Multiple sequence alignment - TraesCS2A01G206400

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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 TraesCS2A01G206400 chr2A 100.000 3298 0 0 1 3298 185283768 185287065 0.000000e+00 6091.0
1 TraesCS2A01G206400 chr2A 86.614 127 17 0 1251 1377 612835015 612834889 1.230000e-29 141.0
2 TraesCS2A01G206400 chr2D 91.112 3274 144 70 65 3298 165469430 165466264 0.000000e+00 4298.0
3 TraesCS2A01G206400 chr2D 86.614 127 17 0 1251 1377 471055935 471055809 1.230000e-29 141.0
4 TraesCS2A01G206400 chr2D 85.600 125 14 4 1249 1371 417625380 417625502 9.610000e-26 128.0
5 TraesCS2A01G206400 chr2D 97.674 43 0 1 9 51 165469466 165469425 4.570000e-09 73.1
6 TraesCS2A01G206400 chr7D 84.783 138 19 2 1508 1644 13029169 13029033 1.600000e-28 137.0
7 TraesCS2A01G206400 chr7D 84.783 138 19 2 1508 1644 13066900 13066764 1.600000e-28 137.0
8 TraesCS2A01G206400 chr7D 81.752 137 23 2 1509 1644 13097810 13097675 2.690000e-21 113.0
9 TraesCS2A01G206400 chr7D 97.297 37 1 0 1030 1066 566989745 566989781 2.750000e-06 63.9
10 TraesCS2A01G206400 chr7A 84.783 138 19 2 1508 1644 12454993 12454857 1.600000e-28 137.0
11 TraesCS2A01G206400 chr7A 84.672 137 19 2 1509 1644 12652387 12652252 5.740000e-28 135.0
12 TraesCS2A01G206400 chr7A 83.333 138 21 2 1508 1644 12429304 12429168 3.450000e-25 126.0
13 TraesCS2A01G206400 chr7A 97.222 36 1 0 1031 1066 653589545 653589580 9.880000e-06 62.1
14 TraesCS2A01G206400 chr4A 84.783 138 19 2 1508 1644 724782969 724783105 1.600000e-28 137.0
15 TraesCS2A01G206400 chr2B 85.827 127 18 0 1251 1377 550214166 550214040 5.740000e-28 135.0
16 TraesCS2A01G206400 chr2B 85.600 125 14 4 1249 1371 489849204 489849326 9.610000e-26 128.0
17 TraesCS2A01G206400 chr5A 86.885 122 12 4 1251 1370 414934545 414934426 2.060000e-27 134.0
18 TraesCS2A01G206400 chr5D 86.179 123 13 4 1251 1371 319254580 319254700 2.670000e-26 130.0
19 TraesCS2A01G206400 chr5B 86.179 123 13 4 1251 1371 369485739 369485859 2.670000e-26 130.0
20 TraesCS2A01G206400 chr4D 84.496 129 18 2 1508 1635 506606765 506606638 3.450000e-25 126.0
21 TraesCS2A01G206400 chr1A 80.952 147 13 11 1510 1650 463461337 463461200 5.820000e-18 102.0
22 TraesCS2A01G206400 chr1A 85.714 77 11 0 998 1074 551593139 551593063 7.590000e-12 82.4
23 TraesCS2A01G206400 chr1D 85.714 77 11 0 998 1074 459880645 459880569 7.590000e-12 82.4
24 TraesCS2A01G206400 chr7B 81.707 82 15 0 1030 1111 619592503 619592422 5.910000e-08 69.4


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 TraesCS2A01G206400 chr2A 185283768 185287065 3297 False 6091.00 6091 100.000 1 3298 1 chr2A.!!$F1 3297
1 TraesCS2A01G206400 chr2D 165466264 165469466 3202 True 2185.55 4298 94.393 9 3298 2 chr2D.!!$R2 3289

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
978 1005 0.030908 CGCCCAATCCGTCTCTACTC 59.969 60.0 0.0 0.0 0.0 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2953 3028 0.034337 GGGTAACTGTTGGTCGCTCA 59.966 55.0 2.69 0.0 0.0 4.26 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
177 179 2.284417 GGCGAAACACGAGTCAATATCC 59.716 50.000 0.00 0.00 45.77 2.59
180 182 4.034048 GCGAAACACGAGTCAATATCCATT 59.966 41.667 0.00 0.00 45.77 3.16
200 202 5.466819 CATTGATTGGATTGGATTGGATCG 58.533 41.667 0.00 0.00 0.00 3.69
201 203 3.489355 TGATTGGATTGGATTGGATCGG 58.511 45.455 0.00 0.00 0.00 4.18
202 204 3.138098 TGATTGGATTGGATTGGATCGGA 59.862 43.478 0.00 0.00 0.00 4.55
203 205 3.882102 TTGGATTGGATTGGATCGGAT 57.118 42.857 0.00 0.00 0.00 4.18
204 206 3.144657 TGGATTGGATTGGATCGGATG 57.855 47.619 0.00 0.00 0.00 3.51
205 207 2.442878 TGGATTGGATTGGATCGGATGT 59.557 45.455 0.00 0.00 0.00 3.06
209 211 5.163416 GGATTGGATTGGATCGGATGTTTTT 60.163 40.000 0.00 0.00 0.00 1.94
230 232 1.847328 CCCGCCAAGAAATTTACCCT 58.153 50.000 0.00 0.00 0.00 4.34
231 233 1.476488 CCCGCCAAGAAATTTACCCTG 59.524 52.381 0.00 0.00 0.00 4.45
232 234 1.135112 CCGCCAAGAAATTTACCCTGC 60.135 52.381 0.00 0.00 0.00 4.85
233 235 1.135112 CGCCAAGAAATTTACCCTGCC 60.135 52.381 0.00 0.00 0.00 4.85
235 237 2.534990 CCAAGAAATTTACCCTGCCCA 58.465 47.619 0.00 0.00 0.00 5.36
239 243 3.964411 AGAAATTTACCCTGCCCAGTAC 58.036 45.455 0.00 0.00 0.00 2.73
249 253 0.618458 TGCCCAGTACATCCTTGGTC 59.382 55.000 0.00 0.00 0.00 4.02
293 298 6.930667 AATACAGTACAGTTGACCGTTTTT 57.069 33.333 0.00 0.00 0.00 1.94
308 313 4.229096 CCGTTTTTCACTCCATCATTGTG 58.771 43.478 0.00 0.00 0.00 3.33
324 329 6.072112 TCATTGTGTTTTGTTTCCTAGCTC 57.928 37.500 0.00 0.00 0.00 4.09
325 330 4.545823 TTGTGTTTTGTTTCCTAGCTCG 57.454 40.909 0.00 0.00 0.00 5.03
326 331 3.537580 TGTGTTTTGTTTCCTAGCTCGT 58.462 40.909 0.00 0.00 0.00 4.18
327 332 4.695396 TGTGTTTTGTTTCCTAGCTCGTA 58.305 39.130 0.00 0.00 0.00 3.43
340 345 0.179134 GCTCGTACGTTCAGCCTGAT 60.179 55.000 16.05 0.00 0.00 2.90
352 357 3.556999 TCAGCCTGATGGAGTCTAGTAC 58.443 50.000 0.00 0.00 34.57 2.73
353 358 3.203263 TCAGCCTGATGGAGTCTAGTACT 59.797 47.826 0.00 0.00 42.80 2.73
354 359 4.412528 TCAGCCTGATGGAGTCTAGTACTA 59.587 45.833 1.89 1.89 39.07 1.82
366 371 6.936335 GGAGTCTAGTACTAGATTCTACCACC 59.064 46.154 35.39 24.72 43.90 4.61
387 392 4.111916 CCATCGGTAAAAATGGCATGTTC 58.888 43.478 2.78 0.00 36.31 3.18
405 410 2.205022 TCCTGATGGAACTGGCAAAG 57.795 50.000 0.00 0.00 39.87 2.77
408 413 0.776810 TGATGGAACTGGCAAAGGGA 59.223 50.000 0.00 0.00 0.00 4.20
409 414 1.146774 TGATGGAACTGGCAAAGGGAA 59.853 47.619 0.00 0.00 0.00 3.97
410 415 1.821136 GATGGAACTGGCAAAGGGAAG 59.179 52.381 0.00 0.00 0.00 3.46
411 416 0.827507 TGGAACTGGCAAAGGGAAGC 60.828 55.000 0.00 0.00 0.00 3.86
413 418 2.477972 GAACTGGCAAAGGGAAGCGC 62.478 60.000 0.00 0.00 0.00 5.92
414 419 2.985282 CTGGCAAAGGGAAGCGCA 60.985 61.111 11.47 0.00 0.00 6.09
415 420 3.273080 CTGGCAAAGGGAAGCGCAC 62.273 63.158 11.47 2.54 0.00 5.34
449 475 4.887748 AGGATCGACACATGTGATTATCC 58.112 43.478 31.94 30.66 36.56 2.59
450 476 4.590647 AGGATCGACACATGTGATTATCCT 59.409 41.667 31.98 31.98 39.01 3.24
451 477 5.775195 AGGATCGACACATGTGATTATCCTA 59.225 40.000 34.00 16.61 40.40 2.94
452 478 6.071672 AGGATCGACACATGTGATTATCCTAG 60.072 42.308 34.00 16.47 40.40 3.02
453 479 6.294787 GGATCGACACATGTGATTATCCTAGT 60.295 42.308 31.94 5.36 35.09 2.57
454 480 6.073327 TCGACACATGTGATTATCCTAGTC 57.927 41.667 31.94 13.41 0.00 2.59
455 481 5.592688 TCGACACATGTGATTATCCTAGTCA 59.407 40.000 31.94 3.87 0.00 3.41
466 492 6.811665 TGATTATCCTAGTCAGTCAAAACACG 59.188 38.462 0.00 0.00 0.00 4.49
477 503 4.730042 CAGTCAAAACACGAGACAATGTTG 59.270 41.667 0.00 0.00 39.00 3.33
482 508 0.110688 CACGAGACAATGTTGCACGG 60.111 55.000 0.00 0.00 0.00 4.94
555 581 4.457496 CGTGCCGTGGGATCTGCT 62.457 66.667 0.00 0.00 0.00 4.24
560 586 2.825836 CGTGGGATCTGCTTGGCC 60.826 66.667 0.00 0.00 0.00 5.36
614 640 2.049802 TTGTCTTCCGGTCGCGAC 60.050 61.111 30.67 30.67 0.00 5.19
649 675 0.530650 CCATCCTCATCCAACGGACG 60.531 60.000 0.00 0.00 32.98 4.79
655 681 1.516386 CATCCAACGGACGAGACGG 60.516 63.158 0.00 0.00 32.98 4.79
657 683 1.930908 ATCCAACGGACGAGACGGTC 61.931 60.000 0.00 0.00 32.98 4.79
810 837 1.954382 CGCCCTTTATAAGCCTTTCCC 59.046 52.381 0.00 0.00 0.00 3.97
858 885 1.481428 CCTCTACCTCCATCCATCCGT 60.481 57.143 0.00 0.00 0.00 4.69
863 890 1.050988 CCTCCATCCATCCGTCCAGT 61.051 60.000 0.00 0.00 0.00 4.00
885 912 5.355350 AGTTTTCAGTTTTCACACTCTCCTG 59.645 40.000 0.00 0.00 0.00 3.86
886 913 3.475566 TCAGTTTTCACACTCTCCTGG 57.524 47.619 0.00 0.00 0.00 4.45
887 914 1.876156 CAGTTTTCACACTCTCCTGGC 59.124 52.381 0.00 0.00 0.00 4.85
888 915 1.771255 AGTTTTCACACTCTCCTGGCT 59.229 47.619 0.00 0.00 0.00 4.75
910 937 1.818674 GCTAGCTAGCTCCTCTCCATC 59.181 57.143 33.71 4.79 45.62 3.51
914 941 1.203050 GCTAGCTCCTCTCCATCCTCT 60.203 57.143 7.70 0.00 0.00 3.69
916 943 2.675658 AGCTCCTCTCCATCCTCTAC 57.324 55.000 0.00 0.00 0.00 2.59
917 944 1.856259 AGCTCCTCTCCATCCTCTACA 59.144 52.381 0.00 0.00 0.00 2.74
918 945 2.158475 AGCTCCTCTCCATCCTCTACAG 60.158 54.545 0.00 0.00 0.00 2.74
919 946 2.238521 CTCCTCTCCATCCTCTACAGC 58.761 57.143 0.00 0.00 0.00 4.40
920 947 0.958091 CCTCTCCATCCTCTACAGCG 59.042 60.000 0.00 0.00 0.00 5.18
953 980 3.182312 GAGCCTTTTCCTGCTCGC 58.818 61.111 0.00 0.00 43.94 5.03
954 981 2.360475 AGCCTTTTCCTGCTCGCC 60.360 61.111 0.00 0.00 30.33 5.54
977 1004 0.395311 TCGCCCAATCCGTCTCTACT 60.395 55.000 0.00 0.00 0.00 2.57
978 1005 0.030908 CGCCCAATCCGTCTCTACTC 59.969 60.000 0.00 0.00 0.00 2.59
980 1007 2.584236 GCCCAATCCGTCTCTACTCTA 58.416 52.381 0.00 0.00 0.00 2.43
982 1009 3.552875 CCCAATCCGTCTCTACTCTACA 58.447 50.000 0.00 0.00 0.00 2.74
983 1010 3.566322 CCCAATCCGTCTCTACTCTACAG 59.434 52.174 0.00 0.00 0.00 2.74
984 1011 4.200874 CCAATCCGTCTCTACTCTACAGT 58.799 47.826 0.00 0.00 36.55 3.55
987 1014 4.283363 TCCGTCTCTACTCTACAGTTGT 57.717 45.455 0.00 0.00 33.62 3.32
988 1015 5.411831 TCCGTCTCTACTCTACAGTTGTA 57.588 43.478 0.00 0.00 33.62 2.41
1151 1178 0.739561 GGTAAGCGACTCGGACTCAT 59.260 55.000 0.00 0.00 0.00 2.90
1152 1179 1.534175 GGTAAGCGACTCGGACTCATG 60.534 57.143 0.00 0.00 0.00 3.07
1172 1199 2.567049 GCTGCTTGCTCTGCCAAG 59.433 61.111 0.00 0.00 43.88 3.61
1173 1200 2.266627 GCTGCTTGCTCTGCCAAGT 61.267 57.895 0.00 0.00 43.17 3.16
1174 1201 1.803366 GCTGCTTGCTCTGCCAAGTT 61.803 55.000 0.00 0.00 43.17 2.66
1175 1202 0.039437 CTGCTTGCTCTGCCAAGTTG 60.039 55.000 0.00 0.00 43.17 3.16
1176 1203 1.288127 GCTTGCTCTGCCAAGTTGG 59.712 57.895 18.17 18.17 43.17 3.77
1177 1204 1.458639 GCTTGCTCTGCCAAGTTGGT 61.459 55.000 22.85 0.00 43.17 3.67
1178 1205 1.035139 CTTGCTCTGCCAAGTTGGTT 58.965 50.000 22.85 0.00 40.46 3.67
1179 1206 2.229792 CTTGCTCTGCCAAGTTGGTTA 58.770 47.619 22.85 11.64 40.46 2.85
1180 1207 1.896220 TGCTCTGCCAAGTTGGTTAG 58.104 50.000 22.85 19.69 40.46 2.34
1181 1208 1.142870 TGCTCTGCCAAGTTGGTTAGT 59.857 47.619 22.85 0.00 40.46 2.24
1182 1209 2.230660 GCTCTGCCAAGTTGGTTAGTT 58.769 47.619 22.85 0.00 40.46 2.24
1183 1210 3.181449 TGCTCTGCCAAGTTGGTTAGTTA 60.181 43.478 22.85 9.68 40.46 2.24
1184 1211 3.437049 GCTCTGCCAAGTTGGTTAGTTAG 59.563 47.826 22.85 15.13 40.46 2.34
1185 1212 4.642429 CTCTGCCAAGTTGGTTAGTTAGT 58.358 43.478 22.85 0.00 40.46 2.24
1186 1213 5.043737 TCTGCCAAGTTGGTTAGTTAGTT 57.956 39.130 22.85 0.00 40.46 2.24
1187 1214 6.177310 TCTGCCAAGTTGGTTAGTTAGTTA 57.823 37.500 22.85 3.07 40.46 2.24
1188 1215 6.775708 TCTGCCAAGTTGGTTAGTTAGTTAT 58.224 36.000 22.85 0.00 40.46 1.89
1189 1216 6.877322 TCTGCCAAGTTGGTTAGTTAGTTATC 59.123 38.462 22.85 2.34 40.46 1.75
1190 1217 5.941647 TGCCAAGTTGGTTAGTTAGTTATCC 59.058 40.000 22.85 1.91 40.46 2.59
1210 1237 0.830648 ACCGATCGATCCCACACAAT 59.169 50.000 18.66 0.00 0.00 2.71
1211 1238 2.036387 ACCGATCGATCCCACACAATA 58.964 47.619 18.66 0.00 0.00 1.90
1212 1239 2.432874 ACCGATCGATCCCACACAATAA 59.567 45.455 18.66 0.00 0.00 1.40
1214 1241 4.065088 CCGATCGATCCCACACAATAATT 58.935 43.478 18.66 0.00 0.00 1.40
1216 1243 5.699001 CCGATCGATCCCACACAATAATTAA 59.301 40.000 18.66 0.00 0.00 1.40
1217 1244 6.347402 CCGATCGATCCCACACAATAATTAAC 60.347 42.308 18.66 0.00 0.00 2.01
1231 1280 3.896648 AATTAACTGTGTTGCGTCTGG 57.103 42.857 0.00 0.00 0.00 3.86
1246 1295 1.149174 CTGGGTGTGTGCAGACCTT 59.851 57.895 12.00 0.00 43.64 3.50
1351 1400 2.603021 GAGGAGACCATCATCCAGCTA 58.397 52.381 0.00 0.00 38.12 3.32
1386 1458 4.150098 CGGCAACAAGTAAGAACTACTCAC 59.850 45.833 0.00 0.00 40.14 3.51
1424 1496 2.611225 ACGTAGTACTAGCTAGGCGT 57.389 50.000 24.35 20.14 41.94 5.68
1425 1497 2.478831 ACGTAGTACTAGCTAGGCGTC 58.521 52.381 24.35 11.21 41.94 5.19
1426 1498 2.102252 ACGTAGTACTAGCTAGGCGTCT 59.898 50.000 24.35 16.88 41.94 4.18
1427 1499 2.730928 CGTAGTACTAGCTAGGCGTCTC 59.269 54.545 24.35 9.28 0.00 3.36
1428 1500 3.552684 CGTAGTACTAGCTAGGCGTCTCT 60.553 52.174 24.35 13.89 0.00 3.10
1429 1501 2.841215 AGTACTAGCTAGGCGTCTCTG 58.159 52.381 24.35 0.00 0.00 3.35
1430 1502 2.171027 AGTACTAGCTAGGCGTCTCTGT 59.829 50.000 24.35 3.84 0.00 3.41
1431 1503 2.131776 ACTAGCTAGGCGTCTCTGTT 57.868 50.000 24.35 0.00 0.00 3.16
1432 1504 1.746220 ACTAGCTAGGCGTCTCTGTTG 59.254 52.381 24.35 0.00 0.00 3.33
1433 1505 0.456221 TAGCTAGGCGTCTCTGTTGC 59.544 55.000 0.00 0.00 0.00 4.17
1434 1506 1.216710 GCTAGGCGTCTCTGTTGCT 59.783 57.895 0.00 0.00 0.00 3.91
1435 1507 0.456221 GCTAGGCGTCTCTGTTGCTA 59.544 55.000 0.00 0.00 0.00 3.49
1436 1508 1.067821 GCTAGGCGTCTCTGTTGCTAT 59.932 52.381 0.00 0.00 0.00 2.97
1437 1509 2.293677 GCTAGGCGTCTCTGTTGCTATA 59.706 50.000 0.00 0.00 0.00 1.31
1438 1510 3.610585 GCTAGGCGTCTCTGTTGCTATAG 60.611 52.174 0.00 0.00 0.00 1.31
1439 1511 1.067821 AGGCGTCTCTGTTGCTATAGC 59.932 52.381 18.18 18.18 42.50 2.97
1478 1550 0.883370 ACGGTTTCCTGGCGAGTTTC 60.883 55.000 0.00 0.00 0.00 2.78
1479 1551 0.882927 CGGTTTCCTGGCGAGTTTCA 60.883 55.000 0.00 0.00 0.00 2.69
1487 1559 3.191162 TCCTGGCGAGTTTCATTTTGATG 59.809 43.478 0.00 0.00 0.00 3.07
1488 1560 3.057315 CCTGGCGAGTTTCATTTTGATGT 60.057 43.478 0.00 0.00 0.00 3.06
1489 1561 3.899734 TGGCGAGTTTCATTTTGATGTG 58.100 40.909 0.00 0.00 0.00 3.21
1490 1562 2.663119 GGCGAGTTTCATTTTGATGTGC 59.337 45.455 0.00 0.00 0.00 4.57
1491 1563 3.568538 GCGAGTTTCATTTTGATGTGCT 58.431 40.909 0.00 0.00 0.00 4.40
1492 1564 3.983344 GCGAGTTTCATTTTGATGTGCTT 59.017 39.130 0.00 0.00 0.00 3.91
1493 1565 4.445385 GCGAGTTTCATTTTGATGTGCTTT 59.555 37.500 0.00 0.00 0.00 3.51
1688 1760 3.078836 GCCGCCTACTACCCCACA 61.079 66.667 0.00 0.00 0.00 4.17
1977 2049 1.977854 AGCAACTACACCAGGATCACA 59.022 47.619 0.00 0.00 0.00 3.58
2105 2177 1.741770 CAGCCCGGTCACAAGTAGC 60.742 63.158 0.00 0.00 0.00 3.58
2106 2178 2.214216 AGCCCGGTCACAAGTAGCA 61.214 57.895 0.00 0.00 0.00 3.49
2107 2179 1.302192 GCCCGGTCACAAGTAGCAA 60.302 57.895 0.00 0.00 0.00 3.91
2208 2280 2.252260 CAACCTTCTGCGCCAACG 59.748 61.111 4.18 0.00 44.07 4.10
2219 2291 2.202349 GCCAACGCGAGCAACATC 60.202 61.111 15.93 0.00 0.00 3.06
2297 2369 3.445805 TGGATGTGAGCGACTACATGTAA 59.554 43.478 7.06 0.00 37.63 2.41
2322 2394 5.239087 TGAAAAATACAAGTACGGGTTCCAC 59.761 40.000 0.00 0.00 0.00 4.02
2323 2395 3.339253 AATACAAGTACGGGTTCCACC 57.661 47.619 0.00 0.00 37.60 4.61
2324 2396 2.014010 TACAAGTACGGGTTCCACCT 57.986 50.000 0.00 0.00 38.64 4.00
2345 2417 2.492019 CATCTGCATGCATGTGGAAG 57.508 50.000 26.79 18.32 0.00 3.46
2349 2421 1.333931 CTGCATGCATGTGGAAGCTAG 59.666 52.381 26.79 0.21 31.38 3.42
2352 2424 1.945394 CATGCATGTGGAAGCTAGGTC 59.055 52.381 18.91 0.00 0.00 3.85
2378 2453 0.168788 TTCATCACGTACCGACCGAC 59.831 55.000 0.00 0.00 0.00 4.79
2389 2464 2.114411 GACCGACAGGGGGCAAAA 59.886 61.111 0.00 0.00 43.47 2.44
2390 2465 2.203437 ACCGACAGGGGGCAAAAC 60.203 61.111 0.00 0.00 43.47 2.43
2391 2466 2.203422 CCGACAGGGGGCAAAACA 60.203 61.111 0.00 0.00 0.00 2.83
2392 2467 1.606313 CCGACAGGGGGCAAAACAT 60.606 57.895 0.00 0.00 0.00 2.71
2393 2468 1.586028 CGACAGGGGGCAAAACATG 59.414 57.895 0.00 0.00 0.00 3.21
2408 2483 6.906584 CAAAACATGCATACGATGATGATC 57.093 37.500 0.00 0.00 0.00 2.92
2409 2484 6.665465 CAAAACATGCATACGATGATGATCT 58.335 36.000 0.00 0.00 0.00 2.75
2410 2485 6.477669 AAACATGCATACGATGATGATCTC 57.522 37.500 0.00 0.00 0.00 2.75
2411 2486 4.171754 ACATGCATACGATGATGATCTCG 58.828 43.478 0.00 11.03 40.62 4.04
2412 2487 4.082571 ACATGCATACGATGATGATCTCGA 60.083 41.667 16.93 0.00 38.24 4.04
2490 2565 7.494952 ACTGGTTACTGTTAGAAACTTCACTTC 59.505 37.037 0.00 0.00 0.00 3.01
2493 2568 7.494952 GGTTACTGTTAGAAACTTCACTTCTGT 59.505 37.037 0.00 0.00 34.90 3.41
2658 2733 5.412904 CCAGTGAAGAAAAATAGGGTCACTC 59.587 44.000 1.28 0.00 42.80 3.51
2659 2734 5.412904 CAGTGAAGAAAAATAGGGTCACTCC 59.587 44.000 1.28 0.00 42.80 3.85
2660 2735 4.392138 GTGAAGAAAAATAGGGTCACTCCG 59.608 45.833 0.00 0.00 37.00 4.63
2661 2736 3.629142 AGAAAAATAGGGTCACTCCGG 57.371 47.619 0.00 0.00 37.00 5.14
2663 2738 3.329814 AGAAAAATAGGGTCACTCCGGTT 59.670 43.478 0.00 0.00 37.00 4.44
2664 2739 2.781681 AAATAGGGTCACTCCGGTTG 57.218 50.000 0.00 0.00 37.00 3.77
2665 2740 0.252197 AATAGGGTCACTCCGGTTGC 59.748 55.000 0.00 0.00 37.00 4.17
2666 2741 0.617820 ATAGGGTCACTCCGGTTGCT 60.618 55.000 0.00 0.00 37.00 3.91
2667 2742 0.834687 TAGGGTCACTCCGGTTGCTT 60.835 55.000 0.00 0.00 37.00 3.91
2668 2743 1.228154 GGGTCACTCCGGTTGCTTT 60.228 57.895 0.00 0.00 37.00 3.51
2669 2744 0.822121 GGGTCACTCCGGTTGCTTTT 60.822 55.000 0.00 0.00 37.00 2.27
2670 2745 0.591659 GGTCACTCCGGTTGCTTTTC 59.408 55.000 0.00 0.00 0.00 2.29
2671 2746 1.594331 GTCACTCCGGTTGCTTTTCT 58.406 50.000 0.00 0.00 0.00 2.52
2672 2747 1.947456 GTCACTCCGGTTGCTTTTCTT 59.053 47.619 0.00 0.00 0.00 2.52
2673 2748 3.135994 GTCACTCCGGTTGCTTTTCTTA 58.864 45.455 0.00 0.00 0.00 2.10
2674 2749 3.186613 GTCACTCCGGTTGCTTTTCTTAG 59.813 47.826 0.00 0.00 0.00 2.18
2675 2750 3.070446 TCACTCCGGTTGCTTTTCTTAGA 59.930 43.478 0.00 0.00 0.00 2.10
2676 2751 3.813166 CACTCCGGTTGCTTTTCTTAGAA 59.187 43.478 0.00 0.00 0.00 2.10
2677 2752 4.455877 CACTCCGGTTGCTTTTCTTAGAAT 59.544 41.667 0.00 0.00 0.00 2.40
2678 2753 4.455877 ACTCCGGTTGCTTTTCTTAGAATG 59.544 41.667 0.00 0.00 0.00 2.67
2679 2754 3.190535 TCCGGTTGCTTTTCTTAGAATGC 59.809 43.478 0.00 11.57 0.00 3.56
2680 2755 3.191371 CCGGTTGCTTTTCTTAGAATGCT 59.809 43.478 16.75 0.00 32.63 3.79
2681 2756 4.394920 CCGGTTGCTTTTCTTAGAATGCTA 59.605 41.667 16.75 9.84 32.63 3.49
2682 2757 5.324697 CGGTTGCTTTTCTTAGAATGCTAC 58.675 41.667 18.21 18.21 35.93 3.58
2683 2758 5.122396 CGGTTGCTTTTCTTAGAATGCTACT 59.878 40.000 22.02 0.00 36.46 2.57
2684 2759 6.348540 CGGTTGCTTTTCTTAGAATGCTACTT 60.349 38.462 22.02 0.00 36.46 2.24
2685 2760 7.371159 GGTTGCTTTTCTTAGAATGCTACTTT 58.629 34.615 22.02 0.00 36.46 2.66
2686 2761 7.867909 GGTTGCTTTTCTTAGAATGCTACTTTT 59.132 33.333 22.02 0.00 36.46 2.27
2687 2762 9.893305 GTTGCTTTTCTTAGAATGCTACTTTTA 57.107 29.630 18.72 1.60 34.81 1.52
2742 2817 8.082242 TCTTTAGTTTAATTTTGCTGCCTCTTC 58.918 33.333 0.00 0.00 0.00 2.87
2763 2838 9.877178 CTCTTCTATTTCATTGGTTACTGTACT 57.123 33.333 0.00 0.00 0.00 2.73
2764 2839 9.653287 TCTTCTATTTCATTGGTTACTGTACTG 57.347 33.333 0.00 0.00 0.00 2.74
2773 2848 5.483685 TGGTTACTGTACTGCTGAGAATT 57.516 39.130 0.00 0.00 0.00 2.17
2882 2957 7.392953 TGGTCACATGACAAGCAATTATTCTTA 59.607 33.333 13.77 0.00 46.47 2.10
2913 2988 4.506802 GGGAAAATAGACTGGAGTTGGTGT 60.507 45.833 0.00 0.00 0.00 4.16
2924 2999 3.568007 TGGAGTTGGTGTGCAACTTAATC 59.432 43.478 0.00 0.00 42.28 1.75
2946 3021 4.079850 CTGCTGCCTGCTCCGTCT 62.080 66.667 0.00 0.00 43.37 4.18
2953 3028 2.037053 CCTGCTCCGTCTGATCGAT 58.963 57.895 0.00 0.00 0.00 3.59
2976 3051 1.636988 CGACCAACAGTTACCCGATC 58.363 55.000 0.00 0.00 0.00 3.69
2983 3058 0.528924 CAGTTACCCGATCGACCACA 59.471 55.000 18.66 0.00 0.00 4.17
2984 3059 1.136305 CAGTTACCCGATCGACCACAT 59.864 52.381 18.66 0.00 0.00 3.21
3024 3103 7.766278 TCTGTAAGTCAAAGAGAAATCTATGGC 59.234 37.037 0.00 0.00 33.76 4.40
3039 3118 9.578439 GAAATCTATGGCAATGGATTAATTAGC 57.422 33.333 12.66 0.00 41.62 3.09
3140 3219 0.615850 TGGTCAGGTCAACACACACA 59.384 50.000 0.00 0.00 0.00 3.72
3169 3248 4.453093 GCTGCATGAGCCTAGGTC 57.547 61.111 11.31 7.48 42.54 3.85
3172 3251 0.529337 CTGCATGAGCCTAGGTCGTG 60.529 60.000 20.57 20.57 46.06 4.35
3173 3252 1.227380 GCATGAGCCTAGGTCGTGG 60.227 63.158 23.59 10.16 44.26 4.94
3174 3253 1.961180 GCATGAGCCTAGGTCGTGGT 61.961 60.000 23.59 2.44 44.26 4.16
3175 3254 1.399714 CATGAGCCTAGGTCGTGGTA 58.600 55.000 11.31 0.00 41.56 3.25
3177 3256 0.038599 TGAGCCTAGGTCGTGGTACA 59.961 55.000 11.31 0.00 32.15 2.90
3222 3301 5.199024 TGTACGTACACACATACCAAAGT 57.801 39.130 24.10 0.00 0.00 2.66
3236 3315 7.910162 CACATACCAAAGTAACTCAATGTATGC 59.090 37.037 0.00 0.00 38.41 3.14
3256 3335 7.655732 TGTATGCATGCATTCTTAGTTATACGT 59.344 33.333 36.23 11.32 37.82 3.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.305064 GGCCAACTCTTATCTCTAGCTCG 60.305 52.174 0.00 0.00 0.00 5.03
3 4 2.288518 CCGGCCAACTCTTATCTCTAGC 60.289 54.545 2.24 0.00 0.00 3.42
4 5 2.297597 CCCGGCCAACTCTTATCTCTAG 59.702 54.545 2.24 0.00 0.00 2.43
5 6 2.317040 CCCGGCCAACTCTTATCTCTA 58.683 52.381 2.24 0.00 0.00 2.43
6 7 1.123928 CCCGGCCAACTCTTATCTCT 58.876 55.000 2.24 0.00 0.00 3.10
7 8 0.533085 GCCCGGCCAACTCTTATCTC 60.533 60.000 2.24 0.00 0.00 2.75
8 9 1.527370 GCCCGGCCAACTCTTATCT 59.473 57.895 2.24 0.00 0.00 1.98
9 10 4.142780 GCCCGGCCAACTCTTATC 57.857 61.111 2.24 0.00 0.00 1.75
118 119 3.408851 GTTGACGAACGTCCCCGC 61.409 66.667 21.54 7.94 43.97 6.13
159 160 6.662414 TCAATGGATATTGACTCGTGTTTC 57.338 37.500 0.00 0.00 45.77 2.78
177 179 5.466819 CGATCCAATCCAATCCAATCAATG 58.533 41.667 0.00 0.00 0.00 2.82
180 182 3.138098 TCCGATCCAATCCAATCCAATCA 59.862 43.478 0.00 0.00 0.00 2.57
185 187 3.146104 ACATCCGATCCAATCCAATCC 57.854 47.619 0.00 0.00 0.00 3.01
199 201 2.126110 GGCGGGCAAAAACATCCG 60.126 61.111 0.00 0.00 44.70 4.18
200 202 0.670239 CTTGGCGGGCAAAAACATCC 60.670 55.000 18.03 0.00 0.00 3.51
201 203 0.316841 TCTTGGCGGGCAAAAACATC 59.683 50.000 18.03 0.00 0.00 3.06
202 204 0.755686 TTCTTGGCGGGCAAAAACAT 59.244 45.000 18.03 0.00 0.00 2.71
203 205 0.537188 TTTCTTGGCGGGCAAAAACA 59.463 45.000 18.03 0.23 0.00 2.83
204 206 1.877637 ATTTCTTGGCGGGCAAAAAC 58.122 45.000 18.03 0.00 0.00 2.43
205 207 2.629336 AATTTCTTGGCGGGCAAAAA 57.371 40.000 18.03 18.55 0.00 1.94
209 211 0.892063 GGTAAATTTCTTGGCGGGCA 59.108 50.000 0.00 0.00 0.00 5.36
230 232 0.618458 GACCAAGGATGTACTGGGCA 59.382 55.000 0.00 0.00 34.71 5.36
231 233 0.912486 AGACCAAGGATGTACTGGGC 59.088 55.000 3.41 0.00 34.71 5.36
232 234 5.148502 ACTATAGACCAAGGATGTACTGGG 58.851 45.833 6.78 0.00 37.59 4.45
233 235 7.005296 ACTACTATAGACCAAGGATGTACTGG 58.995 42.308 6.78 0.00 0.00 4.00
235 237 8.947305 ACTACTACTATAGACCAAGGATGTACT 58.053 37.037 6.78 0.00 0.00 2.73
287 292 4.858935 ACACAATGATGGAGTGAAAAACG 58.141 39.130 0.00 0.00 37.05 3.60
293 298 5.850557 AACAAAACACAATGATGGAGTGA 57.149 34.783 0.00 0.00 37.05 3.41
308 313 3.737774 ACGTACGAGCTAGGAAACAAAAC 59.262 43.478 24.41 0.00 0.00 2.43
324 329 0.172578 TCCATCAGGCTGAACGTACG 59.827 55.000 22.84 15.01 33.74 3.67
325 330 1.204941 ACTCCATCAGGCTGAACGTAC 59.795 52.381 22.84 0.00 33.74 3.67
326 331 1.476891 GACTCCATCAGGCTGAACGTA 59.523 52.381 22.84 6.66 33.74 3.57
327 332 0.247736 GACTCCATCAGGCTGAACGT 59.752 55.000 22.84 15.14 33.74 3.99
340 345 7.419981 GGTGGTAGAATCTAGTACTAGACTCCA 60.420 44.444 28.90 25.99 44.11 3.86
352 357 6.401047 TTTACCGATGGTGGTAGAATCTAG 57.599 41.667 0.00 0.00 44.93 2.43
353 358 6.795144 TTTTACCGATGGTGGTAGAATCTA 57.205 37.500 0.00 0.00 44.93 1.98
354 359 5.687166 TTTTACCGATGGTGGTAGAATCT 57.313 39.130 0.00 0.00 44.93 2.40
366 371 4.111916 GGAACATGCCATTTTTACCGATG 58.888 43.478 0.00 0.00 0.00 3.84
387 392 1.180029 CCTTTGCCAGTTCCATCAGG 58.820 55.000 0.00 0.00 0.00 3.86
398 403 3.294493 GTGCGCTTCCCTTTGCCA 61.294 61.111 9.73 0.00 0.00 4.92
405 410 1.142097 GGAGTAGAGTGCGCTTCCC 59.858 63.158 9.73 0.00 0.00 3.97
411 416 1.517257 CCTTGCGGAGTAGAGTGCG 60.517 63.158 0.00 0.00 0.00 5.34
413 418 1.268794 CGATCCTTGCGGAGTAGAGTG 60.269 57.143 0.00 0.00 44.06 3.51
414 419 1.025812 CGATCCTTGCGGAGTAGAGT 58.974 55.000 0.00 0.00 44.06 3.24
415 420 1.002251 GTCGATCCTTGCGGAGTAGAG 60.002 57.143 0.00 0.00 44.06 2.43
449 475 4.607955 TGTCTCGTGTTTTGACTGACTAG 58.392 43.478 0.00 0.00 0.00 2.57
450 476 4.642445 TGTCTCGTGTTTTGACTGACTA 57.358 40.909 0.00 0.00 0.00 2.59
451 477 3.520290 TGTCTCGTGTTTTGACTGACT 57.480 42.857 0.00 0.00 0.00 3.41
452 478 4.034048 ACATTGTCTCGTGTTTTGACTGAC 59.966 41.667 0.00 0.00 0.00 3.51
453 479 4.188462 ACATTGTCTCGTGTTTTGACTGA 58.812 39.130 0.00 0.00 0.00 3.41
454 480 4.536364 ACATTGTCTCGTGTTTTGACTG 57.464 40.909 0.00 0.00 0.00 3.51
455 481 4.730613 GCAACATTGTCTCGTGTTTTGACT 60.731 41.667 0.00 0.00 36.48 3.41
466 492 1.875963 CCCCGTGCAACATTGTCTC 59.124 57.895 0.00 0.00 35.74 3.36
676 703 2.505118 GGCTGCGTCTCGTCTCAC 60.505 66.667 0.00 0.00 0.00 3.51
810 837 3.901797 GAAGGTGTGTGGGGGCGAG 62.902 68.421 0.00 0.00 0.00 5.03
858 885 5.253330 AGAGTGTGAAAACTGAAAACTGGA 58.747 37.500 0.00 0.00 0.00 3.86
863 890 4.640201 CCAGGAGAGTGTGAAAACTGAAAA 59.360 41.667 0.00 0.00 0.00 2.29
910 937 3.764810 CTCGCAGCCGCTGTAGAGG 62.765 68.421 26.59 15.50 36.00 3.69
914 941 2.428960 TTTGTCTCGCAGCCGCTGTA 62.429 55.000 21.29 9.47 35.30 2.74
916 943 3.043713 TTTGTCTCGCAGCCGCTG 61.044 61.111 16.47 16.47 35.30 5.18
917 944 3.044305 GTTTGTCTCGCAGCCGCT 61.044 61.111 0.00 0.00 35.30 5.52
918 945 3.044305 AGTTTGTCTCGCAGCCGC 61.044 61.111 0.00 0.00 0.00 6.53
919 946 1.621301 CTCAGTTTGTCTCGCAGCCG 61.621 60.000 0.00 0.00 0.00 5.52
920 947 1.905922 GCTCAGTTTGTCTCGCAGCC 61.906 60.000 0.00 0.00 0.00 4.85
953 980 4.189580 ACGGATTGGGCGATGGGG 62.190 66.667 0.00 0.00 0.00 4.96
954 981 2.591715 GACGGATTGGGCGATGGG 60.592 66.667 0.00 0.00 0.00 4.00
977 1004 6.849588 TCTAATCGCGTATACAACTGTAGA 57.150 37.500 5.77 1.74 33.52 2.59
978 1005 6.523546 CCATCTAATCGCGTATACAACTGTAG 59.476 42.308 5.77 0.00 33.52 2.74
980 1007 5.220381 CCATCTAATCGCGTATACAACTGT 58.780 41.667 5.77 0.00 0.00 3.55
982 1009 4.321750 CCCCATCTAATCGCGTATACAACT 60.322 45.833 5.77 0.00 0.00 3.16
983 1010 3.924686 CCCCATCTAATCGCGTATACAAC 59.075 47.826 5.77 0.00 0.00 3.32
984 1011 3.615592 GCCCCATCTAATCGCGTATACAA 60.616 47.826 5.77 0.00 0.00 2.41
987 1014 1.133598 CGCCCCATCTAATCGCGTATA 59.866 52.381 5.77 0.00 38.12 1.47
988 1015 0.108804 CGCCCCATCTAATCGCGTAT 60.109 55.000 5.77 0.00 38.12 3.06
1035 1062 2.046217 GTCCACGGCCCCTTCTTC 60.046 66.667 0.00 0.00 0.00 2.87
1075 1102 1.661112 GTGCTTCTTGATGTAGGCGAC 59.339 52.381 0.00 0.00 0.00 5.19
1124 1151 1.152383 GAGTCGCTTACCGGCATTCC 61.152 60.000 0.00 0.00 45.91 3.01
1126 1153 1.518572 CGAGTCGCTTACCGGCATT 60.519 57.895 0.00 0.00 45.91 3.56
1168 1195 6.373495 GGTGGATAACTAACTAACCAACTTGG 59.627 42.308 6.24 6.24 45.02 3.61
1171 1198 5.481473 TCGGTGGATAACTAACTAACCAACT 59.519 40.000 0.00 0.00 31.02 3.16
1172 1199 5.723295 TCGGTGGATAACTAACTAACCAAC 58.277 41.667 0.00 0.00 30.11 3.77
1173 1200 5.999205 TCGGTGGATAACTAACTAACCAA 57.001 39.130 0.00 0.00 0.00 3.67
1174 1201 5.221106 CGATCGGTGGATAACTAACTAACCA 60.221 44.000 7.38 0.00 31.51 3.67
1175 1202 5.009010 TCGATCGGTGGATAACTAACTAACC 59.991 44.000 16.41 0.00 31.51 2.85
1176 1203 6.064846 TCGATCGGTGGATAACTAACTAAC 57.935 41.667 16.41 0.00 31.51 2.34
1177 1204 6.072286 GGATCGATCGGTGGATAACTAACTAA 60.072 42.308 18.81 0.00 31.51 2.24
1178 1205 5.413833 GGATCGATCGGTGGATAACTAACTA 59.586 44.000 18.81 0.00 31.51 2.24
1179 1206 4.217983 GGATCGATCGGTGGATAACTAACT 59.782 45.833 18.81 0.00 31.51 2.24
1180 1207 4.483311 GGATCGATCGGTGGATAACTAAC 58.517 47.826 18.81 0.00 31.51 2.34
1181 1208 3.508793 GGGATCGATCGGTGGATAACTAA 59.491 47.826 18.81 0.00 31.51 2.24
1182 1209 3.087031 GGGATCGATCGGTGGATAACTA 58.913 50.000 18.81 0.00 31.51 2.24
1183 1210 1.893801 GGGATCGATCGGTGGATAACT 59.106 52.381 18.81 0.00 31.51 2.24
1184 1211 1.616865 TGGGATCGATCGGTGGATAAC 59.383 52.381 18.81 1.91 31.51 1.89
1185 1212 1.616865 GTGGGATCGATCGGTGGATAA 59.383 52.381 18.81 0.00 31.51 1.75
1186 1213 1.254026 GTGGGATCGATCGGTGGATA 58.746 55.000 18.81 0.00 31.51 2.59
1187 1214 0.759060 TGTGGGATCGATCGGTGGAT 60.759 55.000 18.81 0.20 34.96 3.41
1188 1215 1.380650 TGTGGGATCGATCGGTGGA 60.381 57.895 18.81 0.00 0.00 4.02
1189 1216 1.227263 GTGTGGGATCGATCGGTGG 60.227 63.158 18.81 0.00 0.00 4.61
1190 1217 0.108377 TTGTGTGGGATCGATCGGTG 60.108 55.000 18.81 0.00 0.00 4.94
1210 1237 3.749088 CCCAGACGCAACACAGTTAATTA 59.251 43.478 0.00 0.00 0.00 1.40
1211 1238 2.552315 CCCAGACGCAACACAGTTAATT 59.448 45.455 0.00 0.00 0.00 1.40
1212 1239 2.151202 CCCAGACGCAACACAGTTAAT 58.849 47.619 0.00 0.00 0.00 1.40
1214 1241 0.466543 ACCCAGACGCAACACAGTTA 59.533 50.000 0.00 0.00 0.00 2.24
1216 1243 1.523711 CACCCAGACGCAACACAGT 60.524 57.895 0.00 0.00 0.00 3.55
1217 1244 1.523711 ACACCCAGACGCAACACAG 60.524 57.895 0.00 0.00 0.00 3.66
1231 1280 1.510480 GCTCAAGGTCTGCACACACC 61.510 60.000 0.00 0.00 0.00 4.16
1246 1295 4.069232 CTCTTCCCGCACCGCTCA 62.069 66.667 0.00 0.00 0.00 4.26
1351 1400 1.672356 GTTGCCGAGGATGCTGTGT 60.672 57.895 0.00 0.00 0.00 3.72
1386 1458 3.675225 ACGTCGAGTTGAATGATGTGAAG 59.325 43.478 0.00 0.00 31.01 3.02
1414 1486 0.456221 GCAACAGAGACGCCTAGCTA 59.544 55.000 0.00 0.00 0.00 3.32
1415 1487 1.216710 GCAACAGAGACGCCTAGCT 59.783 57.895 0.00 0.00 0.00 3.32
1416 1488 0.456221 TAGCAACAGAGACGCCTAGC 59.544 55.000 0.00 0.00 0.00 3.42
1417 1489 3.610585 GCTATAGCAACAGAGACGCCTAG 60.611 52.174 20.01 0.00 41.59 3.02
1418 1490 2.293677 GCTATAGCAACAGAGACGCCTA 59.706 50.000 20.01 0.00 41.59 3.93
1419 1491 1.067821 GCTATAGCAACAGAGACGCCT 59.932 52.381 20.01 0.00 41.59 5.52
1420 1492 1.492720 GCTATAGCAACAGAGACGCC 58.507 55.000 20.01 0.00 41.59 5.68
1444 1516 2.956964 CGTACGCCTAGCTGCTGC 60.957 66.667 13.43 7.62 40.05 5.25
1445 1517 2.278857 CCGTACGCCTAGCTGCTG 60.279 66.667 13.43 2.21 0.00 4.41
1446 1518 1.885163 AAACCGTACGCCTAGCTGCT 61.885 55.000 10.49 7.57 0.00 4.24
1447 1519 1.419107 GAAACCGTACGCCTAGCTGC 61.419 60.000 10.49 0.00 0.00 5.25
1448 1520 0.804933 GGAAACCGTACGCCTAGCTG 60.805 60.000 10.49 0.00 0.00 4.24
1449 1521 0.969409 AGGAAACCGTACGCCTAGCT 60.969 55.000 10.49 0.00 0.00 3.32
1450 1522 0.804933 CAGGAAACCGTACGCCTAGC 60.805 60.000 10.49 0.00 0.00 3.42
1451 1523 0.179119 CCAGGAAACCGTACGCCTAG 60.179 60.000 10.49 0.00 0.00 3.02
1452 1524 1.892338 CCAGGAAACCGTACGCCTA 59.108 57.895 10.49 0.00 0.00 3.93
1453 1525 2.660802 CCAGGAAACCGTACGCCT 59.339 61.111 10.49 8.12 0.00 5.52
1454 1526 3.122971 GCCAGGAAACCGTACGCC 61.123 66.667 10.49 5.57 0.00 5.68
1455 1527 3.484547 CGCCAGGAAACCGTACGC 61.485 66.667 10.49 0.00 0.00 4.42
1456 1528 1.804326 CTCGCCAGGAAACCGTACG 60.804 63.158 8.69 8.69 0.00 3.67
1457 1529 0.320160 AACTCGCCAGGAAACCGTAC 60.320 55.000 0.00 0.00 0.00 3.67
1458 1530 0.393820 AAACTCGCCAGGAAACCGTA 59.606 50.000 0.00 0.00 0.00 4.02
1459 1531 0.883370 GAAACTCGCCAGGAAACCGT 60.883 55.000 0.00 0.00 0.00 4.83
1460 1532 0.882927 TGAAACTCGCCAGGAAACCG 60.883 55.000 0.00 0.00 0.00 4.44
1670 1742 4.217159 GTGGGGTAGTAGGCGGCG 62.217 72.222 0.51 0.51 0.00 6.46
2105 2177 3.421569 CGTTGCAGTTGTTGTTGTTGTTG 60.422 43.478 0.00 0.00 0.00 3.33
2106 2178 2.728839 CGTTGCAGTTGTTGTTGTTGTT 59.271 40.909 0.00 0.00 0.00 2.83
2107 2179 2.287909 ACGTTGCAGTTGTTGTTGTTGT 60.288 40.909 0.00 0.00 0.00 3.32
2187 2259 3.423154 GGCGCAGAAGGTTGTCGG 61.423 66.667 10.83 0.00 0.00 4.79
2190 2262 2.542907 CGTTGGCGCAGAAGGTTGT 61.543 57.895 10.83 0.00 0.00 3.32
2208 2280 4.210304 GGCGTCGATGTTGCTCGC 62.210 66.667 6.48 6.13 44.95 5.03
2297 2369 6.005198 TGGAACCCGTACTTGTATTTTTCAT 58.995 36.000 0.00 0.00 0.00 2.57
2300 2372 5.694231 GTGGAACCCGTACTTGTATTTTT 57.306 39.130 0.00 0.00 0.00 1.94
2326 2398 1.536072 GCTTCCACATGCATGCAGATG 60.536 52.381 26.69 23.70 0.00 2.90
2327 2399 0.744874 GCTTCCACATGCATGCAGAT 59.255 50.000 26.69 13.61 0.00 2.90
2328 2400 0.323087 AGCTTCCACATGCATGCAGA 60.323 50.000 26.69 19.51 0.00 4.26
2329 2401 1.333931 CTAGCTTCCACATGCATGCAG 59.666 52.381 26.69 19.15 0.00 4.41
2345 2417 2.924290 GTGATGAACTGTTCGACCTAGC 59.076 50.000 15.18 1.56 0.00 3.42
2349 2421 1.779569 ACGTGATGAACTGTTCGACC 58.220 50.000 15.18 7.64 0.00 4.79
2389 2464 4.082571 TCGAGATCATCATCGTATGCATGT 60.083 41.667 10.16 0.00 39.86 3.21
2390 2465 4.418392 TCGAGATCATCATCGTATGCATG 58.582 43.478 10.16 0.00 39.86 4.06
2391 2466 4.708726 TCGAGATCATCATCGTATGCAT 57.291 40.909 3.79 3.79 39.86 3.96
2392 2467 4.229876 GTTCGAGATCATCATCGTATGCA 58.770 43.478 0.00 0.00 39.86 3.96
2393 2468 3.299281 CGTTCGAGATCATCATCGTATGC 59.701 47.826 0.00 0.00 39.86 3.14
2394 2469 4.712763 TCGTTCGAGATCATCATCGTATG 58.287 43.478 0.00 0.00 39.86 2.39
2395 2470 4.691216 TCTCGTTCGAGATCATCATCGTAT 59.309 41.667 18.89 0.00 39.86 3.06
2396 2471 4.056050 TCTCGTTCGAGATCATCATCGTA 58.944 43.478 18.89 0.00 39.86 3.43
2397 2472 2.872858 TCTCGTTCGAGATCATCATCGT 59.127 45.455 18.89 0.00 39.86 3.73
2398 2473 3.478063 CTCTCGTTCGAGATCATCATCG 58.522 50.000 22.11 7.26 40.07 3.84
2399 2474 3.233578 GCTCTCGTTCGAGATCATCATC 58.766 50.000 22.11 5.65 40.07 2.92
2400 2475 2.030363 GGCTCTCGTTCGAGATCATCAT 60.030 50.000 22.11 0.00 40.07 2.45
2401 2476 1.335182 GGCTCTCGTTCGAGATCATCA 59.665 52.381 22.11 2.75 40.07 3.07
2402 2477 1.661743 CGGCTCTCGTTCGAGATCATC 60.662 57.143 22.11 12.81 40.07 2.92
2403 2478 0.309302 CGGCTCTCGTTCGAGATCAT 59.691 55.000 22.11 0.00 40.07 2.45
2404 2479 1.722082 CGGCTCTCGTTCGAGATCA 59.278 57.895 22.11 4.06 40.07 2.92
2405 2480 4.599417 CGGCTCTCGTTCGAGATC 57.401 61.111 22.11 18.33 40.07 2.75
2603 2678 4.907809 CATATGATGCAAGTGAGAGGGAT 58.092 43.478 0.00 0.00 0.00 3.85
2658 2733 3.191371 AGCATTCTAAGAAAAGCAACCGG 59.809 43.478 0.00 0.00 0.00 5.28
2659 2734 4.425577 AGCATTCTAAGAAAAGCAACCG 57.574 40.909 0.00 0.00 0.00 4.44
2660 2735 6.502136 AGTAGCATTCTAAGAAAAGCAACC 57.498 37.500 0.00 0.00 0.00 3.77
2661 2736 8.803201 AAAAGTAGCATTCTAAGAAAAGCAAC 57.197 30.769 0.00 0.00 0.00 4.17
2669 2744 9.944376 ACAGACAATAAAAGTAGCATTCTAAGA 57.056 29.630 0.00 0.00 0.00 2.10
2673 2748 8.850156 ACAAACAGACAATAAAAGTAGCATTCT 58.150 29.630 0.00 0.00 0.00 2.40
2674 2749 9.463443 AACAAACAGACAATAAAAGTAGCATTC 57.537 29.630 0.00 0.00 0.00 2.67
2675 2750 9.463443 GAACAAACAGACAATAAAAGTAGCATT 57.537 29.630 0.00 0.00 0.00 3.56
2676 2751 8.850156 AGAACAAACAGACAATAAAAGTAGCAT 58.150 29.630 0.00 0.00 0.00 3.79
2677 2752 8.220755 AGAACAAACAGACAATAAAAGTAGCA 57.779 30.769 0.00 0.00 0.00 3.49
2678 2753 8.958043 CAAGAACAAACAGACAATAAAAGTAGC 58.042 33.333 0.00 0.00 0.00 3.58
2681 2756 9.353999 GAACAAGAACAAACAGACAATAAAAGT 57.646 29.630 0.00 0.00 0.00 2.66
2682 2757 9.352784 TGAACAAGAACAAACAGACAATAAAAG 57.647 29.630 0.00 0.00 0.00 2.27
2683 2758 9.868277 ATGAACAAGAACAAACAGACAATAAAA 57.132 25.926 0.00 0.00 0.00 1.52
2684 2759 9.868277 AATGAACAAGAACAAACAGACAATAAA 57.132 25.926 0.00 0.00 0.00 1.40
2685 2760 9.515020 GAATGAACAAGAACAAACAGACAATAA 57.485 29.630 0.00 0.00 0.00 1.40
2686 2761 7.855409 CGAATGAACAAGAACAAACAGACAATA 59.145 33.333 0.00 0.00 0.00 1.90
2687 2762 6.692681 CGAATGAACAAGAACAAACAGACAAT 59.307 34.615 0.00 0.00 0.00 2.71
2688 2763 6.027131 CGAATGAACAAGAACAAACAGACAA 58.973 36.000 0.00 0.00 0.00 3.18
2742 2817 7.549134 TCAGCAGTACAGTAACCAATGAAATAG 59.451 37.037 0.00 0.00 0.00 1.73
2788 2863 5.350547 TCTCCCTCCCTTTGATTTCTTCTA 58.649 41.667 0.00 0.00 0.00 2.10
2802 2877 2.677542 AGTTGGTTTTTCTCCCTCCC 57.322 50.000 0.00 0.00 0.00 4.30
2882 2957 5.566469 TCCAGTCTATTTTCCCAACGATTT 58.434 37.500 0.00 0.00 0.00 2.17
2953 3028 0.034337 GGGTAACTGTTGGTCGCTCA 59.966 55.000 2.69 0.00 0.00 4.26
2976 3051 8.020819 ACAGAAAAACAAATACATATGTGGTCG 58.979 33.333 18.81 7.06 0.00 4.79
3024 3103 8.139350 TGATGAAGCTTGCTAATTAATCCATTG 58.861 33.333 2.10 0.00 0.00 2.82
3039 3118 7.373493 AGGAATGTAAACTTTGATGAAGCTTG 58.627 34.615 2.10 0.00 39.04 4.01
3096 3175 9.932207 CATACCCAAACAAGACGGTTATATATA 57.068 33.333 0.00 0.00 0.00 0.86
3097 3176 7.881232 CCATACCCAAACAAGACGGTTATATAT 59.119 37.037 0.00 0.00 0.00 0.86
3098 3177 7.147514 ACCATACCCAAACAAGACGGTTATATA 60.148 37.037 0.00 0.00 0.00 0.86
3099 3178 6.059484 CCATACCCAAACAAGACGGTTATAT 58.941 40.000 0.00 0.00 0.00 0.86
3140 3219 1.001974 TCATGCAGCCTTGTACGAGTT 59.998 47.619 9.32 0.00 0.00 3.01
3169 3248 1.375523 GCCTTGGAGGTGTACCACG 60.376 63.158 3.56 0.00 37.80 4.94
3172 3251 0.331616 ATTGGCCTTGGAGGTGTACC 59.668 55.000 3.32 0.00 37.80 3.34
3173 3252 1.271926 ACATTGGCCTTGGAGGTGTAC 60.272 52.381 3.32 0.00 37.80 2.90
3174 3253 1.072266 ACATTGGCCTTGGAGGTGTA 58.928 50.000 3.32 0.00 37.80 2.90
3175 3254 0.540365 CACATTGGCCTTGGAGGTGT 60.540 55.000 3.32 0.00 37.80 4.16
3177 3256 0.540365 CACACATTGGCCTTGGAGGT 60.540 55.000 3.32 0.00 37.80 3.85
3178 3257 0.540365 ACACACATTGGCCTTGGAGG 60.540 55.000 3.32 0.00 38.80 4.30
3179 3258 2.086869 CTACACACATTGGCCTTGGAG 58.913 52.381 3.32 2.07 0.00 3.86
3180 3259 1.423541 ACTACACACATTGGCCTTGGA 59.576 47.619 3.32 0.00 0.00 3.53
3181 3260 1.541147 CACTACACACATTGGCCTTGG 59.459 52.381 3.32 0.00 0.00 3.61
3210 3289 7.910162 GCATACATTGAGTTACTTTGGTATGTG 59.090 37.037 18.77 6.53 39.15 3.21
3222 3301 6.947644 AGAATGCATGCATACATTGAGTTA 57.052 33.333 32.36 0.15 36.65 2.24
3236 3315 7.117667 TGCCATACGTATAACTAAGAATGCATG 59.882 37.037 7.96 0.00 0.00 4.06
3256 3335 7.324935 ACGTACGGAAATAATGATATGCCATA 58.675 34.615 21.06 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.