Multiple sequence alignment - TraesCS4D01G024400

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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 TraesCS4D01G024400 chr4D 100.000 3713 0 0 1 3713 10768639 10764927 0.000000e+00 6857.0
1 TraesCS4D01G024400 chr4D 100.000 222 0 0 4019 4240 10764621 10764400 1.100000e-110 411.0
2 TraesCS4D01G024400 chr4B 96.927 2571 56 15 1151 3713 20280908 20278353 0.000000e+00 4289.0
3 TraesCS4D01G024400 chr4B 91.781 584 36 8 1 574 20281962 20281381 0.000000e+00 802.0
4 TraesCS4D01G024400 chr4B 86.897 435 23 14 631 1050 20281352 20280937 1.390000e-124 457.0
5 TraesCS4D01G024400 chr4B 100.000 55 0 0 4019 4073 20277676 20277622 7.500000e-18 102.0
6 TraesCS4D01G024400 chr4B 100.000 55 0 0 4019 4073 20278223 20278169 7.500000e-18 102.0
7 TraesCS4D01G024400 chrUn 95.004 1361 57 4 2355 3713 308088350 308089701 0.000000e+00 2126.0
8 TraesCS4D01G024400 chrUn 90.847 1180 81 14 1155 2324 308086638 308087800 0.000000e+00 1555.0
9 TraesCS4D01G024400 chrUn 91.105 371 12 7 222 571 432032994 432033364 2.290000e-132 483.0
10 TraesCS4D01G024400 chrUn 88.629 299 23 6 800 1090 432033659 432033954 1.880000e-93 353.0
11 TraesCS4D01G024400 chrUn 88.294 299 24 6 800 1090 308086332 308086627 8.730000e-92 348.0
12 TraesCS4D01G024400 chrUn 91.556 225 14 3 1 220 480012169 480012393 5.330000e-79 305.0
13 TraesCS4D01G024400 chrUn 93.258 178 11 1 1155 1332 432033965 432034141 1.170000e-65 261.0
14 TraesCS4D01G024400 chrUn 100.000 55 0 0 4019 4073 308089827 308089881 7.500000e-18 102.0
15 TraesCS4D01G024400 chrUn 100.000 28 0 0 763 790 308086280 308086307 8.000000e-03 52.8
16 TraesCS4D01G024400 chrUn 100.000 28 0 0 763 790 432033607 432033634 8.000000e-03 52.8
17 TraesCS4D01G024400 chr4A 95.004 1361 57 4 2355 3713 592546193 592547544 0.000000e+00 2126.0
18 TraesCS4D01G024400 chr4A 94.636 1361 63 3 2355 3713 593115002 593116354 0.000000e+00 2100.0
19 TraesCS4D01G024400 chr4A 91.349 1179 71 17 1158 2324 591499077 591497918 0.000000e+00 1583.0
20 TraesCS4D01G024400 chr4A 91.186 1180 77 14 1155 2324 592830408 592831570 0.000000e+00 1578.0
21 TraesCS4D01G024400 chr4A 91.117 1182 74 17 1155 2324 593113290 593114452 0.000000e+00 1572.0
22 TraesCS4D01G024400 chr4A 90.847 1180 81 14 1155 2324 592544481 592545643 0.000000e+00 1555.0
23 TraesCS4D01G024400 chr4A 94.211 570 33 0 2355 2924 591497371 591496802 0.000000e+00 870.0
24 TraesCS4D01G024400 chr4A 91.290 597 26 10 1 571 592829211 592829807 0.000000e+00 791.0
25 TraesCS4D01G024400 chr4A 90.369 623 29 12 1 592 591500614 591499992 0.000000e+00 789.0
26 TraesCS4D01G024400 chr4A 90.369 623 29 12 1 592 593111650 593112272 0.000000e+00 789.0
27 TraesCS4D01G024400 chr4A 91.122 597 27 10 1 571 592543281 592543877 0.000000e+00 785.0
28 TraesCS4D01G024400 chr4A 86.802 394 26 8 720 1090 593112889 593113279 2.360000e-112 416.0
29 TraesCS4D01G024400 chr4A 85.901 383 28 8 731 1090 591499470 591499091 6.650000e-103 385.0
30 TraesCS4D01G024400 chr4A 88.629 299 23 6 800 1090 592830102 592830397 1.880000e-93 353.0
31 TraesCS4D01G024400 chr4A 88.294 299 24 6 800 1090 592544175 592544470 8.730000e-92 348.0
32 TraesCS4D01G024400 chr4A 100.000 55 0 0 4019 4073 592547670 592547724 7.500000e-18 102.0
33 TraesCS4D01G024400 chr4A 100.000 55 0 0 4019 4073 592834040 592834094 7.500000e-18 102.0
34 TraesCS4D01G024400 chr4A 100.000 55 0 0 4019 4073 593116482 593116536 7.500000e-18 102.0
35 TraesCS4D01G024400 chr4A 100.000 28 0 0 763 790 592544123 592544150 8.000000e-03 52.8
36 TraesCS4D01G024400 chr4A 100.000 28 0 0 763 790 592830050 592830077 8.000000e-03 52.8
37 TraesCS4D01G024400 chr6B 90.609 1363 113 8 2354 3713 183333216 183331866 0.000000e+00 1794.0
38 TraesCS4D01G024400 chr6B 90.222 1217 94 14 1113 2324 183334541 183333345 0.000000e+00 1565.0
39 TraesCS4D01G024400 chr6B 87.305 449 26 19 635 1063 183334996 183334559 6.370000e-133 484.0
40 TraesCS4D01G024400 chr6B 89.565 230 15 7 158 386 698040458 698040237 2.500000e-72 283.0
41 TraesCS4D01G024400 chr6D 90.549 1365 107 11 2354 3713 98128710 98127363 0.000000e+00 1786.0
42 TraesCS4D01G024400 chr6D 90.386 1217 92 14 1113 2324 98130034 98128838 0.000000e+00 1576.0
43 TraesCS4D01G024400 chr6D 86.784 454 21 23 637 1063 98130493 98130052 1.780000e-128 470.0
44 TraesCS4D01G024400 chr6D 98.291 117 2 0 4072 4188 147675570 147675686 5.560000e-49 206.0
45 TraesCS4D01G024400 chr6D 98.291 117 2 0 4072 4188 366701106 366701222 5.560000e-49 206.0
46 TraesCS4D01G024400 chr6A 90.365 1370 111 9 2354 3713 117413292 117411934 0.000000e+00 1779.0
47 TraesCS4D01G024400 chr6A 89.227 1216 109 13 1113 2324 117414618 117413421 0.000000e+00 1500.0
48 TraesCS4D01G024400 chr6A 86.695 466 22 20 627 1063 117415090 117414636 8.250000e-132 481.0
49 TraesCS4D01G024400 chr7A 80.963 872 156 9 2397 3263 556319715 556320581 0.000000e+00 682.0
50 TraesCS4D01G024400 chr7D 99.145 117 1 0 4072 4188 199358703 199358587 1.190000e-50 211.0
51 TraesCS4D01G024400 chr3A 98.305 118 1 1 4071 4188 455782826 455782942 5.560000e-49 206.0
52 TraesCS4D01G024400 chr1D 97.479 119 3 0 4071 4189 408872520 408872402 2.000000e-48 204.0
53 TraesCS4D01G024400 chr2A 95.200 125 6 0 4065 4189 250318869 250318745 9.300000e-47 198.0
54 TraesCS4D01G024400 chr2A 95.200 125 6 0 4065 4189 250338505 250338381 9.300000e-47 198.0
55 TraesCS4D01G024400 chr2A 96.970 33 0 1 584 615 757825364 757825396 2.000000e-03 54.7
56 TraesCS4D01G024400 chr1A 95.238 126 4 2 4064 4188 329250256 329250132 9.300000e-47 198.0
57 TraesCS4D01G024400 chr7B 94.574 129 4 2 4072 4200 716093675 716093550 3.340000e-46 196.0
58 TraesCS4D01G024400 chr2B 97.297 37 1 0 594 630 39156772 39156808 3.540000e-06 63.9
59 TraesCS4D01G024400 chr1B 88.235 51 4 2 580 630 277446148 277446196 4.580000e-05 60.2
60 TraesCS4D01G024400 chr3D 94.595 37 2 0 594 630 44884146 44884110 1.650000e-04 58.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G024400 chr4D 10764400 10768639 4239 True 3634.000000 6857 100.000000 1 4240 2 chr4D.!!$R1 4239
1 TraesCS4D01G024400 chr4B 20277622 20281962 4340 True 1150.400000 4289 95.121000 1 4073 5 chr4B.!!$R1 4072
2 TraesCS4D01G024400 chrUn 308086280 308089881 3601 False 836.760000 2126 94.829000 763 4073 5 chrUn.!!$F2 3310
3 TraesCS4D01G024400 chrUn 432032994 432034141 1147 False 287.450000 483 93.248000 222 1332 4 chrUn.!!$F3 1110
4 TraesCS4D01G024400 chr4A 593111650 593116536 4886 False 995.800000 2100 92.584800 1 4073 5 chr4A.!!$F3 4072
5 TraesCS4D01G024400 chr4A 591496802 591500614 3812 True 906.750000 1583 90.457500 1 2924 4 chr4A.!!$R1 2923
6 TraesCS4D01G024400 chr4A 592543281 592547724 4443 False 828.133333 2126 94.211167 1 4073 6 chr4A.!!$F1 4072
7 TraesCS4D01G024400 chr4A 592829211 592834094 4883 False 575.360000 1578 94.221000 1 4073 5 chr4A.!!$F2 4072
8 TraesCS4D01G024400 chr6B 183331866 183334996 3130 True 1281.000000 1794 89.378667 635 3713 3 chr6B.!!$R2 3078
9 TraesCS4D01G024400 chr6D 98127363 98130493 3130 True 1277.333333 1786 89.239667 637 3713 3 chr6D.!!$R1 3076
10 TraesCS4D01G024400 chr6A 117411934 117415090 3156 True 1253.333333 1779 88.762333 627 3713 3 chr6A.!!$R1 3086
11 TraesCS4D01G024400 chr7A 556319715 556320581 866 False 682.000000 682 80.963000 2397 3263 1 chr7A.!!$F1 866

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
547 579 0.814010 AACGGTGTGTGTCTGCTTCC 60.814 55.000 0.00 0.00 0.0 3.46 F
722 1286 3.446873 TGAGTGAGAGAGAGAGGAAATGC 59.553 47.826 0.00 0.00 0.0 3.56 F
1710 2332 0.179086 TTGCGACTCTGAACACTGCA 60.179 50.000 0.00 0.00 0.0 4.41 F
2559 3718 1.520787 GTATGGGCCTCGTTCGTGG 60.521 63.158 4.53 8.64 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1430 2042 0.716108 GCATTCACAGAACTCGACGG 59.284 55.000 0.00 0.00 0.00 4.79 R
2559 3718 1.133407 CCCAGCGACTGAGTAGAAGAC 59.867 57.143 8.20 0.00 32.44 3.01 R
3152 4311 1.562942 AGAGCAGCCATCATCCAGAAA 59.437 47.619 0.00 0.00 0.00 2.52 R
4074 5489 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20 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
35 36 5.922960 ACTTAATGTTCATATAGGGGCCA 57.077 39.130 4.39 0.00 0.00 5.36
56 57 2.437716 CACCCCGGCGCTACAAAT 60.438 61.111 7.64 0.00 0.00 2.32
89 90 7.602644 CCGGCTGTAGATGCTCTAATAAATTTA 59.397 37.037 0.00 0.00 29.58 1.40
120 123 7.373617 TGCATATACTCTTCTCAATGGGTAA 57.626 36.000 0.00 0.00 0.00 2.85
122 125 8.097038 TGCATATACTCTTCTCAATGGGTAATC 58.903 37.037 0.00 0.00 0.00 1.75
128 134 6.600822 ACTCTTCTCAATGGGTAATCAATGTG 59.399 38.462 0.00 0.00 0.00 3.21
196 202 2.044492 TGGAAGGAGTAGGACAGGACAT 59.956 50.000 0.00 0.00 0.00 3.06
396 422 1.561542 ACATCTTCTGGACCACCATCC 59.438 52.381 0.00 0.00 45.87 3.51
414 440 1.224592 CCCATCCCTCCACCTTTCG 59.775 63.158 0.00 0.00 0.00 3.46
468 495 5.071653 TCCCTCCGACATAATCAATCAATCA 59.928 40.000 0.00 0.00 0.00 2.57
476 503 8.718734 CGACATAATCAATCAATCATCACAGAT 58.281 33.333 0.00 0.00 0.00 2.90
522 553 1.093972 CACCAGCGCCATTGATTGTA 58.906 50.000 2.29 0.00 0.00 2.41
545 577 1.714899 GCAACGGTGTGTGTCTGCTT 61.715 55.000 0.66 0.00 0.00 3.91
547 579 0.814010 AACGGTGTGTGTCTGCTTCC 60.814 55.000 0.00 0.00 0.00 3.46
596 636 9.750783 AATAGTCAGGTCCACGTATATATTACT 57.249 33.333 0.00 0.00 0.00 2.24
597 637 7.684937 AGTCAGGTCCACGTATATATTACTC 57.315 40.000 0.00 0.00 0.00 2.59
598 638 6.658391 AGTCAGGTCCACGTATATATTACTCC 59.342 42.308 0.00 0.00 0.00 3.85
599 639 6.658391 GTCAGGTCCACGTATATATTACTCCT 59.342 42.308 0.00 0.00 0.00 3.69
600 640 7.176340 GTCAGGTCCACGTATATATTACTCCTT 59.824 40.741 0.00 0.00 0.00 3.36
601 641 7.392673 TCAGGTCCACGTATATATTACTCCTTC 59.607 40.741 0.00 0.00 0.00 3.46
602 642 6.662663 AGGTCCACGTATATATTACTCCTTCC 59.337 42.308 0.00 0.00 0.00 3.46
603 643 6.404074 GGTCCACGTATATATTACTCCTTCCG 60.404 46.154 0.00 0.00 0.00 4.30
604 644 6.150140 GTCCACGTATATATTACTCCTTCCGT 59.850 42.308 0.00 0.00 0.00 4.69
605 645 6.372659 TCCACGTATATATTACTCCTTCCGTC 59.627 42.308 0.00 0.00 0.00 4.79
606 646 6.404074 CCACGTATATATTACTCCTTCCGTCC 60.404 46.154 0.00 0.00 0.00 4.79
607 647 5.649831 ACGTATATATTACTCCTTCCGTCCC 59.350 44.000 0.00 0.00 0.00 4.46
608 648 5.649395 CGTATATATTACTCCTTCCGTCCCA 59.351 44.000 0.00 0.00 0.00 4.37
609 649 6.320672 CGTATATATTACTCCTTCCGTCCCAT 59.679 42.308 0.00 0.00 0.00 4.00
610 650 7.500227 CGTATATATTACTCCTTCCGTCCCATA 59.500 40.741 0.00 0.00 0.00 2.74
611 651 9.193806 GTATATATTACTCCTTCCGTCCCATAA 57.806 37.037 0.00 0.00 0.00 1.90
612 652 8.855804 ATATATTACTCCTTCCGTCCCATAAT 57.144 34.615 0.00 0.00 0.00 1.28
613 653 9.947189 ATATATTACTCCTTCCGTCCCATAATA 57.053 33.333 0.00 0.00 0.00 0.98
614 654 8.855804 ATATTACTCCTTCCGTCCCATAATAT 57.144 34.615 0.00 0.00 0.00 1.28
615 655 4.891992 ACTCCTTCCGTCCCATAATATG 57.108 45.455 0.00 0.00 0.00 1.78
685 836 4.787551 TGCTCCTACAAAAGTTGGAGAAA 58.212 39.130 23.69 11.92 44.73 2.52
686 837 4.821805 TGCTCCTACAAAAGTTGGAGAAAG 59.178 41.667 23.69 9.59 44.73 2.62
718 878 4.887071 GCTTATGAGTGAGAGAGAGAGGAA 59.113 45.833 0.00 0.00 0.00 3.36
722 1286 3.446873 TGAGTGAGAGAGAGAGGAAATGC 59.553 47.826 0.00 0.00 0.00 3.56
990 1590 4.354893 AATCCTCATCTGCTCCATCTTC 57.645 45.455 0.00 0.00 0.00 2.87
1067 1676 7.727186 TCTCCAACCGTATAATCAGGTATACTT 59.273 37.037 2.25 0.00 37.26 2.24
1090 1699 6.827586 TTCTTACTCTCCACTTCTCTTCTC 57.172 41.667 0.00 0.00 0.00 2.87
1091 1700 6.134535 TCTTACTCTCCACTTCTCTTCTCT 57.865 41.667 0.00 0.00 0.00 3.10
1093 1702 7.691213 TCTTACTCTCCACTTCTCTTCTCTTA 58.309 38.462 0.00 0.00 0.00 2.10
1095 1704 9.621629 CTTACTCTCCACTTCTCTTCTCTTATA 57.378 37.037 0.00 0.00 0.00 0.98
1099 1708 9.354673 CTCTCCACTTCTCTTCTCTTATATCTT 57.645 37.037 0.00 0.00 0.00 2.40
1100 1709 9.130661 TCTCCACTTCTCTTCTCTTATATCTTG 57.869 37.037 0.00 0.00 0.00 3.02
1101 1710 9.130661 CTCCACTTCTCTTCTCTTATATCTTGA 57.869 37.037 0.00 0.00 0.00 3.02
1102 1711 9.653516 TCCACTTCTCTTCTCTTATATCTTGAT 57.346 33.333 0.00 0.00 0.00 2.57
1103 1712 9.695526 CCACTTCTCTTCTCTTATATCTTGATG 57.304 37.037 0.00 0.00 0.00 3.07
1108 1717 8.575589 TCTCTTCTCTTATATCTTGATGACTGC 58.424 37.037 0.00 0.00 0.00 4.40
1109 1718 8.242729 TCTTCTCTTATATCTTGATGACTGCA 57.757 34.615 0.00 0.00 0.00 4.41
1110 1719 8.868103 TCTTCTCTTATATCTTGATGACTGCAT 58.132 33.333 0.00 0.00 37.47 3.96
1132 1741 9.399797 TGCATCATATGAGAATAGTTTCAGTTT 57.600 29.630 11.78 0.00 34.08 2.66
1139 1748 6.884187 TGAGAATAGTTTCAGTTTAACACGC 58.116 36.000 0.00 0.00 34.08 5.34
1143 1752 4.442350 AGTTTCAGTTTAACACGCGTAC 57.558 40.909 13.44 6.14 0.00 3.67
1184 1793 3.695060 TCCTCCACGAGAGATTTACAGTC 59.305 47.826 8.50 0.00 46.50 3.51
1197 1806 8.632679 AGAGATTTACAGTCTCAAATTTGCAAA 58.367 29.630 15.44 15.44 43.57 3.68
1332 1942 4.809426 GCGTGCTACATGATTTTAGGTACT 59.191 41.667 0.00 0.00 46.37 2.73
1333 1943 5.276868 GCGTGCTACATGATTTTAGGTACTG 60.277 44.000 0.00 0.00 41.52 2.74
1334 1944 5.810587 CGTGCTACATGATTTTAGGTACTGT 59.189 40.000 0.00 0.00 41.52 3.55
1335 1945 6.976349 CGTGCTACATGATTTTAGGTACTGTA 59.024 38.462 0.00 0.00 41.52 2.74
1336 1946 7.043590 CGTGCTACATGATTTTAGGTACTGTAC 60.044 40.741 9.46 9.46 41.52 2.90
1355 1966 5.988287 TGTACCAGATATCAGCAATTCACA 58.012 37.500 5.32 0.00 0.00 3.58
1372 1983 3.485394 TCACAAATGCAAACTGCTCCTA 58.515 40.909 0.00 0.00 45.31 2.94
1391 2003 8.816894 TGCTCCTATTTTTCTCTTCTTCTCTTA 58.183 33.333 0.00 0.00 0.00 2.10
1430 2042 3.620374 CACCTGAACACATACATCTCAGC 59.380 47.826 0.00 0.00 33.64 4.26
1443 2056 0.889638 TCTCAGCCGTCGAGTTCTGT 60.890 55.000 0.00 0.00 0.00 3.41
1518 2131 0.465460 TGCTCCACGAAAGCAAGGTT 60.465 50.000 8.31 0.00 46.29 3.50
1575 2188 1.291132 GCTTCCTCGCACCACTTATC 58.709 55.000 0.00 0.00 0.00 1.75
1657 2270 4.142622 CGGTCTACACCATCGTAAGTACAA 60.143 45.833 0.00 0.00 44.02 2.41
1710 2332 0.179086 TTGCGACTCTGAACACTGCA 60.179 50.000 0.00 0.00 0.00 4.41
2027 2649 2.030401 CGGTTTCGCGATCCCAACA 61.030 57.895 19.67 0.00 0.00 3.33
2246 2868 7.170489 AGTCACAATATTCAGCATACGAATCAG 59.830 37.037 0.00 0.00 34.89 2.90
2255 2877 4.742167 CAGCATACGAATCAGTTCAGGTAG 59.258 45.833 0.00 0.00 33.86 3.18
2559 3718 1.520787 GTATGGGCCTCGTTCGTGG 60.521 63.158 4.53 8.64 0.00 4.94
3152 4311 6.213195 TGAATGAAGGGCATTTGGACTATTTT 59.787 34.615 0.00 0.00 46.90 1.82
3676 4859 9.468532 TTGTGATAGAATATTCTGATCGTCTTG 57.531 33.333 25.22 0.00 38.19 3.02
4073 5488 4.852650 GCTTCTCGTCCGCTTATAATCTAC 59.147 45.833 0.00 0.00 0.00 2.59
4074 5489 5.335035 GCTTCTCGTCCGCTTATAATCTACT 60.335 44.000 0.00 0.00 0.00 2.57
4075 5490 5.859521 TCTCGTCCGCTTATAATCTACTC 57.140 43.478 0.00 0.00 0.00 2.59
4076 5491 4.694509 TCTCGTCCGCTTATAATCTACTCC 59.305 45.833 0.00 0.00 0.00 3.85
4077 5492 3.755378 TCGTCCGCTTATAATCTACTCCC 59.245 47.826 0.00 0.00 0.00 4.30
4078 5493 3.757493 CGTCCGCTTATAATCTACTCCCT 59.243 47.826 0.00 0.00 0.00 4.20
4079 5494 4.142643 CGTCCGCTTATAATCTACTCCCTC 60.143 50.000 0.00 0.00 0.00 4.30
4080 5495 4.158209 GTCCGCTTATAATCTACTCCCTCC 59.842 50.000 0.00 0.00 0.00 4.30
4081 5496 3.128938 CCGCTTATAATCTACTCCCTCCG 59.871 52.174 0.00 0.00 0.00 4.63
4082 5497 3.757493 CGCTTATAATCTACTCCCTCCGT 59.243 47.826 0.00 0.00 0.00 4.69
4083 5498 4.142643 CGCTTATAATCTACTCCCTCCGTC 60.143 50.000 0.00 0.00 0.00 4.79
4084 5499 4.158209 GCTTATAATCTACTCCCTCCGTCC 59.842 50.000 0.00 0.00 0.00 4.79
4085 5500 2.267174 TAATCTACTCCCTCCGTCCG 57.733 55.000 0.00 0.00 0.00 4.79
4086 5501 0.467659 AATCTACTCCCTCCGTCCGG 60.468 60.000 0.00 0.00 0.00 5.14
4087 5502 1.351080 ATCTACTCCCTCCGTCCGGA 61.351 60.000 0.00 0.00 42.90 5.14
4088 5503 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
4089 5504 0.682209 CTACTCCCTCCGTCCGGAAA 60.682 60.000 5.23 0.00 44.66 3.13
4090 5505 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
4091 5506 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
4092 5507 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
4093 5508 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
4094 5509 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
4095 5510 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
4096 5511 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
4097 5512 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
4098 5513 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
4099 5514 1.135315 CCGTCCGGAAATACTTGTCGA 60.135 52.381 5.23 0.00 37.50 4.20
4100 5515 2.598589 CGTCCGGAAATACTTGTCGAA 58.401 47.619 5.23 0.00 0.00 3.71
4101 5516 2.597305 CGTCCGGAAATACTTGTCGAAG 59.403 50.000 5.23 0.00 35.07 3.79
4102 5517 3.671433 CGTCCGGAAATACTTGTCGAAGA 60.671 47.826 5.23 0.00 32.98 2.87
4103 5518 4.240096 GTCCGGAAATACTTGTCGAAGAA 58.760 43.478 5.23 0.00 39.69 2.52
4104 5519 4.687483 GTCCGGAAATACTTGTCGAAGAAA 59.313 41.667 5.23 0.00 39.69 2.52
4105 5520 5.350640 GTCCGGAAATACTTGTCGAAGAAAT 59.649 40.000 5.23 0.00 39.69 2.17
4106 5521 5.350365 TCCGGAAATACTTGTCGAAGAAATG 59.650 40.000 0.00 0.00 39.69 2.32
4107 5522 5.447279 CCGGAAATACTTGTCGAAGAAATGG 60.447 44.000 0.00 0.00 39.69 3.16
4108 5523 5.447279 CGGAAATACTTGTCGAAGAAATGGG 60.447 44.000 0.00 0.00 39.69 4.00
4109 5524 5.414765 GGAAATACTTGTCGAAGAAATGGGT 59.585 40.000 0.00 0.00 39.69 4.51
4110 5525 6.596497 GGAAATACTTGTCGAAGAAATGGGTA 59.404 38.462 0.00 0.00 39.69 3.69
4111 5526 7.120138 GGAAATACTTGTCGAAGAAATGGGTAA 59.880 37.037 0.00 0.00 39.69 2.85
4112 5527 7.989416 AATACTTGTCGAAGAAATGGGTAAA 57.011 32.000 0.00 0.00 39.69 2.01
4113 5528 7.989416 ATACTTGTCGAAGAAATGGGTAAAA 57.011 32.000 0.00 0.00 39.69 1.52
4114 5529 6.068473 ACTTGTCGAAGAAATGGGTAAAAC 57.932 37.500 0.00 0.00 39.69 2.43
4115 5530 5.826208 ACTTGTCGAAGAAATGGGTAAAACT 59.174 36.000 0.00 0.00 39.69 2.66
4116 5531 5.682943 TGTCGAAGAAATGGGTAAAACTG 57.317 39.130 0.00 0.00 39.69 3.16
4117 5532 4.517453 TGTCGAAGAAATGGGTAAAACTGG 59.483 41.667 0.00 0.00 39.69 4.00
4118 5533 4.758165 GTCGAAGAAATGGGTAAAACTGGA 59.242 41.667 0.00 0.00 39.69 3.86
4119 5534 5.414765 GTCGAAGAAATGGGTAAAACTGGAT 59.585 40.000 0.00 0.00 39.69 3.41
4120 5535 5.414454 TCGAAGAAATGGGTAAAACTGGATG 59.586 40.000 0.00 0.00 0.00 3.51
4121 5536 5.183140 CGAAGAAATGGGTAAAACTGGATGT 59.817 40.000 0.00 0.00 0.00 3.06
4122 5537 6.373216 CGAAGAAATGGGTAAAACTGGATGTA 59.627 38.462 0.00 0.00 0.00 2.29
4123 5538 7.067008 CGAAGAAATGGGTAAAACTGGATGTAT 59.933 37.037 0.00 0.00 0.00 2.29
4124 5539 7.881775 AGAAATGGGTAAAACTGGATGTATC 57.118 36.000 0.00 0.00 0.00 2.24
4125 5540 7.643123 AGAAATGGGTAAAACTGGATGTATCT 58.357 34.615 0.00 0.00 0.00 1.98
4126 5541 8.778059 AGAAATGGGTAAAACTGGATGTATCTA 58.222 33.333 0.00 0.00 0.00 1.98
4127 5542 8.747538 AAATGGGTAAAACTGGATGTATCTAC 57.252 34.615 0.00 0.00 0.00 2.59
4128 5543 6.877668 TGGGTAAAACTGGATGTATCTACA 57.122 37.500 0.00 0.00 40.98 2.74
4129 5544 7.260387 TGGGTAAAACTGGATGTATCTACAA 57.740 36.000 0.00 0.00 39.99 2.41
4130 5545 7.107542 TGGGTAAAACTGGATGTATCTACAAC 58.892 38.462 0.00 0.00 39.99 3.32
4131 5546 7.037873 TGGGTAAAACTGGATGTATCTACAACT 60.038 37.037 0.00 0.00 39.99 3.16
4132 5547 8.480501 GGGTAAAACTGGATGTATCTACAACTA 58.519 37.037 0.00 0.00 39.99 2.24
4133 5548 9.880157 GGTAAAACTGGATGTATCTACAACTAA 57.120 33.333 0.00 0.00 39.99 2.24
4138 5553 8.438676 ACTGGATGTATCTACAACTAAAATGC 57.561 34.615 0.00 0.00 39.99 3.56
4139 5554 7.224753 ACTGGATGTATCTACAACTAAAATGCG 59.775 37.037 0.00 0.00 39.99 4.73
4140 5555 7.045416 TGGATGTATCTACAACTAAAATGCGT 58.955 34.615 0.00 0.00 39.99 5.24
4141 5556 7.223971 TGGATGTATCTACAACTAAAATGCGTC 59.776 37.037 0.00 0.00 39.99 5.19
4142 5557 7.438459 GGATGTATCTACAACTAAAATGCGTCT 59.562 37.037 0.00 0.00 39.99 4.18
4143 5558 9.459640 GATGTATCTACAACTAAAATGCGTCTA 57.540 33.333 0.00 0.00 39.99 2.59
4144 5559 8.851960 TGTATCTACAACTAAAATGCGTCTAG 57.148 34.615 0.00 0.00 32.40 2.43
4145 5560 8.680001 TGTATCTACAACTAAAATGCGTCTAGA 58.320 33.333 0.00 0.00 32.40 2.43
4146 5561 9.680315 GTATCTACAACTAAAATGCGTCTAGAT 57.320 33.333 0.00 0.00 0.00 1.98
4148 5563 9.680315 ATCTACAACTAAAATGCGTCTAGATAC 57.320 33.333 0.00 0.00 0.00 2.24
4149 5564 8.680001 TCTACAACTAAAATGCGTCTAGATACA 58.320 33.333 0.00 0.00 0.00 2.29
4150 5565 9.464714 CTACAACTAAAATGCGTCTAGATACAT 57.535 33.333 0.00 0.00 0.00 2.29
4151 5566 8.354011 ACAACTAAAATGCGTCTAGATACATC 57.646 34.615 10.00 0.00 0.00 3.06
4152 5567 7.438459 ACAACTAAAATGCGTCTAGATACATCC 59.562 37.037 10.00 0.00 0.00 3.51
4153 5568 7.050970 ACTAAAATGCGTCTAGATACATCCA 57.949 36.000 10.00 0.00 0.00 3.41
4154 5569 7.671302 ACTAAAATGCGTCTAGATACATCCAT 58.329 34.615 10.00 4.20 0.00 3.41
4155 5570 8.150945 ACTAAAATGCGTCTAGATACATCCATT 58.849 33.333 10.00 8.72 0.00 3.16
4156 5571 7.807977 AAAATGCGTCTAGATACATCCATTT 57.192 32.000 10.00 9.00 0.00 2.32
4157 5572 7.426929 AAATGCGTCTAGATACATCCATTTC 57.573 36.000 10.00 0.00 0.00 2.17
4158 5573 5.791336 TGCGTCTAGATACATCCATTTCT 57.209 39.130 0.00 0.00 0.00 2.52
4159 5574 5.773575 TGCGTCTAGATACATCCATTTCTC 58.226 41.667 0.00 0.00 0.00 2.87
4160 5575 5.164954 GCGTCTAGATACATCCATTTCTCC 58.835 45.833 0.00 0.00 0.00 3.71
4161 5576 5.394802 CGTCTAGATACATCCATTTCTCCG 58.605 45.833 0.00 0.00 0.00 4.63
4162 5577 5.181433 CGTCTAGATACATCCATTTCTCCGA 59.819 44.000 0.00 0.00 0.00 4.55
4163 5578 6.383415 GTCTAGATACATCCATTTCTCCGAC 58.617 44.000 0.00 0.00 0.00 4.79
4164 5579 6.016192 GTCTAGATACATCCATTTCTCCGACA 60.016 42.308 0.00 0.00 0.00 4.35
4165 5580 5.614324 AGATACATCCATTTCTCCGACAA 57.386 39.130 0.00 0.00 0.00 3.18
4166 5581 5.605534 AGATACATCCATTTCTCCGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
4167 5582 3.703001 ACATCCATTTCTCCGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
4168 5583 4.819105 ACATCCATTTCTCCGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
4169 5584 5.359194 ACATCCATTTCTCCGACAAGTAT 57.641 39.130 0.00 0.00 0.00 2.12
4170 5585 5.745227 ACATCCATTTCTCCGACAAGTATT 58.255 37.500 0.00 0.00 0.00 1.89
4171 5586 6.180472 ACATCCATTTCTCCGACAAGTATTT 58.820 36.000 0.00 0.00 0.00 1.40
4172 5587 6.316390 ACATCCATTTCTCCGACAAGTATTTC 59.684 38.462 0.00 0.00 0.00 2.17
4173 5588 5.183228 TCCATTTCTCCGACAAGTATTTCC 58.817 41.667 0.00 0.00 0.00 3.13
4174 5589 4.034048 CCATTTCTCCGACAAGTATTTCCG 59.966 45.833 0.00 0.00 0.00 4.30
4175 5590 2.953466 TCTCCGACAAGTATTTCCGG 57.047 50.000 0.00 0.00 41.36 5.14
4176 5591 2.449464 TCTCCGACAAGTATTTCCGGA 58.551 47.619 0.00 0.00 45.74 5.14
4177 5592 2.165030 TCTCCGACAAGTATTTCCGGAC 59.835 50.000 1.83 0.00 43.47 4.79
4178 5593 1.135315 TCCGACAAGTATTTCCGGACG 60.135 52.381 1.83 0.00 43.47 4.79
4179 5594 1.274596 CGACAAGTATTTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
4180 5595 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
4181 5596 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
4182 5597 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
4183 5598 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
4184 5599 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
4185 5600 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
4186 5601 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
4187 5602 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
4194 5609 1.424684 GGACGGAGGGAGTAGTAGGAT 59.575 57.143 0.00 0.00 0.00 3.24
4200 5615 6.856757 ACGGAGGGAGTAGTAGGATAATAAA 58.143 40.000 0.00 0.00 0.00 1.40
4226 5641 4.631234 AGAATGTAATCTGGTACCCCTCA 58.369 43.478 10.07 0.82 0.00 3.86
4227 5642 5.227593 AGAATGTAATCTGGTACCCCTCAT 58.772 41.667 10.07 3.19 0.00 2.90
4238 5653 6.901300 TCTGGTACCCCTCATATCCATATTAC 59.099 42.308 10.07 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.699634 GCTCTGGCCCCTATATGAACA 59.300 52.381 0.00 0.00 0.00 3.18
20 21 1.699634 TGCTCTGGCCCCTATATGAAC 59.300 52.381 0.00 0.00 37.74 3.18
47 48 1.571919 CCGGAAGAGGATTTGTAGCG 58.428 55.000 0.00 0.00 0.00 4.26
56 57 1.403814 CATCTACAGCCGGAAGAGGA 58.596 55.000 5.05 0.00 0.00 3.71
89 90 9.499479 CATTGAGAAGAGTATATGCAACCTATT 57.501 33.333 0.00 0.00 0.00 1.73
124 127 9.699410 TCCATCTTTTACTCCATAATTTCACAT 57.301 29.630 0.00 0.00 0.00 3.21
196 202 7.121168 GGGAGTGATAAACAAAAGATGTGATGA 59.879 37.037 0.00 0.00 42.99 2.92
396 422 1.224592 CGAAAGGTGGAGGGATGGG 59.775 63.158 0.00 0.00 0.00 4.00
414 440 4.859629 ATAAAGAGATGCGACGAAAACC 57.140 40.909 0.00 0.00 0.00 3.27
468 495 5.489792 ACCAGTTACTGTGAATCTGTGAT 57.510 39.130 11.68 0.00 0.00 3.06
476 503 3.071023 CCTGAGGAACCAGTTACTGTGAA 59.929 47.826 11.68 0.00 32.95 3.18
522 553 1.065401 CAGACACACACCGTTGCAAAT 59.935 47.619 0.00 0.00 0.00 2.32
585 625 7.657023 ATGGGACGGAAGGAGTAATATATAC 57.343 40.000 0.00 0.00 0.00 1.47
592 632 5.247564 CCATATTATGGGACGGAAGGAGTAA 59.752 44.000 14.04 0.00 46.86 2.24
594 634 3.583086 CCATATTATGGGACGGAAGGAGT 59.417 47.826 14.04 0.00 46.86 3.85
595 635 4.207891 CCATATTATGGGACGGAAGGAG 57.792 50.000 14.04 0.00 46.86 3.69
607 647 3.173965 ACTCCCTCCGTCCCATATTATG 58.826 50.000 0.00 0.00 0.00 1.90
608 648 3.562108 ACTCCCTCCGTCCCATATTAT 57.438 47.619 0.00 0.00 0.00 1.28
609 649 3.400322 ACTACTCCCTCCGTCCCATATTA 59.600 47.826 0.00 0.00 0.00 0.98
610 650 2.179424 ACTACTCCCTCCGTCCCATATT 59.821 50.000 0.00 0.00 0.00 1.28
611 651 1.787676 ACTACTCCCTCCGTCCCATAT 59.212 52.381 0.00 0.00 0.00 1.78
612 652 1.133575 CACTACTCCCTCCGTCCCATA 60.134 57.143 0.00 0.00 0.00 2.74
613 653 0.397254 CACTACTCCCTCCGTCCCAT 60.397 60.000 0.00 0.00 0.00 4.00
614 654 1.000019 CACTACTCCCTCCGTCCCA 60.000 63.158 0.00 0.00 0.00 4.37
615 655 0.614134 AACACTACTCCCTCCGTCCC 60.614 60.000 0.00 0.00 0.00 4.46
616 656 0.531200 CAACACTACTCCCTCCGTCC 59.469 60.000 0.00 0.00 0.00 4.79
617 657 1.542492 TCAACACTACTCCCTCCGTC 58.458 55.000 0.00 0.00 0.00 4.79
618 658 1.617357 GTTCAACACTACTCCCTCCGT 59.383 52.381 0.00 0.00 0.00 4.69
619 659 1.616865 TGTTCAACACTACTCCCTCCG 59.383 52.381 0.00 0.00 0.00 4.63
620 660 2.897969 TCTGTTCAACACTACTCCCTCC 59.102 50.000 0.00 0.00 0.00 4.30
621 661 4.602340 TTCTGTTCAACACTACTCCCTC 57.398 45.455 0.00 0.00 0.00 4.30
622 662 4.593206 TGATTCTGTTCAACACTACTCCCT 59.407 41.667 0.00 0.00 0.00 4.20
623 663 4.894784 TGATTCTGTTCAACACTACTCCC 58.105 43.478 0.00 0.00 0.00 4.30
624 664 6.706270 TCTTTGATTCTGTTCAACACTACTCC 59.294 38.462 0.00 0.00 35.42 3.85
625 665 7.715265 TCTTTGATTCTGTTCAACACTACTC 57.285 36.000 0.00 0.00 35.42 2.59
660 700 4.137543 CTCCAACTTTTGTAGGAGCAAGT 58.862 43.478 0.00 0.00 40.98 3.16
661 701 4.389374 TCTCCAACTTTTGTAGGAGCAAG 58.611 43.478 0.00 0.00 45.69 4.01
662 702 4.431416 TCTCCAACTTTTGTAGGAGCAA 57.569 40.909 0.00 0.00 45.69 3.91
663 703 4.431416 TTCTCCAACTTTTGTAGGAGCA 57.569 40.909 0.00 0.00 45.69 4.26
664 704 4.216472 CCTTTCTCCAACTTTTGTAGGAGC 59.784 45.833 0.00 0.00 45.69 4.70
698 849 5.301551 GCATTTCCTCTCTCTCTCACTCATA 59.698 44.000 0.00 0.00 0.00 2.15
722 1286 4.802051 CAGGACCCACGCCCATGG 62.802 72.222 4.14 4.14 39.71 3.66
990 1590 1.022735 CTGCTTCCATGGCTGCTTAG 58.977 55.000 22.91 13.17 0.00 2.18
1067 1676 6.548321 AGAGAAGAGAAGTGGAGAGTAAGAA 58.452 40.000 0.00 0.00 0.00 2.52
1100 1709 8.774890 AACTATTCTCATATGATGCAGTCATC 57.225 34.615 5.72 0.00 44.23 2.92
1101 1710 9.217278 GAAACTATTCTCATATGATGCAGTCAT 57.783 33.333 5.72 13.68 40.31 3.06
1102 1711 8.206189 TGAAACTATTCTCATATGATGCAGTCA 58.794 33.333 5.72 0.00 37.58 3.41
1103 1712 8.599055 TGAAACTATTCTCATATGATGCAGTC 57.401 34.615 5.72 0.00 36.48 3.51
1104 1713 8.209584 ACTGAAACTATTCTCATATGATGCAGT 58.790 33.333 5.72 6.93 36.48 4.40
1105 1714 8.604640 ACTGAAACTATTCTCATATGATGCAG 57.395 34.615 5.72 6.29 36.48 4.41
1106 1715 8.969260 AACTGAAACTATTCTCATATGATGCA 57.031 30.769 5.72 0.00 36.48 3.96
1123 1732 4.442350 AGTACGCGTGTTAAACTGAAAC 57.558 40.909 24.59 7.18 0.00 2.78
1132 1741 3.631145 ACTGAAGAAGTACGCGTGTTA 57.369 42.857 24.59 0.00 37.36 2.41
1133 1742 2.503920 ACTGAAGAAGTACGCGTGTT 57.496 45.000 24.59 15.52 37.36 3.32
1134 1743 2.034305 AGAACTGAAGAAGTACGCGTGT 59.966 45.455 24.59 6.91 38.56 4.49
1139 1748 3.154489 CGACGAGAACTGAAGAAGTACG 58.846 50.000 0.00 0.00 38.56 3.67
1143 1752 2.586900 GACCGACGAGAACTGAAGAAG 58.413 52.381 0.00 0.00 0.00 2.85
1184 1793 7.277098 CAGGATATCCAGTTTTGCAAATTTGAG 59.723 37.037 23.81 8.60 38.89 3.02
1197 1806 4.620723 TCACAGTACCAGGATATCCAGTT 58.379 43.478 23.81 7.00 38.89 3.16
1332 1942 5.988287 TGTGAATTGCTGATATCTGGTACA 58.012 37.500 11.15 0.00 0.00 2.90
1333 1943 6.925610 TTGTGAATTGCTGATATCTGGTAC 57.074 37.500 11.15 0.00 0.00 3.34
1334 1944 7.469043 GCATTTGTGAATTGCTGATATCTGGTA 60.469 37.037 11.15 0.00 0.00 3.25
1335 1945 6.682113 GCATTTGTGAATTGCTGATATCTGGT 60.682 38.462 11.15 0.00 0.00 4.00
1336 1946 5.690409 GCATTTGTGAATTGCTGATATCTGG 59.310 40.000 11.15 2.43 0.00 3.86
1341 1952 6.366604 CAGTTTGCATTTGTGAATTGCTGATA 59.633 34.615 0.00 0.00 0.00 2.15
1343 1954 4.508492 CAGTTTGCATTTGTGAATTGCTGA 59.492 37.500 0.00 0.00 0.00 4.26
1430 2042 0.716108 GCATTCACAGAACTCGACGG 59.284 55.000 0.00 0.00 0.00 4.79
1590 2203 5.465051 CAGTATCTTCCCAGATATGTGTCG 58.535 45.833 0.00 0.00 42.82 4.35
1657 2270 1.553690 ATCTGGTGGGTTAGCTGCGT 61.554 55.000 0.00 0.00 0.00 5.24
1710 2332 2.493278 CGAGCATCCCCTGTCAAATTTT 59.507 45.455 0.00 0.00 0.00 1.82
2027 2649 2.357836 CCCAAGGCCATGAGCACT 59.642 61.111 10.18 0.00 46.50 4.40
2443 3602 1.390123 CCGTGCATGTCTTGTCTAACG 59.610 52.381 4.96 0.00 0.00 3.18
2543 3702 3.310860 GACCACGAACGAGGCCCAT 62.311 63.158 0.00 0.00 0.00 4.00
2559 3718 1.133407 CCCAGCGACTGAGTAGAAGAC 59.867 57.143 8.20 0.00 32.44 3.01
3096 4255 1.703014 ATCCATCCAGGCGCATCACT 61.703 55.000 10.83 0.00 37.29 3.41
3152 4311 1.562942 AGAGCAGCCATCATCCAGAAA 59.437 47.619 0.00 0.00 0.00 2.52
3676 4859 7.617041 ACAATTGACTATGAAAGTAGCCTTC 57.383 36.000 13.59 0.00 39.07 3.46
4073 5488 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
4074 5489 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
4075 5490 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
4076 5491 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
4077 5492 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
4078 5493 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
4079 5494 1.135315 TCGACAAGTATTTCCGGACGG 60.135 52.381 1.83 3.96 0.00 4.79
4080 5495 2.267188 TCGACAAGTATTTCCGGACG 57.733 50.000 1.83 0.27 0.00 4.79
4081 5496 3.841643 TCTTCGACAAGTATTTCCGGAC 58.158 45.455 1.83 0.00 0.00 4.79
4082 5497 4.524316 TTCTTCGACAAGTATTTCCGGA 57.476 40.909 0.00 0.00 0.00 5.14
4083 5498 5.447279 CCATTTCTTCGACAAGTATTTCCGG 60.447 44.000 0.00 0.00 0.00 5.14
4084 5499 5.447279 CCCATTTCTTCGACAAGTATTTCCG 60.447 44.000 0.00 0.00 0.00 4.30
4085 5500 5.414765 ACCCATTTCTTCGACAAGTATTTCC 59.585 40.000 0.00 0.00 0.00 3.13
4086 5501 6.496338 ACCCATTTCTTCGACAAGTATTTC 57.504 37.500 0.00 0.00 0.00 2.17
4087 5502 7.989416 TTACCCATTTCTTCGACAAGTATTT 57.011 32.000 0.00 0.00 0.00 1.40
4088 5503 7.989416 TTTACCCATTTCTTCGACAAGTATT 57.011 32.000 0.00 0.00 0.00 1.89
4089 5504 7.664318 AGTTTTACCCATTTCTTCGACAAGTAT 59.336 33.333 0.00 0.00 0.00 2.12
4090 5505 6.993902 AGTTTTACCCATTTCTTCGACAAGTA 59.006 34.615 0.00 0.00 0.00 2.24
4091 5506 5.826208 AGTTTTACCCATTTCTTCGACAAGT 59.174 36.000 0.00 0.00 0.00 3.16
4092 5507 6.142817 CAGTTTTACCCATTTCTTCGACAAG 58.857 40.000 0.00 0.00 0.00 3.16
4093 5508 5.009210 CCAGTTTTACCCATTTCTTCGACAA 59.991 40.000 0.00 0.00 0.00 3.18
4094 5509 4.517453 CCAGTTTTACCCATTTCTTCGACA 59.483 41.667 0.00 0.00 0.00 4.35
4095 5510 4.758165 TCCAGTTTTACCCATTTCTTCGAC 59.242 41.667 0.00 0.00 0.00 4.20
4096 5511 4.975631 TCCAGTTTTACCCATTTCTTCGA 58.024 39.130 0.00 0.00 0.00 3.71
4097 5512 5.183140 ACATCCAGTTTTACCCATTTCTTCG 59.817 40.000 0.00 0.00 0.00 3.79
4098 5513 6.590234 ACATCCAGTTTTACCCATTTCTTC 57.410 37.500 0.00 0.00 0.00 2.87
4099 5514 8.116026 AGATACATCCAGTTTTACCCATTTCTT 58.884 33.333 0.00 0.00 0.00 2.52
4100 5515 7.643123 AGATACATCCAGTTTTACCCATTTCT 58.357 34.615 0.00 0.00 0.00 2.52
4101 5516 7.881775 AGATACATCCAGTTTTACCCATTTC 57.118 36.000 0.00 0.00 0.00 2.17
4102 5517 8.333235 TGTAGATACATCCAGTTTTACCCATTT 58.667 33.333 0.00 0.00 0.00 2.32
4103 5518 7.867921 TGTAGATACATCCAGTTTTACCCATT 58.132 34.615 0.00 0.00 0.00 3.16
4104 5519 7.446106 TGTAGATACATCCAGTTTTACCCAT 57.554 36.000 0.00 0.00 0.00 4.00
4105 5520 6.877668 TGTAGATACATCCAGTTTTACCCA 57.122 37.500 0.00 0.00 0.00 4.51
4106 5521 7.336396 AGTTGTAGATACATCCAGTTTTACCC 58.664 38.462 0.00 0.00 35.89 3.69
4107 5522 9.880157 TTAGTTGTAGATACATCCAGTTTTACC 57.120 33.333 0.00 0.00 35.89 2.85
4112 5527 8.893727 GCATTTTAGTTGTAGATACATCCAGTT 58.106 33.333 0.00 0.00 35.89 3.16
4113 5528 7.224753 CGCATTTTAGTTGTAGATACATCCAGT 59.775 37.037 0.00 0.00 35.89 4.00
4114 5529 7.224753 ACGCATTTTAGTTGTAGATACATCCAG 59.775 37.037 0.00 0.00 35.89 3.86
4115 5530 7.045416 ACGCATTTTAGTTGTAGATACATCCA 58.955 34.615 0.00 0.00 35.89 3.41
4116 5531 7.438459 AGACGCATTTTAGTTGTAGATACATCC 59.562 37.037 0.00 0.00 35.89 3.51
4117 5532 8.354011 AGACGCATTTTAGTTGTAGATACATC 57.646 34.615 0.00 0.00 35.89 3.06
4118 5533 9.464714 CTAGACGCATTTTAGTTGTAGATACAT 57.535 33.333 0.00 0.00 35.89 2.29
4119 5534 8.680001 TCTAGACGCATTTTAGTTGTAGATACA 58.320 33.333 0.00 0.00 0.00 2.29
4120 5535 9.680315 ATCTAGACGCATTTTAGTTGTAGATAC 57.320 33.333 0.00 0.00 31.17 2.24
4122 5537 9.680315 GTATCTAGACGCATTTTAGTTGTAGAT 57.320 33.333 0.00 0.00 34.34 1.98
4123 5538 8.680001 TGTATCTAGACGCATTTTAGTTGTAGA 58.320 33.333 0.00 0.00 0.00 2.59
4124 5539 8.851960 TGTATCTAGACGCATTTTAGTTGTAG 57.148 34.615 0.00 0.00 0.00 2.74
4125 5540 9.459640 GATGTATCTAGACGCATTTTAGTTGTA 57.540 33.333 10.93 0.00 0.00 2.41
4126 5541 7.438459 GGATGTATCTAGACGCATTTTAGTTGT 59.562 37.037 10.93 0.00 0.00 3.32
4127 5542 7.438160 TGGATGTATCTAGACGCATTTTAGTTG 59.562 37.037 10.93 0.00 0.00 3.16
4128 5543 7.497595 TGGATGTATCTAGACGCATTTTAGTT 58.502 34.615 10.93 0.00 0.00 2.24
4129 5544 7.050970 TGGATGTATCTAGACGCATTTTAGT 57.949 36.000 10.93 0.00 0.00 2.24
4130 5545 8.539770 AATGGATGTATCTAGACGCATTTTAG 57.460 34.615 10.93 0.00 0.00 1.85
4131 5546 8.902540 AAATGGATGTATCTAGACGCATTTTA 57.097 30.769 10.93 3.77 0.00 1.52
4132 5547 7.716998 AGAAATGGATGTATCTAGACGCATTTT 59.283 33.333 10.93 8.42 0.00 1.82
4133 5548 7.220030 AGAAATGGATGTATCTAGACGCATTT 58.780 34.615 10.93 0.00 0.00 2.32
4134 5549 6.763355 AGAAATGGATGTATCTAGACGCATT 58.237 36.000 10.93 0.00 0.00 3.56
4135 5550 6.352016 AGAAATGGATGTATCTAGACGCAT 57.648 37.500 9.78 9.78 0.00 4.73
4136 5551 5.279006 GGAGAAATGGATGTATCTAGACGCA 60.279 44.000 0.00 0.00 0.00 5.24
4137 5552 5.164954 GGAGAAATGGATGTATCTAGACGC 58.835 45.833 0.00 0.00 0.00 5.19
4138 5553 5.181433 TCGGAGAAATGGATGTATCTAGACG 59.819 44.000 0.00 0.00 0.00 4.18
4139 5554 6.016192 TGTCGGAGAAATGGATGTATCTAGAC 60.016 42.308 0.00 0.00 39.69 2.59
4140 5555 6.068670 TGTCGGAGAAATGGATGTATCTAGA 58.931 40.000 0.00 0.00 39.69 2.43
4141 5556 6.332735 TGTCGGAGAAATGGATGTATCTAG 57.667 41.667 0.00 0.00 39.69 2.43
4142 5557 6.323996 ACTTGTCGGAGAAATGGATGTATCTA 59.676 38.462 0.00 0.00 39.69 1.98
4143 5558 5.129485 ACTTGTCGGAGAAATGGATGTATCT 59.871 40.000 0.00 0.00 39.69 1.98
4144 5559 5.360591 ACTTGTCGGAGAAATGGATGTATC 58.639 41.667 0.00 0.00 39.69 2.24
4145 5560 5.359194 ACTTGTCGGAGAAATGGATGTAT 57.641 39.130 0.00 0.00 39.69 2.29
4146 5561 4.819105 ACTTGTCGGAGAAATGGATGTA 57.181 40.909 0.00 0.00 39.69 2.29
4147 5562 3.703001 ACTTGTCGGAGAAATGGATGT 57.297 42.857 0.00 0.00 39.69 3.06
4148 5563 6.238484 GGAAATACTTGTCGGAGAAATGGATG 60.238 42.308 0.00 0.00 39.69 3.51
4149 5564 5.823045 GGAAATACTTGTCGGAGAAATGGAT 59.177 40.000 0.00 0.00 39.69 3.41
4150 5565 5.183228 GGAAATACTTGTCGGAGAAATGGA 58.817 41.667 0.00 0.00 39.69 3.41
4151 5566 4.034048 CGGAAATACTTGTCGGAGAAATGG 59.966 45.833 0.00 0.00 39.69 3.16
4152 5567 4.034048 CCGGAAATACTTGTCGGAGAAATG 59.966 45.833 0.00 0.00 42.94 2.32
4153 5568 4.081309 TCCGGAAATACTTGTCGGAGAAAT 60.081 41.667 0.00 0.00 43.84 2.17
4154 5569 3.258872 TCCGGAAATACTTGTCGGAGAAA 59.741 43.478 0.00 0.00 43.84 2.52
4155 5570 2.827322 TCCGGAAATACTTGTCGGAGAA 59.173 45.455 0.00 0.00 43.84 2.87
4156 5571 2.449464 TCCGGAAATACTTGTCGGAGA 58.551 47.619 0.00 0.00 43.84 3.71
4157 5572 2.953466 TCCGGAAATACTTGTCGGAG 57.047 50.000 0.00 0.00 43.84 4.63
4158 5573 1.135315 CGTCCGGAAATACTTGTCGGA 60.135 52.381 5.23 0.00 46.06 4.55
4159 5574 1.274596 CGTCCGGAAATACTTGTCGG 58.725 55.000 5.23 0.00 41.80 4.79
4160 5575 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
4161 5576 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
4162 5577 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
4163 5578 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
4164 5579 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
4165 5580 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
4166 5581 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
4167 5582 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
4168 5583 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
4169 5584 0.682209 CTACTCCCTCCGTCCGGAAA 60.682 60.000 5.23 0.00 44.66 3.13
4170 5585 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
4171 5586 0.982852 TACTACTCCCTCCGTCCGGA 60.983 60.000 0.00 0.00 42.90 5.14
4172 5587 0.534652 CTACTACTCCCTCCGTCCGG 60.535 65.000 0.00 0.00 0.00 5.14
4173 5588 0.534652 CCTACTACTCCCTCCGTCCG 60.535 65.000 0.00 0.00 0.00 4.79
4174 5589 0.842635 TCCTACTACTCCCTCCGTCC 59.157 60.000 0.00 0.00 0.00 4.79
4175 5590 2.955342 ATCCTACTACTCCCTCCGTC 57.045 55.000 0.00 0.00 0.00 4.79
4176 5591 6.460103 TTATTATCCTACTACTCCCTCCGT 57.540 41.667 0.00 0.00 0.00 4.69
4177 5592 7.201714 CGATTTATTATCCTACTACTCCCTCCG 60.202 44.444 0.00 0.00 0.00 4.63
4178 5593 7.833183 TCGATTTATTATCCTACTACTCCCTCC 59.167 40.741 0.00 0.00 0.00 4.30
4179 5594 8.804912 TCGATTTATTATCCTACTACTCCCTC 57.195 38.462 0.00 0.00 0.00 4.30
4180 5595 8.613034 TCTCGATTTATTATCCTACTACTCCCT 58.387 37.037 0.00 0.00 0.00 4.20
4181 5596 8.804912 TCTCGATTTATTATCCTACTACTCCC 57.195 38.462 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.