Multiple sequence alignment - TraesCS3D01G402400

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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 TraesCS3D01G402400 chr3D 100.000 5275 0 0 603 5877 516869556 516864282 0.000000e+00 9742.0
1 TraesCS3D01G402400 chr3D 93.351 376 14 5 3111 3475 596798052 596797677 4.000000e-151 545.0
2 TraesCS3D01G402400 chr3D 100.000 200 0 0 1 200 516870158 516869959 2.590000e-98 370.0
3 TraesCS3D01G402400 chr3D 95.197 229 9 2 2049 2275 511426620 511426392 1.560000e-95 361.0
4 TraesCS3D01G402400 chr3D 89.236 288 24 4 2067 2350 574451547 574451831 2.610000e-93 353.0
5 TraesCS3D01G402400 chr3D 94.488 127 1 1 1446 1566 105420808 105420934 2.160000e-44 191.0
6 TraesCS3D01G402400 chr3D 90.566 53 4 1 2015 2066 352144120 352144172 1.060000e-07 69.4
7 TraesCS3D01G402400 chr6D 94.770 1434 41 16 2065 3474 471833061 471834484 0.000000e+00 2202.0
8 TraesCS3D01G402400 chr6D 93.648 1228 45 13 2271 3477 465183038 465181823 0.000000e+00 1805.0
9 TraesCS3D01G402400 chr6D 93.607 1220 42 13 2272 3474 32152752 32151552 0.000000e+00 1788.0
10 TraesCS3D01G402400 chr6D 93.509 1217 42 9 2271 3474 11040547 11039355 0.000000e+00 1775.0
11 TraesCS3D01G402400 chr6D 92.951 1220 48 15 2272 3475 27105774 27104577 0.000000e+00 1742.0
12 TraesCS3D01G402400 chr6D 92.882 1138 21 18 2340 3474 7324235 7325315 0.000000e+00 1598.0
13 TraesCS3D01G402400 chr6D 96.670 961 25 5 2279 3236 5322620 5321664 0.000000e+00 1591.0
14 TraesCS3D01G402400 chr6D 92.734 1101 32 13 2393 3481 36738775 36739839 0.000000e+00 1546.0
15 TraesCS3D01G402400 chr6D 97.741 841 13 1 1441 2275 5323855 5323015 0.000000e+00 1443.0
16 TraesCS3D01G402400 chr6D 95.290 828 22 10 2663 3474 471867574 471868400 0.000000e+00 1297.0
17 TraesCS3D01G402400 chr6D 93.810 840 28 9 2655 3474 447544073 447544908 0.000000e+00 1242.0
18 TraesCS3D01G402400 chr6D 89.106 716 53 13 2765 3477 435829368 435828675 0.000000e+00 867.0
19 TraesCS3D01G402400 chr7D 92.287 1452 34 16 2066 3474 612323023 612321607 0.000000e+00 1989.0
20 TraesCS3D01G402400 chr7D 94.676 1221 36 12 2272 3474 9819023 9820232 0.000000e+00 1868.0
21 TraesCS3D01G402400 chr7D 92.874 1263 33 22 2066 3313 30816961 30818181 0.000000e+00 1781.0
22 TraesCS3D01G402400 chr7D 73.445 418 85 25 4226 4630 65437675 65438079 3.690000e-27 134.0
23 TraesCS3D01G402400 chr7D 90.244 82 7 1 1986 2066 131468451 131468370 8.050000e-19 106.0
24 TraesCS3D01G402400 chr1D 92.216 1426 51 16 2067 3474 29819185 29817802 0.000000e+00 1964.0
25 TraesCS3D01G402400 chr1D 95.290 1189 36 13 2272 3457 380753397 380754568 0.000000e+00 1868.0
26 TraesCS3D01G402400 chr1D 93.306 1225 49 20 2272 3474 16876924 16875711 0.000000e+00 1777.0
27 TraesCS3D01G402400 chr1D 93.782 1190 51 10 2138 3313 31996635 31997815 0.000000e+00 1766.0
28 TraesCS3D01G402400 chr1D 93.176 1231 38 15 2271 3475 466416622 466415412 0.000000e+00 1766.0
29 TraesCS3D01G402400 chr1D 94.811 1137 37 8 2351 3474 66108054 66106927 0.000000e+00 1753.0
30 TraesCS3D01G402400 chr1D 93.240 1213 46 17 2272 3474 487455061 487453875 0.000000e+00 1753.0
31 TraesCS3D01G402400 chr1D 83.394 825 133 4 4059 4881 18431346 18430524 0.000000e+00 761.0
32 TraesCS3D01G402400 chr1D 83.466 756 90 25 2730 3474 13677070 13677801 0.000000e+00 671.0
33 TraesCS3D01G402400 chr1D 96.000 325 7 1 1441 1759 412433443 412433119 1.880000e-144 523.0
34 TraesCS3D01G402400 chr1D 95.636 275 6 3 2066 2335 2673217 2673490 2.510000e-118 436.0
35 TraesCS3D01G402400 chr1D 83.259 448 53 14 3037 3477 6433116 6432684 5.520000e-105 392.0
36 TraesCS3D01G402400 chr3A 91.884 1417 94 15 3793 5203 652018363 652016962 0.000000e+00 1960.0
37 TraesCS3D01G402400 chr3A 85.398 1445 148 37 2065 3478 357092139 357093551 0.000000e+00 1441.0
38 TraesCS3D01G402400 chr3A 91.242 491 24 6 719 1209 652020138 652019667 0.000000e+00 651.0
39 TraesCS3D01G402400 chr3A 78.962 732 89 40 1230 1952 652019466 652018791 6.990000e-119 438.0
40 TraesCS3D01G402400 chr3A 89.139 267 27 2 5227 5492 652016804 652016539 1.220000e-86 331.0
41 TraesCS3D01G402400 chr3A 83.776 339 31 8 5542 5860 652016066 652015732 3.440000e-77 300.0
42 TraesCS3D01G402400 chr3A 86.897 145 6 5 1084 1228 640388215 640388346 3.670000e-32 150.0
43 TraesCS3D01G402400 chr3A 92.857 98 7 0 30 127 652021622 652021525 6.140000e-30 143.0
44 TraesCS3D01G402400 chr3A 97.015 67 2 0 603 669 652020204 652020138 4.810000e-21 113.0
45 TraesCS3D01G402400 chr3A 100.000 28 0 0 1 28 717862902 717862929 1.100000e-02 52.8
46 TraesCS3D01G402400 chr5D 93.663 1294 42 12 2067 3341 63117144 63115872 0.000000e+00 1899.0
47 TraesCS3D01G402400 chr5D 97.285 221 6 0 2055 2275 507169418 507169198 5.560000e-100 375.0
48 TraesCS3D01G402400 chr5D 98.565 209 3 0 2067 2275 515576534 515576326 2.590000e-98 370.0
49 TraesCS3D01G402400 chr5D 96.818 220 6 1 2056 2275 505012805 505012587 3.350000e-97 366.0
50 TraesCS3D01G402400 chr5D 87.952 83 9 1 1983 2064 353482983 353483065 4.850000e-16 97.1
51 TraesCS3D01G402400 chr2D 95.017 1204 41 10 2272 3474 629368253 629369438 0.000000e+00 1873.0
52 TraesCS3D01G402400 chr2D 74.272 412 82 24 4229 4628 73009684 73009285 1.020000e-32 152.0
53 TraesCS3D01G402400 chr2D 75.836 269 53 12 4229 4493 73317074 73317334 6.180000e-25 126.0
54 TraesCS3D01G402400 chr2D 71.010 614 132 41 4229 4819 73312433 73313023 8.050000e-19 106.0
55 TraesCS3D01G402400 chrUn 95.217 1108 26 10 2383 3474 98637065 98638161 0.000000e+00 1727.0
56 TraesCS3D01G402400 chrUn 94.936 1086 39 7 2403 3474 102545817 102544734 0.000000e+00 1687.0
57 TraesCS3D01G402400 chrUn 91.894 1209 44 16 2272 3474 132052034 132053194 0.000000e+00 1640.0
58 TraesCS3D01G402400 chrUn 93.006 1101 37 13 2400 3474 134436841 134437927 0.000000e+00 1570.0
59 TraesCS3D01G402400 chrUn 93.371 1056 31 11 2456 3474 95814099 95815152 0.000000e+00 1526.0
60 TraesCS3D01G402400 chrUn 91.741 1114 28 26 2401 3479 89964713 89963629 0.000000e+00 1489.0
61 TraesCS3D01G402400 chrUn 93.728 861 32 8 2635 3491 33145275 33146117 0.000000e+00 1271.0
62 TraesCS3D01G402400 chrUn 93.564 808 23 9 2680 3474 26264013 26264804 0.000000e+00 1177.0
63 TraesCS3D01G402400 chrUn 83.906 727 61 16 2765 3474 8770537 8769850 1.380000e-180 643.0
64 TraesCS3D01G402400 chrUn 99.043 209 2 0 2067 2275 89965689 89965481 5.560000e-100 375.0
65 TraesCS3D01G402400 chrUn 93.023 43 1 2 1704 1745 94859848 94859889 1.770000e-05 62.1
66 TraesCS3D01G402400 chr3B 95.869 944 30 3 4000 4934 680468893 680469836 0.000000e+00 1519.0
67 TraesCS3D01G402400 chr3B 94.955 555 25 2 603 1155 680466412 680466965 0.000000e+00 867.0
68 TraesCS3D01G402400 chr3B 90.076 393 36 3 5137 5527 680474154 680474545 1.890000e-139 507.0
69 TraesCS3D01G402400 chr3B 96.949 295 8 1 1254 1548 680466969 680467262 1.470000e-135 494.0
70 TraesCS3D01G402400 chr3B 88.089 403 37 9 3075 3474 655301334 655301728 8.920000e-128 468.0
71 TraesCS3D01G402400 chr3B 92.258 155 12 0 27 181 680466162 680466316 2.760000e-53 220.0
72 TraesCS3D01G402400 chr3B 78.358 134 20 2 1690 1814 749494027 749494160 1.760000e-10 78.7
73 TraesCS3D01G402400 chr3B 90.566 53 4 1 2015 2066 450843955 450844007 1.060000e-07 69.4
74 TraesCS3D01G402400 chr3B 100.000 36 0 0 165 200 680466308 680466343 3.800000e-07 67.6
75 TraesCS3D01G402400 chr7B 83.063 1482 108 46 2066 3474 59683384 59684795 0.000000e+00 1214.0
76 TraesCS3D01G402400 chr7B 86.920 711 54 13 2769 3474 608209292 608209968 0.000000e+00 761.0
77 TraesCS3D01G402400 chr7B 72.771 415 87 25 4229 4630 7038018 7037617 3.720000e-22 117.0
78 TraesCS3D01G402400 chr4D 96.444 675 11 6 2811 3475 418850420 418849749 0.000000e+00 1101.0
79 TraesCS3D01G402400 chr4B 87.268 809 57 23 2679 3474 20283378 20284153 0.000000e+00 881.0
80 TraesCS3D01G402400 chr1A 83.090 822 133 6 4059 4877 20417120 20416302 0.000000e+00 743.0
81 TraesCS3D01G402400 chr1A 87.374 594 57 9 2887 3474 572733151 572732570 0.000000e+00 665.0
82 TraesCS3D01G402400 chr1A 87.205 594 58 9 2887 3474 572736447 572735866 0.000000e+00 660.0
83 TraesCS3D01G402400 chr1B 81.585 820 145 6 4059 4875 27236985 27236169 0.000000e+00 673.0
84 TraesCS3D01G402400 chr1B 90.566 53 4 1 2015 2066 560219635 560219687 1.060000e-07 69.4
85 TraesCS3D01G402400 chr1B 92.500 40 1 2 1 40 322488032 322487995 8.230000e-04 56.5
86 TraesCS3D01G402400 chr5A 85.671 663 41 13 2765 3417 584963378 584963996 0.000000e+00 649.0
87 TraesCS3D01G402400 chr5A 84.286 70 9 2 1683 1751 309694139 309694071 3.800000e-07 67.6
88 TraesCS3D01G402400 chr7A 73.445 418 85 25 4226 4630 69568620 69569024 3.690000e-27 134.0
89 TraesCS3D01G402400 chr7A 84.722 72 11 0 1681 1752 171416878 171416949 8.170000e-09 73.1
90 TraesCS3D01G402400 chr2B 73.558 416 82 27 4229 4630 110417184 110416783 3.690000e-27 134.0
91 TraesCS3D01G402400 chr2B 74.060 266 59 10 4230 4492 111041404 111041146 3.750000e-17 100.0
92 TraesCS3D01G402400 chr2B 94.340 53 2 1 2015 2066 353585103 353585155 4.880000e-11 80.5
93 TraesCS3D01G402400 chr2B 100.000 28 0 0 1 28 748491967 748491940 1.100000e-02 52.8
94 TraesCS3D01G402400 chr4A 92.391 92 5 2 1976 2066 625404870 625404780 4.780000e-26 130.0
95 TraesCS3D01G402400 chr4A 87.500 72 9 0 1681 1752 599357455 599357384 3.770000e-12 84.2
96 TraesCS3D01G402400 chr5B 91.566 83 4 3 1983 2062 708237947 708237865 1.730000e-20 111.0
97 TraesCS3D01G402400 chr5B 86.957 69 7 2 1681 1748 131015924 131015991 6.320000e-10 76.8
98 TraesCS3D01G402400 chr6B 80.412 97 18 1 5585 5681 190655245 190655340 8.170000e-09 73.1


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G402400 chr3D 516864282 516870158 5876 True 5056.000000 9742 100.000000 1 5877 2 chr3D.!!$R3 5876
1 TraesCS3D01G402400 chr6D 471833061 471834484 1423 False 2202.000000 2202 94.770000 2065 3474 1 chr6D.!!$F4 1409
2 TraesCS3D01G402400 chr6D 465181823 465183038 1215 True 1805.000000 1805 93.648000 2271 3477 1 chr6D.!!$R5 1206
3 TraesCS3D01G402400 chr6D 32151552 32152752 1200 True 1788.000000 1788 93.607000 2272 3474 1 chr6D.!!$R3 1202
4 TraesCS3D01G402400 chr6D 11039355 11040547 1192 True 1775.000000 1775 93.509000 2271 3474 1 chr6D.!!$R1 1203
5 TraesCS3D01G402400 chr6D 27104577 27105774 1197 True 1742.000000 1742 92.951000 2272 3475 1 chr6D.!!$R2 1203
6 TraesCS3D01G402400 chr6D 7324235 7325315 1080 False 1598.000000 1598 92.882000 2340 3474 1 chr6D.!!$F1 1134
7 TraesCS3D01G402400 chr6D 36738775 36739839 1064 False 1546.000000 1546 92.734000 2393 3481 1 chr6D.!!$F2 1088
8 TraesCS3D01G402400 chr6D 5321664 5323855 2191 True 1517.000000 1591 97.205500 1441 3236 2 chr6D.!!$R6 1795
9 TraesCS3D01G402400 chr6D 471867574 471868400 826 False 1297.000000 1297 95.290000 2663 3474 1 chr6D.!!$F5 811
10 TraesCS3D01G402400 chr6D 447544073 447544908 835 False 1242.000000 1242 93.810000 2655 3474 1 chr6D.!!$F3 819
11 TraesCS3D01G402400 chr6D 435828675 435829368 693 True 867.000000 867 89.106000 2765 3477 1 chr6D.!!$R4 712
12 TraesCS3D01G402400 chr7D 612321607 612323023 1416 True 1989.000000 1989 92.287000 2066 3474 1 chr7D.!!$R2 1408
13 TraesCS3D01G402400 chr7D 9819023 9820232 1209 False 1868.000000 1868 94.676000 2272 3474 1 chr7D.!!$F1 1202
14 TraesCS3D01G402400 chr7D 30816961 30818181 1220 False 1781.000000 1781 92.874000 2066 3313 1 chr7D.!!$F2 1247
15 TraesCS3D01G402400 chr1D 29817802 29819185 1383 True 1964.000000 1964 92.216000 2067 3474 1 chr1D.!!$R4 1407
16 TraesCS3D01G402400 chr1D 380753397 380754568 1171 False 1868.000000 1868 95.290000 2272 3457 1 chr1D.!!$F4 1185
17 TraesCS3D01G402400 chr1D 16875711 16876924 1213 True 1777.000000 1777 93.306000 2272 3474 1 chr1D.!!$R2 1202
18 TraesCS3D01G402400 chr1D 31996635 31997815 1180 False 1766.000000 1766 93.782000 2138 3313 1 chr1D.!!$F3 1175
19 TraesCS3D01G402400 chr1D 466415412 466416622 1210 True 1766.000000 1766 93.176000 2271 3475 1 chr1D.!!$R7 1204
20 TraesCS3D01G402400 chr1D 66106927 66108054 1127 True 1753.000000 1753 94.811000 2351 3474 1 chr1D.!!$R5 1123
21 TraesCS3D01G402400 chr1D 487453875 487455061 1186 True 1753.000000 1753 93.240000 2272 3474 1 chr1D.!!$R8 1202
22 TraesCS3D01G402400 chr1D 18430524 18431346 822 True 761.000000 761 83.394000 4059 4881 1 chr1D.!!$R3 822
23 TraesCS3D01G402400 chr1D 13677070 13677801 731 False 671.000000 671 83.466000 2730 3474 1 chr1D.!!$F2 744
24 TraesCS3D01G402400 chr3A 357092139 357093551 1412 False 1441.000000 1441 85.398000 2065 3478 1 chr3A.!!$F1 1413
25 TraesCS3D01G402400 chr3A 652015732 652021622 5890 True 562.285714 1960 89.267857 30 5860 7 chr3A.!!$R1 5830
26 TraesCS3D01G402400 chr5D 63115872 63117144 1272 True 1899.000000 1899 93.663000 2067 3341 1 chr5D.!!$R1 1274
27 TraesCS3D01G402400 chr2D 629368253 629369438 1185 False 1873.000000 1873 95.017000 2272 3474 1 chr2D.!!$F3 1202
28 TraesCS3D01G402400 chrUn 98637065 98638161 1096 False 1727.000000 1727 95.217000 2383 3474 1 chrUn.!!$F5 1091
29 TraesCS3D01G402400 chrUn 102544734 102545817 1083 True 1687.000000 1687 94.936000 2403 3474 1 chrUn.!!$R2 1071
30 TraesCS3D01G402400 chrUn 132052034 132053194 1160 False 1640.000000 1640 91.894000 2272 3474 1 chrUn.!!$F6 1202
31 TraesCS3D01G402400 chrUn 134436841 134437927 1086 False 1570.000000 1570 93.006000 2400 3474 1 chrUn.!!$F7 1074
32 TraesCS3D01G402400 chrUn 95814099 95815152 1053 False 1526.000000 1526 93.371000 2456 3474 1 chrUn.!!$F4 1018
33 TraesCS3D01G402400 chrUn 33145275 33146117 842 False 1271.000000 1271 93.728000 2635 3491 1 chrUn.!!$F2 856
34 TraesCS3D01G402400 chrUn 26264013 26264804 791 False 1177.000000 1177 93.564000 2680 3474 1 chrUn.!!$F1 794
35 TraesCS3D01G402400 chrUn 89963629 89965689 2060 True 932.000000 1489 95.392000 2067 3479 2 chrUn.!!$R3 1412
36 TraesCS3D01G402400 chrUn 8769850 8770537 687 True 643.000000 643 83.906000 2765 3474 1 chrUn.!!$R1 709
37 TraesCS3D01G402400 chr3B 680466162 680469836 3674 False 633.520000 1519 96.006200 27 4934 5 chr3B.!!$F5 4907
38 TraesCS3D01G402400 chr7B 59683384 59684795 1411 False 1214.000000 1214 83.063000 2066 3474 1 chr7B.!!$F1 1408
39 TraesCS3D01G402400 chr7B 608209292 608209968 676 False 761.000000 761 86.920000 2769 3474 1 chr7B.!!$F2 705
40 TraesCS3D01G402400 chr4D 418849749 418850420 671 True 1101.000000 1101 96.444000 2811 3475 1 chr4D.!!$R1 664
41 TraesCS3D01G402400 chr4B 20283378 20284153 775 False 881.000000 881 87.268000 2679 3474 1 chr4B.!!$F1 795
42 TraesCS3D01G402400 chr1A 20416302 20417120 818 True 743.000000 743 83.090000 4059 4877 1 chr1A.!!$R1 818
43 TraesCS3D01G402400 chr1A 572732570 572736447 3877 True 662.500000 665 87.289500 2887 3474 2 chr1A.!!$R2 587
44 TraesCS3D01G402400 chr1B 27236169 27236985 816 True 673.000000 673 81.585000 4059 4875 1 chr1B.!!$R1 816
45 TraesCS3D01G402400 chr5A 584963378 584963996 618 False 649.000000 649 85.671000 2765 3417 1 chr5A.!!$F1 652

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
819 1988 1.421268 TCCACAGGTGCTCTTGAACAT 59.579 47.619 4.78 0.00 0.0 2.71 F
1443 2800 0.037590 CACCGGAATCCCAAACCTCA 59.962 55.000 9.46 0.00 0.0 3.86 F
1765 3183 0.257328 TGACAACTTGAACCCTGGCA 59.743 50.000 0.00 0.00 0.0 4.92 F
2059 3953 2.351418 CTGCGACGCTTATTTTGGATCA 59.649 45.455 22.08 0.00 0.0 2.92 F
3837 10524 4.075682 TGATTTCGCACCATTGAACCTAA 58.924 39.130 0.00 0.00 0.0 2.69 F
4662 11379 1.073216 CAGTTCTCGCAGCTGTACCG 61.073 60.000 16.64 10.78 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1736 3153 0.583438 CAAGTTGTCACTGGTGCTCG 59.417 55.0 0.00 0.0 31.60 5.03 R
2632 5647 7.683437 TTTTGAAAATGTTTAACGGGGTTTT 57.317 28.0 0.00 0.0 0.00 2.43 R
3489 10065 6.281405 TGTTCAGGTTGAAAGAGAGTAAGAC 58.719 40.0 0.00 0.0 38.22 3.01 R
4057 10774 0.324738 TCTTCCCCTCGAGTCTGCAT 60.325 55.0 12.31 0.0 0.00 3.96 R
4768 11485 0.248907 CGTACTTGGCATCGTCGGAT 60.249 55.0 0.00 0.0 0.00 4.18 R
5499 12360 0.460284 CACTGACCGCCGCTTAGATT 60.460 55.0 0.00 0.0 0.00 2.40 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 4.725790 AGAGGGAGCATGTTAAAATTGC 57.274 40.909 0.00 0.00 36.63 3.56
67 68 4.697352 GGTATGAGAGTGAACTTGCACATT 59.303 41.667 0.00 0.00 41.19 2.71
70 71 5.173774 TGAGAGTGAACTTGCACATTTTC 57.826 39.130 0.00 0.00 41.19 2.29
130 1291 9.855021 AGAACAAGTATTTGCACCATAATAAAC 57.145 29.630 0.00 0.00 37.85 2.01
134 1295 9.853555 CAAGTATTTGCACCATAATAAACTTCA 57.146 29.630 0.00 0.00 0.00 3.02
678 1847 1.923850 TCCCTATCGGCTAGCTATCCT 59.076 52.381 15.72 0.00 0.00 3.24
717 1886 8.677300 GCCTTCTTATTGTTATTTGTCAGATCA 58.323 33.333 0.00 0.00 0.00 2.92
753 1922 4.100189 GCTAGCTTCATCCTTCCTTGACTA 59.900 45.833 7.70 0.00 0.00 2.59
794 1963 8.422973 CAGAAATCTCTGTGATTCTTCCTAAG 57.577 38.462 5.52 0.00 43.99 2.18
819 1988 1.421268 TCCACAGGTGCTCTTGAACAT 59.579 47.619 4.78 0.00 0.00 2.71
820 1989 2.637382 TCCACAGGTGCTCTTGAACATA 59.363 45.455 4.78 0.00 0.00 2.29
848 2017 7.483375 CGATTATGATCTCTCCTGTAATTCGTC 59.517 40.741 0.00 0.00 0.00 4.20
849 2018 4.553756 TGATCTCTCCTGTAATTCGTCG 57.446 45.455 0.00 0.00 0.00 5.12
921 2090 6.713520 TGAAGTATGCATGTTTTGTTTTTGC 58.286 32.000 10.16 0.00 0.00 3.68
928 2097 3.921969 TGTTTTGTTTTTGCGATGCAG 57.078 38.095 0.00 0.00 40.61 4.41
950 2119 2.120232 CAACGATCGGCTGTATCACTC 58.880 52.381 20.98 0.00 0.00 3.51
971 2140 5.042463 TCATGGTAGTTGTTTCTTGTCCA 57.958 39.130 0.00 0.00 0.00 4.02
1172 2343 2.445145 TCTCCAGGGTGTTTTGATTCCA 59.555 45.455 0.00 0.00 0.00 3.53
1209 2380 4.801164 TGATCATGTCATCCTGAGAGAGA 58.199 43.478 0.00 0.00 0.00 3.10
1210 2381 5.395611 TGATCATGTCATCCTGAGAGAGAT 58.604 41.667 0.00 0.00 0.00 2.75
1211 2382 6.550163 TGATCATGTCATCCTGAGAGAGATA 58.450 40.000 0.00 0.00 0.00 1.98
1212 2383 6.660094 TGATCATGTCATCCTGAGAGAGATAG 59.340 42.308 0.00 0.00 0.00 2.08
1213 2384 6.198237 TCATGTCATCCTGAGAGAGATAGA 57.802 41.667 0.00 0.00 0.00 1.98
1214 2385 6.792424 TCATGTCATCCTGAGAGAGATAGAT 58.208 40.000 0.00 0.00 0.00 1.98
1215 2386 7.926705 TCATGTCATCCTGAGAGAGATAGATA 58.073 38.462 0.00 0.00 0.00 1.98
1216 2387 8.048514 TCATGTCATCCTGAGAGAGATAGATAG 58.951 40.741 0.00 0.00 0.00 2.08
1217 2388 7.566658 TGTCATCCTGAGAGAGATAGATAGA 57.433 40.000 0.00 0.00 0.00 1.98
1218 2389 8.161640 TGTCATCCTGAGAGAGATAGATAGAT 57.838 38.462 0.00 0.00 0.00 1.98
1219 2390 9.278011 TGTCATCCTGAGAGAGATAGATAGATA 57.722 37.037 0.00 0.00 0.00 1.98
1220 2391 9.770097 GTCATCCTGAGAGAGATAGATAGATAG 57.230 40.741 0.00 0.00 0.00 2.08
1221 2392 9.728100 TCATCCTGAGAGAGATAGATAGATAGA 57.272 37.037 0.00 0.00 0.00 1.98
1239 2596 7.969690 AGATAGATAGAGAGAGAGAGAGAGG 57.030 44.000 0.00 0.00 0.00 3.69
1240 2597 6.900186 AGATAGATAGAGAGAGAGAGAGAGGG 59.100 46.154 0.00 0.00 0.00 4.30
1241 2598 4.171234 AGATAGAGAGAGAGAGAGAGGGG 58.829 52.174 0.00 0.00 0.00 4.79
1242 2599 1.522900 AGAGAGAGAGAGAGAGGGGG 58.477 60.000 0.00 0.00 0.00 5.40
1300 2657 1.229428 CCAGCGATGTTGTCACTTGT 58.771 50.000 0.00 0.00 0.00 3.16
1404 2761 2.359975 CGGGAGTTCCAGCAACCC 60.360 66.667 0.00 0.00 35.28 4.11
1443 2800 0.037590 CACCGGAATCCCAAACCTCA 59.962 55.000 9.46 0.00 0.00 3.86
1505 2864 2.936202 TCAGCAAAATAGGATGCCCTC 58.064 47.619 0.00 0.00 43.14 4.30
1573 2965 2.979240 AGAAAACCTCAGCGAGATTCC 58.021 47.619 7.07 0.00 0.00 3.01
1658 3051 4.566545 TTCACCCTTATAAATGCATGCG 57.433 40.909 14.09 0.00 0.00 4.73
1765 3183 0.257328 TGACAACTTGAACCCTGGCA 59.743 50.000 0.00 0.00 0.00 4.92
2059 3953 2.351418 CTGCGACGCTTATTTTGGATCA 59.649 45.455 22.08 0.00 0.00 2.92
2158 4066 5.376625 GACTAATATGAGCATTGGTCCCAA 58.623 41.667 12.99 0.39 39.30 4.12
2529 5537 7.387673 TCGACTTTATTTGCAAAATCTCTCTGA 59.612 33.333 17.19 5.94 0.00 3.27
2632 5647 6.057321 AGTTACATCCGAATTTAACTGGGA 57.943 37.500 0.00 0.00 37.12 4.37
3489 10065 8.693120 TCTACTAGTGGGAGTATATGTTCTTG 57.307 38.462 5.39 0.00 31.56 3.02
3514 10090 6.761714 GTCTTACTCTCTTTCAACCTGAACAA 59.238 38.462 0.00 0.00 35.89 2.83
3590 10166 6.978343 TCCACTCGTTCCTTTATGTTATTG 57.022 37.500 0.00 0.00 0.00 1.90
3653 10234 7.984422 TGAGAGACATGTGTGAATTTTATGT 57.016 32.000 1.15 0.00 34.91 2.29
3830 10514 4.880886 TGTCTATGATTTCGCACCATTG 57.119 40.909 0.00 0.00 0.00 2.82
3837 10524 4.075682 TGATTTCGCACCATTGAACCTAA 58.924 39.130 0.00 0.00 0.00 2.69
3839 10526 5.184864 TGATTTCGCACCATTGAACCTAAAT 59.815 36.000 0.00 0.00 0.00 1.40
3840 10527 5.461032 TTTCGCACCATTGAACCTAAATT 57.539 34.783 0.00 0.00 0.00 1.82
3841 10528 6.576662 TTTCGCACCATTGAACCTAAATTA 57.423 33.333 0.00 0.00 0.00 1.40
3844 10531 7.164230 TCGCACCATTGAACCTAAATTATTT 57.836 32.000 0.00 0.00 0.00 1.40
3910 10597 4.335416 ACGATTTATTGGGCTCATATGGG 58.665 43.478 2.13 0.00 0.00 4.00
4050 10767 4.650754 AATCTCGATAAGTTGCTACCGT 57.349 40.909 0.00 0.00 0.00 4.83
4057 10774 5.297527 TCGATAAGTTGCTACCGTCTCATTA 59.702 40.000 0.00 0.00 0.00 1.90
4369 11086 2.191641 GTGGCCAGCCTGGATCTC 59.808 66.667 16.85 2.91 40.96 2.75
4480 11197 1.597302 CTCCATCCTCTGCATGGCG 60.597 63.158 0.00 0.00 40.77 5.69
4567 11284 4.680237 CTGGTCAAGACGGCCGCA 62.680 66.667 28.58 12.45 0.00 5.69
4662 11379 1.073216 CAGTTCTCGCAGCTGTACCG 61.073 60.000 16.64 10.78 0.00 4.02
4804 11521 2.943978 CGTCTCCGGCCAGAACCTT 61.944 63.158 2.24 0.00 0.00 3.50
4896 11621 4.030216 TGAGTGATTGCCCACTACTGATA 58.970 43.478 3.89 0.00 46.45 2.15
4900 11625 4.023707 GTGATTGCCCACTACTGATATTGC 60.024 45.833 0.00 0.00 34.38 3.56
4940 11666 3.073209 TGGGATGTACAAAACTGCCTGTA 59.927 43.478 0.00 0.00 0.00 2.74
4944 11670 5.163652 GGATGTACAAAACTGCCTGTATTCC 60.164 44.000 0.00 0.00 31.57 3.01
4949 11675 3.788227 AAACTGCCTGTATTCCTGTGA 57.212 42.857 0.00 0.00 0.00 3.58
4951 11677 3.788227 ACTGCCTGTATTCCTGTGAAA 57.212 42.857 0.00 0.00 33.32 2.69
4953 11679 2.749621 CTGCCTGTATTCCTGTGAAACC 59.250 50.000 0.00 0.00 34.36 3.27
4957 11683 3.191371 CCTGTATTCCTGTGAAACCTTGC 59.809 47.826 0.00 0.00 34.36 4.01
4964 11690 3.896888 TCCTGTGAAACCTTGCAATGAAT 59.103 39.130 8.84 0.00 34.36 2.57
4965 11691 5.076182 TCCTGTGAAACCTTGCAATGAATA 58.924 37.500 8.84 0.00 34.36 1.75
4981 11707 4.046938 TGAATAGTGGATTCGACAGCTC 57.953 45.455 1.54 0.00 46.15 4.09
4982 11708 3.447229 TGAATAGTGGATTCGACAGCTCA 59.553 43.478 1.54 0.00 46.15 4.26
5003 11729 2.499205 CATCTCCAACGCGGCCTA 59.501 61.111 12.47 0.00 33.14 3.93
5004 11730 1.883084 CATCTCCAACGCGGCCTAC 60.883 63.158 12.47 0.00 33.14 3.18
5008 11734 1.227883 TCCAACGCGGCCTACAAAA 60.228 52.632 12.47 0.00 33.14 2.44
5009 11735 0.606944 TCCAACGCGGCCTACAAAAT 60.607 50.000 12.47 0.00 33.14 1.82
5010 11736 0.455972 CCAACGCGGCCTACAAAATG 60.456 55.000 12.47 0.00 0.00 2.32
5037 11763 9.561069 GATATTGTATTTGTCTATGGACTGGTT 57.439 33.333 10.82 0.00 42.54 3.67
5038 11764 7.630242 ATTGTATTTGTCTATGGACTGGTTG 57.370 36.000 10.82 0.00 42.54 3.77
5056 11782 2.062971 TGGGACCAGTCTACGGATAC 57.937 55.000 0.00 0.00 0.00 2.24
5059 11785 3.145286 GGGACCAGTCTACGGATACTAC 58.855 54.545 0.00 0.00 0.00 2.73
5065 11791 5.921004 CAGTCTACGGATACTACTGGTAC 57.079 47.826 0.00 0.00 35.12 3.34
5066 11792 5.363101 CAGTCTACGGATACTACTGGTACA 58.637 45.833 0.00 0.00 35.12 2.90
5080 11806 0.179081 GGTACAGGAGCCGACCATTC 60.179 60.000 0.00 0.00 31.89 2.67
5082 11808 1.066430 GTACAGGAGCCGACCATTCAA 60.066 52.381 0.00 0.00 0.00 2.69
5085 11811 1.749258 GGAGCCGACCATTCAACCC 60.749 63.158 0.00 0.00 0.00 4.11
5088 11814 1.303317 GCCGACCATTCAACCCTGT 60.303 57.895 0.00 0.00 0.00 4.00
5089 11815 1.305930 GCCGACCATTCAACCCTGTC 61.306 60.000 0.00 0.00 0.00 3.51
5091 11817 1.271379 CCGACCATTCAACCCTGTCTT 60.271 52.381 0.00 0.00 0.00 3.01
5092 11818 2.076863 CGACCATTCAACCCTGTCTTC 58.923 52.381 0.00 0.00 0.00 2.87
5097 11823 5.070685 ACCATTCAACCCTGTCTTCTTAAC 58.929 41.667 0.00 0.00 0.00 2.01
5099 11825 2.762745 TCAACCCTGTCTTCTTAACGC 58.237 47.619 0.00 0.00 0.00 4.84
5101 11827 3.139077 CAACCCTGTCTTCTTAACGCTT 58.861 45.455 0.00 0.00 0.00 4.68
5102 11828 2.767505 ACCCTGTCTTCTTAACGCTTG 58.232 47.619 0.00 0.00 0.00 4.01
5109 11835 6.268825 TGTCTTCTTAACGCTTGTCTCTAT 57.731 37.500 0.00 0.00 0.00 1.98
5136 11862 8.514330 TTTTTCTAAGTCTGGAGCACTAAAAA 57.486 30.769 0.00 0.00 0.00 1.94
5163 11889 3.950397 AGCATATCAAACCTTCCACGAA 58.050 40.909 0.00 0.00 0.00 3.85
5230 12081 8.702163 ACAGTTCAATTGAAGTTTCGAAATTT 57.298 26.923 23.08 17.34 35.65 1.82
5263 12123 0.322975 ACTCCGGCTATGATCCATGC 59.677 55.000 0.00 0.00 0.00 4.06
5264 12124 0.738762 CTCCGGCTATGATCCATGCG 60.739 60.000 0.00 0.00 0.00 4.73
5281 12141 5.095490 CCATGCGACTGGAATTTTCTAAAC 58.905 41.667 0.00 0.00 38.69 2.01
5289 12149 9.382244 CGACTGGAATTTTCTAAACTTTAAGTG 57.618 33.333 0.00 0.00 0.00 3.16
5333 12193 4.670896 AAAATCCAACAACCTCCACTTG 57.329 40.909 0.00 0.00 0.00 3.16
5339 12199 2.525105 ACAACCTCCACTTGTTGGTT 57.475 45.000 7.23 0.00 46.97 3.67
5342 12202 2.052782 ACCTCCACTTGTTGGTTCAC 57.947 50.000 0.00 0.00 46.97 3.18
5354 12214 0.250295 TGGTTCACCTCTTCAAGCGG 60.250 55.000 0.00 0.00 36.82 5.52
5361 12221 1.294659 CCTCTTCAAGCGGCACTGTC 61.295 60.000 1.45 0.00 0.00 3.51
5374 12234 2.612972 GGCACTGTCGATCTTTTCCTCA 60.613 50.000 0.00 0.00 0.00 3.86
5392 12252 4.287067 TCCTCAAACTTTCTGTAGAGCCAT 59.713 41.667 0.00 0.00 32.76 4.40
5393 12253 5.483937 TCCTCAAACTTTCTGTAGAGCCATA 59.516 40.000 0.00 0.00 32.76 2.74
5421 12282 2.364317 CCGCCTCCCTTCCTCTCA 60.364 66.667 0.00 0.00 0.00 3.27
5426 12287 2.821245 CGCCTCCCTTCCTCTCATCTAT 60.821 54.545 0.00 0.00 0.00 1.98
5449 12310 3.239861 CCTCTGGCAAGGTCTTGTC 57.760 57.895 8.24 8.24 44.84 3.18
5451 12312 0.397941 CTCTGGCAAGGTCTTGTCCA 59.602 55.000 18.53 18.53 44.04 4.02
5460 12321 1.351350 AGGTCTTGTCCAAGCCCTTAC 59.649 52.381 3.84 0.00 43.61 2.34
5461 12322 1.439679 GTCTTGTCCAAGCCCTTACG 58.560 55.000 2.09 0.00 38.28 3.18
5485 12346 2.522436 TCCGTCCCCGTCTTGTGT 60.522 61.111 0.00 0.00 0.00 3.72
5492 12353 2.030562 CCGTCTTGTGTTCCGGCT 59.969 61.111 0.00 0.00 33.20 5.52
5493 12354 2.027625 CCGTCTTGTGTTCCGGCTC 61.028 63.158 0.00 0.00 33.20 4.70
5494 12355 2.027625 CGTCTTGTGTTCCGGCTCC 61.028 63.158 0.00 0.00 0.00 4.70
5495 12356 1.070786 GTCTTGTGTTCCGGCTCCA 59.929 57.895 0.00 0.00 0.00 3.86
5496 12357 0.321653 GTCTTGTGTTCCGGCTCCAT 60.322 55.000 0.00 0.00 0.00 3.41
5497 12358 0.036388 TCTTGTGTTCCGGCTCCATC 60.036 55.000 0.00 0.00 0.00 3.51
5498 12359 0.036010 CTTGTGTTCCGGCTCCATCT 60.036 55.000 0.00 0.00 0.00 2.90
5499 12360 1.207089 CTTGTGTTCCGGCTCCATCTA 59.793 52.381 0.00 0.00 0.00 1.98
5500 12361 1.271856 TGTGTTCCGGCTCCATCTAA 58.728 50.000 0.00 0.00 0.00 2.10
5501 12362 1.837439 TGTGTTCCGGCTCCATCTAAT 59.163 47.619 0.00 0.00 0.00 1.73
5502 12363 2.158957 TGTGTTCCGGCTCCATCTAATC 60.159 50.000 0.00 0.00 0.00 1.75
5503 12364 2.103263 GTGTTCCGGCTCCATCTAATCT 59.897 50.000 0.00 0.00 0.00 2.40
5507 12368 2.563179 TCCGGCTCCATCTAATCTAAGC 59.437 50.000 0.00 0.00 0.00 3.09
5510 12371 2.342179 GCTCCATCTAATCTAAGCGGC 58.658 52.381 0.00 0.00 0.00 6.53
5511 12372 2.600731 CTCCATCTAATCTAAGCGGCG 58.399 52.381 0.51 0.51 0.00 6.46
5512 12373 1.272490 TCCATCTAATCTAAGCGGCGG 59.728 52.381 9.78 0.00 0.00 6.13
5513 12374 1.000955 CCATCTAATCTAAGCGGCGGT 59.999 52.381 5.44 5.44 0.00 5.68
5514 12375 2.329379 CATCTAATCTAAGCGGCGGTC 58.671 52.381 13.68 0.00 0.00 4.79
5515 12376 1.395635 TCTAATCTAAGCGGCGGTCA 58.604 50.000 13.68 0.00 0.00 4.02
5516 12377 1.337071 TCTAATCTAAGCGGCGGTCAG 59.663 52.381 13.68 7.72 0.00 3.51
5517 12378 1.067212 CTAATCTAAGCGGCGGTCAGT 59.933 52.381 13.68 0.00 0.00 3.41
5519 12380 2.907897 ATCTAAGCGGCGGTCAGTGC 62.908 60.000 13.68 0.00 0.00 4.40
5520 12381 3.932580 CTAAGCGGCGGTCAGTGCA 62.933 63.158 13.68 0.00 0.00 4.57
5525 12386 2.280797 GGCGGTCAGTGCAGAACA 60.281 61.111 0.00 0.00 0.00 3.18
5592 12876 3.418047 AGAAAATACGGTCCTGTTTGGG 58.582 45.455 0.00 0.00 36.20 4.12
5608 12892 6.287589 TGTTTGGGTTGTGATTAACTTTGT 57.712 33.333 0.00 0.00 0.00 2.83
5632 12916 5.931146 TCACATGTTGCCACATTATTTTTCC 59.069 36.000 0.00 0.00 41.16 3.13
5646 12930 9.470399 ACATTATTTTTCCCGAACTTACCTTAT 57.530 29.630 0.00 0.00 0.00 1.73
5669 12953 9.601217 TTATTTGAGGTGCTCTAATTCTTAGTC 57.399 33.333 0.00 0.00 37.23 2.59
5676 12960 6.651225 GGTGCTCTAATTCTTAGTCACACTTT 59.349 38.462 16.08 0.00 38.39 2.66
5685 12969 2.464157 AGTCACACTTTAGCTGCCTC 57.536 50.000 0.00 0.00 0.00 4.70
5687 12971 2.304180 AGTCACACTTTAGCTGCCTCAT 59.696 45.455 0.00 0.00 0.00 2.90
5688 12972 3.515502 AGTCACACTTTAGCTGCCTCATA 59.484 43.478 0.00 0.00 0.00 2.15
5689 12973 3.619038 GTCACACTTTAGCTGCCTCATAC 59.381 47.826 0.00 0.00 0.00 2.39
5690 12974 3.515502 TCACACTTTAGCTGCCTCATACT 59.484 43.478 0.00 0.00 0.00 2.12
5691 12975 4.020218 TCACACTTTAGCTGCCTCATACTT 60.020 41.667 0.00 0.00 0.00 2.24
5717 13021 1.329171 TGGCATGTGGGGCTTATTGC 61.329 55.000 0.00 0.00 41.94 3.56
5721 13025 2.313317 CATGTGGGGCTTATTGCTCAT 58.687 47.619 0.00 0.00 46.01 2.90
5722 13026 3.489355 CATGTGGGGCTTATTGCTCATA 58.511 45.455 0.00 0.00 46.01 2.15
5723 13027 3.660970 TGTGGGGCTTATTGCTCATAA 57.339 42.857 0.00 0.00 46.01 1.90
5730 13034 6.383726 TGGGGCTTATTGCTCATAAAAAGATT 59.616 34.615 0.00 0.00 46.01 2.40
5735 13039 9.793252 GCTTATTGCTCATAAAAAGATTCTTGA 57.207 29.630 0.00 0.00 38.95 3.02
5741 13045 8.454106 TGCTCATAAAAAGATTCTTGACTTAGC 58.546 33.333 0.00 6.38 0.00 3.09
5743 13047 9.985318 CTCATAAAAAGATTCTTGACTTAGCTG 57.015 33.333 0.00 0.00 0.00 4.24
5785 13089 3.540314 AGCTCATCTGCTCCTGTTAAG 57.460 47.619 0.00 0.00 39.34 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.951747 AGCAATTTTAACATGCTCCCTCTTA 59.048 36.000 0.00 0.00 46.98 2.10
1 2 4.774200 AGCAATTTTAACATGCTCCCTCTT 59.226 37.500 0.00 0.00 46.98 2.85
2 3 4.347607 AGCAATTTTAACATGCTCCCTCT 58.652 39.130 0.00 0.00 46.98 3.69
3 4 4.725790 AGCAATTTTAACATGCTCCCTC 57.274 40.909 0.00 0.00 46.98 4.30
45 46 5.869753 AATGTGCAAGTTCACTCTCATAC 57.130 39.130 0.00 0.00 37.81 2.39
53 54 6.529125 CCATCATAGAAAATGTGCAAGTTCAC 59.471 38.462 0.00 0.00 37.48 3.18
67 68 9.645128 AAATCATGTTATGGACCATCATAGAAA 57.355 29.630 11.17 0.00 32.05 2.52
70 71 7.040271 TGCAAATCATGTTATGGACCATCATAG 60.040 37.037 11.17 5.07 32.05 2.23
610 1779 4.838486 CGACGAGCCGGAGCAGTC 62.838 72.222 5.05 7.71 43.56 3.51
678 1847 1.303561 GAAGGCATGCACCACCTCA 60.304 57.895 21.36 0.00 31.86 3.86
793 1962 1.428869 AGAGCACCTGTGGACTTTCT 58.571 50.000 0.00 0.00 0.00 2.52
794 1963 1.876156 CAAGAGCACCTGTGGACTTTC 59.124 52.381 0.00 0.00 0.00 2.62
820 1989 8.187480 CGAATTACAGGAGAGATCATAATCGAT 58.813 37.037 0.00 0.00 36.97 3.59
843 2012 1.216977 CAGTATGCACCCCGACGAA 59.783 57.895 0.00 0.00 0.00 3.85
921 2090 1.920051 CCGATCGTTGTCTGCATCG 59.080 57.895 15.09 0.00 38.69 3.84
928 2097 1.852895 GTGATACAGCCGATCGTTGTC 59.147 52.381 21.18 11.74 0.00 3.18
950 2119 4.821805 AGTGGACAAGAAACAACTACCATG 59.178 41.667 0.00 0.00 0.00 3.66
971 2140 2.812011 GCAATCGTCCCACTACAAAAGT 59.188 45.455 0.00 0.00 39.81 2.66
1213 2384 9.653516 CCTCTCTCTCTCTCTCTATCTATCTAT 57.346 40.741 0.00 0.00 0.00 1.98
1214 2385 8.061920 CCCTCTCTCTCTCTCTCTATCTATCTA 58.938 44.444 0.00 0.00 0.00 1.98
1215 2386 6.900186 CCCTCTCTCTCTCTCTCTATCTATCT 59.100 46.154 0.00 0.00 0.00 1.98
1216 2387 6.098982 CCCCTCTCTCTCTCTCTCTATCTATC 59.901 50.000 0.00 0.00 0.00 2.08
1217 2388 5.966935 CCCCTCTCTCTCTCTCTCTATCTAT 59.033 48.000 0.00 0.00 0.00 1.98
1218 2389 5.342017 CCCCTCTCTCTCTCTCTCTATCTA 58.658 50.000 0.00 0.00 0.00 1.98
1219 2390 4.171234 CCCCTCTCTCTCTCTCTCTATCT 58.829 52.174 0.00 0.00 0.00 1.98
1220 2391 3.264450 CCCCCTCTCTCTCTCTCTCTATC 59.736 56.522 0.00 0.00 0.00 2.08
1221 2392 3.260205 CCCCCTCTCTCTCTCTCTCTAT 58.740 54.545 0.00 0.00 0.00 1.98
1222 2393 2.701551 CCCCCTCTCTCTCTCTCTCTA 58.298 57.143 0.00 0.00 0.00 2.43
1242 2599 2.329399 ACCTCTCTCTCCCTCCCCC 61.329 68.421 0.00 0.00 0.00 5.40
1243 2600 1.075600 CACCTCTCTCTCCCTCCCC 60.076 68.421 0.00 0.00 0.00 4.81
1244 2601 1.075600 CCACCTCTCTCTCCCTCCC 60.076 68.421 0.00 0.00 0.00 4.30
1245 2602 0.927767 TACCACCTCTCTCTCCCTCC 59.072 60.000 0.00 0.00 0.00 4.30
1249 2606 2.380941 GAACCTACCACCTCTCTCTCC 58.619 57.143 0.00 0.00 0.00 3.71
1300 2657 2.698855 GCTATGAGCAGAAACCCTGA 57.301 50.000 0.00 0.00 45.78 3.86
1325 2682 7.040892 TGGAGAGACAATGATTGAACAGAAAAG 60.041 37.037 12.80 0.00 0.00 2.27
1404 2761 1.019278 AGCATACAGACAAACGGGCG 61.019 55.000 0.00 0.00 0.00 6.13
1443 2800 4.070009 GAGAGAAAAATAACACCGGTGGT 58.930 43.478 36.47 33.93 35.62 4.16
1505 2864 8.665685 ACGCTAATTTAGTCAAGGTTTTAGATG 58.334 33.333 5.38 0.00 0.00 2.90
1658 3051 2.268298 CGTCTATGGTAAGGTGTGTGC 58.732 52.381 0.00 0.00 0.00 4.57
1736 3153 0.583438 CAAGTTGTCACTGGTGCTCG 59.417 55.000 0.00 0.00 31.60 5.03
2039 3933 2.351418 CTGATCCAAAATAAGCGTCGCA 59.649 45.455 21.09 0.00 0.00 5.10
2045 3939 4.336713 GTGTCCCTCTGATCCAAAATAAGC 59.663 45.833 0.00 0.00 0.00 3.09
2059 3953 4.283722 CCTGTTTTGTACTAGTGTCCCTCT 59.716 45.833 5.39 0.00 0.00 3.69
2142 4050 2.026641 CGAATTGGGACCAATGCTCAT 58.973 47.619 16.72 1.30 44.86 2.90
2158 4066 0.748005 AATGCCTTAGCCGCACGAAT 60.748 50.000 0.00 0.00 39.49 3.34
2632 5647 7.683437 TTTTGAAAATGTTTAACGGGGTTTT 57.317 28.000 0.00 0.00 0.00 2.43
3489 10065 6.281405 TGTTCAGGTTGAAAGAGAGTAAGAC 58.719 40.000 0.00 0.00 38.22 3.01
3803 10487 6.754193 TGGTGCGAAATCATAGACATACATA 58.246 36.000 0.00 0.00 0.00 2.29
3875 10562 9.048446 GCCCAATAAATCGTAGATACTTAACAA 57.952 33.333 0.00 0.00 45.12 2.83
3890 10577 3.448660 GGCCCATATGAGCCCAATAAATC 59.551 47.826 17.12 0.00 43.76 2.17
3893 10580 2.603075 GGCCCATATGAGCCCAATAA 57.397 50.000 17.12 0.00 43.76 1.40
3910 10597 8.301720 TCAAGAAATGCAATTATGATATCAGGC 58.698 33.333 11.78 9.71 33.67 4.85
4050 10767 2.625314 CCCTCGAGTCTGCATAATGAGA 59.375 50.000 12.31 0.00 0.00 3.27
4057 10774 0.324738 TCTTCCCCTCGAGTCTGCAT 60.325 55.000 12.31 0.00 0.00 3.96
4159 10876 2.355837 GCAGAGTTGACGTCGGCA 60.356 61.111 11.62 0.00 35.46 5.69
4480 11197 3.805891 GAGGAGGCCGCTGATGCTC 62.806 68.421 6.40 0.00 36.97 4.26
4732 11449 3.925630 CTTGGCCACATCCACCGCT 62.926 63.158 3.88 0.00 35.50 5.52
4768 11485 0.248907 CGTACTTGGCATCGTCGGAT 60.249 55.000 0.00 0.00 0.00 4.18
4804 11521 4.555709 AAGCCGCCGTCCACAACA 62.556 61.111 0.00 0.00 0.00 3.33
4896 11621 1.286880 GAGCACAAACGCAGGCAAT 59.713 52.632 0.00 0.00 0.00 3.56
4900 11625 1.956170 AGACGAGCACAAACGCAGG 60.956 57.895 0.00 0.00 0.00 4.85
4940 11666 3.896888 TCATTGCAAGGTTTCACAGGAAT 59.103 39.130 11.36 0.00 31.93 3.01
4944 11670 5.860182 CACTATTCATTGCAAGGTTTCACAG 59.140 40.000 11.36 4.13 0.00 3.66
4949 11675 6.610075 AATCCACTATTCATTGCAAGGTTT 57.390 33.333 11.36 2.57 0.00 3.27
4951 11677 4.336433 CGAATCCACTATTCATTGCAAGGT 59.664 41.667 11.36 0.00 43.68 3.50
4953 11679 5.065090 TGTCGAATCCACTATTCATTGCAAG 59.935 40.000 4.94 0.00 43.68 4.01
4957 11683 4.813161 AGCTGTCGAATCCACTATTCATTG 59.187 41.667 0.00 0.00 43.68 2.82
4964 11690 1.751351 CCTGAGCTGTCGAATCCACTA 59.249 52.381 0.00 0.00 0.00 2.74
4965 11691 0.534412 CCTGAGCTGTCGAATCCACT 59.466 55.000 0.00 0.00 0.00 4.00
4981 11707 3.197790 CGCGTTGGAGATGCCCTG 61.198 66.667 0.00 0.00 36.93 4.45
4982 11708 4.473520 CCGCGTTGGAGATGCCCT 62.474 66.667 4.92 0.00 42.00 5.19
5008 11734 9.730705 CAGTCCATAGACAAATACAATATCCAT 57.269 33.333 0.00 0.00 46.15 3.41
5009 11735 8.156820 CCAGTCCATAGACAAATACAATATCCA 58.843 37.037 0.00 0.00 46.15 3.41
5010 11736 8.157476 ACCAGTCCATAGACAAATACAATATCC 58.843 37.037 0.00 0.00 46.15 2.59
5037 11763 1.567649 AGTATCCGTAGACTGGTCCCA 59.432 52.381 0.00 0.00 0.00 4.37
5038 11764 2.361643 AGTATCCGTAGACTGGTCCC 57.638 55.000 0.00 0.00 0.00 4.46
5048 11774 4.744867 GCTCCTGTACCAGTAGTATCCGTA 60.745 50.000 0.00 0.00 32.28 4.02
5051 11777 2.892215 GGCTCCTGTACCAGTAGTATCC 59.108 54.545 0.00 0.00 32.28 2.59
5056 11782 0.739561 GTCGGCTCCTGTACCAGTAG 59.260 60.000 0.00 0.00 0.00 2.57
5059 11785 1.330655 ATGGTCGGCTCCTGTACCAG 61.331 60.000 0.00 0.00 44.78 4.00
5062 11788 0.535335 TGAATGGTCGGCTCCTGTAC 59.465 55.000 0.00 0.00 0.00 2.90
5063 11789 1.066430 GTTGAATGGTCGGCTCCTGTA 60.066 52.381 0.00 0.00 0.00 2.74
5064 11790 0.321653 GTTGAATGGTCGGCTCCTGT 60.322 55.000 0.00 0.00 0.00 4.00
5065 11791 1.026718 GGTTGAATGGTCGGCTCCTG 61.027 60.000 0.00 0.00 0.00 3.86
5066 11792 1.299976 GGTTGAATGGTCGGCTCCT 59.700 57.895 0.00 0.00 0.00 3.69
5080 11806 2.767505 AGCGTTAAGAAGACAGGGTTG 58.232 47.619 0.00 0.00 0.00 3.77
5082 11808 2.104281 ACAAGCGTTAAGAAGACAGGGT 59.896 45.455 0.00 0.00 0.00 4.34
5085 11811 4.551388 AGAGACAAGCGTTAAGAAGACAG 58.449 43.478 0.00 0.00 0.00 3.51
5088 11814 8.603242 AAAAATAGAGACAAGCGTTAAGAAGA 57.397 30.769 0.00 0.00 0.00 2.87
5135 11861 8.567948 CGTGGAAGGTTTGATATGCTATTATTT 58.432 33.333 0.00 0.00 0.00 1.40
5136 11862 7.936847 TCGTGGAAGGTTTGATATGCTATTATT 59.063 33.333 0.00 0.00 0.00 1.40
5137 11863 7.450074 TCGTGGAAGGTTTGATATGCTATTAT 58.550 34.615 0.00 0.00 0.00 1.28
5138 11864 6.822442 TCGTGGAAGGTTTGATATGCTATTA 58.178 36.000 0.00 0.00 0.00 0.98
5152 11878 7.461182 TTGAATATTTTCATTCGTGGAAGGT 57.539 32.000 0.00 0.00 41.38 3.50
5158 11884 7.114920 GCTGCATTTGAATATTTTCATTCGTG 58.885 34.615 0.00 0.00 41.38 4.35
5160 11886 7.009815 AGTGCTGCATTTGAATATTTTCATTCG 59.990 33.333 5.27 0.00 41.38 3.34
5163 11889 8.472413 ACTAGTGCTGCATTTGAATATTTTCAT 58.528 29.630 12.83 0.00 41.38 2.57
5203 11929 6.429791 TTCGAAACTTCAATTGAACTGTCA 57.570 33.333 16.91 0.00 0.00 3.58
5204 11930 7.914537 ATTTCGAAACTTCAATTGAACTGTC 57.085 32.000 16.91 11.46 0.00 3.51
5223 12074 8.417176 CGGAGTTGAATTCAAGTTTAAATTTCG 58.583 33.333 25.50 15.75 39.43 3.46
5230 12081 4.394729 AGCCGGAGTTGAATTCAAGTTTA 58.605 39.130 25.50 1.35 39.43 2.01
5263 12123 9.382244 CACTTAAAGTTTAGAAAATTCCAGTCG 57.618 33.333 0.00 0.00 0.00 4.18
5264 12124 9.678941 CCACTTAAAGTTTAGAAAATTCCAGTC 57.321 33.333 0.00 0.00 0.00 3.51
5272 12132 9.191479 TGGTGATTCCACTTAAAGTTTAGAAAA 57.809 29.630 0.00 0.00 41.93 2.29
5289 12149 5.343307 AATTTAATGGCTGTGGTGATTCC 57.657 39.130 0.00 0.00 0.00 3.01
5300 12160 8.382405 AGGTTGTTGGATTTTAATTTAATGGCT 58.618 29.630 0.00 0.00 0.00 4.75
5306 12166 8.485578 AGTGGAGGTTGTTGGATTTTAATTTA 57.514 30.769 0.00 0.00 0.00 1.40
5307 12167 7.373617 AGTGGAGGTTGTTGGATTTTAATTT 57.626 32.000 0.00 0.00 0.00 1.82
5333 12193 1.264288 CGCTTGAAGAGGTGAACCAAC 59.736 52.381 0.00 0.00 38.89 3.77
5339 12199 1.301716 GTGCCGCTTGAAGAGGTGA 60.302 57.895 16.28 1.02 37.51 4.02
5342 12202 1.294659 GACAGTGCCGCTTGAAGAGG 61.295 60.000 10.83 10.83 38.30 3.69
5354 12214 2.688507 TGAGGAAAAGATCGACAGTGC 58.311 47.619 0.00 0.00 0.00 4.40
5361 12221 6.305693 ACAGAAAGTTTGAGGAAAAGATCG 57.694 37.500 0.00 0.00 0.00 3.69
5405 12265 0.758685 AGATGAGAGGAAGGGAGGCG 60.759 60.000 0.00 0.00 0.00 5.52
5406 12266 2.390225 TAGATGAGAGGAAGGGAGGC 57.610 55.000 0.00 0.00 0.00 4.70
5407 12267 4.904251 TGAAATAGATGAGAGGAAGGGAGG 59.096 45.833 0.00 0.00 0.00 4.30
5408 12268 5.221621 GGTGAAATAGATGAGAGGAAGGGAG 60.222 48.000 0.00 0.00 0.00 4.30
5421 12282 4.162040 CCTTGCCAGAGGTGAAATAGAT 57.838 45.455 0.00 0.00 31.89 1.98
5485 12346 3.006967 GCTTAGATTAGATGGAGCCGGAA 59.993 47.826 5.05 0.00 0.00 4.30
5492 12353 1.272490 CCGCCGCTTAGATTAGATGGA 59.728 52.381 0.00 0.00 0.00 3.41
5493 12354 1.000955 ACCGCCGCTTAGATTAGATGG 59.999 52.381 0.00 0.00 0.00 3.51
5494 12355 2.288213 TGACCGCCGCTTAGATTAGATG 60.288 50.000 0.00 0.00 0.00 2.90
5495 12356 1.961394 TGACCGCCGCTTAGATTAGAT 59.039 47.619 0.00 0.00 0.00 1.98
5496 12357 1.337071 CTGACCGCCGCTTAGATTAGA 59.663 52.381 0.00 0.00 0.00 2.10
5497 12358 1.067212 ACTGACCGCCGCTTAGATTAG 59.933 52.381 0.00 0.00 0.00 1.73
5498 12359 1.108776 ACTGACCGCCGCTTAGATTA 58.891 50.000 0.00 0.00 0.00 1.75
5499 12360 0.460284 CACTGACCGCCGCTTAGATT 60.460 55.000 0.00 0.00 0.00 2.40
5500 12361 1.141881 CACTGACCGCCGCTTAGAT 59.858 57.895 0.00 0.00 0.00 1.98
5501 12362 2.571757 CACTGACCGCCGCTTAGA 59.428 61.111 0.00 0.00 0.00 2.10
5502 12363 3.188786 GCACTGACCGCCGCTTAG 61.189 66.667 0.00 0.00 0.00 2.18
5503 12364 3.932580 CTGCACTGACCGCCGCTTA 62.933 63.158 0.00 0.00 0.00 3.09
5507 12368 3.414700 GTTCTGCACTGACCGCCG 61.415 66.667 0.00 0.00 0.00 6.46
5581 12865 4.583073 AGTTAATCACAACCCAAACAGGAC 59.417 41.667 0.00 0.00 41.22 3.85
5582 12866 4.798882 AGTTAATCACAACCCAAACAGGA 58.201 39.130 0.00 0.00 41.22 3.86
5584 12868 6.337356 ACAAAGTTAATCACAACCCAAACAG 58.663 36.000 0.00 0.00 0.00 3.16
5617 12901 4.450082 AGTTCGGGAAAAATAATGTGGC 57.550 40.909 0.00 0.00 0.00 5.01
5658 12942 6.594159 GGCAGCTAAAGTGTGACTAAGAATTA 59.406 38.462 0.00 0.00 0.00 1.40
5669 12953 3.866651 AGTATGAGGCAGCTAAAGTGTG 58.133 45.455 0.00 0.00 0.00 3.82
5676 12960 6.655003 GCCATATAAAAAGTATGAGGCAGCTA 59.345 38.462 0.00 0.00 32.52 3.32
5685 12969 6.690530 CCCCACATGCCATATAAAAAGTATG 58.309 40.000 0.00 0.00 0.00 2.39
5687 12971 4.586841 GCCCCACATGCCATATAAAAAGTA 59.413 41.667 0.00 0.00 0.00 2.24
5688 12972 3.387699 GCCCCACATGCCATATAAAAAGT 59.612 43.478 0.00 0.00 0.00 2.66
5689 12973 3.642848 AGCCCCACATGCCATATAAAAAG 59.357 43.478 0.00 0.00 0.00 2.27
5690 12974 3.652055 AGCCCCACATGCCATATAAAAA 58.348 40.909 0.00 0.00 0.00 1.94
5691 12975 3.326946 AGCCCCACATGCCATATAAAA 57.673 42.857 0.00 0.00 0.00 1.52
5717 13021 9.985318 CAGCTAAGTCAAGAATCTTTTTATGAG 57.015 33.333 0.00 0.00 0.00 2.90
5721 13025 7.607991 CCTCCAGCTAAGTCAAGAATCTTTTTA 59.392 37.037 0.00 0.00 0.00 1.52
5722 13026 6.432472 CCTCCAGCTAAGTCAAGAATCTTTTT 59.568 38.462 0.00 0.00 0.00 1.94
5723 13027 5.942826 CCTCCAGCTAAGTCAAGAATCTTTT 59.057 40.000 0.00 0.00 0.00 2.27
5730 13034 2.828520 CTGTCCTCCAGCTAAGTCAAGA 59.171 50.000 0.00 0.00 33.59 3.02
5741 13045 2.581354 CGGAAGGCTGTCCTCCAG 59.419 66.667 12.02 0.00 43.40 3.86
5756 13060 3.842923 AGATGAGCTCCACGCCGG 61.843 66.667 12.15 0.00 40.39 6.13
5778 13082 8.600449 TTGCCAATTTTATTGTTCCTTAACAG 57.400 30.769 0.00 0.00 45.99 3.16
5785 13089 7.548780 TGCTATTCTTGCCAATTTTATTGTTCC 59.451 33.333 0.00 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.