Multiple sequence alignment - TraesCS7D01G342900

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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 TraesCS7D01G342900 chr7D 100.000 3143 0 0 1 3143 439631210 439634352 0.000000e+00 5805.0
1 TraesCS7D01G342900 chr7D 98.837 172 2 0 2931 3102 439633969 439634140 1.090000e-79 307.0
2 TraesCS7D01G342900 chr7D 98.837 172 2 0 2760 2931 439634140 439634311 1.090000e-79 307.0
3 TraesCS7D01G342900 chr7B 88.335 1646 96 38 1337 2928 457383258 457384861 0.000000e+00 1888.0
4 TraesCS7D01G342900 chr7B 92.308 663 49 2 1 661 69354147 69353485 0.000000e+00 941.0
5 TraesCS7D01G342900 chr7B 92.296 662 48 3 1 661 714612184 714611525 0.000000e+00 937.0
6 TraesCS7D01G342900 chr7B 86.545 602 50 17 663 1250 457382676 457383260 4.420000e-178 634.0
7 TraesCS7D01G342900 chr7B 89.524 210 16 4 2933 3141 457384700 457384904 8.650000e-66 261.0
8 TraesCS7D01G342900 chr7B 85.263 95 7 4 1247 1340 103891528 103891440 1.200000e-14 91.6
9 TraesCS7D01G342900 chr2D 97.734 662 14 1 1 661 7177937 7178598 0.000000e+00 1138.0
10 TraesCS7D01G342900 chr3D 96.380 663 20 3 1 662 610529173 610529832 0.000000e+00 1088.0
11 TraesCS7D01G342900 chr3D 88.372 86 4 2 1249 1334 381989073 381989152 7.170000e-17 99.0
12 TraesCS7D01G342900 chr3D 84.536 97 8 3 1248 1343 157099356 157099446 4.320000e-14 89.8
13 TraesCS7D01G342900 chr5B 93.202 662 43 2 1 661 265286403 265287063 0.000000e+00 972.0
14 TraesCS7D01G342900 chr4B 92.900 662 45 2 1 661 595296726 595297386 0.000000e+00 961.0
15 TraesCS7D01G342900 chr4B 87.912 91 8 2 1246 1334 30730986 30731075 1.540000e-18 104.0
16 TraesCS7D01G342900 chr2B 92.296 662 49 2 2 661 57913262 57912601 0.000000e+00 939.0
17 TraesCS7D01G342900 chr2B 92.145 662 48 3 1 661 153900015 153899357 0.000000e+00 931.0
18 TraesCS7D01G342900 chr5A 92.042 666 45 3 1 665 481319825 481319167 0.000000e+00 929.0
19 TraesCS7D01G342900 chr7A 87.198 828 51 17 1532 2304 490865728 490866555 0.000000e+00 891.0
20 TraesCS7D01G342900 chr7A 87.671 511 27 11 663 1164 490864827 490865310 2.120000e-156 562.0
21 TraesCS7D01G342900 chr3A 88.636 88 4 4 1247 1334 672085984 672085903 5.550000e-18 102.0
22 TraesCS7D01G342900 chr3A 86.170 94 6 6 1247 1334 661792641 661792733 9.280000e-16 95.3
23 TraesCS7D01G342900 chr3A 83.838 99 10 3 1239 1337 360822561 360822469 4.320000e-14 89.8
24 TraesCS7D01G342900 chr2A 86.517 89 7 3 1249 1337 78845862 78845779 3.340000e-15 93.5
25 TraesCS7D01G342900 chr5D 82.524 103 12 5 1232 1334 457676006 457676102 5.590000e-13 86.1


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G342900 chr7D 439631210 439634352 3142 False 2139.666667 5805 99.224667 1 3143 3 chr7D.!!$F1 3142
1 TraesCS7D01G342900 chr7B 69353485 69354147 662 True 941.000000 941 92.308000 1 661 1 chr7B.!!$R1 660
2 TraesCS7D01G342900 chr7B 714611525 714612184 659 True 937.000000 937 92.296000 1 661 1 chr7B.!!$R3 660
3 TraesCS7D01G342900 chr7B 457382676 457384904 2228 False 927.666667 1888 88.134667 663 3141 3 chr7B.!!$F1 2478
4 TraesCS7D01G342900 chr2D 7177937 7178598 661 False 1138.000000 1138 97.734000 1 661 1 chr2D.!!$F1 660
5 TraesCS7D01G342900 chr3D 610529173 610529832 659 False 1088.000000 1088 96.380000 1 662 1 chr3D.!!$F3 661
6 TraesCS7D01G342900 chr5B 265286403 265287063 660 False 972.000000 972 93.202000 1 661 1 chr5B.!!$F1 660
7 TraesCS7D01G342900 chr4B 595296726 595297386 660 False 961.000000 961 92.900000 1 661 1 chr4B.!!$F2 660
8 TraesCS7D01G342900 chr2B 57912601 57913262 661 True 939.000000 939 92.296000 2 661 1 chr2B.!!$R1 659
9 TraesCS7D01G342900 chr2B 153899357 153900015 658 True 931.000000 931 92.145000 1 661 1 chr2B.!!$R2 660
10 TraesCS7D01G342900 chr5A 481319167 481319825 658 True 929.000000 929 92.042000 1 665 1 chr5A.!!$R1 664
11 TraesCS7D01G342900 chr7A 490864827 490866555 1728 False 726.500000 891 87.434500 663 2304 2 chr7A.!!$F1 1641

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
102 103 1.065701 GCCGATCTCGAGCTAGTTTCA 59.934 52.381 7.81 0.0 43.02 2.69 F
1261 1314 0.179054 GCCAAATACTCCCTCCGTCC 60.179 60.000 0.00 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1549 1769 0.681733 ATACCTGAGCCGTATGCCTG 59.318 55.0 0.0 0.0 42.71 4.85 R
2918 3200 0.106819 GTGATGGCCCTGAGCAGAAT 60.107 55.0 0.0 0.0 46.50 2.40 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 103 1.065701 GCCGATCTCGAGCTAGTTTCA 59.934 52.381 7.81 0.00 43.02 2.69
368 370 8.414003 GGCTAAATTTCTCCTGTTTAATTAGGG 58.586 37.037 0.00 0.00 34.76 3.53
382 387 2.806945 TTAGGGCTCCATGTTTCCTG 57.193 50.000 0.00 0.00 0.00 3.86
656 663 1.800805 CCTCGAGCTTTTCTTGCAGA 58.199 50.000 6.99 0.00 0.00 4.26
709 719 9.484806 AACTAACTAGCTATTAAAGGGTCACTA 57.515 33.333 0.00 0.00 0.00 2.74
758 768 9.942526 AAGTAAAGGATTTTAATCTCCCATCAT 57.057 29.630 2.77 0.00 40.09 2.45
849 896 4.096833 GTGGAACATGCATGCTGATTCTAA 59.903 41.667 26.53 11.73 44.52 2.10
913 960 8.713271 GTGATTAAATGCTATAGGCTAAGACAC 58.287 37.037 0.00 0.00 42.39 3.67
914 961 8.428852 TGATTAAATGCTATAGGCTAAGACACA 58.571 33.333 0.00 0.00 42.39 3.72
926 973 4.034510 GGCTAAGACACACTATTGATGCAC 59.965 45.833 0.00 0.00 0.00 4.57
928 975 5.352569 GCTAAGACACACTATTGATGCACTT 59.647 40.000 0.00 0.00 0.00 3.16
932 979 5.180117 AGACACACTATTGATGCACTTTCAC 59.820 40.000 0.00 0.00 0.00 3.18
935 982 5.643348 CACACTATTGATGCACTTTCACCTA 59.357 40.000 0.00 0.00 0.00 3.08
936 983 6.317140 CACACTATTGATGCACTTTCACCTAT 59.683 38.462 0.00 0.00 0.00 2.57
964 1011 7.337689 AGCAATAATTCATAGTTGTTCTCAGCA 59.662 33.333 0.00 0.00 0.00 4.41
978 1025 4.771590 TCTCAGCAATGTGGAAATTGTC 57.228 40.909 0.00 0.00 39.33 3.18
1044 1091 1.947013 CATGTCATGCGAGGGATGC 59.053 57.895 0.00 0.00 0.00 3.91
1086 1133 3.037549 TCTTGGCAAAATGGAAGGTTGT 58.962 40.909 0.00 0.00 0.00 3.32
1088 1135 4.651503 TCTTGGCAAAATGGAAGGTTGTTA 59.348 37.500 0.00 0.00 0.00 2.41
1091 1138 6.672266 TGGCAAAATGGAAGGTTGTTATAA 57.328 33.333 0.00 0.00 0.00 0.98
1097 1144 7.611213 AAATGGAAGGTTGTTATAACTCTCG 57.389 36.000 16.33 0.00 0.00 4.04
1164 1217 5.535783 CCCATGCAACTGGAATTGATACATA 59.464 40.000 7.97 0.00 38.69 2.29
1204 1257 6.003326 TCTAATGCCTTCAACAGACAATTCA 58.997 36.000 0.00 0.00 0.00 2.57
1211 1264 5.587844 CCTTCAACAGACAATTCATAGAGGG 59.412 44.000 0.00 0.00 0.00 4.30
1250 1303 5.994668 TCCCAATTTTTCAGTTGCCAAATAC 59.005 36.000 0.00 0.00 0.00 1.89
1251 1304 5.997129 CCCAATTTTTCAGTTGCCAAATACT 59.003 36.000 0.00 0.00 0.00 2.12
1252 1305 6.147656 CCCAATTTTTCAGTTGCCAAATACTC 59.852 38.462 0.00 0.00 0.00 2.59
1253 1306 6.147656 CCAATTTTTCAGTTGCCAAATACTCC 59.852 38.462 0.00 0.00 0.00 3.85
1254 1307 4.864704 TTTTCAGTTGCCAAATACTCCC 57.135 40.909 0.00 0.00 0.00 4.30
1255 1308 3.806949 TTCAGTTGCCAAATACTCCCT 57.193 42.857 0.00 0.00 0.00 4.20
1256 1309 3.350219 TCAGTTGCCAAATACTCCCTC 57.650 47.619 0.00 0.00 0.00 4.30
1257 1310 2.026262 TCAGTTGCCAAATACTCCCTCC 60.026 50.000 0.00 0.00 0.00 4.30
1258 1311 1.065418 AGTTGCCAAATACTCCCTCCG 60.065 52.381 0.00 0.00 0.00 4.63
1259 1312 0.988832 TTGCCAAATACTCCCTCCGT 59.011 50.000 0.00 0.00 0.00 4.69
1260 1313 0.539986 TGCCAAATACTCCCTCCGTC 59.460 55.000 0.00 0.00 0.00 4.79
1261 1314 0.179054 GCCAAATACTCCCTCCGTCC 60.179 60.000 0.00 0.00 0.00 4.79
1262 1315 0.468648 CCAAATACTCCCTCCGTCCC 59.531 60.000 0.00 0.00 0.00 4.46
1263 1316 1.200519 CAAATACTCCCTCCGTCCCA 58.799 55.000 0.00 0.00 0.00 4.37
1264 1317 1.557832 CAAATACTCCCTCCGTCCCAA 59.442 52.381 0.00 0.00 0.00 4.12
1265 1318 1.961133 AATACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
1266 1319 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
1267 1320 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
1268 1321 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
1269 1322 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
1270 1323 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
1271 1324 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
1272 1325 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
1273 1326 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
1274 1327 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
1275 1328 2.671396 CTCCGTCCCAAAATAAGTGTCG 59.329 50.000 0.00 0.00 0.00 4.35
1276 1329 2.037511 TCCGTCCCAAAATAAGTGTCGT 59.962 45.455 0.00 0.00 0.00 4.34
1277 1330 2.809696 CCGTCCCAAAATAAGTGTCGTT 59.190 45.455 0.00 0.00 0.00 3.85
1278 1331 3.364565 CCGTCCCAAAATAAGTGTCGTTG 60.365 47.826 0.00 0.00 0.00 4.10
1279 1332 3.561503 GTCCCAAAATAAGTGTCGTTGC 58.438 45.455 0.00 0.00 0.00 4.17
1280 1333 3.252458 GTCCCAAAATAAGTGTCGTTGCT 59.748 43.478 0.00 0.00 0.00 3.91
1281 1334 3.886505 TCCCAAAATAAGTGTCGTTGCTT 59.113 39.130 0.00 0.00 0.00 3.91
1282 1335 4.339814 TCCCAAAATAAGTGTCGTTGCTTT 59.660 37.500 0.00 0.00 0.00 3.51
1283 1336 5.531659 TCCCAAAATAAGTGTCGTTGCTTTA 59.468 36.000 0.00 0.00 0.00 1.85
1284 1337 5.856455 CCCAAAATAAGTGTCGTTGCTTTAG 59.144 40.000 0.00 0.00 0.00 1.85
1285 1338 6.435428 CCAAAATAAGTGTCGTTGCTTTAGT 58.565 36.000 0.00 0.00 0.00 2.24
1286 1339 7.308109 CCCAAAATAAGTGTCGTTGCTTTAGTA 60.308 37.037 0.00 0.00 0.00 1.82
1287 1340 7.532884 CCAAAATAAGTGTCGTTGCTTTAGTAC 59.467 37.037 0.00 0.00 0.00 2.73
1288 1341 7.958053 AAATAAGTGTCGTTGCTTTAGTACT 57.042 32.000 0.00 0.00 0.00 2.73
1289 1342 6.946229 ATAAGTGTCGTTGCTTTAGTACTG 57.054 37.500 5.39 0.00 0.00 2.74
1290 1343 4.317671 AGTGTCGTTGCTTTAGTACTGT 57.682 40.909 5.39 0.00 0.00 3.55
1291 1344 5.443185 AGTGTCGTTGCTTTAGTACTGTA 57.557 39.130 5.39 0.00 0.00 2.74
1292 1345 5.218139 AGTGTCGTTGCTTTAGTACTGTAC 58.782 41.667 9.93 9.93 0.00 2.90
1293 1346 4.977963 GTGTCGTTGCTTTAGTACTGTACA 59.022 41.667 19.27 0.00 0.00 2.90
1294 1347 5.459762 GTGTCGTTGCTTTAGTACTGTACAA 59.540 40.000 19.27 9.16 0.00 2.41
1295 1348 5.459762 TGTCGTTGCTTTAGTACTGTACAAC 59.540 40.000 19.27 12.91 34.15 3.32
1296 1349 5.689068 GTCGTTGCTTTAGTACTGTACAACT 59.311 40.000 19.27 5.57 35.07 3.16
1297 1350 6.199719 GTCGTTGCTTTAGTACTGTACAACTT 59.800 38.462 19.27 2.05 35.07 2.66
1298 1351 6.757947 TCGTTGCTTTAGTACTGTACAACTTT 59.242 34.615 19.27 1.69 35.07 2.66
1299 1352 6.844279 CGTTGCTTTAGTACTGTACAACTTTG 59.156 38.462 19.27 6.15 35.07 2.77
1300 1353 7.464977 CGTTGCTTTAGTACTGTACAACTTTGT 60.465 37.037 19.27 0.00 44.86 2.83
1301 1354 8.819974 GTTGCTTTAGTACTGTACAACTTTGTA 58.180 33.333 19.27 0.00 42.35 2.41
1316 1369 8.905103 ACAACTTTGTACTAAATCAACAACAC 57.095 30.769 0.00 0.00 40.16 3.32
1317 1370 8.736244 ACAACTTTGTACTAAATCAACAACACT 58.264 29.630 0.00 0.00 40.16 3.55
1318 1371 9.567848 CAACTTTGTACTAAATCAACAACACTT 57.432 29.630 0.00 0.00 33.10 3.16
1330 1383 9.868277 AAATCAACAACACTTATTTTTGAGACA 57.132 25.926 0.00 0.00 0.00 3.41
1331 1384 9.520204 AATCAACAACACTTATTTTTGAGACAG 57.480 29.630 0.00 0.00 0.00 3.51
1332 1385 8.275015 TCAACAACACTTATTTTTGAGACAGA 57.725 30.769 0.00 0.00 0.00 3.41
1333 1386 8.397906 TCAACAACACTTATTTTTGAGACAGAG 58.602 33.333 0.00 0.00 0.00 3.35
1334 1387 8.397906 CAACAACACTTATTTTTGAGACAGAGA 58.602 33.333 0.00 0.00 0.00 3.10
1335 1388 8.147642 ACAACACTTATTTTTGAGACAGAGAG 57.852 34.615 0.00 0.00 0.00 3.20
1364 1417 5.508567 TGGCTTGATTGAATGGATCTTGTA 58.491 37.500 0.00 0.00 0.00 2.41
1382 1435 6.650120 TCTTGTAGTTAAGCTCCCATTTAGG 58.350 40.000 0.00 0.00 37.03 2.69
1449 1503 0.961019 TGCACCTGAATGCTTTGGAC 59.039 50.000 0.00 0.00 46.28 4.02
1483 1537 8.674263 TTATTTTTGAACACATGCTTTGGATT 57.326 26.923 0.00 0.00 0.00 3.01
1544 1764 6.914259 ACAATAAAAGCTAAAAGACAGCCTC 58.086 36.000 0.00 0.00 39.99 4.70
1549 1769 4.209307 AGCTAAAAGACAGCCTCCTTAC 57.791 45.455 0.00 0.00 39.99 2.34
1590 1810 7.704899 GGTATATTTTGTTGGTCTAATGGCAAC 59.295 37.037 0.00 0.00 0.00 4.17
1668 1890 9.624373 AGTTAATTCATACTTTCTGCATCTGAT 57.376 29.630 0.00 0.00 0.00 2.90
1756 1979 4.075682 TGGTTGAAATGGCTCATCGTTTA 58.924 39.130 0.00 0.00 0.00 2.01
1768 1991 7.438564 TGGCTCATCGTTTAGCTATATTGTTA 58.561 34.615 0.00 0.00 38.80 2.41
1802 2025 4.286808 CCCATTTGGAACCTGGAAATTTCT 59.713 41.667 17.42 0.00 37.39 2.52
1953 2208 5.757808 GGAATTGTTACATTGCAAACAGGTT 59.242 36.000 1.71 2.60 36.96 3.50
1971 2227 5.163499 ACAGGTTTTGGCGTTGAATCTAAAA 60.163 36.000 0.00 0.00 0.00 1.52
2302 2579 1.818060 TGTGTGCATCTTATGGTTGGC 59.182 47.619 0.00 0.00 0.00 4.52
2303 2580 1.818060 GTGTGCATCTTATGGTTGGCA 59.182 47.619 0.00 0.00 0.00 4.92
2304 2581 2.230992 GTGTGCATCTTATGGTTGGCAA 59.769 45.455 0.00 0.00 0.00 4.52
2305 2582 2.230992 TGTGCATCTTATGGTTGGCAAC 59.769 45.455 21.92 21.92 0.00 4.17
2306 2583 2.493278 GTGCATCTTATGGTTGGCAACT 59.507 45.455 27.77 13.31 37.61 3.16
2307 2584 3.056607 GTGCATCTTATGGTTGGCAACTT 60.057 43.478 27.77 18.34 37.61 2.66
2308 2585 3.056678 TGCATCTTATGGTTGGCAACTTG 60.057 43.478 27.77 14.97 37.61 3.16
2309 2586 3.056607 GCATCTTATGGTTGGCAACTTGT 60.057 43.478 27.77 16.65 37.61 3.16
2317 2594 2.288395 GGTTGGCAACTTGTCATTCCTG 60.288 50.000 27.77 0.00 29.04 3.86
2339 2616 4.039004 TGCACTGTAAATCTGCAATGGTTT 59.961 37.500 0.00 0.00 37.97 3.27
2359 2636 2.585330 TGATCAGTTTGCCACATGTGT 58.415 42.857 23.79 2.19 0.00 3.72
2371 2648 4.082841 TGCCACATGTGTTGATAATGTGTC 60.083 41.667 23.79 2.39 46.28 3.67
2372 2649 4.156556 GCCACATGTGTTGATAATGTGTCT 59.843 41.667 23.79 0.00 46.28 3.41
2395 2672 0.318955 GTGGTTGCTGTTGATGCACC 60.319 55.000 0.00 0.00 40.40 5.01
2421 2703 5.296151 TGGATAAGCTCATACCTTCCTTG 57.704 43.478 0.00 0.00 0.00 3.61
2438 2720 5.743636 TCCTTGGGAAGAAAATGAATTGG 57.256 39.130 0.00 0.00 0.00 3.16
2499 2781 6.966435 ATTTATTTTGCGAAAATGTGGAGG 57.034 33.333 2.54 0.00 41.01 4.30
2529 2811 3.658725 TGGAATAGAGGAAGAGGGGAAG 58.341 50.000 0.00 0.00 0.00 3.46
2618 2900 6.318900 GGGTGGATCCACTTTTAGTTTGATAG 59.681 42.308 37.26 0.00 45.52 2.08
2652 2934 3.991773 GTGAAAGTGTGTGTTCGCCTATA 59.008 43.478 0.00 0.00 0.00 1.31
2662 2944 6.434340 TGTGTGTTCGCCTATATCAGATAGAT 59.566 38.462 0.00 0.00 40.86 1.98
2675 2957 3.898123 TCAGATAGATCTACCCCTTGTGC 59.102 47.826 4.10 0.00 34.85 4.57
2682 2964 0.748005 CTACCCCTTGTGCGGATTGG 60.748 60.000 0.00 0.00 0.00 3.16
2692 2974 4.497473 TGTGCGGATTGGAGTTTAAAAG 57.503 40.909 0.00 0.00 0.00 2.27
2753 3035 2.158608 AGTTGGGAAAAGTCTGAGGGTG 60.159 50.000 0.00 0.00 0.00 4.61
2759 3041 0.532862 AAAGTCTGAGGGTGTGTGCG 60.533 55.000 0.00 0.00 0.00 5.34
2760 3042 2.996168 AAGTCTGAGGGTGTGTGCGC 62.996 60.000 0.00 0.00 0.00 6.09
2786 3068 8.906867 CCATCACCATCTTTTGTTTAGTCATAT 58.093 33.333 0.00 0.00 0.00 1.78
2789 3071 9.295825 TCACCATCTTTTGTTTAGTCATATTGT 57.704 29.630 0.00 0.00 0.00 2.71
2790 3072 9.345517 CACCATCTTTTGTTTAGTCATATTGTG 57.654 33.333 0.00 0.00 0.00 3.33
2791 3073 9.077885 ACCATCTTTTGTTTAGTCATATTGTGT 57.922 29.630 0.00 0.00 0.00 3.72
2792 3074 9.345517 CCATCTTTTGTTTAGTCATATTGTGTG 57.654 33.333 0.00 0.00 0.00 3.82
2793 3075 9.897744 CATCTTTTGTTTAGTCATATTGTGTGT 57.102 29.630 0.00 0.00 0.00 3.72
2861 3143 9.716531 TTATGATAAAGAGATATGCTGTTCCTG 57.283 33.333 0.00 0.00 0.00 3.86
2862 3144 7.365497 TGATAAAGAGATATGCTGTTCCTGA 57.635 36.000 0.00 0.00 0.00 3.86
2863 3145 7.212976 TGATAAAGAGATATGCTGTTCCTGAC 58.787 38.462 0.00 0.00 0.00 3.51
2864 3146 4.414337 AAGAGATATGCTGTTCCTGACC 57.586 45.455 0.00 0.00 0.00 4.02
2865 3147 3.378512 AGAGATATGCTGTTCCTGACCA 58.621 45.455 0.00 0.00 0.00 4.02
2866 3148 3.972638 AGAGATATGCTGTTCCTGACCAT 59.027 43.478 0.00 0.00 0.00 3.55
2867 3149 4.063689 GAGATATGCTGTTCCTGACCATG 58.936 47.826 0.00 0.00 0.00 3.66
2868 3150 3.457380 AGATATGCTGTTCCTGACCATGT 59.543 43.478 0.00 0.00 0.00 3.21
2869 3151 2.592102 ATGCTGTTCCTGACCATGTT 57.408 45.000 0.00 0.00 0.00 2.71
2870 3152 2.363306 TGCTGTTCCTGACCATGTTT 57.637 45.000 0.00 0.00 0.00 2.83
2871 3153 1.955778 TGCTGTTCCTGACCATGTTTG 59.044 47.619 0.00 0.00 0.00 2.93
2882 3164 2.660189 CCATGTTTGGCCATCTGAAC 57.340 50.000 6.09 8.92 35.85 3.18
2883 3165 1.894466 CCATGTTTGGCCATCTGAACA 59.106 47.619 20.14 20.14 35.85 3.18
2884 3166 2.299582 CCATGTTTGGCCATCTGAACAA 59.700 45.455 21.36 2.27 35.85 2.83
2885 3167 3.244146 CCATGTTTGGCCATCTGAACAAA 60.244 43.478 21.36 1.52 35.85 2.83
2886 3168 4.378774 CATGTTTGGCCATCTGAACAAAA 58.621 39.130 21.36 0.73 35.83 2.44
2887 3169 4.478206 TGTTTGGCCATCTGAACAAAAA 57.522 36.364 16.56 0.00 34.95 1.94
2888 3170 5.033589 TGTTTGGCCATCTGAACAAAAAT 57.966 34.783 16.56 0.00 34.95 1.82
2889 3171 4.815308 TGTTTGGCCATCTGAACAAAAATG 59.185 37.500 16.56 0.00 34.95 2.32
2890 3172 4.686191 TTGGCCATCTGAACAAAAATGT 57.314 36.364 6.09 0.00 0.00 2.71
2891 3173 4.255833 TGGCCATCTGAACAAAAATGTC 57.744 40.909 0.00 0.00 0.00 3.06
2892 3174 3.640498 TGGCCATCTGAACAAAAATGTCA 59.360 39.130 0.00 0.00 0.00 3.58
2893 3175 4.283978 TGGCCATCTGAACAAAAATGTCAT 59.716 37.500 0.00 0.00 0.00 3.06
2894 3176 4.628333 GGCCATCTGAACAAAAATGTCATG 59.372 41.667 0.00 0.00 0.00 3.07
2895 3177 4.628333 GCCATCTGAACAAAAATGTCATGG 59.372 41.667 0.00 0.00 32.86 3.66
2896 3178 5.786311 CCATCTGAACAAAAATGTCATGGT 58.214 37.500 0.00 0.00 0.00 3.55
2897 3179 5.636121 CCATCTGAACAAAAATGTCATGGTG 59.364 40.000 0.00 0.00 0.00 4.17
2898 3180 6.448852 CATCTGAACAAAAATGTCATGGTGA 58.551 36.000 0.00 0.00 0.00 4.02
2899 3181 6.653526 TCTGAACAAAAATGTCATGGTGAT 57.346 33.333 0.00 0.00 0.00 3.06
2900 3182 6.680810 TCTGAACAAAAATGTCATGGTGATC 58.319 36.000 0.00 0.00 0.00 2.92
2901 3183 6.491062 TCTGAACAAAAATGTCATGGTGATCT 59.509 34.615 0.00 0.00 0.00 2.75
2902 3184 7.014518 TCTGAACAAAAATGTCATGGTGATCTT 59.985 33.333 0.00 0.00 0.00 2.40
2903 3185 7.499292 TGAACAAAAATGTCATGGTGATCTTT 58.501 30.769 0.00 0.00 0.00 2.52
2904 3186 7.986320 TGAACAAAAATGTCATGGTGATCTTTT 59.014 29.630 0.00 0.00 29.82 2.27
2905 3187 8.735692 AACAAAAATGTCATGGTGATCTTTTT 57.264 26.923 0.00 8.26 35.32 1.94
2906 3188 8.145316 ACAAAAATGTCATGGTGATCTTTTTG 57.855 30.769 23.31 23.31 44.71 2.44
2907 3189 7.769970 ACAAAAATGTCATGGTGATCTTTTTGT 59.230 29.630 24.04 24.04 45.65 2.83
2908 3190 8.614346 CAAAAATGTCATGGTGATCTTTTTGTT 58.386 29.630 20.33 3.18 40.64 2.83
2909 3191 8.735692 AAAATGTCATGGTGATCTTTTTGTTT 57.264 26.923 0.00 0.00 0.00 2.83
2910 3192 9.829507 AAAATGTCATGGTGATCTTTTTGTTTA 57.170 25.926 0.00 0.00 0.00 2.01
2911 3193 9.829507 AAATGTCATGGTGATCTTTTTGTTTAA 57.170 25.926 0.00 0.00 0.00 1.52
2912 3194 9.829507 AATGTCATGGTGATCTTTTTGTTTAAA 57.170 25.926 0.00 0.00 0.00 1.52
2913 3195 8.870160 TGTCATGGTGATCTTTTTGTTTAAAG 57.130 30.769 0.00 0.00 36.64 1.85
2914 3196 8.474025 TGTCATGGTGATCTTTTTGTTTAAAGT 58.526 29.630 0.00 0.00 36.67 2.66
2915 3197 9.313118 GTCATGGTGATCTTTTTGTTTAAAGTT 57.687 29.630 0.00 0.00 36.67 2.66
2916 3198 9.528018 TCATGGTGATCTTTTTGTTTAAAGTTC 57.472 29.630 0.00 0.00 36.67 3.01
2917 3199 9.533253 CATGGTGATCTTTTTGTTTAAAGTTCT 57.467 29.630 0.00 0.00 35.95 3.01
2928 3210 9.950680 TTTTGTTTAAAGTTCTATTCTGCTCAG 57.049 29.630 0.00 0.00 0.00 3.35
2929 3211 7.672983 TGTTTAAAGTTCTATTCTGCTCAGG 57.327 36.000 0.00 0.00 0.00 3.86
2930 3212 6.655003 TGTTTAAAGTTCTATTCTGCTCAGGG 59.345 38.462 0.00 0.00 0.00 4.45
2931 3213 2.998316 AGTTCTATTCTGCTCAGGGC 57.002 50.000 0.00 0.00 42.22 5.19
2932 3214 1.488393 AGTTCTATTCTGCTCAGGGCC 59.512 52.381 0.00 0.00 40.92 5.80
2933 3215 1.210478 GTTCTATTCTGCTCAGGGCCA 59.790 52.381 6.18 0.00 40.92 5.36
2934 3216 1.811778 TCTATTCTGCTCAGGGCCAT 58.188 50.000 6.18 0.00 40.92 4.40
2935 3217 1.696336 TCTATTCTGCTCAGGGCCATC 59.304 52.381 6.18 0.00 40.92 3.51
2936 3218 1.419012 CTATTCTGCTCAGGGCCATCA 59.581 52.381 6.18 0.00 40.92 3.07
2937 3219 0.106819 ATTCTGCTCAGGGCCATCAC 60.107 55.000 6.18 0.00 40.92 3.06
2938 3220 2.124403 CTGCTCAGGGCCATCACC 60.124 66.667 6.18 0.00 40.92 4.02
2939 3221 2.934932 TGCTCAGGGCCATCACCA 60.935 61.111 6.18 0.00 40.92 4.17
2940 3222 2.280404 CTGCTCAGGGCCATCACCAT 62.280 60.000 6.18 0.00 40.92 3.55
2941 3223 1.527844 GCTCAGGGCCATCACCATC 60.528 63.158 6.18 0.00 34.27 3.51
2942 3224 1.992519 GCTCAGGGCCATCACCATCT 61.993 60.000 6.18 0.00 34.27 2.90
2943 3225 0.549950 CTCAGGGCCATCACCATCTT 59.450 55.000 6.18 0.00 0.00 2.40
2944 3226 1.002069 TCAGGGCCATCACCATCTTT 58.998 50.000 6.18 0.00 0.00 2.52
2945 3227 1.358787 TCAGGGCCATCACCATCTTTT 59.641 47.619 6.18 0.00 0.00 2.27
2946 3228 1.479323 CAGGGCCATCACCATCTTTTG 59.521 52.381 6.18 0.00 0.00 2.44
2947 3229 1.077663 AGGGCCATCACCATCTTTTGT 59.922 47.619 6.18 0.00 0.00 2.83
2948 3230 1.901833 GGGCCATCACCATCTTTTGTT 59.098 47.619 4.39 0.00 0.00 2.83
2949 3231 2.302733 GGGCCATCACCATCTTTTGTTT 59.697 45.455 4.39 0.00 0.00 2.83
2950 3232 3.513515 GGGCCATCACCATCTTTTGTTTA 59.486 43.478 4.39 0.00 0.00 2.01
2951 3233 4.381932 GGGCCATCACCATCTTTTGTTTAG 60.382 45.833 4.39 0.00 0.00 1.85
2952 3234 4.220602 GGCCATCACCATCTTTTGTTTAGT 59.779 41.667 0.00 0.00 0.00 2.24
2953 3235 5.402398 GCCATCACCATCTTTTGTTTAGTC 58.598 41.667 0.00 0.00 0.00 2.59
2954 3236 5.048083 GCCATCACCATCTTTTGTTTAGTCA 60.048 40.000 0.00 0.00 0.00 3.41
2955 3237 6.350445 GCCATCACCATCTTTTGTTTAGTCAT 60.350 38.462 0.00 0.00 0.00 3.06
2956 3238 7.148086 GCCATCACCATCTTTTGTTTAGTCATA 60.148 37.037 0.00 0.00 0.00 2.15
2957 3239 8.906867 CCATCACCATCTTTTGTTTAGTCATAT 58.093 33.333 0.00 0.00 0.00 1.78
3033 3315 7.365497 TGATAAAGAGATATGCTGTTCCTGA 57.635 36.000 0.00 0.00 0.00 3.86
3038 3320 4.063689 GAGATATGCTGTTCCTGACCATG 58.936 47.826 0.00 0.00 0.00 3.66
3060 3342 4.815308 TGTTTGGCCATCTGAACAAAAATG 59.185 37.500 16.56 0.00 34.95 2.32
3071 3353 6.680810 TCTGAACAAAAATGTCATGGTGATC 58.319 36.000 0.00 0.00 0.00 2.92
3078 3360 7.769970 ACAAAAATGTCATGGTGATCTTTTTGT 59.230 29.630 24.04 24.04 45.65 2.83
3080 3362 8.735692 AAAATGTCATGGTGATCTTTTTGTTT 57.264 26.923 0.00 0.00 0.00 2.83
3081 3363 9.829507 AAAATGTCATGGTGATCTTTTTGTTTA 57.170 25.926 0.00 0.00 0.00 2.01
3099 3381 7.672983 TTGTTTAAAGTTCTATCCTGCTCAG 57.327 36.000 0.00 0.00 0.00 3.35
3110 3392 1.700042 CCTGCTCAGGGTGGGGATAC 61.700 65.000 8.03 0.00 44.87 2.24
3132 3414 9.988815 GATACCATCTCTTCTACATGTGTAAAT 57.011 33.333 9.11 0.00 0.00 1.40
3133 3415 9.770097 ATACCATCTCTTCTACATGTGTAAATG 57.230 33.333 9.11 3.88 0.00 2.32
3134 3416 7.624549 ACCATCTCTTCTACATGTGTAAATGT 58.375 34.615 9.11 0.00 43.21 2.71
3135 3417 7.550551 ACCATCTCTTCTACATGTGTAAATGTG 59.449 37.037 9.11 0.00 40.93 3.21
3136 3418 7.765819 CCATCTCTTCTACATGTGTAAATGTGA 59.234 37.037 9.11 1.30 40.93 3.58
3137 3419 8.598924 CATCTCTTCTACATGTGTAAATGTGAC 58.401 37.037 9.11 0.00 40.93 3.67
3138 3420 7.666623 TCTCTTCTACATGTGTAAATGTGACA 58.333 34.615 9.11 0.00 40.93 3.58
3139 3421 7.598869 TCTCTTCTACATGTGTAAATGTGACAC 59.401 37.037 9.11 0.00 46.07 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
368 370 6.509418 TTTTACATACAGGAAACATGGAGC 57.491 37.500 0.00 0.00 0.00 4.70
656 663 9.010029 CAATTTTTCATAGTGGTACAACTAGGT 57.990 33.333 18.98 0.30 44.16 3.08
740 750 8.199449 TGCTTCAAATGATGGGAGATTAAAATC 58.801 33.333 0.00 0.00 35.64 2.17
751 761 1.470285 CGGCTTGCTTCAAATGATGGG 60.470 52.381 0.00 0.00 0.00 4.00
758 768 0.820871 ACCAAACGGCTTGCTTCAAA 59.179 45.000 0.00 0.00 33.27 2.69
913 960 6.932356 ATAGGTGAAAGTGCATCAATAGTG 57.068 37.500 0.00 0.00 0.00 2.74
914 961 7.227512 GCTTATAGGTGAAAGTGCATCAATAGT 59.772 37.037 0.00 0.00 0.00 2.12
962 1009 3.296322 TTCCGACAATTTCCACATTGC 57.704 42.857 0.00 0.00 37.63 3.56
964 1011 7.461182 TCTTAATTCCGACAATTTCCACATT 57.539 32.000 0.00 0.00 0.00 2.71
978 1025 5.801350 TCACAGAGCAAATCTTAATTCCG 57.199 39.130 0.00 0.00 35.47 4.30
1035 1082 2.892425 GCTCCAACGCATCCCTCG 60.892 66.667 0.00 0.00 0.00 4.63
1044 1091 1.635663 CCCGCTTAACAGCTCCAACG 61.636 60.000 0.00 0.00 44.85 4.10
1204 1257 2.406559 AGCATCTCAAGTGCCCTCTAT 58.593 47.619 0.00 0.00 43.50 1.98
1211 1264 1.538047 TGGGAAAGCATCTCAAGTGC 58.462 50.000 0.00 0.00 34.88 4.40
1250 1303 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
1251 1304 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
1252 1305 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
1253 1306 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
1254 1307 2.671396 CGACACTTATTTTGGGACGGAG 59.329 50.000 0.00 0.00 0.00 4.63
1255 1308 2.037511 ACGACACTTATTTTGGGACGGA 59.962 45.455 0.00 0.00 0.00 4.69
1256 1309 2.419667 ACGACACTTATTTTGGGACGG 58.580 47.619 0.00 0.00 0.00 4.79
1257 1310 3.805823 CAACGACACTTATTTTGGGACG 58.194 45.455 0.00 0.00 0.00 4.79
1258 1311 3.252458 AGCAACGACACTTATTTTGGGAC 59.748 43.478 0.00 0.00 0.00 4.46
1259 1312 3.482436 AGCAACGACACTTATTTTGGGA 58.518 40.909 0.00 0.00 0.00 4.37
1260 1313 3.915437 AGCAACGACACTTATTTTGGG 57.085 42.857 0.00 0.00 0.00 4.12
1261 1314 6.435428 ACTAAAGCAACGACACTTATTTTGG 58.565 36.000 0.00 0.00 0.00 3.28
1262 1315 8.280497 AGTACTAAAGCAACGACACTTATTTTG 58.720 33.333 0.00 0.00 0.00 2.44
1263 1316 8.280497 CAGTACTAAAGCAACGACACTTATTTT 58.720 33.333 0.00 0.00 0.00 1.82
1264 1317 7.440255 ACAGTACTAAAGCAACGACACTTATTT 59.560 33.333 0.00 0.00 0.00 1.40
1265 1318 6.927381 ACAGTACTAAAGCAACGACACTTATT 59.073 34.615 0.00 0.00 0.00 1.40
1266 1319 6.453092 ACAGTACTAAAGCAACGACACTTAT 58.547 36.000 0.00 0.00 0.00 1.73
1267 1320 5.835257 ACAGTACTAAAGCAACGACACTTA 58.165 37.500 0.00 0.00 0.00 2.24
1268 1321 4.690122 ACAGTACTAAAGCAACGACACTT 58.310 39.130 0.00 0.00 0.00 3.16
1269 1322 4.317671 ACAGTACTAAAGCAACGACACT 57.682 40.909 0.00 0.00 0.00 3.55
1270 1323 4.977963 TGTACAGTACTAAAGCAACGACAC 59.022 41.667 12.07 0.00 0.00 3.67
1271 1324 5.185668 TGTACAGTACTAAAGCAACGACA 57.814 39.130 12.07 0.00 0.00 4.35
1272 1325 5.689068 AGTTGTACAGTACTAAAGCAACGAC 59.311 40.000 12.07 10.76 39.46 4.34
1273 1326 5.835257 AGTTGTACAGTACTAAAGCAACGA 58.165 37.500 12.07 2.26 39.46 3.85
1274 1327 6.520792 AAGTTGTACAGTACTAAAGCAACG 57.479 37.500 12.07 0.00 39.46 4.10
1275 1328 7.691158 ACAAAGTTGTACAGTACTAAAGCAAC 58.309 34.615 12.07 16.97 40.16 4.17
1276 1329 7.852971 ACAAAGTTGTACAGTACTAAAGCAA 57.147 32.000 12.07 0.00 40.16 3.91
1290 1343 9.991388 GTGTTGTTGATTTAGTACAAAGTTGTA 57.009 29.630 0.00 0.00 42.35 2.41
1291 1344 8.736244 AGTGTTGTTGATTTAGTACAAAGTTGT 58.264 29.630 1.75 1.75 44.86 3.32
1292 1345 9.567848 AAGTGTTGTTGATTTAGTACAAAGTTG 57.432 29.630 0.00 0.00 33.96 3.16
1304 1357 9.868277 TGTCTCAAAAATAAGTGTTGTTGATTT 57.132 25.926 0.00 0.00 0.00 2.17
1305 1358 9.520204 CTGTCTCAAAAATAAGTGTTGTTGATT 57.480 29.630 0.00 0.00 0.00 2.57
1306 1359 8.902806 TCTGTCTCAAAAATAAGTGTTGTTGAT 58.097 29.630 0.00 0.00 0.00 2.57
1307 1360 8.275015 TCTGTCTCAAAAATAAGTGTTGTTGA 57.725 30.769 0.00 0.00 0.00 3.18
1308 1361 8.397906 TCTCTGTCTCAAAAATAAGTGTTGTTG 58.602 33.333 0.00 0.00 0.00 3.33
1309 1362 8.506168 TCTCTGTCTCAAAAATAAGTGTTGTT 57.494 30.769 0.00 0.00 0.00 2.83
1310 1363 7.987458 TCTCTCTGTCTCAAAAATAAGTGTTGT 59.013 33.333 0.00 0.00 0.00 3.32
1311 1364 8.370493 TCTCTCTGTCTCAAAAATAAGTGTTG 57.630 34.615 0.00 0.00 0.00 3.33
1313 1366 9.868277 CTATCTCTCTGTCTCAAAAATAAGTGT 57.132 33.333 0.00 0.00 0.00 3.55
1318 1371 8.147058 GCCATCTATCTCTCTGTCTCAAAAATA 58.853 37.037 0.00 0.00 0.00 1.40
1319 1372 6.991531 GCCATCTATCTCTCTGTCTCAAAAAT 59.008 38.462 0.00 0.00 0.00 1.82
1320 1373 6.155910 AGCCATCTATCTCTCTGTCTCAAAAA 59.844 38.462 0.00 0.00 0.00 1.94
1321 1374 5.660417 AGCCATCTATCTCTCTGTCTCAAAA 59.340 40.000 0.00 0.00 0.00 2.44
1322 1375 5.207354 AGCCATCTATCTCTCTGTCTCAAA 58.793 41.667 0.00 0.00 0.00 2.69
1323 1376 4.802307 AGCCATCTATCTCTCTGTCTCAA 58.198 43.478 0.00 0.00 0.00 3.02
1324 1377 4.451891 AGCCATCTATCTCTCTGTCTCA 57.548 45.455 0.00 0.00 0.00 3.27
1325 1378 4.826733 TCAAGCCATCTATCTCTCTGTCTC 59.173 45.833 0.00 0.00 0.00 3.36
1326 1379 4.802307 TCAAGCCATCTATCTCTCTGTCT 58.198 43.478 0.00 0.00 0.00 3.41
1327 1380 5.726980 ATCAAGCCATCTATCTCTCTGTC 57.273 43.478 0.00 0.00 0.00 3.51
1328 1381 5.601729 TCAATCAAGCCATCTATCTCTCTGT 59.398 40.000 0.00 0.00 0.00 3.41
1329 1382 6.099159 TCAATCAAGCCATCTATCTCTCTG 57.901 41.667 0.00 0.00 0.00 3.35
1330 1383 6.744175 TTCAATCAAGCCATCTATCTCTCT 57.256 37.500 0.00 0.00 0.00 3.10
1331 1384 6.372103 CCATTCAATCAAGCCATCTATCTCTC 59.628 42.308 0.00 0.00 0.00 3.20
1332 1385 6.044054 TCCATTCAATCAAGCCATCTATCTCT 59.956 38.462 0.00 0.00 0.00 3.10
1333 1386 6.236409 TCCATTCAATCAAGCCATCTATCTC 58.764 40.000 0.00 0.00 0.00 2.75
1334 1387 6.196918 TCCATTCAATCAAGCCATCTATCT 57.803 37.500 0.00 0.00 0.00 1.98
1335 1388 6.885376 AGATCCATTCAATCAAGCCATCTATC 59.115 38.462 0.00 0.00 0.00 2.08
1364 1417 4.726825 TGGATCCTAAATGGGAGCTTAACT 59.273 41.667 14.23 0.00 41.12 2.24
1382 1435 1.821136 CTTTGGGAAAGCCAGTGGATC 59.179 52.381 15.20 7.43 35.15 3.36
1449 1503 9.008289 GCATGTGTTCAAAAATAAAAAGGTTTG 57.992 29.630 0.00 0.00 33.26 2.93
1483 1537 7.060383 TCCAATGCTTTTGGAATCAAGTTTA 57.940 32.000 16.36 0.00 44.90 2.01
1549 1769 0.681733 ATACCTGAGCCGTATGCCTG 59.318 55.000 0.00 0.00 42.71 4.85
1553 1773 6.293407 CCAACAAAATATACCTGAGCCGTATG 60.293 42.308 0.00 0.00 0.00 2.39
1558 1778 5.193679 AGACCAACAAAATATACCTGAGCC 58.806 41.667 0.00 0.00 0.00 4.70
1563 1783 7.122715 TGCCATTAGACCAACAAAATATACCT 58.877 34.615 0.00 0.00 0.00 3.08
1590 1810 7.445121 TCACCAATCTTACTATATCCAAGCTG 58.555 38.462 0.00 0.00 0.00 4.24
1622 1844 3.448660 ACTGTCATCTCGGTTCATGATGA 59.551 43.478 0.00 0.00 42.65 2.92
1668 1890 6.866010 ATTAATCAATCGAGCTATGCACAA 57.134 33.333 0.00 0.00 0.00 3.33
1732 1955 2.290260 ACGATGAGCCATTTCAACCAGA 60.290 45.455 0.00 0.00 0.00 3.86
1756 1979 8.620177 TGGGCCCTAAAATATAACAATATAGCT 58.380 33.333 25.70 0.00 0.00 3.32
1768 1991 4.658435 GGTTCCAAATGGGCCCTAAAATAT 59.342 41.667 25.70 3.22 36.21 1.28
1772 1995 1.435168 AGGTTCCAAATGGGCCCTAAA 59.565 47.619 25.70 2.00 35.07 1.85
1802 2025 8.233868 CGATAATAAATCACACAAAAGTGGTGA 58.766 33.333 0.00 0.00 44.73 4.02
1921 2175 5.306678 TGCAATGTAACAATTCCCTTTCCTT 59.693 36.000 0.00 0.00 0.00 3.36
1953 2208 7.332182 ACAAAAGTTTTTAGATTCAACGCCAAA 59.668 29.630 0.00 0.00 0.00 3.28
1971 2227 4.526650 ACACCTGAAGAAACCACAAAAGTT 59.473 37.500 0.00 0.00 0.00 2.66
2182 2454 1.676615 GCATTTCAACTGGGCCATTGG 60.677 52.381 20.93 9.83 0.00 3.16
2302 2579 2.620115 ACAGTGCAGGAATGACAAGTTG 59.380 45.455 0.00 0.00 0.00 3.16
2303 2580 2.936202 ACAGTGCAGGAATGACAAGTT 58.064 42.857 0.00 0.00 0.00 2.66
2304 2581 2.645838 ACAGTGCAGGAATGACAAGT 57.354 45.000 0.00 0.00 0.00 3.16
2305 2582 5.413833 AGATTTACAGTGCAGGAATGACAAG 59.586 40.000 0.00 0.00 0.00 3.16
2306 2583 5.181811 CAGATTTACAGTGCAGGAATGACAA 59.818 40.000 0.00 0.00 0.00 3.18
2307 2584 4.696877 CAGATTTACAGTGCAGGAATGACA 59.303 41.667 0.00 0.00 0.00 3.58
2308 2585 4.437930 GCAGATTTACAGTGCAGGAATGAC 60.438 45.833 0.00 0.00 37.16 3.06
2309 2586 3.691118 GCAGATTTACAGTGCAGGAATGA 59.309 43.478 0.00 0.00 37.16 2.57
2317 2594 3.855689 ACCATTGCAGATTTACAGTGC 57.144 42.857 0.00 0.00 37.73 4.40
2339 2616 2.585330 ACACATGTGGCAAACTGATCA 58.415 42.857 28.64 0.00 34.19 2.92
2359 2636 5.982516 GCAACCACAAAAGACACATTATCAA 59.017 36.000 0.00 0.00 0.00 2.57
2371 2648 2.540931 GCATCAACAGCAACCACAAAAG 59.459 45.455 0.00 0.00 0.00 2.27
2372 2649 2.093816 TGCATCAACAGCAACCACAAAA 60.094 40.909 0.00 0.00 39.39 2.44
2395 2672 3.325293 AGGTATGAGCTTATCCATGCG 57.675 47.619 0.00 0.00 0.00 4.73
2401 2678 4.348168 TCCCAAGGAAGGTATGAGCTTATC 59.652 45.833 0.00 0.00 35.86 1.75
2476 2758 6.696411 TCCTCCACATTTTCGCAAAATAAAT 58.304 32.000 6.55 0.00 38.97 1.40
2478 2760 5.713792 TCCTCCACATTTTCGCAAAATAA 57.286 34.783 6.55 0.00 38.97 1.40
2479 2761 5.652014 AGATCCTCCACATTTTCGCAAAATA 59.348 36.000 6.55 0.00 38.97 1.40
2480 2762 4.463891 AGATCCTCCACATTTTCGCAAAAT 59.536 37.500 0.00 2.29 41.57 1.82
2481 2763 3.826157 AGATCCTCCACATTTTCGCAAAA 59.174 39.130 0.00 0.00 34.41 2.44
2482 2764 3.420893 AGATCCTCCACATTTTCGCAAA 58.579 40.909 0.00 0.00 0.00 3.68
2483 2765 3.071874 AGATCCTCCACATTTTCGCAA 57.928 42.857 0.00 0.00 0.00 4.85
2484 2766 2.787473 AGATCCTCCACATTTTCGCA 57.213 45.000 0.00 0.00 0.00 5.10
2485 2767 2.356069 GGAAGATCCTCCACATTTTCGC 59.644 50.000 5.41 0.00 35.36 4.70
2486 2768 3.878778 AGGAAGATCCTCCACATTTTCG 58.121 45.455 12.97 0.00 45.66 3.46
2529 2811 4.020128 ACCAAAGAGATACAGACTTGGGTC 60.020 45.833 0.00 0.00 42.23 4.46
2535 2817 8.974060 TTTTGTTAACCAAAGAGATACAGACT 57.026 30.769 2.48 0.00 43.63 3.24
2597 2879 8.738645 ACATCTATCAAACTAAAAGTGGATCC 57.261 34.615 4.20 4.20 29.50 3.36
2618 2900 7.362662 ACACACACTTTCACAATCAATACATC 58.637 34.615 0.00 0.00 0.00 3.06
2630 2912 1.014352 AGGCGAACACACACTTTCAC 58.986 50.000 0.00 0.00 0.00 3.18
2652 2934 4.530161 GCACAAGGGGTAGATCTATCTGAT 59.470 45.833 12.74 0.00 37.76 2.90
2675 2957 6.267496 ACCATTCTTTTAAACTCCAATCCG 57.733 37.500 0.00 0.00 0.00 4.18
2682 2964 7.664318 TCCACTCCTAACCATTCTTTTAAACTC 59.336 37.037 0.00 0.00 0.00 3.01
2692 2974 5.104259 ACTCAATCCACTCCTAACCATTC 57.896 43.478 0.00 0.00 0.00 2.67
2723 3005 2.091885 ACTTTTCCCAACTCAAGCTGGA 60.092 45.455 0.93 0.00 33.20 3.86
2724 3006 2.294512 GACTTTTCCCAACTCAAGCTGG 59.705 50.000 0.00 0.00 0.00 4.85
2731 3013 2.106684 ACCCTCAGACTTTTCCCAACTC 59.893 50.000 0.00 0.00 0.00 3.01
2737 3019 2.222027 CACACACCCTCAGACTTTTCC 58.778 52.381 0.00 0.00 0.00 3.13
2753 3035 1.308069 AAGATGGTGATGGCGCACAC 61.308 55.000 10.83 15.82 40.52 3.82
2759 3041 5.048083 TGACTAAACAAAAGATGGTGATGGC 60.048 40.000 0.00 0.00 0.00 4.40
2760 3042 6.573664 TGACTAAACAAAAGATGGTGATGG 57.426 37.500 0.00 0.00 0.00 3.51
2835 3117 9.716531 CAGGAACAGCATATCTCTTTATCATAA 57.283 33.333 0.00 0.00 0.00 1.90
2836 3118 9.093458 TCAGGAACAGCATATCTCTTTATCATA 57.907 33.333 0.00 0.00 0.00 2.15
2837 3119 7.877097 GTCAGGAACAGCATATCTCTTTATCAT 59.123 37.037 0.00 0.00 0.00 2.45
2838 3120 7.212976 GTCAGGAACAGCATATCTCTTTATCA 58.787 38.462 0.00 0.00 0.00 2.15
2839 3121 6.648725 GGTCAGGAACAGCATATCTCTTTATC 59.351 42.308 0.00 0.00 0.00 1.75
2840 3122 6.100279 TGGTCAGGAACAGCATATCTCTTTAT 59.900 38.462 0.00 0.00 0.00 1.40
2841 3123 5.425217 TGGTCAGGAACAGCATATCTCTTTA 59.575 40.000 0.00 0.00 0.00 1.85
2842 3124 4.225942 TGGTCAGGAACAGCATATCTCTTT 59.774 41.667 0.00 0.00 0.00 2.52
2843 3125 3.776969 TGGTCAGGAACAGCATATCTCTT 59.223 43.478 0.00 0.00 0.00 2.85
2844 3126 3.378512 TGGTCAGGAACAGCATATCTCT 58.621 45.455 0.00 0.00 0.00 3.10
2845 3127 3.827008 TGGTCAGGAACAGCATATCTC 57.173 47.619 0.00 0.00 0.00 2.75
2846 3128 3.457380 ACATGGTCAGGAACAGCATATCT 59.543 43.478 0.00 0.00 30.75 1.98
2847 3129 3.813443 ACATGGTCAGGAACAGCATATC 58.187 45.455 0.00 0.00 30.75 1.63
2848 3130 3.939740 ACATGGTCAGGAACAGCATAT 57.060 42.857 0.00 0.00 30.75 1.78
2849 3131 3.719268 AACATGGTCAGGAACAGCATA 57.281 42.857 0.00 0.00 30.75 3.14
2850 3132 2.559668 CAAACATGGTCAGGAACAGCAT 59.440 45.455 0.00 0.00 32.08 3.79
2851 3133 1.955778 CAAACATGGTCAGGAACAGCA 59.044 47.619 0.00 0.00 0.00 4.41
2852 3134 1.270550 CCAAACATGGTCAGGAACAGC 59.729 52.381 0.00 0.00 0.00 4.40
2853 3135 1.270550 GCCAAACATGGTCAGGAACAG 59.729 52.381 6.38 0.00 0.00 3.16
2854 3136 1.327303 GCCAAACATGGTCAGGAACA 58.673 50.000 6.38 0.00 0.00 3.18
2855 3137 0.603065 GGCCAAACATGGTCAGGAAC 59.397 55.000 6.38 0.00 32.88 3.62
2856 3138 0.187117 TGGCCAAACATGGTCAGGAA 59.813 50.000 0.61 0.00 38.86 3.36
2857 3139 1.849832 TGGCCAAACATGGTCAGGA 59.150 52.632 0.61 0.00 38.86 3.86
2858 3140 4.517663 TGGCCAAACATGGTCAGG 57.482 55.556 0.61 0.00 38.86 3.86
2861 3143 1.838112 TCAGATGGCCAAACATGGTC 58.162 50.000 10.96 0.00 0.00 4.02
2862 3144 1.895131 GTTCAGATGGCCAAACATGGT 59.105 47.619 10.96 0.00 0.00 3.55
2863 3145 1.894466 TGTTCAGATGGCCAAACATGG 59.106 47.619 10.96 1.59 0.00 3.66
2864 3146 3.663995 TTGTTCAGATGGCCAAACATG 57.336 42.857 18.90 11.50 32.16 3.21
2865 3147 4.686191 TTTTGTTCAGATGGCCAAACAT 57.314 36.364 18.90 0.00 32.16 2.71
2866 3148 4.478206 TTTTTGTTCAGATGGCCAAACA 57.522 36.364 10.96 13.67 0.00 2.83
2867 3149 4.815846 ACATTTTTGTTCAGATGGCCAAAC 59.184 37.500 10.96 10.69 0.00 2.93
2868 3150 5.033589 ACATTTTTGTTCAGATGGCCAAA 57.966 34.783 10.96 0.00 0.00 3.28
2869 3151 4.100653 TGACATTTTTGTTCAGATGGCCAA 59.899 37.500 10.96 0.00 0.00 4.52
2870 3152 3.640498 TGACATTTTTGTTCAGATGGCCA 59.360 39.130 8.56 8.56 0.00 5.36
2871 3153 4.255833 TGACATTTTTGTTCAGATGGCC 57.744 40.909 0.00 0.00 0.00 5.36
2872 3154 4.628333 CCATGACATTTTTGTTCAGATGGC 59.372 41.667 0.00 0.00 0.00 4.40
2873 3155 5.636121 CACCATGACATTTTTGTTCAGATGG 59.364 40.000 0.00 0.00 35.07 3.51
2874 3156 6.448852 TCACCATGACATTTTTGTTCAGATG 58.551 36.000 0.00 0.00 0.00 2.90
2875 3157 6.653526 TCACCATGACATTTTTGTTCAGAT 57.346 33.333 0.00 0.00 0.00 2.90
2876 3158 6.491062 AGATCACCATGACATTTTTGTTCAGA 59.509 34.615 0.00 0.00 0.00 3.27
2877 3159 6.684686 AGATCACCATGACATTTTTGTTCAG 58.315 36.000 0.00 0.00 0.00 3.02
2878 3160 6.653526 AGATCACCATGACATTTTTGTTCA 57.346 33.333 0.00 0.00 0.00 3.18
2879 3161 7.951530 AAAGATCACCATGACATTTTTGTTC 57.048 32.000 0.00 0.00 0.00 3.18
2880 3162 8.614346 CAAAAAGATCACCATGACATTTTTGTT 58.386 29.630 21.23 3.21 42.55 2.83
2881 3163 8.145316 CAAAAAGATCACCATGACATTTTTGT 57.855 30.769 21.23 0.00 42.55 2.83
2882 3164 8.145316 ACAAAAAGATCACCATGACATTTTTG 57.855 30.769 24.34 24.34 46.71 2.44
2883 3165 8.735692 AACAAAAAGATCACCATGACATTTTT 57.264 26.923 0.00 8.60 37.61 1.94
2884 3166 8.735692 AAACAAAAAGATCACCATGACATTTT 57.264 26.923 0.00 0.00 32.24 1.82
2885 3167 9.829507 TTAAACAAAAAGATCACCATGACATTT 57.170 25.926 0.00 0.00 0.00 2.32
2886 3168 9.829507 TTTAAACAAAAAGATCACCATGACATT 57.170 25.926 0.00 0.00 0.00 2.71
2887 3169 9.480053 CTTTAAACAAAAAGATCACCATGACAT 57.520 29.630 0.00 0.00 38.50 3.06
2888 3170 8.474025 ACTTTAAACAAAAAGATCACCATGACA 58.526 29.630 0.00 0.00 38.50 3.58
2889 3171 8.871686 ACTTTAAACAAAAAGATCACCATGAC 57.128 30.769 0.00 0.00 38.50 3.06
2890 3172 9.528018 GAACTTTAAACAAAAAGATCACCATGA 57.472 29.630 0.00 0.00 37.87 3.07
2891 3173 9.533253 AGAACTTTAAACAAAAAGATCACCATG 57.467 29.630 3.51 0.00 39.45 3.66
2902 3184 9.950680 CTGAGCAGAATAGAACTTTAAACAAAA 57.049 29.630 0.00 0.00 0.00 2.44
2903 3185 8.567948 CCTGAGCAGAATAGAACTTTAAACAAA 58.432 33.333 0.00 0.00 0.00 2.83
2904 3186 7.174946 CCCTGAGCAGAATAGAACTTTAAACAA 59.825 37.037 0.00 0.00 0.00 2.83
2905 3187 6.655003 CCCTGAGCAGAATAGAACTTTAAACA 59.345 38.462 0.00 0.00 0.00 2.83
2906 3188 6.403746 GCCCTGAGCAGAATAGAACTTTAAAC 60.404 42.308 0.00 0.00 42.97 2.01
2907 3189 5.648092 GCCCTGAGCAGAATAGAACTTTAAA 59.352 40.000 0.00 0.00 42.97 1.52
2908 3190 5.186198 GCCCTGAGCAGAATAGAACTTTAA 58.814 41.667 0.00 0.00 42.97 1.52
2909 3191 4.384208 GGCCCTGAGCAGAATAGAACTTTA 60.384 45.833 0.00 0.00 46.50 1.85
2910 3192 3.615155 GCCCTGAGCAGAATAGAACTTT 58.385 45.455 0.00 0.00 42.97 2.66
2911 3193 2.092699 GGCCCTGAGCAGAATAGAACTT 60.093 50.000 0.00 0.00 46.50 2.66
2912 3194 1.488393 GGCCCTGAGCAGAATAGAACT 59.512 52.381 0.00 0.00 46.50 3.01
2913 3195 1.210478 TGGCCCTGAGCAGAATAGAAC 59.790 52.381 0.00 0.00 46.50 3.01
2914 3196 1.583556 TGGCCCTGAGCAGAATAGAA 58.416 50.000 0.00 0.00 46.50 2.10
2915 3197 1.696336 GATGGCCCTGAGCAGAATAGA 59.304 52.381 0.00 0.00 46.50 1.98
2916 3198 1.419012 TGATGGCCCTGAGCAGAATAG 59.581 52.381 0.00 0.00 46.50 1.73
2917 3199 1.141657 GTGATGGCCCTGAGCAGAATA 59.858 52.381 0.00 0.00 46.50 1.75
2918 3200 0.106819 GTGATGGCCCTGAGCAGAAT 60.107 55.000 0.00 0.00 46.50 2.40
2919 3201 1.300963 GTGATGGCCCTGAGCAGAA 59.699 57.895 0.00 0.00 46.50 3.02
2920 3202 2.673200 GGTGATGGCCCTGAGCAGA 61.673 63.158 0.00 0.00 46.50 4.26
2921 3203 2.124403 GGTGATGGCCCTGAGCAG 60.124 66.667 0.00 0.00 46.50 4.24
2922 3204 2.274948 GATGGTGATGGCCCTGAGCA 62.275 60.000 0.00 0.00 46.50 4.26
2923 3205 1.527844 GATGGTGATGGCCCTGAGC 60.528 63.158 0.00 0.00 42.60 4.26
2924 3206 0.549950 AAGATGGTGATGGCCCTGAG 59.450 55.000 0.00 0.00 0.00 3.35
2925 3207 1.002069 AAAGATGGTGATGGCCCTGA 58.998 50.000 0.00 0.00 0.00 3.86
2926 3208 1.479323 CAAAAGATGGTGATGGCCCTG 59.521 52.381 0.00 0.00 0.00 4.45
2927 3209 1.077663 ACAAAAGATGGTGATGGCCCT 59.922 47.619 0.00 0.00 0.00 5.19
2928 3210 1.560505 ACAAAAGATGGTGATGGCCC 58.439 50.000 0.00 0.00 0.00 5.80
2929 3211 3.683365 AAACAAAAGATGGTGATGGCC 57.317 42.857 0.00 0.00 0.00 5.36
2930 3212 5.048083 TGACTAAACAAAAGATGGTGATGGC 60.048 40.000 0.00 0.00 0.00 4.40
2931 3213 6.573664 TGACTAAACAAAAGATGGTGATGG 57.426 37.500 0.00 0.00 0.00 3.51
2934 3216 9.295825 ACAATATGACTAAACAAAAGATGGTGA 57.704 29.630 0.00 0.00 0.00 4.02
2935 3217 9.345517 CACAATATGACTAAACAAAAGATGGTG 57.654 33.333 0.00 0.00 0.00 4.17
2936 3218 9.077885 ACACAATATGACTAAACAAAAGATGGT 57.922 29.630 0.00 0.00 0.00 3.55
2937 3219 9.345517 CACACAATATGACTAAACAAAAGATGG 57.654 33.333 0.00 0.00 0.00 3.51
2938 3220 9.897744 ACACACAATATGACTAAACAAAAGATG 57.102 29.630 0.00 0.00 0.00 2.90
3010 3292 6.648725 GGTCAGGAACAGCATATCTCTTTATC 59.351 42.308 0.00 0.00 0.00 1.75
3023 3305 1.270550 CCAAACATGGTCAGGAACAGC 59.729 52.381 0.00 0.00 0.00 4.40
3024 3306 1.270550 GCCAAACATGGTCAGGAACAG 59.729 52.381 6.38 0.00 0.00 3.16
3025 3307 1.327303 GCCAAACATGGTCAGGAACA 58.673 50.000 6.38 0.00 0.00 3.18
3026 3308 0.603065 GGCCAAACATGGTCAGGAAC 59.397 55.000 6.38 0.00 32.88 3.62
3033 3315 1.895131 GTTCAGATGGCCAAACATGGT 59.105 47.619 10.96 0.00 0.00 3.55
3038 3320 4.815846 ACATTTTTGTTCAGATGGCCAAAC 59.184 37.500 10.96 10.69 0.00 2.93
3045 3327 6.448852 TCACCATGACATTTTTGTTCAGATG 58.551 36.000 0.00 0.00 0.00 2.90
3046 3328 6.653526 TCACCATGACATTTTTGTTCAGAT 57.346 33.333 0.00 0.00 0.00 2.90
3047 3329 6.491062 AGATCACCATGACATTTTTGTTCAGA 59.509 34.615 0.00 0.00 0.00 3.27
3060 3342 8.871686 ACTTTAAACAAAAAGATCACCATGAC 57.128 30.769 0.00 0.00 38.50 3.06
3071 3353 9.399403 GAGCAGGATAGAACTTTAAACAAAAAG 57.601 33.333 0.00 0.00 41.35 2.27
3110 3392 7.765819 TCACATTTACACATGTAGAAGAGATGG 59.234 37.037 0.00 0.00 35.51 3.51


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

AutoCloner maintained by Alex Coulton.