Multiple sequence alignment - TraesCS4A01G272100

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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 TraesCS4A01G272100 chr4A 100.000 3575 0 0 1 3575 583760270 583756696 0.000000e+00 6602.0
1 TraesCS4A01G272100 chr4B 89.376 1346 91 25 1259 2568 28715430 28716759 0.000000e+00 1646.0
2 TraesCS4A01G272100 chr4B 86.824 850 49 30 2746 3575 28716809 28717615 0.000000e+00 891.0
3 TraesCS4A01G272100 chr4B 90.169 295 17 9 1 286 28714205 28714496 1.210000e-99 374.0
4 TraesCS4A01G272100 chr4B 85.920 348 15 12 890 1220 28715091 28715421 1.230000e-89 340.0
5 TraesCS4A01G272100 chr4D 87.953 1104 76 26 893 1973 16797358 16798427 0.000000e+00 1249.0
6 TraesCS4A01G272100 chr4D 89.286 952 55 24 2648 3575 16799002 16799930 0.000000e+00 1149.0
7 TraesCS4A01G272100 chr4D 89.976 419 34 4 2150 2568 16798562 16798972 5.250000e-148 534.0
8 TraesCS4A01G272100 chr4D 86.822 387 16 18 1 382 16796493 16796849 2.000000e-107 399.0
9 TraesCS4A01G272100 chr2A 97.419 155 4 0 3324 3478 12281434 12281280 7.610000e-67 265.0
10 TraesCS4A01G272100 chr2A 82.400 125 18 4 512 633 679852992 679852869 4.880000e-19 106.0
11 TraesCS4A01G272100 chr6B 89.583 48 4 1 509 555 708003976 708003929 3.850000e-05 60.2


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 TraesCS4A01G272100 chr4A 583756696 583760270 3574 True 6602.00 6602 100.00000 1 3575 1 chr4A.!!$R1 3574
1 TraesCS4A01G272100 chr4B 28714205 28717615 3410 False 812.75 1646 88.07225 1 3575 4 chr4B.!!$F1 3574
2 TraesCS4A01G272100 chr4D 16796493 16799930 3437 False 832.75 1249 88.50925 1 3575 4 chr4D.!!$F1 3574

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
237 246 0.179108 GCTATCCGACTTCCAAGCGT 60.179 55.0 0.0 0.0 0.0 5.07 F
1017 1140 0.035056 CCAAGGCAGAAGATTCCGGT 60.035 55.0 0.0 0.0 0.0 5.28 F
1019 1142 0.035056 AAGGCAGAAGATTCCGGTGG 60.035 55.0 0.0 0.0 0.0 4.61 F
2215 2432 0.039527 GGTTCAACCGTGTGGCAATC 60.040 55.0 0.0 0.0 39.7 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1566 1721 0.250295 CGCCCTTCTGTCAAGTTCCA 60.250 55.0 0.00 0.0 0.00 3.53 R
2434 2651 0.040067 CTTGAGCCGGAGCAACAAAC 60.040 55.0 5.05 0.0 43.56 2.93 R
2447 2664 0.169009 GACGGCATGGAAACTTGAGC 59.831 55.0 0.00 0.0 37.69 4.26 R
3063 3297 0.039798 CCGTGTCCGTCTTTTCTCGA 60.040 55.0 0.00 0.0 0.00 4.04 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
17 20 4.547859 GCCTCAGGCGACATTGAT 57.452 55.556 0.00 0.00 39.62 2.57
18 21 3.686622 GCCTCAGGCGACATTGATA 57.313 52.632 0.00 0.00 39.62 2.15
19 22 2.175878 GCCTCAGGCGACATTGATAT 57.824 50.000 0.00 0.00 39.62 1.63
56 59 1.614241 CCCCAGCGTGTACTAGCCTT 61.614 60.000 9.02 0.00 0.00 4.35
58 61 1.338769 CCCAGCGTGTACTAGCCTTTT 60.339 52.381 9.02 0.00 0.00 2.27
80 86 3.884037 TCAGGCCTTCTCTTTTCCTTT 57.116 42.857 0.00 0.00 0.00 3.11
81 87 3.490348 TCAGGCCTTCTCTTTTCCTTTG 58.510 45.455 0.00 0.00 0.00 2.77
142 148 1.095600 GAAACGGAATGGCTCCCTTC 58.904 55.000 0.00 0.00 41.87 3.46
224 233 2.018542 TGCAGTTACCGTTGCTATCC 57.981 50.000 0.00 0.00 40.87 2.59
227 236 2.190981 CAGTTACCGTTGCTATCCGAC 58.809 52.381 0.00 0.00 0.00 4.79
237 246 0.179108 GCTATCCGACTTCCAAGCGT 60.179 55.000 0.00 0.00 0.00 5.07
244 253 2.607187 CGACTTCCAAGCGTGAGTATT 58.393 47.619 0.00 0.00 0.00 1.89
286 296 2.292569 CTGGCCATGCTGTCATTACATC 59.707 50.000 5.51 0.00 34.37 3.06
287 297 1.610522 GGCCATGCTGTCATTACATCC 59.389 52.381 0.00 0.00 34.37 3.51
289 299 2.551459 GCCATGCTGTCATTACATCCTC 59.449 50.000 0.00 0.00 34.37 3.71
293 303 3.521560 TGCTGTCATTACATCCTCGTTC 58.478 45.455 0.00 0.00 34.37 3.95
295 305 3.733988 GCTGTCATTACATCCTCGTTCGA 60.734 47.826 0.00 0.00 34.37 3.71
296 306 4.421058 CTGTCATTACATCCTCGTTCGAA 58.579 43.478 0.00 0.00 34.37 3.71
297 307 4.811908 TGTCATTACATCCTCGTTCGAAA 58.188 39.130 0.00 0.00 0.00 3.46
298 308 5.231702 TGTCATTACATCCTCGTTCGAAAA 58.768 37.500 0.00 0.00 0.00 2.29
299 309 5.697178 TGTCATTACATCCTCGTTCGAAAAA 59.303 36.000 0.00 0.00 0.00 1.94
346 357 3.664107 TGTTTAGAGATGTGGTGTGCTC 58.336 45.455 0.00 0.00 0.00 4.26
445 459 6.439636 AGCTCTACAGAATGGCCATAATTA 57.560 37.500 21.15 7.34 43.62 1.40
451 465 5.140454 ACAGAATGGCCATAATTAAGGGAC 58.860 41.667 21.15 7.10 43.62 4.46
455 469 4.534647 TGGCCATAATTAAGGGACATGT 57.465 40.909 0.00 0.00 33.91 3.21
459 473 5.705905 GGCCATAATTAAGGGACATGTAGTC 59.294 44.000 8.74 0.00 46.83 2.59
485 512 7.045416 TCTAAACTTGAGCTTGTGAACAGTAA 58.955 34.615 0.00 0.00 0.00 2.24
488 515 6.509418 ACTTGAGCTTGTGAACAGTAAAAA 57.491 33.333 0.00 0.00 0.00 1.94
557 598 9.634163 AATTTTCTACATTCGTGTAAATTTCCC 57.366 29.630 0.00 0.00 0.00 3.97
558 599 7.989416 TTTCTACATTCGTGTAAATTTCCCT 57.011 32.000 0.00 0.00 0.00 4.20
586 627 4.660789 AAACATTCATAATGCTCTGGGC 57.339 40.909 0.00 0.00 42.69 5.36
614 655 7.969508 ACAAAAACAAATTTGATGCTCCAAAAG 59.030 29.630 24.64 5.02 41.73 2.27
617 658 5.927819 ACAAATTTGATGCTCCAAAAGGAA 58.072 33.333 24.64 0.00 39.20 3.36
621 662 8.354426 CAAATTTGATGCTCCAAAAGGAATTTT 58.646 29.630 13.08 2.14 39.20 1.82
686 743 6.954616 TTCATCATTAAAAGTTGCATGCAG 57.045 33.333 21.50 5.95 0.00 4.41
697 754 1.297664 TGCATGCAGGCAAACAAAAC 58.702 45.000 25.72 0.00 41.65 2.43
702 759 4.370917 CATGCAGGCAAACAAAACTAAGT 58.629 39.130 0.00 0.00 0.00 2.24
705 762 5.344884 TGCAGGCAAACAAAACTAAGTAAC 58.655 37.500 0.00 0.00 0.00 2.50
708 765 6.198403 GCAGGCAAACAAAACTAAGTAACTTC 59.802 38.462 0.00 0.00 0.00 3.01
788 846 5.808042 TCATAGAACAAGCATTTGAGCTC 57.192 39.130 6.82 6.82 45.89 4.09
796 854 4.095483 ACAAGCATTTGAGCTCGGAATTAG 59.905 41.667 9.64 2.97 45.89 1.73
810 868 7.337942 AGCTCGGAATTAGAAGAACATTTTCAT 59.662 33.333 0.00 0.00 33.72 2.57
811 869 8.612619 GCTCGGAATTAGAAGAACATTTTCATA 58.387 33.333 0.00 0.00 33.72 2.15
821 879 8.956426 AGAAGAACATTTTCATAATTTAGCCGA 58.044 29.630 0.00 0.00 33.72 5.54
855 962 2.673368 GACAATCAAAATCGAGCCGAGT 59.327 45.455 3.76 0.00 39.91 4.18
856 963 2.416547 ACAATCAAAATCGAGCCGAGTG 59.583 45.455 3.76 0.00 39.91 3.51
862 969 0.320374 AATCGAGCCGAGTGGAAACA 59.680 50.000 3.76 0.00 39.91 2.83
880 987 7.398829 TGGAAACACTTATTATTGAGCCTACA 58.601 34.615 0.00 0.00 33.40 2.74
883 990 7.849804 AACACTTATTATTGAGCCTACACTG 57.150 36.000 0.00 0.00 0.00 3.66
884 991 7.182817 ACACTTATTATTGAGCCTACACTGA 57.817 36.000 0.00 0.00 0.00 3.41
885 992 7.268586 ACACTTATTATTGAGCCTACACTGAG 58.731 38.462 0.00 0.00 0.00 3.35
886 993 7.093289 ACACTTATTATTGAGCCTACACTGAGT 60.093 37.037 0.00 0.00 0.00 3.41
887 994 7.223582 CACTTATTATTGAGCCTACACTGAGTG 59.776 40.741 11.70 11.70 39.75 3.51
888 995 4.471904 TTATTGAGCCTACACTGAGTGG 57.528 45.455 17.92 0.00 37.94 4.00
889 996 0.321671 TTGAGCCTACACTGAGTGGC 59.678 55.000 17.92 10.94 41.68 5.01
904 1011 2.884639 GAGTGGCTTTTTGTAGGCTCAA 59.115 45.455 0.00 0.00 41.03 3.02
905 1012 3.500343 AGTGGCTTTTTGTAGGCTCAAT 58.500 40.909 0.00 0.00 41.03 2.57
906 1013 3.897505 AGTGGCTTTTTGTAGGCTCAATT 59.102 39.130 0.00 0.00 41.03 2.32
910 1017 5.303078 TGGCTTTTTGTAGGCTCAATTACAA 59.697 36.000 0.00 0.00 41.03 2.41
944 1051 0.686789 GCCCAAAATCAAGCCCAAGT 59.313 50.000 0.00 0.00 0.00 3.16
949 1056 3.392882 CAAAATCAAGCCCAAGTCCAAC 58.607 45.455 0.00 0.00 0.00 3.77
950 1057 2.380064 AATCAAGCCCAAGTCCAACA 57.620 45.000 0.00 0.00 0.00 3.33
951 1058 2.610438 ATCAAGCCCAAGTCCAACAT 57.390 45.000 0.00 0.00 0.00 2.71
1000 1123 1.074775 CCCCCTCGGGTTCTATCCA 60.075 63.158 0.55 0.00 45.50 3.41
1001 1124 0.693092 CCCCCTCGGGTTCTATCCAA 60.693 60.000 0.55 0.00 45.50 3.53
1003 1126 0.759346 CCCTCGGGTTCTATCCAAGG 59.241 60.000 0.00 0.00 34.06 3.61
1015 1138 2.338577 ATCCAAGGCAGAAGATTCCG 57.661 50.000 0.00 0.00 0.00 4.30
1016 1139 0.253044 TCCAAGGCAGAAGATTCCGG 59.747 55.000 0.00 0.00 0.00 5.14
1017 1140 0.035056 CCAAGGCAGAAGATTCCGGT 60.035 55.000 0.00 0.00 0.00 5.28
1018 1141 1.089920 CAAGGCAGAAGATTCCGGTG 58.910 55.000 0.00 0.00 0.00 4.94
1019 1142 0.035056 AAGGCAGAAGATTCCGGTGG 60.035 55.000 0.00 0.00 0.00 4.61
1020 1143 1.452108 GGCAGAAGATTCCGGTGGG 60.452 63.158 0.00 0.00 0.00 4.61
1021 1144 1.602237 GCAGAAGATTCCGGTGGGA 59.398 57.895 0.00 0.00 41.83 4.37
1091 1222 4.468769 ATGGTCTCCGGCCCCGTA 62.469 66.667 5.93 0.00 37.81 4.02
1112 1243 3.612607 ACCTCGTCCCTCCCCCTT 61.613 66.667 0.00 0.00 0.00 3.95
1185 1316 4.806339 CCGCCCTCTTCCTCCCCT 62.806 72.222 0.00 0.00 0.00 4.79
1186 1317 2.689034 CGCCCTCTTCCTCCCCTT 60.689 66.667 0.00 0.00 0.00 3.95
1187 1318 2.736826 CGCCCTCTTCCTCCCCTTC 61.737 68.421 0.00 0.00 0.00 3.46
1190 1321 0.692756 CCCTCTTCCTCCCCTTCCTC 60.693 65.000 0.00 0.00 0.00 3.71
1195 1326 1.772561 TTCCTCCCCTTCCTCCCCTT 61.773 60.000 0.00 0.00 0.00 3.95
1235 1369 1.267574 TGGGAAGGAGCTAGTGCCAG 61.268 60.000 0.46 0.00 40.80 4.85
1238 1372 0.179124 GAAGGAGCTAGTGCCAGTCG 60.179 60.000 5.91 0.00 40.80 4.18
1242 1376 1.380524 GAGCTAGTGCCAGTCGAGTA 58.619 55.000 0.00 0.00 40.80 2.59
1247 1381 0.675837 AGTGCCAGTCGAGTACGCTA 60.676 55.000 11.54 0.00 39.58 4.26
1264 1398 1.460504 CTACTAGGTCTCGGCACACA 58.539 55.000 0.00 0.00 0.00 3.72
1286 1420 0.787183 GCTTGCGTTGTCTGTCTCTC 59.213 55.000 0.00 0.00 0.00 3.20
1290 1424 2.227194 TGCGTTGTCTGTCTCTCTGTA 58.773 47.619 0.00 0.00 0.00 2.74
1291 1425 2.820197 TGCGTTGTCTGTCTCTCTGTAT 59.180 45.455 0.00 0.00 0.00 2.29
1292 1426 3.175152 GCGTTGTCTGTCTCTCTGTATG 58.825 50.000 0.00 0.00 0.00 2.39
1303 1437 5.952347 TGTCTCTCTGTATGTGTAGTTCCAT 59.048 40.000 0.00 0.00 0.00 3.41
1334 1469 0.468771 GGATGCTGGAAGAATGGGGG 60.469 60.000 0.00 0.00 26.21 5.40
1335 1470 0.259938 GATGCTGGAAGAATGGGGGT 59.740 55.000 0.00 0.00 26.21 4.95
1350 1485 1.302033 GGGTGAGCTGGTGTCTGTG 60.302 63.158 0.00 0.00 0.00 3.66
1352 1487 0.882042 GGTGAGCTGGTGTCTGTGTG 60.882 60.000 0.00 0.00 0.00 3.82
1353 1488 0.882042 GTGAGCTGGTGTCTGTGTGG 60.882 60.000 0.00 0.00 0.00 4.17
1356 1491 1.893808 GCTGGTGTCTGTGTGGGTG 60.894 63.158 0.00 0.00 0.00 4.61
1357 1492 1.893808 CTGGTGTCTGTGTGGGTGC 60.894 63.158 0.00 0.00 0.00 5.01
1358 1493 2.329539 CTGGTGTCTGTGTGGGTGCT 62.330 60.000 0.00 0.00 0.00 4.40
1360 1495 1.447317 GGTGTCTGTGTGGGTGCTTG 61.447 60.000 0.00 0.00 0.00 4.01
1361 1496 1.823470 TGTCTGTGTGGGTGCTTGC 60.823 57.895 0.00 0.00 0.00 4.01
1362 1497 1.526917 GTCTGTGTGGGTGCTTGCT 60.527 57.895 0.00 0.00 0.00 3.91
1393 1544 5.125900 CCATGAATGTCCTAGCACATTTTGA 59.874 40.000 13.25 2.03 45.23 2.69
1405 1556 8.338259 CCTAGCACATTTTGACTGATAATGTAC 58.662 37.037 0.00 0.00 39.70 2.90
1406 1557 7.686438 AGCACATTTTGACTGATAATGTACA 57.314 32.000 0.00 0.00 39.70 2.90
1407 1558 8.109705 AGCACATTTTGACTGATAATGTACAA 57.890 30.769 0.00 0.00 39.70 2.41
1408 1559 8.742777 AGCACATTTTGACTGATAATGTACAAT 58.257 29.630 0.00 0.00 39.70 2.71
1409 1560 9.357652 GCACATTTTGACTGATAATGTACAATT 57.642 29.630 0.00 0.00 39.70 2.32
1479 1633 7.881775 ATTTTTCTTCGCTATATGTCCCTTT 57.118 32.000 0.00 0.00 0.00 3.11
1486 1640 8.251026 TCTTCGCTATATGTCCCTTTATATGTG 58.749 37.037 0.00 0.00 0.00 3.21
1496 1650 8.141298 TGTCCCTTTATATGTGTTTACAGAGA 57.859 34.615 0.00 0.00 40.79 3.10
1593 1751 3.830192 CAGAAGGGCGGCATTGGC 61.830 66.667 15.43 0.00 40.13 4.52
1692 1850 1.070601 CAGTACATCCATGGCATCGGA 59.929 52.381 17.18 17.18 35.27 4.55
1698 1856 1.227943 CCATGGCATCGGACGGAAT 60.228 57.895 0.00 0.00 0.00 3.01
1734 1892 4.803452 TCCTTTTGGACCTCAGTTTTGAT 58.197 39.130 0.00 0.00 45.19 2.57
1782 1940 2.415608 GGAGGTCATCACGCTCCGA 61.416 63.158 0.00 0.00 33.11 4.55
1823 1981 6.725364 ACATGATTGAAGGAGACCTTGTAAT 58.275 36.000 7.81 8.17 44.82 1.89
1824 1982 7.177878 ACATGATTGAAGGAGACCTTGTAATT 58.822 34.615 7.81 0.00 44.82 1.40
1830 1988 4.479786 AGGAGACCTTGTAATTGCTCTC 57.520 45.455 3.00 3.00 0.00 3.20
1832 1990 4.472833 AGGAGACCTTGTAATTGCTCTCAT 59.527 41.667 11.00 3.34 0.00 2.90
1844 2002 3.939740 TGCTCTCATCCCTTTGCTAAT 57.060 42.857 0.00 0.00 0.00 1.73
1938 2114 3.679824 AGGACCTGTTTAGTTCTTCCG 57.320 47.619 0.00 0.00 0.00 4.30
1945 2121 6.527423 ACCTGTTTAGTTCTTCCGACATTTA 58.473 36.000 0.00 0.00 0.00 1.40
2147 2324 5.485353 AGGACATGTTTAGTTCTCTCCATGA 59.515 40.000 0.00 0.00 35.04 3.07
2154 2331 6.813649 TGTTTAGTTCTCTCCATGATTCTTCG 59.186 38.462 0.00 0.00 0.00 3.79
2215 2432 0.039527 GGTTCAACCGTGTGGCAATC 60.040 55.000 0.00 0.00 39.70 2.67
2308 2525 2.682856 GACAAAGAACAACTGCAGGACA 59.317 45.455 19.93 0.00 0.00 4.02
2411 2628 3.436243 ACCTCCTGTTTGGTTTTTGTGA 58.564 40.909 0.00 0.00 37.07 3.58
2430 2647 1.331138 GAGCTACATCACGACGCTACT 59.669 52.381 0.00 0.00 0.00 2.57
2434 2651 0.376152 ACATCACGACGCTACTACCG 59.624 55.000 0.00 0.00 0.00 4.02
2437 2654 0.874390 TCACGACGCTACTACCGTTT 59.126 50.000 0.00 0.00 39.30 3.60
2439 2656 0.593128 ACGACGCTACTACCGTTTGT 59.407 50.000 0.00 0.00 39.30 2.83
2441 2658 1.384409 CGACGCTACTACCGTTTGTTG 59.616 52.381 0.00 0.00 39.30 3.33
2447 2664 0.601841 ACTACCGTTTGTTGCTCCGG 60.602 55.000 0.00 0.00 45.72 5.14
2448 2665 1.908066 CTACCGTTTGTTGCTCCGGC 61.908 60.000 0.00 0.00 44.14 6.13
2536 2753 9.677567 GAGTTTATAGTCATGACATCTCTTCTC 57.322 37.037 27.02 19.21 0.00 2.87
2546 2763 8.813951 TCATGACATCTCTTCTCTTATATGCAT 58.186 33.333 3.79 3.79 0.00 3.96
2554 2771 9.093458 TCTCTTCTCTTATATGCATTGATGGTA 57.907 33.333 3.54 0.00 0.00 3.25
2594 2811 8.582657 TTTTCCGATAAAGGGTAAATCATCAA 57.417 30.769 0.00 0.00 0.00 2.57
2614 2831 0.110554 GGTTACATGCGCGTTTCGTT 60.111 50.000 8.43 0.00 41.07 3.85
2632 2849 4.109050 TCGTTCCAAGCACAAATGTTTTC 58.891 39.130 0.00 0.00 0.00 2.29
2635 2852 4.998671 TCCAAGCACAAATGTTTTCTGA 57.001 36.364 0.00 0.00 0.00 3.27
2640 2857 5.070770 AGCACAAATGTTTTCTGAACACA 57.929 34.783 11.37 11.37 32.37 3.72
2644 2861 7.927629 AGCACAAATGTTTTCTGAACACATATT 59.072 29.630 19.24 13.55 30.74 1.28
2691 2908 1.197721 GATGCAAAGACAGGTCAACCG 59.802 52.381 1.84 0.00 42.08 4.44
2697 2914 1.079336 GACAGGTCAACCGGCTACC 60.079 63.158 0.00 6.89 42.08 3.18
2716 2933 4.592485 ACCGATGACTGGATTAGCTTAG 57.408 45.455 0.00 0.00 0.00 2.18
2717 2934 4.215908 ACCGATGACTGGATTAGCTTAGA 58.784 43.478 0.00 0.00 0.00 2.10
2718 2935 4.038162 ACCGATGACTGGATTAGCTTAGAC 59.962 45.833 0.00 0.00 0.00 2.59
2719 2936 4.038042 CCGATGACTGGATTAGCTTAGACA 59.962 45.833 0.00 0.00 0.00 3.41
2720 2937 4.979197 CGATGACTGGATTAGCTTAGACAC 59.021 45.833 0.00 0.00 0.00 3.67
2723 2940 4.160439 TGACTGGATTAGCTTAGACACCAG 59.840 45.833 0.00 0.00 45.78 4.00
2724 2941 4.744795 CTGGATTAGCTTAGACACCAGT 57.255 45.455 0.00 0.00 38.67 4.00
2728 2945 4.323562 GGATTAGCTTAGACACCAGTGGTT 60.324 45.833 13.62 4.23 31.02 3.67
2729 2946 2.550830 AGCTTAGACACCAGTGGTTG 57.449 50.000 13.62 11.00 31.02 3.77
2731 2948 2.969950 AGCTTAGACACCAGTGGTTGTA 59.030 45.455 13.62 4.75 31.02 2.41
2732 2949 3.006967 AGCTTAGACACCAGTGGTTGTAG 59.993 47.826 13.62 9.81 31.02 2.74
2733 2950 3.006537 GCTTAGACACCAGTGGTTGTAGA 59.993 47.826 13.62 3.46 31.02 2.59
2735 2952 5.794894 CTTAGACACCAGTGGTTGTAGAAT 58.205 41.667 13.62 4.76 31.02 2.40
2741 2961 3.818773 ACCAGTGGTTGTAGAATTTTCCG 59.181 43.478 9.70 0.00 27.29 4.30
2808 3028 0.902516 GACAGAGGAGCTCCAGTGGT 60.903 60.000 33.90 24.17 38.89 4.16
2814 3034 4.874521 AGCTCCAGTGGTAGCTCA 57.125 55.556 22.87 0.00 45.92 4.26
2823 3043 3.195610 CCAGTGGTAGCTCAGTAATGTGA 59.804 47.826 0.00 0.00 0.00 3.58
2824 3044 4.177026 CAGTGGTAGCTCAGTAATGTGAC 58.823 47.826 0.00 0.00 0.00 3.67
2849 3069 5.239525 ACTGTCAGGTTTGATTGCTAGTTTC 59.760 40.000 4.53 0.00 35.39 2.78
2854 3074 5.940470 CAGGTTTGATTGCTAGTTTCCTACT 59.060 40.000 0.00 0.00 41.04 2.57
2855 3075 5.940470 AGGTTTGATTGCTAGTTTCCTACTG 59.060 40.000 0.00 0.00 37.73 2.74
2856 3076 5.705905 GGTTTGATTGCTAGTTTCCTACTGT 59.294 40.000 0.00 0.00 37.73 3.55
2858 3078 7.148457 GGTTTGATTGCTAGTTTCCTACTGTAC 60.148 40.741 0.00 0.00 37.73 2.90
2859 3079 5.974108 TGATTGCTAGTTTCCTACTGTACC 58.026 41.667 0.00 0.00 37.73 3.34
2860 3080 5.482526 TGATTGCTAGTTTCCTACTGTACCA 59.517 40.000 0.00 0.00 37.73 3.25
2861 3081 5.401531 TTGCTAGTTTCCTACTGTACCAG 57.598 43.478 0.00 0.00 37.73 4.00
2863 3083 5.269991 TGCTAGTTTCCTACTGTACCAGAT 58.730 41.667 0.00 0.00 37.73 2.90
2865 3085 6.320672 TGCTAGTTTCCTACTGTACCAGATAC 59.679 42.308 0.00 0.00 37.73 2.24
2867 3087 7.147949 GCTAGTTTCCTACTGTACCAGATACAA 60.148 40.741 0.00 0.00 43.35 2.41
2868 3088 7.549147 AGTTTCCTACTGTACCAGATACAAA 57.451 36.000 0.00 0.00 43.35 2.83
2869 3089 7.612677 AGTTTCCTACTGTACCAGATACAAAG 58.387 38.462 0.00 0.00 43.35 2.77
2870 3090 7.234988 AGTTTCCTACTGTACCAGATACAAAGT 59.765 37.037 0.00 0.00 43.35 2.66
2871 3091 7.549147 TTCCTACTGTACCAGATACAAAGTT 57.451 36.000 0.00 0.00 43.35 2.66
2872 3092 8.654485 TTCCTACTGTACCAGATACAAAGTTA 57.346 34.615 0.00 0.00 43.35 2.24
2873 3093 8.654485 TCCTACTGTACCAGATACAAAGTTAA 57.346 34.615 0.00 0.00 43.35 2.01
2874 3094 8.746530 TCCTACTGTACCAGATACAAAGTTAAG 58.253 37.037 0.00 0.00 43.35 1.85
2875 3095 8.529476 CCTACTGTACCAGATACAAAGTTAAGT 58.471 37.037 0.00 0.00 43.35 2.24
2878 3098 9.871238 ACTGTACCAGATACAAAGTTAAGTATG 57.129 33.333 5.82 0.00 43.35 2.39
2909 3137 0.536460 TCCAAGGCACCGAAAACCTC 60.536 55.000 0.00 0.00 31.86 3.85
2913 3141 0.693049 AGGCACCGAAAACCTCTGAT 59.307 50.000 0.00 0.00 0.00 2.90
2933 3161 4.019501 TGATTTTGGGATGAATTTGGGGTG 60.020 41.667 0.00 0.00 0.00 4.61
2992 3223 3.829886 TCTGAATTTGACCGACAATGC 57.170 42.857 0.00 0.00 38.36 3.56
2996 3227 0.447801 ATTTGACCGACAATGCGAGC 59.552 50.000 0.00 0.00 38.36 5.03
2998 3229 1.014044 TTGACCGACAATGCGAGCTC 61.014 55.000 2.73 2.73 33.18 4.09
3053 3287 2.642700 CACTCAAAAACCCCGCGG 59.357 61.111 21.04 21.04 0.00 6.46
3055 3289 2.983592 CTCAAAAACCCCGCGGCT 60.984 61.111 22.85 3.02 0.00 5.52
3068 3302 3.132139 CGGCTCCTTCCGTCGAGA 61.132 66.667 0.00 0.00 44.18 4.04
3069 3303 2.697761 CGGCTCCTTCCGTCGAGAA 61.698 63.158 0.00 0.00 44.18 2.87
3070 3304 1.590147 GGCTCCTTCCGTCGAGAAA 59.410 57.895 0.00 0.00 0.00 2.52
3071 3305 0.037605 GGCTCCTTCCGTCGAGAAAA 60.038 55.000 0.00 0.00 0.00 2.29
3072 3306 1.351153 GCTCCTTCCGTCGAGAAAAG 58.649 55.000 0.00 0.00 0.00 2.27
3073 3307 1.067776 GCTCCTTCCGTCGAGAAAAGA 60.068 52.381 0.00 0.00 0.00 2.52
3074 3308 2.597520 CTCCTTCCGTCGAGAAAAGAC 58.402 52.381 0.00 0.00 35.41 3.01
3082 3316 0.039798 TCGAGAAAAGACGGACACGG 60.040 55.000 0.00 0.00 46.48 4.94
3114 3348 1.336755 ACGCACACACAAAAATCCCTC 59.663 47.619 0.00 0.00 0.00 4.30
3117 3351 1.269448 CACACACAAAAATCCCTCCCG 59.731 52.381 0.00 0.00 0.00 5.14
3119 3353 1.269448 CACACAAAAATCCCTCCCGTG 59.731 52.381 0.00 0.00 0.00 4.94
3505 3751 1.344763 AGGTGAGGTGACCTTCTTTCG 59.655 52.381 5.21 0.00 44.53 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 17 5.538813 GGCATCGGGGACTGTATATATATCA 59.461 44.000 0.00 0.00 35.30 2.15
15 18 5.047235 GGGCATCGGGGACTGTATATATATC 60.047 48.000 0.00 0.00 35.30 1.63
17 20 4.220724 GGGCATCGGGGACTGTATATATA 58.779 47.826 0.00 0.00 35.30 0.86
18 21 3.039011 GGGCATCGGGGACTGTATATAT 58.961 50.000 0.00 0.00 35.30 0.86
19 22 2.463752 GGGCATCGGGGACTGTATATA 58.536 52.381 0.00 0.00 35.30 0.86
56 59 4.546674 AGGAAAAGAGAAGGCCTGAAAAA 58.453 39.130 5.69 0.00 0.00 1.94
58 61 3.884037 AGGAAAAGAGAAGGCCTGAAA 57.116 42.857 5.69 0.00 0.00 2.69
61 64 2.029560 GCAAAGGAAAAGAGAAGGCCTG 60.030 50.000 5.69 0.00 0.00 4.85
62 65 2.158400 AGCAAAGGAAAAGAGAAGGCCT 60.158 45.455 0.00 0.00 0.00 5.19
63 66 2.242926 AGCAAAGGAAAAGAGAAGGCC 58.757 47.619 0.00 0.00 0.00 5.19
64 67 6.951062 ATATAGCAAAGGAAAAGAGAAGGC 57.049 37.500 0.00 0.00 0.00 4.35
177 183 1.279496 ACAGGGAAGCAGATACAGCA 58.721 50.000 0.00 0.00 0.00 4.41
224 233 2.279582 ATACTCACGCTTGGAAGTCG 57.720 50.000 0.00 0.00 0.00 4.18
227 236 4.755411 TCCTTAATACTCACGCTTGGAAG 58.245 43.478 0.00 0.00 0.00 3.46
244 253 5.163301 CCAGGCTGCTAGTAGAAAATCCTTA 60.163 44.000 12.54 0.00 0.00 2.69
296 306 9.657419 AATTTAGCCAATTCAGATTCGATTTTT 57.343 25.926 0.00 0.00 27.71 1.94
297 307 9.657419 AAATTTAGCCAATTCAGATTCGATTTT 57.343 25.926 0.00 0.00 33.60 1.82
298 308 9.657419 AAAATTTAGCCAATTCAGATTCGATTT 57.343 25.926 0.00 0.00 33.60 2.17
299 309 9.657419 AAAAATTTAGCCAATTCAGATTCGATT 57.343 25.926 0.00 0.00 33.60 3.34
300 310 9.090692 CAAAAATTTAGCCAATTCAGATTCGAT 57.909 29.630 0.00 0.00 33.60 3.59
301 311 8.087750 ACAAAAATTTAGCCAATTCAGATTCGA 58.912 29.630 0.00 0.00 33.60 3.71
302 312 8.243289 ACAAAAATTTAGCCAATTCAGATTCG 57.757 30.769 0.00 0.00 33.60 3.34
312 322 9.474920 CACATCTCTAAACAAAAATTTAGCCAA 57.525 29.630 0.00 0.00 40.52 4.52
313 323 8.087750 CCACATCTCTAAACAAAAATTTAGCCA 58.912 33.333 0.00 0.00 40.52 4.75
314 324 8.088365 ACCACATCTCTAAACAAAAATTTAGCC 58.912 33.333 0.00 0.00 40.52 3.93
315 325 8.915654 CACCACATCTCTAAACAAAAATTTAGC 58.084 33.333 0.00 0.00 40.52 3.09
316 326 9.965824 ACACCACATCTCTAAACAAAAATTTAG 57.034 29.630 0.00 0.00 41.59 1.85
317 327 9.743057 CACACCACATCTCTAAACAAAAATTTA 57.257 29.630 0.00 0.00 0.00 1.40
318 328 7.224557 GCACACCACATCTCTAAACAAAAATTT 59.775 33.333 0.00 0.00 0.00 1.82
321 331 5.359576 AGCACACCACATCTCTAAACAAAAA 59.640 36.000 0.00 0.00 0.00 1.94
387 399 8.466798 GCCCTAAAAATGTAGAGCTTTCAAATA 58.533 33.333 0.00 0.00 0.00 1.40
388 400 7.179160 AGCCCTAAAAATGTAGAGCTTTCAAAT 59.821 33.333 0.00 0.00 31.69 2.32
389 401 6.493458 AGCCCTAAAAATGTAGAGCTTTCAAA 59.507 34.615 0.00 0.00 31.69 2.69
390 402 6.010219 AGCCCTAAAAATGTAGAGCTTTCAA 58.990 36.000 0.00 0.00 31.69 2.69
391 403 5.570320 AGCCCTAAAAATGTAGAGCTTTCA 58.430 37.500 0.00 0.00 31.69 2.69
392 404 6.516739 AAGCCCTAAAAATGTAGAGCTTTC 57.483 37.500 0.00 0.00 40.96 2.62
393 405 6.918067 AAAGCCCTAAAAATGTAGAGCTTT 57.082 33.333 6.35 6.35 45.17 3.51
394 406 6.918067 AAAAGCCCTAAAAATGTAGAGCTT 57.082 33.333 0.00 0.00 44.34 3.74
395 407 6.918067 AAAAAGCCCTAAAAATGTAGAGCT 57.082 33.333 0.00 0.00 36.80 4.09
437 451 7.967908 AGAGACTACATGTCCCTTAATTATGG 58.032 38.462 0.00 9.90 46.46 2.74
445 459 6.497259 TCAAGTTTAGAGACTACATGTCCCTT 59.503 38.462 0.00 0.00 46.46 3.95
451 465 6.870965 ACAAGCTCAAGTTTAGAGACTACATG 59.129 38.462 0.00 0.00 35.09 3.21
455 469 6.650427 TCACAAGCTCAAGTTTAGAGACTA 57.350 37.500 0.00 0.00 35.09 2.59
459 473 5.525378 ACTGTTCACAAGCTCAAGTTTAGAG 59.475 40.000 0.00 0.00 36.21 2.43
578 619 2.307934 TTGTTTTTGTTGCCCAGAGC 57.692 45.000 0.00 0.00 44.14 4.09
579 620 5.353678 TCAAATTTGTTTTTGTTGCCCAGAG 59.646 36.000 17.47 0.00 37.73 3.35
581 622 5.557891 TCAAATTTGTTTTTGTTGCCCAG 57.442 34.783 17.47 0.00 37.73 4.45
582 623 5.678107 GCATCAAATTTGTTTTTGTTGCCCA 60.678 36.000 17.47 0.00 46.61 5.36
584 625 5.869853 GCATCAAATTTGTTTTTGTTGCC 57.130 34.783 17.47 5.05 46.61 4.52
586 627 6.783162 TGGAGCATCAAATTTGTTTTTGTTG 58.217 32.000 17.47 6.86 38.46 3.33
587 628 6.998968 TGGAGCATCAAATTTGTTTTTGTT 57.001 29.167 17.47 9.41 37.73 2.83
588 629 6.998968 TTGGAGCATCAAATTTGTTTTTGT 57.001 29.167 17.47 0.00 37.73 2.83
589 630 7.432838 CCTTTTGGAGCATCAAATTTGTTTTTG 59.567 33.333 17.47 11.87 44.07 2.44
642 697 8.812513 ATGAAATCACATTTGGATGTCTAGAA 57.187 30.769 0.00 0.00 44.55 2.10
643 698 8.442632 GATGAAATCACATTTGGATGTCTAGA 57.557 34.615 0.00 0.00 44.55 2.43
686 743 7.255569 ACAGAAGTTACTTAGTTTTGTTTGCC 58.744 34.615 0.00 0.00 32.25 4.52
760 818 6.671190 TCAAATGCTTGTTCTATGAACACTG 58.329 36.000 11.99 9.49 33.94 3.66
772 830 1.896220 TCCGAGCTCAAATGCTTGTT 58.104 45.000 15.40 0.00 44.17 2.83
774 832 3.498927 AATTCCGAGCTCAAATGCTTG 57.501 42.857 15.40 0.00 44.17 4.01
796 854 9.736023 ATCGGCTAAATTATGAAAATGTTCTTC 57.264 29.630 0.00 0.00 34.60 2.87
832 890 2.930040 TCGGCTCGATTTTGATTGTCTC 59.070 45.455 0.00 0.00 0.00 3.36
833 891 2.932614 CTCGGCTCGATTTTGATTGTCT 59.067 45.455 0.00 0.00 34.61 3.41
836 894 2.223112 CCACTCGGCTCGATTTTGATTG 60.223 50.000 0.00 0.00 34.61 2.67
838 896 1.207089 TCCACTCGGCTCGATTTTGAT 59.793 47.619 0.00 0.00 34.61 2.57
842 949 1.270625 TGTTTCCACTCGGCTCGATTT 60.271 47.619 0.00 0.00 34.61 2.17
846 953 3.550656 GTGTTTCCACTCGGCTCG 58.449 61.111 0.00 0.00 38.61 5.03
855 962 7.335924 GTGTAGGCTCAATAATAAGTGTTTCCA 59.664 37.037 0.00 0.00 0.00 3.53
856 963 7.553044 AGTGTAGGCTCAATAATAAGTGTTTCC 59.447 37.037 0.00 0.00 0.00 3.13
862 969 7.268586 CACTCAGTGTAGGCTCAATAATAAGT 58.731 38.462 0.00 0.00 0.00 2.24
865 972 5.453339 GCCACTCAGTGTAGGCTCAATAATA 60.453 44.000 3.56 0.00 38.73 0.98
867 974 3.369471 GCCACTCAGTGTAGGCTCAATAA 60.369 47.826 3.56 0.00 38.73 1.40
869 976 1.065854 GCCACTCAGTGTAGGCTCAAT 60.066 52.381 3.56 0.00 38.73 2.57
870 977 0.321671 GCCACTCAGTGTAGGCTCAA 59.678 55.000 3.56 0.00 38.73 3.02
871 978 0.542938 AGCCACTCAGTGTAGGCTCA 60.543 55.000 16.38 0.00 44.17 4.26
872 979 0.610687 AAGCCACTCAGTGTAGGCTC 59.389 55.000 20.39 0.00 45.56 4.70
873 980 4.549155 AGCCACTCAGTGTAGGCT 57.451 55.556 16.38 16.38 43.37 4.58
874 981 1.897560 AAAAGCCACTCAGTGTAGGC 58.102 50.000 3.56 13.05 40.61 3.93
875 982 3.214328 ACAAAAAGCCACTCAGTGTAGG 58.786 45.455 3.56 0.00 0.00 3.18
876 983 4.452455 CCTACAAAAAGCCACTCAGTGTAG 59.548 45.833 3.56 0.00 37.68 2.74
877 984 4.385825 CCTACAAAAAGCCACTCAGTGTA 58.614 43.478 3.56 0.00 0.00 2.90
878 985 3.214328 CCTACAAAAAGCCACTCAGTGT 58.786 45.455 3.56 0.00 0.00 3.55
880 987 2.158608 AGCCTACAAAAAGCCACTCAGT 60.159 45.455 0.00 0.00 0.00 3.41
883 990 2.504367 TGAGCCTACAAAAAGCCACTC 58.496 47.619 0.00 0.00 0.00 3.51
884 991 2.656947 TGAGCCTACAAAAAGCCACT 57.343 45.000 0.00 0.00 0.00 4.00
885 992 3.942130 ATTGAGCCTACAAAAAGCCAC 57.058 42.857 0.00 0.00 33.44 5.01
886 993 4.830046 TGTAATTGAGCCTACAAAAAGCCA 59.170 37.500 0.00 0.00 33.44 4.75
887 994 5.385509 TGTAATTGAGCCTACAAAAAGCC 57.614 39.130 0.00 0.00 33.44 4.35
888 995 7.201350 CGAATTGTAATTGAGCCTACAAAAAGC 60.201 37.037 0.00 0.00 40.42 3.51
889 996 7.273381 CCGAATTGTAATTGAGCCTACAAAAAG 59.727 37.037 0.00 0.00 40.42 2.27
944 1051 2.244117 GAGGCTGCTCCGATGTTGGA 62.244 60.000 0.00 0.00 40.77 3.53
949 1056 2.108566 CTGGAGGCTGCTCCGATG 59.891 66.667 7.74 0.00 46.18 3.84
950 1057 3.859414 GCTGGAGGCTGCTCCGAT 61.859 66.667 7.74 0.00 46.18 4.18
1000 1123 0.035056 CCACCGGAATCTTCTGCCTT 60.035 55.000 9.46 0.00 32.15 4.35
1001 1124 1.604378 CCACCGGAATCTTCTGCCT 59.396 57.895 9.46 0.00 32.15 4.75
1003 1126 0.035439 TTCCCACCGGAATCTTCTGC 60.035 55.000 9.46 0.00 43.57 4.26
1015 1138 2.719354 GTGCGTGTGTTTCCCACC 59.281 61.111 0.00 0.00 43.85 4.61
1016 1139 1.782028 GAGGTGCGTGTGTTTCCCAC 61.782 60.000 0.00 0.00 44.78 4.61
1017 1140 1.525077 GAGGTGCGTGTGTTTCCCA 60.525 57.895 0.00 0.00 0.00 4.37
1018 1141 2.258726 GGAGGTGCGTGTGTTTCCC 61.259 63.158 0.00 0.00 0.00 3.97
1019 1142 1.227853 AGGAGGTGCGTGTGTTTCC 60.228 57.895 0.00 0.00 0.00 3.13
1020 1143 1.557443 CGAGGAGGTGCGTGTGTTTC 61.557 60.000 0.00 0.00 0.00 2.78
1021 1144 1.594293 CGAGGAGGTGCGTGTGTTT 60.594 57.895 0.00 0.00 0.00 2.83
1022 1145 2.029073 CGAGGAGGTGCGTGTGTT 59.971 61.111 0.00 0.00 0.00 3.32
1185 1316 0.475048 ACGAAAGGGAAGGGGAGGAA 60.475 55.000 0.00 0.00 0.00 3.36
1186 1317 1.160145 ACGAAAGGGAAGGGGAGGA 59.840 57.895 0.00 0.00 0.00 3.71
1187 1318 1.299976 CACGAAAGGGAAGGGGAGG 59.700 63.158 0.00 0.00 35.60 4.30
1190 1321 1.971695 GTGCACGAAAGGGAAGGGG 60.972 63.158 0.00 0.00 35.60 4.79
1235 1369 2.794350 GAGACCTAGTAGCGTACTCGAC 59.206 54.545 1.69 0.00 40.14 4.20
1238 1372 2.134346 CCGAGACCTAGTAGCGTACTC 58.866 57.143 1.69 0.00 40.14 2.59
1242 1376 1.077930 TGCCGAGACCTAGTAGCGT 60.078 57.895 0.00 0.00 0.00 5.07
1247 1381 1.533469 GGTGTGTGCCGAGACCTAGT 61.533 60.000 0.00 0.00 0.00 2.57
1264 1398 2.203015 ACAGACAACGCAAGCGGT 60.203 55.556 19.30 9.73 44.69 5.68
1286 1420 7.095060 GGCATATCAATGGAACTACACATACAG 60.095 40.741 0.00 0.00 33.38 2.74
1290 1424 5.072741 GGGCATATCAATGGAACTACACAT 58.927 41.667 0.00 0.00 33.38 3.21
1291 1425 4.460263 GGGCATATCAATGGAACTACACA 58.540 43.478 0.00 0.00 33.38 3.72
1292 1426 3.498397 CGGGCATATCAATGGAACTACAC 59.502 47.826 0.00 0.00 33.38 2.90
1303 1437 0.250858 CAGCATCCCGGGCATATCAA 60.251 55.000 18.49 0.00 0.00 2.57
1334 1469 0.882042 CCACACAGACACCAGCTCAC 60.882 60.000 0.00 0.00 0.00 3.51
1335 1470 1.447217 CCACACAGACACCAGCTCA 59.553 57.895 0.00 0.00 0.00 4.26
1350 1485 1.832167 TTCCCAAGCAAGCACCCAC 60.832 57.895 0.00 0.00 0.00 4.61
1352 1487 2.574018 GGTTCCCAAGCAAGCACCC 61.574 63.158 0.00 0.00 0.00 4.61
1353 1488 1.187567 ATGGTTCCCAAGCAAGCACC 61.188 55.000 0.00 0.00 42.83 5.01
1356 1491 0.968405 TTCATGGTTCCCAAGCAAGC 59.032 50.000 0.00 0.00 42.83 4.01
1357 1492 2.564062 ACATTCATGGTTCCCAAGCAAG 59.436 45.455 0.00 0.00 42.83 4.01
1358 1493 2.562298 GACATTCATGGTTCCCAAGCAA 59.438 45.455 0.00 0.00 42.83 3.91
1360 1495 1.478105 GGACATTCATGGTTCCCAAGC 59.522 52.381 0.00 0.00 36.95 4.01
1361 1496 3.091633 AGGACATTCATGGTTCCCAAG 57.908 47.619 0.00 0.00 36.95 3.61
1362 1497 3.624707 GCTAGGACATTCATGGTTCCCAA 60.625 47.826 0.00 0.00 36.95 4.12
1393 1544 9.979578 TGCAAAGAAAAATTGTACATTATCAGT 57.020 25.926 0.00 0.00 0.00 3.41
1501 1655 9.770097 CCTACACACATCTACATATCAAAGAAT 57.230 33.333 0.00 0.00 0.00 2.40
1508 1662 7.142021 CAGTCACCTACACACATCTACATATC 58.858 42.308 0.00 0.00 0.00 1.63
1566 1721 0.250295 CGCCCTTCTGTCAAGTTCCA 60.250 55.000 0.00 0.00 0.00 3.53
1728 1886 5.300792 GTCCTTGGTGACCTTGTTATCAAAA 59.699 40.000 2.11 0.00 32.87 2.44
1731 1889 4.015872 GTCCTTGGTGACCTTGTTATCA 57.984 45.455 2.11 0.00 0.00 2.15
1782 1940 3.650942 TCATGTACTTGGTGACCTCCTTT 59.349 43.478 2.11 0.00 0.00 3.11
1823 1981 3.719268 TTAGCAAAGGGATGAGAGCAA 57.281 42.857 0.00 0.00 0.00 3.91
1824 1982 3.939740 ATTAGCAAAGGGATGAGAGCA 57.060 42.857 0.00 0.00 0.00 4.26
1830 1988 7.009179 TCATACTCCTATTAGCAAAGGGATG 57.991 40.000 0.00 0.00 33.40 3.51
1832 1990 7.633018 AATCATACTCCTATTAGCAAAGGGA 57.367 36.000 0.00 0.00 33.40 4.20
1844 2002 9.964354 CATGGAATGGAATAAATCATACTCCTA 57.036 33.333 0.00 0.00 41.79 2.94
1915 2083 6.096001 GTCGGAAGAACTAAACAGGTCCTATA 59.904 42.308 0.00 0.00 45.01 1.31
1916 2084 5.021458 TCGGAAGAACTAAACAGGTCCTAT 58.979 41.667 0.00 0.00 37.03 2.57
1938 2114 9.511022 GTGAAATGCGTGTTTTAAATAAATGTC 57.489 29.630 0.00 0.00 0.00 3.06
1945 2121 8.810652 ATAACAGTGAAATGCGTGTTTTAAAT 57.189 26.923 0.00 0.00 34.92 1.40
1984 2161 9.515226 TGAAGATGCTACTTTTATACCTTTTGT 57.485 29.630 0.00 0.00 0.00 2.83
2036 2213 9.253832 ACAACATGGGATAAATTCTAAACATGA 57.746 29.630 15.08 0.00 38.19 3.07
2125 2302 7.768120 AGAATCATGGAGAGAACTAAACATGTC 59.232 37.037 0.00 0.00 35.88 3.06
2147 2324 7.115378 GCAATGTTCAGTTCATTTTCGAAGAAT 59.885 33.333 0.00 0.00 36.05 2.40
2154 2331 3.996363 GGGGCAATGTTCAGTTCATTTTC 59.004 43.478 0.00 0.00 33.92 2.29
2212 2429 3.831911 GGATCTCCTTCATCCTCTCGATT 59.168 47.826 0.00 0.00 37.44 3.34
2215 2432 1.539388 CGGATCTCCTTCATCCTCTCG 59.461 57.143 0.00 0.00 38.18 4.04
2308 2525 0.476611 AAGCCCTCTTCCCCTTGAGT 60.477 55.000 0.00 0.00 0.00 3.41
2411 2628 1.380524 AGTAGCGTCGTGATGTAGCT 58.619 50.000 0.00 0.00 41.45 3.32
2430 2647 4.364817 CCGGAGCAACAAACGGTA 57.635 55.556 0.00 0.00 41.34 4.02
2434 2651 0.040067 CTTGAGCCGGAGCAACAAAC 60.040 55.000 5.05 0.00 43.56 2.93
2437 2654 0.465460 AAACTTGAGCCGGAGCAACA 60.465 50.000 5.05 0.00 43.56 3.33
2439 2656 0.889186 GGAAACTTGAGCCGGAGCAA 60.889 55.000 5.05 7.52 43.56 3.91
2441 2658 0.678048 ATGGAAACTTGAGCCGGAGC 60.678 55.000 5.05 0.00 40.32 4.70
2447 2664 0.169009 GACGGCATGGAAACTTGAGC 59.831 55.000 0.00 0.00 37.69 4.26
2448 2665 0.443869 CGACGGCATGGAAACTTGAG 59.556 55.000 0.00 0.00 37.69 3.02
2478 2695 3.985127 TCCGACCATATCCCCGTAATAT 58.015 45.455 0.00 0.00 0.00 1.28
2480 2697 2.314071 TCCGACCATATCCCCGTAAT 57.686 50.000 0.00 0.00 0.00 1.89
2481 2698 1.897133 CATCCGACCATATCCCCGTAA 59.103 52.381 0.00 0.00 0.00 3.18
2482 2699 1.552578 CATCCGACCATATCCCCGTA 58.447 55.000 0.00 0.00 0.00 4.02
2483 2700 1.827399 GCATCCGACCATATCCCCGT 61.827 60.000 0.00 0.00 0.00 5.28
2484 2701 1.079127 GCATCCGACCATATCCCCG 60.079 63.158 0.00 0.00 0.00 5.73
2510 2727 9.677567 GAGAAGAGATGTCATGACTATAAACTC 57.322 37.037 25.55 17.42 0.00 3.01
2568 2785 8.582657 TGATGATTTACCCTTTATCGGAAAAA 57.417 30.769 0.00 0.00 0.00 1.94
2569 2786 8.582657 TTGATGATTTACCCTTTATCGGAAAA 57.417 30.769 0.00 0.00 0.00 2.29
2570 2787 7.284489 CCTTGATGATTTACCCTTTATCGGAAA 59.716 37.037 0.00 0.00 0.00 3.13
2571 2788 6.770785 CCTTGATGATTTACCCTTTATCGGAA 59.229 38.462 0.00 0.00 0.00 4.30
2572 2789 6.126594 ACCTTGATGATTTACCCTTTATCGGA 60.127 38.462 0.00 0.00 0.00 4.55
2573 2790 6.062095 ACCTTGATGATTTACCCTTTATCGG 58.938 40.000 0.00 0.00 0.00 4.18
2574 2791 7.568199 AACCTTGATGATTTACCCTTTATCG 57.432 36.000 0.00 0.00 0.00 2.92
2575 2792 9.403583 TGTAACCTTGATGATTTACCCTTTATC 57.596 33.333 0.00 0.00 0.00 1.75
2576 2793 9.936329 ATGTAACCTTGATGATTTACCCTTTAT 57.064 29.630 0.00 0.00 0.00 1.40
2577 2794 9.184523 CATGTAACCTTGATGATTTACCCTTTA 57.815 33.333 0.00 0.00 0.00 1.85
2578 2795 7.363793 GCATGTAACCTTGATGATTTACCCTTT 60.364 37.037 0.00 0.00 0.00 3.11
2579 2796 6.096846 GCATGTAACCTTGATGATTTACCCTT 59.903 38.462 0.00 0.00 0.00 3.95
2580 2797 5.594317 GCATGTAACCTTGATGATTTACCCT 59.406 40.000 0.00 0.00 0.00 4.34
2581 2798 5.505654 CGCATGTAACCTTGATGATTTACCC 60.506 44.000 0.00 0.00 0.00 3.69
2582 2799 5.510671 CGCATGTAACCTTGATGATTTACC 58.489 41.667 0.00 0.00 0.00 2.85
2583 2800 4.970003 GCGCATGTAACCTTGATGATTTAC 59.030 41.667 0.30 0.00 0.00 2.01
2594 2811 0.947180 ACGAAACGCGCATGTAACCT 60.947 50.000 5.73 0.00 46.04 3.50
2614 2831 4.998671 TCAGAAAACATTTGTGCTTGGA 57.001 36.364 0.00 0.00 0.00 3.53
2691 2908 2.610727 GCTAATCCAGTCATCGGTAGCC 60.611 54.545 0.00 0.00 0.00 3.93
2697 2914 4.979197 GTGTCTAAGCTAATCCAGTCATCG 59.021 45.833 0.00 0.00 0.00 3.84
2707 2924 4.041691 ACAACCACTGGTGTCTAAGCTAAT 59.958 41.667 0.00 0.00 35.34 1.73
2716 2933 5.278315 GGAAAATTCTACAACCACTGGTGTC 60.278 44.000 0.00 0.00 35.34 3.67
2717 2934 4.583073 GGAAAATTCTACAACCACTGGTGT 59.417 41.667 0.00 5.14 35.34 4.16
2718 2935 4.320202 CGGAAAATTCTACAACCACTGGTG 60.320 45.833 0.00 0.00 35.34 4.17
2719 2936 3.818773 CGGAAAATTCTACAACCACTGGT 59.181 43.478 0.00 0.00 37.65 4.00
2720 2937 4.069304 TCGGAAAATTCTACAACCACTGG 58.931 43.478 0.00 0.00 0.00 4.00
2723 2940 4.857037 GCAATCGGAAAATTCTACAACCAC 59.143 41.667 0.00 0.00 0.00 4.16
2724 2941 4.082463 GGCAATCGGAAAATTCTACAACCA 60.082 41.667 0.00 0.00 0.00 3.67
2728 2945 5.649557 CAATGGCAATCGGAAAATTCTACA 58.350 37.500 0.00 0.00 0.00 2.74
2729 2946 4.504097 GCAATGGCAATCGGAAAATTCTAC 59.496 41.667 0.00 0.00 40.72 2.59
2731 2948 3.524541 GCAATGGCAATCGGAAAATTCT 58.475 40.909 0.00 0.00 40.72 2.40
2732 2949 3.931285 GCAATGGCAATCGGAAAATTC 57.069 42.857 0.00 0.00 40.72 2.17
2762 2982 3.188492 TGCAAACAAAATGACTGCACAG 58.812 40.909 0.00 0.00 35.05 3.66
2808 3028 4.522789 TGACAGTGTCACATTACTGAGCTA 59.477 41.667 22.06 0.00 45.46 3.32
2814 3034 4.689612 AACCTGACAGTGTCACATTACT 57.310 40.909 22.06 1.26 37.67 2.24
2823 3043 2.936202 AGCAATCAAACCTGACAGTGT 58.064 42.857 0.00 0.00 33.30 3.55
2824 3044 4.067896 ACTAGCAATCAAACCTGACAGTG 58.932 43.478 0.93 0.00 33.30 3.66
2854 3074 9.865321 GACATACTTAACTTTGTATCTGGTACA 57.135 33.333 0.00 0.00 41.46 2.90
2855 3075 9.865321 TGACATACTTAACTTTGTATCTGGTAC 57.135 33.333 0.00 0.00 0.00 3.34
2858 3078 8.338259 GCATGACATACTTAACTTTGTATCTGG 58.662 37.037 0.00 0.00 0.00 3.86
2859 3079 8.882736 TGCATGACATACTTAACTTTGTATCTG 58.117 33.333 0.00 0.00 0.00 2.90
2860 3080 9.448438 TTGCATGACATACTTAACTTTGTATCT 57.552 29.630 0.00 0.00 0.00 1.98
2867 3087 8.584157 TGGATTTTTGCATGACATACTTAACTT 58.416 29.630 0.00 0.00 0.00 2.66
2868 3088 8.121305 TGGATTTTTGCATGACATACTTAACT 57.879 30.769 0.00 0.00 0.00 2.24
2869 3089 8.755696 TTGGATTTTTGCATGACATACTTAAC 57.244 30.769 0.00 0.00 0.00 2.01
2870 3090 8.034215 CCTTGGATTTTTGCATGACATACTTAA 58.966 33.333 0.00 0.00 0.00 1.85
2871 3091 7.546358 CCTTGGATTTTTGCATGACATACTTA 58.454 34.615 0.00 0.00 0.00 2.24
2872 3092 6.400568 CCTTGGATTTTTGCATGACATACTT 58.599 36.000 0.00 0.00 0.00 2.24
2873 3093 5.625197 GCCTTGGATTTTTGCATGACATACT 60.625 40.000 0.00 0.00 0.00 2.12
2874 3094 4.567959 GCCTTGGATTTTTGCATGACATAC 59.432 41.667 0.00 0.00 0.00 2.39
2875 3095 4.222366 TGCCTTGGATTTTTGCATGACATA 59.778 37.500 0.00 0.00 0.00 2.29
2876 3096 3.008157 TGCCTTGGATTTTTGCATGACAT 59.992 39.130 0.00 0.00 0.00 3.06
2877 3097 2.367894 TGCCTTGGATTTTTGCATGACA 59.632 40.909 0.00 0.00 0.00 3.58
2878 3098 2.738314 GTGCCTTGGATTTTTGCATGAC 59.262 45.455 0.00 0.00 34.04 3.06
2909 3137 4.225717 ACCCCAAATTCATCCCAAAATCAG 59.774 41.667 0.00 0.00 0.00 2.90
2913 3141 3.321950 ACACCCCAAATTCATCCCAAAA 58.678 40.909 0.00 0.00 0.00 2.44
2933 3161 7.360361 ACTTTGCACAAAATTACTACTGCTAC 58.640 34.615 0.00 0.00 0.00 3.58
3012 3246 3.083848 TATAGCGCGTGGGGTGGTG 62.084 63.158 8.43 0.00 37.45 4.17
3013 3247 2.760799 TATAGCGCGTGGGGTGGT 60.761 61.111 8.43 0.00 40.53 4.16
3053 3287 1.067776 TCTTTTCTCGACGGAAGGAGC 60.068 52.381 0.00 0.00 0.00 4.70
3055 3289 2.719426 GTCTTTTCTCGACGGAAGGA 57.281 50.000 0.00 0.00 0.00 3.36
3062 3296 1.050767 CGTGTCCGTCTTTTCTCGAC 58.949 55.000 0.00 0.00 0.00 4.20
3063 3297 0.039798 CCGTGTCCGTCTTTTCTCGA 60.040 55.000 0.00 0.00 0.00 4.04
3065 3299 0.319641 AGCCGTGTCCGTCTTTTCTC 60.320 55.000 0.00 0.00 0.00 2.87
3066 3300 0.600255 CAGCCGTGTCCGTCTTTTCT 60.600 55.000 0.00 0.00 0.00 2.52
3067 3301 1.860078 CAGCCGTGTCCGTCTTTTC 59.140 57.895 0.00 0.00 0.00 2.29
3068 3302 2.251642 GCAGCCGTGTCCGTCTTTT 61.252 57.895 0.00 0.00 0.00 2.27
3069 3303 2.665185 GCAGCCGTGTCCGTCTTT 60.665 61.111 0.00 0.00 0.00 2.52
3098 3332 1.133606 ACGGGAGGGATTTTTGTGTGT 60.134 47.619 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.