 0.00 29.39 4.35
161 162 1.475751 CCCAAGGAGATGACGGGAATG 60.476 57.143 0.00 0.00 39.44 2.67
186 187 2.717809 GCAACTTCGTCGACTCCGC 61.718 63.158 14.70 3.90 35.37 5.54
214 215 3.699038 GGGATAGATTCGAGGAGGATCAG 59.301 52.174 0.00 0.00 36.25 2.90
217 218 3.593442 AGATTCGAGGAGGATCAGAGT 57.407 47.619 0.00 0.00 36.25 3.24
219 220 2.060050 TTCGAGGAGGATCAGAGTCC 57.940 55.000 0.00 0.00 36.25 3.85
291 304 8.376803 AGTCTAACCTAAACTACTAGCCAAAT 57.623 34.615 0.00 0.00 0.00 2.32
335 350 2.524394 ACCAGCCGACAGAGTGGT 60.524 61.111 0.00 0.00 38.53 4.16
336 351 2.140792 ACCAGCCGACAGAGTGGTT 61.141 57.895 0.00 0.00 40.54 3.67
343 358 1.825474 CCGACAGAGTGGTTGGTAGAT 59.175 52.381 0.00 0.00 37.52 1.98
356 371 2.871796 TGGTAGATGGGAGGGGAATTT 58.128 47.619 0.00 0.00 0.00 1.82
366 381 3.159472 GGAGGGGAATTTACGTTTGGTT 58.841 45.455 0.00 0.00 0.00 3.67
410 426 7.737972 TTCTTGAAATTAATGAGTCGTCCAA 57.262 32.000 0.00 0.00 0.00 3.53
418 434 3.558931 ATGAGTCGTCCAATGGCATTA 57.441 42.857 13.23 0.00 0.00 1.90
452 471 6.831769 TCAAGAATTTTCAGAGTTATCACGC 58.168 36.000 0.00 0.00 0.00 5.34
492 511 2.950990 AGGATTAGGGTGTCCTCTGT 57.049 50.000 0.00 0.00 40.87 3.41
503 522 1.822990 TGTCCTCTGTGAATCGTACCC 59.177 52.381 0.00 0.00 0.00 3.69
511 530 1.153229 GAATCGTACCCTGGGGCAC 60.153 63.158 18.88 13.31 39.32 5.01
630 685 2.815647 CGAAGGAACCAGAGCCGC 60.816 66.667 0.00 0.00 0.00 6.53
632 687 2.032681 AAGGAACCAGAGCCGCAC 59.967 61.111 0.00 0.00 0.00 5.34
633 688 2.731691 GAAGGAACCAGAGCCGCACA 62.732 60.000 0.00 0.00 0.00 4.57
635 690 1.220749 GGAACCAGAGCCGCACATA 59.779 57.895 0.00 0.00 0.00 2.29
637 692 0.108138 GAACCAGAGCCGCACATAGT 60.108 55.000 0.00 0.00 0.00 2.12
638 693 1.136305 GAACCAGAGCCGCACATAGTA 59.864 52.381 0.00 0.00 0.00 1.82
639 694 0.747255 ACCAGAGCCGCACATAGTAG 59.253 55.000 0.00 0.00 0.00 2.57
641 696 1.137086 CCAGAGCCGCACATAGTAGTT 59.863 52.381 0.00 0.00 0.00 2.24
642 697 2.418746 CCAGAGCCGCACATAGTAGTTT 60.419 50.000 0.00 0.00 0.00 2.66
643 698 2.860735 CAGAGCCGCACATAGTAGTTTC 59.139 50.000 0.00 0.00 0.00 2.78
644 699 2.761208 AGAGCCGCACATAGTAGTTTCT 59.239 45.455 0.00 0.00 0.00 2.52
645 700 3.195825 AGAGCCGCACATAGTAGTTTCTT 59.804 43.478 0.00 0.00 0.00 2.52
646 701 3.933332 GAGCCGCACATAGTAGTTTCTTT 59.067 43.478 0.00 0.00 0.00 2.52
647 702 4.324267 AGCCGCACATAGTAGTTTCTTTT 58.676 39.130 0.00 0.00 0.00 2.27
648 703 4.154195 AGCCGCACATAGTAGTTTCTTTTG 59.846 41.667 0.00 0.00 0.00 2.44
656 899 6.307318 ACATAGTAGTTTCTTTTGCTCGTACG 59.693 38.462 9.53 9.53 0.00 3.67
684 927 2.729360 TGAAAGCACACAGACGTAATCG 59.271 45.455 0.00 0.00 43.34 3.34
704 947 4.890088 TCGTTTTAGTACAGCAGAACCAT 58.110 39.130 0.00 0.00 0.00 3.55
705 948 6.028146 TCGTTTTAGTACAGCAGAACCATA 57.972 37.500 0.00 0.00 0.00 2.74
706 949 6.636705 TCGTTTTAGTACAGCAGAACCATAT 58.363 36.000 0.00 0.00 0.00 1.78
707 950 7.101054 TCGTTTTAGTACAGCAGAACCATATT 58.899 34.615 0.00 0.00 0.00 1.28
708 951 8.252417 TCGTTTTAGTACAGCAGAACCATATTA 58.748 33.333 0.00 0.00 0.00 0.98
847 1158 1.303643 CCCCTTTGACCAGCTCCAC 60.304 63.158 0.00 0.00 0.00 4.02
931 1259 1.669115 CCTGCACTCAACCACCTCG 60.669 63.158 0.00 0.00 0.00 4.63
1017 1347 4.335315 ACATCACGAGCAAAAGAAGAAACA 59.665 37.500 0.00 0.00 0.00 2.83
1030 1360 4.253685 AGAAGAAACACATACCACCATCG 58.746 43.478 0.00 0.00 0.00 3.84
1427 1761 1.760086 CGTGCTCTCCTGGGAGGAT 60.760 63.158 15.66 0.00 44.81 3.24
1609 1943 8.972262 ATACATGCTCGTGAATAATACTACTG 57.028 34.615 0.00 0.00 0.00 2.74
1655 1991 0.524392 CTTCGCTACTCAGACAGCCG 60.524 60.000 0.00 0.00 34.15 5.52
1697 2080 5.105834 AGCGACTCGTACAATTAGTATCC 57.894 43.478 0.00 0.00 34.67 2.59
1698 2081 3.904824 GCGACTCGTACAATTAGTATCCG 59.095 47.826 0.00 0.00 34.67 4.18
1699 2082 3.904824 CGACTCGTACAATTAGTATCCGC 59.095 47.826 0.00 0.00 34.67 5.54
1700 2083 4.319333 CGACTCGTACAATTAGTATCCGCT 60.319 45.833 0.00 0.00 34.67 5.52
1701 2084 5.105834 ACTCGTACAATTAGTATCCGCTC 57.894 43.478 0.00 0.00 34.67 5.03
1702 2085 4.023365 ACTCGTACAATTAGTATCCGCTCC 60.023 45.833 0.00 0.00 34.67 4.70
1703 2086 3.254166 TCGTACAATTAGTATCCGCTCCC 59.746 47.826 0.00 0.00 34.67 4.30
1704 2087 3.255149 CGTACAATTAGTATCCGCTCCCT 59.745 47.826 0.00 0.00 34.67 4.20
1705 2088 4.615452 CGTACAATTAGTATCCGCTCCCTC 60.615 50.000 0.00 0.00 34.67 4.30
1706 2089 2.633481 ACAATTAGTATCCGCTCCCTCC 59.367 50.000 0.00 0.00 0.00 4.30
1707 2090 1.546961 ATTAGTATCCGCTCCCTCCG 58.453 55.000 0.00 0.00 0.00 4.63
1708 2091 0.184451 TTAGTATCCGCTCCCTCCGT 59.816 55.000 0.00 0.00 0.00 4.69
1709 2092 0.250640 TAGTATCCGCTCCCTCCGTC 60.251 60.000 0.00 0.00 0.00 4.79
1710 2093 1.528776 GTATCCGCTCCCTCCGTCT 60.529 63.158 0.00 0.00 0.00 4.18
1711 2094 1.228184 TATCCGCTCCCTCCGTCTC 60.228 63.158 0.00 0.00 0.00 3.36
1712 2095 1.991339 TATCCGCTCCCTCCGTCTCA 61.991 60.000 0.00 0.00 0.00 3.27
1713 2096 2.648613 ATCCGCTCCCTCCGTCTCAT 62.649 60.000 0.00 0.00 0.00 2.90
1714 2097 1.528542 CCGCTCCCTCCGTCTCATA 60.529 63.158 0.00 0.00 0.00 2.15
1715 2098 1.107538 CCGCTCCCTCCGTCTCATAA 61.108 60.000 0.00 0.00 0.00 1.90
1716 2099 0.962489 CGCTCCCTCCGTCTCATAAT 59.038 55.000 0.00 0.00 0.00 1.28
1717 2100 2.160205 CGCTCCCTCCGTCTCATAATA 58.840 52.381 0.00 0.00 0.00 0.98
1718 2101 2.755655 CGCTCCCTCCGTCTCATAATAT 59.244 50.000 0.00 0.00 0.00 1.28
1719 2102 3.945921 CGCTCCCTCCGTCTCATAATATA 59.054 47.826 0.00 0.00 0.00 0.86
1720 2103 4.398358 CGCTCCCTCCGTCTCATAATATAA 59.602 45.833 0.00 0.00 0.00 0.98
1721 2104 5.105877 CGCTCCCTCCGTCTCATAATATAAA 60.106 44.000 0.00 0.00 0.00 1.40
1722 2105 6.571731 CGCTCCCTCCGTCTCATAATATAAAA 60.572 42.308 0.00 0.00 0.00 1.52
1723 2106 6.814146 GCTCCCTCCGTCTCATAATATAAAAG 59.186 42.308 0.00 0.00 0.00 2.27
1724 2107 6.698380 TCCCTCCGTCTCATAATATAAAAGC 58.302 40.000 0.00 0.00 0.00 3.51
1725 2108 5.577164 CCCTCCGTCTCATAATATAAAAGCG 59.423 44.000 0.00 0.00 0.00 4.68
1726 2109 6.157211 CCTCCGTCTCATAATATAAAAGCGT 58.843 40.000 0.00 0.00 0.00 5.07
1727 2110 6.308282 CCTCCGTCTCATAATATAAAAGCGTC 59.692 42.308 0.00 0.00 0.00 5.19
1728 2111 6.978338 TCCGTCTCATAATATAAAAGCGTCT 58.022 36.000 0.00 0.00 0.00 4.18
1729 2112 7.431249 TCCGTCTCATAATATAAAAGCGTCTT 58.569 34.615 0.00 0.00 0.00 3.01
1730 2113 7.924412 TCCGTCTCATAATATAAAAGCGTCTTT 59.076 33.333 0.00 0.00 0.00 2.52
1731 2114 8.548721 CCGTCTCATAATATAAAAGCGTCTTTT 58.451 33.333 17.46 17.46 0.00 2.27
1894 2291 1.203237 TCTTGATCAATGGCCGGAGA 58.797 50.000 5.05 0.00 0.00 3.71
2017 2419 9.395707 CGAGCGTACTCTATCAATTATTTTAGT 57.604 33.333 0.00 0.00 41.09 2.24
2087 2489 1.226295 CGTGCTGATGACGACGCTA 60.226 57.895 0.00 0.00 39.21 4.26
2118 2520 4.849329 CGGTGCGGTACTCGGCTC 62.849 72.222 6.00 2.78 39.97 4.70
2119 2521 3.755628 GGTGCGGTACTCGGCTCA 61.756 66.667 6.00 0.00 39.97 4.26
2199 2601 2.040464 GGGAGATGGGGCTGGAGA 60.040 66.667 0.00 0.00 0.00 3.71
2637 3412 0.318784 GGACATGATCGCGACCCTAC 60.319 60.000 12.93 1.37 0.00 3.18
2649 3435 1.196354 CGACCCTACTAGGCGTATTCG 59.804 57.143 0.00 0.00 40.37 3.34
2809 3616 7.772757 AGTCCAAAACATTTCAGCCAAAATTTA 59.227 29.630 0.00 0.00 0.00 1.40
2835 3642 7.757526 CATCTAAATCTAGAGATGTACGGAGG 58.242 42.308 10.22 0.00 42.71 4.30
2836 3643 6.239396 TCTAAATCTAGAGATGTACGGAGGG 58.761 44.000 0.00 0.00 34.49 4.30
2932 3743 3.378427 GGTACACCATTCATTGCTCTTCC 59.622 47.826 0.00 0.00 35.64 3.46
2968 3781 2.380084 TCTAAGTGTGGGTCGAATGC 57.620 50.000 0.00 0.00 0.00 3.56
2991 3804 4.083537 CGAAGCTGCAATTTAGTGTGGTTA 60.084 41.667 1.02 0.00 0.00 2.85
3007 3821 7.309920 AGTGTGGTTAGTTGTTACAGTTTTTG 58.690 34.615 0.00 0.00 0.00 2.44
3010 3824 8.142551 TGTGGTTAGTTGTTACAGTTTTTGTTT 58.857 29.630 0.00 0.00 41.29 2.83
3013 3827 9.800299 GGTTAGTTGTTACAGTTTTTGTTTTTG 57.200 29.630 0.00 0.00 41.29 2.44
3159 3974 5.227569 ACGCTGATCCCACAAATCATATA 57.772 39.130 0.00 0.00 32.91 0.86
3161 3976 5.645067 ACGCTGATCCCACAAATCATATATG 59.355 40.000 6.36 6.36 32.91 1.78
3178 3993 6.685147 TCATATATGAGGAGAGATCCTACCCT 59.315 42.308 11.49 0.00 40.86 4.34
3207 4027 2.943653 CACTCGGGTTGGCGAAAC 59.056 61.111 0.00 0.00 38.12 2.78
3259 4090 8.450578 CAAACTTGCATCCTATTTATAGACCA 57.549 34.615 0.00 0.00 32.05 4.02
3276 4107 4.981812 AGACCATCCTTTTTAAGTCCGTT 58.018 39.130 0.00 0.00 0.00 4.44
3318 4149 5.202746 TCCCCTAAGAGCAACTAAGACTA 57.797 43.478 0.00 0.00 0.00 2.59
3324 4155 7.201652 CCCTAAGAGCAACTAAGACTAATTTGC 60.202 40.741 6.70 6.70 42.35 3.68
3365 4196 5.954335 ACGGATTCTTCCTGCAAATAAAAG 58.046 37.500 0.00 0.00 40.17 2.27
3383 4215 3.764237 AAGTTACTTGTGTGACCCGAT 57.236 42.857 0.00 0.00 33.75 4.18
3472 4311 7.742767 AGGTAATTATCGGTTAAACCTAGCAT 58.257 34.615 0.00 0.00 35.66 3.79
3484 4323 0.531532 CCTAGCATTGTGAGAGGGCG 60.532 60.000 0.00 0.00 0.00 6.13
3501 4340 2.288518 GGGCGCATAACAAAAACCTGAA 60.289 45.455 10.83 0.00 0.00 3.02
3502 4341 3.584834 GGCGCATAACAAAAACCTGAAT 58.415 40.909 10.83 0.00 0.00 2.57
3571 4410 1.689984 TTGGTCACAGAAAGCATGCA 58.310 45.000 21.98 0.00 0.00 3.96
3710 4549 9.626045 AAAAACAGTTTGTTAACTTTCAGAGAG 57.374 29.630 7.22 0.00 41.85 3.20
3711 4550 8.561738 AAACAGTTTGTTAACTTTCAGAGAGA 57.438 30.769 7.22 0.00 41.85 3.10
3712 4551 8.738645 AACAGTTTGTTAACTTTCAGAGAGAT 57.261 30.769 7.22 0.00 41.85 2.75
3713 4552 8.738645 ACAGTTTGTTAACTTTCAGAGAGATT 57.261 30.769 7.22 0.00 41.85 2.40
3714 4553 8.831550 ACAGTTTGTTAACTTTCAGAGAGATTC 58.168 33.333 7.22 0.00 41.85 2.52
3715 4554 8.286097 CAGTTTGTTAACTTTCAGAGAGATTCC 58.714 37.037 7.22 0.00 41.85 3.01
3716 4555 7.445707 AGTTTGTTAACTTTCAGAGAGATTCCC 59.554 37.037 7.22 0.00 41.85 3.97
3717 4556 6.688073 TGTTAACTTTCAGAGAGATTCCCT 57.312 37.500 7.22 0.00 0.00 4.20
3718 4557 6.467677 TGTTAACTTTCAGAGAGATTCCCTG 58.532 40.000 7.22 0.00 0.00 4.45
3719 4558 3.625649 ACTTTCAGAGAGATTCCCTGC 57.374 47.619 0.00 0.00 0.00 4.85
3720 4559 2.909006 ACTTTCAGAGAGATTCCCTGCA 59.091 45.455 0.00 0.00 0.00 4.41
3721 4560 3.328931 ACTTTCAGAGAGATTCCCTGCAA 59.671 43.478 0.00 0.00 0.00 4.08
3722 4561 4.202503 ACTTTCAGAGAGATTCCCTGCAAA 60.203 41.667 0.00 0.00 0.00 3.68
3723 4562 4.371624 TTCAGAGAGATTCCCTGCAAAA 57.628 40.909 0.00 0.00 0.00 2.44
3724 4563 4.371624 TCAGAGAGATTCCCTGCAAAAA 57.628 40.909 0.00 0.00 0.00 1.94
3763 4602 4.008539 GCAATTGCGAAAGAAGTAGGAG 57.991 45.455 15.87 0.00 0.00 3.69
3764 4603 3.437049 GCAATTGCGAAAGAAGTAGGAGT 59.563 43.478 15.87 0.00 0.00 3.85
3765 4604 4.630069 GCAATTGCGAAAGAAGTAGGAGTA 59.370 41.667 15.87 0.00 0.00 2.59
3766 4605 5.220491 GCAATTGCGAAAGAAGTAGGAGTAG 60.220 44.000 15.87 0.00 0.00 2.57
3767 4606 5.662674 ATTGCGAAAGAAGTAGGAGTAGT 57.337 39.130 0.00 0.00 0.00 2.73
3768 4607 4.698583 TGCGAAAGAAGTAGGAGTAGTC 57.301 45.455 0.00 0.00 0.00 2.59
3769 4608 4.333690 TGCGAAAGAAGTAGGAGTAGTCT 58.666 43.478 0.00 0.00 0.00 3.24
3770 4609 4.765856 TGCGAAAGAAGTAGGAGTAGTCTT 59.234 41.667 0.00 0.00 0.00 3.01
3771 4610 5.243283 TGCGAAAGAAGTAGGAGTAGTCTTT 59.757 40.000 0.00 0.00 0.00 2.52
3772 4611 6.157904 GCGAAAGAAGTAGGAGTAGTCTTTT 58.842 40.000 0.00 0.00 0.00 2.27
3773 4612 6.645827 GCGAAAGAAGTAGGAGTAGTCTTTTT 59.354 38.462 0.00 0.00 0.00 1.94
3850 6426 8.840321 GGAACTGTGCATTCACTATACATTTAT 58.160 33.333 0.00 0.00 43.49 1.40
3866 6442 4.647853 ACATTTATAGTGGCACCTCTACGA 59.352 41.667 15.27 0.00 0.00 3.43
3896 6477 0.456995 GTGCTCGAGTCACTGGTAGC 60.457 60.000 23.86 6.00 0.00 3.58
3911 6505 0.248702 GTAGCGACTAGGAGCACTGC 60.249 60.000 13.04 0.00 35.48 4.40
3912 6506 0.394488 TAGCGACTAGGAGCACTGCT 60.394 55.000 2.22 2.22 43.88 4.24
3913 6507 0.394488 AGCGACTAGGAGCACTGCTA 60.394 55.000 2.71 0.00 39.88 3.49
3914 6508 0.248702 GCGACTAGGAGCACTGCTAC 60.249 60.000 4.92 4.92 39.88 3.58
3915 6509 0.028242 CGACTAGGAGCACTGCTACG 59.972 60.000 7.65 0.00 45.59 3.51
3916 6510 0.248702 GACTAGGAGCACTGCTACGC 60.249 60.000 7.65 0.00 45.59 4.42
3917 6511 1.298713 CTAGGAGCACTGCTACGCG 60.299 63.158 3.53 3.53 45.59 6.01
3918 6512 1.715862 CTAGGAGCACTGCTACGCGA 61.716 60.000 15.93 0.00 45.59 5.87
3920 6514 2.179517 GAGCACTGCTACGCGACT 59.820 61.111 15.93 0.00 39.88 4.18
3922 6516 2.126463 GCACTGCTACGCGACTGA 60.126 61.111 15.93 0.00 0.00 3.41
3923 6517 1.733041 GCACTGCTACGCGACTGAA 60.733 57.895 15.93 0.00 0.00 3.02
3924 6518 1.678269 GCACTGCTACGCGACTGAAG 61.678 60.000 15.93 8.71 0.00 3.02
3926 6520 0.109689 ACTGCTACGCGACTGAAGAC 60.110 55.000 15.93 0.00 0.00 3.01
3927 6521 0.798771 CTGCTACGCGACTGAAGACC 60.799 60.000 15.93 0.00 0.00 3.85
3929 6523 1.071567 GCTACGCGACTGAAGACCAC 61.072 60.000 15.93 0.00 0.00 4.16
3930 6524 0.522180 CTACGCGACTGAAGACCACT 59.478 55.000 15.93 0.00 0.00 4.00
4004 6602 1.339929 GAACATTCGTTTTGGCAGGGT 59.660 47.619 0.00 0.00 34.75 4.34
4116 6760 0.250038 TTCAGTGGTGACAGCTGAGC 60.250 55.000 23.35 12.52 43.93 4.26
4134 6778 1.133668 AGCCTGAAAGCTCAGTTTGGT 60.134 47.619 2.63 0.00 46.71 3.67
4168 6812 2.508716 TGGAGGGATCGTGTAGTACTCT 59.491 50.000 0.00 0.00 0.00 3.24
4169 6813 3.713248 TGGAGGGATCGTGTAGTACTCTA 59.287 47.826 0.00 0.00 0.00 2.43
4170 6814 4.064388 GGAGGGATCGTGTAGTACTCTAC 58.936 52.174 0.00 0.00 44.72 2.59
4171 6815 4.202346 GGAGGGATCGTGTAGTACTCTACT 60.202 50.000 0.00 0.00 44.74 2.57
4172 6816 4.959723 AGGGATCGTGTAGTACTCTACTC 58.040 47.826 0.00 0.00 44.74 2.59
4483 7414 5.023452 TGTTCCTATCTTCCTCACTTGCTA 58.977 41.667 0.00 0.00 0.00 3.49
4510 7441 9.488124 GACTTAGATTACTACAGTCAAAGTACG 57.512 37.037 0.00 0.00 37.09 3.67
4520 7451 5.425630 ACAGTCAAAGTACGGAAGAAACTT 58.574 37.500 0.00 0.00 40.61 2.66
4571 7511 6.610741 TTTCTTTGCTTGTTTGTTTGTTGT 57.389 29.167 0.00 0.00 0.00 3.32
4627 7567 1.210478 CTGATGAACCCTTCCGACCAT 59.790 52.381 0.00 0.00 0.00 3.55
4809 8165 1.003233 GGGAAGAAGATGACCACCGTT 59.997 52.381 0.00 0.00 0.00 4.44
4848 8204 1.840635 GTGGCCTCCTACAAATCCTCT 59.159 52.381 3.32 0.00 0.00 3.69
4851 8207 1.210478 GCCTCCTACAAATCCTCTGCA 59.790 52.381 0.00 0.00 0.00 4.41
4889 8245 4.730081 GCAGATCGCCGACATACA 57.270 55.556 0.00 0.00 32.94 2.29
4926 8286 2.019249 CCGGACTCCACGTACATTCTA 58.981 52.381 0.00 0.00 0.00 2.10
4971 8331 9.586150 CTGAATTTAGCTAATTATAAGCGTGTG 57.414 33.333 7.08 0.00 44.87 3.82
4988 8356 1.080298 GTGTGTGGTTTGTCGTGTGA 58.920 50.000 0.00 0.00 0.00 3.58
5168 8536 3.243873 GCACCATCTTCTATGACATCGGA 60.244 47.826 0.00 0.00 0.00 4.55
5250 8627 5.278463 GCCATTGATCACTGTTGTGTTAACT 60.278 40.000 11.65 0.00 44.14 2.24
5293 8678 2.437359 GCTCGTGGCTCCATGCTT 60.437 61.111 3.27 0.00 42.39 3.91
5302 8687 2.017049 GGCTCCATGCTTATGTTCGTT 58.983 47.619 0.00 0.00 42.39 3.85
5662 9639 0.683973 AGGGCCTGATGATGATCGTC 59.316 55.000 4.50 8.06 33.13 4.20
5956 9933 1.002773 GGGTACAACAAGTGGGTCGAT 59.997 52.381 0.00 0.00 0.00 3.59
5966 9943 3.210528 GGGTCGATCTCGCGGTCT 61.211 66.667 6.13 0.00 39.60 3.85
6154 10148 9.683069 AGAGATCATCACAATTGTTTTGTTAAC 57.317 29.630 8.77 0.00 0.00 2.01
6160 10154 6.037098 TCACAATTGTTTTGTTAACGGAAGG 58.963 36.000 8.77 0.00 0.00 3.46
6372 10373 7.450074 GTTCACCCCCTAATTTTCATTTTTCT 58.550 34.615 0.00 0.00 0.00 2.52
6393 10394 8.722342 TTTCTAAAAATTGATTACACGAGCAC 57.278 30.769 0.00 0.00 0.00 4.40
6417 10418 5.124457 CCCATCAAGTTCCTGTTAAGACATG 59.876 44.000 0.00 0.00 34.72 3.21
6460 10461 3.251571 GTTAACGAGCACCCTCTAACAG 58.748 50.000 0.00 0.00 35.90 3.16
6484 10485 5.163874 GCAAGAGACATCTACTGAGCAAAAG 60.164 44.000 0.00 0.00 33.45 2.27
6509 10510 5.818678 AGACCTTATTACAGAACCACACA 57.181 39.130 0.00 0.00 0.00 3.72
6515 10516 3.916359 TTACAGAACCACACAACCAGA 57.084 42.857 0.00 0.00 0.00 3.86
6649 10650 1.977594 GCGCACAAGAATACACCCCG 61.978 60.000 0.30 0.00 0.00 5.73
6697 10698 3.845178 AGCTTGACGTCGTTGATGATAA 58.155 40.909 11.62 0.00 0.00 1.75
6852 10853 4.195416 GCTTTTTCCACCATTCCAAAACA 58.805 39.130 0.00 0.00 0.00 2.83
6853 10854 4.637977 GCTTTTTCCACCATTCCAAAACAA 59.362 37.500 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.269778 CGTATCGGCACATGGACAGAT 60.270 52.381 0.00 2.97 0.00 2.90
22 23 1.883084 CAAGGCGCTGGTCCGTATC 60.883 63.158 7.64 0.00 0.00 2.24
23 24 1.324740 TACAAGGCGCTGGTCCGTAT 61.325 55.000 7.64 0.00 0.00 3.06
51 52 0.534203 TCAAGGGCTCAACAACGACC 60.534 55.000 0.00 0.00 0.00 4.79
113 114 4.010349 GAGGTTAGGGTTTCTTGTCATGG 58.990 47.826 0.00 0.00 0.00 3.66
120 121 3.527434 CGCGAGGTTAGGGTTTCTT 57.473 52.632 0.00 0.00 0.00 2.52
137 138 1.141881 CGTCATCTCCTTGGGACCG 59.858 63.158 0.00 0.00 0.00 4.79
138 139 1.522569 CCGTCATCTCCTTGGGACC 59.477 63.158 0.00 0.00 0.00 4.46
155 156 3.190535 ACGAAGTTGCAATGTACATTCCC 59.809 43.478 18.25 12.47 37.78 3.97
186 187 1.178276 CTCGAATCTATCCCTCGGGG 58.822 60.000 0.00 0.00 46.11 5.73
214 215 1.805345 TCGAGTTCGTCTTCTGGACTC 59.195 52.381 1.07 0.00 42.44 3.36
217 218 2.501261 TCTTCGAGTTCGTCTTCTGGA 58.499 47.619 1.07 0.00 40.80 3.86
219 220 4.084889 TCATCTTCGAGTTCGTCTTCTG 57.915 45.455 1.07 0.00 40.80 3.02
256 257 9.149225 GTAGTTTAGGTTAGACTTTTTAGCCTC 57.851 37.037 0.00 0.00 34.19 4.70
326 341 1.909302 CCCATCTACCAACCACTCTGT 59.091 52.381 0.00 0.00 0.00 3.41
335 350 2.605825 ATTCCCCTCCCATCTACCAA 57.394 50.000 0.00 0.00 0.00 3.67
336 351 2.605825 AATTCCCCTCCCATCTACCA 57.394 50.000 0.00 0.00 0.00 3.25
343 358 2.555670 CCAAACGTAAATTCCCCTCCCA 60.556 50.000 0.00 0.00 0.00 4.37
356 371 5.999205 TGTATCTTCCCTAACCAAACGTA 57.001 39.130 0.00 0.00 0.00 3.57
366 381 9.931698 TCAAGAAACTACTATGTATCTTCCCTA 57.068 33.333 0.00 0.00 0.00 3.53
401 417 1.065491 TGCTAATGCCATTGGACGACT 60.065 47.619 6.95 0.00 38.71 4.18
403 419 2.121291 TTGCTAATGCCATTGGACGA 57.879 45.000 6.95 0.00 38.71 4.20
404 420 2.164219 ACTTTGCTAATGCCATTGGACG 59.836 45.455 6.95 0.00 38.71 4.79
410 426 4.951715 TCTTGATGACTTTGCTAATGCCAT 59.048 37.500 0.00 0.00 38.71 4.40
418 434 7.014038 ACTCTGAAAATTCTTGATGACTTTGCT 59.986 33.333 0.00 0.00 29.69 3.91
452 471 2.440409 AGCTAGGGCAACATCACAAAG 58.560 47.619 0.00 0.00 41.70 2.77
492 511 1.613928 TGCCCCAGGGTACGATTCA 60.614 57.895 4.22 0.00 37.65 2.57
503 522 4.087892 CTCACCCTCGTGCCCCAG 62.088 72.222 0.00 0.00 40.04 4.45
511 530 2.036475 CCCAATAGATGACTCACCCTCG 59.964 54.545 0.00 0.00 0.00 4.63
621 676 0.747255 ACTACTATGTGCGGCTCTGG 59.253 55.000 0.00 0.00 0.00 3.86
627 682 4.154195 AGCAAAAGAAACTACTATGTGCGG 59.846 41.667 0.00 0.00 34.72 5.69
628 683 5.283060 AGCAAAAGAAACTACTATGTGCG 57.717 39.130 0.00 0.00 34.72 5.34
629 684 5.107065 ACGAGCAAAAGAAACTACTATGTGC 60.107 40.000 0.00 0.00 0.00 4.57
630 685 6.467723 ACGAGCAAAAGAAACTACTATGTG 57.532 37.500 0.00 0.00 0.00 3.21
632 687 6.525628 TCGTACGAGCAAAAGAAACTACTATG 59.474 38.462 15.28 0.00 0.00 2.23
633 688 6.615088 TCGTACGAGCAAAAGAAACTACTAT 58.385 36.000 15.28 0.00 0.00 2.12
635 690 4.863491 TCGTACGAGCAAAAGAAACTACT 58.137 39.130 15.28 0.00 0.00 2.57
637 692 4.149396 GCTTCGTACGAGCAAAAGAAACTA 59.851 41.667 24.93 6.16 0.00 2.24
638 693 3.059800 GCTTCGTACGAGCAAAAGAAACT 60.060 43.478 24.93 0.00 0.00 2.66
639 694 3.216031 GCTTCGTACGAGCAAAAGAAAC 58.784 45.455 24.93 5.07 0.00 2.78
641 696 2.475818 TGCTTCGTACGAGCAAAAGAA 58.524 42.857 28.11 13.49 35.46 2.52
642 697 2.143008 TGCTTCGTACGAGCAAAAGA 57.857 45.000 28.11 10.67 35.46 2.52
643 698 2.941891 TTGCTTCGTACGAGCAAAAG 57.058 45.000 33.03 23.39 44.24 2.27
647 702 2.073117 TTCATTGCTTCGTACGAGCA 57.927 45.000 27.18 27.18 36.72 4.26
648 703 2.784665 GCTTTCATTGCTTCGTACGAGC 60.785 50.000 23.84 23.84 0.00 5.03
656 899 3.303406 GTCTGTGTGCTTTCATTGCTTC 58.697 45.455 0.00 0.00 0.00 3.86
684 927 9.379791 ACTAATATGGTTCTGCTGTACTAAAAC 57.620 33.333 0.00 0.00 0.00 2.43
847 1158 5.443185 TTCTTGAATGCCTCTTTGAACAG 57.557 39.130 0.00 0.00 0.00 3.16
931 1259 6.228616 AGACTGCTTAAATAGAGGGAAGAC 57.771 41.667 0.00 0.00 0.00 3.01
1017 1347 1.485124 TCAGCTCGATGGTGGTATGT 58.515 50.000 12.10 0.00 43.76 2.29
1319 1653 1.652930 GCTGATCTCGAGCGACGAC 60.653 63.158 7.81 0.00 46.45 4.34
1538 1872 2.026262 GTCTAGAAGGGTGGATTTGCCA 60.026 50.000 0.00 0.00 46.96 4.92
1644 1980 2.125350 GAAGGCCGGCTGTCTGAG 60.125 66.667 28.56 0.00 0.00 3.35
1655 1991 1.300233 CGACGCTATCAGGAAGGCC 60.300 63.158 0.00 0.00 0.00 5.19
1697 2080 0.962489 ATTATGAGACGGAGGGAGCG 59.038 55.000 0.00 0.00 0.00 5.03
1698 2081 5.916661 TTATATTATGAGACGGAGGGAGC 57.083 43.478 0.00 0.00 0.00 4.70
1699 2082 6.814146 GCTTTTATATTATGAGACGGAGGGAG 59.186 42.308 0.00 0.00 0.00 4.30
1700 2083 6.571731 CGCTTTTATATTATGAGACGGAGGGA 60.572 42.308 0.00 0.00 0.00 4.20
1701 2084 5.577164 CGCTTTTATATTATGAGACGGAGGG 59.423 44.000 0.00 0.00 0.00 4.30
1702 2085 6.157211 ACGCTTTTATATTATGAGACGGAGG 58.843 40.000 0.00 0.00 0.00 4.30
1703 2086 7.085116 AGACGCTTTTATATTATGAGACGGAG 58.915 38.462 0.00 0.00 0.00 4.63
1704 2087 6.978338 AGACGCTTTTATATTATGAGACGGA 58.022 36.000 0.00 0.00 0.00 4.69
1705 2088 7.639162 AAGACGCTTTTATATTATGAGACGG 57.361 36.000 0.00 0.00 0.00 4.79
1813 2201 2.922740 TTTTGTACCACGGAAGCTCT 57.077 45.000 0.00 0.00 0.00 4.09
2663 3449 9.284594 CAAATAATTTGTATTACCACCGTTCAG 57.715 33.333 0.00 0.00 35.94 3.02
2664 3450 9.011095 TCAAATAATTTGTATTACCACCGTTCA 57.989 29.630 0.00 0.00 41.36 3.18
2829 3636 9.281371 GCTTTTTATTATTATTACTCCCTCCGT 57.719 33.333 0.00 0.00 0.00 4.69
2830 3637 9.503399 AGCTTTTTATTATTATTACTCCCTCCG 57.497 33.333 0.00 0.00 0.00 4.63
2882 3693 2.102420 CCCAACCAAACCTGAAGAAACC 59.898 50.000 0.00 0.00 0.00 3.27
2893 3704 2.076207 ACCCAAGTACCCAACCAAAC 57.924 50.000 0.00 0.00 0.00 2.93
2968 3781 2.226437 ACCACACTAAATTGCAGCTTCG 59.774 45.455 0.00 0.00 0.00 3.79
2974 3787 6.458232 AACAACTAACCACACTAAATTGCA 57.542 33.333 0.00 0.00 0.00 4.08
2983 3796 7.085746 ACAAAAACTGTAACAACTAACCACAC 58.914 34.615 0.00 0.00 36.10 3.82
3139 3953 6.318144 CCTCATATATGATTTGTGGGATCAGC 59.682 42.308 15.71 0.00 36.99 4.26
3140 3954 7.627311 TCCTCATATATGATTTGTGGGATCAG 58.373 38.462 15.71 0.04 36.99 2.90
3178 3993 4.077184 CGAGTGCGGGGGCAACTA 62.077 66.667 0.00 0.00 0.00 2.24
3254 4075 4.635699 ACGGACTTAAAAAGGATGGTCT 57.364 40.909 0.00 0.00 0.00 3.85
3282 4113 8.061304 TGCTCTTAGGGGAAAATTAGAATTCAT 58.939 33.333 8.44 0.00 0.00 2.57
3296 4127 4.062490 AGTCTTAGTTGCTCTTAGGGGA 57.938 45.455 0.00 0.00 0.00 4.81
3365 4196 3.810941 TGAAATCGGGTCACACAAGTAAC 59.189 43.478 0.00 0.00 0.00 2.50
3472 4311 0.323302 TGTTATGCGCCCTCTCACAA 59.677 50.000 4.18 0.00 0.00 3.33
3484 4323 6.806739 GTCTGGTATTCAGGTTTTTGTTATGC 59.193 38.462 0.00 0.00 43.53 3.14
3501 4340 4.100344 TGCATTATGGTGTACGTCTGGTAT 59.900 41.667 0.00 0.00 32.74 2.73
3502 4341 3.447944 TGCATTATGGTGTACGTCTGGTA 59.552 43.478 0.00 0.00 0.00 3.25
3602 4441 6.589139 AGAACGGTAAGTACTAAATCAGCAAC 59.411 38.462 0.00 0.00 0.00 4.17
3604 4443 6.097356 CAGAACGGTAAGTACTAAATCAGCA 58.903 40.000 0.00 0.00 0.00 4.41
3689 4528 8.286097 GGAATCTCTCTGAAAGTTAACAAACTG 58.714 37.037 8.61 3.00 32.47 3.16
3690 4529 7.445707 GGGAATCTCTCTGAAAGTTAACAAACT 59.554 37.037 8.61 0.00 33.76 2.66
3691 4530 7.445707 AGGGAATCTCTCTGAAAGTTAACAAAC 59.554 37.037 8.61 0.00 33.76 2.93
3694 4533 6.688073 AGGGAATCTCTCTGAAAGTTAACA 57.312 37.500 8.61 0.00 33.76 2.41
3725 4564 5.803967 GCAATTGCGATCTCTCTGAATTTTT 59.196 36.000 15.87 0.00 0.00 1.94
3726 4565 5.338365 GCAATTGCGATCTCTCTGAATTTT 58.662 37.500 15.87 0.00 0.00 1.82
3727 4566 4.918037 GCAATTGCGATCTCTCTGAATTT 58.082 39.130 15.87 0.00 0.00 1.82
3728 4567 4.548991 GCAATTGCGATCTCTCTGAATT 57.451 40.909 15.87 0.00 0.00 2.17
3742 4581 3.437049 ACTCCTACTTCTTTCGCAATTGC 59.563 43.478 20.76 20.76 37.78 3.56
3778 4617 1.298863 CTGTCGCCGTACGGTATGG 60.299 63.158 33.34 19.92 43.89 2.74
3779 4618 0.657312 TACTGTCGCCGTACGGTATG 59.343 55.000 33.34 23.20 43.89 2.39
3780 4619 1.378531 TTACTGTCGCCGTACGGTAT 58.621 50.000 33.34 15.77 40.13 2.73
3781 4620 1.378531 ATTACTGTCGCCGTACGGTA 58.621 50.000 33.34 20.31 43.89 4.02
3782 4621 0.527565 AATTACTGTCGCCGTACGGT 59.472 50.000 33.34 16.46 43.89 4.83
3850 6426 1.028330 CCGTCGTAGAGGTGCCACTA 61.028 60.000 0.00 0.00 41.34 2.74
3866 6442 2.029073 CGAGCACAGTTCCACCGT 59.971 61.111 0.00 0.00 0.00 4.83
3896 6477 0.028242 CGTAGCAGTGCTCCTAGTCG 59.972 60.000 23.64 13.48 40.44 4.18
3911 6505 0.522180 AGTGGTCTTCAGTCGCGTAG 59.478 55.000 5.77 0.00 0.00 3.51
3912 6506 0.240145 CAGTGGTCTTCAGTCGCGTA 59.760 55.000 5.77 0.00 0.00 4.42
3913 6507 1.007271 CAGTGGTCTTCAGTCGCGT 60.007 57.895 5.77 0.00 0.00 6.01
3914 6508 2.375766 GCAGTGGTCTTCAGTCGCG 61.376 63.158 0.00 0.00 0.00 5.87
3915 6509 1.300931 TGCAGTGGTCTTCAGTCGC 60.301 57.895 0.00 0.00 0.00 5.19
3916 6510 0.249447 TGTGCAGTGGTCTTCAGTCG 60.249 55.000 0.00 0.00 0.00 4.18
3917 6511 1.869767 CTTGTGCAGTGGTCTTCAGTC 59.130 52.381 0.00 0.00 0.00 3.51
3918 6512 1.486310 TCTTGTGCAGTGGTCTTCAGT 59.514 47.619 0.00 0.00 0.00 3.41
3920 6514 2.771089 GATCTTGTGCAGTGGTCTTCA 58.229 47.619 0.00 0.00 0.00 3.02
3922 6516 1.344438 TCGATCTTGTGCAGTGGTCTT 59.656 47.619 0.00 0.00 0.00 3.01
3923 6517 0.969149 TCGATCTTGTGCAGTGGTCT 59.031 50.000 0.00 0.00 0.00 3.85
3924 6518 1.929836 GATCGATCTTGTGCAGTGGTC 59.070 52.381 18.29 0.00 0.00 4.02
3926 6520 0.926155 CGATCGATCTTGTGCAGTGG 59.074 55.000 22.43 0.00 0.00 4.00
3927 6521 1.913317 TCGATCGATCTTGTGCAGTG 58.087 50.000 22.43 4.50 0.00 3.66
3929 6523 2.029728 GGTTTCGATCGATCTTGTGCAG 59.970 50.000 20.18 5.91 0.00 4.41
3930 6524 1.999735 GGTTTCGATCGATCTTGTGCA 59.000 47.619 20.18 0.00 0.00 4.57
4004 6602 4.939509 CATGATCGATCAATGCATGCTA 57.060 40.909 30.41 4.71 40.69 3.49
4116 6760 2.689983 ACAACCAAACTGAGCTTTCAGG 59.310 45.455 7.77 0.00 41.76 3.86
4134 6778 1.202964 TCCCTCCACAGTCGTCTACAA 60.203 52.381 0.00 0.00 0.00 2.41
4168 6812 4.883585 ACAGTGGATTACCGAATACGAGTA 59.116 41.667 0.00 0.00 42.66 2.59
4169 6813 3.698040 ACAGTGGATTACCGAATACGAGT 59.302 43.478 0.00 0.00 42.66 4.18
4170 6814 4.042398 CACAGTGGATTACCGAATACGAG 58.958 47.826 0.00 0.00 42.66 4.18
4171 6815 3.735820 GCACAGTGGATTACCGAATACGA 60.736 47.826 1.84 0.00 42.66 3.43
4172 6816 2.538449 GCACAGTGGATTACCGAATACG 59.462 50.000 1.84 0.00 39.42 3.06
4178 6826 1.086696 CTTGGCACAGTGGATTACCG 58.913 55.000 1.84 0.00 42.39 4.02
4419 7348 9.897744 AATTTCACATAATCATTAGCAATACCG 57.102 29.630 0.00 0.00 0.00 4.02
4510 7441 4.097892 TCAGTGGCTTCAAAAGTTTCTTCC 59.902 41.667 0.00 0.00 0.00 3.46
4520 7451 4.734398 AACACAATTCAGTGGCTTCAAA 57.266 36.364 0.00 0.00 43.72 2.69
4571 7511 2.151202 CCCGCTCAAAGCAAAGAACTA 58.849 47.619 0.00 0.00 42.58 2.24
4627 7567 2.992124 TGTTGACGGTCCTCAGAAAA 57.008 45.000 5.55 0.00 0.00 2.29
4809 8165 1.801512 CAGCGCGTCGATGTTCTCA 60.802 57.895 8.43 0.00 38.50 3.27
4848 8204 0.182299 TCACCTTGTCCATGTGTGCA 59.818 50.000 0.00 0.00 0.00 4.57
4851 8207 0.884704 GCGTCACCTTGTCCATGTGT 60.885 55.000 0.00 0.00 0.00 3.72
4889 8245 2.657237 GGCTACTCACAGTGCCGT 59.343 61.111 0.00 0.00 34.49 5.68
4953 8313 4.570772 CCACACACACGCTTATAATTAGCT 59.429 41.667 0.00 0.00 36.49 3.32
4971 8331 3.181505 TGAAATCACACGACAAACCACAC 60.182 43.478 0.00 0.00 0.00 3.82
4988 8356 0.921256 CCACCTCCCCTCCCTGAAAT 60.921 60.000 0.00 0.00 0.00 2.17
5093 8461 3.130227 CGGAGCCAGTAGTAGCCC 58.870 66.667 0.00 0.00 0.00 5.19
5168 8536 5.188555 CACCTGTATGGATCCATAGCTATGT 59.811 44.000 30.90 20.53 39.29 2.29
5203 8571 1.541147 TGGTAACTACAACGGGAGACG 59.459 52.381 0.00 0.00 43.97 4.18
5250 8627 4.338964 ACATGCAGAGTTTTCAATCACACA 59.661 37.500 0.00 0.00 0.00 3.72
5293 8678 1.349688 AGGAAGGCACCAACGAACATA 59.650 47.619 0.00 0.00 0.00 2.29
5956 9933 2.257371 CCGAACAAGACCGCGAGA 59.743 61.111 8.23 0.00 0.00 4.04
5966 9943 4.229304 ACAATATGACCATCCCGAACAA 57.771 40.909 0.00 0.00 0.00 2.83
6154 10148 3.074412 ACTCATAAGCAACAACCTTCCG 58.926 45.455 0.00 0.00 0.00 4.30
6160 10154 6.645415 ACACTACAGTACTCATAAGCAACAAC 59.355 38.462 0.00 0.00 0.00 3.32
6209 10203 3.250040 GCACTTCTTTCTTTTGCGGACTA 59.750 43.478 0.00 0.00 0.00 2.59
6294 10289 2.004017 CGACAAACCGCTTATAGCCAA 58.996 47.619 0.00 0.00 38.18 4.52
6372 10373 5.473846 TGGGTGCTCGTGTAATCAATTTTTA 59.526 36.000 0.00 0.00 0.00 1.52
6388 10389 1.271597 ACAGGAACTTGATGGGTGCTC 60.272 52.381 0.00 0.00 34.60 4.26
6393 10394 4.651778 TGTCTTAACAGGAACTTGATGGG 58.348 43.478 0.00 0.00 34.60 4.00
6417 10418 2.590073 CGTCATGTGACACTGAGACTC 58.410 52.381 13.07 0.00 44.99 3.36
6460 10461 3.516981 TGCTCAGTAGATGTCTCTTGC 57.483 47.619 0.00 0.00 32.66 4.01
6484 10485 5.811100 GTGTGGTTCTGTAATAAGGTCTAGC 59.189 44.000 0.00 0.00 0.00 3.42
6509 10510 2.052782 AAAAGCTTCGGTGTCTGGTT 57.947 45.000 0.00 0.00 0.00 3.67
6697 10698 0.978146 CCTCCGGTCCTTCTCCATGT 60.978 60.000 0.00 0.00 0.00 3.21
6836 10837 3.969976 TGGATTTGTTTTGGAATGGTGGA 59.030 39.130 0.00 0.00 0.00 4.02
6852 10853 3.453353 CCTCTTGGCATTTGGATGGATTT 59.547 43.478 0.00 0.00 33.72 2.17
6853 10854 3.036091 CCTCTTGGCATTTGGATGGATT 58.964 45.455 0.00 0.00 33.72 3.01


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

AutoCloner maintained by Alex Coulton.