Multiple sequence alignment - TraesCS3D01G314000

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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 TraesCS3D01G314000 chr3D 100.000 3339 0 0 1869 5207 427818713 427815375 0.000000e+00 6167.0
1 TraesCS3D01G314000 chr3D 100.000 1586 0 0 1 1586 427820581 427818996 0.000000e+00 2929.0
2 TraesCS3D01G314000 chr3D 84.499 529 70 12 3 523 395834575 395834051 3.600000e-141 512.0
3 TraesCS3D01G314000 chr3A 96.009 3007 76 10 1995 4988 557948066 557951041 0.000000e+00 4848.0
4 TraesCS3D01G314000 chr3A 90.383 1175 64 24 97 1257 557946611 557947750 0.000000e+00 1498.0
5 TraesCS3D01G314000 chr3A 94.660 206 7 2 5006 5207 557951100 557951305 3.030000e-82 316.0
6 TraesCS3D01G314000 chr3A 91.743 109 8 1 1394 1501 557947862 557947970 3.250000e-32 150.0
7 TraesCS3D01G314000 chr3B 93.987 3193 119 33 1994 5158 559342997 559339850 0.000000e+00 4765.0
8 TraesCS3D01G314000 chr3B 87.393 936 75 17 578 1502 559344047 559343144 0.000000e+00 1035.0
9 TraesCS3D01G314000 chr3B 91.231 536 44 2 14 546 559344585 559344050 0.000000e+00 726.0
10 TraesCS3D01G314000 chr3B 100.000 66 0 0 1924 1989 559343153 559343088 7.080000e-24 122.0
11 TraesCS3D01G314000 chr6D 85.057 522 67 10 4 520 304689035 304688520 5.980000e-144 521.0
12 TraesCS3D01G314000 chr6D 84.837 521 70 7 3 519 464465484 464465999 2.780000e-142 516.0
13 TraesCS3D01G314000 chr2A 84.733 524 72 8 1 519 55952817 55953337 7.730000e-143 518.0
14 TraesCS3D01G314000 chr2A 89.450 218 21 2 3691 3907 746852175 746851959 1.850000e-69 274.0
15 TraesCS3D01G314000 chr6B 84.704 523 72 6 1 519 51009532 51010050 2.780000e-142 516.0
16 TraesCS3D01G314000 chr6B 88.489 139 16 0 3706 3844 107771869 107771731 8.970000e-38 169.0
17 TraesCS3D01G314000 chr5D 84.733 524 71 7 3 522 129238992 129239510 2.780000e-142 516.0
18 TraesCS3D01G314000 chr5D 93.258 89 6 0 3755 3843 476462586 476462674 1.180000e-26 132.0
19 TraesCS3D01G314000 chr2B 84.674 522 73 7 3 519 105901859 105901340 1.000000e-141 514.0
20 TraesCS3D01G314000 chr2B 89.427 227 20 4 3684 3908 751842026 751841802 3.070000e-72 283.0
21 TraesCS3D01G314000 chr2D 89.908 218 18 3 3691 3904 616635075 616634858 1.430000e-70 278.0
22 TraesCS3D01G314000 chrUn 88.489 139 16 0 3706 3844 98211657 98211519 8.970000e-38 169.0
23 TraesCS3D01G314000 chr6A 88.489 139 16 0 3706 3844 53156881 53156743 8.970000e-38 169.0
24 TraesCS3D01G314000 chr6A 92.857 56 4 0 1869 1924 617656426 617656481 1.200000e-11 82.4
25 TraesCS3D01G314000 chr7D 100.000 85 0 0 1502 1586 565636728 565636812 1.940000e-34 158.0
26 TraesCS3D01G314000 chr7D 98.864 88 0 1 1500 1586 565622181 565622268 6.980000e-34 156.0
27 TraesCS3D01G314000 chr7D 98.824 85 1 0 1502 1586 565623981 565624065 9.030000e-33 152.0
28 TraesCS3D01G314000 chr7D 100.000 82 0 0 1502 1583 565638053 565638134 9.030000e-33 152.0
29 TraesCS3D01G314000 chr7D 97.647 85 2 0 1502 1586 565637868 565637952 4.200000e-31 147.0
30 TraesCS3D01G314000 chr7D 97.619 84 2 0 1503 1586 54923801 54923718 1.510000e-30 145.0
31 TraesCS3D01G314000 chr7D 95.402 87 2 1 1502 1586 565624168 565624254 2.530000e-28 137.0
32 TraesCS3D01G314000 chr7D 98.214 56 1 0 1869 1924 565623921 565623976 1.190000e-16 99.0
33 TraesCS3D01G314000 chr7D 98.214 56 1 0 1869 1924 565637993 565638048 1.190000e-16 99.0
34 TraesCS3D01G314000 chr7D 98.214 56 1 0 1869 1924 565639422 565639477 1.190000e-16 99.0
35 TraesCS3D01G314000 chr7D 98.148 54 1 0 1871 1924 565636855 565636908 1.540000e-15 95.3
36 TraesCS3D01G314000 chr7D 96.429 56 2 0 1869 1924 565622310 565622365 5.550000e-15 93.5
37 TraesCS3D01G314000 chr7D 96.429 56 2 0 1869 1924 565624108 565624163 5.550000e-15 93.5
38 TraesCS3D01G314000 chr1D 98.851 87 1 0 1500 1586 416093176 416093262 6.980000e-34 156.0
39 TraesCS3D01G314000 chr1D 95.000 60 2 1 1869 1927 416093304 416093363 5.550000e-15 93.5
40 TraesCS3D01G314000 chr7A 97.619 84 2 0 1503 1586 256015862 256015779 1.510000e-30 145.0
41 TraesCS3D01G314000 chr5A 96.296 54 1 1 1872 1925 593077428 593077376 2.580000e-13 87.9


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 TraesCS3D01G314000 chr3D 427815375 427820581 5206 True 4548 6167 100.00000 1 5207 2 chr3D.!!$R2 5206
1 TraesCS3D01G314000 chr3D 395834051 395834575 524 True 512 512 84.49900 3 523 1 chr3D.!!$R1 520
2 TraesCS3D01G314000 chr3A 557946611 557951305 4694 False 1703 4848 93.19875 97 5207 4 chr3A.!!$F1 5110
3 TraesCS3D01G314000 chr3B 559339850 559344585 4735 True 1662 4765 93.15275 14 5158 4 chr3B.!!$R1 5144
4 TraesCS3D01G314000 chr6D 304688520 304689035 515 True 521 521 85.05700 4 520 1 chr6D.!!$R1 516
5 TraesCS3D01G314000 chr6D 464465484 464465999 515 False 516 516 84.83700 3 519 1 chr6D.!!$F1 516
6 TraesCS3D01G314000 chr2A 55952817 55953337 520 False 518 518 84.73300 1 519 1 chr2A.!!$F1 518
7 TraesCS3D01G314000 chr6B 51009532 51010050 518 False 516 516 84.70400 1 519 1 chr6B.!!$F1 518
8 TraesCS3D01G314000 chr5D 129238992 129239510 518 False 516 516 84.73300 3 522 1 chr5D.!!$F1 519
9 TraesCS3D01G314000 chr2B 105901340 105901859 519 True 514 514 84.67400 3 519 1 chr2B.!!$R1 516

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
630 642 0.341961 ACAGGTAGGCCCCATGACTA 59.658 55.000 11.23 0.0 34.57 2.59 F
1488 1516 0.028505 CATGCGCTGAAGAAATCCCG 59.971 55.000 9.73 0.0 0.00 5.14 F
1523 1551 0.101759 GCGATGCTAGACCCACGTAA 59.898 55.000 0.00 0.0 0.00 3.18 F
1917 1945 0.169672 GCTCGTTCGTAGGTGTAGCA 59.830 55.000 0.00 0.0 0.00 3.49 F
2046 2176 0.636733 CGCATGCAAATTTGACGAGC 59.363 50.000 22.31 16.4 0.00 5.03 F
2125 2255 1.131504 GAGCTCGAGAGTGATGTCGTT 59.868 52.381 18.75 0.0 37.46 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1504 1532 0.101759 TTACGTGGGTCTAGCATCGC 59.898 55.000 0.00 0.0 0.00 4.58 R
3343 3478 4.176752 GTCCCCAGCCCGTCCATC 62.177 72.222 0.00 0.0 0.00 3.51 R
3617 3752 1.068541 GGAGCAAACCGAAATGTGTCC 60.069 52.381 0.00 0.0 0.00 4.02 R
3987 4126 2.283966 ACCACCTCCTCGTCCTGG 60.284 66.667 0.00 0.0 0.00 4.45 R
4191 4330 2.411904 CCTCTCTATTTGCCGCTCATC 58.588 52.381 0.00 0.0 0.00 2.92 R
4238 4379 0.537188 ATAACTCTGGCGTGAGGTGG 59.463 55.000 7.93 0.0 38.32 4.61 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
30 32 4.295051 TCCGCTTTTAGATGTGTTTTTGC 58.705 39.130 0.00 0.00 0.00 3.68
105 109 4.469945 TGAAGATGGAATAACGTTCTCCCT 59.530 41.667 20.88 14.17 0.00 4.20
271 276 3.881089 TCTACATTACTCTTCATCGGCGA 59.119 43.478 13.87 13.87 0.00 5.54
392 398 0.896479 TGACGGTGGGACATCTTCGA 60.896 55.000 0.00 0.00 40.91 3.71
424 430 1.681793 GCTTCTGGTCATCGCTAGGTA 59.318 52.381 0.00 0.00 0.00 3.08
512 521 5.526506 AATAGATTGGATGCTTTTCTGCC 57.473 39.130 0.00 0.00 0.00 4.85
547 559 3.653835 AGCCCACCCTCTATTTTCTTC 57.346 47.619 0.00 0.00 0.00 2.87
548 560 2.092914 AGCCCACCCTCTATTTTCTTCG 60.093 50.000 0.00 0.00 0.00 3.79
563 575 1.134367 TCTTCGTAGATTCGCCACTGG 59.866 52.381 0.00 0.00 35.04 4.00
564 576 1.134367 CTTCGTAGATTCGCCACTGGA 59.866 52.381 0.00 0.00 35.04 3.86
565 577 1.399714 TCGTAGATTCGCCACTGGAT 58.600 50.000 0.00 0.00 0.00 3.41
566 578 2.578786 TCGTAGATTCGCCACTGGATA 58.421 47.619 0.00 0.00 0.00 2.59
567 579 2.292569 TCGTAGATTCGCCACTGGATAC 59.707 50.000 0.00 0.00 0.00 2.24
568 580 5.701569 TTCGTAGATTCGCCACTGGATACA 61.702 45.833 0.00 0.00 41.02 2.29
630 642 0.341961 ACAGGTAGGCCCCATGACTA 59.658 55.000 11.23 0.00 34.57 2.59
631 643 0.759346 CAGGTAGGCCCCATGACTAC 59.241 60.000 0.00 1.49 37.07 2.73
795 810 1.142465 CAGCTACGTACTCCCTCCCTA 59.858 57.143 0.00 0.00 0.00 3.53
806 821 2.615773 CTCCCTACCTCCCTCCCC 59.384 72.222 0.00 0.00 0.00 4.81
833 848 1.078143 AACCGCCATCTCTTCCTGC 60.078 57.895 0.00 0.00 0.00 4.85
918 933 2.242708 CCACTAGACAGAGACCCTACCT 59.757 54.545 0.00 0.00 0.00 3.08
919 934 3.309265 CCACTAGACAGAGACCCTACCTT 60.309 52.174 0.00 0.00 0.00 3.50
998 1015 7.112779 GTGGAATAATTCTGGGAGAAGAAGAA 58.887 38.462 0.00 0.00 39.47 2.52
999 1016 7.281999 GTGGAATAATTCTGGGAGAAGAAGAAG 59.718 40.741 0.00 0.00 39.47 2.85
1000 1017 7.182749 TGGAATAATTCTGGGAGAAGAAGAAGA 59.817 37.037 0.00 0.00 39.47 2.87
1064 1081 3.035363 TCGAAGGCCTCACATGGTTATA 58.965 45.455 5.23 0.00 0.00 0.98
1081 1098 5.435041 TGGTTATACCCCTTCCTCATTTCAT 59.565 40.000 0.00 0.00 37.50 2.57
1082 1099 6.621931 TGGTTATACCCCTTCCTCATTTCATA 59.378 38.462 0.00 0.00 37.50 2.15
1083 1100 7.129660 TGGTTATACCCCTTCCTCATTTCATAA 59.870 37.037 0.00 0.00 37.50 1.90
1084 1101 8.170730 GGTTATACCCCTTCCTCATTTCATAAT 58.829 37.037 0.00 0.00 30.04 1.28
1085 1102 9.588096 GTTATACCCCTTCCTCATTTCATAATT 57.412 33.333 0.00 0.00 0.00 1.40
1086 1103 9.807921 TTATACCCCTTCCTCATTTCATAATTC 57.192 33.333 0.00 0.00 0.00 2.17
1087 1104 6.091076 ACCCCTTCCTCATTTCATAATTCA 57.909 37.500 0.00 0.00 0.00 2.57
1132 1152 4.828829 TCTCCCTCGGTTGATTTTTCTAC 58.171 43.478 0.00 0.00 0.00 2.59
1170 1190 5.689514 ACTTCGAGATGCAGAATTATTCTCG 59.310 40.000 21.70 21.70 44.47 4.04
1176 1196 7.418840 AGATGCAGAATTATTCTCGATGTTC 57.581 36.000 4.24 0.00 38.11 3.18
1177 1197 7.215789 AGATGCAGAATTATTCTCGATGTTCT 58.784 34.615 4.24 0.25 38.11 3.01
1178 1198 7.714377 AGATGCAGAATTATTCTCGATGTTCTT 59.286 33.333 4.24 0.00 38.11 2.52
1179 1199 8.893219 ATGCAGAATTATTCTCGATGTTCTTA 57.107 30.769 4.24 0.00 38.11 2.10
1180 1200 8.893219 TGCAGAATTATTCTCGATGTTCTTAT 57.107 30.769 4.24 0.00 38.11 1.73
1182 1202 7.743838 GCAGAATTATTCTCGATGTTCTTATGC 59.256 37.037 4.24 0.00 38.11 3.14
1184 1204 9.499479 AGAATTATTCTCGATGTTCTTATGCAT 57.501 29.630 3.79 3.79 34.07 3.96
1218 1245 3.239449 TCTTTCTCTAGGCACAACTGGA 58.761 45.455 0.00 0.00 0.00 3.86
1219 1246 3.006967 TCTTTCTCTAGGCACAACTGGAC 59.993 47.826 0.00 0.00 0.00 4.02
1221 1248 0.976641 CTCTAGGCACAACTGGACCA 59.023 55.000 0.00 0.00 0.00 4.02
1253 1281 3.386402 TGTGGGTTCTATATCATCACGCA 59.614 43.478 0.00 0.00 0.00 5.24
1257 1285 6.256539 GTGGGTTCTATATCATCACGCATATG 59.743 42.308 0.00 0.00 33.48 1.78
1258 1286 6.070824 TGGGTTCTATATCATCACGCATATGT 60.071 38.462 4.29 0.00 0.00 2.29
1260 1288 8.144478 GGGTTCTATATCATCACGCATATGTAT 58.856 37.037 4.29 0.00 0.00 2.29
1261 1289 9.534565 GGTTCTATATCATCACGCATATGTATT 57.465 33.333 4.29 0.00 0.00 1.89
1273 1301 5.125417 ACGCATATGTATTTTGCCTCAGTTT 59.875 36.000 4.29 0.00 32.76 2.66
1277 1305 9.533253 GCATATGTATTTTGCCTCAGTTTAAAT 57.467 29.630 4.29 0.00 0.00 1.40
1333 1361 9.277565 CATGATTTTAAGAACATAGTTTCCACG 57.722 33.333 0.00 0.00 0.00 4.94
1345 1373 2.561858 AGTTTCCACGGTTAGAGGAGAC 59.438 50.000 0.00 0.00 42.37 3.36
1383 1411 2.028190 CCATGTCTAGGCGGCTCG 59.972 66.667 17.67 10.11 0.00 5.03
1386 1414 0.032678 CATGTCTAGGCGGCTCGATT 59.967 55.000 17.67 3.81 0.00 3.34
1390 1418 0.821517 TCTAGGCGGCTCGATTTGAA 59.178 50.000 17.67 0.00 0.00 2.69
1408 1436 6.852858 TTTGAAATGCGGATATCGATTGTA 57.147 33.333 1.71 0.00 42.43 2.41
1409 1437 6.466308 TTGAAATGCGGATATCGATTGTAG 57.534 37.500 1.71 0.00 42.43 2.74
1429 1457 7.716799 TGTAGAGAAAATGTAATGCCCATTT 57.283 32.000 0.00 0.00 42.68 2.32
1435 1463 8.144862 AGAAAATGTAATGCCCATTTTAAGGA 57.855 30.769 10.17 0.00 46.84 3.36
1441 1469 7.740805 TGTAATGCCCATTTTAAGGAAAGTTT 58.259 30.769 0.00 0.00 32.50 2.66
1485 1513 2.486951 ATGCATGCGCTGAAGAAATC 57.513 45.000 14.09 0.00 39.64 2.17
1488 1516 0.028505 CATGCGCTGAAGAAATCCCG 59.971 55.000 9.73 0.00 0.00 5.14
1489 1517 1.718757 ATGCGCTGAAGAAATCCCGC 61.719 55.000 9.73 0.00 43.71 6.13
1490 1518 2.703409 CGCTGAAGAAATCCCGCG 59.297 61.111 0.00 0.00 39.47 6.46
1491 1519 2.405191 GCTGAAGAAATCCCGCGC 59.595 61.111 0.00 0.00 0.00 6.86
1492 1520 2.703409 CTGAAGAAATCCCGCGCG 59.297 61.111 25.67 25.67 0.00 6.86
1493 1521 3.440356 CTGAAGAAATCCCGCGCGC 62.440 63.158 27.36 23.91 0.00 6.86
1494 1522 4.237809 GAAGAAATCCCGCGCGCC 62.238 66.667 27.36 9.60 0.00 6.53
1503 1531 4.397090 CCGCGCGCCACAAAATGA 62.397 61.111 27.36 0.00 0.00 2.57
1504 1532 2.871080 CGCGCGCCACAAAATGAG 60.871 61.111 27.72 2.72 0.00 2.90
1505 1533 3.174573 GCGCGCCACAAAATGAGC 61.175 61.111 23.24 0.00 0.00 4.26
1506 1534 2.871080 CGCGCCACAAAATGAGCG 60.871 61.111 0.00 12.66 45.33 5.03
1507 1535 2.560861 GCGCCACAAAATGAGCGA 59.439 55.556 18.43 0.00 45.37 4.93
1508 1536 1.137404 GCGCCACAAAATGAGCGAT 59.863 52.632 18.43 0.00 45.37 4.58
1509 1537 1.135699 GCGCCACAAAATGAGCGATG 61.136 55.000 18.43 0.00 45.37 3.84
1510 1538 1.135699 CGCCACAAAATGAGCGATGC 61.136 55.000 11.94 0.00 45.37 3.91
1511 1539 0.171903 GCCACAAAATGAGCGATGCT 59.828 50.000 0.00 0.00 43.88 3.79
1512 1540 1.401552 GCCACAAAATGAGCGATGCTA 59.598 47.619 0.00 0.00 39.88 3.49
1513 1541 2.540361 GCCACAAAATGAGCGATGCTAG 60.540 50.000 0.00 0.00 39.88 3.42
1514 1542 2.938451 CCACAAAATGAGCGATGCTAGA 59.062 45.455 0.00 0.00 39.88 2.43
1515 1543 3.242543 CCACAAAATGAGCGATGCTAGAC 60.243 47.826 0.00 0.00 39.88 2.59
1516 1544 2.939103 ACAAAATGAGCGATGCTAGACC 59.061 45.455 0.00 0.00 39.88 3.85
1517 1545 2.246719 AAATGAGCGATGCTAGACCC 57.753 50.000 0.00 0.00 39.88 4.46
1518 1546 1.123077 AATGAGCGATGCTAGACCCA 58.877 50.000 0.00 0.00 39.88 4.51
1519 1547 0.390860 ATGAGCGATGCTAGACCCAC 59.609 55.000 0.00 0.00 39.88 4.61
1520 1548 1.299468 GAGCGATGCTAGACCCACG 60.299 63.158 0.00 0.00 39.88 4.94
1521 1549 2.005960 GAGCGATGCTAGACCCACGT 62.006 60.000 0.00 0.00 39.88 4.49
1522 1550 0.750546 AGCGATGCTAGACCCACGTA 60.751 55.000 0.00 0.00 36.99 3.57
1523 1551 0.101759 GCGATGCTAGACCCACGTAA 59.898 55.000 0.00 0.00 0.00 3.18
1524 1552 1.470285 GCGATGCTAGACCCACGTAAA 60.470 52.381 0.00 0.00 0.00 2.01
1525 1553 2.460918 CGATGCTAGACCCACGTAAAG 58.539 52.381 0.00 0.00 0.00 1.85
1526 1554 2.159282 CGATGCTAGACCCACGTAAAGT 60.159 50.000 0.00 0.00 0.00 2.66
1527 1555 3.675228 CGATGCTAGACCCACGTAAAGTT 60.675 47.826 0.00 0.00 0.00 2.66
1528 1556 4.439153 CGATGCTAGACCCACGTAAAGTTA 60.439 45.833 0.00 0.00 0.00 2.24
1529 1557 4.178545 TGCTAGACCCACGTAAAGTTAC 57.821 45.455 0.00 0.00 0.00 2.50
1551 1579 5.526010 CGTGAGATTTTTACGTAAAGGCT 57.474 39.130 19.31 16.83 33.48 4.58
1552 1580 5.313623 CGTGAGATTTTTACGTAAAGGCTG 58.686 41.667 19.31 5.10 33.48 4.85
1553 1581 5.119588 CGTGAGATTTTTACGTAAAGGCTGA 59.880 40.000 19.31 10.37 33.48 4.26
1554 1582 6.304882 GTGAGATTTTTACGTAAAGGCTGAC 58.695 40.000 19.31 16.74 0.00 3.51
1555 1583 6.147328 GTGAGATTTTTACGTAAAGGCTGACT 59.853 38.462 19.31 13.73 0.00 3.41
1556 1584 6.708949 TGAGATTTTTACGTAAAGGCTGACTT 59.291 34.615 19.31 0.00 42.52 3.01
1557 1585 6.899114 AGATTTTTACGTAAAGGCTGACTTG 58.101 36.000 19.31 0.00 39.96 3.16
1558 1586 5.427036 TTTTTACGTAAAGGCTGACTTGG 57.573 39.130 19.31 0.00 39.96 3.61
1559 1587 3.756933 TTACGTAAAGGCTGACTTGGT 57.243 42.857 5.31 0.00 39.96 3.67
1560 1588 1.878953 ACGTAAAGGCTGACTTGGTG 58.121 50.000 0.00 0.00 39.96 4.17
1561 1589 1.156736 CGTAAAGGCTGACTTGGTGG 58.843 55.000 0.00 0.00 39.96 4.61
1562 1590 1.542547 CGTAAAGGCTGACTTGGTGGT 60.543 52.381 0.00 0.00 39.96 4.16
1563 1591 2.289195 CGTAAAGGCTGACTTGGTGGTA 60.289 50.000 0.00 0.00 39.96 3.25
1564 1592 2.568623 AAAGGCTGACTTGGTGGTAG 57.431 50.000 0.00 0.00 39.96 3.18
1565 1593 1.435256 AAGGCTGACTTGGTGGTAGT 58.565 50.000 0.00 0.00 38.21 2.73
1566 1594 1.435256 AGGCTGACTTGGTGGTAGTT 58.565 50.000 0.00 0.00 0.00 2.24
1567 1595 2.616524 AGGCTGACTTGGTGGTAGTTA 58.383 47.619 0.00 0.00 0.00 2.24
1568 1596 2.976882 AGGCTGACTTGGTGGTAGTTAA 59.023 45.455 0.00 0.00 0.00 2.01
1569 1597 3.587506 AGGCTGACTTGGTGGTAGTTAAT 59.412 43.478 0.00 0.00 0.00 1.40
1570 1598 4.042934 AGGCTGACTTGGTGGTAGTTAATT 59.957 41.667 0.00 0.00 0.00 1.40
1571 1599 4.156008 GGCTGACTTGGTGGTAGTTAATTG 59.844 45.833 0.00 0.00 0.00 2.32
1572 1600 4.156008 GCTGACTTGGTGGTAGTTAATTGG 59.844 45.833 0.00 0.00 0.00 3.16
1573 1601 5.556915 CTGACTTGGTGGTAGTTAATTGGA 58.443 41.667 0.00 0.00 0.00 3.53
1574 1602 6.134535 TGACTTGGTGGTAGTTAATTGGAT 57.865 37.500 0.00 0.00 0.00 3.41
1575 1603 6.548321 TGACTTGGTGGTAGTTAATTGGATT 58.452 36.000 0.00 0.00 0.00 3.01
1576 1604 7.691213 TGACTTGGTGGTAGTTAATTGGATTA 58.309 34.615 0.00 0.00 0.00 1.75
1577 1605 7.827236 TGACTTGGTGGTAGTTAATTGGATTAG 59.173 37.037 0.00 0.00 0.00 1.73
1578 1606 7.116736 ACTTGGTGGTAGTTAATTGGATTAGG 58.883 38.462 0.00 0.00 0.00 2.69
1579 1607 6.894735 TGGTGGTAGTTAATTGGATTAGGA 57.105 37.500 0.00 0.00 0.00 2.94
1580 1608 7.460214 TGGTGGTAGTTAATTGGATTAGGAT 57.540 36.000 0.00 0.00 0.00 3.24
1581 1609 7.878495 TGGTGGTAGTTAATTGGATTAGGATT 58.122 34.615 0.00 0.00 0.00 3.01
1582 1610 9.005318 TGGTGGTAGTTAATTGGATTAGGATTA 57.995 33.333 0.00 0.00 0.00 1.75
1583 1611 9.503399 GGTGGTAGTTAATTGGATTAGGATTAG 57.497 37.037 0.00 0.00 0.00 1.73
1903 1931 3.114693 CGTAAGTCTTCGTAAGCTCGT 57.885 47.619 0.00 0.00 37.18 4.18
1904 1932 3.486584 CGTAAGTCTTCGTAAGCTCGTT 58.513 45.455 0.00 0.00 37.18 3.85
1905 1933 3.537613 CGTAAGTCTTCGTAAGCTCGTTC 59.462 47.826 0.00 0.00 37.18 3.95
1906 1934 2.244281 AGTCTTCGTAAGCTCGTTCG 57.756 50.000 0.00 0.00 37.18 3.95
1907 1935 1.534595 AGTCTTCGTAAGCTCGTTCGT 59.465 47.619 0.00 0.00 37.18 3.85
1908 1936 2.738846 AGTCTTCGTAAGCTCGTTCGTA 59.261 45.455 0.00 0.00 37.18 3.43
1909 1937 3.089982 GTCTTCGTAAGCTCGTTCGTAG 58.910 50.000 0.00 0.00 37.18 3.51
1910 1938 2.094894 TCTTCGTAAGCTCGTTCGTAGG 59.905 50.000 0.00 0.00 37.18 3.18
1911 1939 1.442769 TCGTAAGCTCGTTCGTAGGT 58.557 50.000 0.00 0.00 37.18 3.08
1912 1940 1.129251 TCGTAAGCTCGTTCGTAGGTG 59.871 52.381 0.00 0.00 37.18 4.00
1913 1941 1.135859 CGTAAGCTCGTTCGTAGGTGT 60.136 52.381 0.00 0.00 0.00 4.16
1914 1942 2.094258 CGTAAGCTCGTTCGTAGGTGTA 59.906 50.000 0.00 0.00 0.00 2.90
1915 1943 2.915738 AAGCTCGTTCGTAGGTGTAG 57.084 50.000 0.00 0.00 0.00 2.74
1916 1944 0.450983 AGCTCGTTCGTAGGTGTAGC 59.549 55.000 0.00 0.00 0.00 3.58
1917 1945 0.169672 GCTCGTTCGTAGGTGTAGCA 59.830 55.000 0.00 0.00 0.00 3.49
1918 1946 1.202268 GCTCGTTCGTAGGTGTAGCAT 60.202 52.381 0.00 0.00 0.00 3.79
1919 1947 2.734492 GCTCGTTCGTAGGTGTAGCATT 60.734 50.000 0.00 0.00 0.00 3.56
1920 1948 3.488047 GCTCGTTCGTAGGTGTAGCATTA 60.488 47.826 0.00 0.00 0.00 1.90
1921 1949 4.792057 GCTCGTTCGTAGGTGTAGCATTAT 60.792 45.833 0.00 0.00 0.00 1.28
1922 1950 5.252969 TCGTTCGTAGGTGTAGCATTATT 57.747 39.130 0.00 0.00 0.00 1.40
1992 2020 7.122799 TGTTTCGATCTATAAGATCCGATCCAT 59.877 37.037 10.52 2.11 46.42 3.41
2014 2138 6.851837 CCATATACTTCTCAGTCGTAGTTTCG 59.148 42.308 0.00 0.00 34.06 3.46
2046 2176 0.636733 CGCATGCAAATTTGACGAGC 59.363 50.000 22.31 16.40 0.00 5.03
2049 2179 2.280708 GCATGCAAATTTGACGAGCATC 59.719 45.455 22.31 7.87 43.43 3.91
2073 2203 3.490896 CAGATGTTTACGTGATCCATCCG 59.509 47.826 13.48 4.13 33.95 4.18
2116 2246 1.999071 GCATGACCGAGCTCGAGAGT 61.999 60.000 36.59 25.32 43.02 3.24
2125 2255 1.131504 GAGCTCGAGAGTGATGTCGTT 59.868 52.381 18.75 0.00 37.46 3.85
2252 2387 2.532193 CGCGCGTTAATGTGACTAACTG 60.532 50.000 24.19 0.00 0.00 3.16
2258 2393 5.808540 GCGTTAATGTGACTAACTGATGGTA 59.191 40.000 0.00 0.00 0.00 3.25
2276 2411 4.805219 TGGTACATCGATCGTCATTATGG 58.195 43.478 15.94 0.00 0.00 2.74
2299 2434 2.345244 CAGTTCCCGCTGCTGAGT 59.655 61.111 0.00 0.00 32.39 3.41
2395 2530 1.153568 GCTGCAGCTGGACGACATA 60.154 57.895 31.33 0.00 38.21 2.29
3343 3478 2.161808 ACTGGACTACTTCATGTCGTCG 59.838 50.000 0.00 0.00 40.85 5.12
3617 3752 2.276201 TCAAGGTCACAACAACTCACG 58.724 47.619 0.00 0.00 0.00 4.35
3625 3760 2.354510 CACAACAACTCACGGACACATT 59.645 45.455 0.00 0.00 0.00 2.71
3626 3761 3.013921 ACAACAACTCACGGACACATTT 58.986 40.909 0.00 0.00 0.00 2.32
3680 3819 7.815068 TGTCTCTCTCTTACTTAACATTTGAGC 59.185 37.037 0.00 0.00 0.00 4.26
4238 4379 6.183360 GCCCCAAAAAGTAGAGTATGAAATCC 60.183 42.308 0.00 0.00 0.00 3.01
4241 4382 7.148069 CCCAAAAAGTAGAGTATGAAATCCCAC 60.148 40.741 0.00 0.00 0.00 4.61
4248 4389 1.940613 GTATGAAATCCCACCTCACGC 59.059 52.381 0.00 0.00 0.00 5.34
4257 4398 0.537188 CCACCTCACGCCAGAGTTAT 59.463 55.000 0.07 0.00 33.75 1.89
4258 4399 1.754803 CCACCTCACGCCAGAGTTATA 59.245 52.381 0.07 0.00 33.75 0.98
4259 4400 2.167693 CCACCTCACGCCAGAGTTATAA 59.832 50.000 0.07 0.00 33.75 0.98
4400 4541 8.848474 AACTAGTTTTAGCACTTCACATACAT 57.152 30.769 1.12 0.00 0.00 2.29
4439 4581 1.509644 TTGCAAGCAAGCTCGTCAGG 61.510 55.000 2.89 0.00 34.99 3.86
4528 4670 4.331168 CCTAGGAAAGAAATGAAGCACTCG 59.669 45.833 1.05 0.00 0.00 4.18
4602 4754 3.838317 GCCACCCACAGATATGTATAGGA 59.162 47.826 9.61 0.00 0.00 2.94
4833 4985 0.472471 AAGGAAACAGAAGGCACGGA 59.528 50.000 0.00 0.00 0.00 4.69
4846 4998 1.613270 GCACGGAAAAAGGTTATGCG 58.387 50.000 0.00 0.00 0.00 4.73
4929 5081 6.945435 TCCAACAAAGTAAAATATCTGCCAGA 59.055 34.615 0.00 0.00 0.00 3.86
4939 5091 9.860898 GTAAAATATCTGCCAGAAGAAAATGTT 57.139 29.630 0.00 0.00 0.00 2.71
4941 5093 9.783081 AAAATATCTGCCAGAAGAAAATGTTTT 57.217 25.926 0.00 0.00 0.00 2.43
4942 5094 9.783081 AAATATCTGCCAGAAGAAAATGTTTTT 57.217 25.926 0.00 0.00 0.00 1.94
5002 5186 3.379445 GACGCGGGTCTGGAAGGA 61.379 66.667 23.96 0.00 40.15 3.36
5003 5187 2.683933 ACGCGGGTCTGGAAGGAT 60.684 61.111 12.47 0.00 0.00 3.24
5004 5188 2.202932 CGCGGGTCTGGAAGGATG 60.203 66.667 0.00 0.00 0.00 3.51
5037 5230 1.068127 CAGCCATGCCAAATTAGCTCC 59.932 52.381 0.00 0.00 0.00 4.70
5125 5320 5.710099 CCCACTGTAACACCAGAAACAATAT 59.290 40.000 0.00 0.00 36.30 1.28
5175 5372 8.774546 ATGAGTTGTAGATAAGAGGAGATGAA 57.225 34.615 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 14 7.452231 ACAAAACGCAAAAACACATCTAAAAG 58.548 30.769 0.00 0.00 0.00 2.27
79 83 5.395324 GGAGAACGTTATTCCATCTTCAGGA 60.395 44.000 20.70 0.00 0.00 3.86
105 109 3.488569 CGGAATGGGGGCTAGGCA 61.489 66.667 19.14 0.00 0.00 4.75
209 213 1.887198 AGACACACGAAGGAGACGAAT 59.113 47.619 0.00 0.00 34.70 3.34
271 276 2.186826 GCACCAGAACAGCAACCGT 61.187 57.895 0.00 0.00 0.00 4.83
392 398 2.421424 GACCAGAAGCAATGAAGCGAAT 59.579 45.455 0.00 0.00 40.15 3.34
547 559 2.034179 TGTATCCAGTGGCGAATCTACG 59.966 50.000 3.51 0.00 0.00 3.51
548 560 3.553096 CCTGTATCCAGTGGCGAATCTAC 60.553 52.174 3.51 0.29 36.95 2.59
563 575 1.202533 CCATCGGTCACACCCTGTATC 60.203 57.143 0.00 0.00 33.75 2.24
564 576 0.830648 CCATCGGTCACACCCTGTAT 59.169 55.000 0.00 0.00 33.75 2.29
565 577 0.251877 TCCATCGGTCACACCCTGTA 60.252 55.000 0.00 0.00 33.75 2.74
566 578 1.535444 TCCATCGGTCACACCCTGT 60.535 57.895 0.00 0.00 33.75 4.00
567 579 1.079127 GTCCATCGGTCACACCCTG 60.079 63.158 0.00 0.00 33.75 4.45
568 580 2.291043 GGTCCATCGGTCACACCCT 61.291 63.158 0.00 0.00 33.75 4.34
569 581 2.119484 TTGGTCCATCGGTCACACCC 62.119 60.000 0.00 0.00 33.75 4.61
570 582 0.673644 CTTGGTCCATCGGTCACACC 60.674 60.000 0.00 0.00 34.05 4.16
571 583 0.320374 TCTTGGTCCATCGGTCACAC 59.680 55.000 0.00 0.00 0.00 3.82
572 584 1.052617 TTCTTGGTCCATCGGTCACA 58.947 50.000 0.00 0.00 0.00 3.58
573 585 1.270625 TGTTCTTGGTCCATCGGTCAC 60.271 52.381 0.00 0.00 0.00 3.67
574 586 1.052617 TGTTCTTGGTCCATCGGTCA 58.947 50.000 0.00 0.00 0.00 4.02
575 587 1.439679 GTGTTCTTGGTCCATCGGTC 58.560 55.000 0.00 0.00 0.00 4.79
576 588 0.320421 CGTGTTCTTGGTCCATCGGT 60.320 55.000 0.00 0.00 0.00 4.69
648 663 5.577945 CAGCCTGCATGTTCGATTTTTAATT 59.422 36.000 0.00 0.00 0.00 1.40
650 665 4.484236 CAGCCTGCATGTTCGATTTTTAA 58.516 39.130 0.00 0.00 0.00 1.52
651 666 3.673052 GCAGCCTGCATGTTCGATTTTTA 60.673 43.478 12.82 0.00 44.26 1.52
833 848 2.291741 GGAGCGAGCAAGGATTTATTGG 59.708 50.000 0.00 0.00 0.00 3.16
998 1015 1.064906 CCAGCTTCATGGTCACCATCT 60.065 52.381 6.26 0.00 43.15 2.90
999 1016 1.386533 CCAGCTTCATGGTCACCATC 58.613 55.000 6.26 0.00 43.15 3.51
1000 1017 0.033796 CCCAGCTTCATGGTCACCAT 60.034 55.000 2.35 2.35 46.37 3.55
1064 1081 6.091076 TGAATTATGAAATGAGGAAGGGGT 57.909 37.500 0.00 0.00 0.00 4.95
1085 1102 9.742144 GAGGAGTAATCAACTAGGAGTATATGA 57.258 37.037 0.00 0.00 39.07 2.15
1086 1103 9.747898 AGAGGAGTAATCAACTAGGAGTATATG 57.252 37.037 0.00 0.00 39.07 1.78
1087 1104 9.969001 GAGAGGAGTAATCAACTAGGAGTATAT 57.031 37.037 0.00 0.00 39.07 0.86
1145 1165 7.475771 GAGAATAATTCTGCATCTCGAAGTT 57.524 36.000 0.00 0.00 40.87 2.66
1170 1190 7.696755 TCACATGTACAATGCATAAGAACATC 58.303 34.615 0.00 0.00 0.00 3.06
1176 1196 9.229784 GAAAGATTCACATGTACAATGCATAAG 57.770 33.333 0.00 0.00 0.00 1.73
1177 1197 8.959548 AGAAAGATTCACATGTACAATGCATAA 58.040 29.630 0.00 0.00 0.00 1.90
1178 1198 8.510243 AGAAAGATTCACATGTACAATGCATA 57.490 30.769 0.00 0.00 0.00 3.14
1179 1199 7.338703 AGAGAAAGATTCACATGTACAATGCAT 59.661 33.333 0.00 0.00 0.00 3.96
1180 1200 6.656270 AGAGAAAGATTCACATGTACAATGCA 59.344 34.615 0.00 0.00 0.00 3.96
1182 1202 8.824781 CCTAGAGAAAGATTCACATGTACAATG 58.175 37.037 0.00 1.47 0.00 2.82
1184 1204 6.818644 GCCTAGAGAAAGATTCACATGTACAA 59.181 38.462 0.00 0.00 0.00 2.41
1185 1205 6.070824 TGCCTAGAGAAAGATTCACATGTACA 60.071 38.462 0.00 0.00 0.00 2.90
1310 1338 7.813645 ACCGTGGAAACTATGTTCTTAAAATC 58.186 34.615 0.00 0.00 0.00 2.17
1311 1339 7.754851 ACCGTGGAAACTATGTTCTTAAAAT 57.245 32.000 0.00 0.00 0.00 1.82
1320 1348 4.091549 TCCTCTAACCGTGGAAACTATGT 58.908 43.478 0.00 0.00 32.57 2.29
1333 1361 4.210746 GTGTTTTTGTCGTCTCCTCTAACC 59.789 45.833 0.00 0.00 0.00 2.85
1345 1373 3.433615 GGAGATGAGGAGTGTTTTTGTCG 59.566 47.826 0.00 0.00 0.00 4.35
1383 1411 6.373779 ACAATCGATATCCGCATTTCAAATC 58.626 36.000 0.00 0.00 38.37 2.17
1386 1414 6.220201 TCTACAATCGATATCCGCATTTCAA 58.780 36.000 0.00 0.00 38.37 2.69
1390 1418 5.644977 TCTCTACAATCGATATCCGCATT 57.355 39.130 0.00 0.00 38.37 3.56
1429 1457 5.776173 TTCGCCAATGAAACTTTCCTTAA 57.224 34.783 0.00 0.00 0.00 1.85
1435 1463 5.200368 ACTTGATTCGCCAATGAAACTTT 57.800 34.783 0.00 0.00 0.00 2.66
1441 1469 2.488204 TGGACTTGATTCGCCAATGA 57.512 45.000 0.00 0.00 0.00 2.57
1488 1516 3.174573 GCTCATTTTGTGGCGCGC 61.175 61.111 25.94 25.94 0.00 6.86
1489 1517 2.582202 ATCGCTCATTTTGTGGCGCG 62.582 55.000 0.00 0.00 42.99 6.86
1490 1518 1.135699 CATCGCTCATTTTGTGGCGC 61.136 55.000 0.00 0.00 42.99 6.53
1491 1519 1.135699 GCATCGCTCATTTTGTGGCG 61.136 55.000 0.00 0.00 43.93 5.69
1492 1520 0.171903 AGCATCGCTCATTTTGTGGC 59.828 50.000 0.00 0.00 30.62 5.01
1493 1521 2.938451 TCTAGCATCGCTCATTTTGTGG 59.062 45.455 0.00 0.00 40.44 4.17
1494 1522 3.242543 GGTCTAGCATCGCTCATTTTGTG 60.243 47.826 0.00 0.00 40.44 3.33
1495 1523 2.939103 GGTCTAGCATCGCTCATTTTGT 59.061 45.455 0.00 0.00 40.44 2.83
1496 1524 2.289002 GGGTCTAGCATCGCTCATTTTG 59.711 50.000 0.00 0.00 40.44 2.44
1497 1525 2.092968 TGGGTCTAGCATCGCTCATTTT 60.093 45.455 0.00 0.00 40.44 1.82
1498 1526 1.486310 TGGGTCTAGCATCGCTCATTT 59.514 47.619 0.00 0.00 40.44 2.32
1499 1527 1.123077 TGGGTCTAGCATCGCTCATT 58.877 50.000 0.00 0.00 40.44 2.57
1500 1528 0.390860 GTGGGTCTAGCATCGCTCAT 59.609 55.000 0.00 0.00 40.44 2.90
1501 1529 1.816537 GTGGGTCTAGCATCGCTCA 59.183 57.895 0.00 0.00 40.44 4.26
1502 1530 1.299468 CGTGGGTCTAGCATCGCTC 60.299 63.158 0.00 0.00 40.44 5.03
1503 1531 0.750546 TACGTGGGTCTAGCATCGCT 60.751 55.000 0.00 0.00 43.41 4.93
1504 1532 0.101759 TTACGTGGGTCTAGCATCGC 59.898 55.000 0.00 0.00 0.00 4.58
1505 1533 2.159282 ACTTTACGTGGGTCTAGCATCG 60.159 50.000 0.00 0.00 0.00 3.84
1506 1534 3.521947 ACTTTACGTGGGTCTAGCATC 57.478 47.619 0.00 0.00 0.00 3.91
1507 1535 3.975168 AACTTTACGTGGGTCTAGCAT 57.025 42.857 0.00 0.00 0.00 3.79
1508 1536 4.178545 GTAACTTTACGTGGGTCTAGCA 57.821 45.455 0.00 0.00 0.00 3.49
1527 1555 6.089820 CAGCCTTTACGTAAAAATCTCACGTA 59.910 38.462 20.47 2.38 46.23 3.57
1529 1557 5.119588 TCAGCCTTTACGTAAAAATCTCACG 59.880 40.000 20.47 7.32 41.32 4.35
1530 1558 6.147328 AGTCAGCCTTTACGTAAAAATCTCAC 59.853 38.462 20.47 13.68 0.00 3.51
1531 1559 6.228258 AGTCAGCCTTTACGTAAAAATCTCA 58.772 36.000 20.47 3.30 0.00 3.27
1532 1560 6.723131 AGTCAGCCTTTACGTAAAAATCTC 57.277 37.500 20.47 10.28 0.00 2.75
1533 1561 6.072673 CCAAGTCAGCCTTTACGTAAAAATCT 60.073 38.462 20.47 14.16 0.00 2.40
1534 1562 6.084277 CCAAGTCAGCCTTTACGTAAAAATC 58.916 40.000 20.47 12.40 0.00 2.17
1535 1563 5.533528 ACCAAGTCAGCCTTTACGTAAAAAT 59.466 36.000 20.47 7.67 0.00 1.82
1536 1564 4.883006 ACCAAGTCAGCCTTTACGTAAAAA 59.117 37.500 20.47 2.81 0.00 1.94
1537 1565 4.273969 CACCAAGTCAGCCTTTACGTAAAA 59.726 41.667 20.47 3.89 0.00 1.52
1538 1566 3.810941 CACCAAGTCAGCCTTTACGTAAA 59.189 43.478 19.12 19.12 0.00 2.01
1539 1567 3.395639 CACCAAGTCAGCCTTTACGTAA 58.604 45.455 3.29 3.29 0.00 3.18
1540 1568 2.289195 CCACCAAGTCAGCCTTTACGTA 60.289 50.000 0.00 0.00 0.00 3.57
1541 1569 1.542547 CCACCAAGTCAGCCTTTACGT 60.543 52.381 0.00 0.00 0.00 3.57
1542 1570 1.156736 CCACCAAGTCAGCCTTTACG 58.843 55.000 0.00 0.00 0.00 3.18
1543 1571 2.271944 ACCACCAAGTCAGCCTTTAC 57.728 50.000 0.00 0.00 0.00 2.01
1544 1572 2.976882 ACTACCACCAAGTCAGCCTTTA 59.023 45.455 0.00 0.00 0.00 1.85
1545 1573 1.774856 ACTACCACCAAGTCAGCCTTT 59.225 47.619 0.00 0.00 0.00 3.11
1546 1574 1.435256 ACTACCACCAAGTCAGCCTT 58.565 50.000 0.00 0.00 0.00 4.35
1547 1575 1.435256 AACTACCACCAAGTCAGCCT 58.565 50.000 0.00 0.00 0.00 4.58
1548 1576 3.412237 TTAACTACCACCAAGTCAGCC 57.588 47.619 0.00 0.00 0.00 4.85
1549 1577 4.156008 CCAATTAACTACCACCAAGTCAGC 59.844 45.833 0.00 0.00 0.00 4.26
1550 1578 5.556915 TCCAATTAACTACCACCAAGTCAG 58.443 41.667 0.00 0.00 0.00 3.51
1551 1579 5.570205 TCCAATTAACTACCACCAAGTCA 57.430 39.130 0.00 0.00 0.00 3.41
1552 1580 7.282450 CCTAATCCAATTAACTACCACCAAGTC 59.718 40.741 0.00 0.00 0.00 3.01
1553 1581 7.037153 TCCTAATCCAATTAACTACCACCAAGT 60.037 37.037 0.00 0.00 0.00 3.16
1554 1582 7.343357 TCCTAATCCAATTAACTACCACCAAG 58.657 38.462 0.00 0.00 0.00 3.61
1555 1583 7.273457 TCCTAATCCAATTAACTACCACCAA 57.727 36.000 0.00 0.00 0.00 3.67
1556 1584 6.894735 TCCTAATCCAATTAACTACCACCA 57.105 37.500 0.00 0.00 0.00 4.17
1557 1585 9.503399 CTAATCCTAATCCAATTAACTACCACC 57.497 37.037 0.00 0.00 0.00 4.61
1868 1896 7.115947 CGAAGACTTACGTAACTTTTCCTCAAT 59.884 37.037 3.29 0.00 0.00 2.57
1869 1897 6.418819 CGAAGACTTACGTAACTTTTCCTCAA 59.581 38.462 3.29 0.00 0.00 3.02
1870 1898 5.916883 CGAAGACTTACGTAACTTTTCCTCA 59.083 40.000 3.29 0.00 0.00 3.86
1871 1899 5.917447 ACGAAGACTTACGTAACTTTTCCTC 59.083 40.000 3.29 0.00 40.92 3.71
1872 1900 5.836347 ACGAAGACTTACGTAACTTTTCCT 58.164 37.500 3.29 0.00 40.92 3.36
1873 1901 7.618139 GCTTACGAAGACTTACGTAACTTTTCC 60.618 40.741 19.54 0.00 45.48 3.13
1874 1902 7.114106 AGCTTACGAAGACTTACGTAACTTTTC 59.886 37.037 19.54 6.11 45.48 2.29
1875 1903 6.920210 AGCTTACGAAGACTTACGTAACTTTT 59.080 34.615 19.54 0.00 45.48 2.27
1876 1904 6.442112 AGCTTACGAAGACTTACGTAACTTT 58.558 36.000 19.54 0.00 45.48 2.66
1877 1905 6.006759 AGCTTACGAAGACTTACGTAACTT 57.993 37.500 19.54 7.38 45.48 2.66
1878 1906 5.619625 AGCTTACGAAGACTTACGTAACT 57.380 39.130 19.54 18.09 45.48 2.24
1879 1907 4.490191 CGAGCTTACGAAGACTTACGTAAC 59.510 45.833 19.54 16.96 45.48 2.50
1881 1909 3.679980 ACGAGCTTACGAAGACTTACGTA 59.320 43.478 12.73 12.73 42.61 3.57
1882 1910 2.481952 ACGAGCTTACGAAGACTTACGT 59.518 45.455 14.22 14.22 44.72 3.57
1883 1911 3.114693 ACGAGCTTACGAAGACTTACG 57.885 47.619 1.33 0.00 37.03 3.18
1884 1912 3.537613 CGAACGAGCTTACGAAGACTTAC 59.462 47.826 1.33 0.00 37.03 2.34
1885 1913 3.187227 ACGAACGAGCTTACGAAGACTTA 59.813 43.478 1.33 0.00 37.03 2.24
1886 1914 2.031333 ACGAACGAGCTTACGAAGACTT 60.031 45.455 1.33 0.00 37.03 3.01
1887 1915 1.534595 ACGAACGAGCTTACGAAGACT 59.465 47.619 1.33 0.00 37.03 3.24
1888 1916 1.961079 ACGAACGAGCTTACGAAGAC 58.039 50.000 1.33 0.00 37.03 3.01
1889 1917 2.094894 CCTACGAACGAGCTTACGAAGA 59.905 50.000 1.33 0.00 37.03 2.87
1890 1918 2.159599 ACCTACGAACGAGCTTACGAAG 60.160 50.000 1.33 0.00 37.03 3.79
1891 1919 1.806542 ACCTACGAACGAGCTTACGAA 59.193 47.619 1.33 0.00 37.03 3.85
1892 1920 1.129251 CACCTACGAACGAGCTTACGA 59.871 52.381 1.33 0.00 37.03 3.43
1893 1921 1.135859 ACACCTACGAACGAGCTTACG 60.136 52.381 0.14 0.00 39.31 3.18
1894 1922 2.626088 ACACCTACGAACGAGCTTAC 57.374 50.000 0.14 0.00 0.00 2.34
1895 1923 2.096496 GCTACACCTACGAACGAGCTTA 59.904 50.000 0.14 0.00 0.00 3.09
1896 1924 1.135460 GCTACACCTACGAACGAGCTT 60.135 52.381 0.14 0.00 0.00 3.74
1897 1925 0.450983 GCTACACCTACGAACGAGCT 59.549 55.000 0.14 0.00 0.00 4.09
1898 1926 0.169672 TGCTACACCTACGAACGAGC 59.830 55.000 0.14 0.00 0.00 5.03
1899 1927 2.846039 ATGCTACACCTACGAACGAG 57.154 50.000 0.14 0.00 0.00 4.18
1900 1928 4.906065 ATAATGCTACACCTACGAACGA 57.094 40.909 0.14 0.00 0.00 3.85
1901 1929 5.311016 CAATAATGCTACACCTACGAACG 57.689 43.478 0.00 0.00 0.00 3.95
1918 1946 8.779303 CCTATACGATGTATTTTGTGGCAATAA 58.221 33.333 0.00 0.00 0.00 1.40
1919 1947 7.934665 ACCTATACGATGTATTTTGTGGCAATA 59.065 33.333 0.00 0.00 0.00 1.90
1920 1948 6.770785 ACCTATACGATGTATTTTGTGGCAAT 59.229 34.615 0.00 0.00 0.00 3.56
1921 1949 6.116806 ACCTATACGATGTATTTTGTGGCAA 58.883 36.000 0.00 0.00 0.00 4.52
1922 1950 5.676552 ACCTATACGATGTATTTTGTGGCA 58.323 37.500 0.00 0.00 0.00 4.92
1992 2020 7.038048 TCTCGAAACTACGACTGAGAAGTATA 58.962 38.462 0.00 0.00 37.37 1.47
2014 2138 1.922903 CATGCGTGCTCGTGATCTC 59.077 57.895 10.18 0.00 39.49 2.75
2042 2172 1.860950 CGTAAACATCTGGGATGCTCG 59.139 52.381 7.35 4.41 0.00 5.03
2046 2176 3.809832 GGATCACGTAAACATCTGGGATG 59.190 47.826 6.04 6.04 0.00 3.51
2049 2179 3.260475 TGGATCACGTAAACATCTGGG 57.740 47.619 0.00 0.00 0.00 4.45
2073 2203 3.149981 CTCCTGGGGAAAAAGTCAAGAC 58.850 50.000 0.00 0.00 0.00 3.01
2125 2255 2.753452 GGACATGTCTCCTACTTCGACA 59.247 50.000 24.50 0.00 41.36 4.35
2181 2311 2.252127 AATGCGAAATGTGACGGCGG 62.252 55.000 13.24 0.00 0.00 6.13
2252 2387 5.516696 CCATAATGACGATCGATGTACCATC 59.483 44.000 24.34 6.63 0.00 3.51
2258 2393 2.037121 TGCCCATAATGACGATCGATGT 59.963 45.455 24.34 0.00 0.00 3.06
2735 2870 4.194720 GAGCGCGTCCCTGTCGAT 62.195 66.667 8.43 0.00 0.00 3.59
3343 3478 4.176752 GTCCCCAGCCCGTCCATC 62.177 72.222 0.00 0.00 0.00 3.51
3617 3752 1.068541 GGAGCAAACCGAAATGTGTCC 60.069 52.381 0.00 0.00 0.00 4.02
3987 4126 2.283966 ACCACCTCCTCGTCCTGG 60.284 66.667 0.00 0.00 0.00 4.45
4191 4330 2.411904 CCTCTCTATTTGCCGCTCATC 58.588 52.381 0.00 0.00 0.00 2.92
4238 4379 0.537188 ATAACTCTGGCGTGAGGTGG 59.463 55.000 7.93 0.00 38.32 4.61
4241 4382 5.707242 TCTATTATAACTCTGGCGTGAGG 57.293 43.478 11.14 0.00 38.32 3.86
4248 4389 7.176865 TGGGAGACGAATCTATTATAACTCTGG 59.823 40.741 0.00 0.00 34.34 3.86
4257 4398 9.627123 AAATGAAAATGGGAGACGAATCTATTA 57.373 29.630 0.00 0.00 34.34 0.98
4258 4399 8.408601 CAAATGAAAATGGGAGACGAATCTATT 58.591 33.333 0.00 0.00 34.34 1.73
4259 4400 7.557719 ACAAATGAAAATGGGAGACGAATCTAT 59.442 33.333 0.00 0.00 34.34 1.98
4439 4581 6.821388 AGATACAACTTCCACCATCACTATC 58.179 40.000 0.00 0.00 0.00 2.08
4602 4754 3.472652 TGGCGTCTTGTCTTTGTACATT 58.527 40.909 0.00 0.00 0.00 2.71
4846 4998 1.084289 GGTGATCCAGGTGCGTTTAC 58.916 55.000 0.00 0.00 0.00 2.01
4942 5094 9.754382 AGTCATTTACGTTGTCTCTACTTAAAA 57.246 29.630 0.00 0.00 0.00 1.52
4945 5097 9.224267 ACTAGTCATTTACGTTGTCTCTACTTA 57.776 33.333 0.00 0.00 0.00 2.24
4946 5098 8.108551 ACTAGTCATTTACGTTGTCTCTACTT 57.891 34.615 0.00 0.00 0.00 2.24
4947 5099 7.389884 TGACTAGTCATTTACGTTGTCTCTACT 59.610 37.037 21.74 0.00 34.14 2.57
4948 5100 7.524912 TGACTAGTCATTTACGTTGTCTCTAC 58.475 38.462 21.74 0.00 34.14 2.59
4949 5101 7.677454 TGACTAGTCATTTACGTTGTCTCTA 57.323 36.000 21.74 0.00 34.14 2.43
5001 5185 0.108945 GCTGCTTTTCTGGGTGCATC 60.109 55.000 0.00 0.00 34.79 3.91
5002 5186 1.538687 GGCTGCTTTTCTGGGTGCAT 61.539 55.000 0.00 0.00 34.79 3.96
5003 5187 2.202395 GGCTGCTTTTCTGGGTGCA 61.202 57.895 0.00 0.00 0.00 4.57
5004 5188 1.538687 ATGGCTGCTTTTCTGGGTGC 61.539 55.000 0.00 0.00 0.00 5.01
5033 5226 6.224584 GGGTAAGTATTTCTGTCTATGGAGC 58.775 44.000 0.00 0.00 0.00 4.70
5037 5230 6.126883 TGTGGGGGTAAGTATTTCTGTCTATG 60.127 42.308 0.00 0.00 0.00 2.23
5125 5320 6.472016 TCACATTATCTAACTTTGCCTGTCA 58.528 36.000 0.00 0.00 0.00 3.58
5175 5372 8.336235 TCTTTTCAAATCATAGATAGGTGGGTT 58.664 33.333 0.00 0.00 0.00 4.11


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

AutoCloner maintained by Alex Coulton.