Multiple sequence alignment - TraesCS2D01G130500

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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 TraesCS2D01G130500 chr2D 100.000 4031 0 0 1 4031 75749744 75753774 0.000000e+00 7444.0
1 TraesCS2D01G130500 chr2A 90.590 2646 190 25 774 3377 75644648 75642020 0.000000e+00 3452.0
2 TraesCS2D01G130500 chr2A 86.535 557 49 11 2840 3377 75639330 75638781 1.250000e-164 590.0
3 TraesCS2D01G130500 chr2A 90.687 451 29 9 198 640 31773648 31774093 4.490000e-164 588.0
4 TraesCS2D01G130500 chr2A 90.541 296 14 6 3537 3823 75637127 75636837 2.940000e-101 379.0
5 TraesCS2D01G130500 chr2A 96.795 156 5 0 3876 4031 75636341 75636186 1.110000e-65 261.0
6 TraesCS2D01G130500 chr2A 93.197 147 5 3 3656 3802 75641219 75641078 1.140000e-50 211.0
7 TraesCS2D01G130500 chr2A 83.744 203 14 9 3836 4031 75640141 75639951 1.490000e-39 174.0
8 TraesCS2D01G130500 chr2A 92.437 119 5 3 3375 3490 75637378 75637261 2.490000e-37 167.0
9 TraesCS2D01G130500 chr2A 89.916 119 8 2 3505 3623 75641336 75641222 2.510000e-32 150.0
10 TraesCS2D01G130500 chr2A 100.000 36 0 0 3505 3540 75637274 75637239 2.600000e-07 67.6
11 TraesCS2D01G130500 chr2B 93.088 2199 132 13 1141 3323 116411903 116409709 0.000000e+00 3201.0
12 TraesCS2D01G130500 chr2B 90.669 643 49 8 1 640 709837503 709836869 0.000000e+00 845.0
13 TraesCS2D01G130500 chr2B 88.992 645 58 9 1 640 142395481 142394845 0.000000e+00 785.0
14 TraesCS2D01G130500 chr2B 90.030 331 13 10 3505 3823 116396305 116395983 1.040000e-110 411.0
15 TraesCS2D01G130500 chr2B 89.000 300 15 5 846 1145 116416203 116415922 4.960000e-94 355.0
16 TraesCS2D01G130500 chr2B 94.118 204 6 2 3827 4029 116395936 116395738 5.060000e-79 305.0
17 TraesCS2D01G130500 chr2B 92.437 119 5 2 3375 3490 116396409 116396292 2.490000e-37 167.0
18 TraesCS2D01G130500 chr2B 93.548 62 4 0 712 773 709836890 709836829 4.290000e-15 93.5
19 TraesCS2D01G130500 chr3B 90.358 643 50 9 1 640 58850090 58849457 0.000000e+00 833.0
20 TraesCS2D01G130500 chr3B 74.412 680 142 18 1953 2625 89063821 89064475 3.090000e-66 263.0
21 TraesCS2D01G130500 chr7B 86.462 650 58 15 1 640 594176398 594177027 0.000000e+00 686.0
22 TraesCS2D01G130500 chr7B 88.235 442 41 7 1 439 594175902 594176335 5.970000e-143 518.0
23 TraesCS2D01G130500 chr5A 86.562 640 58 9 1 633 41881601 41882219 0.000000e+00 680.0
24 TraesCS2D01G130500 chr4D 87.564 587 54 12 63 640 31648874 31648298 0.000000e+00 662.0
25 TraesCS2D01G130500 chr4D 88.945 398 32 9 1 393 501310704 501311094 7.840000e-132 481.0
26 TraesCS2D01G130500 chr1A 85.248 644 63 12 1 640 452919942 452919327 5.680000e-178 634.0
27 TraesCS2D01G130500 chr6B 86.789 545 55 13 104 640 600634287 600633752 3.470000e-165 592.0
28 TraesCS2D01G130500 chr6B 85.000 520 50 14 129 640 528087286 528087785 1.670000e-138 503.0
29 TraesCS2D01G130500 chr6B 92.593 108 8 0 1 108 600639535 600639428 5.390000e-34 156.0
30 TraesCS2D01G130500 chr6D 72.548 1417 325 51 1250 2640 264441251 264442629 1.740000e-108 403.0
31 TraesCS2D01G130500 chr7D 88.660 97 9 2 3276 3371 54659705 54659800 2.550000e-22 117.0
32 TraesCS2D01G130500 chr7A 87.129 101 13 0 3277 3377 58336203 58336103 9.160000e-22 115.0
33 TraesCS2D01G130500 chr7A 91.463 82 6 1 635 716 6483261 6483341 1.180000e-20 111.0
34 TraesCS2D01G130500 chr4A 87.838 74 8 1 643 716 736890511 736890583 7.180000e-13 86.1


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G130500 chr2D 75749744 75753774 4030 False 7444.000000 7444 100.000000 1 4031 1 chr2D.!!$F1 4030
1 TraesCS2D01G130500 chr2A 75636186 75644648 8462 True 605.733333 3452 91.528333 774 4031 9 chr2A.!!$R1 3257
2 TraesCS2D01G130500 chr2B 116409709 116411903 2194 True 3201.000000 3201 93.088000 1141 3323 1 chr2B.!!$R1 2182
3 TraesCS2D01G130500 chr2B 142394845 142395481 636 True 785.000000 785 88.992000 1 640 1 chr2B.!!$R3 639
4 TraesCS2D01G130500 chr2B 709836829 709837503 674 True 469.250000 845 92.108500 1 773 2 chr2B.!!$R5 772
5 TraesCS2D01G130500 chr2B 116395738 116396409 671 True 294.333333 411 92.195000 3375 4029 3 chr2B.!!$R4 654
6 TraesCS2D01G130500 chr3B 58849457 58850090 633 True 833.000000 833 90.358000 1 640 1 chr3B.!!$R1 639
7 TraesCS2D01G130500 chr3B 89063821 89064475 654 False 263.000000 263 74.412000 1953 2625 1 chr3B.!!$F1 672
8 TraesCS2D01G130500 chr7B 594175902 594177027 1125 False 602.000000 686 87.348500 1 640 2 chr7B.!!$F1 639
9 TraesCS2D01G130500 chr5A 41881601 41882219 618 False 680.000000 680 86.562000 1 633 1 chr5A.!!$F1 632
10 TraesCS2D01G130500 chr4D 31648298 31648874 576 True 662.000000 662 87.564000 63 640 1 chr4D.!!$R1 577
11 TraesCS2D01G130500 chr1A 452919327 452919942 615 True 634.000000 634 85.248000 1 640 1 chr1A.!!$R1 639
12 TraesCS2D01G130500 chr6B 600633752 600634287 535 True 592.000000 592 86.789000 104 640 1 chr6B.!!$R1 536
13 TraesCS2D01G130500 chr6D 264441251 264442629 1378 False 403.000000 403 72.548000 1250 2640 1 chr6D.!!$F1 1390

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
692 1202 0.036306 GGGTCACCGTCTCACCATTT 59.964 55.0 0.0 0.0 31.06 2.32 F
1639 2188 0.319900 CAACGTGACCCTGTCTCCTG 60.320 60.0 0.0 0.0 33.15 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2023 2572 0.250124 CTGAACCCTTGTGTGGCGTA 60.250 55.0 0.0 0.0 0.00 4.42 R
3293 7101 0.108709 TGTCGTTACATACCGGCACC 60.109 55.0 0.0 0.0 33.16 5.01 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
28 29 6.830873 AGCAATGCATTTAAGTCTTCTCTT 57.169 33.333 9.83 0.00 0.00 2.85
38 39 6.665992 TTAAGTCTTCTCTTCCACTAAGCA 57.334 37.500 0.00 0.00 34.97 3.91
83 84 5.475719 CACCAATTCTCTCAACATGCAAAT 58.524 37.500 0.00 0.00 0.00 2.32
85 86 6.425721 CACCAATTCTCTCAACATGCAAATTT 59.574 34.615 0.00 0.00 0.00 1.82
143 145 6.479884 AGTTTTCTCTCTCATTAAGCCATGT 58.520 36.000 0.00 0.00 0.00 3.21
247 251 9.410556 TGTCACATCATATATTCATGTTAGTCG 57.589 33.333 4.82 0.00 0.00 4.18
266 271 9.493206 GTTAGTCGTTCTTTACATTTTTGTTCA 57.507 29.630 0.00 0.00 0.00 3.18
468 976 3.319137 TCCTCAATGAAGAAGACACCG 57.681 47.619 0.00 0.00 0.00 4.94
659 1169 9.573133 ACATATTCTTTTAGTTGCTAATTGTGC 57.427 29.630 0.00 0.00 0.00 4.57
660 1170 9.571810 CATATTCTTTTAGTTGCTAATTGTGCA 57.428 29.630 4.21 4.21 38.80 4.57
661 1171 9.793252 ATATTCTTTTAGTTGCTAATTGTGCAG 57.207 29.630 7.76 0.00 41.71 4.41
662 1172 6.633500 TCTTTTAGTTGCTAATTGTGCAGT 57.367 33.333 7.76 3.82 41.71 4.40
663 1173 6.437928 TCTTTTAGTTGCTAATTGTGCAGTG 58.562 36.000 7.76 0.00 41.71 3.66
664 1174 2.712057 AGTTGCTAATTGTGCAGTGC 57.288 45.000 8.58 8.58 41.71 4.40
665 1175 1.955778 AGTTGCTAATTGTGCAGTGCA 59.044 42.857 15.37 15.37 41.71 4.57
666 1176 2.030540 AGTTGCTAATTGTGCAGTGCAG 60.031 45.455 20.42 6.75 40.08 4.41
667 1177 0.241749 TGCTAATTGTGCAGTGCAGC 59.758 50.000 20.42 17.56 40.08 5.25
668 1178 0.241749 GCTAATTGTGCAGTGCAGCA 59.758 50.000 20.42 16.47 40.08 4.41
674 1184 3.585020 TGCAGTGCAGCACAACGG 61.585 61.111 27.35 14.11 40.11 4.44
675 1185 4.332637 GCAGTGCAGCACAACGGG 62.333 66.667 27.35 11.74 36.74 5.28
676 1186 2.901840 CAGTGCAGCACAACGGGT 60.902 61.111 27.35 2.28 36.74 5.28
677 1187 2.591715 AGTGCAGCACAACGGGTC 60.592 61.111 27.35 0.00 36.74 4.46
678 1188 2.899838 GTGCAGCACAACGGGTCA 60.900 61.111 21.22 0.00 34.08 4.02
679 1189 2.899838 TGCAGCACAACGGGTCAC 60.900 61.111 0.00 0.00 0.00 3.67
680 1190 3.660111 GCAGCACAACGGGTCACC 61.660 66.667 0.00 0.00 0.00 4.02
690 1200 3.388841 GGGTCACCGTCTCACCAT 58.611 61.111 0.00 0.00 31.06 3.55
691 1201 1.677552 GGGTCACCGTCTCACCATT 59.322 57.895 0.00 0.00 31.06 3.16
692 1202 0.036306 GGGTCACCGTCTCACCATTT 59.964 55.000 0.00 0.00 31.06 2.32
693 1203 1.544759 GGGTCACCGTCTCACCATTTT 60.545 52.381 0.00 0.00 31.06 1.82
694 1204 1.535462 GGTCACCGTCTCACCATTTTG 59.465 52.381 0.00 0.00 0.00 2.44
695 1205 2.218603 GTCACCGTCTCACCATTTTGT 58.781 47.619 0.00 0.00 0.00 2.83
696 1206 2.032030 GTCACCGTCTCACCATTTTGTG 60.032 50.000 0.00 0.00 37.59 3.33
697 1207 1.946768 CACCGTCTCACCATTTTGTGT 59.053 47.619 0.00 0.00 37.51 3.72
698 1208 1.946768 ACCGTCTCACCATTTTGTGTG 59.053 47.619 0.00 0.00 37.51 3.82
699 1209 1.334960 CCGTCTCACCATTTTGTGTGC 60.335 52.381 0.00 0.00 37.51 4.57
700 1210 1.333308 CGTCTCACCATTTTGTGTGCA 59.667 47.619 0.00 0.00 37.51 4.57
701 1211 2.731217 GTCTCACCATTTTGTGTGCAC 58.269 47.619 10.75 10.75 37.51 4.57
702 1212 1.680735 TCTCACCATTTTGTGTGCACC 59.319 47.619 15.69 6.37 37.51 5.01
703 1213 1.682854 CTCACCATTTTGTGTGCACCT 59.317 47.619 15.69 0.00 37.51 4.00
704 1214 2.101249 CTCACCATTTTGTGTGCACCTT 59.899 45.455 15.69 0.00 37.51 3.50
705 1215 2.499289 TCACCATTTTGTGTGCACCTTT 59.501 40.909 15.69 0.00 37.51 3.11
706 1216 3.055530 TCACCATTTTGTGTGCACCTTTT 60.056 39.130 15.69 0.00 37.51 2.27
707 1217 4.160439 TCACCATTTTGTGTGCACCTTTTA 59.840 37.500 15.69 0.00 37.51 1.52
708 1218 4.872691 CACCATTTTGTGTGCACCTTTTAA 59.127 37.500 15.69 2.72 0.00 1.52
709 1219 5.006552 CACCATTTTGTGTGCACCTTTTAAG 59.993 40.000 15.69 0.00 0.00 1.85
710 1220 9.928855 TCACCATTTTGTGTGCACCTTTTAAGG 62.929 40.741 15.69 11.47 43.13 2.69
722 1232 4.813296 CCTTTTAAGGGCACGTATCATC 57.187 45.455 0.32 0.00 42.66 2.92
723 1233 4.451900 CCTTTTAAGGGCACGTATCATCT 58.548 43.478 0.32 0.00 42.66 2.90
724 1234 5.607477 CCTTTTAAGGGCACGTATCATCTA 58.393 41.667 0.32 0.00 42.66 1.98
725 1235 6.053005 CCTTTTAAGGGCACGTATCATCTAA 58.947 40.000 0.32 0.00 42.66 2.10
726 1236 6.540914 CCTTTTAAGGGCACGTATCATCTAAA 59.459 38.462 0.32 0.00 42.66 1.85
727 1237 6.913873 TTTAAGGGCACGTATCATCTAAAC 57.086 37.500 0.00 0.00 0.00 2.01
728 1238 4.481368 AAGGGCACGTATCATCTAAACA 57.519 40.909 0.00 0.00 0.00 2.83
729 1239 4.689612 AGGGCACGTATCATCTAAACAT 57.310 40.909 0.00 0.00 0.00 2.71
730 1240 5.801531 AGGGCACGTATCATCTAAACATA 57.198 39.130 0.00 0.00 0.00 2.29
731 1241 6.360370 AGGGCACGTATCATCTAAACATAT 57.640 37.500 0.00 0.00 0.00 1.78
732 1242 6.769512 AGGGCACGTATCATCTAAACATATT 58.230 36.000 0.00 0.00 0.00 1.28
745 1255 6.194235 TCTAAACATATTGCCAACCATTCCT 58.806 36.000 0.00 0.00 0.00 3.36
747 1257 2.431782 ACATATTGCCAACCATTCCTGC 59.568 45.455 0.00 0.00 0.00 4.85
754 1264 0.675083 CAACCATTCCTGCAGCAACA 59.325 50.000 8.66 0.00 0.00 3.33
794 1304 1.594862 GGAAGAAACGAGCGGATCATG 59.405 52.381 0.00 0.00 0.00 3.07
808 1318 2.413502 GGATCATGTCGAGTAGCTAGCG 60.414 54.545 9.55 9.11 0.00 4.26
809 1319 1.664873 TCATGTCGAGTAGCTAGCGT 58.335 50.000 9.55 0.00 0.00 5.07
810 1320 1.598132 TCATGTCGAGTAGCTAGCGTC 59.402 52.381 9.55 6.88 0.00 5.19
811 1321 1.330829 CATGTCGAGTAGCTAGCGTCA 59.669 52.381 9.55 14.67 0.00 4.35
812 1322 1.445871 TGTCGAGTAGCTAGCGTCAA 58.554 50.000 9.55 0.00 0.00 3.18
813 1323 1.397343 TGTCGAGTAGCTAGCGTCAAG 59.603 52.381 9.55 2.64 0.00 3.02
844 1369 2.053627 CGCCTTGAATGTGAGCAAAAC 58.946 47.619 0.00 0.00 0.00 2.43
862 1387 5.672819 GCAAAACAATATCCGTACTCACCAC 60.673 44.000 0.00 0.00 0.00 4.16
883 1408 6.151691 CCACAAAAGTCAATGAATGATTCGT 58.848 36.000 0.18 0.00 40.97 3.85
898 1423 1.388547 TTCGTGCTGGCTTTGACTTT 58.611 45.000 0.00 0.00 0.00 2.66
899 1424 1.388547 TCGTGCTGGCTTTGACTTTT 58.611 45.000 0.00 0.00 0.00 2.27
900 1425 1.065401 TCGTGCTGGCTTTGACTTTTG 59.935 47.619 0.00 0.00 0.00 2.44
901 1426 1.065401 CGTGCTGGCTTTGACTTTTGA 59.935 47.619 0.00 0.00 0.00 2.69
902 1427 2.287788 CGTGCTGGCTTTGACTTTTGAT 60.288 45.455 0.00 0.00 0.00 2.57
903 1428 3.058293 CGTGCTGGCTTTGACTTTTGATA 60.058 43.478 0.00 0.00 0.00 2.15
904 1429 4.556501 CGTGCTGGCTTTGACTTTTGATAA 60.557 41.667 0.00 0.00 0.00 1.75
905 1430 5.288804 GTGCTGGCTTTGACTTTTGATAAA 58.711 37.500 0.00 0.00 0.00 1.40
918 1443 4.695217 TTTGATAAATGACAAGTCGCCC 57.305 40.909 0.00 0.00 0.00 6.13
931 1456 0.461961 GTCGCCCTAGTTCATCAGCT 59.538 55.000 0.00 0.00 0.00 4.24
932 1457 0.747255 TCGCCCTAGTTCATCAGCTC 59.253 55.000 0.00 0.00 0.00 4.09
998 1532 5.362143 AGATCGATCGATATCCAACCATCAT 59.638 40.000 29.45 4.08 34.60 2.45
1003 1537 5.488262 TCGATATCCAACCATCATCATGT 57.512 39.130 0.00 0.00 0.00 3.21
1004 1538 5.482006 TCGATATCCAACCATCATCATGTC 58.518 41.667 0.00 0.00 0.00 3.06
1005 1539 4.633126 CGATATCCAACCATCATCATGTCC 59.367 45.833 0.00 0.00 0.00 4.02
1021 1555 1.970640 TGTCCTCAGTGCTGCTTCTAA 59.029 47.619 0.00 0.00 0.00 2.10
1023 1557 3.008375 TGTCCTCAGTGCTGCTTCTAAAT 59.992 43.478 0.00 0.00 0.00 1.40
1024 1558 3.620821 GTCCTCAGTGCTGCTTCTAAATC 59.379 47.826 0.00 0.00 0.00 2.17
1040 1574 1.270907 AATCTCTTCCTCAGCACCGT 58.729 50.000 0.00 0.00 0.00 4.83
1054 1588 1.202498 GCACCGTAGCCCTTAACCTAG 60.202 57.143 0.00 0.00 0.00 3.02
1060 1594 0.621862 AGCCCTTAACCTAGCAGCCT 60.622 55.000 0.00 0.00 0.00 4.58
1104 1638 0.544357 TCTTCTCCGGCTTCAAGGGA 60.544 55.000 0.00 0.00 0.00 4.20
1107 1641 2.927856 TCCGGCTTCAAGGGAGCA 60.928 61.111 0.00 0.00 0.00 4.26
1166 1700 3.980583 GTCTTGTCGACCTCACCAA 57.019 52.632 14.12 0.00 36.62 3.67
1167 1701 1.499049 GTCTTGTCGACCTCACCAAC 58.501 55.000 14.12 0.00 36.62 3.77
1191 1725 0.980423 AGGAGACTCTCAAAGGCCAC 59.020 55.000 5.01 0.00 32.90 5.01
1206 1740 1.819632 CCACGCATTCTACCCTGCC 60.820 63.158 0.00 0.00 34.89 4.85
1228 1762 1.509923 CTACGGTTCCGTGAGTCCC 59.490 63.158 24.37 0.00 42.91 4.46
1272 1815 1.325355 TCTCCGTCTCCTTCGTGTTT 58.675 50.000 0.00 0.00 0.00 2.83
1464 2013 2.504899 CTGCACGACATCGACGCT 60.505 61.111 8.54 0.00 43.02 5.07
1484 2033 1.024579 AACCATGTCGGGATCAACGC 61.025 55.000 4.37 1.61 40.22 4.84
1511 2060 1.784525 GTCGTCTCCAACAAGTCCAG 58.215 55.000 0.00 0.00 0.00 3.86
1614 2163 1.451567 CTACGAGAGGGAGCCGACA 60.452 63.158 0.00 0.00 0.00 4.35
1638 2187 0.469331 TCAACGTGACCCTGTCTCCT 60.469 55.000 0.00 0.00 33.15 3.69
1639 2188 0.319900 CAACGTGACCCTGTCTCCTG 60.320 60.000 0.00 0.00 33.15 3.86
1641 2190 0.759436 ACGTGACCCTGTCTCCTGTT 60.759 55.000 0.00 0.00 33.15 3.16
1734 2283 2.124942 CTTGGCTTCGGCTCCTCC 60.125 66.667 0.00 0.00 41.44 4.30
1827 2376 0.724549 TCGACATCCGAAATTTGCCG 59.275 50.000 0.00 0.00 45.43 5.69
1876 2425 1.623834 GGTCCAAGGTCCTGGAGATCT 60.624 57.143 9.58 0.00 46.29 2.75
1899 2448 0.393267 TACCATTAGCAACGGCCACC 60.393 55.000 2.24 0.00 42.56 4.61
1916 2465 3.374402 CTCTGTCCTCGCCGTGGT 61.374 66.667 4.98 0.00 0.00 4.16
2023 2572 5.478679 CGATTCCCATACAAGGATCTCTACT 59.521 44.000 0.00 0.00 32.10 2.57
2190 2739 0.387202 CTGAGGTCGTCAGCATAGGG 59.613 60.000 9.49 0.00 46.41 3.53
2306 2855 7.112122 AGCCTTGACAAATACTTGTATCATCA 58.888 34.615 0.00 0.00 45.98 3.07
2314 2863 7.042456 ACAAATACTTGTATCATCATCGTCAGC 60.042 37.037 0.00 0.00 44.14 4.26
2331 2883 1.063972 GCACGACAACAAGCTGCAA 59.936 52.632 1.02 0.00 0.00 4.08
2333 2885 0.592247 CACGACAACAAGCTGCAACC 60.592 55.000 1.02 0.00 0.00 3.77
2334 2886 0.748005 ACGACAACAAGCTGCAACCT 60.748 50.000 1.02 0.00 0.00 3.50
2335 2887 1.225855 CGACAACAAGCTGCAACCTA 58.774 50.000 1.02 0.00 0.00 3.08
2343 2895 4.087182 ACAAGCTGCAACCTACTACTCTA 58.913 43.478 1.02 0.00 0.00 2.43
2361 2913 4.195416 CTCTAAATTGGGCTCAGAGGTTC 58.805 47.826 0.00 0.00 31.15 3.62
2373 2925 4.695396 CTCAGAGGTTCAAGATCATCAGG 58.305 47.826 0.00 0.00 0.00 3.86
2391 2943 2.583593 GGCGTCGCATCTGGACTC 60.584 66.667 20.50 0.00 32.24 3.36
2646 3198 4.576463 GGCATATTCATCCTTGAAGTCGTT 59.424 41.667 0.00 0.00 44.75 3.85
2768 3320 3.885297 GTGGATATTGAACTCCATGGTGG 59.115 47.826 17.76 11.57 43.20 4.61
2769 3321 2.887152 GGATATTGAACTCCATGGTGGC 59.113 50.000 17.76 9.82 37.47 5.01
2805 3357 2.283298 GCATGCTTAGCACTCAAGCTA 58.717 47.619 9.82 0.00 46.85 3.32
2830 3382 2.741985 TGTGCTCGCACCCATTCG 60.742 61.111 18.35 0.00 45.63 3.34
2836 3388 2.358125 CGCACCCATTCGTGGACA 60.358 61.111 0.00 0.00 34.16 4.02
2860 3412 1.160329 GCCTACCATGCGCCAAGTAG 61.160 60.000 16.61 16.61 33.50 2.57
2874 3426 3.619979 GCCAAGTAGTGCAGTACCTTGAT 60.620 47.826 27.56 12.48 0.00 2.57
2885 3437 4.643795 CCTTGATGGTGACCGCAT 57.356 55.556 0.00 0.00 0.00 4.73
2895 3447 1.803334 GTGACCGCATAACACCAGAA 58.197 50.000 0.00 0.00 0.00 3.02
3039 6831 1.673168 GTGGAAGATGACTCCATGCC 58.327 55.000 0.00 0.00 35.82 4.40
3043 6835 2.703007 GGAAGATGACTCCATGCCTAGT 59.297 50.000 0.00 0.00 32.09 2.57
3063 6864 2.331893 CGGCGCCATTTGGTTCTCA 61.332 57.895 28.98 0.00 37.57 3.27
3070 6871 4.202050 GCGCCATTTGGTTCTCATAAGATT 60.202 41.667 0.00 0.00 37.57 2.40
3076 6877 6.652205 TTTGGTTCTCATAAGATTAGGGGT 57.348 37.500 0.00 0.00 0.00 4.95
3080 6881 7.136885 TGGTTCTCATAAGATTAGGGGTCTTA 58.863 38.462 0.00 0.00 41.08 2.10
3108 6909 2.109834 ACATCCTCCAATTGGACCACAA 59.890 45.455 23.63 7.44 44.54 3.33
3130 6931 9.573133 CACAATATTTTCTATTCTGTGGGTTTC 57.427 33.333 0.00 0.00 0.00 2.78
3231 7035 2.554032 GCCCCTGTATTGTATGCATGTC 59.446 50.000 10.16 3.02 0.00 3.06
3246 7050 1.416401 CATGTCCGGGTTAGTAGGCAT 59.584 52.381 0.00 0.00 0.00 4.40
3248 7056 1.910671 TGTCCGGGTTAGTAGGCATTT 59.089 47.619 0.00 0.00 0.00 2.32
3252 7060 4.753610 GTCCGGGTTAGTAGGCATTTTATC 59.246 45.833 0.00 0.00 0.00 1.75
3257 7065 6.479660 CGGGTTAGTAGGCATTTTATCGTAAA 59.520 38.462 0.00 0.00 0.00 2.01
3263 7071 3.379057 AGGCATTTTATCGTAAAACCCCG 59.621 43.478 5.47 0.00 0.00 5.73
3270 7078 2.967397 GTAAAACCCCGGGCTTGC 59.033 61.111 17.73 7.78 0.00 4.01
3293 7101 4.116961 TGCCGAAAGTGATAATTCTACCG 58.883 43.478 0.00 0.00 0.00 4.02
3329 7140 1.873591 GACAATGTATCCACCATCCGC 59.126 52.381 0.00 0.00 0.00 5.54
3332 7143 1.140312 ATGTATCCACCATCCGCCTT 58.860 50.000 0.00 0.00 0.00 4.35
3338 7149 2.124151 ACCATCCGCCTTGGCATC 60.124 61.111 12.45 0.00 37.81 3.91
3339 7150 2.124193 CCATCCGCCTTGGCATCA 60.124 61.111 12.45 0.00 37.80 3.07
3340 7151 1.753848 CCATCCGCCTTGGCATCAA 60.754 57.895 12.45 0.00 37.80 2.57
3355 7166 3.759527 CATCAAGATTGGTGCAGTGAG 57.240 47.619 0.00 0.00 31.79 3.51
3383 8599 7.042725 TGCAGTATAAAGATGCGAAATAGTGAC 60.043 37.037 0.00 0.00 42.92 3.67
3384 8600 7.042725 GCAGTATAAAGATGCGAAATAGTGACA 60.043 37.037 0.00 0.00 0.00 3.58
3387 8603 5.786401 AAAGATGCGAAATAGTGACACTC 57.214 39.130 12.39 0.00 0.00 3.51
3388 8604 4.456280 AGATGCGAAATAGTGACACTCA 57.544 40.909 12.39 2.96 0.00 3.41
3390 8606 5.423015 AGATGCGAAATAGTGACACTCATT 58.577 37.500 12.39 8.40 0.00 2.57
3391 8607 5.877012 AGATGCGAAATAGTGACACTCATTT 59.123 36.000 12.39 15.03 0.00 2.32
3392 8608 7.041721 AGATGCGAAATAGTGACACTCATTTA 58.958 34.615 12.39 0.00 0.00 1.40
3393 8609 7.549134 AGATGCGAAATAGTGACACTCATTTAA 59.451 33.333 12.39 6.85 0.00 1.52
3452 8670 4.036734 TCACTCATTTCAAAGAACTGTGGC 59.963 41.667 0.00 0.00 0.00 5.01
3479 8697 3.701800 GGACTCTCCCTCTCCAACT 57.298 57.895 0.00 0.00 0.00 3.16
3480 8698 1.480789 GGACTCTCCCTCTCCAACTC 58.519 60.000 0.00 0.00 0.00 3.01
3481 8699 1.006639 GGACTCTCCCTCTCCAACTCT 59.993 57.143 0.00 0.00 0.00 3.24
3482 8700 2.242708 GGACTCTCCCTCTCCAACTCTA 59.757 54.545 0.00 0.00 0.00 2.43
3483 8701 3.309265 GGACTCTCCCTCTCCAACTCTAA 60.309 52.174 0.00 0.00 0.00 2.10
3484 8702 4.345854 GACTCTCCCTCTCCAACTCTAAA 58.654 47.826 0.00 0.00 0.00 1.85
3485 8703 4.753186 ACTCTCCCTCTCCAACTCTAAAA 58.247 43.478 0.00 0.00 0.00 1.52
3486 8704 5.346270 ACTCTCCCTCTCCAACTCTAAAAT 58.654 41.667 0.00 0.00 0.00 1.82
3487 8705 6.503944 ACTCTCCCTCTCCAACTCTAAAATA 58.496 40.000 0.00 0.00 0.00 1.40
3488 8706 6.609616 ACTCTCCCTCTCCAACTCTAAAATAG 59.390 42.308 0.00 0.00 0.00 1.73
3489 8707 5.364157 TCTCCCTCTCCAACTCTAAAATAGC 59.636 44.000 0.00 0.00 0.00 2.97
3490 8708 5.281314 TCCCTCTCCAACTCTAAAATAGCT 58.719 41.667 0.00 0.00 0.00 3.32
3491 8709 5.726793 TCCCTCTCCAACTCTAAAATAGCTT 59.273 40.000 0.00 0.00 0.00 3.74
3492 8710 6.901300 TCCCTCTCCAACTCTAAAATAGCTTA 59.099 38.462 0.00 0.00 0.00 3.09
3493 8711 6.987404 CCCTCTCCAACTCTAAAATAGCTTAC 59.013 42.308 0.00 0.00 0.00 2.34
3494 8712 6.987404 CCTCTCCAACTCTAAAATAGCTTACC 59.013 42.308 0.00 0.00 0.00 2.85
3495 8713 6.885922 TCTCCAACTCTAAAATAGCTTACCC 58.114 40.000 0.00 0.00 0.00 3.69
3496 8714 5.667466 TCCAACTCTAAAATAGCTTACCCG 58.333 41.667 0.00 0.00 0.00 5.28
3497 8715 4.272748 CCAACTCTAAAATAGCTTACCCGC 59.727 45.833 0.00 0.00 0.00 6.13
3498 8716 4.748277 ACTCTAAAATAGCTTACCCGCA 57.252 40.909 0.00 0.00 0.00 5.69
3499 8717 5.093849 ACTCTAAAATAGCTTACCCGCAA 57.906 39.130 0.00 0.00 0.00 4.85
3500 8718 5.493809 ACTCTAAAATAGCTTACCCGCAAA 58.506 37.500 0.00 0.00 0.00 3.68
3501 8719 5.941647 ACTCTAAAATAGCTTACCCGCAAAA 59.058 36.000 0.00 0.00 0.00 2.44
3502 8720 6.431852 ACTCTAAAATAGCTTACCCGCAAAAA 59.568 34.615 0.00 0.00 0.00 1.94
3597 8930 2.143876 CCCCCTTGTATGGGTCAAAG 57.856 55.000 0.00 0.00 45.70 2.77
3611 8944 1.181098 TCAAAGCAAAGGAGCAGCCC 61.181 55.000 0.00 0.00 37.37 5.19
3625 8958 1.478288 GCAGCCCAGCCTCAAGATTAT 60.478 52.381 0.00 0.00 0.00 1.28
3654 8988 7.992180 AGCAAACAGAAAACAATAAAGACTG 57.008 32.000 0.00 0.00 0.00 3.51
3658 8992 6.942532 ACAGAAAACAATAAAGACTGCAGA 57.057 33.333 23.35 0.00 0.00 4.26
3717 9060 0.036765 TGGATTGGACGTACTGGTGC 60.037 55.000 0.00 0.00 0.00 5.01
3753 9096 6.969993 ACAACAGTGTATATTTTGGTTGGT 57.030 33.333 0.00 0.00 38.66 3.67
3755 9098 7.206687 ACAACAGTGTATATTTTGGTTGGTTG 58.793 34.615 0.00 0.00 38.66 3.77
3759 9102 7.070074 ACAGTGTATATTTTGGTTGGTTGGAAA 59.930 33.333 0.00 0.00 0.00 3.13
3820 9163 3.449737 ACGGATAAAGACGGGATGAAAGA 59.550 43.478 0.00 0.00 0.00 2.52
3823 9166 4.383770 GGATAAAGACGGGATGAAAGACCA 60.384 45.833 0.00 0.00 0.00 4.02
3825 9168 0.250513 AGACGGGATGAAAGACCAGC 59.749 55.000 0.00 0.00 0.00 4.85
3826 9169 0.744771 GACGGGATGAAAGACCAGCC 60.745 60.000 0.00 0.00 41.63 4.85
3827 9170 1.815421 CGGGATGAAAGACCAGCCG 60.815 63.158 0.00 0.00 43.19 5.52
3828 9171 1.299976 GGGATGAAAGACCAGCCGT 59.700 57.895 0.00 0.00 43.19 5.68
3861 9251 6.015519 AGTGATTGCTTGCAACACCTTAAATA 60.016 34.615 23.53 0.00 32.76 1.40
3862 9252 6.813152 GTGATTGCTTGCAACACCTTAAATAT 59.187 34.615 19.95 1.36 0.00 1.28
3863 9253 7.973388 GTGATTGCTTGCAACACCTTAAATATA 59.027 33.333 19.95 0.00 0.00 0.86
3864 9254 8.526978 TGATTGCTTGCAACACCTTAAATATAA 58.473 29.630 10.37 0.00 0.00 0.98
3898 9685 2.634453 TGTGGCTGATCTGTTCTCTTGA 59.366 45.455 1.27 0.00 0.00 3.02
3998 9785 4.350346 GCATCGCATGTTAACTTATTGCA 58.650 39.130 7.22 0.00 32.94 4.08
4004 9791 5.163864 CGCATGTTAACTTATTGCAGTCTCA 60.164 40.000 7.22 0.00 32.94 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 3.005684 CAGGTTTTGCATTGCTTAGTGGA 59.994 43.478 10.49 0.00 0.00 4.02
83 84 0.547075 TGGGACGTTGAGGTGGAAAA 59.453 50.000 0.00 0.00 0.00 2.29
85 86 1.052124 AGTGGGACGTTGAGGTGGAA 61.052 55.000 0.00 0.00 0.00 3.53
143 145 9.653287 CAAGACTCACTTATGTGGTAGATTTTA 57.347 33.333 8.74 0.00 43.94 1.52
380 392 3.963724 CGTTGTTGCGGTAACTTTGTTAG 59.036 43.478 10.27 0.00 40.05 2.34
407 420 4.141620 ACTGAGGATGACTCTCTCTCTCTC 60.142 50.000 0.00 0.00 46.72 3.20
408 421 3.782523 ACTGAGGATGACTCTCTCTCTCT 59.217 47.826 0.00 0.00 46.72 3.10
409 422 4.156455 ACTGAGGATGACTCTCTCTCTC 57.844 50.000 0.00 0.00 46.72 3.20
410 423 4.721776 AGTACTGAGGATGACTCTCTCTCT 59.278 45.833 0.00 0.00 46.72 3.10
448 956 2.028112 CCGGTGTCTTCTTCATTGAGGA 60.028 50.000 0.00 0.00 0.00 3.71
640 1150 5.117592 GCACTGCACAATTAGCAACTAAAAG 59.882 40.000 6.26 0.00 42.17 2.27
641 1151 4.981674 GCACTGCACAATTAGCAACTAAAA 59.018 37.500 6.26 0.00 42.17 1.52
642 1152 4.037327 TGCACTGCACAATTAGCAACTAAA 59.963 37.500 0.00 0.00 42.17 1.85
643 1153 3.567585 TGCACTGCACAATTAGCAACTAA 59.432 39.130 0.00 0.00 42.17 2.24
644 1154 3.145286 TGCACTGCACAATTAGCAACTA 58.855 40.909 0.00 0.00 42.17 2.24
645 1155 1.955778 TGCACTGCACAATTAGCAACT 59.044 42.857 0.00 0.00 42.17 3.16
646 1156 2.322161 CTGCACTGCACAATTAGCAAC 58.678 47.619 0.00 1.04 42.17 4.17
647 1157 1.336148 GCTGCACTGCACAATTAGCAA 60.336 47.619 0.00 0.00 42.17 3.91
648 1158 0.241749 GCTGCACTGCACAATTAGCA 59.758 50.000 0.00 4.86 40.19 3.49
649 1159 0.241749 TGCTGCACTGCACAATTAGC 59.758 50.000 0.00 1.58 38.12 3.09
657 1167 3.585020 CCGTTGTGCTGCACTGCA 61.585 61.111 30.43 13.96 41.05 4.41
658 1168 4.332637 CCCGTTGTGCTGCACTGC 62.333 66.667 30.43 21.48 35.11 4.40
659 1169 2.896801 GACCCGTTGTGCTGCACTG 61.897 63.158 30.43 20.20 35.11 3.66
660 1170 2.591715 GACCCGTTGTGCTGCACT 60.592 61.111 30.43 11.79 35.11 4.40
661 1171 2.899838 TGACCCGTTGTGCTGCAC 60.900 61.111 25.15 25.15 34.56 4.57
662 1172 2.899838 GTGACCCGTTGTGCTGCA 60.900 61.111 0.00 0.00 0.00 4.41
663 1173 3.660111 GGTGACCCGTTGTGCTGC 61.660 66.667 0.00 0.00 0.00 5.25
673 1183 0.036306 AAATGGTGAGACGGTGACCC 59.964 55.000 0.00 0.00 0.00 4.46
674 1184 1.535462 CAAAATGGTGAGACGGTGACC 59.465 52.381 0.00 0.00 0.00 4.02
675 1185 2.032030 CACAAAATGGTGAGACGGTGAC 60.032 50.000 0.00 0.00 41.32 3.67
676 1186 2.217750 CACAAAATGGTGAGACGGTGA 58.782 47.619 0.00 0.00 41.32 4.02
677 1187 1.946768 ACACAAAATGGTGAGACGGTG 59.053 47.619 0.00 0.00 41.32 4.94
678 1188 1.946768 CACACAAAATGGTGAGACGGT 59.053 47.619 0.00 0.00 41.32 4.83
679 1189 1.334960 GCACACAAAATGGTGAGACGG 60.335 52.381 0.00 0.00 41.32 4.79
680 1190 1.333308 TGCACACAAAATGGTGAGACG 59.667 47.619 0.00 0.00 41.32 4.18
681 1191 2.543653 GGTGCACACAAAATGGTGAGAC 60.544 50.000 20.43 0.00 41.32 3.36
682 1192 1.680735 GGTGCACACAAAATGGTGAGA 59.319 47.619 20.43 0.00 41.32 3.27
683 1193 1.682854 AGGTGCACACAAAATGGTGAG 59.317 47.619 20.43 0.00 41.32 3.51
684 1194 1.774110 AGGTGCACACAAAATGGTGA 58.226 45.000 20.43 0.00 41.32 4.02
685 1195 2.600470 AAGGTGCACACAAAATGGTG 57.400 45.000 20.43 0.00 44.35 4.17
686 1196 3.625649 AAAAGGTGCACACAAAATGGT 57.374 38.095 20.43 0.00 0.00 3.55
687 1197 4.511082 CCTTAAAAGGTGCACACAAAATGG 59.489 41.667 20.43 9.02 41.41 3.16
688 1198 4.511082 CCCTTAAAAGGTGCACACAAAATG 59.489 41.667 20.43 3.48 44.98 2.32
689 1199 4.702831 CCCTTAAAAGGTGCACACAAAAT 58.297 39.130 20.43 1.76 44.98 1.82
690 1200 3.680196 GCCCTTAAAAGGTGCACACAAAA 60.680 43.478 20.43 5.03 44.98 2.44
691 1201 2.159028 GCCCTTAAAAGGTGCACACAAA 60.159 45.455 20.43 4.31 44.98 2.83
692 1202 1.410882 GCCCTTAAAAGGTGCACACAA 59.589 47.619 20.43 3.59 44.98 3.33
693 1203 1.036707 GCCCTTAAAAGGTGCACACA 58.963 50.000 20.43 0.00 44.98 3.72
694 1204 1.036707 TGCCCTTAAAAGGTGCACAC 58.963 50.000 20.43 8.23 44.98 3.82
695 1205 3.522483 TGCCCTTAAAAGGTGCACA 57.478 47.368 20.43 0.00 44.98 4.57
697 1207 0.466555 ACGTGCCCTTAAAAGGTGCA 60.467 50.000 16.27 16.27 44.98 4.57
698 1208 1.525941 TACGTGCCCTTAAAAGGTGC 58.474 50.000 7.94 10.63 44.98 5.01
699 1209 3.340034 TGATACGTGCCCTTAAAAGGTG 58.660 45.455 7.94 1.22 44.98 4.00
700 1210 3.706600 TGATACGTGCCCTTAAAAGGT 57.293 42.857 7.94 0.00 44.98 3.50
701 1211 4.451900 AGATGATACGTGCCCTTAAAAGG 58.548 43.478 0.00 1.47 46.06 3.11
702 1212 7.065324 TGTTTAGATGATACGTGCCCTTAAAAG 59.935 37.037 0.00 0.00 0.00 2.27
703 1213 6.879993 TGTTTAGATGATACGTGCCCTTAAAA 59.120 34.615 0.00 0.00 0.00 1.52
704 1214 6.408035 TGTTTAGATGATACGTGCCCTTAAA 58.592 36.000 0.00 0.00 0.00 1.52
705 1215 5.979993 TGTTTAGATGATACGTGCCCTTAA 58.020 37.500 0.00 0.00 0.00 1.85
706 1216 5.601583 TGTTTAGATGATACGTGCCCTTA 57.398 39.130 0.00 0.00 0.00 2.69
707 1217 4.481368 TGTTTAGATGATACGTGCCCTT 57.519 40.909 0.00 0.00 0.00 3.95
708 1218 4.689612 ATGTTTAGATGATACGTGCCCT 57.310 40.909 0.00 0.00 0.00 5.19
709 1219 6.620733 GCAATATGTTTAGATGATACGTGCCC 60.621 42.308 0.00 0.00 0.00 5.36
710 1220 6.307155 GCAATATGTTTAGATGATACGTGCC 58.693 40.000 0.00 0.00 0.00 5.01
711 1221 6.073276 TGGCAATATGTTTAGATGATACGTGC 60.073 38.462 0.00 0.00 0.00 5.34
712 1222 7.420184 TGGCAATATGTTTAGATGATACGTG 57.580 36.000 0.00 0.00 0.00 4.49
713 1223 7.041372 GGTTGGCAATATGTTTAGATGATACGT 60.041 37.037 1.92 0.00 0.00 3.57
714 1224 7.041440 TGGTTGGCAATATGTTTAGATGATACG 60.041 37.037 1.92 0.00 0.00 3.06
715 1225 8.165239 TGGTTGGCAATATGTTTAGATGATAC 57.835 34.615 1.92 0.00 0.00 2.24
716 1226 8.938801 ATGGTTGGCAATATGTTTAGATGATA 57.061 30.769 1.92 0.00 0.00 2.15
717 1227 7.844493 ATGGTTGGCAATATGTTTAGATGAT 57.156 32.000 1.92 0.00 0.00 2.45
718 1228 7.201902 GGAATGGTTGGCAATATGTTTAGATGA 60.202 37.037 1.92 0.00 0.00 2.92
719 1229 6.925165 GGAATGGTTGGCAATATGTTTAGATG 59.075 38.462 1.92 0.00 0.00 2.90
720 1230 6.840705 AGGAATGGTTGGCAATATGTTTAGAT 59.159 34.615 1.92 0.00 0.00 1.98
721 1231 6.096705 CAGGAATGGTTGGCAATATGTTTAGA 59.903 38.462 1.92 0.00 0.00 2.10
722 1232 6.275335 CAGGAATGGTTGGCAATATGTTTAG 58.725 40.000 1.92 0.00 0.00 1.85
723 1233 5.395103 GCAGGAATGGTTGGCAATATGTTTA 60.395 40.000 1.92 0.00 0.00 2.01
724 1234 4.623647 GCAGGAATGGTTGGCAATATGTTT 60.624 41.667 1.92 0.00 0.00 2.83
725 1235 3.118665 GCAGGAATGGTTGGCAATATGTT 60.119 43.478 1.92 0.00 0.00 2.71
726 1236 2.431782 GCAGGAATGGTTGGCAATATGT 59.568 45.455 1.92 0.00 0.00 2.29
727 1237 2.431419 TGCAGGAATGGTTGGCAATATG 59.569 45.455 1.92 0.00 0.00 1.78
728 1238 2.696707 CTGCAGGAATGGTTGGCAATAT 59.303 45.455 5.57 0.00 33.58 1.28
729 1239 2.101783 CTGCAGGAATGGTTGGCAATA 58.898 47.619 5.57 0.00 33.58 1.90
730 1240 0.899720 CTGCAGGAATGGTTGGCAAT 59.100 50.000 5.57 0.00 33.58 3.56
731 1241 1.818959 GCTGCAGGAATGGTTGGCAA 61.819 55.000 17.12 0.00 33.58 4.52
732 1242 2.277591 GCTGCAGGAATGGTTGGCA 61.278 57.895 17.12 0.00 0.00 4.92
747 1257 2.625823 AATTCCCCGCGTGTTGCTG 61.626 57.895 4.92 0.00 43.27 4.41
754 1264 0.108329 CACTAGACAATTCCCCGCGT 60.108 55.000 4.92 0.00 0.00 6.01
794 1304 1.856807 GCTTGACGCTAGCTACTCGAC 60.857 57.143 13.93 10.56 35.74 4.20
808 1318 2.658707 GCGACCACACGAGCTTGAC 61.659 63.158 8.31 0.00 35.09 3.18
809 1319 2.355837 GCGACCACACGAGCTTGA 60.356 61.111 8.31 0.00 35.09 3.02
810 1320 3.414700 GGCGACCACACGAGCTTG 61.415 66.667 0.00 0.00 35.09 4.01
811 1321 3.165160 AAGGCGACCACACGAGCTT 62.165 57.895 0.00 0.00 35.09 3.74
812 1322 3.616721 AAGGCGACCACACGAGCT 61.617 61.111 0.00 0.00 35.09 4.09
813 1323 3.414700 CAAGGCGACCACACGAGC 61.415 66.667 0.00 0.00 35.09 5.03
815 1325 0.948623 CATTCAAGGCGACCACACGA 60.949 55.000 0.00 0.00 35.09 4.35
816 1326 1.227999 ACATTCAAGGCGACCACACG 61.228 55.000 0.00 0.00 0.00 4.49
844 1369 5.642063 ACTTTTGTGGTGAGTACGGATATTG 59.358 40.000 0.00 0.00 0.00 1.90
862 1387 5.860182 AGCACGAATCATTCATTGACTTTTG 59.140 36.000 0.00 0.00 37.11 2.44
883 1408 5.528043 TTTATCAAAAGTCAAAGCCAGCA 57.472 34.783 0.00 0.00 0.00 4.41
898 1423 3.950397 AGGGCGACTTGTCATTTATCAA 58.050 40.909 0.00 0.00 0.00 2.57
899 1424 3.627395 AGGGCGACTTGTCATTTATCA 57.373 42.857 0.00 0.00 0.00 2.15
900 1425 4.694339 ACTAGGGCGACTTGTCATTTATC 58.306 43.478 0.00 0.00 28.74 1.75
901 1426 4.755266 ACTAGGGCGACTTGTCATTTAT 57.245 40.909 0.00 0.00 28.74 1.40
902 1427 4.020928 TGAACTAGGGCGACTTGTCATTTA 60.021 41.667 0.00 0.00 33.98 1.40
903 1428 3.244422 TGAACTAGGGCGACTTGTCATTT 60.244 43.478 0.00 0.00 33.98 2.32
904 1429 2.301870 TGAACTAGGGCGACTTGTCATT 59.698 45.455 0.00 0.00 33.98 2.57
905 1430 1.899814 TGAACTAGGGCGACTTGTCAT 59.100 47.619 0.00 0.00 33.98 3.06
940 1465 7.205992 TGCAAATTATAGTCTCTCTACAGCTG 58.794 38.462 13.48 13.48 0.00 4.24
946 1471 6.015434 TGGCGATGCAAATTATAGTCTCTCTA 60.015 38.462 0.00 0.00 0.00 2.43
953 1478 3.213506 TGCTGGCGATGCAAATTATAGT 58.786 40.909 0.00 0.00 37.51 2.12
998 1532 0.689055 AAGCAGCACTGAGGACATGA 59.311 50.000 0.00 0.00 0.00 3.07
1003 1537 3.517100 AGATTTAGAAGCAGCACTGAGGA 59.483 43.478 0.81 0.00 0.00 3.71
1004 1538 3.870419 GAGATTTAGAAGCAGCACTGAGG 59.130 47.826 0.81 0.00 0.00 3.86
1005 1539 4.757594 AGAGATTTAGAAGCAGCACTGAG 58.242 43.478 0.81 0.00 0.00 3.35
1021 1555 1.270907 ACGGTGCTGAGGAAGAGATT 58.729 50.000 0.00 0.00 0.00 2.40
1023 1557 1.464734 CTACGGTGCTGAGGAAGAGA 58.535 55.000 0.00 0.00 0.00 3.10
1024 1558 0.179124 GCTACGGTGCTGAGGAAGAG 60.179 60.000 0.00 0.00 0.00 2.85
1040 1574 1.129058 GGCTGCTAGGTTAAGGGCTA 58.871 55.000 0.00 0.00 0.00 3.93
1060 1594 1.078214 CATCTTCTCCGGCAGCCAA 60.078 57.895 13.30 0.00 0.00 4.52
1104 1638 1.227999 CGTCCACGGTGATGTTTGCT 61.228 55.000 10.28 0.00 35.37 3.91
1149 1683 0.031585 CGTTGGTGAGGTCGACAAGA 59.968 55.000 18.91 0.00 0.00 3.02
1158 1692 3.612247 CTCCTGGCCGTTGGTGAGG 62.612 68.421 0.00 0.00 0.00 3.86
1161 1695 2.358737 GTCTCCTGGCCGTTGGTG 60.359 66.667 0.00 1.46 0.00 4.17
1166 1700 0.832135 TTTGAGAGTCTCCTGGCCGT 60.832 55.000 17.57 0.00 0.00 5.68
1167 1701 0.108424 CTTTGAGAGTCTCCTGGCCG 60.108 60.000 17.57 0.00 0.00 6.13
1191 1725 2.203209 GGGGCAGGGTAGAATGCG 60.203 66.667 0.00 0.00 43.49 4.73
1242 1785 2.531206 GAGACGGAGAAGGATTTCACG 58.469 52.381 0.00 0.00 39.93 4.35
1272 1815 1.209621 GGTAGTTGGGGTAGATGGCA 58.790 55.000 0.00 0.00 0.00 4.92
1392 1941 3.236618 GACGTGGTTGCTGGCGTTC 62.237 63.158 0.00 0.00 37.71 3.95
1464 2013 1.741055 GCGTTGATCCCGACATGGTTA 60.741 52.381 6.11 0.00 35.15 2.85
1484 2033 1.300620 TTGGAGACGACGCTGTTGG 60.301 57.895 0.00 0.00 0.00 3.77
1614 2163 0.391597 ACAGGGTCACGTTGATTCGT 59.608 50.000 0.00 0.00 45.10 3.85
1764 2313 0.327591 AAGAGAAGCTCCAGCCAAGG 59.672 55.000 0.00 0.00 43.38 3.61
1827 2376 2.125350 CCAAGACGAGGCAGCCTC 60.125 66.667 29.53 29.53 46.44 4.70
1876 2425 1.813786 GGCCGTTGCTAATGGTAACAA 59.186 47.619 0.00 0.00 44.95 2.83
1899 2448 2.932234 AACCACGGCGAGGACAGAG 61.932 63.158 29.75 2.30 0.00 3.35
2001 2550 6.434652 CGTAGTAGAGATCCTTGTATGGGAAT 59.565 42.308 0.00 0.00 36.37 3.01
2023 2572 0.250124 CTGAACCCTTGTGTGGCGTA 60.250 55.000 0.00 0.00 0.00 4.42
2241 2790 0.755327 ACACCAGAAACAGTTGGCCC 60.755 55.000 0.00 0.00 38.03 5.80
2314 2863 0.592247 GGTTGCAGCTTGTTGTCGTG 60.592 55.000 0.00 0.00 0.00 4.35
2331 2883 5.278061 TGAGCCCAATTTAGAGTAGTAGGT 58.722 41.667 0.00 0.00 0.00 3.08
2333 2885 6.239176 CCTCTGAGCCCAATTTAGAGTAGTAG 60.239 46.154 0.00 0.00 34.51 2.57
2334 2886 5.598830 CCTCTGAGCCCAATTTAGAGTAGTA 59.401 44.000 0.00 0.00 34.51 1.82
2335 2887 4.407296 CCTCTGAGCCCAATTTAGAGTAGT 59.593 45.833 0.00 0.00 34.51 2.73
2343 2895 2.978156 TGAACCTCTGAGCCCAATTT 57.022 45.000 0.00 0.00 0.00 1.82
2361 2913 0.877649 CGACGCCCCTGATGATCTTG 60.878 60.000 0.00 0.00 0.00 3.02
2373 2925 4.148825 AGTCCAGATGCGACGCCC 62.149 66.667 18.69 9.33 35.33 6.13
2487 3039 0.591170 ACCGTGCAAGACCAAAATCG 59.409 50.000 0.00 0.00 0.00 3.34
2646 3198 0.466372 TGATTGGCCGTTGTCCACAA 60.466 50.000 0.00 0.00 32.45 3.33
2768 3320 4.458295 AGCATGCCTCATTTACATCATAGC 59.542 41.667 15.66 0.00 0.00 2.97
2769 3321 6.570672 AAGCATGCCTCATTTACATCATAG 57.429 37.500 15.66 0.00 0.00 2.23
2805 3357 1.587054 GTGCGAGCACAGTAGTCCT 59.413 57.895 21.73 0.00 45.53 3.85
2830 3382 1.562672 ATGGTAGGCCTGGTGTCCAC 61.563 60.000 17.99 2.69 35.27 4.02
2836 3388 4.489771 GCGCATGGTAGGCCTGGT 62.490 66.667 17.99 0.00 35.27 4.00
2885 3437 5.483937 ACTGGTGATGATAGTTCTGGTGTTA 59.516 40.000 0.00 0.00 0.00 2.41
2895 3447 2.501723 GGTGTCCACTGGTGATGATAGT 59.498 50.000 1.93 0.00 0.00 2.12
2937 3489 3.555518 GTCAAAACCTTCGTTCTGCATC 58.444 45.455 0.00 0.00 0.00 3.91
2943 6727 1.302366 ACGGGTCAAAACCTTCGTTC 58.698 50.000 0.00 0.00 45.66 3.95
3039 6831 2.180204 CCAAATGGCGCCGGACTAG 61.180 63.158 23.90 9.20 0.00 2.57
3043 6835 3.059386 GAACCAAATGGCGCCGGA 61.059 61.111 23.90 5.15 39.32 5.14
3048 6840 5.505173 AATCTTATGAGAACCAAATGGCG 57.495 39.130 0.00 0.00 35.07 5.69
3052 6844 7.129504 AGACCCCTAATCTTATGAGAACCAAAT 59.870 37.037 0.00 0.00 35.07 2.32
3070 6871 3.391296 GGATGTTGCAGATAAGACCCCTA 59.609 47.826 0.00 0.00 0.00 3.53
3076 6877 4.842531 TTGGAGGATGTTGCAGATAAGA 57.157 40.909 0.00 0.00 0.00 2.10
3080 6881 3.028850 CCAATTGGAGGATGTTGCAGAT 58.971 45.455 20.50 0.00 37.39 2.90
3108 6909 6.039382 GGCGAAACCCACAGAATAGAAAATAT 59.961 38.462 0.00 0.00 0.00 1.28
3117 6918 1.674322 CCGGCGAAACCCACAGAAT 60.674 57.895 9.30 0.00 33.26 2.40
3120 6921 0.885596 TTTACCGGCGAAACCCACAG 60.886 55.000 9.30 0.00 33.26 3.66
3130 6931 5.163794 ACAAATATTCAGAAGTTTACCGGCG 60.164 40.000 0.00 0.00 0.00 6.46
3192 6996 3.613030 GGGCAATGCTTCCATGAAAAAT 58.387 40.909 4.82 0.00 0.00 1.82
3200 7004 0.630673 ATACAGGGGCAATGCTTCCA 59.369 50.000 17.07 1.45 0.00 3.53
3204 7008 3.225104 CATACAATACAGGGGCAATGCT 58.775 45.455 4.82 0.00 0.00 3.79
3206 7010 2.957680 TGCATACAATACAGGGGCAATG 59.042 45.455 0.00 0.00 0.00 2.82
3207 7011 3.311167 TGCATACAATACAGGGGCAAT 57.689 42.857 0.00 0.00 0.00 3.56
3231 7035 3.744426 CGATAAAATGCCTACTAACCCGG 59.256 47.826 0.00 0.00 0.00 5.73
3246 7050 2.090760 GCCCGGGGTTTTACGATAAAA 58.909 47.619 25.28 0.00 0.00 1.52
3248 7056 0.911053 AGCCCGGGGTTTTACGATAA 59.089 50.000 22.45 0.00 0.00 1.75
3252 7060 2.985117 GCAAGCCCGGGGTTTTACG 61.985 63.158 34.93 23.76 33.16 3.18
3270 7078 4.209288 CGGTAGAATTATCACTTTCGGCAG 59.791 45.833 0.00 0.00 0.00 4.85
3293 7101 0.108709 TGTCGTTACATACCGGCACC 60.109 55.000 0.00 0.00 33.16 5.01
3332 7143 1.179152 CTGCACCAATCTTGATGCCA 58.821 50.000 6.80 0.00 37.26 4.92
3338 7149 2.606308 GCAACTCACTGCACCAATCTTG 60.606 50.000 0.00 0.00 42.17 3.02
3339 7150 1.610522 GCAACTCACTGCACCAATCTT 59.389 47.619 0.00 0.00 42.17 2.40
3340 7151 1.242076 GCAACTCACTGCACCAATCT 58.758 50.000 0.00 0.00 42.17 2.40
3341 7152 3.780925 GCAACTCACTGCACCAATC 57.219 52.632 0.00 0.00 42.17 2.67
3350 7161 4.568359 CGCATCTTTATACTGCAACTCACT 59.432 41.667 0.00 0.00 35.64 3.41
3355 7166 7.584123 CACTATTTCGCATCTTTATACTGCAAC 59.416 37.037 0.00 0.00 35.64 4.17
3360 7171 8.198109 AGTGTCACTATTTCGCATCTTTATACT 58.802 33.333 2.87 0.00 0.00 2.12
3370 7181 7.428282 TTTAAATGAGTGTCACTATTTCGCA 57.572 32.000 5.21 0.00 0.00 5.10
3421 8639 6.064846 TCTTTGAAATGAGTGAAAGCAGTC 57.935 37.500 0.00 0.00 43.38 3.51
3452 8670 4.950479 GGAGAGTCCCATGCAGTG 57.050 61.111 0.00 0.00 0.00 3.66
3476 8694 5.093849 TGCGGGTAAGCTATTTTAGAGTT 57.906 39.130 0.00 0.00 38.13 3.01
3477 8695 4.748277 TGCGGGTAAGCTATTTTAGAGT 57.252 40.909 0.00 0.00 38.13 3.24
3478 8696 6.431198 TTTTGCGGGTAAGCTATTTTAGAG 57.569 37.500 0.00 0.00 38.13 2.43
3479 8697 6.821031 TTTTTGCGGGTAAGCTATTTTAGA 57.179 33.333 0.00 0.00 38.13 2.10
3597 8930 3.756727 GCTGGGCTGCTCCTTTGC 61.757 66.667 0.00 1.58 34.39 3.68
3611 8944 6.441093 TTGCTAACAATAATCTTGAGGCTG 57.559 37.500 0.00 0.00 0.00 4.85
3625 8958 9.862371 TCTTTATTGTTTTCTGTTTGCTAACAA 57.138 25.926 14.52 0.00 43.33 2.83
3643 8977 8.633075 TTTTGAAAAGTCTGCAGTCTTTATTG 57.367 30.769 30.37 0.00 33.52 1.90
3654 8988 6.729187 AGTGTCATACTTTTGAAAAGTCTGC 58.271 36.000 24.86 19.41 35.67 4.26
3680 9014 6.400568 CAATCCAAGTGGCATGAAAAATACT 58.599 36.000 0.00 0.00 34.44 2.12
3681 9015 5.581874 CCAATCCAAGTGGCATGAAAAATAC 59.418 40.000 0.00 0.00 34.44 1.89
3683 9017 4.286549 TCCAATCCAAGTGGCATGAAAAAT 59.713 37.500 0.00 0.00 35.99 1.82
3684 9018 3.645212 TCCAATCCAAGTGGCATGAAAAA 59.355 39.130 0.00 0.00 35.99 1.94
3685 9019 3.006752 GTCCAATCCAAGTGGCATGAAAA 59.993 43.478 0.00 0.00 35.99 2.29
3686 9020 2.562298 GTCCAATCCAAGTGGCATGAAA 59.438 45.455 0.00 0.00 35.99 2.69
3753 9096 0.385751 TCGCACCGCAAAATTTCCAA 59.614 45.000 0.00 0.00 0.00 3.53
3755 9098 0.239879 TCTCGCACCGCAAAATTTCC 59.760 50.000 0.00 0.00 0.00 3.13
3759 9102 3.263941 GGTCTCGCACCGCAAAAT 58.736 55.556 0.00 0.00 34.56 1.82
3789 9132 5.047092 TCCCGTCTTTATCCGTAGAACTTTT 60.047 40.000 0.00 0.00 0.00 2.27
3820 9163 0.681564 CACTCTCTCCTACGGCTGGT 60.682 60.000 0.00 0.00 0.00 4.00
3823 9166 2.028130 CAATCACTCTCTCCTACGGCT 58.972 52.381 0.00 0.00 0.00 5.52
3825 9168 2.028130 AGCAATCACTCTCTCCTACGG 58.972 52.381 0.00 0.00 0.00 4.02
3826 9169 3.443037 CAAGCAATCACTCTCTCCTACG 58.557 50.000 0.00 0.00 0.00 3.51
3827 9170 3.194062 GCAAGCAATCACTCTCTCCTAC 58.806 50.000 0.00 0.00 0.00 3.18
3828 9171 2.833943 TGCAAGCAATCACTCTCTCCTA 59.166 45.455 0.00 0.00 0.00 2.94
3834 9224 1.610522 GGTGTTGCAAGCAATCACTCT 59.389 47.619 24.99 0.00 37.70 3.24
3898 9685 0.033366 GCCTTTTCAATGGCACGGTT 59.967 50.000 10.78 0.00 45.65 4.44
3998 9785 9.936759 TTTTTACCTTTTTGTTGAATTGAGACT 57.063 25.926 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.