Multiple sequence alignment - TraesCS4A01G402700

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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 TraesCS4A01G402700 chr4A 100.000 3860 0 0 1 3860 676458237 676454378 0.000000e+00 7129.0
1 TraesCS4A01G402700 chr4A 94.509 692 29 5 1737 2427 676528352 676527669 0.000000e+00 1059.0
2 TraesCS4A01G402700 chr4A 83.772 684 91 7 3018 3682 400753873 400753191 7.040000e-177 630.0
3 TraesCS4A01G402700 chr4A 92.131 305 16 2 1434 1731 676528978 676528675 1.280000e-114 424.0
4 TraesCS4A01G402700 chr4A 89.021 337 34 3 766 1100 676494241 676493906 7.720000e-112 414.0
5 TraesCS4A01G402700 chr4A 92.509 267 19 1 1148 1413 676493905 676493639 7.830000e-102 381.0
6 TraesCS4A01G402700 chr4A 88.936 235 15 5 2187 2414 676362453 676362223 2.940000e-71 279.0
7 TraesCS4A01G402700 chr4A 93.377 151 7 3 1192 1339 676529128 676528978 1.810000e-53 220.0
8 TraesCS4A01G402700 chr4A 86.325 117 10 4 2600 2712 572709951 572709837 5.240000e-24 122.0
9 TraesCS4A01G402700 chr7D 91.009 1001 67 8 1435 2427 59091884 59090899 0.000000e+00 1328.0
10 TraesCS4A01G402700 chr7D 92.533 750 47 5 1 741 34031625 34032374 0.000000e+00 1066.0
11 TraesCS4A01G402700 chr7D 92.154 752 49 6 1 742 555165570 555164819 0.000000e+00 1053.0
12 TraesCS4A01G402700 chr7D 86.722 836 83 11 3018 3833 161465196 161464369 0.000000e+00 904.0
13 TraesCS4A01G402700 chr7D 88.946 588 49 8 1753 2330 58992889 58992308 0.000000e+00 712.0
14 TraesCS4A01G402700 chr7D 84.438 694 82 17 1629 2311 58938129 58937451 0.000000e+00 660.0
15 TraesCS4A01G402700 chr7D 89.167 360 34 5 755 1111 58994414 58994057 9.840000e-121 444.0
16 TraesCS4A01G402700 chr7D 91.195 318 21 4 1186 1496 58994057 58993740 3.560000e-115 425.0
17 TraesCS4A01G402700 chr7D 91.837 245 13 1 1494 1731 58993480 58993236 6.180000e-88 335.0
18 TraesCS4A01G402700 chr7D 90.991 111 8 2 1230 1338 59091996 59091886 8.640000e-32 148.0
19 TraesCS4A01G402700 chr7D 89.691 97 10 0 1336 1432 605166838 605166934 1.460000e-24 124.0
20 TraesCS4A01G402700 chr7A 91.037 993 68 9 1431 2414 63710036 63711016 0.000000e+00 1321.0
21 TraesCS4A01G402700 chr7A 90.621 821 49 16 911 1731 63578984 63578192 0.000000e+00 1064.0
22 TraesCS4A01G402700 chr7A 87.561 820 77 16 1607 2412 63554315 63553507 0.000000e+00 926.0
23 TraesCS4A01G402700 chr7A 86.996 669 64 12 3187 3834 183488111 183487445 0.000000e+00 732.0
24 TraesCS4A01G402700 chr7A 88.702 593 51 11 1737 2319 63577864 63577278 0.000000e+00 710.0
25 TraesCS4A01G402700 chr7A 94.969 159 7 1 755 912 63579400 63579242 8.280000e-62 248.0
26 TraesCS4A01G402700 chr6B 92.182 857 52 4 3018 3860 499007738 499006883 0.000000e+00 1197.0
27 TraesCS4A01G402700 chr6B 90.115 607 49 8 2422 3019 499008264 499007660 0.000000e+00 778.0
28 TraesCS4A01G402700 chr6B 87.255 102 11 2 1332 1432 55105530 55105630 8.760000e-22 115.0
29 TraesCS4A01G402700 chr6B 89.394 66 3 2 1121 1186 104317871 104317810 3.200000e-11 80.5
30 TraesCS4A01G402700 chr2D 92.952 752 42 6 1 742 635194353 635193603 0.000000e+00 1085.0
31 TraesCS4A01G402700 chr2D 92.810 751 45 5 1 742 635196594 635195844 0.000000e+00 1079.0
32 TraesCS4A01G402700 chr2D 92.810 751 45 5 1 742 635198835 635198085 0.000000e+00 1079.0
33 TraesCS4A01G402700 chr2D 92.676 751 46 5 1 742 635201075 635200325 0.000000e+00 1074.0
34 TraesCS4A01G402700 chr2D 92.277 751 49 5 1 742 635192112 635191362 0.000000e+00 1057.0
35 TraesCS4A01G402700 chr2D 92.277 751 49 5 1 742 635203316 635202566 0.000000e+00 1057.0
36 TraesCS4A01G402700 chr2D 82.963 135 17 5 2573 2704 575946544 575946675 2.440000e-22 117.0
37 TraesCS4A01G402700 chr2D 78.947 114 18 6 763 873 564479267 564479157 5.350000e-09 73.1
38 TraesCS4A01G402700 chr1B 91.689 758 50 10 1 749 73869016 73868263 0.000000e+00 1038.0
39 TraesCS4A01G402700 chr1B 87.039 841 84 13 3018 3834 642731462 642730623 0.000000e+00 926.0
40 TraesCS4A01G402700 chr1B 85.816 839 91 13 3021 3834 16853133 16853968 0.000000e+00 865.0
41 TraesCS4A01G402700 chr1B 85.903 681 69 13 3176 3834 450448493 450449168 0.000000e+00 701.0
42 TraesCS4A01G402700 chr1B 83.419 585 75 19 2452 3018 642731965 642731385 1.230000e-144 523.0
43 TraesCS4A01G402700 chr1B 82.848 309 38 13 2718 3018 16852908 16853209 2.960000e-66 263.0
44 TraesCS4A01G402700 chr1B 75.896 307 59 10 766 1064 655122767 655122468 4.020000e-30 143.0
45 TraesCS4A01G402700 chr1B 87.273 110 13 1 1328 1437 540341545 540341653 1.460000e-24 124.0
46 TraesCS4A01G402700 chr1B 84.298 121 19 0 1316 1436 217778062 217777942 6.770000e-23 119.0
47 TraesCS4A01G402700 chr1B 86.111 108 15 0 1326 1433 683383489 683383596 2.440000e-22 117.0
48 TraesCS4A01G402700 chr1B 76.991 113 21 5 762 873 587498250 587498142 4.160000e-05 60.2
49 TraesCS4A01G402700 chr7B 87.753 841 82 9 3013 3833 595163174 595164013 0.000000e+00 963.0
50 TraesCS4A01G402700 chr7B 85.610 410 44 8 2611 3005 595162429 595162838 2.150000e-112 416.0
51 TraesCS4A01G402700 chr7B 84.670 424 49 11 2611 3019 595162835 595163257 3.590000e-110 409.0
52 TraesCS4A01G402700 chr7B 80.602 299 39 16 2729 3019 612890393 612890680 3.020000e-51 213.0
53 TraesCS4A01G402700 chr7B 89.552 67 4 3 1114 1179 384380568 384380504 8.890000e-12 82.4
54 TraesCS4A01G402700 chr7B 83.333 78 12 1 796 873 12529742 12529818 1.920000e-08 71.3
55 TraesCS4A01G402700 chr5B 85.256 841 100 12 3018 3834 41956064 41955224 0.000000e+00 845.0
56 TraesCS4A01G402700 chr5B 87.793 213 25 1 3621 3833 387350086 387349875 8.280000e-62 248.0
57 TraesCS4A01G402700 chr5B 93.443 61 4 0 1108 1168 264286815 264286875 1.480000e-14 91.6
58 TraesCS4A01G402700 chr4B 87.147 708 68 10 3147 3834 385969239 385968535 0.000000e+00 782.0
59 TraesCS4A01G402700 chr6A 86.345 725 74 13 3018 3720 88803948 88803227 0.000000e+00 767.0
60 TraesCS4A01G402700 chr3B 84.293 573 79 6 3015 3576 322727779 322728351 2.030000e-152 549.0
61 TraesCS4A01G402700 chr3B 88.732 213 23 1 3621 3833 322728455 322728666 3.830000e-65 259.0
62 TraesCS4A01G402700 chr1D 78.930 617 99 22 2422 3019 80553612 80553008 1.300000e-104 390.0
63 TraesCS4A01G402700 chr1D 78.182 110 18 6 766 873 462688640 462688535 8.950000e-07 65.8
64 TraesCS4A01G402700 chr2A 84.694 294 31 6 3576 3860 10490291 10490003 8.160000e-72 281.0
65 TraesCS4A01G402700 chr2A 83.582 268 34 4 3575 3833 24890098 24890364 3.850000e-60 243.0
66 TraesCS4A01G402700 chr2A 77.692 390 62 17 2648 3019 205199978 205199596 8.400000e-52 215.0
67 TraesCS4A01G402700 chr5D 78.960 423 66 16 2617 3019 264501078 264501497 2.290000e-67 267.0
68 TraesCS4A01G402700 chr2B 78.598 271 42 10 2592 2848 377106162 377105894 8.580000e-37 165.0
69 TraesCS4A01G402700 chr2B 89.109 101 9 2 1336 1435 257534764 257534863 1.460000e-24 124.0
70 TraesCS4A01G402700 chr2B 89.231 65 6 1 1116 1180 15721477 15721540 3.200000e-11 80.5
71 TraesCS4A01G402700 chrUn 76.254 299 56 11 2573 2859 40740841 40740546 1.120000e-30 145.0
72 TraesCS4A01G402700 chrUn 76.254 299 56 11 2573 2859 40747064 40747359 1.120000e-30 145.0
73 TraesCS4A01G402700 chrUn 76.254 299 56 11 2573 2859 303400395 303400100 1.120000e-30 145.0
74 TraesCS4A01G402700 chrUn 89.231 65 6 1 1116 1180 349616255 349616318 3.200000e-11 80.5
75 TraesCS4A01G402700 chr3D 88.732 71 6 2 1115 1185 120290006 120289938 6.870000e-13 86.1
76 TraesCS4A01G402700 chr5A 90.476 63 5 1 1116 1177 475527343 475527281 8.890000e-12 82.4
77 TraesCS4A01G402700 chr5A 80.000 100 16 3 775 873 231310693 231310597 1.920000e-08 71.3
78 TraesCS4A01G402700 chr6D 83.333 84 12 2 1096 1178 425931334 425931252 4.140000e-10 76.8


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 TraesCS4A01G402700 chr4A 676454378 676458237 3859 True 7129.000000 7129 100.000000 1 3860 1 chr4A.!!$R4 3859
1 TraesCS4A01G402700 chr4A 400753191 400753873 682 True 630.000000 630 83.772000 3018 3682 1 chr4A.!!$R1 664
2 TraesCS4A01G402700 chr4A 676527669 676529128 1459 True 567.666667 1059 93.339000 1192 2427 3 chr4A.!!$R6 1235
3 TraesCS4A01G402700 chr4A 676493639 676494241 602 True 397.500000 414 90.765000 766 1413 2 chr4A.!!$R5 647
4 TraesCS4A01G402700 chr7D 34031625 34032374 749 False 1066.000000 1066 92.533000 1 741 1 chr7D.!!$F1 740
5 TraesCS4A01G402700 chr7D 555164819 555165570 751 True 1053.000000 1053 92.154000 1 742 1 chr7D.!!$R3 741
6 TraesCS4A01G402700 chr7D 161464369 161465196 827 True 904.000000 904 86.722000 3018 3833 1 chr7D.!!$R2 815
7 TraesCS4A01G402700 chr7D 59090899 59091996 1097 True 738.000000 1328 91.000000 1230 2427 2 chr7D.!!$R5 1197
8 TraesCS4A01G402700 chr7D 58937451 58938129 678 True 660.000000 660 84.438000 1629 2311 1 chr7D.!!$R1 682
9 TraesCS4A01G402700 chr7D 58992308 58994414 2106 True 479.000000 712 90.286250 755 2330 4 chr7D.!!$R4 1575
10 TraesCS4A01G402700 chr7A 63710036 63711016 980 False 1321.000000 1321 91.037000 1431 2414 1 chr7A.!!$F1 983
11 TraesCS4A01G402700 chr7A 63553507 63554315 808 True 926.000000 926 87.561000 1607 2412 1 chr7A.!!$R1 805
12 TraesCS4A01G402700 chr7A 183487445 183488111 666 True 732.000000 732 86.996000 3187 3834 1 chr7A.!!$R2 647
13 TraesCS4A01G402700 chr7A 63577278 63579400 2122 True 674.000000 1064 91.430667 755 2319 3 chr7A.!!$R3 1564
14 TraesCS4A01G402700 chr6B 499006883 499008264 1381 True 987.500000 1197 91.148500 2422 3860 2 chr6B.!!$R2 1438
15 TraesCS4A01G402700 chr2D 635191362 635203316 11954 True 1071.833333 1085 92.633667 1 742 6 chr2D.!!$R2 741
16 TraesCS4A01G402700 chr1B 73868263 73869016 753 True 1038.000000 1038 91.689000 1 749 1 chr1B.!!$R1 748
17 TraesCS4A01G402700 chr1B 642730623 642731965 1342 True 724.500000 926 85.229000 2452 3834 2 chr1B.!!$R5 1382
18 TraesCS4A01G402700 chr1B 450448493 450449168 675 False 701.000000 701 85.903000 3176 3834 1 chr1B.!!$F1 658
19 TraesCS4A01G402700 chr1B 16852908 16853968 1060 False 564.000000 865 84.332000 2718 3834 2 chr1B.!!$F4 1116
20 TraesCS4A01G402700 chr7B 595162429 595164013 1584 False 596.000000 963 86.011000 2611 3833 3 chr7B.!!$F3 1222
21 TraesCS4A01G402700 chr5B 41955224 41956064 840 True 845.000000 845 85.256000 3018 3834 1 chr5B.!!$R1 816
22 TraesCS4A01G402700 chr4B 385968535 385969239 704 True 782.000000 782 87.147000 3147 3834 1 chr4B.!!$R1 687
23 TraesCS4A01G402700 chr6A 88803227 88803948 721 True 767.000000 767 86.345000 3018 3720 1 chr6A.!!$R1 702
24 TraesCS4A01G402700 chr3B 322727779 322728666 887 False 404.000000 549 86.512500 3015 3833 2 chr3B.!!$F1 818
25 TraesCS4A01G402700 chr1D 80553008 80553612 604 True 390.000000 390 78.930000 2422 3019 1 chr1D.!!$R1 597

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
752 9725 0.233074 CGCAAACCATCGATCATCCG 59.767 55.000 0.0 0.0 0.00 4.18 F
2246 13645 1.271543 TGCATCAACCTTCTGTCCAGG 60.272 52.381 0.0 0.0 37.45 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2250 13649 1.007842 TGTAGCACATCTCTACCCCCA 59.992 52.381 0.0 0.0 36.47 4.96 R
3804 15756 2.380084 TAATCCACAAGCACGGAGAC 57.620 50.000 0.0 0.0 33.97 3.36 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
64 9033 0.590682 TGCGCGCATATTATGTTGGG 59.409 50.000 33.09 7.79 0.00 4.12
115 9085 7.389330 CACTATATATGAGAGGCCTAGGATACG 59.611 44.444 14.75 0.00 46.39 3.06
185 9155 5.625568 ACTACAAGTCCAACTGTAACCTT 57.374 39.130 0.00 0.00 0.00 3.50
220 9190 8.495949 ACAATATTCGACACAACTCTAACAAAG 58.504 33.333 0.00 0.00 0.00 2.77
230 9200 4.772886 ACTCTAACAAAGTCCACCTTGT 57.227 40.909 0.00 0.00 32.32 3.16
367 9337 4.953579 TGCAACTTGTAGTCCCTTCTTTTT 59.046 37.500 0.00 0.00 0.00 1.94
389 9359 6.507958 TTTTGATCACAGTCAACACTCAAA 57.492 33.333 0.00 0.00 37.80 2.69
425 9395 8.358895 GTTCCTTGTTACTCTAGTTTGTACTCT 58.641 37.037 0.00 0.00 35.78 3.24
460 9431 1.414550 TCCGTCAACTCCATCACACAA 59.585 47.619 0.00 0.00 0.00 3.33
461 9432 1.531149 CCGTCAACTCCATCACACAAC 59.469 52.381 0.00 0.00 0.00 3.32
545 9517 2.086054 ACTCAACATCACCGCTCTTC 57.914 50.000 0.00 0.00 0.00 2.87
551 9523 1.347707 ACATCACCGCTCTTCCTTGAA 59.652 47.619 0.00 0.00 0.00 2.69
598 9570 4.558226 TCACCATTGCTTGTAGTCATCT 57.442 40.909 0.00 0.00 0.00 2.90
616 9588 2.596452 TCTCGAGTCAAATTCGCAGTC 58.404 47.619 13.13 0.00 37.94 3.51
639 9611 3.055819 GTCTCACCACATGTATGACCACT 60.056 47.826 0.00 0.00 0.00 4.00
670 9642 2.509336 GTCTCCATGTCCCGTGCG 60.509 66.667 0.00 0.00 0.00 5.34
671 9643 4.451150 TCTCCATGTCCCGTGCGC 62.451 66.667 0.00 0.00 0.00 6.09
707 9680 0.816825 TATTACCGCGTCGAGCCTCT 60.817 55.000 4.92 0.00 44.76 3.69
719 9692 4.459089 GCCTCTGCTGTCCCGGTC 62.459 72.222 0.00 0.00 33.53 4.79
736 9709 1.602605 TCGAGTCTCAAGGGTCGCA 60.603 57.895 0.00 0.00 32.41 5.10
738 9711 0.319555 CGAGTCTCAAGGGTCGCAAA 60.320 55.000 0.00 0.00 0.00 3.68
750 9723 2.652662 GTCGCAAACCATCGATCATC 57.347 50.000 0.00 0.00 37.06 2.92
751 9724 1.261619 GTCGCAAACCATCGATCATCC 59.738 52.381 0.00 0.00 37.06 3.51
752 9725 0.233074 CGCAAACCATCGATCATCCG 59.767 55.000 0.00 0.00 0.00 4.18
753 9726 1.581934 GCAAACCATCGATCATCCGA 58.418 50.000 0.00 0.00 43.16 4.55
881 9855 2.560542 TGCACACAACCAAACTTCAACT 59.439 40.909 0.00 0.00 0.00 3.16
966 10200 2.024655 ACCTATGTCGAAGGAGGTGGTA 60.025 50.000 8.64 0.00 40.86 3.25
1064 10299 4.090930 CCATCTTAAACAGTGGTTCGTACG 59.909 45.833 9.53 9.53 35.82 3.67
1126 10361 8.033038 TGCATACAACGGAATATAATCTACTCC 58.967 37.037 0.00 0.00 0.00 3.85
1128 10363 8.750298 CATACAACGGAATATAATCTACTCCCT 58.250 37.037 0.00 0.00 0.00 4.20
1155 10390 9.828039 CCGTTCCTAAATATAAGTCCTTTTAGT 57.172 33.333 0.00 0.00 32.35 2.24
1195 10430 4.455877 GCTACATAAACATGCCCTGGATAC 59.544 45.833 0.00 0.00 0.00 2.24
1366 10611 5.103000 CCGTCTCAAAATAAGTGTCTCGAT 58.897 41.667 0.00 0.00 0.00 3.59
1511 11018 6.707161 TCCGCTTGTAAGTTGTAACAGTTAAT 59.293 34.615 0.00 0.00 0.00 1.40
1516 11023 9.659830 CTTGTAAGTTGTAACAGTTAATTGTCC 57.340 33.333 3.87 0.00 0.00 4.02
1539 11046 4.328440 CGCTGCTAATAAGTATCTGGATGC 59.672 45.833 0.00 0.00 0.00 3.91
1542 11049 6.096673 TGCTAATAAGTATCTGGATGCGAA 57.903 37.500 0.00 0.00 0.00 4.70
1581 11088 3.921119 TTCATGCATTTCTGACACACC 57.079 42.857 0.00 0.00 0.00 4.16
1582 11089 2.161855 TCATGCATTTCTGACACACCC 58.838 47.619 0.00 0.00 0.00 4.61
1626 11140 1.412343 GGAGAACCCTTTGCTGCAAAA 59.588 47.619 25.93 11.98 32.75 2.44
1680 11223 5.871396 TGAGATCAATGGAGGTAGGTTAC 57.129 43.478 0.00 0.00 0.00 2.50
1919 13019 6.993902 ACCATAGGTTACCCAAATATGTTACG 59.006 38.462 0.00 0.00 27.29 3.18
1953 13053 3.483421 TCACAGTTCTCCGTGACTTCTA 58.517 45.455 0.00 0.00 37.23 2.10
1972 13072 8.728088 ACTTCTAAGCGAAATATGTTTGTTTG 57.272 30.769 0.00 0.00 0.00 2.93
1973 13073 8.564574 ACTTCTAAGCGAAATATGTTTGTTTGA 58.435 29.630 0.00 0.00 0.00 2.69
1974 13074 9.393249 CTTCTAAGCGAAATATGTTTGTTTGAA 57.607 29.630 0.00 0.00 0.00 2.69
1999 13343 4.694339 ACTGCTGAGGGTTAATCGTATTC 58.306 43.478 0.00 0.00 0.00 1.75
2063 13456 3.636381 GCAAAAGAAAGACCTGAAGCAG 58.364 45.455 0.00 0.00 0.00 4.24
2198 13591 3.663908 CAAAAGCGAGCTATGAAGAACG 58.336 45.455 0.00 0.00 0.00 3.95
2245 13644 1.808945 GTGCATCAACCTTCTGTCCAG 59.191 52.381 0.00 0.00 0.00 3.86
2246 13645 1.271543 TGCATCAACCTTCTGTCCAGG 60.272 52.381 0.00 0.00 37.45 4.45
2248 13647 2.704572 CATCAACCTTCTGTCCAGGAC 58.295 52.381 13.35 13.35 35.14 3.85
2249 13648 2.103153 TCAACCTTCTGTCCAGGACT 57.897 50.000 20.82 0.00 35.14 3.85
2250 13649 2.408565 TCAACCTTCTGTCCAGGACTT 58.591 47.619 20.82 2.38 35.14 3.01
2251 13650 2.104792 TCAACCTTCTGTCCAGGACTTG 59.895 50.000 20.82 14.59 35.14 3.16
2262 13662 1.344496 CCAGGACTTGGGGGTAGAGAT 60.344 57.143 0.00 0.00 43.75 2.75
2287 13689 3.301835 GCTACATAAACGTGCACGATGAG 60.302 47.826 42.94 28.99 43.02 2.90
2414 13817 5.815740 GGTGTATGTGGTACTCTGTAAATGG 59.184 44.000 0.00 0.00 34.27 3.16
2416 13819 5.486063 TGTATGTGGTACTCTGTAAATGGGT 59.514 40.000 0.00 0.00 34.27 4.51
2419 13822 2.026636 TGGTACTCTGTAAATGGGTGGC 60.027 50.000 0.00 0.00 0.00 5.01
2446 13849 6.373759 TCACTACAATATCTAAGCTCCCTCA 58.626 40.000 0.00 0.00 0.00 3.86
2481 13884 3.861797 CGCTCCGGGGCTGGTATT 61.862 66.667 26.87 0.00 0.00 1.89
2489 13894 1.208535 CGGGGCTGGTATTGTCAACTA 59.791 52.381 0.00 0.00 0.00 2.24
2640 14046 4.719026 ACACTCATCCCTATGAATGCAT 57.281 40.909 0.00 0.00 41.91 3.96
2728 14146 6.377996 TGATGAAGTTTCCAATAGTTCATGGG 59.622 38.462 9.85 0.00 42.68 4.00
2749 14167 3.324117 GAACGTCTCCTTCCACTAAACC 58.676 50.000 0.00 0.00 0.00 3.27
2788 14207 5.192927 CCTGTAATAAATCAGGGAAGTGCA 58.807 41.667 3.58 0.00 45.11 4.57
2792 14211 0.883833 AAATCAGGGAAGTGCAAGCG 59.116 50.000 0.00 0.00 0.00 4.68
2801 14220 0.443869 AAGTGCAAGCGCTAATGTCG 59.556 50.000 12.05 0.00 39.64 4.35
2802 14221 1.060937 GTGCAAGCGCTAATGTCGG 59.939 57.895 12.05 0.00 39.64 4.79
2904 14332 4.340666 TGTAACACCCTAACTTCGTGTGTA 59.659 41.667 0.00 0.00 40.50 2.90
2938 14367 8.948631 ATATGTTATGTGTCACTTACTCCTTG 57.051 34.615 4.27 0.00 0.00 3.61
2939 14368 6.413783 TGTTATGTGTCACTTACTCCTTGA 57.586 37.500 4.27 0.00 0.00 3.02
2940 14369 6.822442 TGTTATGTGTCACTTACTCCTTGAA 58.178 36.000 4.27 0.00 0.00 2.69
2941 14370 6.704493 TGTTATGTGTCACTTACTCCTTGAAC 59.296 38.462 4.27 0.00 0.00 3.18
2942 14371 5.552870 ATGTGTCACTTACTCCTTGAACT 57.447 39.130 4.27 0.00 0.00 3.01
2943 14372 6.665992 ATGTGTCACTTACTCCTTGAACTA 57.334 37.500 4.27 0.00 0.00 2.24
2944 14373 6.474140 TGTGTCACTTACTCCTTGAACTAA 57.526 37.500 4.27 0.00 0.00 2.24
2945 14374 6.880484 TGTGTCACTTACTCCTTGAACTAAA 58.120 36.000 4.27 0.00 0.00 1.85
2946 14375 7.332557 TGTGTCACTTACTCCTTGAACTAAAA 58.667 34.615 4.27 0.00 0.00 1.52
2947 14376 7.279313 TGTGTCACTTACTCCTTGAACTAAAAC 59.721 37.037 4.27 0.00 0.00 2.43
2948 14377 6.764560 TGTCACTTACTCCTTGAACTAAAACC 59.235 38.462 0.00 0.00 0.00 3.27
2949 14378 6.764560 GTCACTTACTCCTTGAACTAAAACCA 59.235 38.462 0.00 0.00 0.00 3.67
2950 14379 6.764560 TCACTTACTCCTTGAACTAAAACCAC 59.235 38.462 0.00 0.00 0.00 4.16
2951 14380 6.540914 CACTTACTCCTTGAACTAAAACCACA 59.459 38.462 0.00 0.00 0.00 4.17
2952 14381 7.066525 CACTTACTCCTTGAACTAAAACCACAA 59.933 37.037 0.00 0.00 0.00 3.33
2953 14382 5.830000 ACTCCTTGAACTAAAACCACAAC 57.170 39.130 0.00 0.00 0.00 3.32
2954 14383 5.506708 ACTCCTTGAACTAAAACCACAACT 58.493 37.500 0.00 0.00 0.00 3.16
2955 14384 5.949952 ACTCCTTGAACTAAAACCACAACTT 59.050 36.000 0.00 0.00 0.00 2.66
2956 14385 6.436218 ACTCCTTGAACTAAAACCACAACTTT 59.564 34.615 0.00 0.00 0.00 2.66
2957 14386 7.039293 ACTCCTTGAACTAAAACCACAACTTTT 60.039 33.333 0.00 0.00 0.00 2.27
2958 14387 8.350852 TCCTTGAACTAAAACCACAACTTTTA 57.649 30.769 0.00 0.00 0.00 1.52
2959 14388 8.973182 TCCTTGAACTAAAACCACAACTTTTAT 58.027 29.630 0.00 0.00 0.00 1.40
2960 14389 9.594478 CCTTGAACTAAAACCACAACTTTTATT 57.406 29.630 0.00 0.00 0.00 1.40
2972 14401 9.793259 ACCACAACTTTTATTTTAGATCAGAGA 57.207 29.630 0.00 0.00 0.00 3.10
3050 14480 7.917505 CCACAACATTTATTTTAGATCAGAGCC 59.082 37.037 0.00 0.00 0.00 4.70
3138 14975 0.112995 ATGCGGCCAACCATATCCAT 59.887 50.000 2.24 0.00 34.57 3.41
3545 15429 4.586841 TCCCCTTCTTTTGTGTGGTAATTG 59.413 41.667 0.00 0.00 0.00 2.32
3604 15538 2.080286 ATCGTCTTCGGAACTTGGTG 57.920 50.000 0.00 0.00 37.69 4.17
3606 15540 0.032952 CGTCTTCGGAACTTGGTGGA 59.967 55.000 0.00 0.00 0.00 4.02
3609 15543 1.070134 TCTTCGGAACTTGGTGGACTG 59.930 52.381 0.00 0.00 0.00 3.51
3620 15554 1.317613 GGTGGACTGCATCAACACAA 58.682 50.000 11.40 0.00 32.02 3.33
3639 15582 4.937620 CACAACATAGGTCTGCAGTACAAT 59.062 41.667 14.67 5.75 0.00 2.71
3804 15756 2.683968 TGCTTCACTGCTTAAGTACCG 58.316 47.619 4.02 0.00 36.83 4.02
3834 15786 3.821033 GCTTGTGGATTAACAACCTCACT 59.179 43.478 0.00 0.00 35.16 3.41
3841 15793 5.013079 TGGATTAACAACCTCACTCTGTCAT 59.987 40.000 0.00 0.00 0.00 3.06
3856 15808 5.819379 ACTCTGTCATGCAGTTTATACATGG 59.181 40.000 14.21 0.00 45.23 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 6775 8.822805 ACGATGTAACCTATCCCAACATAATAT 58.177 33.333 0.00 0.00 31.19 1.28
64 9033 5.506982 GGGTAGACACACGATGTAACCTATC 60.507 48.000 18.81 9.29 43.56 2.08
185 9155 5.785243 TGTGTCGAATATTGTGTACAAGGA 58.215 37.500 0.00 0.00 39.47 3.36
220 9190 4.120589 GGAGAATATTCGACAAGGTGGAC 58.879 47.826 9.78 0.00 0.00 4.02
230 9200 4.223144 TCAGGATGGTGGAGAATATTCGA 58.777 43.478 9.78 0.00 36.16 3.71
367 9337 5.414144 TGTTTGAGTGTTGACTGTGATCAAA 59.586 36.000 0.00 0.00 40.22 2.69
372 9342 5.697473 TTTTGTTTGAGTGTTGACTGTGA 57.303 34.783 0.00 0.00 30.16 3.58
425 9395 3.427573 TGACGGATACTCTGGAAGTTGA 58.572 45.455 0.00 0.00 39.55 3.18
460 9431 1.080501 CACGCAGGTCAGTGATCGT 60.081 57.895 0.00 1.57 40.56 3.73
461 9432 0.388520 TTCACGCAGGTCAGTGATCG 60.389 55.000 0.00 0.92 45.40 3.69
545 9517 3.152341 AGTTTCAGACAGGCATTCAAGG 58.848 45.455 0.00 0.00 0.00 3.61
551 9523 3.152341 CCTTCAAGTTTCAGACAGGCAT 58.848 45.455 0.00 0.00 0.00 4.40
598 9570 1.335597 ACGACTGCGAATTTGACTCGA 60.336 47.619 11.81 0.00 41.64 4.04
616 9588 2.094234 TGGTCATACATGTGGTGAGACG 60.094 50.000 9.11 0.00 36.22 4.18
639 9611 4.075793 AGACGGGCCAGGGCTCTA 62.076 66.667 13.81 0.00 39.97 2.43
685 9658 1.298863 GCTCGACGCGGTAATAGCA 60.299 57.895 12.47 0.00 34.19 3.49
707 9680 3.371063 GACTCGACCGGGACAGCA 61.371 66.667 6.32 0.00 0.00 4.41
717 9690 1.153997 GCGACCCTTGAGACTCGAC 60.154 63.158 0.00 0.00 0.00 4.20
719 9692 0.319555 TTTGCGACCCTTGAGACTCG 60.320 55.000 0.00 0.00 0.00 4.18
736 9709 2.430694 TCACTCGGATGATCGATGGTTT 59.569 45.455 0.54 0.00 38.55 3.27
738 9711 1.692411 TCACTCGGATGATCGATGGT 58.308 50.000 0.54 0.00 38.55 3.55
742 9715 4.655762 AATTCTTCACTCGGATGATCGA 57.344 40.909 0.00 0.00 37.60 3.59
743 9716 7.413475 AAATAATTCTTCACTCGGATGATCG 57.587 36.000 0.00 0.00 30.61 3.69
744 9717 9.443283 CAAAAATAATTCTTCACTCGGATGATC 57.557 33.333 0.00 0.00 30.61 2.92
745 9718 8.408601 CCAAAAATAATTCTTCACTCGGATGAT 58.591 33.333 0.00 0.00 30.61 2.45
746 9719 7.609918 TCCAAAAATAATTCTTCACTCGGATGA 59.390 33.333 0.00 0.00 0.00 2.92
748 9721 7.393234 TGTCCAAAAATAATTCTTCACTCGGAT 59.607 33.333 0.00 0.00 0.00 4.18
749 9722 6.712998 TGTCCAAAAATAATTCTTCACTCGGA 59.287 34.615 0.00 0.00 0.00 4.55
750 9723 6.908825 TGTCCAAAAATAATTCTTCACTCGG 58.091 36.000 0.00 0.00 0.00 4.63
751 9724 8.795786 TTTGTCCAAAAATAATTCTTCACTCG 57.204 30.769 0.00 0.00 0.00 4.18
752 9725 9.196552 CCTTTGTCCAAAAATAATTCTTCACTC 57.803 33.333 0.00 0.00 0.00 3.51
753 9726 8.150296 CCCTTTGTCCAAAAATAATTCTTCACT 58.850 33.333 0.00 0.00 0.00 3.41
966 10200 4.082679 GCAGTATAATCTTCGGATCGGTCT 60.083 45.833 0.00 0.00 32.82 3.85
1032 10267 5.705441 CCACTGTTTAAGATGGTGTGTATGT 59.295 40.000 0.00 0.00 0.00 2.29
1033 10268 5.705441 ACCACTGTTTAAGATGGTGTGTATG 59.295 40.000 0.00 0.00 38.27 2.39
1064 10299 3.181479 TGGTCTATGCTACATCCAACGAC 60.181 47.826 0.00 0.00 0.00 4.34
1126 10361 6.667558 AGGACTTATATTTAGGAACGGAGG 57.332 41.667 0.00 0.00 0.00 4.30
1154 10389 6.925610 TGTAGCACTTCATATTGGAATCAC 57.074 37.500 0.00 0.00 0.00 3.06
1155 10390 9.625747 TTTATGTAGCACTTCATATTGGAATCA 57.374 29.630 0.00 0.00 0.00 2.57
1195 10430 4.447724 ACTGAATTTACTACACAGCACACG 59.552 41.667 0.00 0.00 32.67 4.49
1312 10552 2.821969 CTGCTTACATGGCTGAAGGTTT 59.178 45.455 0.00 0.00 0.00 3.27
1399 10644 7.837863 TCCATTCGAAAATAAGTGTCTCTAGT 58.162 34.615 0.00 0.00 0.00 2.57
1402 10647 6.070767 TCCTCCATTCGAAAATAAGTGTCTCT 60.071 38.462 0.00 0.00 0.00 3.10
1417 10662 8.129211 GGTTTTATGAAATACTTCCTCCATTCG 58.871 37.037 0.00 0.00 0.00 3.34
1419 10664 8.893563 TGGTTTTATGAAATACTTCCTCCATT 57.106 30.769 0.00 0.00 0.00 3.16
1421 10666 6.889722 CCTGGTTTTATGAAATACTTCCTCCA 59.110 38.462 0.00 0.00 0.00 3.86
1511 11018 5.289595 CAGATACTTATTAGCAGCGGACAA 58.710 41.667 0.00 0.00 0.00 3.18
1516 11023 4.328440 GCATCCAGATACTTATTAGCAGCG 59.672 45.833 0.00 0.00 0.00 5.18
1539 11046 3.700109 TCTGTCCCCAGAGCTTCG 58.300 61.111 0.00 0.00 42.80 3.79
1581 11088 7.430441 CCGGTCCTGTAATTTTTAATATTGGG 58.570 38.462 0.00 0.00 0.00 4.12
1582 11089 7.285858 TCCCGGTCCTGTAATTTTTAATATTGG 59.714 37.037 0.00 0.00 0.00 3.16
1680 11223 7.792374 ATAGTTACACATATCACAGCCAAAG 57.208 36.000 0.00 0.00 0.00 2.77
1953 13053 7.920682 AGTTCTTCAAACAAACATATTTCGCTT 59.079 29.630 0.00 0.00 0.00 4.68
1972 13072 3.619038 CGATTAACCCTCAGCAGTTCTTC 59.381 47.826 0.00 0.00 0.00 2.87
1973 13073 3.008049 ACGATTAACCCTCAGCAGTTCTT 59.992 43.478 0.00 0.00 0.00 2.52
1974 13074 2.567615 ACGATTAACCCTCAGCAGTTCT 59.432 45.455 0.00 0.00 0.00 3.01
2063 13456 1.896220 TGATCTGTTTCACCACCTGC 58.104 50.000 0.00 0.00 0.00 4.85
2214 13613 1.083489 TTGATGCACCGAACCGATTC 58.917 50.000 0.00 0.00 0.00 2.52
2245 13644 1.486726 CACATCTCTACCCCCAAGTCC 59.513 57.143 0.00 0.00 0.00 3.85
2246 13645 1.134371 GCACATCTCTACCCCCAAGTC 60.134 57.143 0.00 0.00 0.00 3.01
2248 13647 1.207791 AGCACATCTCTACCCCCAAG 58.792 55.000 0.00 0.00 0.00 3.61
2249 13648 2.116238 GTAGCACATCTCTACCCCCAA 58.884 52.381 0.00 0.00 32.38 4.12
2250 13649 1.007842 TGTAGCACATCTCTACCCCCA 59.992 52.381 0.00 0.00 36.47 4.96
2251 13650 1.789523 TGTAGCACATCTCTACCCCC 58.210 55.000 0.00 0.00 36.47 5.40
2287 13689 5.591472 AGTGTACACCAAAAGTCCCTTAAAC 59.409 40.000 22.28 0.00 0.00 2.01
2414 13817 4.357918 AGATATTGTAGTGATGGCCACC 57.642 45.455 8.16 0.00 46.87 4.61
2416 13819 5.307976 AGCTTAGATATTGTAGTGATGGCCA 59.692 40.000 8.56 8.56 0.00 5.36
2419 13822 6.212388 AGGGAGCTTAGATATTGTAGTGATGG 59.788 42.308 0.00 0.00 0.00 3.51
2481 13884 1.617322 AGAGACGTGGCTAGTTGACA 58.383 50.000 0.00 0.00 0.00 3.58
2489 13894 6.282199 TCTAAGAAAATAAGAGACGTGGCT 57.718 37.500 0.00 0.00 0.00 4.75
2575 13981 5.587043 AGTTCAATTGTACCGTGTTCAAGAA 59.413 36.000 11.17 0.00 0.00 2.52
2594 14000 3.548214 GCTCGTATATGTGAGCGAGTTCA 60.548 47.826 13.23 0.00 47.00 3.18
2728 14146 3.324117 GGTTTAGTGGAAGGAGACGTTC 58.676 50.000 0.00 0.00 0.00 3.95
2749 14167 1.079127 AGGCCTTTCGTCGATGTGG 60.079 57.895 0.00 7.06 0.00 4.17
2781 14200 1.527793 CGACATTAGCGCTTGCACTTC 60.528 52.381 18.68 4.23 42.66 3.01
2788 14207 0.818296 AGACTCCGACATTAGCGCTT 59.182 50.000 18.68 0.00 0.00 4.68
2792 14211 1.112113 TCCCAGACTCCGACATTAGC 58.888 55.000 0.00 0.00 0.00 3.09
2801 14220 4.876752 AGTCCAGTCCCAGACTCC 57.123 61.111 0.00 0.00 41.37 3.85
2874 14301 6.991531 ACGAAGTTAGGGTGTTACACAAATAA 59.008 34.615 17.67 9.48 37.78 1.40
2881 14308 3.132646 ACACACGAAGTTAGGGTGTTACA 59.867 43.478 17.19 0.00 40.25 2.41
2904 14332 9.502091 AAGTGACACATAACATATAAGTGTTGT 57.498 29.630 8.59 0.00 42.86 3.32
2914 14342 8.129496 TCAAGGAGTAAGTGACACATAACATA 57.871 34.615 8.59 0.00 0.00 2.29
2915 14343 7.004555 TCAAGGAGTAAGTGACACATAACAT 57.995 36.000 8.59 0.00 0.00 2.71
2946 14375 9.793259 TCTCTGATCTAAAATAAAAGTTGTGGT 57.207 29.630 0.00 0.00 0.00 4.16
3004 14433 6.403049 TGTGGTTTTAGTACATGATCGACAT 58.597 36.000 0.00 0.00 40.17 3.06
3005 14434 5.785243 TGTGGTTTTAGTACATGATCGACA 58.215 37.500 0.00 0.00 0.00 4.35
3006 14435 6.146510 TGTTGTGGTTTTAGTACATGATCGAC 59.853 38.462 0.00 0.00 0.00 4.20
3007 14436 6.224584 TGTTGTGGTTTTAGTACATGATCGA 58.775 36.000 0.00 0.00 0.00 3.59
3008 14437 6.474819 TGTTGTGGTTTTAGTACATGATCG 57.525 37.500 0.00 0.00 0.00 3.69
3081 14918 4.142609 ACCAGATGTACATGATGGACAC 57.857 45.455 30.28 7.39 45.23 3.67
3138 14975 6.368791 GCGATGATACATCACTTTTATAGGCA 59.631 38.462 11.39 0.00 40.03 4.75
3604 15538 3.127548 CCTATGTTGTGTTGATGCAGTCC 59.872 47.826 0.00 0.00 0.00 3.85
3606 15540 3.753272 GACCTATGTTGTGTTGATGCAGT 59.247 43.478 0.00 0.00 0.00 4.40
3609 15543 3.426695 GCAGACCTATGTTGTGTTGATGC 60.427 47.826 0.00 0.00 0.00 3.91
3620 15554 5.683876 AGAATTGTACTGCAGACCTATGT 57.316 39.130 23.35 0.00 0.00 2.29
3639 15582 5.102870 AGGGAGAGGAAGGAGATATCAAGAA 60.103 44.000 5.32 0.00 0.00 2.52
3804 15756 2.380084 TAATCCACAAGCACGGAGAC 57.620 50.000 0.00 0.00 33.97 3.36


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

AutoCloner maintained by Alex Coulton.