Multiple sequence alignment - TraesCS7D01G021800

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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 TraesCS7D01G021800 chr7D 100.000 2582 0 0 1 2582 10466609 10464028 0.000000e+00 4769.0
1 TraesCS7D01G021800 chr7D 76.964 1706 268 54 783 2401 8818639 8820306 0.000000e+00 857.0
2 TraesCS7D01G021800 chr7D 78.723 1363 222 37 1071 2384 10963566 10962223 0.000000e+00 848.0
3 TraesCS7D01G021800 chr7D 76.706 1700 281 60 921 2568 8870072 8871708 0.000000e+00 839.0
4 TraesCS7D01G021800 chr7D 78.382 1360 226 33 1080 2401 10974144 10972815 0.000000e+00 821.0
5 TraesCS7D01G021800 chr7D 77.877 1347 227 42 1080 2393 10150994 10149686 0.000000e+00 771.0
6 TraesCS7D01G021800 chr7D 77.580 1347 216 49 1080 2357 10910332 10909003 0.000000e+00 736.0
7 TraesCS7D01G021800 chr7D 77.248 1301 227 41 1082 2329 1520441 1519157 0.000000e+00 699.0
8 TraesCS7D01G021800 chr7D 76.308 1051 199 30 1164 2184 1205736 1206766 1.370000e-142 516.0
9 TraesCS7D01G021800 chr7D 79.173 701 123 15 1071 1759 9354923 9355612 5.030000e-127 464.0
10 TraesCS7D01G021800 chr7D 84.706 170 26 0 2404 2573 10972782 10972613 1.230000e-38 171.0
11 TraesCS7D01G021800 chr7D 84.906 159 20 3 2416 2571 9235844 9236001 9.560000e-35 158.0
12 TraesCS7D01G021800 chr7A 92.172 1533 91 16 1071 2582 9669782 9668258 0.000000e+00 2139.0
13 TraesCS7D01G021800 chr7A 78.162 1360 229 37 1080 2401 10169864 10168535 0.000000e+00 804.0
14 TraesCS7D01G021800 chr7A 76.026 1560 250 57 780 2267 9381806 9383313 0.000000e+00 695.0
15 TraesCS7D01G021800 chr7A 76.008 1488 259 44 859 2300 9494122 9495557 0.000000e+00 680.0
16 TraesCS7D01G021800 chr7A 76.552 1369 243 40 1080 2400 114688660 114687322 0.000000e+00 678.0
17 TraesCS7D01G021800 chr7A 87.931 290 20 2 753 1037 9676238 9675959 6.890000e-86 327.0
18 TraesCS7D01G021800 chr7A 87.586 290 21 2 753 1037 9678836 9678557 3.210000e-84 322.0
19 TraesCS7D01G021800 chr7A 92.063 189 13 2 264 450 5431528 5431340 5.480000e-67 265.0
20 TraesCS7D01G021800 chr7A 80.620 258 43 3 5 262 9381281 9381531 2.620000e-45 193.0
21 TraesCS7D01G021800 chr7A 78.305 295 46 13 2295 2573 10105521 10105229 9.500000e-40 174.0
22 TraesCS7D01G021800 chr7A 81.081 185 27 5 2406 2582 10156237 10156053 9.630000e-30 141.0
23 TraesCS7D01G021800 chr7A 83.117 154 19 4 2419 2571 9687187 9687040 1.610000e-27 134.0
24 TraesCS7D01G021800 chr7A 83.810 105 17 0 2406 2510 10167550 10167446 1.630000e-17 100.0
25 TraesCS7D01G021800 chr4A 77.723 2020 295 77 466 2403 729818730 729820676 0.000000e+00 1094.0
26 TraesCS7D01G021800 chr4A 76.885 2003 326 69 471 2401 729925047 729926984 0.000000e+00 1007.0
27 TraesCS7D01G021800 chr4A 76.746 2047 297 85 461 2400 729156771 729158745 0.000000e+00 977.0
28 TraesCS7D01G021800 chr4A 78.667 1350 237 32 1080 2393 728645336 728644002 0.000000e+00 850.0
29 TraesCS7D01G021800 chr4A 78.529 1346 223 30 1080 2390 729972565 729971251 0.000000e+00 824.0
30 TraesCS7D01G021800 chr4A 80.197 1116 184 23 1080 2176 728352981 728351884 0.000000e+00 802.0
31 TraesCS7D01G021800 chr4A 78.475 1259 226 25 1071 2297 729827582 729828827 0.000000e+00 782.0
32 TraesCS7D01G021800 chr4A 78.003 1332 225 33 1080 2377 729880958 729882255 0.000000e+00 774.0
33 TraesCS7D01G021800 chr4A 76.555 1527 249 61 815 2266 730004642 730003150 0.000000e+00 736.0
34 TraesCS7D01G021800 chr4A 76.495 1221 223 36 1071 2242 730322861 730324066 7.900000e-170 606.0
35 TraesCS7D01G021800 chr4A 75.041 1234 233 43 1403 2573 727711493 727712714 1.070000e-138 503.0
36 TraesCS7D01G021800 chr4A 76.974 899 130 33 791 1652 729677558 729678416 2.360000e-120 442.0
37 TraesCS7D01G021800 chr4A 86.545 275 30 2 792 1060 730061513 730061240 1.940000e-76 296.0
38 TraesCS7D01G021800 chr4A 90.503 179 14 2 2406 2582 728351483 728351306 1.540000e-57 233.0
39 TraesCS7D01G021800 chr4A 85.294 170 22 1 2416 2582 729238209 729238378 3.420000e-39 172.0
40 TraesCS7D01G021800 chr4A 87.179 156 15 2 2431 2582 742717659 742717813 3.420000e-39 172.0
41 TraesCS7D01G021800 chr4A 94.444 108 5 1 533 639 730005022 730004915 5.720000e-37 165.0
42 TraesCS7D01G021800 chr4A 90.769 65 5 1 558 621 730061575 730061511 4.580000e-13 86.1
43 TraesCS7D01G021800 chr4A 94.118 51 0 2 561 610 730005077 730005029 9.910000e-10 75.0
44 TraesCS7D01G021800 chr4A 92.857 42 3 0 2362 2403 742717604 742717645 7.710000e-06 62.1
45 TraesCS7D01G021800 chr5A 79.120 1614 231 48 789 2319 691820781 691822371 0.000000e+00 1016.0
46 TraesCS7D01G021800 chr5A 95.745 188 7 1 264 450 22234235 22234048 4.180000e-78 302.0
47 TraesCS7D01G021800 chr5A 93.617 188 12 0 263 450 646899558 646899745 5.440000e-72 281.0
48 TraesCS7D01G021800 chr4B 78.676 1632 232 58 791 2326 654201712 654203323 0.000000e+00 979.0
49 TraesCS7D01G021800 chr4B 93.194 191 9 1 264 450 483912485 483912295 7.040000e-71 278.0
50 TraesCS7D01G021800 chr4D 80.592 1283 200 22 1080 2326 507352129 507350860 0.000000e+00 944.0
51 TraesCS7D01G021800 chr7B 77.990 1363 229 38 1080 2401 68160591 68159259 0.000000e+00 789.0
52 TraesCS7D01G021800 chr1A 76.058 898 138 48 1080 1941 589182051 589181195 1.860000e-106 396.0
53 TraesCS7D01G021800 chr3B 96.809 188 6 0 263 450 67381521 67381708 5.360000e-82 315.0
54 TraesCS7D01G021800 chr1D 97.312 186 4 1 265 450 335042013 335042197 5.360000e-82 315.0
55 TraesCS7D01G021800 chr1D 88.500 200 18 5 253 449 24026425 24026622 1.190000e-58 237.0
56 TraesCS7D01G021800 chr3A 95.767 189 6 2 263 450 55217933 55218120 1.160000e-78 303.0
57 TraesCS7D01G021800 chr2A 91.005 189 14 2 265 450 748820817 748821005 4.270000e-63 252.0


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 TraesCS7D01G021800 chr7D 10464028 10466609 2581 True 4769.000000 4769 100.000000 1 2582 1 chr7D.!!$R3 2581
1 TraesCS7D01G021800 chr7D 8818639 8820306 1667 False 857.000000 857 76.964000 783 2401 1 chr7D.!!$F2 1618
2 TraesCS7D01G021800 chr7D 10962223 10963566 1343 True 848.000000 848 78.723000 1071 2384 1 chr7D.!!$R5 1313
3 TraesCS7D01G021800 chr7D 8870072 8871708 1636 False 839.000000 839 76.706000 921 2568 1 chr7D.!!$F3 1647
4 TraesCS7D01G021800 chr7D 10149686 10150994 1308 True 771.000000 771 77.877000 1080 2393 1 chr7D.!!$R2 1313
5 TraesCS7D01G021800 chr7D 10909003 10910332 1329 True 736.000000 736 77.580000 1080 2357 1 chr7D.!!$R4 1277
6 TraesCS7D01G021800 chr7D 1519157 1520441 1284 True 699.000000 699 77.248000 1082 2329 1 chr7D.!!$R1 1247
7 TraesCS7D01G021800 chr7D 1205736 1206766 1030 False 516.000000 516 76.308000 1164 2184 1 chr7D.!!$F1 1020
8 TraesCS7D01G021800 chr7D 10972613 10974144 1531 True 496.000000 821 81.544000 1080 2573 2 chr7D.!!$R6 1493
9 TraesCS7D01G021800 chr7D 9354923 9355612 689 False 464.000000 464 79.173000 1071 1759 1 chr7D.!!$F5 688
10 TraesCS7D01G021800 chr7A 9668258 9669782 1524 True 2139.000000 2139 92.172000 1071 2582 1 chr7A.!!$R2 1511
11 TraesCS7D01G021800 chr7A 9494122 9495557 1435 False 680.000000 680 76.008000 859 2300 1 chr7A.!!$F1 1441
12 TraesCS7D01G021800 chr7A 114687322 114688660 1338 True 678.000000 678 76.552000 1080 2400 1 chr7A.!!$R6 1320
13 TraesCS7D01G021800 chr7A 10167446 10169864 2418 True 452.000000 804 80.986000 1080 2510 2 chr7A.!!$R8 1430
14 TraesCS7D01G021800 chr7A 9381281 9383313 2032 False 444.000000 695 78.323000 5 2267 2 chr7A.!!$F2 2262
15 TraesCS7D01G021800 chr7A 9675959 9678836 2877 True 324.500000 327 87.758500 753 1037 2 chr7A.!!$R7 284
16 TraesCS7D01G021800 chr4A 729818730 729820676 1946 False 1094.000000 1094 77.723000 466 2403 1 chr4A.!!$F5 1937
17 TraesCS7D01G021800 chr4A 729925047 729926984 1937 False 1007.000000 1007 76.885000 471 2401 1 chr4A.!!$F8 1930
18 TraesCS7D01G021800 chr4A 729156771 729158745 1974 False 977.000000 977 76.746000 461 2400 1 chr4A.!!$F2 1939
19 TraesCS7D01G021800 chr4A 728644002 728645336 1334 True 850.000000 850 78.667000 1080 2393 1 chr4A.!!$R1 1313
20 TraesCS7D01G021800 chr4A 729971251 729972565 1314 True 824.000000 824 78.529000 1080 2390 1 chr4A.!!$R2 1310
21 TraesCS7D01G021800 chr4A 729827582 729828827 1245 False 782.000000 782 78.475000 1071 2297 1 chr4A.!!$F6 1226
22 TraesCS7D01G021800 chr4A 729880958 729882255 1297 False 774.000000 774 78.003000 1080 2377 1 chr4A.!!$F7 1297
23 TraesCS7D01G021800 chr4A 730322861 730324066 1205 False 606.000000 606 76.495000 1071 2242 1 chr4A.!!$F9 1171
24 TraesCS7D01G021800 chr4A 728351306 728352981 1675 True 517.500000 802 85.350000 1080 2582 2 chr4A.!!$R3 1502
25 TraesCS7D01G021800 chr4A 727711493 727712714 1221 False 503.000000 503 75.041000 1403 2573 1 chr4A.!!$F1 1170
26 TraesCS7D01G021800 chr4A 729677558 729678416 858 False 442.000000 442 76.974000 791 1652 1 chr4A.!!$F4 861
27 TraesCS7D01G021800 chr4A 730003150 730005077 1927 True 325.333333 736 88.372333 533 2266 3 chr4A.!!$R4 1733
28 TraesCS7D01G021800 chr5A 691820781 691822371 1590 False 1016.000000 1016 79.120000 789 2319 1 chr5A.!!$F2 1530
29 TraesCS7D01G021800 chr4B 654201712 654203323 1611 False 979.000000 979 78.676000 791 2326 1 chr4B.!!$F1 1535
30 TraesCS7D01G021800 chr4D 507350860 507352129 1269 True 944.000000 944 80.592000 1080 2326 1 chr4D.!!$R1 1246
31 TraesCS7D01G021800 chr7B 68159259 68160591 1332 True 789.000000 789 77.990000 1080 2401 1 chr7B.!!$R1 1321
32 TraesCS7D01G021800 chr1A 589181195 589182051 856 True 396.000000 396 76.058000 1080 1941 1 chr1A.!!$R1 861

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
97 98 0.035056 CCGGCCCATCCCTCATTATC 60.035 60.0 0.0 0.0 0.0 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1818 4066 0.251922 TGTAAGCACCCCTAGGACGT 60.252 55.0 11.48 2.58 36.73 4.34 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
67 68 4.265056 AACGCTCCCGCCCTTGTT 62.265 61.111 0.00 0.00 38.22 2.83
74 75 2.348998 CCGCCCTTGTTGAGCTCT 59.651 61.111 16.19 0.00 0.00 4.09
78 79 1.362406 GCCCTTGTTGAGCTCTACGC 61.362 60.000 20.79 14.82 39.57 4.42
95 96 2.829384 GCCGGCCCATCCCTCATTA 61.829 63.158 18.11 0.00 0.00 1.90
96 97 2.078452 CCGGCCCATCCCTCATTAT 58.922 57.895 0.00 0.00 0.00 1.28
97 98 0.035056 CCGGCCCATCCCTCATTATC 60.035 60.000 0.00 0.00 0.00 1.75
101 102 2.616510 GGCCCATCCCTCATTATCGAAG 60.617 54.545 0.00 0.00 0.00 3.79
103 104 2.616510 CCCATCCCTCATTATCGAAGCC 60.617 54.545 0.00 0.00 0.00 4.35
115 116 2.592308 GAAGCCCGAGCCATCCTT 59.408 61.111 0.00 0.00 41.25 3.36
124 125 0.106318 GAGCCATCCTTGAGCCCATT 60.106 55.000 0.00 0.00 0.00 3.16
135 136 0.182061 GAGCCCATTGAGGATGAGCA 59.818 55.000 0.00 0.00 41.55 4.26
143 144 0.545071 TGAGGATGAGCAGGTGGTGA 60.545 55.000 0.00 0.00 0.00 4.02
147 148 0.176680 GATGAGCAGGTGGTGACGAT 59.823 55.000 0.00 0.00 0.00 3.73
153 154 1.014044 CAGGTGGTGACGATGAACCG 61.014 60.000 0.00 0.00 39.47 4.44
156 157 3.186047 GGTGACGATGAACCGCCG 61.186 66.667 0.00 0.00 0.00 6.46
177 178 3.462021 GCAGGATCTTTATTCGTGAGCT 58.538 45.455 0.00 0.00 32.17 4.09
185 186 5.651530 TCTTTATTCGTGAGCTAGAGTTGG 58.348 41.667 0.00 0.00 0.00 3.77
188 189 1.464734 TCGTGAGCTAGAGTTGGAGG 58.535 55.000 0.00 0.00 0.00 4.30
198 199 3.133141 AGAGTTGGAGGAGACTTTTGC 57.867 47.619 0.00 0.00 44.43 3.68
203 204 1.768275 TGGAGGAGACTTTTGCAGACA 59.232 47.619 0.00 0.00 44.43 3.41
205 206 3.214328 GGAGGAGACTTTTGCAGACAAA 58.786 45.455 0.00 0.00 44.43 2.83
207 208 3.217626 AGGAGACTTTTGCAGACAAAGG 58.782 45.455 12.69 0.00 46.08 3.11
208 209 3.117888 AGGAGACTTTTGCAGACAAAGGA 60.118 43.478 12.69 0.00 46.08 3.36
210 211 3.620488 AGACTTTTGCAGACAAAGGACA 58.380 40.909 12.69 0.00 46.08 4.02
211 212 4.016444 AGACTTTTGCAGACAAAGGACAA 58.984 39.130 12.69 0.00 46.08 3.18
212 213 4.096984 AGACTTTTGCAGACAAAGGACAAG 59.903 41.667 12.69 0.00 46.08 3.16
214 215 2.727123 TTGCAGACAAAGGACAAGGA 57.273 45.000 0.00 0.00 31.21 3.36
215 216 2.957402 TGCAGACAAAGGACAAGGAT 57.043 45.000 0.00 0.00 0.00 3.24
216 217 2.507484 TGCAGACAAAGGACAAGGATG 58.493 47.619 0.00 0.00 0.00 3.51
218 219 2.485814 GCAGACAAAGGACAAGGATGAC 59.514 50.000 0.00 0.00 0.00 3.06
253 254 2.264480 CAATGACCACGAGGCCGA 59.736 61.111 0.00 0.00 39.06 5.54
256 257 2.593468 AATGACCACGAGGCCGATGG 62.593 60.000 18.35 18.35 40.38 3.51
257 258 3.771160 GACCACGAGGCCGATGGT 61.771 66.667 23.74 23.74 45.66 3.55
258 259 3.310860 GACCACGAGGCCGATGGTT 62.311 63.158 24.16 11.99 44.25 3.67
259 260 2.511600 CCACGAGGCCGATGGTTC 60.512 66.667 13.29 0.00 39.50 3.62
260 261 2.579201 CACGAGGCCGATGGTTCT 59.421 61.111 0.00 0.00 39.50 3.01
262 263 1.982395 ACGAGGCCGATGGTTCTGA 60.982 57.895 0.00 0.00 39.50 3.27
263 264 1.519455 CGAGGCCGATGGTTCTGAC 60.519 63.158 0.00 0.00 38.22 3.51
264 265 1.596934 GAGGCCGATGGTTCTGACA 59.403 57.895 0.00 0.00 0.00 3.58
265 266 0.460987 GAGGCCGATGGTTCTGACAG 60.461 60.000 0.00 0.00 0.00 3.51
266 267 1.194781 AGGCCGATGGTTCTGACAGT 61.195 55.000 1.59 0.00 0.00 3.55
268 269 1.021390 GCCGATGGTTCTGACAGTGG 61.021 60.000 1.59 0.00 0.00 4.00
270 271 1.354337 CGATGGTTCTGACAGTGGCG 61.354 60.000 1.59 0.00 0.00 5.69
271 272 1.003355 ATGGTTCTGACAGTGGCGG 60.003 57.895 0.00 0.00 0.00 6.13
272 273 1.480212 ATGGTTCTGACAGTGGCGGA 61.480 55.000 2.36 2.36 0.00 5.54
288 289 2.245159 CGGAGCTTGAGCATAATCCA 57.755 50.000 5.70 0.00 45.16 3.41
289 290 2.564771 CGGAGCTTGAGCATAATCCAA 58.435 47.619 5.70 0.00 45.16 3.53
290 291 2.547211 CGGAGCTTGAGCATAATCCAAG 59.453 50.000 5.70 0.00 45.16 3.61
291 292 3.742327 CGGAGCTTGAGCATAATCCAAGA 60.742 47.826 5.70 0.00 45.16 3.02
292 293 3.563390 GGAGCTTGAGCATAATCCAAGAC 59.437 47.826 5.70 0.00 45.16 3.01
293 294 3.201290 AGCTTGAGCATAATCCAAGACG 58.799 45.455 5.70 0.00 45.16 4.18
294 295 2.289002 GCTTGAGCATAATCCAAGACGG 59.711 50.000 0.00 0.00 41.59 4.79
295 296 2.620251 TGAGCATAATCCAAGACGGG 57.380 50.000 0.00 0.00 34.36 5.28
296 297 2.115427 TGAGCATAATCCAAGACGGGA 58.885 47.619 0.00 0.00 42.21 5.14
297 298 2.158957 TGAGCATAATCCAAGACGGGAC 60.159 50.000 0.00 0.00 40.44 4.46
299 300 1.134220 GCATAATCCAAGACGGGACCA 60.134 52.381 0.00 0.00 40.44 4.02
300 301 2.487265 GCATAATCCAAGACGGGACCAT 60.487 50.000 0.00 0.00 40.44 3.55
301 302 3.820557 CATAATCCAAGACGGGACCATT 58.179 45.455 0.00 0.00 40.44 3.16
303 304 3.560636 AATCCAAGACGGGACCATTAG 57.439 47.619 0.00 0.00 40.44 1.73
304 305 0.539986 TCCAAGACGGGACCATTAGC 59.460 55.000 0.00 0.00 34.36 3.09
305 306 0.541863 CCAAGACGGGACCATTAGCT 59.458 55.000 0.00 0.00 0.00 3.32
306 307 1.656652 CAAGACGGGACCATTAGCTG 58.343 55.000 0.00 0.00 0.00 4.24
307 308 1.207089 CAAGACGGGACCATTAGCTGA 59.793 52.381 0.00 0.00 0.00 4.26
308 309 1.568504 AGACGGGACCATTAGCTGAA 58.431 50.000 0.00 0.00 0.00 3.02
309 310 1.482593 AGACGGGACCATTAGCTGAAG 59.517 52.381 0.00 0.00 0.00 3.02
310 311 0.541863 ACGGGACCATTAGCTGAAGG 59.458 55.000 0.00 0.00 0.00 3.46
311 312 0.179045 CGGGACCATTAGCTGAAGGG 60.179 60.000 4.66 5.11 44.98 3.95
312 313 1.213296 GGGACCATTAGCTGAAGGGA 58.787 55.000 4.66 0.00 41.85 4.20
314 315 1.141858 GGACCATTAGCTGAAGGGAGG 59.858 57.143 4.66 0.00 41.85 4.30
315 316 0.548510 ACCATTAGCTGAAGGGAGGC 59.451 55.000 4.66 0.00 41.85 4.70
316 317 0.548031 CCATTAGCTGAAGGGAGGCA 59.452 55.000 0.00 0.00 41.85 4.75
319 320 3.294214 CATTAGCTGAAGGGAGGCAAAT 58.706 45.455 0.00 0.00 0.00 2.32
320 321 3.456380 TTAGCTGAAGGGAGGCAAATT 57.544 42.857 0.00 0.00 0.00 1.82
322 323 3.456380 AGCTGAAGGGAGGCAAATTAA 57.544 42.857 0.00 0.00 0.00 1.40
323 324 3.986435 AGCTGAAGGGAGGCAAATTAAT 58.014 40.909 0.00 0.00 0.00 1.40
324 325 5.129368 AGCTGAAGGGAGGCAAATTAATA 57.871 39.130 0.00 0.00 0.00 0.98
325 326 5.136105 AGCTGAAGGGAGGCAAATTAATAG 58.864 41.667 0.00 0.00 0.00 1.73
327 328 4.803452 TGAAGGGAGGCAAATTAATAGGG 58.197 43.478 0.00 0.00 0.00 3.53
328 329 4.480537 TGAAGGGAGGCAAATTAATAGGGA 59.519 41.667 0.00 0.00 0.00 4.20
329 330 5.043732 TGAAGGGAGGCAAATTAATAGGGAA 60.044 40.000 0.00 0.00 0.00 3.97
330 331 5.066913 AGGGAGGCAAATTAATAGGGAAG 57.933 43.478 0.00 0.00 0.00 3.46
331 332 4.140924 AGGGAGGCAAATTAATAGGGAAGG 60.141 45.833 0.00 0.00 0.00 3.46
332 333 4.141018 GGGAGGCAAATTAATAGGGAAGGA 60.141 45.833 0.00 0.00 0.00 3.36
333 334 5.073428 GGAGGCAAATTAATAGGGAAGGAG 58.927 45.833 0.00 0.00 0.00 3.69
335 336 4.140924 AGGCAAATTAATAGGGAAGGAGGG 60.141 45.833 0.00 0.00 0.00 4.30
336 337 4.152647 GCAAATTAATAGGGAAGGAGGGG 58.847 47.826 0.00 0.00 0.00 4.79
337 338 4.152647 CAAATTAATAGGGAAGGAGGGGC 58.847 47.826 0.00 0.00 0.00 5.80
338 339 2.910360 TTAATAGGGAAGGAGGGGCT 57.090 50.000 0.00 0.00 0.00 5.19
343 344 0.650558 AGGGAAGGAGGGGCTAATCT 59.349 55.000 0.00 0.00 0.00 2.40
344 345 1.060729 GGGAAGGAGGGGCTAATCTC 58.939 60.000 0.00 0.00 0.00 2.75
345 346 1.415273 GGGAAGGAGGGGCTAATCTCT 60.415 57.143 0.00 0.00 0.00 3.10
349 350 4.228010 GAAGGAGGGGCTAATCTCTAGTT 58.772 47.826 0.00 0.00 0.00 2.24
350 351 4.288324 AGGAGGGGCTAATCTCTAGTTT 57.712 45.455 0.00 0.00 0.00 2.66
351 352 5.420215 AGGAGGGGCTAATCTCTAGTTTA 57.580 43.478 0.00 0.00 0.00 2.01
353 354 6.210522 AGGAGGGGCTAATCTCTAGTTTAAA 58.789 40.000 0.00 0.00 0.00 1.52
355 356 6.126854 GGAGGGGCTAATCTCTAGTTTAAACA 60.127 42.308 20.06 5.82 0.00 2.83
356 357 6.651086 AGGGGCTAATCTCTAGTTTAAACAC 58.349 40.000 20.06 0.00 0.00 3.32
357 358 6.444171 AGGGGCTAATCTCTAGTTTAAACACT 59.556 38.462 20.06 3.08 0.00 3.55
358 359 7.622479 AGGGGCTAATCTCTAGTTTAAACACTA 59.378 37.037 20.06 4.14 0.00 2.74
359 360 7.927092 GGGGCTAATCTCTAGTTTAAACACTAG 59.073 40.741 20.06 13.37 45.43 2.57
360 361 8.476447 GGGCTAATCTCTAGTTTAAACACTAGT 58.524 37.037 20.06 1.88 44.68 2.57
361 362 9.872721 GGCTAATCTCTAGTTTAAACACTAGTT 57.127 33.333 20.06 9.74 44.68 2.24
365 366 9.872721 AATCTCTAGTTTAAACACTAGTTAGGC 57.127 33.333 20.06 0.00 44.68 3.93
367 368 7.673082 TCTCTAGTTTAAACACTAGTTAGGCCT 59.327 37.037 20.06 11.78 44.68 5.19
368 369 8.884124 TCTAGTTTAAACACTAGTTAGGCCTA 57.116 34.615 20.06 8.91 44.68 3.93
369 370 9.312904 TCTAGTTTAAACACTAGTTAGGCCTAA 57.687 33.333 21.68 21.68 44.68 2.69
370 371 9.933723 CTAGTTTAAACACTAGTTAGGCCTAAA 57.066 33.333 26.78 11.65 40.99 1.85
372 373 9.803507 AGTTTAAACACTAGTTAGGCCTAAAAT 57.196 29.630 26.78 19.66 36.84 1.82
377 378 6.818233 ACACTAGTTAGGCCTAAAATAGAGC 58.182 40.000 33.02 19.91 0.00 4.09
378 379 6.383147 ACACTAGTTAGGCCTAAAATAGAGCA 59.617 38.462 33.02 10.85 0.00 4.26
379 380 7.071321 ACACTAGTTAGGCCTAAAATAGAGCAT 59.929 37.037 33.02 18.94 0.00 3.79
381 382 9.327731 ACTAGTTAGGCCTAAAATAGAGCATAT 57.672 33.333 33.02 18.22 0.00 1.78
384 385 8.885346 AGTTAGGCCTAAAATAGAGCATATTCT 58.115 33.333 26.78 11.23 0.00 2.40
385 386 9.508642 GTTAGGCCTAAAATAGAGCATATTCTT 57.491 33.333 26.78 0.00 0.00 2.52
408 409 8.862085 TCTTTAATGGTTGTAAAAGTTAAGGGG 58.138 33.333 0.00 0.00 32.15 4.79
409 410 7.541916 TTAATGGTTGTAAAAGTTAAGGGGG 57.458 36.000 0.00 0.00 0.00 5.40
429 430 3.068064 CCATTGCCCCCGTTGGTC 61.068 66.667 0.00 0.00 0.00 4.02
431 432 1.301623 CATTGCCCCCGTTGGTCTA 59.698 57.895 0.00 0.00 0.00 2.59
432 433 1.029947 CATTGCCCCCGTTGGTCTAC 61.030 60.000 0.00 0.00 0.00 2.59
433 434 1.493854 ATTGCCCCCGTTGGTCTACA 61.494 55.000 0.00 0.00 0.00 2.74
434 435 2.046604 GCCCCCGTTGGTCTACAC 60.047 66.667 0.00 0.00 0.00 2.90
436 437 2.277591 CCCCCGTTGGTCTACACGA 61.278 63.158 0.00 0.00 0.00 4.35
437 438 1.667151 CCCCGTTGGTCTACACGAA 59.333 57.895 0.00 0.00 0.00 3.85
438 439 0.389426 CCCCGTTGGTCTACACGAAG 60.389 60.000 0.00 0.00 0.00 3.79
439 440 1.012486 CCCGTTGGTCTACACGAAGC 61.012 60.000 0.00 0.00 0.00 3.86
440 441 0.038526 CCGTTGGTCTACACGAAGCT 60.039 55.000 0.00 0.00 0.00 3.74
442 443 1.711206 GTTGGTCTACACGAAGCTCC 58.289 55.000 0.00 0.00 0.00 4.70
444 445 1.516603 GGTCTACACGAAGCTCCGC 60.517 63.158 0.00 0.00 0.00 5.54
445 446 1.516603 GTCTACACGAAGCTCCGCC 60.517 63.158 0.00 0.00 0.00 6.13
446 447 1.974875 TCTACACGAAGCTCCGCCA 60.975 57.895 0.00 0.00 0.00 5.69
448 449 2.214181 CTACACGAAGCTCCGCCACT 62.214 60.000 0.00 0.00 0.00 4.00
450 451 4.379243 ACGAAGCTCCGCCACTGG 62.379 66.667 0.00 0.00 0.00 4.00
457 458 2.525629 TCCGCCACTGGGTTCTGA 60.526 61.111 0.00 0.00 36.17 3.27
461 462 0.742281 CGCCACTGGGTTCTGATGAG 60.742 60.000 0.00 0.00 36.17 2.90
464 465 1.279496 CACTGGGTTCTGATGAGGGA 58.721 55.000 0.00 0.00 0.00 4.20
500 501 5.193930 TCCCTCAGACAAGGAGTAGATAGAA 59.806 44.000 0.00 0.00 38.87 2.10
509 510 8.312669 ACAAGGAGTAGATAGAATAGTTTGCT 57.687 34.615 0.00 0.00 0.00 3.91
545 546 8.921205 ACATTTATTACCGGATGTAGTTCTAGT 58.079 33.333 9.46 0.00 31.41 2.57
700 711 8.407064 AGGTTATAAGAAATAGTGAGTCAGACG 58.593 37.037 0.00 0.00 0.00 4.18
717 728 2.037144 GACGTATAGGGGGCAAGAAGA 58.963 52.381 0.00 0.00 0.00 2.87
721 732 3.877508 CGTATAGGGGGCAAGAAGAAAAG 59.122 47.826 0.00 0.00 0.00 2.27
722 733 2.215942 TAGGGGGCAAGAAGAAAAGC 57.784 50.000 0.00 0.00 0.00 3.51
727 738 2.908688 GGCAAGAAGAAAAGCCCAAA 57.091 45.000 0.00 0.00 41.25 3.28
728 739 2.483876 GGCAAGAAGAAAAGCCCAAAC 58.516 47.619 0.00 0.00 41.25 2.93
729 740 2.127251 GCAAGAAGAAAAGCCCAAACG 58.873 47.619 0.00 0.00 0.00 3.60
730 741 2.742774 CAAGAAGAAAAGCCCAAACGG 58.257 47.619 0.00 0.00 0.00 4.44
731 742 2.358322 AGAAGAAAAGCCCAAACGGA 57.642 45.000 0.00 0.00 0.00 4.69
732 743 2.230660 AGAAGAAAAGCCCAAACGGAG 58.769 47.619 0.00 0.00 0.00 4.63
734 745 1.318576 AGAAAAGCCCAAACGGAGTG 58.681 50.000 0.00 0.00 45.00 3.51
735 746 1.029681 GAAAAGCCCAAACGGAGTGT 58.970 50.000 0.00 0.00 45.00 3.55
736 747 1.407618 GAAAAGCCCAAACGGAGTGTT 59.592 47.619 0.00 0.00 45.00 3.32
778 2642 2.543578 GCTTGAGCGTCCACATTCA 58.456 52.632 0.00 0.00 0.00 2.57
810 2684 4.135153 TCGCTCCCAGAAGCTCGC 62.135 66.667 0.00 0.00 40.23 5.03
975 2995 2.323599 CATCTGCAGATCTGACCCCTA 58.676 52.381 26.44 5.11 31.21 3.53
988 3036 1.461655 CCCCTACCTAGGCCCTTCC 60.462 68.421 9.30 0.00 42.26 3.46
1034 3105 1.900486 GAAAGGGGAGGTCTTCGAGAA 59.100 52.381 0.00 0.00 0.00 2.87
1061 3132 4.219999 GCCGAGGCTGGAGAGCTC 62.220 72.222 5.27 5.27 45.44 4.09
1062 3133 3.898509 CCGAGGCTGGAGAGCTCG 61.899 72.222 8.37 0.00 45.44 5.03
1063 3134 3.898509 CGAGGCTGGAGAGCTCGG 61.899 72.222 8.37 1.48 45.44 4.63
1064 3135 2.441164 GAGGCTGGAGAGCTCGGA 60.441 66.667 8.37 0.00 45.44 4.55
1065 3136 1.832167 GAGGCTGGAGAGCTCGGAT 60.832 63.158 8.37 0.00 45.44 4.18
1067 3138 2.280052 GCTGGAGAGCTCGGATGC 60.280 66.667 8.37 8.46 42.52 3.91
1095 3193 3.583526 ACATCATCATCCTGGAGATCCTG 59.416 47.826 1.52 7.45 36.82 3.86
1153 3251 4.753662 TCTCCGTACCCTGGCGCT 62.754 66.667 7.64 0.00 0.00 5.92
1381 3533 0.314935 CGGCTGCACCAAGAATTTGT 59.685 50.000 0.50 0.00 39.03 2.83
1463 3633 3.650950 GGTGGAGCTGCCCCTCAA 61.651 66.667 1.53 0.00 34.97 3.02
1464 3634 2.360475 GTGGAGCTGCCCCTCAAC 60.360 66.667 1.53 0.00 34.97 3.18
1465 3635 3.650950 TGGAGCTGCCCCTCAACC 61.651 66.667 1.53 0.00 34.97 3.77
1818 4066 4.580167 CCCGAAGATTTGCTATGATTGGAA 59.420 41.667 0.00 0.00 0.00 3.53
1824 4072 3.627395 TTGCTATGATTGGAACGTCCT 57.373 42.857 0.00 0.00 37.46 3.85
1870 4143 4.220602 AGCTTCCAATAACAACAACATCCC 59.779 41.667 0.00 0.00 0.00 3.85
1953 4234 3.119245 ACGTACTGCCAACATCGATAAGT 60.119 43.478 0.00 0.00 0.00 2.24
2042 4326 2.550978 GTTCCATGTGGAGGTGATACG 58.449 52.381 1.49 0.00 46.36 3.06
2069 4360 4.997905 AGCGTATGATATGCAACATCAC 57.002 40.909 17.99 4.90 43.07 3.06
2133 4448 6.381994 ACAACGATTTCTACCCTATGTTCCTA 59.618 38.462 0.00 0.00 0.00 2.94
2230 5627 2.177394 TCGGCTGAACTATTTGTGCA 57.823 45.000 0.00 0.00 32.26 4.57
2303 5705 3.381272 TCCTCTTGCTTGGTTTTCAGTTG 59.619 43.478 0.00 0.00 0.00 3.16
2339 5757 7.657761 CCTGGTAAACCTACAGATTAAGCATAG 59.342 40.741 0.02 0.00 36.82 2.23
2421 5881 5.686753 TCTTGTTTGTAACCAGCCTTCTTA 58.313 37.500 0.00 0.00 0.00 2.10
2474 5948 6.599244 CCTAAATCCTAGTGCAGATTGTGAAA 59.401 38.462 0.15 0.00 33.08 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.935481 CAAGGTGCTCCTCCCCCA 60.935 66.667 7.99 0.00 44.35 4.96
78 79 0.035056 GATAATGAGGGATGGGCCGG 60.035 60.000 0.00 0.00 37.63 6.13
85 86 1.276421 CGGGCTTCGATAATGAGGGAT 59.724 52.381 0.00 0.00 42.43 3.85
96 97 3.849951 GGATGGCTCGGGCTTCGA 61.850 66.667 7.48 3.09 46.77 3.71
97 98 3.391665 AAGGATGGCTCGGGCTTCG 62.392 63.158 7.48 0.00 38.73 3.79
101 102 2.203126 CTCAAGGATGGCTCGGGC 60.203 66.667 0.00 0.00 37.82 6.13
103 104 2.203126 GGCTCAAGGATGGCTCGG 60.203 66.667 0.00 0.00 0.00 4.63
106 107 0.396695 CAATGGGCTCAAGGATGGCT 60.397 55.000 0.00 0.00 0.00 4.75
124 125 0.545071 TCACCACCTGCTCATCCTCA 60.545 55.000 0.00 0.00 0.00 3.86
135 136 1.292223 CGGTTCATCGTCACCACCT 59.708 57.895 0.00 0.00 31.84 4.00
147 148 2.463589 AAAGATCCTGCGGCGGTTCA 62.464 55.000 9.78 0.00 0.00 3.18
153 154 1.261619 CACGAATAAAGATCCTGCGGC 59.738 52.381 0.00 0.00 0.00 6.53
156 157 3.462021 AGCTCACGAATAAAGATCCTGC 58.538 45.455 0.00 0.00 0.00 4.85
171 172 2.425668 GTCTCCTCCAACTCTAGCTCAC 59.574 54.545 0.00 0.00 0.00 3.51
175 176 4.249661 CAAAAGTCTCCTCCAACTCTAGC 58.750 47.826 0.00 0.00 0.00 3.42
177 178 3.646162 TGCAAAAGTCTCCTCCAACTCTA 59.354 43.478 0.00 0.00 0.00 2.43
185 186 3.251972 CCTTTGTCTGCAAAAGTCTCCTC 59.748 47.826 8.22 0.00 43.17 3.71
188 189 3.627577 TGTCCTTTGTCTGCAAAAGTCTC 59.372 43.478 8.22 0.85 43.17 3.36
193 194 3.360867 TCCTTGTCCTTTGTCTGCAAAA 58.639 40.909 0.00 0.00 43.17 2.44
198 199 3.077359 GGTCATCCTTGTCCTTTGTCTG 58.923 50.000 0.00 0.00 0.00 3.51
203 204 3.875369 GCATCTGGTCATCCTTGTCCTTT 60.875 47.826 0.00 0.00 32.85 3.11
205 206 1.211457 GCATCTGGTCATCCTTGTCCT 59.789 52.381 0.00 0.00 32.85 3.85
207 208 1.211457 AGGCATCTGGTCATCCTTGTC 59.789 52.381 0.00 0.00 34.23 3.18
208 209 1.211457 GAGGCATCTGGTCATCCTTGT 59.789 52.381 0.00 0.00 34.23 3.16
210 211 1.588239 TGAGGCATCTGGTCATCCTT 58.412 50.000 0.00 0.00 34.23 3.36
211 212 1.420514 CATGAGGCATCTGGTCATCCT 59.579 52.381 0.00 0.00 34.23 3.24
212 213 1.893544 CATGAGGCATCTGGTCATCC 58.106 55.000 0.00 0.00 0.00 3.51
214 215 3.416253 GCATGAGGCATCTGGTCAT 57.584 52.632 0.00 0.00 43.97 3.06
215 216 4.970621 GCATGAGGCATCTGGTCA 57.029 55.556 0.00 0.00 43.97 4.02
253 254 1.003355 CCGCCACTGTCAGAACCAT 60.003 57.895 6.91 0.00 0.00 3.55
256 257 2.029844 GCTCCGCCACTGTCAGAAC 61.030 63.158 6.91 0.00 0.00 3.01
257 258 1.758440 AAGCTCCGCCACTGTCAGAA 61.758 55.000 6.91 0.00 0.00 3.02
258 259 2.210013 AAGCTCCGCCACTGTCAGA 61.210 57.895 6.91 0.00 0.00 3.27
259 260 2.031516 CAAGCTCCGCCACTGTCAG 61.032 63.158 0.00 0.00 0.00 3.51
260 261 2.031012 CAAGCTCCGCCACTGTCA 59.969 61.111 0.00 0.00 0.00 3.58
262 263 2.345244 CTCAAGCTCCGCCACTGT 59.655 61.111 0.00 0.00 0.00 3.55
263 264 3.123620 GCTCAAGCTCCGCCACTG 61.124 66.667 0.00 0.00 38.21 3.66
264 265 1.617018 TATGCTCAAGCTCCGCCACT 61.617 55.000 3.32 0.00 42.66 4.00
265 266 0.744414 TTATGCTCAAGCTCCGCCAC 60.744 55.000 3.32 0.00 42.66 5.01
266 267 0.181114 ATTATGCTCAAGCTCCGCCA 59.819 50.000 3.32 0.00 42.66 5.69
268 269 0.871057 GGATTATGCTCAAGCTCCGC 59.129 55.000 3.32 0.00 42.66 5.54
270 271 3.563390 GTCTTGGATTATGCTCAAGCTCC 59.437 47.826 3.32 2.58 42.66 4.70
271 272 3.247173 CGTCTTGGATTATGCTCAAGCTC 59.753 47.826 3.32 0.00 42.66 4.09
272 273 3.201290 CGTCTTGGATTATGCTCAAGCT 58.799 45.455 3.32 0.00 42.66 3.74
274 275 2.874701 CCCGTCTTGGATTATGCTCAAG 59.125 50.000 0.00 0.00 42.00 3.02
275 276 2.503765 TCCCGTCTTGGATTATGCTCAA 59.496 45.455 0.00 0.00 42.00 3.02
276 277 2.115427 TCCCGTCTTGGATTATGCTCA 58.885 47.619 0.00 0.00 42.00 4.26
278 279 1.141053 GGTCCCGTCTTGGATTATGCT 59.859 52.381 0.00 0.00 42.00 3.79
279 280 1.134220 TGGTCCCGTCTTGGATTATGC 60.134 52.381 0.00 0.00 42.00 3.14
280 281 3.492102 ATGGTCCCGTCTTGGATTATG 57.508 47.619 0.00 0.00 42.00 1.90
281 282 4.505039 GCTAATGGTCCCGTCTTGGATTAT 60.505 45.833 0.00 0.00 42.00 1.28
283 284 2.421529 GCTAATGGTCCCGTCTTGGATT 60.422 50.000 0.00 0.00 42.00 3.01
285 286 0.539986 GCTAATGGTCCCGTCTTGGA 59.460 55.000 0.00 0.00 42.00 3.53
286 287 0.541863 AGCTAATGGTCCCGTCTTGG 59.458 55.000 0.00 0.00 37.55 3.61
287 288 1.207089 TCAGCTAATGGTCCCGTCTTG 59.793 52.381 0.00 0.00 0.00 3.02
288 289 1.568504 TCAGCTAATGGTCCCGTCTT 58.431 50.000 0.00 0.00 0.00 3.01
289 290 1.482593 CTTCAGCTAATGGTCCCGTCT 59.517 52.381 0.00 0.00 0.00 4.18
290 291 1.473434 CCTTCAGCTAATGGTCCCGTC 60.473 57.143 0.00 0.00 0.00 4.79
291 292 0.541863 CCTTCAGCTAATGGTCCCGT 59.458 55.000 0.00 0.00 0.00 5.28
292 293 0.179045 CCCTTCAGCTAATGGTCCCG 60.179 60.000 0.00 0.00 0.00 5.14
293 294 1.141858 CTCCCTTCAGCTAATGGTCCC 59.858 57.143 0.00 0.00 0.00 4.46
294 295 1.141858 CCTCCCTTCAGCTAATGGTCC 59.858 57.143 0.00 0.00 0.00 4.46
295 296 1.475930 GCCTCCCTTCAGCTAATGGTC 60.476 57.143 0.00 0.00 0.00 4.02
296 297 0.548510 GCCTCCCTTCAGCTAATGGT 59.451 55.000 0.00 0.00 0.00 3.55
297 298 0.548031 TGCCTCCCTTCAGCTAATGG 59.452 55.000 0.00 0.00 0.00 3.16
299 300 3.677156 ATTTGCCTCCCTTCAGCTAAT 57.323 42.857 0.00 0.00 0.00 1.73
300 301 3.456380 AATTTGCCTCCCTTCAGCTAA 57.544 42.857 0.00 0.00 0.00 3.09
301 302 4.584638 TTAATTTGCCTCCCTTCAGCTA 57.415 40.909 0.00 0.00 0.00 3.32
303 304 4.279420 CCTATTAATTTGCCTCCCTTCAGC 59.721 45.833 0.00 0.00 0.00 4.26
304 305 4.829492 CCCTATTAATTTGCCTCCCTTCAG 59.171 45.833 0.00 0.00 0.00 3.02
305 306 4.480537 TCCCTATTAATTTGCCTCCCTTCA 59.519 41.667 0.00 0.00 0.00 3.02
306 307 5.061721 TCCCTATTAATTTGCCTCCCTTC 57.938 43.478 0.00 0.00 0.00 3.46
307 308 5.458595 CTTCCCTATTAATTTGCCTCCCTT 58.541 41.667 0.00 0.00 0.00 3.95
308 309 4.140924 CCTTCCCTATTAATTTGCCTCCCT 60.141 45.833 0.00 0.00 0.00 4.20
309 310 4.141018 TCCTTCCCTATTAATTTGCCTCCC 60.141 45.833 0.00 0.00 0.00 4.30
310 311 5.061721 TCCTTCCCTATTAATTTGCCTCC 57.938 43.478 0.00 0.00 0.00 4.30
311 312 5.073428 CCTCCTTCCCTATTAATTTGCCTC 58.927 45.833 0.00 0.00 0.00 4.70
312 313 4.140924 CCCTCCTTCCCTATTAATTTGCCT 60.141 45.833 0.00 0.00 0.00 4.75
314 315 4.152647 CCCCTCCTTCCCTATTAATTTGC 58.847 47.826 0.00 0.00 0.00 3.68
315 316 4.140924 AGCCCCTCCTTCCCTATTAATTTG 60.141 45.833 0.00 0.00 0.00 2.32
316 317 4.062390 AGCCCCTCCTTCCCTATTAATTT 58.938 43.478 0.00 0.00 0.00 1.82
319 320 2.910360 AGCCCCTCCTTCCCTATTAA 57.090 50.000 0.00 0.00 0.00 1.40
320 321 4.111424 AGATTAGCCCCTCCTTCCCTATTA 59.889 45.833 0.00 0.00 0.00 0.98
322 323 2.460691 AGATTAGCCCCTCCTTCCCTAT 59.539 50.000 0.00 0.00 0.00 2.57
323 324 1.873732 AGATTAGCCCCTCCTTCCCTA 59.126 52.381 0.00 0.00 0.00 3.53
324 325 0.650558 AGATTAGCCCCTCCTTCCCT 59.349 55.000 0.00 0.00 0.00 4.20
325 326 1.060729 GAGATTAGCCCCTCCTTCCC 58.939 60.000 0.00 0.00 0.00 3.97
327 328 3.851979 ACTAGAGATTAGCCCCTCCTTC 58.148 50.000 0.00 0.00 0.00 3.46
328 329 4.288324 AACTAGAGATTAGCCCCTCCTT 57.712 45.455 0.00 0.00 0.00 3.36
329 330 4.288324 AAACTAGAGATTAGCCCCTCCT 57.712 45.455 0.00 0.00 0.00 3.69
330 331 6.126854 TGTTTAAACTAGAGATTAGCCCCTCC 60.127 42.308 18.72 0.00 0.00 4.30
331 332 6.762187 GTGTTTAAACTAGAGATTAGCCCCTC 59.238 42.308 18.72 0.00 0.00 4.30
332 333 6.444171 AGTGTTTAAACTAGAGATTAGCCCCT 59.556 38.462 18.72 0.00 0.00 4.79
333 334 6.651086 AGTGTTTAAACTAGAGATTAGCCCC 58.349 40.000 18.72 0.00 0.00 5.80
351 352 7.769507 GCTCTATTTTAGGCCTAACTAGTGTTT 59.230 37.037 25.13 6.37 37.59 2.83
353 354 6.383147 TGCTCTATTTTAGGCCTAACTAGTGT 59.617 38.462 25.13 9.65 0.00 3.55
355 356 7.619512 ATGCTCTATTTTAGGCCTAACTAGT 57.380 36.000 25.13 10.78 0.00 2.57
358 359 8.885346 AGAATATGCTCTATTTTAGGCCTAACT 58.115 33.333 25.13 16.92 0.00 2.24
359 360 9.508642 AAGAATATGCTCTATTTTAGGCCTAAC 57.491 33.333 25.13 11.96 0.00 2.34
382 383 8.862085 CCCCTTAACTTTTACAACCATTAAAGA 58.138 33.333 0.00 0.00 33.12 2.52
383 384 8.092068 CCCCCTTAACTTTTACAACCATTAAAG 58.908 37.037 0.00 0.00 34.58 1.85
384 385 7.964624 CCCCCTTAACTTTTACAACCATTAAA 58.035 34.615 0.00 0.00 0.00 1.52
385 386 7.541916 CCCCCTTAACTTTTACAACCATTAA 57.458 36.000 0.00 0.00 0.00 1.40
419 420 0.389426 CTTCGTGTAGACCAACGGGG 60.389 60.000 0.00 0.00 44.81 5.73
420 421 1.012486 GCTTCGTGTAGACCAACGGG 61.012 60.000 0.00 0.00 41.29 5.28
422 423 1.337821 GAGCTTCGTGTAGACCAACG 58.662 55.000 0.00 0.00 0.00 4.10
423 424 1.711206 GGAGCTTCGTGTAGACCAAC 58.289 55.000 0.00 0.00 0.00 3.77
425 426 1.880894 CGGAGCTTCGTGTAGACCA 59.119 57.895 6.14 0.00 0.00 4.02
426 427 4.787999 CGGAGCTTCGTGTAGACC 57.212 61.111 6.14 0.00 0.00 3.85
439 440 1.903877 ATCAGAACCCAGTGGCGGAG 61.904 60.000 2.61 0.00 33.59 4.63
440 441 1.918293 ATCAGAACCCAGTGGCGGA 60.918 57.895 2.61 0.00 33.59 5.54
442 443 0.742281 CTCATCAGAACCCAGTGGCG 60.742 60.000 2.61 0.00 33.59 5.69
444 445 0.254178 CCCTCATCAGAACCCAGTGG 59.746 60.000 0.63 0.63 37.80 4.00
445 446 1.209019 CTCCCTCATCAGAACCCAGTG 59.791 57.143 0.00 0.00 0.00 3.66
446 447 1.203364 ACTCCCTCATCAGAACCCAGT 60.203 52.381 0.00 0.00 0.00 4.00
448 449 1.279496 CACTCCCTCATCAGAACCCA 58.721 55.000 0.00 0.00 0.00 4.51
450 451 0.908198 AGCACTCCCTCATCAGAACC 59.092 55.000 0.00 0.00 0.00 3.62
464 465 1.306141 TGAGGGAATCGGGAGCACT 60.306 57.895 0.00 0.00 0.00 4.40
476 477 4.727332 TCTATCTACTCCTTGTCTGAGGGA 59.273 45.833 0.00 0.00 37.41 4.20
520 521 9.760077 AACTAGAACTACATCCGGTAATAAATG 57.240 33.333 0.00 0.00 0.00 2.32
521 522 9.978044 GAACTAGAACTACATCCGGTAATAAAT 57.022 33.333 0.00 0.00 0.00 1.40
528 529 3.350833 ACGAACTAGAACTACATCCGGT 58.649 45.455 0.00 0.00 0.00 5.28
665 672 9.653287 CACTATTTCTTATAACCTGTGTCTCAA 57.347 33.333 0.00 0.00 0.00 3.02
666 673 9.031537 TCACTATTTCTTATAACCTGTGTCTCA 57.968 33.333 0.00 0.00 0.00 3.27
668 675 9.036980 ACTCACTATTTCTTATAACCTGTGTCT 57.963 33.333 0.00 0.00 0.00 3.41
669 676 9.303537 GACTCACTATTTCTTATAACCTGTGTC 57.696 37.037 0.00 0.00 0.00 3.67
671 678 9.307121 CTGACTCACTATTTCTTATAACCTGTG 57.693 37.037 0.00 0.00 0.00 3.66
672 679 9.256228 TCTGACTCACTATTTCTTATAACCTGT 57.744 33.333 0.00 0.00 0.00 4.00
673 680 9.522804 GTCTGACTCACTATTTCTTATAACCTG 57.477 37.037 0.00 0.00 0.00 4.00
674 681 8.407064 CGTCTGACTCACTATTTCTTATAACCT 58.593 37.037 6.21 0.00 0.00 3.50
680 687 9.053840 CCTATACGTCTGACTCACTATTTCTTA 57.946 37.037 6.21 0.00 0.00 2.10
681 688 7.013464 CCCTATACGTCTGACTCACTATTTCTT 59.987 40.741 6.21 0.00 0.00 2.52
700 711 3.632604 GCTTTTCTTCTTGCCCCCTATAC 59.367 47.826 0.00 0.00 0.00 1.47
717 728 1.480789 AACACTCCGTTTGGGCTTTT 58.519 45.000 0.00 0.00 32.35 2.27
744 755 5.343249 GCTCAAGCTTTTCTTCACTGAAAA 58.657 37.500 0.00 0.00 41.75 2.29
745 756 4.496341 CGCTCAAGCTTTTCTTCACTGAAA 60.496 41.667 0.00 0.00 39.32 2.69
746 757 3.002656 CGCTCAAGCTTTTCTTCACTGAA 59.997 43.478 0.00 0.00 39.32 3.02
747 758 2.545526 CGCTCAAGCTTTTCTTCACTGA 59.454 45.455 0.00 0.00 39.32 3.41
748 759 2.289002 ACGCTCAAGCTTTTCTTCACTG 59.711 45.455 0.00 0.00 39.32 3.66
750 761 2.349912 GGACGCTCAAGCTTTTCTTCAC 60.350 50.000 0.00 0.00 39.32 3.18
751 762 1.873591 GGACGCTCAAGCTTTTCTTCA 59.126 47.619 0.00 0.00 39.32 3.02
752 763 1.873591 TGGACGCTCAAGCTTTTCTTC 59.126 47.619 0.00 0.00 39.32 2.87
753 764 1.604278 GTGGACGCTCAAGCTTTTCTT 59.396 47.619 0.00 0.00 39.32 2.52
755 766 0.944386 TGTGGACGCTCAAGCTTTTC 59.056 50.000 0.00 0.00 39.32 2.29
756 767 1.609208 ATGTGGACGCTCAAGCTTTT 58.391 45.000 0.00 0.00 39.32 2.27
778 2642 0.033601 AGCGACAGAGACAGGAGGAT 60.034 55.000 0.00 0.00 0.00 3.24
837 2711 1.228184 TTTGGTTTAGGGCGGCGAA 60.228 52.632 12.98 0.00 0.00 4.70
872 2755 3.948086 CTCGCCGTGGTGAGTCGAC 62.948 68.421 19.09 7.70 44.90 4.20
873 2756 3.733960 CTCGCCGTGGTGAGTCGA 61.734 66.667 19.09 3.69 44.90 4.20
908 2791 3.492829 CGAGGAAAATCAGGTAGTAGCCC 60.493 52.174 0.00 0.00 0.00 5.19
975 2995 2.285442 AAGCGGAAGGGCCTAGGT 60.285 61.111 6.41 4.24 0.00 3.08
1010 3081 1.657804 GAAGACCTCCCCTTTCTCCA 58.342 55.000 0.00 0.00 0.00 3.86
1034 3105 2.032681 GCCTCGGCTTGGTGTTCT 59.967 61.111 0.00 0.00 38.26 3.01
1062 3133 2.281070 ATGATGTCGGCCGCATCC 60.281 61.111 36.91 26.72 41.32 3.51
1063 3134 0.952497 ATGATGATGTCGGCCGCATC 60.952 55.000 35.39 35.39 42.10 3.91
1064 3135 0.952497 GATGATGATGTCGGCCGCAT 60.952 55.000 27.51 27.51 0.00 4.73
1065 3136 1.595109 GATGATGATGTCGGCCGCA 60.595 57.895 23.51 22.28 0.00 5.69
1067 3138 0.947660 CAGGATGATGATGTCGGCCG 60.948 60.000 22.12 22.12 39.69 6.13
1075 3173 3.839490 GACAGGATCTCCAGGATGATGAT 59.161 47.826 6.23 0.00 39.69 2.45
1076 3174 3.237746 GACAGGATCTCCAGGATGATGA 58.762 50.000 6.23 0.00 39.69 2.92
1153 3251 1.755395 CGGGGTCGGTGATGAGGTA 60.755 63.158 0.00 0.00 0.00 3.08
1461 3631 1.576421 GCTCTTGCGGTTGAGGTTG 59.424 57.895 0.00 0.00 0.00 3.77
1462 3632 1.600916 GGCTCTTGCGGTTGAGGTT 60.601 57.895 0.00 0.00 40.82 3.50
1463 3633 2.032681 GGCTCTTGCGGTTGAGGT 59.967 61.111 0.00 0.00 40.82 3.85
1464 3634 3.121030 CGGCTCTTGCGGTTGAGG 61.121 66.667 0.00 0.00 40.82 3.86
1465 3635 3.121030 CCGGCTCTTGCGGTTGAG 61.121 66.667 0.00 0.00 40.82 3.02
1818 4066 0.251922 TGTAAGCACCCCTAGGACGT 60.252 55.000 11.48 2.58 36.73 4.34
1824 4072 2.759355 AGCATAGTGTAAGCACCCCTA 58.241 47.619 0.00 0.00 46.35 3.53
1870 4143 6.098679 CACCAGAGTTCTATCTCAGAAACTG 58.901 44.000 0.00 11.87 44.89 3.16
1953 4234 9.031360 GTAATTCTTCATAGTCATGCTCGTAAA 57.969 33.333 0.00 0.00 31.73 2.01
2042 4326 6.466308 TGTTGCATATCATACGCTATCAAC 57.534 37.500 0.00 0.00 33.86 3.18
2088 4379 8.922676 TCGTTGTGTACTATTTTTCTCAAGATC 58.077 33.333 0.00 0.00 0.00 2.75
2133 4448 6.205076 GCATCTGCTAATGATTCTGAGAACAT 59.795 38.462 0.00 0.85 38.21 2.71
2230 5627 7.877097 GCATGATTCAAGTAGATTCAGAGGTAT 59.123 37.037 0.00 0.00 39.29 2.73
2303 5705 1.745653 GGTTTACCAGGCATTGCTCTC 59.254 52.381 8.82 0.00 35.64 3.20
2339 5757 3.624410 ACGGTGTTCTTTGGAGTTAACAC 59.376 43.478 8.61 8.32 46.91 3.32
2474 5948 9.281371 GATTGAACCTTTTAGTAAACTACCAGT 57.719 33.333 0.00 0.00 0.00 4.00
2510 5984 5.571285 AGGTTGAGTAGACATCACACTAGA 58.429 41.667 0.00 0.00 0.00 2.43
2513 5987 6.859112 ATAAGGTTGAGTAGACATCACACT 57.141 37.500 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.