Multiple sequence alignment - TraesCS6D01G121900

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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 TraesCS6D01G121900 chr6D 100.000 4677 0 0 1 4677 86656104 86660780 0.000000e+00 8637.0
1 TraesCS6D01G121900 chr6D 79.253 241 42 6 2479 2714 419600949 419601186 1.350000e-35 161.0
2 TraesCS6D01G121900 chr6A 96.628 2610 81 5 2069 4677 104356350 104358953 0.000000e+00 4325.0
3 TraesCS6D01G121900 chr6A 96.628 2610 81 4 2069 4677 104447238 104444635 0.000000e+00 4325.0
4 TraesCS6D01G121900 chr6A 88.942 841 35 20 1 814 104354332 104355141 0.000000e+00 985.0
5 TraesCS6D01G121900 chr6A 91.261 595 22 12 240 814 104448899 104448315 0.000000e+00 784.0
6 TraesCS6D01G121900 chr6A 95.561 383 12 3 853 1235 104355146 104355523 4.000000e-170 608.0
7 TraesCS6D01G121900 chr6A 95.561 383 12 3 853 1235 104448310 104447933 4.000000e-170 608.0
8 TraesCS6D01G121900 chr6A 85.911 582 61 14 1344 1917 104355577 104356145 6.700000e-168 601.0
9 TraesCS6D01G121900 chr6A 85.911 582 61 14 1344 1917 104447879 104447311 6.700000e-168 601.0
10 TraesCS6D01G121900 chr6A 80.180 222 41 3 2488 2706 412366275 412366496 3.740000e-36 163.0
11 TraesCS6D01G121900 chr6B 97.567 1932 43 3 2750 4677 164358101 164360032 0.000000e+00 3304.0
12 TraesCS6D01G121900 chr6B 92.426 845 26 13 1 814 164356505 164357342 0.000000e+00 1171.0
13 TraesCS6D01G121900 chr6B 92.344 418 24 3 2007 2416 164357680 164358097 5.210000e-164 588.0
14 TraesCS6D01G121900 chr6B 94.030 335 11 3 851 1181 164357345 164357674 2.510000e-137 499.0
15 TraesCS6D01G121900 chr6B 81.435 237 39 5 2481 2714 632443584 632443818 6.180000e-44 189.0
16 TraesCS6D01G121900 chr5B 86.495 622 81 2 3759 4377 684126740 684126119 0.000000e+00 680.0
17 TraesCS6D01G121900 chr5B 85.993 307 43 0 4371 4677 684120915 684120609 3.490000e-86 329.0
18 TraesCS6D01G121900 chr5B 82.934 334 57 0 2071 2404 684131548 684131215 7.610000e-78 302.0
19 TraesCS6D01G121900 chr5B 87.402 127 16 0 2794 2920 684130820 684130694 3.770000e-31 147.0
20 TraesCS6D01G121900 chr5B 87.273 55 7 0 1127 1181 561064775 561064721 3.910000e-06 63.9
21 TraesCS6D01G121900 chr5B 92.500 40 3 0 1127 1166 560444538 560444499 1.820000e-04 58.4
22 TraesCS6D01G121900 chr4D 75.497 755 173 12 3927 4675 15913236 15912488 4.450000e-95 359.0
23 TraesCS6D01G121900 chr4D 72.029 690 143 34 2802 3481 15914627 15913978 4.840000e-35 159.0
24 TraesCS6D01G121900 chr4A 75.510 735 143 20 3924 4654 584679679 584680380 4.510000e-85 326.0
25 TraesCS6D01G121900 chr4A 75.299 753 149 20 3927 4675 584735245 584734526 4.510000e-85 326.0
26 TraesCS6D01G121900 chr4B 73.227 691 135 30 2801 3481 27521791 27521141 6.130000e-49 206.0
27 TraesCS6D01G121900 chr4B 72.688 692 139 30 2801 3482 27249689 27250340 7.990000e-43 185.0
28 TraesCS6D01G121900 chr4B 77.821 257 51 6 3927 4180 27520220 27519967 2.250000e-33 154.0
29 TraesCS6D01G121900 chr2B 81.513 238 39 4 2482 2715 45740937 45740701 1.720000e-44 191.0
30 TraesCS6D01G121900 chr2B 80.357 112 14 6 1558 1665 789613012 789613119 1.400000e-10 78.7
31 TraesCS6D01G121900 chr3D 82.143 224 35 3 2488 2708 495320421 495320642 2.220000e-43 187.0
32 TraesCS6D01G121900 chr7B 80.000 245 38 6 2481 2714 706362097 706361853 2.240000e-38 171.0
33 TraesCS6D01G121900 chr7B 87.719 57 5 2 1343 1399 411498681 411498627 1.090000e-06 65.8
34 TraesCS6D01G121900 chr5D 80.488 205 34 4 2505 2705 417607120 417607322 8.110000e-33 152.0
35 TraesCS6D01G121900 chr5D 82.051 156 25 2 2801 2956 537224589 537224437 3.800000e-26 130.0
36 TraesCS6D01G121900 chr5D 92.500 40 3 0 1127 1166 458097945 458097906 1.820000e-04 58.4
37 TraesCS6D01G121900 chr2A 79.259 135 23 5 1535 1666 39582150 39582018 6.450000e-14 89.8
38 TraesCS6D01G121900 chr2A 77.483 151 29 5 1519 1666 39945334 39945482 8.340000e-13 86.1
39 TraesCS6D01G121900 chr2D 84.000 75 9 3 1610 1682 36226222 36226149 8.400000e-08 69.4
40 TraesCS6D01G121900 chr3A 88.889 45 3 2 1561 1605 111566319 111566361 2.000000e-03 54.7


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 TraesCS6D01G121900 chr6D 86656104 86660780 4676 False 8637.000000 8637 100.000000 1 4677 1 chr6D.!!$F1 4676
1 TraesCS6D01G121900 chr6A 104354332 104358953 4621 False 1629.750000 4325 91.760500 1 4677 4 chr6A.!!$F2 4676
2 TraesCS6D01G121900 chr6A 104444635 104448899 4264 True 1579.500000 4325 92.340250 240 4677 4 chr6A.!!$R1 4437
3 TraesCS6D01G121900 chr6B 164356505 164360032 3527 False 1390.500000 3304 94.091750 1 4677 4 chr6B.!!$F2 4676
4 TraesCS6D01G121900 chr5B 684126119 684131548 5429 True 376.333333 680 85.610333 2071 4377 3 chr5B.!!$R4 2306
5 TraesCS6D01G121900 chr4D 15912488 15914627 2139 True 259.000000 359 73.763000 2802 4675 2 chr4D.!!$R1 1873
6 TraesCS6D01G121900 chr4A 584679679 584680380 701 False 326.000000 326 75.510000 3924 4654 1 chr4A.!!$F1 730
7 TraesCS6D01G121900 chr4A 584734526 584735245 719 True 326.000000 326 75.299000 3927 4675 1 chr4A.!!$R1 748

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
354 371 0.098905 GACAGCGATGACGAGTAGCA 59.901 55.0 8.12 0.0 42.66 3.49 F
1245 1295 0.179129 TTAAATCTCCGACCGCGACC 60.179 55.0 8.23 0.0 40.82 4.79 F
1922 1978 0.037975 CACAAGGGATGCAAAGTGCC 60.038 55.0 0.00 0.0 44.23 5.01 F
2284 2442 0.172578 GACCATCACCATCGACGACA 59.827 55.0 0.00 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1892 1948 0.109532 TCCCTTGTGCGAACCATTCA 59.890 50.000 0.0 0.0 0.00 2.57 R
2995 3382 1.134189 GGGTATGGGTACAAGCTGTCC 60.134 57.143 0.0 0.0 32.25 4.02 R
3082 3469 1.227853 GAACTGTTGGAGCACGGGT 60.228 57.895 0.0 0.0 0.00 5.28 R
4063 7755 1.066858 GTCATCTCGAAGAAGCCACCA 60.067 52.381 0.0 0.0 34.09 4.17 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
20 21 2.933769 GGAACTGGTCGCAAATCAAAG 58.066 47.619 0.00 0.00 0.00 2.77
36 37 7.631377 GCAAATCAAAGGCACATCTAATTAGGT 60.631 37.037 12.54 2.02 0.00 3.08
38 39 7.573968 ATCAAAGGCACATCTAATTAGGTTC 57.426 36.000 12.54 0.00 0.00 3.62
67 68 5.175090 AGTTTAGCAACAGAGCAAGAAAC 57.825 39.130 0.00 0.00 35.05 2.78
76 77 5.349824 ACAGAGCAAGAAACGAAAAGATC 57.650 39.130 0.00 0.00 0.00 2.75
78 79 5.296780 ACAGAGCAAGAAACGAAAAGATCAA 59.703 36.000 0.00 0.00 0.00 2.57
79 80 6.016777 ACAGAGCAAGAAACGAAAAGATCAAT 60.017 34.615 0.00 0.00 0.00 2.57
80 81 6.304922 CAGAGCAAGAAACGAAAAGATCAATG 59.695 38.462 0.00 0.00 0.00 2.82
81 82 5.464168 AGCAAGAAACGAAAAGATCAATGG 58.536 37.500 0.00 0.00 0.00 3.16
102 107 4.959210 TGGTTCATCCTTTCCACAGAAAAA 59.041 37.500 0.00 0.00 41.40 1.94
124 129 6.783708 AACATAGTTTTTGTCACCTTTCCA 57.216 33.333 0.00 0.00 0.00 3.53
236 246 4.469945 TCCATAGGAACTTCCGAAGTCAAT 59.530 41.667 14.18 5.90 42.75 2.57
237 247 5.659525 TCCATAGGAACTTCCGAAGTCAATA 59.340 40.000 14.18 7.74 42.75 1.90
238 248 5.753921 CCATAGGAACTTCCGAAGTCAATAC 59.246 44.000 14.18 0.06 42.75 1.89
242 252 4.804665 GGAACTTCCGAAGTCAATACTAGC 59.195 45.833 14.18 0.00 41.91 3.42
258 268 1.671328 CTAGCACAAGTCGAGATCGGA 59.329 52.381 1.91 0.00 40.29 4.55
290 300 0.179210 GAGAGACGAGACGACAGTGC 60.179 60.000 0.00 0.00 0.00 4.40
354 371 0.098905 GACAGCGATGACGAGTAGCA 59.901 55.000 8.12 0.00 42.66 3.49
516 556 3.510360 TCAAGTAACTACTGGCAGGACTC 59.490 47.826 20.34 4.19 36.50 3.36
517 557 3.459710 AGTAACTACTGGCAGGACTCT 57.540 47.619 20.34 6.43 34.72 3.24
534 574 4.961435 ACTCTACGTACTTAAGAGTGCC 57.039 45.455 15.40 0.00 46.25 5.01
547 587 7.394816 ACTTAAGAGTGCCATAAACAGTGTAT 58.605 34.615 10.09 0.00 33.99 2.29
610 652 8.204836 GTGATCACTTAATAGGTCTACCATGTT 58.795 37.037 18.83 0.00 38.89 2.71
883 929 2.123812 GGTCCTCCGATCCGACCT 60.124 66.667 8.11 0.00 42.39 3.85
990 1040 1.254284 CCAAGGAGCGGAGTGAGAGT 61.254 60.000 0.00 0.00 0.00 3.24
1062 1112 2.042831 GCTCATGCGCAGGAACCTT 61.043 57.895 26.11 0.00 0.00 3.50
1090 1140 4.954970 ACCACTGGCAGCAACCCG 62.955 66.667 15.89 0.00 0.00 5.28
1092 1142 3.663176 CACTGGCAGCAACCCGTG 61.663 66.667 15.89 0.00 0.00 4.94
1176 1226 2.806237 GCCGACCCGAGTAAGGAG 59.194 66.667 0.00 0.00 0.00 3.69
1181 1231 1.404843 GACCCGAGTAAGGAGCATCT 58.595 55.000 0.00 0.00 33.73 2.90
1185 1235 2.288518 CCCGAGTAAGGAGCATCTAAGC 60.289 54.545 0.00 0.00 33.73 3.09
1192 1242 1.287730 GGAGCATCTAAGCGCATCCG 61.288 60.000 11.47 0.00 40.15 4.18
1225 1275 9.715121 TCCTATGTGTTTATATTTACGGGATTC 57.285 33.333 0.00 0.00 0.00 2.52
1237 1287 5.857471 TTACGGGATTCTTAAATCTCCGA 57.143 39.130 22.94 11.66 46.99 4.55
1238 1288 4.056092 ACGGGATTCTTAAATCTCCGAC 57.944 45.455 22.94 1.13 46.99 4.79
1239 1289 3.181468 ACGGGATTCTTAAATCTCCGACC 60.181 47.826 22.94 7.33 46.99 4.79
1240 1290 3.391049 GGGATTCTTAAATCTCCGACCG 58.609 50.000 0.00 0.00 40.99 4.79
1242 1292 1.917273 TTCTTAAATCTCCGACCGCG 58.083 50.000 0.00 0.00 37.24 6.46
1243 1293 1.097232 TCTTAAATCTCCGACCGCGA 58.903 50.000 8.23 0.00 40.82 5.87
1244 1294 1.197910 CTTAAATCTCCGACCGCGAC 58.802 55.000 8.23 0.00 40.82 5.19
1245 1295 0.179129 TTAAATCTCCGACCGCGACC 60.179 55.000 8.23 0.00 40.82 4.79
1246 1296 1.033746 TAAATCTCCGACCGCGACCT 61.034 55.000 8.23 0.00 40.82 3.85
1247 1297 1.033746 AAATCTCCGACCGCGACCTA 61.034 55.000 8.23 0.00 40.82 3.08
1248 1298 1.033746 AATCTCCGACCGCGACCTAA 61.034 55.000 8.23 0.00 40.82 2.69
1249 1299 0.822532 ATCTCCGACCGCGACCTAAT 60.823 55.000 8.23 0.00 40.82 1.73
1250 1300 1.033746 TCTCCGACCGCGACCTAATT 61.034 55.000 8.23 0.00 40.82 1.40
1251 1301 0.664761 CTCCGACCGCGACCTAATTA 59.335 55.000 8.23 0.00 40.82 1.40
1252 1302 1.066002 CTCCGACCGCGACCTAATTAA 59.934 52.381 8.23 0.00 40.82 1.40
1253 1303 1.202290 TCCGACCGCGACCTAATTAAC 60.202 52.381 8.23 0.00 40.82 2.01
1254 1304 1.203065 CGACCGCGACCTAATTAACC 58.797 55.000 8.23 0.00 40.82 2.85
1255 1305 1.469595 CGACCGCGACCTAATTAACCA 60.470 52.381 8.23 0.00 40.82 3.67
1256 1306 2.620242 GACCGCGACCTAATTAACCAA 58.380 47.619 8.23 0.00 0.00 3.67
1257 1307 2.606272 GACCGCGACCTAATTAACCAAG 59.394 50.000 8.23 0.00 0.00 3.61
1258 1308 2.027837 ACCGCGACCTAATTAACCAAGT 60.028 45.455 8.23 0.00 0.00 3.16
1259 1309 2.606272 CCGCGACCTAATTAACCAAGTC 59.394 50.000 8.23 0.00 0.00 3.01
1260 1310 3.255725 CGCGACCTAATTAACCAAGTCA 58.744 45.455 0.00 0.00 0.00 3.41
1261 1311 3.869246 CGCGACCTAATTAACCAAGTCAT 59.131 43.478 0.00 0.00 0.00 3.06
1262 1312 5.045215 CGCGACCTAATTAACCAAGTCATA 58.955 41.667 0.00 0.00 0.00 2.15
1263 1313 5.175126 CGCGACCTAATTAACCAAGTCATAG 59.825 44.000 0.00 0.00 0.00 2.23
1264 1314 6.047231 GCGACCTAATTAACCAAGTCATAGT 58.953 40.000 0.00 0.00 0.00 2.12
1265 1315 6.200475 GCGACCTAATTAACCAAGTCATAGTC 59.800 42.308 0.00 0.00 0.00 2.59
1266 1316 6.417044 CGACCTAATTAACCAAGTCATAGTCG 59.583 42.308 0.00 0.00 0.00 4.18
1267 1317 7.414222 ACCTAATTAACCAAGTCATAGTCGA 57.586 36.000 0.00 0.00 0.00 4.20
1268 1318 8.019656 ACCTAATTAACCAAGTCATAGTCGAT 57.980 34.615 0.00 0.00 0.00 3.59
1269 1319 7.926555 ACCTAATTAACCAAGTCATAGTCGATG 59.073 37.037 0.00 0.00 36.82 3.84
1270 1320 6.604735 AATTAACCAAGTCATAGTCGATGC 57.395 37.500 0.00 0.00 35.29 3.91
1271 1321 3.895232 AACCAAGTCATAGTCGATGCT 57.105 42.857 0.00 0.00 35.29 3.79
1272 1322 6.459670 TTAACCAAGTCATAGTCGATGCTA 57.540 37.500 0.00 0.00 35.29 3.49
1273 1323 4.308899 ACCAAGTCATAGTCGATGCTAC 57.691 45.455 0.00 0.00 35.29 3.58
1274 1324 3.699538 ACCAAGTCATAGTCGATGCTACA 59.300 43.478 0.00 0.00 35.29 2.74
1275 1325 4.342378 ACCAAGTCATAGTCGATGCTACAT 59.658 41.667 0.00 0.00 35.29 2.29
1276 1326 5.163405 ACCAAGTCATAGTCGATGCTACATT 60.163 40.000 0.00 0.00 35.29 2.71
1277 1327 5.403766 CCAAGTCATAGTCGATGCTACATTC 59.596 44.000 0.00 0.00 35.29 2.67
1278 1328 5.774498 AGTCATAGTCGATGCTACATTCA 57.226 39.130 0.00 0.00 35.29 2.57
1279 1329 5.524284 AGTCATAGTCGATGCTACATTCAC 58.476 41.667 0.00 0.00 35.29 3.18
1280 1330 5.067805 AGTCATAGTCGATGCTACATTCACA 59.932 40.000 0.00 0.00 35.29 3.58
1281 1331 5.748630 GTCATAGTCGATGCTACATTCACAA 59.251 40.000 0.00 0.00 35.29 3.33
1282 1332 5.979517 TCATAGTCGATGCTACATTCACAAG 59.020 40.000 0.00 0.00 35.29 3.16
1283 1333 4.456280 AGTCGATGCTACATTCACAAGA 57.544 40.909 0.00 0.00 0.00 3.02
1284 1334 5.016051 AGTCGATGCTACATTCACAAGAT 57.984 39.130 0.00 0.00 0.00 2.40
1285 1335 5.046529 AGTCGATGCTACATTCACAAGATC 58.953 41.667 0.00 0.00 0.00 2.75
1286 1336 5.046529 GTCGATGCTACATTCACAAGATCT 58.953 41.667 0.00 0.00 0.00 2.75
1287 1337 5.521735 GTCGATGCTACATTCACAAGATCTT 59.478 40.000 0.88 0.88 0.00 2.40
1288 1338 6.697455 GTCGATGCTACATTCACAAGATCTTA 59.303 38.462 7.86 0.00 0.00 2.10
1289 1339 6.697455 TCGATGCTACATTCACAAGATCTTAC 59.303 38.462 7.86 0.00 0.00 2.34
1290 1340 6.345329 CGATGCTACATTCACAAGATCTTACG 60.345 42.308 7.86 2.22 0.00 3.18
1291 1341 5.720202 TGCTACATTCACAAGATCTTACGT 58.280 37.500 7.86 0.00 0.00 3.57
1292 1342 5.576774 TGCTACATTCACAAGATCTTACGTG 59.423 40.000 16.23 16.23 0.00 4.49
1293 1343 5.005779 GCTACATTCACAAGATCTTACGTGG 59.994 44.000 20.09 10.69 0.00 4.94
1294 1344 5.147330 ACATTCACAAGATCTTACGTGGA 57.853 39.130 20.09 14.94 0.00 4.02
1295 1345 5.171476 ACATTCACAAGATCTTACGTGGAG 58.829 41.667 20.09 14.28 0.00 3.86
1296 1346 5.047306 ACATTCACAAGATCTTACGTGGAGA 60.047 40.000 20.09 1.57 0.00 3.71
1300 1350 4.500837 CACAAGATCTTACGTGGAGATTCG 59.499 45.833 7.86 10.19 34.13 3.34
1351 1401 4.569761 TCTATATGCTCGGTCACTTGAC 57.430 45.455 0.34 0.34 44.04 3.18
1362 1412 2.069273 GTCACTTGACCGAGACATTGG 58.931 52.381 0.00 0.00 39.07 3.16
1371 1421 5.556915 TGACCGAGACATTGGTTAAATCTT 58.443 37.500 0.00 0.00 43.89 2.40
1373 1423 6.816640 TGACCGAGACATTGGTTAAATCTTAG 59.183 38.462 0.00 0.00 43.89 2.18
1395 1445 3.556775 GTCGACTAAGATCTAGCGACACT 59.443 47.826 23.15 0.90 40.37 3.55
1396 1446 3.803231 TCGACTAAGATCTAGCGACACTC 59.197 47.826 0.00 0.00 0.00 3.51
1398 1448 4.271533 CGACTAAGATCTAGCGACACTCTT 59.728 45.833 0.00 0.00 0.00 2.85
1402 1452 8.314143 ACTAAGATCTAGCGACACTCTTATAC 57.686 38.462 0.00 0.00 30.42 1.47
1407 1457 8.995220 AGATCTAGCGACACTCTTATACTTAAG 58.005 37.037 0.00 0.00 36.87 1.85
1408 1458 8.905660 ATCTAGCGACACTCTTATACTTAAGA 57.094 34.615 10.09 0.00 41.18 2.10
1409 1459 8.728337 TCTAGCGACACTCTTATACTTAAGAA 57.272 34.615 10.09 0.00 42.46 2.52
1410 1460 8.828644 TCTAGCGACACTCTTATACTTAAGAAG 58.171 37.037 10.09 2.72 42.46 2.85
1411 1461 7.627298 AGCGACACTCTTATACTTAAGAAGA 57.373 36.000 10.09 7.17 42.46 2.87
1413 1463 6.913673 GCGACACTCTTATACTTAAGAAGAGG 59.086 42.308 24.98 18.91 46.92 3.69
1417 1467 8.594550 ACACTCTTATACTTAAGAAGAGGCAAA 58.405 33.333 24.98 5.18 46.92 3.68
1418 1468 9.606631 CACTCTTATACTTAAGAAGAGGCAAAT 57.393 33.333 24.98 10.11 46.92 2.32
1427 1477 9.359653 ACTTAAGAAGAGGCAAATGCATATTAT 57.640 29.630 10.09 0.00 44.36 1.28
1435 1485 9.895138 AGAGGCAAATGCATATTATTTTCTTTT 57.105 25.926 0.00 0.00 44.36 2.27
1481 1532 5.416947 GTCAATACACATCTTACGTTCCCT 58.583 41.667 0.00 0.00 0.00 4.20
1506 1557 2.782615 CGGCCCGAACGAACAATC 59.217 61.111 0.00 0.00 0.00 2.67
1531 1582 1.838077 CCCGACCAGTTAGGAAGGAAT 59.162 52.381 0.00 0.00 41.22 3.01
1532 1583 2.238898 CCCGACCAGTTAGGAAGGAATT 59.761 50.000 0.00 0.00 41.22 2.17
1536 1587 5.484715 CGACCAGTTAGGAAGGAATTAACA 58.515 41.667 0.00 0.00 41.22 2.41
1560 1611 8.903820 ACATTTTAGTTTGCTAAAGAGAACACT 58.096 29.630 0.00 0.00 44.88 3.55
1570 1621 5.163943 GCTAAAGAGAACACTCCAATCGAAC 60.164 44.000 0.00 0.00 0.00 3.95
1574 1625 1.798813 GAACACTCCAATCGAACGCTT 59.201 47.619 0.00 0.00 0.00 4.68
1575 1626 1.429463 ACACTCCAATCGAACGCTTC 58.571 50.000 0.00 0.00 0.00 3.86
1610 1661 4.268405 GCGAAAACAGATAAAATGGCCATG 59.732 41.667 21.63 9.08 0.00 3.66
1627 1678 3.304659 GCCATGCCGTTGTATAAGGATTG 60.305 47.826 0.00 0.00 0.00 2.67
1628 1679 3.304659 CCATGCCGTTGTATAAGGATTGC 60.305 47.826 0.00 0.00 0.00 3.56
1630 1681 2.294074 GCCGTTGTATAAGGATTGCCA 58.706 47.619 0.00 0.00 36.29 4.92
1631 1682 2.884639 GCCGTTGTATAAGGATTGCCAT 59.115 45.455 0.00 0.00 36.29 4.40
1632 1683 3.304659 GCCGTTGTATAAGGATTGCCATG 60.305 47.826 0.00 0.00 36.29 3.66
1730 1781 6.435904 CCATAAGTTTTCAGGGGTTTGTCATA 59.564 38.462 0.00 0.00 0.00 2.15
1731 1782 7.039363 CCATAAGTTTTCAGGGGTTTGTCATAA 60.039 37.037 0.00 0.00 0.00 1.90
1738 1789 4.021544 TCAGGGGTTTGTCATAATTGCAAC 60.022 41.667 0.00 0.00 0.00 4.17
1769 1824 8.518702 AGAATTTCAGTCTAAAAAGAATGCTCC 58.481 33.333 0.00 0.00 34.34 4.70
1783 1838 0.966875 TGCTCCGAATTTGCCATGCT 60.967 50.000 0.00 0.00 0.00 3.79
1820 1875 3.244976 GCCATGCTACATCAACAACAAC 58.755 45.455 0.00 0.00 0.00 3.32
1856 1912 8.476657 TGCAATGATGTAAACATACAAATTGG 57.523 30.769 18.92 9.11 37.89 3.16
1858 1914 7.064371 GCAATGATGTAAACATACAAATTGGCA 59.936 33.333 18.92 0.00 37.89 4.92
1868 1924 5.898972 ACATACAAATTGGCATCCCTAATGT 59.101 36.000 0.00 0.00 37.71 2.71
1869 1925 7.066142 ACATACAAATTGGCATCCCTAATGTA 58.934 34.615 0.00 0.00 37.71 2.29
1870 1926 5.852282 ACAAATTGGCATCCCTAATGTAC 57.148 39.130 0.00 0.00 37.71 2.90
1892 1948 2.159170 GCTTAGAAGGATGCGTGAGAGT 60.159 50.000 0.00 0.00 0.00 3.24
1896 1952 2.499289 AGAAGGATGCGTGAGAGTGAAT 59.501 45.455 0.00 0.00 0.00 2.57
1898 1954 1.134580 AGGATGCGTGAGAGTGAATGG 60.135 52.381 0.00 0.00 0.00 3.16
1901 1957 1.795768 TGCGTGAGAGTGAATGGTTC 58.204 50.000 0.00 0.00 0.00 3.62
1908 1964 2.146342 AGAGTGAATGGTTCGCACAAG 58.854 47.619 6.09 0.00 42.49 3.16
1917 1973 0.313672 GTTCGCACAAGGGATGCAAA 59.686 50.000 0.00 0.00 43.57 3.68
1919 1975 0.537143 TCGCACAAGGGATGCAAAGT 60.537 50.000 0.00 0.00 43.57 2.66
1920 1976 0.387622 CGCACAAGGGATGCAAAGTG 60.388 55.000 0.00 0.00 43.57 3.16
1921 1977 0.668401 GCACAAGGGATGCAAAGTGC 60.668 55.000 10.35 10.35 44.31 4.40
1922 1978 0.037975 CACAAGGGATGCAAAGTGCC 60.038 55.000 0.00 0.00 44.23 5.01
1923 1979 0.178953 ACAAGGGATGCAAAGTGCCT 60.179 50.000 0.00 0.00 44.23 4.75
1924 1980 0.245539 CAAGGGATGCAAAGTGCCTG 59.754 55.000 0.00 0.00 44.23 4.85
1925 1981 0.901580 AAGGGATGCAAAGTGCCTGG 60.902 55.000 0.00 0.00 44.23 4.45
1926 1982 2.353610 GGGATGCAAAGTGCCTGGG 61.354 63.158 0.00 0.00 44.23 4.45
1927 1983 2.353610 GGATGCAAAGTGCCTGGGG 61.354 63.158 0.00 0.00 44.23 4.96
1928 1984 1.607467 GATGCAAAGTGCCTGGGGT 60.607 57.895 0.00 0.00 44.23 4.95
1929 1985 1.598701 GATGCAAAGTGCCTGGGGTC 61.599 60.000 0.00 0.00 44.23 4.46
1930 1986 2.085343 ATGCAAAGTGCCTGGGGTCT 62.085 55.000 0.00 0.00 44.23 3.85
1931 1987 1.531602 GCAAAGTGCCTGGGGTCTT 60.532 57.895 0.00 0.00 37.42 3.01
1932 1988 1.115326 GCAAAGTGCCTGGGGTCTTT 61.115 55.000 0.00 0.00 37.42 2.52
1933 1989 0.961753 CAAAGTGCCTGGGGTCTTTC 59.038 55.000 0.00 0.00 31.29 2.62
1934 1990 0.537371 AAAGTGCCTGGGGTCTTTCG 60.537 55.000 0.00 0.00 29.17 3.46
1935 1991 1.705997 AAGTGCCTGGGGTCTTTCGT 61.706 55.000 0.00 0.00 0.00 3.85
1936 1992 1.228154 GTGCCTGGGGTCTTTCGTT 60.228 57.895 0.00 0.00 0.00 3.85
1937 1993 1.072505 TGCCTGGGGTCTTTCGTTC 59.927 57.895 0.00 0.00 0.00 3.95
1938 1994 1.072505 GCCTGGGGTCTTTCGTTCA 59.927 57.895 0.00 0.00 0.00 3.18
1939 1995 0.955919 GCCTGGGGTCTTTCGTTCAG 60.956 60.000 0.00 0.00 0.00 3.02
1940 1996 0.685097 CCTGGGGTCTTTCGTTCAGA 59.315 55.000 0.00 0.00 0.00 3.27
1941 1997 1.608283 CCTGGGGTCTTTCGTTCAGAC 60.608 57.143 0.00 3.66 40.12 3.51
1957 2013 7.603297 CGTTCAGACGTCAAATTTTTAACAT 57.397 32.000 19.50 0.00 44.08 2.71
1958 2014 8.045750 CGTTCAGACGTCAAATTTTTAACATT 57.954 30.769 19.50 0.00 44.08 2.71
1959 2015 8.198816 CGTTCAGACGTCAAATTTTTAACATTC 58.801 33.333 19.50 0.00 44.08 2.67
1960 2016 8.476925 GTTCAGACGTCAAATTTTTAACATTCC 58.523 33.333 19.50 0.00 0.00 3.01
1961 2017 7.142680 TCAGACGTCAAATTTTTAACATTCCC 58.857 34.615 19.50 0.00 0.00 3.97
1962 2018 6.920758 CAGACGTCAAATTTTTAACATTCCCA 59.079 34.615 19.50 0.00 0.00 4.37
1963 2019 7.114811 CAGACGTCAAATTTTTAACATTCCCAG 59.885 37.037 19.50 0.00 0.00 4.45
1964 2020 6.220201 ACGTCAAATTTTTAACATTCCCAGG 58.780 36.000 0.00 0.00 0.00 4.45
1965 2021 6.041069 ACGTCAAATTTTTAACATTCCCAGGA 59.959 34.615 0.00 0.00 0.00 3.86
1966 2022 6.926272 CGTCAAATTTTTAACATTCCCAGGAA 59.074 34.615 0.68 0.68 38.59 3.36
1967 2023 7.439655 CGTCAAATTTTTAACATTCCCAGGAAA 59.560 33.333 2.65 0.00 37.69 3.13
2003 2059 4.038042 TCTCTCCATCGATTGATACACACC 59.962 45.833 0.00 0.00 32.18 4.16
2056 2115 4.201950 CCGCAAAGTGATTAAGCAAGCTAT 60.202 41.667 0.00 0.00 0.00 2.97
2057 2116 4.966366 CGCAAAGTGATTAAGCAAGCTATC 59.034 41.667 0.00 0.00 0.00 2.08
2061 2120 6.777526 AAGTGATTAAGCAAGCTATCGATC 57.222 37.500 0.00 0.00 0.00 3.69
2063 2122 3.675225 TGATTAAGCAAGCTATCGATCGC 59.325 43.478 13.69 13.69 0.00 4.58
2066 2125 3.303881 AAGCAAGCTATCGATCGCATA 57.696 42.857 22.25 8.46 0.00 3.14
2067 2126 3.516981 AGCAAGCTATCGATCGCATAT 57.483 42.857 22.25 6.84 0.00 1.78
2127 2285 1.153745 CGAAGAGGAGCGGGTTGAG 60.154 63.158 0.00 0.00 0.00 3.02
2284 2442 0.172578 GACCATCACCATCGACGACA 59.827 55.000 0.00 0.00 0.00 4.35
2322 2480 0.999406 CCATCGTCTTCGTCGCAAAT 59.001 50.000 0.00 0.00 38.33 2.32
2334 2492 2.872245 CGTCGCAAATTCATGGGTCTAT 59.128 45.455 0.00 0.00 35.03 1.98
2495 2653 5.556382 CGCTACATGCAAATCTAACGTTAGG 60.556 44.000 29.87 17.46 43.06 2.69
2542 2700 8.594881 ACGTTTTTCATGGCAAATTATGTTAA 57.405 26.923 0.00 0.00 0.00 2.01
2561 2719 5.637810 TGTTAAGCGAGGATGACAAGTTTAG 59.362 40.000 0.00 0.00 0.00 1.85
2573 2731 4.211164 TGACAAGTTTAGTTGACGAGCATG 59.789 41.667 4.40 0.00 0.00 4.06
2580 2738 1.470098 AGTTGACGAGCATGGCAAATC 59.530 47.619 0.00 0.00 0.00 2.17
2581 2739 1.470098 GTTGACGAGCATGGCAAATCT 59.530 47.619 0.00 0.00 0.00 2.40
2584 2742 1.470098 GACGAGCATGGCAAATCTGTT 59.530 47.619 0.00 0.00 0.00 3.16
2618 2776 7.789273 TTTTTGTCATCAAATTGTCATGCTT 57.211 28.000 0.00 0.00 42.14 3.91
2621 2779 7.872163 TTGTCATCAAATTGTCATGCTTAAC 57.128 32.000 0.00 0.00 0.00 2.01
2624 2782 7.381948 TGTCATCAAATTGTCATGCTTAACAAC 59.618 33.333 0.23 0.00 38.14 3.32
2635 2793 9.767684 TGTCATGCTTAACAACTAAATTTATCG 57.232 29.630 0.00 0.00 0.00 2.92
2647 2805 4.955925 AAATTTATCGTCATCGCACCAA 57.044 36.364 0.00 0.00 36.96 3.67
2662 2848 6.641169 TCGCACCAATATAAATTGCCATAA 57.359 33.333 0.00 0.00 41.06 1.90
2666 2852 7.223582 CGCACCAATATAAATTGCCATAAAACA 59.776 33.333 0.00 0.00 41.06 2.83
2715 2902 9.925268 TTTGACGTTAGATTTTTAGTGTTTCTC 57.075 29.630 0.00 0.00 0.00 2.87
3570 4060 1.302033 ACAACCTCGGCAAGCTCAG 60.302 57.895 0.00 0.00 0.00 3.35
3655 4238 4.564406 CCTCACCTGCTAAAGATCAACAGT 60.564 45.833 0.00 0.00 0.00 3.55
3658 4241 4.999950 CACCTGCTAAAGATCAACAGTCTT 59.000 41.667 0.00 0.00 37.52 3.01
3676 4259 5.119279 CAGTCTTCCAAACACATTCGTCTAG 59.881 44.000 0.00 0.00 0.00 2.43
3694 4277 2.032681 GCCACCAGGACGCTTCTT 59.967 61.111 0.00 0.00 36.89 2.52
3841 7403 2.119611 TCGGAGAGGGCTGTCCAA 59.880 61.111 0.00 0.00 42.66 3.53
4057 7749 1.675641 GGCACGCCAAGTCCTCATT 60.676 57.895 2.36 0.00 35.81 2.57
4063 7755 0.462759 GCCAAGTCCTCATTAGCGCT 60.463 55.000 17.26 17.26 0.00 5.92
4180 7872 2.656002 CCGGTAGACCTGATCAAGAGA 58.344 52.381 0.00 0.00 0.00 3.10
4453 8145 1.508545 CGAGCTCGTCAGGTCATGT 59.491 57.895 27.79 0.00 46.03 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.095059 AGATGTGCCTTTGATTTGCGAC 60.095 45.455 0.00 0.00 0.00 5.19
20 21 6.321181 TCATTTGGAACCTAATTAGATGTGCC 59.679 38.462 14.28 12.11 0.00 5.01
36 37 5.278463 GCTCTGTTGCTAAACTCATTTGGAA 60.278 40.000 0.00 0.00 37.19 3.53
38 39 4.022935 TGCTCTGTTGCTAAACTCATTTGG 60.023 41.667 0.00 0.00 37.19 3.28
67 68 5.824904 AGGATGAACCATTGATCTTTTCG 57.175 39.130 0.00 0.00 42.04 3.46
76 77 4.081406 TCTGTGGAAAGGATGAACCATTG 58.919 43.478 0.00 0.00 42.04 2.82
78 79 4.387026 TTCTGTGGAAAGGATGAACCAT 57.613 40.909 0.00 0.00 42.04 3.55
79 80 3.874383 TTCTGTGGAAAGGATGAACCA 57.126 42.857 0.00 0.00 42.04 3.67
80 81 5.163457 TGTTTTTCTGTGGAAAGGATGAACC 60.163 40.000 0.00 0.00 41.66 3.62
81 82 5.901552 TGTTTTTCTGTGGAAAGGATGAAC 58.098 37.500 0.00 0.00 41.66 3.18
102 107 5.068591 GGTGGAAAGGTGACAAAAACTATGT 59.931 40.000 0.00 0.00 0.00 2.29
124 129 6.267699 CCAGAGACAATCTTTTAAAAAGGGGT 59.732 38.462 1.66 0.00 35.47 4.95
236 246 2.612672 CCGATCTCGACTTGTGCTAGTA 59.387 50.000 0.22 0.00 43.02 1.82
237 247 1.402259 CCGATCTCGACTTGTGCTAGT 59.598 52.381 0.22 0.00 43.02 2.57
238 248 1.671328 TCCGATCTCGACTTGTGCTAG 59.329 52.381 0.22 0.00 43.02 3.42
242 252 1.272781 GCTTCCGATCTCGACTTGTG 58.727 55.000 0.22 0.00 43.02 3.33
354 371 1.404035 TGTACGTGCATGCTACTCGAT 59.596 47.619 20.33 10.85 0.00 3.59
516 556 7.031372 TGTTTATGGCACTCTTAAGTACGTAG 58.969 38.462 1.63 0.00 33.25 3.51
517 557 6.923012 TGTTTATGGCACTCTTAAGTACGTA 58.077 36.000 1.63 0.00 33.25 3.57
534 574 5.412640 TCCACCGTACATACACTGTTTATG 58.587 41.667 11.38 11.38 39.39 1.90
547 587 3.066291 AGAAAATGCATCCACCGTACA 57.934 42.857 0.00 0.00 0.00 2.90
610 652 1.517242 TTGCATGTGCGTATGTGTGA 58.483 45.000 0.01 0.00 45.83 3.58
744 790 2.567049 CGCGTCGTCTTCCTTCCT 59.433 61.111 0.00 0.00 0.00 3.36
827 873 4.106925 AGGCTAGCTGCACCCTGC 62.107 66.667 15.72 0.00 45.15 4.85
828 874 2.124819 CAGGCTAGCTGCACCCTG 60.125 66.667 15.72 15.45 45.15 4.45
829 875 4.106925 GCAGGCTAGCTGCACCCT 62.107 66.667 24.94 8.34 46.19 4.34
834 880 2.599645 TAGCAAGGCAGGCTAGCTGC 62.600 60.000 23.03 23.03 46.20 5.25
835 881 1.524002 TAGCAAGGCAGGCTAGCTG 59.476 57.895 15.72 11.82 42.62 4.24
836 882 4.056805 TAGCAAGGCAGGCTAGCT 57.943 55.556 15.72 4.31 42.62 3.32
839 885 1.690219 GGAGCTAGCAAGGCAGGCTA 61.690 60.000 18.83 9.35 42.62 3.93
840 886 2.588989 GAGCTAGCAAGGCAGGCT 59.411 61.111 18.83 8.02 45.18 4.58
841 887 2.515757 GGAGCTAGCAAGGCAGGC 60.516 66.667 18.83 0.00 0.00 4.85
842 888 2.202987 CGGAGCTAGCAAGGCAGG 60.203 66.667 18.83 0.00 0.00 4.85
843 889 2.202987 CCGGAGCTAGCAAGGCAG 60.203 66.667 18.83 3.95 0.00 4.85
844 890 4.473520 GCCGGAGCTAGCAAGGCA 62.474 66.667 30.43 0.00 46.48 4.75
846 892 2.512515 GTGCCGGAGCTAGCAAGG 60.513 66.667 18.83 17.11 41.48 3.61
847 893 2.103042 GTGTGCCGGAGCTAGCAAG 61.103 63.158 18.83 7.31 41.48 4.01
848 894 2.047274 GTGTGCCGGAGCTAGCAA 60.047 61.111 18.83 0.00 41.48 3.91
849 895 4.435436 CGTGTGCCGGAGCTAGCA 62.435 66.667 18.83 1.61 40.80 3.49
867 913 2.194889 GGAGGTCGGATCGGAGGAC 61.195 68.421 2.75 0.14 0.00 3.85
990 1040 1.001974 CACCCGAACATCTTCCTCACA 59.998 52.381 0.00 0.00 0.00 3.58
1062 1112 0.033504 GCCAGTGGTTCAAGTCGAGA 59.966 55.000 11.74 0.00 0.00 4.04
1090 1140 2.357517 CCAGGTGTCGTGGCTCAC 60.358 66.667 0.00 0.00 32.63 3.51
1092 1142 3.311110 TCCCAGGTGTCGTGGCTC 61.311 66.667 3.34 0.00 37.99 4.70
1167 1217 2.223829 TGCGCTTAGATGCTCCTTACTC 60.224 50.000 9.73 0.00 0.00 2.59
1176 1226 1.560860 GGACGGATGCGCTTAGATGC 61.561 60.000 9.73 0.00 0.00 3.91
1181 1231 1.067142 GGATATGGACGGATGCGCTTA 60.067 52.381 9.73 0.00 0.00 3.09
1185 1235 2.166459 ACATAGGATATGGACGGATGCG 59.834 50.000 4.58 4.58 0.00 4.73
1225 1275 1.197910 GTCGCGGTCGGAGATTTAAG 58.802 55.000 6.13 0.00 40.67 1.85
1235 1285 1.203065 GGTTAATTAGGTCGCGGTCG 58.797 55.000 6.13 0.00 0.00 4.79
1237 1287 2.027837 ACTTGGTTAATTAGGTCGCGGT 60.028 45.455 6.13 0.00 0.00 5.68
1238 1288 2.606272 GACTTGGTTAATTAGGTCGCGG 59.394 50.000 6.13 0.00 0.00 6.46
1239 1289 3.255725 TGACTTGGTTAATTAGGTCGCG 58.744 45.455 0.00 0.00 0.00 5.87
1240 1290 6.047231 ACTATGACTTGGTTAATTAGGTCGC 58.953 40.000 0.00 0.00 0.00 5.19
1242 1292 7.486647 TCGACTATGACTTGGTTAATTAGGTC 58.513 38.462 0.00 0.00 0.00 3.85
1243 1293 7.414222 TCGACTATGACTTGGTTAATTAGGT 57.586 36.000 0.00 0.00 0.00 3.08
1244 1294 7.095607 GCATCGACTATGACTTGGTTAATTAGG 60.096 40.741 0.00 0.00 37.86 2.69
1245 1295 7.653713 AGCATCGACTATGACTTGGTTAATTAG 59.346 37.037 0.00 0.00 37.86 1.73
1246 1296 7.497595 AGCATCGACTATGACTTGGTTAATTA 58.502 34.615 0.00 0.00 37.86 1.40
1247 1297 6.349300 AGCATCGACTATGACTTGGTTAATT 58.651 36.000 0.00 0.00 37.86 1.40
1248 1298 5.918608 AGCATCGACTATGACTTGGTTAAT 58.081 37.500 0.00 0.00 37.86 1.40
1249 1299 5.339008 AGCATCGACTATGACTTGGTTAA 57.661 39.130 0.00 0.00 37.86 2.01
1250 1300 5.358725 TGTAGCATCGACTATGACTTGGTTA 59.641 40.000 0.00 0.00 37.86 2.85
1251 1301 3.895232 AGCATCGACTATGACTTGGTT 57.105 42.857 0.00 0.00 37.86 3.67
1252 1302 3.699538 TGTAGCATCGACTATGACTTGGT 59.300 43.478 0.00 0.00 37.86 3.67
1253 1303 4.307443 TGTAGCATCGACTATGACTTGG 57.693 45.455 0.00 0.00 37.86 3.61
1254 1304 5.979517 TGAATGTAGCATCGACTATGACTTG 59.020 40.000 0.00 0.00 37.86 3.16
1255 1305 5.980116 GTGAATGTAGCATCGACTATGACTT 59.020 40.000 0.00 0.00 37.86 3.01
1256 1306 5.067805 TGTGAATGTAGCATCGACTATGACT 59.932 40.000 0.00 0.00 37.86 3.41
1257 1307 5.281727 TGTGAATGTAGCATCGACTATGAC 58.718 41.667 0.00 0.00 37.86 3.06
1258 1308 5.514274 TGTGAATGTAGCATCGACTATGA 57.486 39.130 0.00 0.00 37.86 2.15
1259 1309 5.979517 TCTTGTGAATGTAGCATCGACTATG 59.020 40.000 0.00 0.00 38.74 2.23
1260 1310 6.149129 TCTTGTGAATGTAGCATCGACTAT 57.851 37.500 0.00 0.00 0.00 2.12
1261 1311 5.576447 TCTTGTGAATGTAGCATCGACTA 57.424 39.130 0.00 0.00 0.00 2.59
1262 1312 4.456280 TCTTGTGAATGTAGCATCGACT 57.544 40.909 0.00 0.00 0.00 4.18
1263 1313 5.046529 AGATCTTGTGAATGTAGCATCGAC 58.953 41.667 0.00 0.00 0.00 4.20
1264 1314 5.268118 AGATCTTGTGAATGTAGCATCGA 57.732 39.130 0.00 0.00 0.00 3.59
1265 1315 5.980698 AAGATCTTGTGAATGTAGCATCG 57.019 39.130 7.30 0.00 0.00 3.84
1266 1316 6.477033 ACGTAAGATCTTGTGAATGTAGCATC 59.523 38.462 18.47 0.00 43.62 3.91
1267 1317 6.256539 CACGTAAGATCTTGTGAATGTAGCAT 59.743 38.462 18.47 0.00 43.62 3.79
1268 1318 5.576774 CACGTAAGATCTTGTGAATGTAGCA 59.423 40.000 18.47 0.00 43.62 3.49
1269 1319 5.005779 CCACGTAAGATCTTGTGAATGTAGC 59.994 44.000 21.56 0.71 43.62 3.58
1270 1320 6.330278 TCCACGTAAGATCTTGTGAATGTAG 58.670 40.000 21.56 7.25 43.62 2.74
1271 1321 6.152154 TCTCCACGTAAGATCTTGTGAATGTA 59.848 38.462 21.56 0.00 43.62 2.29
1272 1322 5.047306 TCTCCACGTAAGATCTTGTGAATGT 60.047 40.000 21.56 10.28 43.62 2.71
1273 1323 5.410924 TCTCCACGTAAGATCTTGTGAATG 58.589 41.667 21.56 9.73 43.62 2.67
1274 1324 5.661056 TCTCCACGTAAGATCTTGTGAAT 57.339 39.130 21.56 0.00 43.62 2.57
1275 1325 5.661056 ATCTCCACGTAAGATCTTGTGAA 57.339 39.130 21.56 6.18 43.62 3.18
1276 1326 5.651530 GAATCTCCACGTAAGATCTTGTGA 58.348 41.667 21.56 10.80 43.62 3.58
1277 1327 4.500837 CGAATCTCCACGTAAGATCTTGTG 59.499 45.833 18.47 16.83 43.62 3.33
1278 1328 4.158025 ACGAATCTCCACGTAAGATCTTGT 59.842 41.667 18.47 5.41 40.92 3.16
1279 1329 4.500837 CACGAATCTCCACGTAAGATCTTG 59.499 45.833 18.47 4.73 40.76 3.02
1280 1330 4.673441 CACGAATCTCCACGTAAGATCTT 58.327 43.478 13.56 13.56 40.76 2.40
1281 1331 3.489398 GCACGAATCTCCACGTAAGATCT 60.489 47.826 11.76 0.00 40.76 2.75
1282 1332 2.789893 GCACGAATCTCCACGTAAGATC 59.210 50.000 11.76 6.39 40.76 2.75
1283 1333 2.165641 TGCACGAATCTCCACGTAAGAT 59.834 45.455 6.77 6.77 40.76 2.40
1284 1334 1.542472 TGCACGAATCTCCACGTAAGA 59.458 47.619 2.62 2.62 40.76 2.10
1285 1335 1.990799 TGCACGAATCTCCACGTAAG 58.009 50.000 0.00 0.00 40.76 2.34
1286 1336 2.442212 TTGCACGAATCTCCACGTAA 57.558 45.000 0.00 0.00 40.76 3.18
1287 1337 2.442212 TTTGCACGAATCTCCACGTA 57.558 45.000 0.00 0.00 40.76 3.57
1288 1338 1.588674 TTTTGCACGAATCTCCACGT 58.411 45.000 0.00 0.00 43.50 4.49
1289 1339 2.679355 TTTTTGCACGAATCTCCACG 57.321 45.000 0.00 0.00 0.00 4.94
1327 1377 5.810587 GTCAAGTGACCGAGCATATAGAAAA 59.189 40.000 0.00 0.00 39.07 2.29
1328 1378 5.348986 GTCAAGTGACCGAGCATATAGAAA 58.651 41.667 0.00 0.00 39.07 2.52
1342 1392 2.069273 CCAATGTCTCGGTCAAGTGAC 58.931 52.381 2.69 2.69 44.04 3.67
1351 1401 6.019801 CGACTAAGATTTAACCAATGTCTCGG 60.020 42.308 0.00 0.00 0.00 4.63
1352 1402 6.750501 TCGACTAAGATTTAACCAATGTCTCG 59.249 38.462 0.00 0.00 0.00 4.04
1353 1403 7.760340 AGTCGACTAAGATTTAACCAATGTCTC 59.240 37.037 18.46 0.00 0.00 3.36
1371 1421 4.744137 GTGTCGCTAGATCTTAGTCGACTA 59.256 45.833 21.25 21.25 40.79 2.59
1373 1423 3.556775 AGTGTCGCTAGATCTTAGTCGAC 59.443 47.826 21.27 21.27 40.69 4.20
1388 1438 6.913673 CCTCTTCTTAAGTATAAGAGTGTCGC 59.086 42.308 21.78 0.00 46.15 5.19
1390 1440 7.773149 TGCCTCTTCTTAAGTATAAGAGTGTC 58.227 38.462 21.78 14.62 46.15 3.67
1395 1445 8.046708 TGCATTTGCCTCTTCTTAAGTATAAGA 58.953 33.333 1.63 3.86 41.95 2.10
1396 1446 8.213518 TGCATTTGCCTCTTCTTAAGTATAAG 57.786 34.615 1.63 0.00 41.18 1.73
1407 1457 9.538508 AAGAAAATAATATGCATTTGCCTCTTC 57.461 29.630 3.54 0.94 41.18 2.87
1408 1458 9.895138 AAAGAAAATAATATGCATTTGCCTCTT 57.105 25.926 3.54 2.67 41.18 2.85
1409 1459 9.895138 AAAAGAAAATAATATGCATTTGCCTCT 57.105 25.926 3.54 0.00 41.18 3.69
1489 1540 2.782615 GATTGTTCGTTCGGGCCG 59.217 61.111 22.51 22.51 0.00 6.13
1506 1557 1.217244 CCTAACTGGTCGGGGAACG 59.783 63.158 0.00 0.00 46.11 3.95
1507 1558 0.978907 TTCCTAACTGGTCGGGGAAC 59.021 55.000 0.00 0.00 37.07 3.62
1514 1565 7.939784 AATGTTAATTCCTTCCTAACTGGTC 57.060 36.000 0.00 0.00 37.07 4.02
1515 1566 8.721133 AAAATGTTAATTCCTTCCTAACTGGT 57.279 30.769 0.00 0.00 37.07 4.00
1536 1587 8.568794 GGAGTGTTCTCTTTAGCAAACTAAAAT 58.431 33.333 0.48 0.00 45.42 1.82
1552 1603 1.390463 GCGTTCGATTGGAGTGTTCTC 59.610 52.381 0.00 0.00 39.76 2.87
1570 1621 0.587242 CGCATGACAATTCCGAAGCG 60.587 55.000 0.00 0.00 37.91 4.68
1574 1625 2.550180 TGTTTTCGCATGACAATTCCGA 59.450 40.909 0.00 0.00 0.00 4.55
1575 1626 2.910482 CTGTTTTCGCATGACAATTCCG 59.090 45.455 0.00 0.00 0.00 4.30
1576 1627 4.159377 TCTGTTTTCGCATGACAATTCC 57.841 40.909 0.00 0.00 0.00 3.01
1577 1628 7.795431 TTTATCTGTTTTCGCATGACAATTC 57.205 32.000 0.00 0.00 0.00 2.17
1610 1661 2.294074 TGGCAATCCTTATACAACGGC 58.706 47.619 0.00 0.00 0.00 5.68
1627 1678 7.914465 TGACAATTTTTACTTTGAAACATGGC 58.086 30.769 0.00 0.00 0.00 4.40
1628 1679 9.866936 CATGACAATTTTTACTTTGAAACATGG 57.133 29.630 0.00 0.00 34.00 3.66
1694 1745 9.025041 CCCTGAAAACTTATGGAAATTACTCTT 57.975 33.333 0.00 0.00 0.00 2.85
1709 1760 6.994421 ATTATGACAAACCCCTGAAAACTT 57.006 33.333 0.00 0.00 0.00 2.66
1738 1789 9.635520 ATTCTTTTTAGACTGAAATTCTGCATG 57.364 29.630 0.00 0.00 0.00 4.06
1783 1838 2.285024 GGCAATTTCCCTGCAGCCA 61.285 57.895 8.66 0.00 41.78 4.75
1849 1905 4.792704 GCGTACATTAGGGATGCCAATTTG 60.793 45.833 5.86 0.00 39.47 2.32
1856 1912 4.252971 TCTAAGCGTACATTAGGGATGC 57.747 45.455 12.53 0.00 39.47 3.91
1858 1914 5.145564 TCCTTCTAAGCGTACATTAGGGAT 58.854 41.667 12.53 0.00 32.24 3.85
1892 1948 0.109532 TCCCTTGTGCGAACCATTCA 59.890 50.000 0.00 0.00 0.00 2.57
1896 1952 1.971167 GCATCCCTTGTGCGAACCA 60.971 57.895 0.00 0.00 32.29 3.67
1898 1954 0.313672 TTTGCATCCCTTGTGCGAAC 59.686 50.000 0.00 0.00 45.37 3.95
1901 1957 0.387622 CACTTTGCATCCCTTGTGCG 60.388 55.000 0.00 0.00 45.37 5.34
1917 1973 1.705997 AACGAAAGACCCCAGGCACT 61.706 55.000 0.00 0.00 43.88 4.40
1919 1975 1.072505 GAACGAAAGACCCCAGGCA 59.927 57.895 0.00 0.00 0.00 4.75
1920 1976 0.955919 CTGAACGAAAGACCCCAGGC 60.956 60.000 0.00 0.00 0.00 4.85
1921 1977 0.685097 TCTGAACGAAAGACCCCAGG 59.315 55.000 0.00 0.00 0.00 4.45
1922 1978 1.797025 GTCTGAACGAAAGACCCCAG 58.203 55.000 0.00 0.00 38.50 4.45
1934 1990 8.476925 GGAATGTTAAAAATTTGACGTCTGAAC 58.523 33.333 17.92 5.38 30.13 3.18
1935 1991 7.650104 GGGAATGTTAAAAATTTGACGTCTGAA 59.350 33.333 17.92 11.89 30.13 3.02
1936 1992 7.142680 GGGAATGTTAAAAATTTGACGTCTGA 58.857 34.615 17.92 5.48 30.13 3.27
1937 1993 6.920758 TGGGAATGTTAAAAATTTGACGTCTG 59.079 34.615 17.92 0.00 30.13 3.51
1938 1994 7.045126 TGGGAATGTTAAAAATTTGACGTCT 57.955 32.000 17.92 0.00 30.13 4.18
1939 1995 6.364976 CCTGGGAATGTTAAAAATTTGACGTC 59.635 38.462 9.11 9.11 30.13 4.34
1940 1996 6.041069 TCCTGGGAATGTTAAAAATTTGACGT 59.959 34.615 0.00 0.00 30.13 4.34
1941 1997 6.451393 TCCTGGGAATGTTAAAAATTTGACG 58.549 36.000 0.00 0.00 30.13 4.35
1942 1998 8.669946 TTTCCTGGGAATGTTAAAAATTTGAC 57.330 30.769 2.69 0.00 33.79 3.18
1943 1999 9.686683 TTTTTCCTGGGAATGTTAAAAATTTGA 57.313 25.926 2.69 0.00 33.79 2.69
1985 2041 3.070159 AGGAGGTGTGTATCAATCGATGG 59.930 47.826 0.00 0.00 32.73 3.51
1988 2044 3.767131 TGAAGGAGGTGTGTATCAATCGA 59.233 43.478 0.00 0.00 0.00 3.59
2035 2094 4.966366 CGATAGCTTGCTTAATCACTTTGC 59.034 41.667 0.00 0.00 0.00 3.68
2040 2099 4.433544 GCGATCGATAGCTTGCTTAATCAC 60.434 45.833 21.57 0.00 38.56 3.06
2044 2103 3.092334 TGCGATCGATAGCTTGCTTAA 57.908 42.857 27.21 6.24 42.06 1.85
2063 2122 7.439655 CACTCTCATCATCTGCATCCATATATG 59.560 40.741 5.68 5.68 0.00 1.78
2066 2125 5.338463 CCACTCTCATCATCTGCATCCATAT 60.338 44.000 0.00 0.00 0.00 1.78
2067 2126 4.020485 CCACTCTCATCATCTGCATCCATA 60.020 45.833 0.00 0.00 0.00 2.74
2322 2480 5.506730 TGTTGGTGTTATAGACCCATGAA 57.493 39.130 0.00 0.00 31.43 2.57
2334 2492 4.340666 TCGTAGTGGTACTTGTTGGTGTTA 59.659 41.667 0.00 0.00 0.00 2.41
2404 2562 9.631257 ATGAAACTGATACATGAATATGTCCAA 57.369 29.630 0.00 0.00 44.00 3.53
2469 2627 7.656837 CTAACGTTAGATTTGCATGTAGCGGA 61.657 42.308 27.65 0.00 37.23 5.54
2472 2630 5.293569 ACCTAACGTTAGATTTGCATGTAGC 59.706 40.000 31.97 0.00 37.00 3.58
2474 2632 7.675962 AAACCTAACGTTAGATTTGCATGTA 57.324 32.000 31.97 0.00 33.05 2.29
2518 2676 7.687757 GCTTAACATAATTTGCCATGAAAAACG 59.312 33.333 0.00 0.00 0.00 3.60
2542 2700 3.963428 ACTAAACTTGTCATCCTCGCT 57.037 42.857 0.00 0.00 0.00 4.93
2561 2719 1.470098 AGATTTGCCATGCTCGTCAAC 59.530 47.619 0.00 0.00 0.00 3.18
2617 2775 8.657729 TGCGATGACGATAAATTTAGTTGTTAA 58.342 29.630 3.94 0.00 42.66 2.01
2618 2776 8.111836 GTGCGATGACGATAAATTTAGTTGTTA 58.888 33.333 3.94 0.13 42.66 2.41
2621 2779 5.901884 GGTGCGATGACGATAAATTTAGTTG 59.098 40.000 3.94 0.00 42.66 3.16
2624 2782 5.651172 TGGTGCGATGACGATAAATTTAG 57.349 39.130 3.94 0.00 42.66 1.85
2635 2793 4.917415 GGCAATTTATATTGGTGCGATGAC 59.083 41.667 7.83 0.00 41.21 3.06
2715 2902 7.968405 CGGTGTTTATCCTCCTTTTATTTTCAG 59.032 37.037 0.00 0.00 0.00 3.02
2786 2973 1.399089 CGTCTGCATTGCATGTCATGA 59.601 47.619 17.24 1.69 38.13 3.07
2995 3382 1.134189 GGGTATGGGTACAAGCTGTCC 60.134 57.143 0.00 0.00 32.25 4.02
3082 3469 1.227853 GAACTGTTGGAGCACGGGT 60.228 57.895 0.00 0.00 0.00 5.28
3570 4060 2.092291 TCGATTGCCTTGTCGACGC 61.092 57.895 11.62 9.03 41.44 5.19
3655 4238 4.566004 CCTAGACGAATGTGTTTGGAAGA 58.434 43.478 0.00 0.00 0.00 2.87
3658 4241 2.614481 GGCCTAGACGAATGTGTTTGGA 60.614 50.000 0.00 0.00 0.00 3.53
3676 4259 3.553095 AAGAAGCGTCCTGGTGGCC 62.553 63.158 0.00 0.00 0.00 5.36
3691 4274 1.497991 CGTCGTCTTGCAGGAAAAGA 58.502 50.000 0.00 0.00 0.00 2.52
3694 4277 1.959226 GCCGTCGTCTTGCAGGAAA 60.959 57.895 0.00 0.00 0.00 3.13
3841 7403 1.298993 CAGCTGCCAGATGGTGTCT 59.701 57.895 1.02 0.00 37.80 3.41
4063 7755 1.066858 GTCATCTCGAAGAAGCCACCA 60.067 52.381 0.00 0.00 34.09 4.17
4180 7872 2.203788 TCCTCCTTCGCCACACCT 60.204 61.111 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.