Multiple sequence alignment - TraesCS1A01G101500

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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 TraesCS1A01G101500 chr1A 100.000 6178 0 0 1 6178 97941054 97934877 0.000000e+00 11409.0
1 TraesCS1A01G101500 chr1A 88.917 397 23 12 2206 2583 365645050 365644656 2.610000e-128 470.0
2 TraesCS1A01G101500 chr1A 87.010 408 23 7 2206 2583 10695605 10695198 3.420000e-117 433.0
3 TraesCS1A01G101500 chr1A 87.407 135 11 3 105 235 97872625 97872493 3.860000e-32 150.0
4 TraesCS1A01G101500 chr1A 94.845 97 4 1 6082 6178 208901471 208901376 3.860000e-32 150.0
5 TraesCS1A01G101500 chr6D 95.397 3302 118 14 2206 5494 419880782 419877502 0.000000e+00 5225.0
6 TraesCS1A01G101500 chr6D 94.722 3240 134 18 2275 5494 97821969 97825191 0.000000e+00 5001.0
7 TraesCS1A01G101500 chr6D 90.046 1095 88 13 1097 2186 67693156 67694234 0.000000e+00 1399.0
8 TraesCS1A01G101500 chr6D 88.645 1092 76 24 1100 2186 292035435 292036483 0.000000e+00 1286.0
9 TraesCS1A01G101500 chr6D 92.211 398 15 4 2695 3079 422290334 422289940 3.260000e-152 549.0
10 TraesCS1A01G101500 chr6D 88.679 265 17 8 5495 5755 273916064 273916319 1.670000e-80 311.0
11 TraesCS1A01G101500 chr6D 89.848 197 19 1 1990 2186 431862356 431862551 1.030000e-62 252.0
12 TraesCS1A01G101500 chr6B 94.586 3306 148 18 2206 5491 423013811 423017105 0.000000e+00 5084.0
13 TraesCS1A01G101500 chr6B 89.479 922 61 15 2206 3118 595032638 595031744 0.000000e+00 1133.0
14 TraesCS1A01G101500 chr3D 95.180 3091 116 16 2206 5282 570572309 570575380 0.000000e+00 4852.0
15 TraesCS1A01G101500 chr3D 94.831 2341 103 9 3167 5494 613565838 613563503 0.000000e+00 3637.0
16 TraesCS1A01G101500 chr3D 94.532 2359 105 16 3152 5494 64774764 64777114 0.000000e+00 3620.0
17 TraesCS1A01G101500 chr3D 92.074 1085 68 10 1107 2186 500603177 500604248 0.000000e+00 1511.0
18 TraesCS1A01G101500 chr3D 90.943 1082 61 11 1110 2186 610720503 610719454 0.000000e+00 1421.0
19 TraesCS1A01G101500 chr3D 95.577 633 26 2 2235 2867 64774146 64774776 0.000000e+00 1013.0
20 TraesCS1A01G101500 chr4B 93.943 3104 155 21 2409 5494 553921736 553924824 0.000000e+00 4660.0
21 TraesCS1A01G101500 chr4B 85.539 1058 104 17 1139 2186 99340149 99341167 0.000000e+00 1061.0
22 TraesCS1A01G101500 chr4B 84.037 1090 133 29 1107 2186 200717529 200718587 0.000000e+00 1011.0
23 TraesCS1A01G101500 chr4B 91.329 715 49 5 2413 3118 548266118 548266828 0.000000e+00 965.0
24 TraesCS1A01G101500 chr4B 93.798 129 7 1 2206 2334 553921251 553921378 6.320000e-45 193.0
25 TraesCS1A01G101500 chr4B 77.273 176 25 12 5736 5909 626066469 626066307 8.530000e-14 89.8
26 TraesCS1A01G101500 chr2B 92.860 2395 146 13 3117 5494 732957080 732954694 0.000000e+00 3452.0
27 TraesCS1A01G101500 chr2B 92.768 2392 149 13 3117 5494 693571120 693568739 0.000000e+00 3437.0
28 TraesCS1A01G101500 chr1B 92.645 2393 151 18 3114 5494 664473560 664475939 0.000000e+00 3421.0
29 TraesCS1A01G101500 chr1B 91.750 2400 150 22 3114 5493 50137441 50139812 0.000000e+00 3291.0
30 TraesCS1A01G101500 chr1B 90.759 1699 128 17 3808 5494 603983050 603984731 0.000000e+00 2241.0
31 TraesCS1A01G101500 chr1B 92.245 1109 61 17 1 1106 130347552 130346466 0.000000e+00 1548.0
32 TraesCS1A01G101500 chr3B 91.534 1701 122 12 3808 5494 657653602 657655294 0.000000e+00 2324.0
33 TraesCS1A01G101500 chr3B 90.042 1677 129 13 3844 5494 481634726 481636390 0.000000e+00 2137.0
34 TraesCS1A01G101500 chr3B 86.232 414 19 12 5495 5895 68354808 68354420 1.240000e-111 414.0
35 TraesCS1A01G101500 chr7B 87.441 1696 174 20 3823 5494 606988520 606990200 0.000000e+00 1916.0
36 TraesCS1A01G101500 chr7B 95.789 95 4 0 6082 6176 251146696 251146602 2.980000e-33 154.0
37 TraesCS1A01G101500 chr1D 86.075 1702 170 32 3821 5485 165561979 165563650 0.000000e+00 1768.0
38 TraesCS1A01G101500 chr1D 91.068 1086 74 12 1110 2186 218970688 218969617 0.000000e+00 1447.0
39 TraesCS1A01G101500 chr1D 87.583 1055 110 15 1139 2186 96072048 96073088 0.000000e+00 1203.0
40 TraesCS1A01G101500 chr1D 84.686 1097 123 23 1107 2186 165560160 165561228 0.000000e+00 1053.0
41 TraesCS1A01G101500 chr1D 91.023 557 35 6 148 700 79128076 79127531 0.000000e+00 737.0
42 TraesCS1A01G101500 chr1D 94.805 154 7 1 1 153 79133402 79133249 8.000000e-59 239.0
43 TraesCS1A01G101500 chr1D 89.706 68 6 1 6019 6086 80297264 80297330 1.100000e-12 86.1
44 TraesCS1A01G101500 chr2D 85.756 1713 184 28 3821 5494 407950718 407949027 0.000000e+00 1757.0
45 TraesCS1A01G101500 chr2D 91.408 1094 72 19 1104 2186 498766638 498765556 0.000000e+00 1480.0
46 TraesCS1A01G101500 chr2D 91.252 1086 68 13 1106 2186 594596607 594597670 0.000000e+00 1454.0
47 TraesCS1A01G101500 chr2D 97.087 206 4 2 5486 5690 105584311 105584515 4.580000e-91 346.0
48 TraesCS1A01G101500 chr2D 100.000 28 0 0 6059 6086 85605250 85605277 1.100000e-02 52.8
49 TraesCS1A01G101500 chr5D 92.428 1083 65 8 1110 2186 526659009 526657938 0.000000e+00 1530.0
50 TraesCS1A01G101500 chr5D 91.176 1088 70 16 1107 2186 65978760 65977691 0.000000e+00 1454.0
51 TraesCS1A01G101500 chr5D 91.035 1082 68 10 1110 2186 424150801 424149744 0.000000e+00 1434.0
52 TraesCS1A01G101500 chr5D 86.069 1048 111 21 1147 2186 472476353 472477373 0.000000e+00 1094.0
53 TraesCS1A01G101500 chr5D 88.235 68 7 1 6019 6086 527195344 527195278 5.130000e-11 80.5
54 TraesCS1A01G101500 chr7D 92.343 1084 67 7 1107 2186 34178726 34179797 0.000000e+00 1528.0
55 TraesCS1A01G101500 chr7D 91.193 1090 71 15 1107 2186 54988252 54987178 0.000000e+00 1458.0
56 TraesCS1A01G101500 chr7D 92.803 917 45 11 2217 3116 568858349 568857437 0.000000e+00 1308.0
57 TraesCS1A01G101500 chr7D 98.980 196 2 0 5495 5690 378163856 378164051 9.850000e-93 351.0
58 TraesCS1A01G101500 chr4D 91.529 1086 74 9 1106 2186 274217490 274216418 0.000000e+00 1480.0
59 TraesCS1A01G101500 chr4D 89.124 1085 100 9 1107 2186 47249161 47248090 0.000000e+00 1334.0
60 TraesCS1A01G101500 chr4D 87.097 961 98 16 1102 2055 86594059 86595000 0.000000e+00 1064.0
61 TraesCS1A01G101500 chr4D 86.643 554 54 12 1632 2183 43180449 43180984 4.120000e-166 595.0
62 TraesCS1A01G101500 chr4D 95.327 214 8 1 5495 5706 132677775 132677562 7.670000e-89 339.0
63 TraesCS1A01G101500 chr4D 89.706 68 6 1 6019 6086 339059486 339059420 1.100000e-12 86.1
64 TraesCS1A01G101500 chr5A 91.545 1029 72 7 1106 2130 624157013 624155996 0.000000e+00 1404.0
65 TraesCS1A01G101500 chr5A 90.816 392 22 6 2206 2583 33923181 33922790 4.270000e-141 512.0
66 TraesCS1A01G101500 chr5A 88.804 393 20 8 2206 2583 524707633 524707250 1.570000e-125 460.0
67 TraesCS1A01G101500 chr5A 94.495 218 9 2 5495 5709 598094398 598094615 3.570000e-87 333.0
68 TraesCS1A01G101500 chr5A 88.750 160 10 1 6027 6178 626281006 626281165 8.180000e-44 189.0
69 TraesCS1A01G101500 chr5A 87.195 164 9 2 6027 6178 132296979 132296816 6.360000e-40 176.0
70 TraesCS1A01G101500 chr5A 96.774 93 3 0 6086 6178 349123688 349123780 8.290000e-34 156.0
71 TraesCS1A01G101500 chr6A 88.269 1057 89 21 1144 2186 569390231 569389196 0.000000e+00 1232.0
72 TraesCS1A01G101500 chr6A 87.658 1029 84 16 1107 2128 12716674 12715682 0.000000e+00 1157.0
73 TraesCS1A01G101500 chr6A 89.489 685 31 14 5495 6178 88084596 88085240 0.000000e+00 828.0
74 TraesCS1A01G101500 chr6A 91.538 390 20 3 2206 2583 184592192 184592580 5.490000e-145 525.0
75 TraesCS1A01G101500 chr6A 91.538 390 20 3 2206 2583 494439141 494438753 5.490000e-145 525.0
76 TraesCS1A01G101500 chr6A 96.774 93 3 0 6086 6178 101564725 101564817 8.290000e-34 156.0
77 TraesCS1A01G101500 chr6A 96.739 92 3 0 6087 6178 463536544 463536453 2.980000e-33 154.0
78 TraesCS1A01G101500 chr3A 90.349 487 25 2 5495 5981 742395892 742396356 2.450000e-173 619.0
79 TraesCS1A01G101500 chr3A 91.358 243 12 4 5938 6178 742396278 742396513 2.150000e-84 324.0
80 TraesCS1A01G101500 chr2A 90.863 394 20 4 2206 2583 614231706 614231313 1.190000e-141 514.0
81 TraesCS1A01G101500 chr5B 93.510 339 18 3 2781 3116 62148069 62148406 9.250000e-138 501.0
82 TraesCS1A01G101500 chr4A 94.643 224 8 3 5495 5715 448537784 448537562 1.650000e-90 344.0
83 TraesCS1A01G101500 chr4A 96.774 93 3 0 6086 6178 89395774 89395682 8.290000e-34 156.0


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 TraesCS1A01G101500 chr1A 97934877 97941054 6177 True 11409.0 11409 100.0000 1 6178 1 chr1A.!!$R3 6177
1 TraesCS1A01G101500 chr6D 419877502 419880782 3280 True 5225.0 5225 95.3970 2206 5494 1 chr6D.!!$R1 3288
2 TraesCS1A01G101500 chr6D 97821969 97825191 3222 False 5001.0 5001 94.7220 2275 5494 1 chr6D.!!$F2 3219
3 TraesCS1A01G101500 chr6D 67693156 67694234 1078 False 1399.0 1399 90.0460 1097 2186 1 chr6D.!!$F1 1089
4 TraesCS1A01G101500 chr6D 292035435 292036483 1048 False 1286.0 1286 88.6450 1100 2186 1 chr6D.!!$F4 1086
5 TraesCS1A01G101500 chr6B 423013811 423017105 3294 False 5084.0 5084 94.5860 2206 5491 1 chr6B.!!$F1 3285
6 TraesCS1A01G101500 chr6B 595031744 595032638 894 True 1133.0 1133 89.4790 2206 3118 1 chr6B.!!$R1 912
7 TraesCS1A01G101500 chr3D 570572309 570575380 3071 False 4852.0 4852 95.1800 2206 5282 1 chr3D.!!$F2 3076
8 TraesCS1A01G101500 chr3D 613563503 613565838 2335 True 3637.0 3637 94.8310 3167 5494 1 chr3D.!!$R2 2327
9 TraesCS1A01G101500 chr3D 64774146 64777114 2968 False 2316.5 3620 95.0545 2235 5494 2 chr3D.!!$F3 3259
10 TraesCS1A01G101500 chr3D 500603177 500604248 1071 False 1511.0 1511 92.0740 1107 2186 1 chr3D.!!$F1 1079
11 TraesCS1A01G101500 chr3D 610719454 610720503 1049 True 1421.0 1421 90.9430 1110 2186 1 chr3D.!!$R1 1076
12 TraesCS1A01G101500 chr4B 553921251 553924824 3573 False 2426.5 4660 93.8705 2206 5494 2 chr4B.!!$F4 3288
13 TraesCS1A01G101500 chr4B 99340149 99341167 1018 False 1061.0 1061 85.5390 1139 2186 1 chr4B.!!$F1 1047
14 TraesCS1A01G101500 chr4B 200717529 200718587 1058 False 1011.0 1011 84.0370 1107 2186 1 chr4B.!!$F2 1079
15 TraesCS1A01G101500 chr4B 548266118 548266828 710 False 965.0 965 91.3290 2413 3118 1 chr4B.!!$F3 705
16 TraesCS1A01G101500 chr2B 732954694 732957080 2386 True 3452.0 3452 92.8600 3117 5494 1 chr2B.!!$R2 2377
17 TraesCS1A01G101500 chr2B 693568739 693571120 2381 True 3437.0 3437 92.7680 3117 5494 1 chr2B.!!$R1 2377
18 TraesCS1A01G101500 chr1B 664473560 664475939 2379 False 3421.0 3421 92.6450 3114 5494 1 chr1B.!!$F3 2380
19 TraesCS1A01G101500 chr1B 50137441 50139812 2371 False 3291.0 3291 91.7500 3114 5493 1 chr1B.!!$F1 2379
20 TraesCS1A01G101500 chr1B 603983050 603984731 1681 False 2241.0 2241 90.7590 3808 5494 1 chr1B.!!$F2 1686
21 TraesCS1A01G101500 chr1B 130346466 130347552 1086 True 1548.0 1548 92.2450 1 1106 1 chr1B.!!$R1 1105
22 TraesCS1A01G101500 chr3B 657653602 657655294 1692 False 2324.0 2324 91.5340 3808 5494 1 chr3B.!!$F2 1686
23 TraesCS1A01G101500 chr3B 481634726 481636390 1664 False 2137.0 2137 90.0420 3844 5494 1 chr3B.!!$F1 1650
24 TraesCS1A01G101500 chr7B 606988520 606990200 1680 False 1916.0 1916 87.4410 3823 5494 1 chr7B.!!$F1 1671
25 TraesCS1A01G101500 chr1D 218969617 218970688 1071 True 1447.0 1447 91.0680 1110 2186 1 chr1D.!!$R3 1076
26 TraesCS1A01G101500 chr1D 165560160 165563650 3490 False 1410.5 1768 85.3805 1107 5485 2 chr1D.!!$F3 4378
27 TraesCS1A01G101500 chr1D 96072048 96073088 1040 False 1203.0 1203 87.5830 1139 2186 1 chr1D.!!$F2 1047
28 TraesCS1A01G101500 chr1D 79127531 79128076 545 True 737.0 737 91.0230 148 700 1 chr1D.!!$R1 552
29 TraesCS1A01G101500 chr2D 407949027 407950718 1691 True 1757.0 1757 85.7560 3821 5494 1 chr2D.!!$R1 1673
30 TraesCS1A01G101500 chr2D 498765556 498766638 1082 True 1480.0 1480 91.4080 1104 2186 1 chr2D.!!$R2 1082
31 TraesCS1A01G101500 chr2D 594596607 594597670 1063 False 1454.0 1454 91.2520 1106 2186 1 chr2D.!!$F3 1080
32 TraesCS1A01G101500 chr5D 526657938 526659009 1071 True 1530.0 1530 92.4280 1110 2186 1 chr5D.!!$R3 1076
33 TraesCS1A01G101500 chr5D 65977691 65978760 1069 True 1454.0 1454 91.1760 1107 2186 1 chr5D.!!$R1 1079
34 TraesCS1A01G101500 chr5D 424149744 424150801 1057 True 1434.0 1434 91.0350 1110 2186 1 chr5D.!!$R2 1076
35 TraesCS1A01G101500 chr5D 472476353 472477373 1020 False 1094.0 1094 86.0690 1147 2186 1 chr5D.!!$F1 1039
36 TraesCS1A01G101500 chr7D 34178726 34179797 1071 False 1528.0 1528 92.3430 1107 2186 1 chr7D.!!$F1 1079
37 TraesCS1A01G101500 chr7D 54987178 54988252 1074 True 1458.0 1458 91.1930 1107 2186 1 chr7D.!!$R1 1079
38 TraesCS1A01G101500 chr7D 568857437 568858349 912 True 1308.0 1308 92.8030 2217 3116 1 chr7D.!!$R2 899
39 TraesCS1A01G101500 chr4D 274216418 274217490 1072 True 1480.0 1480 91.5290 1106 2186 1 chr4D.!!$R3 1080
40 TraesCS1A01G101500 chr4D 47248090 47249161 1071 True 1334.0 1334 89.1240 1107 2186 1 chr4D.!!$R1 1079
41 TraesCS1A01G101500 chr4D 86594059 86595000 941 False 1064.0 1064 87.0970 1102 2055 1 chr4D.!!$F2 953
42 TraesCS1A01G101500 chr4D 43180449 43180984 535 False 595.0 595 86.6430 1632 2183 1 chr4D.!!$F1 551
43 TraesCS1A01G101500 chr5A 624155996 624157013 1017 True 1404.0 1404 91.5450 1106 2130 1 chr5A.!!$R4 1024
44 TraesCS1A01G101500 chr6A 569389196 569390231 1035 True 1232.0 1232 88.2690 1144 2186 1 chr6A.!!$R4 1042
45 TraesCS1A01G101500 chr6A 12715682 12716674 992 True 1157.0 1157 87.6580 1107 2128 1 chr6A.!!$R1 1021
46 TraesCS1A01G101500 chr6A 88084596 88085240 644 False 828.0 828 89.4890 5495 6178 1 chr6A.!!$F1 683
47 TraesCS1A01G101500 chr3A 742395892 742396513 621 False 471.5 619 90.8535 5495 6178 2 chr3A.!!$F1 683

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
978 993 0.532115 TCATCGCAGCTAGAAGCACA 59.468 50.000 1.22 0.0 45.56 4.57 F
1764 1831 0.171007 CCCGCGGACTACTTCGTTTA 59.829 55.000 30.73 0.0 0.00 2.01 F
2173 2271 0.105408 CAAGCTGCCAGCCTTTTGTT 59.895 50.000 14.25 0.0 43.77 2.83 F
2432 2824 0.594110 GGTTTTTGTCCCGCGATTCA 59.406 50.000 8.23 0.0 0.00 2.57 F
4039 4609 1.343465 GGAAGTCAGTCCCTTTGTCGA 59.657 52.381 0.00 0.0 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1904 1989 0.108138 AGGCTACAATCCACAGACGC 60.108 55.000 0.00 0.0 0.0 5.19 R
3181 3584 1.454847 GGACCCTGGTTGCACACAA 60.455 57.895 0.00 0.0 0.0 3.33 R
4083 4653 1.830477 CTTCCTCTCCCTCCTCAACAG 59.170 57.143 0.00 0.0 0.0 3.16 R
4294 4897 0.393944 GCCCCTAAAACCCCGAGAAG 60.394 60.000 0.00 0.0 0.0 2.85 R
5909 6567 0.613853 AGCTACAACCGGGACTAGCA 60.614 55.000 21.71 0.0 35.1 3.49 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
32 33 9.288576 CCAGGATTATATAATTCTTGAACTGCA 57.711 33.333 12.88 0.00 29.04 4.41
83 85 9.674068 AGACCTTAGTTTATTTCAGAATTCCTC 57.326 33.333 0.65 0.00 0.00 3.71
106 108 3.445096 GCCTTGTGCATCCTTTATGACTT 59.555 43.478 0.00 0.00 37.86 3.01
110 112 5.627499 TGTGCATCCTTTATGACTTGTTC 57.373 39.130 0.00 0.00 37.86 3.18
122 124 4.214986 TGACTTGTTCTGTTCTGTTCCA 57.785 40.909 0.00 0.00 0.00 3.53
135 137 0.953727 TGTTCCATTGCTGCAGTGAC 59.046 50.000 24.39 16.17 0.00 3.67
139 141 1.672030 CATTGCTGCAGTGACCCGA 60.672 57.895 19.00 0.00 0.00 5.14
250 252 4.575236 GTGTGATGTACTCCGATCTAGTGA 59.425 45.833 7.62 0.00 0.00 3.41
308 311 4.762251 ACCTTAGCAAAATGGTGAGAAGTC 59.238 41.667 3.28 0.00 33.95 3.01
327 330 3.869246 AGTCCTTACAGTGTTTGTTGACG 59.131 43.478 0.00 0.00 41.29 4.35
328 331 3.866910 GTCCTTACAGTGTTTGTTGACGA 59.133 43.478 0.00 0.00 41.29 4.20
329 332 3.866910 TCCTTACAGTGTTTGTTGACGAC 59.133 43.478 0.00 0.00 41.29 4.34
405 412 3.110447 TCACAAAAGGAAAATGCTGCC 57.890 42.857 0.00 0.00 0.00 4.85
435 442 0.671781 GCATGGCGTCTTCAGTGTCT 60.672 55.000 0.00 0.00 0.00 3.41
437 444 0.969149 ATGGCGTCTTCAGTGTCTCA 59.031 50.000 0.00 0.00 0.00 3.27
462 469 1.840635 GGAAATCCTACTCTGCTGGGT 59.159 52.381 0.41 0.41 0.00 4.51
482 489 4.461198 GGTTCTCTTGAGAAAGGGAAACA 58.539 43.478 13.81 0.00 44.43 2.83
529 536 1.988846 AGGGAAGAAAGAGAAGTGGGG 59.011 52.381 0.00 0.00 0.00 4.96
560 567 7.798596 ACATATAAAAGCAACTCTCCATCTG 57.201 36.000 0.00 0.00 0.00 2.90
562 569 1.831580 AAAGCAACTCTCCATCTGCC 58.168 50.000 0.00 0.00 35.33 4.85
666 673 1.927895 CTGTGGCGGTGTAGAGAATC 58.072 55.000 0.00 0.00 0.00 2.52
684 691 0.874390 TCGTCAGAAGTTTGGCATGC 59.126 50.000 9.90 9.90 0.00 4.06
794 801 3.744660 ACATTCCTGTTTGGTCTGAGTC 58.255 45.455 0.00 0.00 37.07 3.36
801 816 2.431419 TGTTTGGTCTGAGTCCGTGTTA 59.569 45.455 0.00 0.00 0.00 2.41
823 838 1.893137 CCCCCTTAAAGTTGAAGCCAC 59.107 52.381 0.00 0.00 0.00 5.01
828 843 3.826157 CCTTAAAGTTGAAGCCACATCCA 59.174 43.478 0.00 0.00 0.00 3.41
829 844 4.082571 CCTTAAAGTTGAAGCCACATCCAG 60.083 45.833 0.00 0.00 0.00 3.86
830 845 2.664402 AAGTTGAAGCCACATCCAGT 57.336 45.000 0.00 0.00 0.00 4.00
845 860 2.608623 TCCAGTGACATGGACTTCAGA 58.391 47.619 0.00 0.00 44.56 3.27
846 861 3.176411 TCCAGTGACATGGACTTCAGAT 58.824 45.455 0.00 0.00 44.56 2.90
847 862 4.352893 TCCAGTGACATGGACTTCAGATA 58.647 43.478 0.00 0.00 44.56 1.98
848 863 4.964897 TCCAGTGACATGGACTTCAGATAT 59.035 41.667 0.00 0.00 44.56 1.63
849 864 5.069648 TCCAGTGACATGGACTTCAGATATC 59.930 44.000 0.00 0.00 44.56 1.63
850 865 5.295950 CAGTGACATGGACTTCAGATATCC 58.704 45.833 0.00 0.00 0.00 2.59
891 906 4.760204 TCGATAGAAGACACAGTCAACAGA 59.240 41.667 0.00 0.00 46.15 3.41
892 907 5.092105 CGATAGAAGACACAGTCAACAGAG 58.908 45.833 0.00 0.00 34.13 3.35
949 964 0.756903 AGGTTCATCCGGGGTATTCG 59.243 55.000 0.00 0.00 41.99 3.34
978 993 0.532115 TCATCGCAGCTAGAAGCACA 59.468 50.000 1.22 0.00 45.56 4.57
998 1013 4.012895 GGTGTGTTCTGGTGCGCG 62.013 66.667 0.00 0.00 0.00 6.86
1001 1016 2.742372 GTGTTCTGGTGCGCGGAT 60.742 61.111 8.83 0.00 0.00 4.18
1003 1018 4.166011 GTTCTGGTGCGCGGATGC 62.166 66.667 8.83 0.00 37.91 3.91
1030 1045 1.227853 GCGGGGATGGATGGTGTAC 60.228 63.158 0.00 0.00 0.00 2.90
1086 1101 0.881118 GAAATTCCTCGCCTTGTGCA 59.119 50.000 0.00 0.00 41.33 4.57
1210 1225 2.872388 CGCTGTGTCCAGGTGTCCT 61.872 63.158 0.00 0.00 39.22 3.85
1217 1232 4.215370 CCAGGTGTCCTCTGGTCA 57.785 61.111 2.21 0.00 44.97 4.02
1219 1234 0.833834 CCAGGTGTCCTCTGGTCAGT 60.834 60.000 2.21 0.00 44.97 3.41
1323 1345 2.119495 GGGACCCACATGTCATAGAGT 58.881 52.381 5.33 0.00 36.97 3.24
1369 1392 1.372499 GCTCGTGCGTAGTGGTTGA 60.372 57.895 0.00 0.00 0.00 3.18
1370 1393 0.736325 GCTCGTGCGTAGTGGTTGAT 60.736 55.000 0.00 0.00 0.00 2.57
1441 1479 1.492599 CATTCCTCCTCTTTCCCCCTC 59.507 57.143 0.00 0.00 0.00 4.30
1442 1480 0.800239 TTCCTCCTCTTTCCCCCTCT 59.200 55.000 0.00 0.00 0.00 3.69
1443 1481 0.340208 TCCTCCTCTTTCCCCCTCTC 59.660 60.000 0.00 0.00 0.00 3.20
1444 1482 0.692756 CCTCCTCTTTCCCCCTCTCC 60.693 65.000 0.00 0.00 0.00 3.71
1445 1483 0.692756 CTCCTCTTTCCCCCTCTCCC 60.693 65.000 0.00 0.00 0.00 4.30
1446 1484 1.694525 CCTCTTTCCCCCTCTCCCC 60.695 68.421 0.00 0.00 0.00 4.81
1447 1485 1.694525 CTCTTTCCCCCTCTCCCCC 60.695 68.421 0.00 0.00 0.00 5.40
1448 1486 2.191846 TCTTTCCCCCTCTCCCCCT 61.192 63.158 0.00 0.00 0.00 4.79
1456 1494 0.999712 CCCTCTCCCCCTTTGCTTTA 59.000 55.000 0.00 0.00 0.00 1.85
1698 1765 2.257676 GAACTCGAGGTCGCGGTT 59.742 61.111 15.99 0.00 39.60 4.44
1764 1831 0.171007 CCCGCGGACTACTTCGTTTA 59.829 55.000 30.73 0.00 0.00 2.01
1851 1932 1.068250 GGGGAGAGCTCGTGCATAC 59.932 63.158 12.58 0.20 42.74 2.39
1866 1947 1.767289 CATACACGTACGGGATGAGC 58.233 55.000 27.01 0.00 0.00 4.26
1948 2037 3.255642 CGGTGGATCTGGTGTTTTTGATT 59.744 43.478 0.00 0.00 0.00 2.57
2016 2110 7.254590 GCAAATTAGGAGCAGTAGTAGACAATG 60.255 40.741 0.00 0.00 0.00 2.82
2059 2155 3.116091 CAGCCTTGTGGTGGTTCTT 57.884 52.632 0.00 0.00 38.83 2.52
2060 2156 1.402787 CAGCCTTGTGGTGGTTCTTT 58.597 50.000 0.00 0.00 38.83 2.52
2099 2196 3.091545 CCTGTTGTGTGCAATTAGGGAT 58.908 45.455 0.00 0.00 37.77 3.85
2173 2271 0.105408 CAAGCTGCCAGCCTTTTGTT 59.895 50.000 14.25 0.00 43.77 2.83
2186 2284 5.047802 CAGCCTTTTGTTATTGATCTGGTGT 60.048 40.000 0.00 0.00 0.00 4.16
2187 2285 5.047802 AGCCTTTTGTTATTGATCTGGTGTG 60.048 40.000 0.00 0.00 0.00 3.82
2188 2286 5.048083 GCCTTTTGTTATTGATCTGGTGTGA 60.048 40.000 0.00 0.00 0.00 3.58
2189 2287 6.615088 CCTTTTGTTATTGATCTGGTGTGAG 58.385 40.000 0.00 0.00 0.00 3.51
2190 2288 5.627499 TTTGTTATTGATCTGGTGTGAGC 57.373 39.130 0.00 0.00 0.00 4.26
2191 2289 3.261580 TGTTATTGATCTGGTGTGAGCG 58.738 45.455 0.00 0.00 0.00 5.03
2192 2290 1.939974 TATTGATCTGGTGTGAGCGC 58.060 50.000 0.00 0.00 0.00 5.92
2193 2291 0.745845 ATTGATCTGGTGTGAGCGCC 60.746 55.000 2.29 0.00 45.23 6.53
2199 2297 4.626081 GGTGTGAGCGCCAGGTGT 62.626 66.667 2.29 0.00 44.43 4.16
2201 2299 4.662961 TGTGAGCGCCAGGTGTCG 62.663 66.667 2.29 0.00 0.00 4.35
2247 2352 3.886505 GTGTAGGTGGTTGTTGGATTTGA 59.113 43.478 0.00 0.00 0.00 2.69
2303 2412 1.340600 CCTCCCTCTCTCTGTCTCGTT 60.341 57.143 0.00 0.00 0.00 3.85
2336 2445 2.488820 GTGTCTAGGTCGACGGGC 59.511 66.667 9.92 4.52 36.71 6.13
2337 2446 3.129502 TGTCTAGGTCGACGGGCG 61.130 66.667 9.92 0.00 42.69 6.13
2338 2447 3.885521 GTCTAGGTCGACGGGCGG 61.886 72.222 9.92 0.00 41.33 6.13
2432 2824 0.594110 GGTTTTTGTCCCGCGATTCA 59.406 50.000 8.23 0.00 0.00 2.57
2475 2867 1.466950 CGCTGCGGGAAGTTTATGAAA 59.533 47.619 15.40 0.00 0.00 2.69
2479 2871 2.757868 TGCGGGAAGTTTATGAAATGGG 59.242 45.455 0.00 0.00 0.00 4.00
2510 2902 3.781079 TTTGCAGTTCTGTGAACTTGG 57.219 42.857 9.89 2.62 0.00 3.61
2593 2985 3.241701 CAGTTGCACAAGTTGTTCGTTT 58.758 40.909 5.57 0.00 0.00 3.60
2609 3002 9.006215 GTTGTTCGTTTTTAGTTGGATATATGC 57.994 33.333 0.00 0.00 0.00 3.14
2924 3318 2.703416 CTCAGTTGGCTGCATCACTTA 58.297 47.619 0.50 0.00 42.29 2.24
3106 3509 3.002246 CACAAGTTGCTCTGCTTTTCGTA 59.998 43.478 1.81 0.00 0.00 3.43
3164 3567 5.417580 AGTCTTGTTGTGTATGTGGTTGTTT 59.582 36.000 0.00 0.00 0.00 2.83
3181 3584 3.904717 TGTTTATGTGTGTTTCCCCTGT 58.095 40.909 0.00 0.00 0.00 4.00
3504 4058 7.319646 TGTTTGTAGTTGCACAAAATTCTTCT 58.680 30.769 3.19 0.00 46.81 2.85
3605 4159 6.221659 ACTGTTCCTAACTGTTTGTACTAGC 58.778 40.000 0.00 0.00 40.09 3.42
3661 4216 3.006537 GCCTATTGATTTGGCTGCATCAT 59.993 43.478 0.50 0.00 43.05 2.45
3672 4227 9.219603 GATTTGGCTGCATCATTATACTAGTTA 57.780 33.333 0.00 0.00 0.00 2.24
3755 4314 3.366440 AGGTTGTCTGTCTACACGTTC 57.634 47.619 0.00 0.00 0.00 3.95
3802 4361 2.614057 GTTGGCTGCATCCATGTACTAC 59.386 50.000 10.67 0.31 35.77 2.73
3836 4395 6.199937 ACTTCATTTTGCGCATCTTCTAAT 57.800 33.333 12.75 1.80 0.00 1.73
3981 4543 8.489489 CAACCTATCCATGTATGCTTATATCCT 58.511 37.037 0.00 0.00 0.00 3.24
4034 4604 2.106684 GGTTCTGGAAGTCAGTCCCTTT 59.893 50.000 0.00 0.00 43.76 3.11
4039 4609 1.343465 GGAAGTCAGTCCCTTTGTCGA 59.657 52.381 0.00 0.00 0.00 4.20
4083 4653 2.253154 GCCACGCCCAAAACGTAC 59.747 61.111 0.00 0.00 42.96 3.67
4119 4690 3.454812 GAGGAAGTTGAGGTAAGGGCATA 59.545 47.826 0.00 0.00 0.00 3.14
4294 4897 9.899226 GGTAAGTAAATCCTTGAATATCAATGC 57.101 33.333 0.00 0.00 35.59 3.56
4303 4906 3.743521 TGAATATCAATGCTTCTCGGGG 58.256 45.455 0.00 0.00 0.00 5.73
4331 4935 3.575256 GGGGCTGATGAATTTATGATGCA 59.425 43.478 0.00 0.00 0.00 3.96
4574 5191 6.607735 ATTGAATTGTTTCTTGCAAACCTG 57.392 33.333 0.00 0.00 32.78 4.00
4672 5295 6.127423 TGTCAGGTCTAGTATGTTTTCCTAGC 60.127 42.308 0.00 0.00 0.00 3.42
4725 5348 3.192844 AGTTGCCATGATGAGCTTTCTTG 59.807 43.478 0.00 0.00 0.00 3.02
4753 5376 3.572255 ACAAAAACGCCATATCAGTTGGT 59.428 39.130 0.00 0.00 36.57 3.67
4887 5535 0.868406 CGTTGAAGGAGTTGAGGTGC 59.132 55.000 0.00 0.00 0.00 5.01
4893 5541 2.753029 GAGTTGAGGTGCCTGCCT 59.247 61.111 0.00 0.00 42.53 4.75
4936 5591 0.251341 CAAGCTGGCAGGTTAAGGGT 60.251 55.000 29.33 6.04 33.64 4.34
4969 5624 3.427503 CGGTTTGTGAAGTTCAACAGCTT 60.428 43.478 7.25 0.00 0.00 3.74
4992 5647 1.488705 ATCCCCGCCACAGAAGTCAA 61.489 55.000 0.00 0.00 0.00 3.18
5153 5808 1.334869 GCTGACAGTGTTCAAAGGGTG 59.665 52.381 3.99 0.00 0.00 4.61
5260 5916 3.192944 TGGAAGTTCTCATCCCCAGATT 58.807 45.455 2.25 0.00 34.68 2.40
5282 5938 8.497745 AGATTAGTACATGGACCAAGATGATTT 58.502 33.333 3.84 0.00 0.00 2.17
5283 5939 8.682936 ATTAGTACATGGACCAAGATGATTTC 57.317 34.615 3.84 0.00 0.00 2.17
5365 6023 3.214328 CACTTTTCTAGCACCAACCACT 58.786 45.455 0.00 0.00 0.00 4.00
5431 6089 6.012113 TCATGGAAACCTCAAGAACATGAAT 58.988 36.000 0.00 0.00 39.90 2.57
5485 6143 1.068541 GCTTTTCGGAACATGGACCAC 60.069 52.381 0.00 0.00 0.00 4.16
5538 6196 7.128883 AGTCATGTACCCCTTTGTATTTATCCT 59.871 37.037 0.00 0.00 0.00 3.24
5692 6350 1.121240 CGTGCTATTGATCCGTCGAC 58.879 55.000 5.18 5.18 0.00 4.20
5695 6353 0.030369 GCTATTGATCCGTCGACCGT 59.970 55.000 10.58 0.00 33.66 4.83
5797 6455 1.805345 CGGATCGATCTAGTACGGCTT 59.195 52.381 23.96 0.00 0.00 4.35
5803 6461 2.612672 CGATCTAGTACGGCTTGTCTCA 59.387 50.000 0.00 0.00 0.00 3.27
5804 6462 3.251245 CGATCTAGTACGGCTTGTCTCAT 59.749 47.826 0.00 0.00 0.00 2.90
5842 6500 2.763448 CCTTCGATCTCCTGGAGTCTTT 59.237 50.000 22.50 7.19 0.00 2.52
5924 6582 2.955881 GCCTGCTAGTCCCGGTTGT 61.956 63.158 0.00 0.00 0.00 3.32
5959 6617 4.379243 CCCGCTCGTCCTGCTTGT 62.379 66.667 0.00 0.00 0.00 3.16
5960 6618 2.571757 CCGCTCGTCCTGCTTGTA 59.428 61.111 0.00 0.00 0.00 2.41
5961 6619 1.517257 CCGCTCGTCCTGCTTGTAG 60.517 63.158 0.00 0.00 0.00 2.74
5962 6620 2.161486 CGCTCGTCCTGCTTGTAGC 61.161 63.158 0.00 0.00 42.82 3.58
5963 6621 1.216710 GCTCGTCCTGCTTGTAGCT 59.783 57.895 0.00 0.00 42.97 3.32
5964 6622 0.804156 GCTCGTCCTGCTTGTAGCTC 60.804 60.000 0.00 0.00 42.97 4.09
5965 6623 0.179124 CTCGTCCTGCTTGTAGCTCC 60.179 60.000 0.00 0.00 42.97 4.70
5966 6624 1.153549 CGTCCTGCTTGTAGCTCCC 60.154 63.158 0.00 0.00 42.97 4.30
5967 6625 1.888436 CGTCCTGCTTGTAGCTCCCA 61.888 60.000 0.00 0.00 42.97 4.37
5968 6626 0.107945 GTCCTGCTTGTAGCTCCCAG 60.108 60.000 0.00 0.00 42.97 4.45
5969 6627 1.451028 CCTGCTTGTAGCTCCCAGC 60.451 63.158 0.00 0.00 42.97 4.85
5970 6628 1.451028 CTGCTTGTAGCTCCCAGCC 60.451 63.158 0.00 0.00 43.77 4.85
5971 6629 2.189191 CTGCTTGTAGCTCCCAGCCA 62.189 60.000 0.00 0.00 43.77 4.75
5972 6630 1.451028 GCTTGTAGCTCCCAGCCAG 60.451 63.158 0.00 0.00 43.77 4.85
5973 6631 1.451028 CTTGTAGCTCCCAGCCAGC 60.451 63.158 0.00 0.00 43.77 4.85
5974 6632 2.883267 CTTGTAGCTCCCAGCCAGCC 62.883 65.000 0.00 0.00 43.77 4.85
5975 6633 4.537433 GTAGCTCCCAGCCAGCCG 62.537 72.222 0.00 0.00 43.77 5.52
6086 6744 2.274948 CTGCCAGCTGCCCCTTGATA 62.275 60.000 8.66 0.00 40.16 2.15
6133 6792 2.210013 TTGCTGTCCCTCGCTGTCT 61.210 57.895 0.00 0.00 0.00 3.41
6169 6828 7.340232 TGATGGTACTAACTACACCGAGTTTAT 59.660 37.037 0.00 0.00 40.22 1.40
6173 6832 5.727434 ACTAACTACACCGAGTTTATTGGG 58.273 41.667 0.00 0.00 40.22 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 4.901197 TGTACTCACCATTGTGTACCAT 57.099 40.909 12.18 0.00 45.84 3.55
37 38 5.938125 GGTCTAAATGTACTCACCATTGTGT 59.062 40.000 0.00 0.00 43.26 3.72
61 62 7.281100 AGGCGAGGAATTCTGAAATAAACTAAG 59.719 37.037 5.23 0.00 0.00 2.18
122 124 0.322816 ATTCGGGTCACTGCAGCAAT 60.323 50.000 15.27 0.00 0.00 3.56
135 137 1.945394 CCAAGCTGAAGATGATTCGGG 59.055 52.381 0.00 0.00 0.00 5.14
139 141 5.690464 ACTAGTCCAAGCTGAAGATGATT 57.310 39.130 0.00 0.00 0.00 2.57
250 252 7.557358 TGCATTATGATACCAAACTGAGAACAT 59.443 33.333 0.00 0.00 0.00 2.71
308 311 3.001939 GGTCGTCAACAAACACTGTAAGG 59.998 47.826 0.00 0.00 37.23 2.69
328 331 9.125026 CCATGTTTTATCTGCTAATAAAGAGGT 57.875 33.333 0.00 0.00 33.77 3.85
329 332 9.342308 TCCATGTTTTATCTGCTAATAAAGAGG 57.658 33.333 0.00 0.00 33.77 3.69
405 412 1.140161 CGCCATGCAAACCAGATGG 59.860 57.895 0.00 0.00 39.84 3.51
435 442 3.449018 GCAGAGTAGGATTTCCAGAGTGA 59.551 47.826 0.00 0.00 38.89 3.41
437 444 3.450457 CAGCAGAGTAGGATTTCCAGAGT 59.550 47.826 0.00 0.00 38.89 3.24
462 469 5.594317 CCTTTGTTTCCCTTTCTCAAGAGAA 59.406 40.000 8.37 8.37 44.94 2.87
560 567 0.528249 CACTTGTGCAAAGTGTGGGC 60.528 55.000 22.81 0.00 41.90 5.36
562 569 0.102844 CCCACTTGTGCAAAGTGTGG 59.897 55.000 26.02 22.80 44.52 4.17
600 607 1.045911 GGATGGGTCTTCGGCTCTCT 61.046 60.000 0.00 0.00 0.00 3.10
653 660 3.127203 ACTTCTGACGATTCTCTACACCG 59.873 47.826 0.00 0.00 0.00 4.94
666 673 0.877071 AGCATGCCAAACTTCTGACG 59.123 50.000 15.66 0.00 0.00 4.35
684 691 2.672996 CCCAACACCCTTCGCCAG 60.673 66.667 0.00 0.00 0.00 4.85
752 759 3.449018 GTCACCTCTATGCTCTTCCTTCA 59.551 47.826 0.00 0.00 0.00 3.02
823 838 3.055602 TCTGAAGTCCATGTCACTGGATG 60.056 47.826 7.11 0.00 46.67 3.51
828 843 5.215069 AGGATATCTGAAGTCCATGTCACT 58.785 41.667 12.43 0.00 34.42 3.41
829 844 5.543507 AGGATATCTGAAGTCCATGTCAC 57.456 43.478 12.43 0.00 34.42 3.67
830 845 5.685861 GCAAGGATATCTGAAGTCCATGTCA 60.686 44.000 14.31 0.00 34.23 3.58
831 846 4.754114 GCAAGGATATCTGAAGTCCATGTC 59.246 45.833 14.31 6.96 34.23 3.06
832 847 4.411540 AGCAAGGATATCTGAAGTCCATGT 59.588 41.667 14.31 4.01 34.23 3.21
833 848 4.755629 CAGCAAGGATATCTGAAGTCCATG 59.244 45.833 12.43 11.50 34.69 3.66
834 849 4.202440 CCAGCAAGGATATCTGAAGTCCAT 60.202 45.833 12.43 0.41 41.22 3.41
835 850 3.135348 CCAGCAAGGATATCTGAAGTCCA 59.865 47.826 12.43 0.00 41.22 4.02
836 851 3.135530 ACCAGCAAGGATATCTGAAGTCC 59.864 47.826 2.05 4.11 41.22 3.85
837 852 4.141846 TGACCAGCAAGGATATCTGAAGTC 60.142 45.833 2.05 3.40 41.22 3.01
838 853 3.776969 TGACCAGCAAGGATATCTGAAGT 59.223 43.478 2.05 0.00 41.22 3.01
839 854 4.378774 CTGACCAGCAAGGATATCTGAAG 58.621 47.826 2.05 0.00 41.22 3.02
840 855 3.135348 CCTGACCAGCAAGGATATCTGAA 59.865 47.826 2.05 0.00 41.22 3.02
841 856 2.702478 CCTGACCAGCAAGGATATCTGA 59.298 50.000 2.05 0.00 41.22 3.27
842 857 2.224475 CCCTGACCAGCAAGGATATCTG 60.224 54.545 2.05 0.00 41.22 2.90
843 858 2.053244 CCCTGACCAGCAAGGATATCT 58.947 52.381 2.05 0.00 41.22 1.98
844 859 1.072965 CCCCTGACCAGCAAGGATATC 59.927 57.143 1.83 0.00 41.22 1.63
845 860 1.143813 CCCCTGACCAGCAAGGATAT 58.856 55.000 1.83 0.00 41.22 1.63
846 861 0.253160 ACCCCTGACCAGCAAGGATA 60.253 55.000 1.83 0.00 41.22 2.59
847 862 1.542375 ACCCCTGACCAGCAAGGAT 60.542 57.895 1.83 0.00 41.22 3.24
848 863 2.121963 ACCCCTGACCAGCAAGGA 60.122 61.111 1.83 0.00 41.22 3.36
849 864 2.034687 CACCCCTGACCAGCAAGG 59.965 66.667 0.00 0.00 45.67 3.61
850 865 2.674380 GCACCCCTGACCAGCAAG 60.674 66.667 0.00 0.00 0.00 4.01
891 906 4.999950 CCAAAGTCTACATCAAGAAGCACT 59.000 41.667 0.00 0.00 0.00 4.40
892 907 4.757149 ACCAAAGTCTACATCAAGAAGCAC 59.243 41.667 0.00 0.00 0.00 4.40
949 964 1.639298 GCTGCGATGAACTGACCACC 61.639 60.000 0.00 0.00 0.00 4.61
950 965 0.671781 AGCTGCGATGAACTGACCAC 60.672 55.000 0.00 0.00 0.00 4.16
978 993 1.724582 GCGCACCAGAACACACCTTT 61.725 55.000 0.30 0.00 0.00 3.11
1007 1022 4.552365 CATCCATCCCCGCACGCT 62.552 66.667 0.00 0.00 0.00 5.07
1011 1026 1.690985 TACACCATCCATCCCCGCA 60.691 57.895 0.00 0.00 0.00 5.69
1014 1029 2.586425 CATTGTACACCATCCATCCCC 58.414 52.381 0.00 0.00 0.00 4.81
1015 1030 2.091885 ACCATTGTACACCATCCATCCC 60.092 50.000 0.00 0.00 0.00 3.85
1016 1031 2.951642 CACCATTGTACACCATCCATCC 59.048 50.000 0.00 0.00 0.00 3.51
1030 1045 6.231211 AGGTCTAAAACTGTACTCACCATTG 58.769 40.000 0.00 0.00 0.00 2.82
1086 1101 3.009916 AGGCAGAACAAGTCATGAAGGAT 59.990 43.478 0.00 0.00 0.00 3.24
1132 1147 1.066114 CGCTCGTTCTCTCCGTTCAC 61.066 60.000 0.00 0.00 0.00 3.18
1210 1225 2.829384 GCCCCACCAACTGACCAGA 61.829 63.158 3.76 0.00 0.00 3.86
1323 1345 2.108168 ACGCTGGAGAACTGCCTAATA 58.892 47.619 0.00 0.00 40.57 0.98
1366 1389 4.054671 GGCACAAAATTCGAAACCATCAA 58.945 39.130 0.00 0.00 0.00 2.57
1369 1392 3.742433 TGGCACAAAATTCGAAACCAT 57.258 38.095 0.00 0.00 31.92 3.55
1441 1479 1.272147 ACAGCTAAAGCAAAGGGGGAG 60.272 52.381 4.54 0.00 45.16 4.30
1442 1480 0.777446 ACAGCTAAAGCAAAGGGGGA 59.223 50.000 4.54 0.00 45.16 4.81
1443 1481 1.273327 CAACAGCTAAAGCAAAGGGGG 59.727 52.381 4.54 0.00 45.16 5.40
1444 1482 1.273327 CCAACAGCTAAAGCAAAGGGG 59.727 52.381 4.54 0.00 45.16 4.79
1445 1483 1.963515 ACCAACAGCTAAAGCAAAGGG 59.036 47.619 4.54 3.32 45.16 3.95
1446 1484 3.383761 CAACCAACAGCTAAAGCAAAGG 58.616 45.455 4.54 3.34 45.16 3.11
1447 1485 3.181476 ACCAACCAACAGCTAAAGCAAAG 60.181 43.478 4.54 0.00 45.16 2.77
1448 1486 2.763448 ACCAACCAACAGCTAAAGCAAA 59.237 40.909 4.54 0.00 45.16 3.68
1456 1494 1.893808 CGAGCACCAACCAACAGCT 60.894 57.895 0.00 0.00 38.43 4.24
1698 1765 0.906282 GTTCGACCTCCCTAACCCCA 60.906 60.000 0.00 0.00 0.00 4.96
1764 1831 2.045340 CCAATCCGGCGGTTTCCT 60.045 61.111 27.32 0.00 0.00 3.36
1851 1932 2.278596 CCGCTCATCCCGTACGTG 60.279 66.667 15.21 2.17 0.00 4.49
1866 1947 1.473965 CCACTCATCCTCCATGAACCG 60.474 57.143 0.00 0.00 41.25 4.44
1873 1954 1.596934 GCGAACCACTCATCCTCCA 59.403 57.895 0.00 0.00 0.00 3.86
1904 1989 0.108138 AGGCTACAATCCACAGACGC 60.108 55.000 0.00 0.00 0.00 5.19
1948 2037 1.302671 CCGCGGGGGAAAAACACTA 60.303 57.895 20.10 0.00 38.47 2.74
2016 2110 7.391554 TGGCAGATTGGCTATATTATCTCAAAC 59.608 37.037 4.25 0.00 44.10 2.93
2059 2155 2.043227 GGGGAAAACACATGACCCAAA 58.957 47.619 0.00 0.00 42.03 3.28
2060 2156 1.219213 AGGGGAAAACACATGACCCAA 59.781 47.619 0.00 0.00 42.03 4.12
2173 2271 1.473257 GGCGCTCACACCAGATCAATA 60.473 52.381 7.64 0.00 0.00 1.90
2195 2293 2.438434 CATTCCCCAGGCGACACC 60.438 66.667 0.00 0.00 39.61 4.16
2196 2294 3.134127 GCATTCCCCAGGCGACAC 61.134 66.667 0.00 0.00 0.00 3.67
2201 2299 1.815817 AACAAACGCATTCCCCAGGC 61.816 55.000 0.00 0.00 0.00 4.85
2247 2352 3.444805 GGACGTCTGCCTCGAGCT 61.445 66.667 16.46 0.00 44.23 4.09
2340 2449 3.772853 TATGCAGCCCGCCACATCC 62.773 63.158 0.00 0.00 41.33 3.51
2341 2450 2.203195 TATGCAGCCCGCCACATC 60.203 61.111 0.00 0.00 41.33 3.06
2342 2451 2.203252 CTATGCAGCCCGCCACAT 60.203 61.111 0.00 0.00 41.33 3.21
2343 2452 3.390183 CTCTATGCAGCCCGCCACA 62.390 63.158 0.00 0.00 41.33 4.17
2344 2453 2.590007 CTCTATGCAGCCCGCCAC 60.590 66.667 0.00 0.00 41.33 5.01
2432 2824 2.947652 CCATGAACAGCGAATCAAGGAT 59.052 45.455 0.00 0.00 36.72 3.24
2444 2836 4.170062 CGCAGCGGCCATGAACAG 62.170 66.667 7.00 0.00 36.38 3.16
2475 2867 0.754472 GCAAATGCATAGCCACCCAT 59.246 50.000 11.84 0.00 41.59 4.00
2510 2902 4.608951 ACTCGAACACAACTAAGAGACAC 58.391 43.478 0.00 0.00 0.00 3.67
3100 3503 7.348279 ACCATATTGGCAACTCGAATACGAAA 61.348 38.462 0.00 0.00 44.23 3.46
3106 3509 4.156455 AGACCATATTGGCAACTCGAAT 57.844 40.909 0.00 0.00 42.67 3.34
3133 3536 5.523552 CACATACACAACAAGACTGACAGAA 59.476 40.000 10.08 0.00 0.00 3.02
3164 3567 3.218453 CACAACAGGGGAAACACACATA 58.782 45.455 0.00 0.00 34.58 2.29
3181 3584 1.454847 GGACCCTGGTTGCACACAA 60.455 57.895 0.00 0.00 0.00 3.33
3605 4159 3.845178 TGAATAGCGTGTAGACAACCAG 58.155 45.455 0.00 0.00 0.00 4.00
3661 4216 7.655521 ACACATGGACAGCTAACTAGTATAA 57.344 36.000 0.00 0.00 0.00 0.98
3672 4227 4.022068 CCATTGTAAAACACATGGACAGCT 60.022 41.667 12.20 0.00 38.18 4.24
3802 4361 4.911610 CGCAAAATGAAGTACAGAACCAAG 59.088 41.667 0.00 0.00 0.00 3.61
4039 4609 3.034030 GCAGCACGCTTTGTCCTT 58.966 55.556 0.00 0.00 37.77 3.36
4083 4653 1.830477 CTTCCTCTCCCTCCTCAACAG 59.170 57.143 0.00 0.00 0.00 3.16
4119 4690 8.522830 CCAAAATAAGGTGAATGTGTAATCAGT 58.477 33.333 0.00 0.00 0.00 3.41
4294 4897 0.393944 GCCCCTAAAACCCCGAGAAG 60.394 60.000 0.00 0.00 0.00 2.85
4303 4906 7.346751 TCATAAATTCATCAGCCCCTAAAAC 57.653 36.000 0.00 0.00 0.00 2.43
4599 5220 4.353737 CAACGATAAAGCATGATGTTGGG 58.646 43.478 0.00 0.00 33.46 4.12
4725 5348 2.141535 TATGGCGTTTTTGTGCAACC 57.858 45.000 0.00 0.00 34.36 3.77
4863 5511 0.756294 TCAACTCCTTCAACGCTGGA 59.244 50.000 0.00 0.00 0.00 3.86
4887 5535 1.077212 CCACATCTTCCCAGGCAGG 60.077 63.158 0.00 0.00 37.03 4.85
4893 5541 1.596934 GTCGCTCCACATCTTCCCA 59.403 57.895 0.00 0.00 0.00 4.37
4969 5624 1.971505 CTTCTGTGGCGGGGATAGCA 61.972 60.000 0.00 0.00 36.08 3.49
4992 5647 4.099419 CCCAAACAACCTTGAAACTAGCTT 59.901 41.667 0.00 0.00 0.00 3.74
5111 5766 1.212688 TCGACACGGATACTTCCCCTA 59.787 52.381 0.00 0.00 39.01 3.53
5153 5808 5.180810 AGACCCCTTTAGGAAGATCAAAC 57.819 43.478 0.00 0.00 38.24 2.93
5260 5916 6.280643 CGAAATCATCTTGGTCCATGTACTA 58.719 40.000 4.76 0.00 0.00 1.82
5431 6089 7.446769 TGTGTTCTACTACAAAAAGGCAGATA 58.553 34.615 0.00 0.00 0.00 1.98
5485 6143 5.883328 TTATAACTCTAACATGCTTCGCG 57.117 39.130 0.00 0.00 0.00 5.87
5538 6196 3.074687 TGCAGGAAACCCCTTATACAACA 59.925 43.478 0.00 0.00 44.85 3.33
5715 6373 1.959226 GCCAGACGAGCGGAAACAA 60.959 57.895 0.00 0.00 0.00 2.83
5791 6449 1.079127 CGGGAATGAGACAAGCCGT 60.079 57.895 0.00 0.00 0.00 5.68
5797 6455 1.202417 GCTTCGATCGGGAATGAGACA 60.202 52.381 16.41 0.00 0.00 3.41
5803 6461 2.819284 GGGGGCTTCGATCGGGAAT 61.819 63.158 16.41 0.00 0.00 3.01
5804 6462 3.476419 GGGGGCTTCGATCGGGAA 61.476 66.667 16.41 1.82 0.00 3.97
5823 6481 3.431415 TCAAAGACTCCAGGAGATCGAA 58.569 45.455 24.45 0.95 33.32 3.71
5909 6567 0.613853 AGCTACAACCGGGACTAGCA 60.614 55.000 21.71 0.00 35.10 3.49
5950 6608 1.903877 GCTGGGAGCTACAAGCAGGA 61.904 60.000 21.36 0.00 45.56 3.86
5951 6609 1.451028 GCTGGGAGCTACAAGCAGG 60.451 63.158 21.36 0.00 45.56 4.85
5952 6610 1.451028 GGCTGGGAGCTACAAGCAG 60.451 63.158 27.03 11.83 45.56 4.24
5953 6611 2.189191 CTGGCTGGGAGCTACAAGCA 62.189 60.000 27.03 11.97 45.56 3.91
5954 6612 1.451028 CTGGCTGGGAGCTACAAGC 60.451 63.158 18.02 18.02 41.99 4.01
5955 6613 1.451028 GCTGGCTGGGAGCTACAAG 60.451 63.158 0.00 0.00 41.99 3.16
5956 6614 2.671070 GCTGGCTGGGAGCTACAA 59.329 61.111 0.00 0.00 41.99 2.41
5957 6615 3.402681 GGCTGGCTGGGAGCTACA 61.403 66.667 0.00 0.00 41.99 2.74
5958 6616 4.537433 CGGCTGGCTGGGAGCTAC 62.537 72.222 0.00 0.00 41.99 3.58
6041 6699 1.546548 GGCTGAAGAAAAGCAGGGACT 60.547 52.381 0.00 0.00 42.69 3.85
6050 6708 1.070786 AGTCGGCGGCTGAAGAAAA 59.929 52.632 15.69 0.00 0.00 2.29
6133 6792 6.620877 AGTTAGTACCATCAAAGATCACCA 57.379 37.500 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.