Multiple sequence alignment - TraesCS1A01G283700

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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 TraesCS1A01G283700 chr1A 100.000 4105 0 0 1 4105 481626893 481630997 0.000000e+00 7581.0
1 TraesCS1A01G283700 chr1A 91.732 641 42 6 2 636 330089616 330088981 0.000000e+00 880.0
2 TraesCS1A01G283700 chr1A 90.029 341 33 1 603 943 330088964 330088625 1.350000e-119 440.0
3 TraesCS1A01G283700 chr1D 92.348 1921 93 16 974 2862 381004781 381006679 0.000000e+00 2684.0
4 TraesCS1A01G283700 chr1D 96.952 689 21 0 3417 4105 381007252 381007940 0.000000e+00 1157.0
5 TraesCS1A01G283700 chr1D 95.896 536 14 5 2856 3384 381006720 381007254 0.000000e+00 861.0
6 TraesCS1A01G283700 chr1D 77.562 1493 227 64 953 2392 456280675 456279238 0.000000e+00 802.0
7 TraesCS1A01G283700 chr1B 94.335 1518 47 8 930 2420 510790598 510792103 0.000000e+00 2290.0
8 TraesCS1A01G283700 chr1B 95.321 1261 43 8 2856 4100 510792637 510793897 0.000000e+00 1988.0
9 TraesCS1A01G283700 chr1B 86.901 939 93 10 2 937 647247834 647246923 0.000000e+00 1026.0
10 TraesCS1A01G283700 chr1B 88.357 627 57 9 2 623 654867512 654866897 0.000000e+00 739.0
11 TraesCS1A01G283700 chr1B 87.421 636 68 9 2 636 527631012 527631636 0.000000e+00 721.0
12 TraesCS1A01G283700 chr1B 88.776 588 59 5 2 589 169000788 169001368 0.000000e+00 713.0
13 TraesCS1A01G283700 chr1B 91.189 454 17 8 2418 2862 510792157 510792596 2.730000e-166 595.0
14 TraesCS1A01G283700 chr3D 79.461 1446 207 55 991 2392 27662997 27664396 0.000000e+00 942.0
15 TraesCS1A01G283700 chr3D 81.113 1186 187 24 1163 2316 28124475 28123295 0.000000e+00 915.0
16 TraesCS1A01G283700 chr3D 77.105 1271 219 45 1382 2608 28224566 28223324 0.000000e+00 669.0
17 TraesCS1A01G283700 chr3D 77.234 1186 208 38 1235 2375 28275286 28276454 4.480000e-179 638.0
18 TraesCS1A01G283700 chr3D 80.155 645 95 17 3483 4105 28277867 28278500 6.260000e-123 451.0
19 TraesCS1A01G283700 chr3D 73.583 1200 250 45 1212 2355 4995449 4996637 8.270000e-107 398.0
20 TraesCS1A01G283700 chr3D 81.837 490 68 16 2916 3388 28122503 28122018 3.850000e-105 392.0
21 TraesCS1A01G283700 chr3D 78.135 622 92 28 2854 3450 28277112 28277714 5.050000e-94 355.0
22 TraesCS1A01G283700 chr3D 80.531 113 20 2 3861 3972 27885042 27884931 7.310000e-13 86.1
23 TraesCS1A01G283700 chr3D 90.000 50 5 0 3896 3945 28487820 28487869 9.520000e-07 65.8
24 TraesCS1A01G283700 chr3B 77.719 1710 257 65 974 2608 47223145 47221485 0.000000e+00 933.0
25 TraesCS1A01G283700 chr3B 78.890 1478 227 43 969 2392 47211306 47209860 0.000000e+00 922.0
26 TraesCS1A01G283700 chr3B 78.602 1159 190 21 1021 2140 46254332 46255471 0.000000e+00 713.0
27 TraesCS1A01G283700 chr3B 80.263 760 135 12 1567 2316 46328528 46329282 3.580000e-155 558.0
28 TraesCS1A01G283700 chr3B 81.719 640 85 18 3483 4105 47272514 47273138 4.740000e-139 505.0
29 TraesCS1A01G283700 chr3B 83.368 481 72 7 1842 2315 46305475 46305954 4.870000e-119 438.0
30 TraesCS1A01G283700 chr3B 81.687 486 63 12 3464 3933 47208716 47208241 8.330000e-102 381.0
31 TraesCS1A01G283700 chr3B 81.345 461 68 15 2932 3380 46330064 46330518 3.900000e-95 359.0
32 TraesCS1A01G283700 chr3B 77.331 622 96 27 2854 3450 47271760 47272361 3.960000e-85 326.0
33 TraesCS1A01G283700 chr3B 75.949 158 28 6 3518 3665 28276465 28276308 5.690000e-09 73.1
34 TraesCS1A01G283700 chr3A 80.667 1200 190 27 1154 2316 38013589 38012395 0.000000e+00 893.0
35 TraesCS1A01G283700 chr3A 90.991 333 29 1 603 935 487474370 487474701 8.090000e-122 448.0
36 TraesCS1A01G283700 chr3A 81.474 475 82 6 1669 2140 38160008 38159537 6.440000e-103 385.0
37 TraesCS1A01G283700 chr3A 80.455 527 58 19 981 1482 38160589 38160083 1.080000e-95 361.0
38 TraesCS1A01G283700 chr3A 82.383 193 22 8 3128 3315 37802379 37802564 1.530000e-34 158.0
39 TraesCS1A01G283700 chr3A 71.210 785 177 39 1579 2340 10486902 10486144 7.110000e-33 152.0
40 TraesCS1A01G283700 chr4A 87.988 641 59 15 2 636 485008150 485007522 0.000000e+00 741.0
41 TraesCS1A01G283700 chr5B 89.456 588 56 4 2 589 538554271 538553690 0.000000e+00 737.0
42 TraesCS1A01G283700 chr4D 87.739 628 64 10 2 628 504103254 504102639 0.000000e+00 721.0
43 TraesCS1A01G283700 chr2B 86.875 640 70 10 2 636 335412635 335412005 0.000000e+00 704.0
44 TraesCS1A01G283700 chr2B 97.059 34 1 0 603 636 1903993 1903960 1.590000e-04 58.4
45 TraesCS1A01G283700 chr2D 85.373 335 31 11 603 935 47288061 47287743 8.510000e-87 331.0
46 TraesCS1A01G283700 chr2D 89.919 248 23 2 689 936 643052464 643052219 6.620000e-83 318.0
47 TraesCS1A01G283700 chr2D 71.777 1435 300 65 1229 2603 35035115 35033726 3.990000e-80 309.0
48 TraesCS1A01G283700 chr2D 88.755 249 26 2 689 936 648110522 648110769 1.850000e-78 303.0
49 TraesCS1A01G283700 chr2D 79.355 465 58 15 3469 3921 650599880 650600318 4.010000e-75 292.0
50 TraesCS1A01G283700 chr2D 71.574 1175 256 56 1229 2355 35231134 35229990 8.810000e-62 248.0
51 TraesCS1A01G283700 chr6D 84.393 346 40 7 600 936 113904509 113904169 1.100000e-85 327.0
52 TraesCS1A01G283700 chr7D 88.327 257 28 2 679 935 465835972 465836226 1.430000e-79 307.0
53 TraesCS1A01G283700 chr7D 88.710 248 27 1 689 936 219288686 219288440 6.670000e-78 302.0
54 TraesCS1A01G283700 chr5D 89.069 247 25 2 689 935 367799971 367799727 5.160000e-79 305.0
55 TraesCS1A01G283700 chrUn 72.255 1193 247 59 1220 2355 197241981 197240816 4.010000e-75 292.0
56 TraesCS1A01G283700 chrUn 71.205 830 165 51 1578 2355 36351675 36350868 1.540000e-29 141.0
57 TraesCS1A01G283700 chrUn 71.205 830 165 51 1578 2355 214883330 214884137 1.540000e-29 141.0
58 TraesCS1A01G283700 chrUn 70.153 784 184 41 1579 2340 35360495 35359740 5.610000e-19 106.0
59 TraesCS1A01G283700 chrUn 70.153 784 184 41 1579 2340 263318734 263317979 5.610000e-19 106.0
60 TraesCS1A01G283700 chrUn 82.540 126 15 4 2548 2666 32289015 32288890 2.020000e-18 104.0
61 TraesCS1A01G283700 chrUn 81.746 126 16 4 2548 2666 225560283 225560158 9.390000e-17 99.0
62 TraesCS1A01G283700 chrUn 81.395 129 17 4 2545 2666 237464084 237464212 9.390000e-17 99.0
63 TraesCS1A01G283700 chrUn 81.395 129 17 4 2545 2666 257675800 257675928 9.390000e-17 99.0
64 TraesCS1A01G283700 chrUn 81.395 129 17 4 2545 2666 279685941 279686069 9.390000e-17 99.0
65 TraesCS1A01G283700 chrUn 81.746 126 16 4 2548 2666 294337923 294337798 9.390000e-17 99.0
66 TraesCS1A01G283700 chr2A 78.710 465 61 15 3469 3921 771972095 771972533 4.040000e-70 276.0
67 TraesCS1A01G283700 chr2A 90.741 54 5 0 4043 4096 772012249 772012302 5.690000e-09 73.1


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 TraesCS1A01G283700 chr1A 481626893 481630997 4104 False 7581.000000 7581 100.000000 1 4105 1 chr1A.!!$F1 4104
1 TraesCS1A01G283700 chr1A 330088625 330089616 991 True 660.000000 880 90.880500 2 943 2 chr1A.!!$R1 941
2 TraesCS1A01G283700 chr1D 381004781 381007940 3159 False 1567.333333 2684 95.065333 974 4105 3 chr1D.!!$F1 3131
3 TraesCS1A01G283700 chr1D 456279238 456280675 1437 True 802.000000 802 77.562000 953 2392 1 chr1D.!!$R1 1439
4 TraesCS1A01G283700 chr1B 510790598 510793897 3299 False 1624.333333 2290 93.615000 930 4100 3 chr1B.!!$F3 3170
5 TraesCS1A01G283700 chr1B 647246923 647247834 911 True 1026.000000 1026 86.901000 2 937 1 chr1B.!!$R1 935
6 TraesCS1A01G283700 chr1B 654866897 654867512 615 True 739.000000 739 88.357000 2 623 1 chr1B.!!$R2 621
7 TraesCS1A01G283700 chr1B 527631012 527631636 624 False 721.000000 721 87.421000 2 636 1 chr1B.!!$F2 634
8 TraesCS1A01G283700 chr1B 169000788 169001368 580 False 713.000000 713 88.776000 2 589 1 chr1B.!!$F1 587
9 TraesCS1A01G283700 chr3D 27662997 27664396 1399 False 942.000000 942 79.461000 991 2392 1 chr3D.!!$F2 1401
10 TraesCS1A01G283700 chr3D 28223324 28224566 1242 True 669.000000 669 77.105000 1382 2608 1 chr3D.!!$R2 1226
11 TraesCS1A01G283700 chr3D 28122018 28124475 2457 True 653.500000 915 81.475000 1163 3388 2 chr3D.!!$R3 2225
12 TraesCS1A01G283700 chr3D 28275286 28278500 3214 False 481.333333 638 78.508000 1235 4105 3 chr3D.!!$F4 2870
13 TraesCS1A01G283700 chr3D 4995449 4996637 1188 False 398.000000 398 73.583000 1212 2355 1 chr3D.!!$F1 1143
14 TraesCS1A01G283700 chr3B 47221485 47223145 1660 True 933.000000 933 77.719000 974 2608 1 chr3B.!!$R2 1634
15 TraesCS1A01G283700 chr3B 46254332 46255471 1139 False 713.000000 713 78.602000 1021 2140 1 chr3B.!!$F1 1119
16 TraesCS1A01G283700 chr3B 47208241 47211306 3065 True 651.500000 922 80.288500 969 3933 2 chr3B.!!$R3 2964
17 TraesCS1A01G283700 chr3B 46328528 46330518 1990 False 458.500000 558 80.804000 1567 3380 2 chr3B.!!$F3 1813
18 TraesCS1A01G283700 chr3B 47271760 47273138 1378 False 415.500000 505 79.525000 2854 4105 2 chr3B.!!$F4 1251
19 TraesCS1A01G283700 chr3A 38012395 38013589 1194 True 893.000000 893 80.667000 1154 2316 1 chr3A.!!$R2 1162
20 TraesCS1A01G283700 chr3A 38159537 38160589 1052 True 373.000000 385 80.964500 981 2140 2 chr3A.!!$R3 1159
21 TraesCS1A01G283700 chr4A 485007522 485008150 628 True 741.000000 741 87.988000 2 636 1 chr4A.!!$R1 634
22 TraesCS1A01G283700 chr5B 538553690 538554271 581 True 737.000000 737 89.456000 2 589 1 chr5B.!!$R1 587
23 TraesCS1A01G283700 chr4D 504102639 504103254 615 True 721.000000 721 87.739000 2 628 1 chr4D.!!$R1 626
24 TraesCS1A01G283700 chr2B 335412005 335412635 630 True 704.000000 704 86.875000 2 636 1 chr2B.!!$R2 634
25 TraesCS1A01G283700 chr2D 35033726 35035115 1389 True 309.000000 309 71.777000 1229 2603 1 chr2D.!!$R1 1374
26 TraesCS1A01G283700 chr2D 35229990 35231134 1144 True 248.000000 248 71.574000 1229 2355 1 chr2D.!!$R2 1126
27 TraesCS1A01G283700 chrUn 197240816 197241981 1165 True 292.000000 292 72.255000 1220 2355 1 chrUn.!!$R4 1135

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
931 1002 0.036199 AGTACCGCCGGTGCATTTTA 60.036 50.000 25.99 0.0 40.76 1.52 F
933 1004 0.036199 TACCGCCGGTGCATTTTACT 60.036 50.000 21.20 0.0 36.19 2.24 F
936 1007 0.802494 CGCCGGTGCATTTTACTCTT 59.198 50.000 0.00 0.0 37.32 2.85 F
937 1008 2.004017 CGCCGGTGCATTTTACTCTTA 58.996 47.619 0.00 0.0 37.32 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2808 3394 1.584724 AACTCATCCCTCCCGATGTT 58.415 50.000 0.00 0.00 40.50 2.71 R
2900 3551 3.639094 GCTCACTACTGATGATGGTACCT 59.361 47.826 14.36 0.00 0.00 3.08 R
3079 3778 2.624316 ATCGTGCAACATTTCAGCTG 57.376 45.000 7.63 7.63 35.74 4.24 R
3395 4113 7.916914 TTATGAAACAGCTAAACTAAGGGAC 57.083 36.000 0.00 0.00 0.00 4.46 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
143 144 2.550830 TTGAGCTCCAACTCTTCCAC 57.449 50.000 12.15 0.00 37.58 4.02
176 183 4.104383 TCAAAGCCTGGAAGATCAACTT 57.896 40.909 0.00 0.00 42.03 2.66
249 256 2.165357 TCCTCTGCAGCTCCTAATGA 57.835 50.000 9.47 0.00 0.00 2.57
298 305 8.049117 AGAAATTGATTATCCAGCAAGTAGACA 58.951 33.333 0.00 0.00 0.00 3.41
348 355 6.830873 AATGGTCCTGAAGATCAAAAGAAG 57.169 37.500 0.00 0.00 39.67 2.85
355 362 5.106396 CCTGAAGATCAAAAGAAGCGAACAT 60.106 40.000 0.00 0.00 0.00 2.71
414 422 6.226787 TCGACCAAAATTAACAAATGCCAAT 58.773 32.000 0.00 0.00 0.00 3.16
423 431 1.624312 ACAAATGCCAATGGATGCACA 59.376 42.857 2.05 0.00 40.88 4.57
440 448 2.912771 CACACCACTTACACCAACAGA 58.087 47.619 0.00 0.00 0.00 3.41
506 514 0.388134 TAGAACTTCACACGAGCGCC 60.388 55.000 2.29 0.00 0.00 6.53
652 714 3.775654 CCTCGGTGGCAGGGAGTC 61.776 72.222 12.24 0.00 0.00 3.36
663 725 1.789523 CAGGGAGTCGGGAATTAGGA 58.210 55.000 0.00 0.00 0.00 2.94
684 755 3.689002 TTGGCATCGGCGGCACATA 62.689 57.895 10.53 0.00 41.78 2.29
685 756 2.669569 GGCATCGGCGGCACATAT 60.670 61.111 10.53 0.00 42.47 1.78
686 757 1.375396 GGCATCGGCGGCACATATA 60.375 57.895 10.53 0.00 42.47 0.86
687 758 0.744414 GGCATCGGCGGCACATATAT 60.744 55.000 10.53 0.00 42.47 0.86
688 759 1.086696 GCATCGGCGGCACATATATT 58.913 50.000 10.53 0.00 0.00 1.28
689 760 1.468520 GCATCGGCGGCACATATATTT 59.531 47.619 10.53 0.00 0.00 1.40
690 761 2.476185 GCATCGGCGGCACATATATTTC 60.476 50.000 10.53 0.00 0.00 2.17
691 762 2.535012 TCGGCGGCACATATATTTCA 57.465 45.000 10.53 0.00 0.00 2.69
692 763 2.412870 TCGGCGGCACATATATTTCAG 58.587 47.619 10.53 0.00 0.00 3.02
693 764 1.464608 CGGCGGCACATATATTTCAGG 59.535 52.381 10.53 0.00 0.00 3.86
694 765 1.812571 GGCGGCACATATATTTCAGGG 59.187 52.381 3.07 0.00 0.00 4.45
695 766 2.504367 GCGGCACATATATTTCAGGGT 58.496 47.619 0.00 0.00 0.00 4.34
696 767 2.226437 GCGGCACATATATTTCAGGGTG 59.774 50.000 0.00 0.00 0.00 4.61
697 768 3.738982 CGGCACATATATTTCAGGGTGA 58.261 45.455 0.00 0.00 0.00 4.02
698 769 4.326826 CGGCACATATATTTCAGGGTGAT 58.673 43.478 0.00 0.00 0.00 3.06
699 770 4.154737 CGGCACATATATTTCAGGGTGATG 59.845 45.833 0.00 0.00 0.00 3.07
700 771 4.460382 GGCACATATATTTCAGGGTGATGG 59.540 45.833 0.00 0.00 0.00 3.51
701 772 5.316167 GCACATATATTTCAGGGTGATGGA 58.684 41.667 0.00 0.00 0.00 3.41
702 773 5.948162 GCACATATATTTCAGGGTGATGGAT 59.052 40.000 0.00 0.00 0.00 3.41
703 774 6.127814 GCACATATATTTCAGGGTGATGGATG 60.128 42.308 0.00 0.00 0.00 3.51
704 775 6.944290 CACATATATTTCAGGGTGATGGATGT 59.056 38.462 0.00 0.00 0.00 3.06
705 776 8.102676 CACATATATTTCAGGGTGATGGATGTA 58.897 37.037 0.00 0.00 0.00 2.29
706 777 8.668653 ACATATATTTCAGGGTGATGGATGTAA 58.331 33.333 0.00 0.00 0.00 2.41
707 778 9.519191 CATATATTTCAGGGTGATGGATGTAAA 57.481 33.333 0.00 0.00 0.00 2.01
712 783 7.822161 TTCAGGGTGATGGATGTAAATTATG 57.178 36.000 0.00 0.00 0.00 1.90
713 784 6.910191 TCAGGGTGATGGATGTAAATTATGT 58.090 36.000 0.00 0.00 0.00 2.29
714 785 6.772233 TCAGGGTGATGGATGTAAATTATGTG 59.228 38.462 0.00 0.00 0.00 3.21
715 786 5.536161 AGGGTGATGGATGTAAATTATGTGC 59.464 40.000 0.00 0.00 0.00 4.57
716 787 5.451908 GGTGATGGATGTAAATTATGTGCG 58.548 41.667 0.00 0.00 0.00 5.34
717 788 4.911610 GTGATGGATGTAAATTATGTGCGC 59.088 41.667 0.00 0.00 0.00 6.09
718 789 3.980646 TGGATGTAAATTATGTGCGCC 57.019 42.857 4.18 0.00 0.00 6.53
719 790 2.289274 TGGATGTAAATTATGTGCGCCG 59.711 45.455 4.18 0.00 0.00 6.46
720 791 2.350388 GGATGTAAATTATGTGCGCCGG 60.350 50.000 4.18 0.00 0.00 6.13
721 792 0.378962 TGTAAATTATGTGCGCCGGC 59.621 50.000 19.07 19.07 40.52 6.13
722 793 0.317519 GTAAATTATGTGCGCCGGCC 60.318 55.000 23.46 14.70 38.85 6.13
723 794 0.464735 TAAATTATGTGCGCCGGCCT 60.465 50.000 23.46 2.91 38.85 5.19
724 795 0.464735 AAATTATGTGCGCCGGCCTA 60.465 50.000 23.46 7.09 38.85 3.93
725 796 0.464735 AATTATGTGCGCCGGCCTAA 60.465 50.000 23.46 11.30 38.85 2.69
726 797 0.250727 ATTATGTGCGCCGGCCTAAT 60.251 50.000 23.46 12.19 38.85 1.73
727 798 0.464735 TTATGTGCGCCGGCCTAATT 60.465 50.000 23.46 5.92 38.85 1.40
728 799 0.464735 TATGTGCGCCGGCCTAATTT 60.465 50.000 23.46 4.13 38.85 1.82
729 800 0.464735 ATGTGCGCCGGCCTAATTTA 60.465 50.000 23.46 0.86 38.85 1.40
730 801 1.354155 GTGCGCCGGCCTAATTTAC 59.646 57.895 23.46 5.73 38.85 2.01
731 802 1.078356 TGCGCCGGCCTAATTTACA 60.078 52.632 23.46 3.36 38.85 2.41
732 803 0.464735 TGCGCCGGCCTAATTTACAT 60.465 50.000 23.46 0.00 38.85 2.29
733 804 1.202663 TGCGCCGGCCTAATTTACATA 60.203 47.619 23.46 0.00 38.85 2.29
734 805 1.874872 GCGCCGGCCTAATTTACATAA 59.125 47.619 23.46 0.00 0.00 1.90
735 806 2.291190 GCGCCGGCCTAATTTACATAAA 59.709 45.455 23.46 0.00 0.00 1.40
736 807 3.057806 GCGCCGGCCTAATTTACATAAAT 60.058 43.478 23.46 0.00 37.49 1.40
737 808 4.154556 GCGCCGGCCTAATTTACATAAATA 59.845 41.667 23.46 0.00 35.00 1.40
738 809 5.335035 GCGCCGGCCTAATTTACATAAATAA 60.335 40.000 23.46 0.00 35.00 1.40
739 810 6.081693 CGCCGGCCTAATTTACATAAATAAC 58.918 40.000 23.46 0.00 35.00 1.89
740 811 6.384224 GCCGGCCTAATTTACATAAATAACC 58.616 40.000 18.11 0.00 35.00 2.85
741 812 6.570957 GCCGGCCTAATTTACATAAATAACCC 60.571 42.308 18.11 0.00 35.00 4.11
742 813 6.071784 CCGGCCTAATTTACATAAATAACCCC 60.072 42.308 0.00 0.00 35.00 4.95
743 814 6.071784 CGGCCTAATTTACATAAATAACCCCC 60.072 42.308 0.00 0.00 35.00 5.40
761 832 4.724697 CGCGAACGCCAGCTGTTG 62.725 66.667 13.81 6.94 37.98 3.33
763 834 4.389576 CGAACGCCAGCTGTTGCC 62.390 66.667 13.81 0.00 40.80 4.52
764 835 2.980233 GAACGCCAGCTGTTGCCT 60.980 61.111 13.81 0.00 40.80 4.75
765 836 2.970974 GAACGCCAGCTGTTGCCTC 61.971 63.158 13.81 4.67 40.80 4.70
768 839 4.704833 GCCAGCTGTTGCCTCGGA 62.705 66.667 13.81 0.00 40.80 4.55
769 840 2.270205 CCAGCTGTTGCCTCGGAT 59.730 61.111 13.81 0.00 40.80 4.18
770 841 1.377725 CCAGCTGTTGCCTCGGATT 60.378 57.895 13.81 0.00 40.80 3.01
771 842 1.651240 CCAGCTGTTGCCTCGGATTG 61.651 60.000 13.81 0.00 40.80 2.67
772 843 1.377725 AGCTGTTGCCTCGGATTGG 60.378 57.895 0.00 0.00 40.80 3.16
773 844 1.675641 GCTGTTGCCTCGGATTGGT 60.676 57.895 0.00 0.00 0.00 3.67
774 845 1.648467 GCTGTTGCCTCGGATTGGTC 61.648 60.000 0.00 0.00 0.00 4.02
775 846 0.321564 CTGTTGCCTCGGATTGGTCA 60.322 55.000 0.00 0.00 0.00 4.02
776 847 0.109532 TGTTGCCTCGGATTGGTCAA 59.890 50.000 0.00 0.00 0.00 3.18
777 848 0.521735 GTTGCCTCGGATTGGTCAAC 59.478 55.000 0.00 0.00 35.87 3.18
778 849 0.109532 TTGCCTCGGATTGGTCAACA 59.890 50.000 0.00 0.00 0.00 3.33
779 850 0.109532 TGCCTCGGATTGGTCAACAA 59.890 50.000 0.00 0.00 44.54 2.83
780 851 0.804989 GCCTCGGATTGGTCAACAAG 59.195 55.000 0.00 0.00 43.48 3.16
781 852 1.882352 GCCTCGGATTGGTCAACAAGT 60.882 52.381 0.00 0.00 43.48 3.16
782 853 1.806542 CCTCGGATTGGTCAACAAGTG 59.193 52.381 0.00 0.00 43.48 3.16
783 854 1.806542 CTCGGATTGGTCAACAAGTGG 59.193 52.381 0.00 0.00 43.48 4.00
784 855 1.142060 TCGGATTGGTCAACAAGTGGT 59.858 47.619 0.00 0.00 43.48 4.16
785 856 1.535462 CGGATTGGTCAACAAGTGGTC 59.465 52.381 0.00 0.00 43.48 4.02
786 857 2.582052 GGATTGGTCAACAAGTGGTCA 58.418 47.619 0.00 0.00 43.48 4.02
787 858 2.955660 GGATTGGTCAACAAGTGGTCAA 59.044 45.455 0.00 0.00 43.48 3.18
788 859 3.383185 GGATTGGTCAACAAGTGGTCAAA 59.617 43.478 0.00 0.00 43.48 2.69
789 860 4.039124 GGATTGGTCAACAAGTGGTCAAAT 59.961 41.667 0.00 0.00 43.48 2.32
790 861 4.383850 TTGGTCAACAAGTGGTCAAATG 57.616 40.909 0.00 0.00 33.18 2.32
791 862 2.692557 TGGTCAACAAGTGGTCAAATGG 59.307 45.455 0.00 0.00 0.00 3.16
792 863 2.955660 GGTCAACAAGTGGTCAAATGGA 59.044 45.455 0.00 0.00 0.00 3.41
793 864 3.004734 GGTCAACAAGTGGTCAAATGGAG 59.995 47.826 0.00 0.00 0.00 3.86
794 865 2.622942 TCAACAAGTGGTCAAATGGAGC 59.377 45.455 0.00 0.00 44.35 4.70
799 870 4.301505 GGTCAAATGGAGCAGCGA 57.698 55.556 0.00 0.00 43.54 4.93
800 871 1.796796 GGTCAAATGGAGCAGCGAC 59.203 57.895 0.00 0.00 43.54 5.19
801 872 1.421485 GTCAAATGGAGCAGCGACG 59.579 57.895 0.00 0.00 0.00 5.12
802 873 1.014044 GTCAAATGGAGCAGCGACGA 61.014 55.000 0.00 0.00 0.00 4.20
803 874 0.737367 TCAAATGGAGCAGCGACGAG 60.737 55.000 0.00 0.00 0.00 4.18
804 875 1.016130 CAAATGGAGCAGCGACGAGT 61.016 55.000 0.00 0.00 0.00 4.18
805 876 1.016130 AAATGGAGCAGCGACGAGTG 61.016 55.000 0.00 0.00 0.00 3.51
806 877 2.842394 AATGGAGCAGCGACGAGTGG 62.842 60.000 0.00 0.00 0.00 4.00
817 888 4.777781 CGAGTGGCGTACGATGAA 57.222 55.556 21.65 0.00 34.64 2.57
818 889 2.275703 CGAGTGGCGTACGATGAAC 58.724 57.895 21.65 10.47 34.64 3.18
819 890 0.455464 CGAGTGGCGTACGATGAACA 60.455 55.000 21.65 6.20 34.64 3.18
820 891 1.269166 GAGTGGCGTACGATGAACAG 58.731 55.000 21.65 0.00 0.00 3.16
821 892 0.736325 AGTGGCGTACGATGAACAGC 60.736 55.000 21.65 0.00 0.00 4.40
822 893 1.803922 TGGCGTACGATGAACAGCG 60.804 57.895 21.65 10.78 46.76 5.18
823 894 1.515519 GGCGTACGATGAACAGCGA 60.516 57.895 21.65 0.58 43.75 4.93
824 895 1.624323 GCGTACGATGAACAGCGAC 59.376 57.895 21.65 11.01 43.75 5.19
825 896 0.797249 GCGTACGATGAACAGCGACT 60.797 55.000 21.65 0.42 43.75 4.18
826 897 0.907837 CGTACGATGAACAGCGACTG 59.092 55.000 18.67 5.47 43.75 3.51
828 899 1.649171 GTACGATGAACAGCGACTGTG 59.351 52.381 18.67 3.78 44.62 3.66
829 900 1.284982 ACGATGAACAGCGACTGTGC 61.285 55.000 18.67 11.13 44.62 4.57
831 902 4.530581 TGAACAGCGACTGTGCAA 57.469 50.000 15.56 3.26 45.90 4.08
832 903 3.005205 TGAACAGCGACTGTGCAAT 57.995 47.368 15.56 1.07 45.90 3.56
833 904 0.867746 TGAACAGCGACTGTGCAATC 59.132 50.000 15.56 9.29 45.90 2.67
834 905 0.867746 GAACAGCGACTGTGCAATCA 59.132 50.000 12.22 0.00 44.62 2.57
835 906 0.588252 AACAGCGACTGTGCAATCAC 59.412 50.000 12.22 0.00 44.62 3.06
836 907 1.131218 CAGCGACTGTGCAATCACG 59.869 57.895 0.00 0.00 46.01 4.35
837 908 1.300931 AGCGACTGTGCAATCACGT 60.301 52.632 0.00 0.00 46.01 4.49
838 909 1.154599 GCGACTGTGCAATCACGTG 60.155 57.895 9.94 9.94 46.01 4.49
839 910 1.831389 GCGACTGTGCAATCACGTGT 61.831 55.000 16.51 0.00 46.01 4.49
840 911 1.414378 CGACTGTGCAATCACGTGTA 58.586 50.000 16.51 2.58 46.01 2.90
841 912 1.386748 CGACTGTGCAATCACGTGTAG 59.613 52.381 16.51 7.81 46.01 2.74
842 913 2.672714 GACTGTGCAATCACGTGTAGA 58.327 47.619 16.51 0.00 46.01 2.59
843 914 2.404215 ACTGTGCAATCACGTGTAGAC 58.596 47.619 16.51 7.15 46.01 2.59
856 927 3.423571 CGTGTAGACGTATTGAGTGACC 58.576 50.000 3.89 0.00 40.91 4.02
857 928 3.120095 CGTGTAGACGTATTGAGTGACCA 60.120 47.826 3.89 0.00 40.91 4.02
858 929 4.438336 CGTGTAGACGTATTGAGTGACCAT 60.438 45.833 3.89 0.00 40.91 3.55
859 930 5.220719 CGTGTAGACGTATTGAGTGACCATA 60.221 44.000 3.89 0.00 40.91 2.74
860 931 6.512903 CGTGTAGACGTATTGAGTGACCATAT 60.513 42.308 3.89 0.00 40.91 1.78
861 932 7.201145 GTGTAGACGTATTGAGTGACCATATT 58.799 38.462 0.00 0.00 0.00 1.28
862 933 8.347771 GTGTAGACGTATTGAGTGACCATATTA 58.652 37.037 0.00 0.00 0.00 0.98
863 934 8.565416 TGTAGACGTATTGAGTGACCATATTAG 58.435 37.037 0.00 0.00 0.00 1.73
864 935 7.584122 AGACGTATTGAGTGACCATATTAGT 57.416 36.000 0.00 0.00 0.00 2.24
865 936 7.649973 AGACGTATTGAGTGACCATATTAGTC 58.350 38.462 0.00 0.00 34.72 2.59
866 937 6.436261 ACGTATTGAGTGACCATATTAGTCG 58.564 40.000 0.00 0.00 37.04 4.18
867 938 6.039047 ACGTATTGAGTGACCATATTAGTCGT 59.961 38.462 0.00 0.00 37.04 4.34
868 939 7.227314 ACGTATTGAGTGACCATATTAGTCGTA 59.773 37.037 0.00 0.00 37.04 3.43
869 940 8.235226 CGTATTGAGTGACCATATTAGTCGTAT 58.765 37.037 0.00 0.00 37.04 3.06
870 941 9.909644 GTATTGAGTGACCATATTAGTCGTATT 57.090 33.333 0.00 0.00 37.04 1.89
872 943 9.832445 ATTGAGTGACCATATTAGTCGTATTTT 57.168 29.630 0.00 0.00 37.04 1.82
891 962 9.698617 CGTATTTTAAAGTATAGTGACCAAAGC 57.301 33.333 0.00 0.00 0.00 3.51
892 963 9.698617 GTATTTTAAAGTATAGTGACCAAAGCG 57.301 33.333 0.00 0.00 0.00 4.68
893 964 7.733402 TTTTAAAGTATAGTGACCAAAGCGT 57.267 32.000 0.00 0.00 0.00 5.07
894 965 6.715344 TTAAAGTATAGTGACCAAAGCGTG 57.285 37.500 0.00 0.00 0.00 5.34
895 966 2.618053 AGTATAGTGACCAAAGCGTGC 58.382 47.619 0.00 0.00 0.00 5.34
896 967 1.664151 GTATAGTGACCAAAGCGTGCC 59.336 52.381 0.00 0.00 0.00 5.01
897 968 0.324943 ATAGTGACCAAAGCGTGCCT 59.675 50.000 0.00 0.00 0.00 4.75
898 969 0.107831 TAGTGACCAAAGCGTGCCTT 59.892 50.000 0.00 0.00 34.51 4.35
899 970 1.166531 AGTGACCAAAGCGTGCCTTC 61.167 55.000 0.00 0.00 31.99 3.46
900 971 1.148273 TGACCAAAGCGTGCCTTCT 59.852 52.632 0.00 0.00 31.99 2.85
901 972 0.465460 TGACCAAAGCGTGCCTTCTT 60.465 50.000 0.00 0.00 31.99 2.52
902 973 0.238553 GACCAAAGCGTGCCTTCTTC 59.761 55.000 0.00 0.00 31.99 2.87
903 974 1.207593 CCAAAGCGTGCCTTCTTCG 59.792 57.895 0.00 0.00 31.99 3.79
908 979 3.642755 CGTGCCTTCTTCGCAAGT 58.357 55.556 0.00 0.00 38.13 3.16
909 980 1.941812 CGTGCCTTCTTCGCAAGTT 59.058 52.632 0.00 0.00 38.13 2.66
910 981 0.110644 CGTGCCTTCTTCGCAAGTTC 60.111 55.000 0.00 0.00 38.13 3.01
911 982 0.944386 GTGCCTTCTTCGCAAGTTCA 59.056 50.000 0.00 0.00 38.13 3.18
912 983 1.333619 GTGCCTTCTTCGCAAGTTCAA 59.666 47.619 0.00 0.00 38.13 2.69
913 984 1.603802 TGCCTTCTTCGCAAGTTCAAG 59.396 47.619 0.00 0.00 39.48 3.02
914 985 1.604278 GCCTTCTTCGCAAGTTCAAGT 59.396 47.619 0.00 0.00 39.48 3.16
915 986 2.806244 GCCTTCTTCGCAAGTTCAAGTA 59.194 45.455 0.00 0.00 39.48 2.24
916 987 3.364068 GCCTTCTTCGCAAGTTCAAGTAC 60.364 47.826 0.00 0.00 39.48 2.73
917 988 3.186613 CCTTCTTCGCAAGTTCAAGTACC 59.813 47.826 0.00 0.00 39.48 3.34
918 989 2.400399 TCTTCGCAAGTTCAAGTACCG 58.600 47.619 0.00 0.00 39.48 4.02
919 990 0.863144 TTCGCAAGTTCAAGTACCGC 59.137 50.000 0.00 0.00 39.48 5.68
920 991 0.947180 TCGCAAGTTCAAGTACCGCC 60.947 55.000 0.00 0.00 39.48 6.13
921 992 1.495951 GCAAGTTCAAGTACCGCCG 59.504 57.895 0.00 0.00 0.00 6.46
922 993 1.908066 GCAAGTTCAAGTACCGCCGG 61.908 60.000 0.00 0.00 0.00 6.13
923 994 0.601841 CAAGTTCAAGTACCGCCGGT 60.602 55.000 15.63 15.63 40.16 5.28
924 995 0.601841 AAGTTCAAGTACCGCCGGTG 60.602 55.000 21.20 8.42 36.19 4.94
925 996 2.357760 TTCAAGTACCGCCGGTGC 60.358 61.111 21.20 19.07 38.59 5.01
926 997 3.166490 TTCAAGTACCGCCGGTGCA 62.166 57.895 25.99 2.70 40.76 4.57
927 998 2.435938 CAAGTACCGCCGGTGCAT 60.436 61.111 25.99 12.09 40.76 3.96
928 999 2.038269 CAAGTACCGCCGGTGCATT 61.038 57.895 25.99 14.00 40.76 3.56
929 1000 1.302993 AAGTACCGCCGGTGCATTT 60.303 52.632 25.99 9.99 40.76 2.32
930 1001 0.891904 AAGTACCGCCGGTGCATTTT 60.892 50.000 25.99 9.25 40.76 1.82
931 1002 0.036199 AGTACCGCCGGTGCATTTTA 60.036 50.000 25.99 0.00 40.76 1.52
932 1003 0.097499 GTACCGCCGGTGCATTTTAC 59.903 55.000 21.20 2.70 38.20 2.01
933 1004 0.036199 TACCGCCGGTGCATTTTACT 60.036 50.000 21.20 0.00 36.19 2.24
934 1005 1.303091 ACCGCCGGTGCATTTTACTC 61.303 55.000 8.62 0.00 37.32 2.59
935 1006 1.024579 CCGCCGGTGCATTTTACTCT 61.025 55.000 10.27 0.00 37.32 3.24
936 1007 0.802494 CGCCGGTGCATTTTACTCTT 59.198 50.000 0.00 0.00 37.32 2.85
937 1008 2.004017 CGCCGGTGCATTTTACTCTTA 58.996 47.619 0.00 0.00 37.32 2.10
1116 1232 2.835895 GAGGAGGGAGCCGGAGTC 60.836 72.222 5.05 0.00 0.00 3.36
1320 1457 4.617520 TCCGCCGTCTGCAAGCAA 62.618 61.111 0.00 0.00 41.33 3.91
2118 2348 4.139786 AGACCATTGACATGCATACCATC 58.860 43.478 0.00 0.00 29.71 3.51
2392 2727 3.632145 ACCTTTGTTGCGATTCTCAAGTT 59.368 39.130 0.00 0.00 0.00 2.66
2459 2930 9.944663 CAGTATAGTTATCTTCACTCTTCACTC 57.055 37.037 0.00 0.00 0.00 3.51
2460 2931 9.914834 AGTATAGTTATCTTCACTCTTCACTCT 57.085 33.333 0.00 0.00 0.00 3.24
2463 2934 7.531857 AGTTATCTTCACTCTTCACTCTTCA 57.468 36.000 0.00 0.00 0.00 3.02
2464 2935 7.375053 AGTTATCTTCACTCTTCACTCTTCAC 58.625 38.462 0.00 0.00 0.00 3.18
2465 2936 7.232534 AGTTATCTTCACTCTTCACTCTTCACT 59.767 37.037 0.00 0.00 0.00 3.41
2525 3007 8.373048 TGTGTTATCGTTCAGTTTAATTGTCT 57.627 30.769 0.00 0.00 0.00 3.41
2526 3008 8.832521 TGTGTTATCGTTCAGTTTAATTGTCTT 58.167 29.630 0.00 0.00 0.00 3.01
2527 3009 9.314501 GTGTTATCGTTCAGTTTAATTGTCTTC 57.685 33.333 0.00 0.00 0.00 2.87
2528 3010 9.047371 TGTTATCGTTCAGTTTAATTGTCTTCA 57.953 29.630 0.00 0.00 0.00 3.02
2610 3095 9.829507 AAAATGTCAAATGGTTAACTCATTCAA 57.170 25.926 17.28 9.60 34.15 2.69
2633 3119 2.229792 TGTTTTTACCTCAGCTGGCTG 58.770 47.619 15.13 15.58 44.86 4.85
2764 3317 9.469807 TTGCATGTAACACACCTTTTATTTAAG 57.530 29.630 0.00 0.00 0.00 1.85
2808 3394 5.717078 TCTGGTAGAGTTTTCGCTTCTTA 57.283 39.130 0.00 0.00 0.00 2.10
3395 4113 7.880160 TCCAAATGTTATATTCCCAGAGTTG 57.120 36.000 0.00 0.00 0.00 3.16
3522 4423 3.253921 TGATGAGTTCACATGCCTTGTTG 59.746 43.478 0.00 0.00 36.00 3.33
3634 4543 2.340427 GGGCTGCTGCACTTGTTAA 58.660 52.632 17.89 0.00 40.03 2.01
3644 4553 3.963665 TGCACTTGTTAATTGACACTGC 58.036 40.909 18.52 18.52 35.49 4.40
3658 4567 1.337703 ACACTGCATTTGTCGCATTGT 59.662 42.857 2.72 2.72 45.18 2.71
4041 4976 9.646427 TGCAATATTTACCTTTTAATGGTTCAC 57.354 29.630 7.83 0.00 38.88 3.18
4069 5004 4.979197 GCCAGAGTACTCATCATTAACTCG 59.021 45.833 24.44 0.00 41.12 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 6.017934 CACTCATTGTACTTGTAGTGCTTGTT 60.018 38.462 0.00 0.00 31.77 2.83
131 132 2.778299 TGGAATTCGTGGAAGAGTTGG 58.222 47.619 0.00 0.00 0.00 3.77
143 144 3.181493 CCAGGCTTTGAAGATGGAATTCG 60.181 47.826 8.83 0.00 36.86 3.34
176 183 2.180946 AGATATGCAGGTGGAGGTGA 57.819 50.000 0.00 0.00 0.00 4.02
298 305 3.192633 GCATTGGGAGTTGGAATACGTTT 59.807 43.478 0.00 0.00 0.00 3.60
355 362 3.149981 TGTGATGGTGATTTTTGGCGTA 58.850 40.909 0.00 0.00 0.00 4.42
414 422 1.544537 GGTGTAAGTGGTGTGCATCCA 60.545 52.381 9.10 9.10 0.00 3.41
423 431 3.637911 TGTTCTGTTGGTGTAAGTGGT 57.362 42.857 0.00 0.00 0.00 4.16
440 448 3.009143 GGGTTGGGTCTTCTACAGATGTT 59.991 47.826 0.00 0.00 32.60 2.71
506 514 2.547211 CTCATAAGATGCCCTTCTTGCG 59.453 50.000 6.67 0.00 36.63 4.85
550 558 0.960861 TCAGTCAGGTCATCGCTCGT 60.961 55.000 0.00 0.00 0.00 4.18
641 703 0.619255 TAATTCCCGACTCCCTGCCA 60.619 55.000 0.00 0.00 0.00 4.92
652 714 3.304659 CGATGCCAAATTCCTAATTCCCG 60.305 47.826 0.00 0.00 0.00 5.14
663 725 3.067439 TGCCGCCGATGCCAAATT 61.067 55.556 0.00 0.00 0.00 1.82
686 757 8.863086 CATAATTTACATCCATCACCCTGAAAT 58.137 33.333 0.00 0.00 0.00 2.17
687 758 7.838696 ACATAATTTACATCCATCACCCTGAAA 59.161 33.333 0.00 0.00 0.00 2.69
688 759 7.285172 CACATAATTTACATCCATCACCCTGAA 59.715 37.037 0.00 0.00 0.00 3.02
689 760 6.772233 CACATAATTTACATCCATCACCCTGA 59.228 38.462 0.00 0.00 0.00 3.86
690 761 6.515531 GCACATAATTTACATCCATCACCCTG 60.516 42.308 0.00 0.00 0.00 4.45
691 762 5.536161 GCACATAATTTACATCCATCACCCT 59.464 40.000 0.00 0.00 0.00 4.34
692 763 5.562696 CGCACATAATTTACATCCATCACCC 60.563 44.000 0.00 0.00 0.00 4.61
693 764 5.451908 CGCACATAATTTACATCCATCACC 58.548 41.667 0.00 0.00 0.00 4.02
694 765 4.911610 GCGCACATAATTTACATCCATCAC 59.088 41.667 0.30 0.00 0.00 3.06
695 766 4.023279 GGCGCACATAATTTACATCCATCA 60.023 41.667 10.83 0.00 0.00 3.07
696 767 4.475944 GGCGCACATAATTTACATCCATC 58.524 43.478 10.83 0.00 0.00 3.51
697 768 3.058293 CGGCGCACATAATTTACATCCAT 60.058 43.478 10.83 0.00 0.00 3.41
698 769 2.289274 CGGCGCACATAATTTACATCCA 59.711 45.455 10.83 0.00 0.00 3.41
699 770 2.350388 CCGGCGCACATAATTTACATCC 60.350 50.000 10.83 0.00 0.00 3.51
700 771 2.916111 CCGGCGCACATAATTTACATC 58.084 47.619 10.83 0.00 0.00 3.06
701 772 1.001815 GCCGGCGCACATAATTTACAT 60.002 47.619 12.58 0.00 34.03 2.29
702 773 0.378962 GCCGGCGCACATAATTTACA 59.621 50.000 12.58 0.00 34.03 2.41
703 774 0.317519 GGCCGGCGCACATAATTTAC 60.318 55.000 22.54 0.00 36.38 2.01
704 775 0.464735 AGGCCGGCGCACATAATTTA 60.465 50.000 22.54 0.00 36.38 1.40
705 776 0.464735 TAGGCCGGCGCACATAATTT 60.465 50.000 22.54 0.00 36.38 1.82
706 777 0.464735 TTAGGCCGGCGCACATAATT 60.465 50.000 22.54 0.00 36.38 1.40
707 778 0.250727 ATTAGGCCGGCGCACATAAT 60.251 50.000 22.54 15.52 36.38 1.28
708 779 0.464735 AATTAGGCCGGCGCACATAA 60.465 50.000 22.54 13.94 36.38 1.90
709 780 0.464735 AAATTAGGCCGGCGCACATA 60.465 50.000 22.54 5.07 36.38 2.29
710 781 0.464735 TAAATTAGGCCGGCGCACAT 60.465 50.000 22.54 6.79 36.38 3.21
711 782 1.078356 TAAATTAGGCCGGCGCACA 60.078 52.632 22.54 4.27 36.38 4.57
712 783 1.354155 GTAAATTAGGCCGGCGCAC 59.646 57.895 22.54 6.73 36.38 5.34
713 784 0.464735 ATGTAAATTAGGCCGGCGCA 60.465 50.000 22.54 7.56 36.38 6.09
714 785 1.515081 TATGTAAATTAGGCCGGCGC 58.485 50.000 22.54 13.90 0.00 6.53
715 786 4.759516 ATTTATGTAAATTAGGCCGGCG 57.240 40.909 22.54 0.00 32.28 6.46
716 787 6.384224 GGTTATTTATGTAAATTAGGCCGGC 58.616 40.000 21.18 21.18 37.16 6.13
717 788 6.071784 GGGGTTATTTATGTAAATTAGGCCGG 60.072 42.308 0.00 0.00 37.16 6.13
718 789 6.071784 GGGGGTTATTTATGTAAATTAGGCCG 60.072 42.308 0.00 0.00 37.16 6.13
719 790 7.235935 GGGGGTTATTTATGTAAATTAGGCC 57.764 40.000 0.00 0.00 37.16 5.19
744 815 4.724697 CAACAGCTGGCGTTCGCG 62.725 66.667 19.93 0.00 44.73 5.87
746 817 4.389576 GGCAACAGCTGGCGTTCG 62.390 66.667 19.93 0.31 41.35 3.95
752 823 1.377725 AATCCGAGGCAACAGCTGG 60.378 57.895 19.93 1.57 41.41 4.85
753 824 1.651240 CCAATCCGAGGCAACAGCTG 61.651 60.000 13.48 13.48 41.41 4.24
754 825 1.377725 CCAATCCGAGGCAACAGCT 60.378 57.895 0.00 0.00 41.41 4.24
755 826 1.648467 GACCAATCCGAGGCAACAGC 61.648 60.000 0.00 0.00 41.41 4.40
756 827 0.321564 TGACCAATCCGAGGCAACAG 60.322 55.000 0.00 0.00 41.41 3.16
757 828 0.109532 TTGACCAATCCGAGGCAACA 59.890 50.000 0.00 0.00 41.41 3.33
758 829 0.521735 GTTGACCAATCCGAGGCAAC 59.478 55.000 0.00 0.00 36.64 4.17
759 830 0.109532 TGTTGACCAATCCGAGGCAA 59.890 50.000 0.00 0.00 0.00 4.52
760 831 0.109532 TTGTTGACCAATCCGAGGCA 59.890 50.000 0.00 0.00 0.00 4.75
761 832 0.804989 CTTGTTGACCAATCCGAGGC 59.195 55.000 0.00 0.00 31.20 4.70
762 833 1.806542 CACTTGTTGACCAATCCGAGG 59.193 52.381 0.00 0.00 31.20 4.63
763 834 1.806542 CCACTTGTTGACCAATCCGAG 59.193 52.381 0.00 0.00 31.20 4.63
764 835 1.142060 ACCACTTGTTGACCAATCCGA 59.858 47.619 0.00 0.00 31.20 4.55
765 836 1.535462 GACCACTTGTTGACCAATCCG 59.465 52.381 0.00 0.00 31.20 4.18
766 837 2.582052 TGACCACTTGTTGACCAATCC 58.418 47.619 0.00 0.00 31.20 3.01
767 838 4.647424 TTTGACCACTTGTTGACCAATC 57.353 40.909 0.00 0.00 31.20 2.67
768 839 4.202243 CCATTTGACCACTTGTTGACCAAT 60.202 41.667 0.00 0.00 31.20 3.16
769 840 3.131933 CCATTTGACCACTTGTTGACCAA 59.868 43.478 0.00 0.00 0.00 3.67
770 841 2.692557 CCATTTGACCACTTGTTGACCA 59.307 45.455 0.00 0.00 0.00 4.02
771 842 2.955660 TCCATTTGACCACTTGTTGACC 59.044 45.455 0.00 0.00 0.00 4.02
772 843 3.550842 GCTCCATTTGACCACTTGTTGAC 60.551 47.826 0.00 0.00 0.00 3.18
773 844 2.622942 GCTCCATTTGACCACTTGTTGA 59.377 45.455 0.00 0.00 0.00 3.18
774 845 2.361757 TGCTCCATTTGACCACTTGTTG 59.638 45.455 0.00 0.00 0.00 3.33
775 846 2.624838 CTGCTCCATTTGACCACTTGTT 59.375 45.455 0.00 0.00 0.00 2.83
776 847 2.233271 CTGCTCCATTTGACCACTTGT 58.767 47.619 0.00 0.00 0.00 3.16
777 848 1.068055 GCTGCTCCATTTGACCACTTG 60.068 52.381 0.00 0.00 0.00 3.16
778 849 1.251251 GCTGCTCCATTTGACCACTT 58.749 50.000 0.00 0.00 0.00 3.16
779 850 0.957395 CGCTGCTCCATTTGACCACT 60.957 55.000 0.00 0.00 0.00 4.00
780 851 0.955428 TCGCTGCTCCATTTGACCAC 60.955 55.000 0.00 0.00 0.00 4.16
781 852 0.955428 GTCGCTGCTCCATTTGACCA 60.955 55.000 0.00 0.00 0.00 4.02
782 853 1.796796 GTCGCTGCTCCATTTGACC 59.203 57.895 0.00 0.00 0.00 4.02
783 854 1.014044 TCGTCGCTGCTCCATTTGAC 61.014 55.000 0.00 0.00 0.00 3.18
784 855 0.737367 CTCGTCGCTGCTCCATTTGA 60.737 55.000 0.00 0.00 0.00 2.69
785 856 1.016130 ACTCGTCGCTGCTCCATTTG 61.016 55.000 0.00 0.00 0.00 2.32
786 857 1.016130 CACTCGTCGCTGCTCCATTT 61.016 55.000 0.00 0.00 0.00 2.32
787 858 1.446792 CACTCGTCGCTGCTCCATT 60.447 57.895 0.00 0.00 0.00 3.16
788 859 2.182791 CACTCGTCGCTGCTCCAT 59.817 61.111 0.00 0.00 0.00 3.41
789 860 4.056125 CCACTCGTCGCTGCTCCA 62.056 66.667 0.00 0.00 0.00 3.86
800 871 0.455464 TGTTCATCGTACGCCACTCG 60.455 55.000 11.24 0.00 45.38 4.18
801 872 1.269166 CTGTTCATCGTACGCCACTC 58.731 55.000 11.24 1.69 0.00 3.51
802 873 0.736325 GCTGTTCATCGTACGCCACT 60.736 55.000 11.24 0.00 0.00 4.00
803 874 1.708027 GCTGTTCATCGTACGCCAC 59.292 57.895 11.24 4.79 0.00 5.01
804 875 1.803922 CGCTGTTCATCGTACGCCA 60.804 57.895 11.24 0.00 0.00 5.69
805 876 1.515519 TCGCTGTTCATCGTACGCC 60.516 57.895 11.24 0.00 0.00 5.68
806 877 0.797249 AGTCGCTGTTCATCGTACGC 60.797 55.000 11.24 0.00 0.00 4.42
807 878 0.907837 CAGTCGCTGTTCATCGTACG 59.092 55.000 9.53 9.53 0.00 3.67
808 879 1.649171 CACAGTCGCTGTTCATCGTAC 59.351 52.381 9.36 0.00 42.59 3.67
809 880 1.977188 CACAGTCGCTGTTCATCGTA 58.023 50.000 9.36 0.00 42.59 3.43
810 881 1.284982 GCACAGTCGCTGTTCATCGT 61.285 55.000 9.36 0.00 42.59 3.73
811 882 1.284297 TGCACAGTCGCTGTTCATCG 61.284 55.000 9.36 1.18 42.59 3.84
812 883 0.867746 TTGCACAGTCGCTGTTCATC 59.132 50.000 11.49 3.63 42.59 2.92
813 884 1.466167 GATTGCACAGTCGCTGTTCAT 59.534 47.619 11.49 4.82 42.59 2.57
814 885 0.867746 GATTGCACAGTCGCTGTTCA 59.132 50.000 9.36 8.57 42.59 3.18
815 886 0.867746 TGATTGCACAGTCGCTGTTC 59.132 50.000 9.36 6.29 42.59 3.18
816 887 0.588252 GTGATTGCACAGTCGCTGTT 59.412 50.000 9.36 0.00 42.59 3.16
817 888 1.560004 CGTGATTGCACAGTCGCTGT 61.560 55.000 6.67 6.67 46.51 4.40
818 889 1.131218 CGTGATTGCACAGTCGCTG 59.869 57.895 5.37 5.47 45.41 5.18
819 890 1.300931 ACGTGATTGCACAGTCGCT 60.301 52.632 5.37 0.00 45.41 4.93
820 891 1.154599 CACGTGATTGCACAGTCGC 60.155 57.895 10.90 0.00 45.41 5.19
821 892 1.386748 CTACACGTGATTGCACAGTCG 59.613 52.381 25.01 0.00 45.41 4.18
822 893 2.408704 GTCTACACGTGATTGCACAGTC 59.591 50.000 25.01 1.88 45.41 3.51
823 894 2.404215 GTCTACACGTGATTGCACAGT 58.596 47.619 25.01 0.00 45.41 3.55
824 895 1.386748 CGTCTACACGTGATTGCACAG 59.613 52.381 25.01 7.16 45.41 3.66
825 896 1.414378 CGTCTACACGTGATTGCACA 58.586 50.000 25.01 0.00 45.41 4.57
836 907 4.430137 TGGTCACTCAATACGTCTACAC 57.570 45.455 0.00 0.00 0.00 2.90
837 908 6.954487 ATATGGTCACTCAATACGTCTACA 57.046 37.500 0.00 0.00 0.00 2.74
838 909 8.566260 ACTAATATGGTCACTCAATACGTCTAC 58.434 37.037 0.00 0.00 0.00 2.59
839 910 8.687292 ACTAATATGGTCACTCAATACGTCTA 57.313 34.615 0.00 0.00 0.00 2.59
840 911 7.520131 CGACTAATATGGTCACTCAATACGTCT 60.520 40.741 0.00 0.00 33.73 4.18
841 912 6.577800 CGACTAATATGGTCACTCAATACGTC 59.422 42.308 0.00 0.00 33.73 4.34
842 913 6.039047 ACGACTAATATGGTCACTCAATACGT 59.961 38.462 0.00 0.00 33.73 3.57
843 914 6.436261 ACGACTAATATGGTCACTCAATACG 58.564 40.000 0.00 0.00 33.73 3.06
844 915 9.909644 AATACGACTAATATGGTCACTCAATAC 57.090 33.333 0.00 0.00 33.73 1.89
846 917 9.832445 AAAATACGACTAATATGGTCACTCAAT 57.168 29.630 0.00 0.00 33.73 2.57
865 936 9.698617 GCTTTGGTCACTATACTTTAAAATACG 57.301 33.333 0.00 0.00 0.00 3.06
866 937 9.698617 CGCTTTGGTCACTATACTTTAAAATAC 57.301 33.333 0.00 0.00 0.00 1.89
867 938 9.439500 ACGCTTTGGTCACTATACTTTAAAATA 57.561 29.630 0.00 0.00 0.00 1.40
868 939 8.234546 CACGCTTTGGTCACTATACTTTAAAAT 58.765 33.333 0.00 0.00 0.00 1.82
869 940 7.577979 CACGCTTTGGTCACTATACTTTAAAA 58.422 34.615 0.00 0.00 0.00 1.52
870 941 6.347888 GCACGCTTTGGTCACTATACTTTAAA 60.348 38.462 0.00 0.00 0.00 1.52
871 942 5.121142 GCACGCTTTGGTCACTATACTTTAA 59.879 40.000 0.00 0.00 0.00 1.52
872 943 4.628333 GCACGCTTTGGTCACTATACTTTA 59.372 41.667 0.00 0.00 0.00 1.85
873 944 3.435671 GCACGCTTTGGTCACTATACTTT 59.564 43.478 0.00 0.00 0.00 2.66
874 945 3.000727 GCACGCTTTGGTCACTATACTT 58.999 45.455 0.00 0.00 0.00 2.24
875 946 2.618053 GCACGCTTTGGTCACTATACT 58.382 47.619 0.00 0.00 0.00 2.12
876 947 1.664151 GGCACGCTTTGGTCACTATAC 59.336 52.381 0.00 0.00 0.00 1.47
877 948 1.553248 AGGCACGCTTTGGTCACTATA 59.447 47.619 0.00 0.00 0.00 1.31
878 949 0.324943 AGGCACGCTTTGGTCACTAT 59.675 50.000 0.00 0.00 0.00 2.12
879 950 0.107831 AAGGCACGCTTTGGTCACTA 59.892 50.000 0.00 0.00 0.00 2.74
880 951 1.152963 AAGGCACGCTTTGGTCACT 60.153 52.632 0.00 0.00 0.00 3.41
881 952 1.166531 AGAAGGCACGCTTTGGTCAC 61.167 55.000 0.00 0.00 0.00 3.67
882 953 0.465460 AAGAAGGCACGCTTTGGTCA 60.465 50.000 0.00 0.00 0.00 4.02
883 954 0.238553 GAAGAAGGCACGCTTTGGTC 59.761 55.000 0.00 0.00 0.00 4.02
884 955 1.507141 CGAAGAAGGCACGCTTTGGT 61.507 55.000 0.00 0.00 0.00 3.67
885 956 1.207593 CGAAGAAGGCACGCTTTGG 59.792 57.895 0.00 0.00 0.00 3.28
886 957 4.826600 CGAAGAAGGCACGCTTTG 57.173 55.556 0.00 0.00 0.00 2.77
891 962 0.110644 GAACTTGCGAAGAAGGCACG 60.111 55.000 3.37 0.00 40.71 5.34
892 963 0.944386 TGAACTTGCGAAGAAGGCAC 59.056 50.000 3.37 0.00 40.71 5.01
893 964 1.603802 CTTGAACTTGCGAAGAAGGCA 59.396 47.619 3.37 0.00 38.93 4.75
894 965 1.604278 ACTTGAACTTGCGAAGAAGGC 59.396 47.619 3.37 0.00 0.00 4.35
895 966 3.186613 GGTACTTGAACTTGCGAAGAAGG 59.813 47.826 0.00 0.00 0.00 3.46
896 967 3.120991 CGGTACTTGAACTTGCGAAGAAG 60.121 47.826 0.00 0.00 0.00 2.85
897 968 2.798283 CGGTACTTGAACTTGCGAAGAA 59.202 45.455 0.00 0.00 0.00 2.52
898 969 2.400399 CGGTACTTGAACTTGCGAAGA 58.600 47.619 0.00 0.00 0.00 2.87
899 970 1.136336 GCGGTACTTGAACTTGCGAAG 60.136 52.381 0.00 0.00 0.00 3.79
900 971 0.863144 GCGGTACTTGAACTTGCGAA 59.137 50.000 0.00 0.00 0.00 4.70
901 972 0.947180 GGCGGTACTTGAACTTGCGA 60.947 55.000 0.00 0.00 0.00 5.10
902 973 1.495951 GGCGGTACTTGAACTTGCG 59.504 57.895 0.00 0.00 0.00 4.85
903 974 1.495951 CGGCGGTACTTGAACTTGC 59.504 57.895 0.00 0.00 0.00 4.01
904 975 0.601841 ACCGGCGGTACTTGAACTTG 60.602 55.000 33.31 0.00 32.11 3.16
905 976 0.601841 CACCGGCGGTACTTGAACTT 60.602 55.000 33.65 0.87 32.11 2.66
906 977 1.005394 CACCGGCGGTACTTGAACT 60.005 57.895 33.65 1.79 32.11 3.01
907 978 2.674084 GCACCGGCGGTACTTGAAC 61.674 63.158 33.65 11.24 32.11 3.18
908 979 2.357760 GCACCGGCGGTACTTGAA 60.358 61.111 33.65 0.00 32.11 2.69
909 980 2.457743 AATGCACCGGCGGTACTTGA 62.458 55.000 33.65 11.13 45.35 3.02
910 981 1.582610 AAATGCACCGGCGGTACTTG 61.583 55.000 33.65 20.67 45.35 3.16
911 982 0.891904 AAAATGCACCGGCGGTACTT 60.892 50.000 33.65 21.76 45.35 2.24
912 983 0.036199 TAAAATGCACCGGCGGTACT 60.036 50.000 33.65 16.32 45.35 2.73
913 984 0.097499 GTAAAATGCACCGGCGGTAC 59.903 55.000 33.65 27.66 45.35 3.34
914 985 0.036199 AGTAAAATGCACCGGCGGTA 60.036 50.000 33.65 18.82 45.35 4.02
915 986 1.302993 AGTAAAATGCACCGGCGGT 60.303 52.632 28.83 28.83 45.35 5.68
916 987 1.024579 AGAGTAAAATGCACCGGCGG 61.025 55.000 27.06 27.06 45.35 6.13
917 988 0.802494 AAGAGTAAAATGCACCGGCG 59.198 50.000 0.00 0.00 45.35 6.46
918 989 4.428615 TTTAAGAGTAAAATGCACCGGC 57.571 40.909 0.00 0.00 41.68 6.13
945 1016 2.202756 CGGGAGCGGAGTTGTAGC 60.203 66.667 0.00 0.00 0.00 3.58
948 1019 3.692406 GGACGGGAGCGGAGTTGT 61.692 66.667 0.00 0.00 0.00 3.32
2182 2476 4.641396 TCATGGCCCACGAATAGAAATAG 58.359 43.478 0.00 0.00 0.00 1.73
2462 2933 8.871862 GCTCATCTATCTAGCAAATGAATAGTG 58.128 37.037 0.00 0.00 36.26 2.74
2463 2934 8.814931 AGCTCATCTATCTAGCAAATGAATAGT 58.185 33.333 0.00 0.00 38.75 2.12
2464 2935 9.656040 AAGCTCATCTATCTAGCAAATGAATAG 57.344 33.333 0.00 0.00 38.75 1.73
2484 2961 4.826274 AACACAGAAGGCTATAAGCTCA 57.174 40.909 0.00 0.00 41.99 4.26
2609 3094 3.005791 GCCAGCTGAGGTAAAAACATGTT 59.994 43.478 17.39 4.92 0.00 2.71
2610 3095 2.558359 GCCAGCTGAGGTAAAAACATGT 59.442 45.455 17.39 0.00 0.00 3.21
2764 3317 1.831580 AAGTGATCTTGGGCTTCAGC 58.168 50.000 0.00 0.00 34.75 4.26
2808 3394 1.584724 AACTCATCCCTCCCGATGTT 58.415 50.000 0.00 0.00 40.50 2.71
2900 3551 3.639094 GCTCACTACTGATGATGGTACCT 59.361 47.826 14.36 0.00 0.00 3.08
3079 3778 2.624316 ATCGTGCAACATTTCAGCTG 57.376 45.000 7.63 7.63 35.74 4.24
3395 4113 7.916914 TTATGAAACAGCTAAACTAAGGGAC 57.083 36.000 0.00 0.00 0.00 4.46
3522 4423 5.890419 ACCTAGGAGTATGTAACAGTGTACC 59.110 44.000 17.98 0.00 0.00 3.34
3634 4543 1.608109 TGCGACAAATGCAGTGTCAAT 59.392 42.857 24.98 0.00 44.66 2.57
3644 4553 6.260377 AGACATTGATACAATGCGACAAATG 58.740 36.000 19.83 0.00 0.00 2.32
3658 4567 9.836864 ATATAAACACTGCTGAAGACATTGATA 57.163 29.630 0.00 0.00 0.00 2.15
3984 4914 3.314635 AGCAAAGCAAAACTCACTCTCAG 59.685 43.478 0.00 0.00 0.00 3.35
4043 4978 5.658634 AGTTAATGATGAGTACTCTGGCTCA 59.341 40.000 23.01 18.51 44.55 4.26
4069 5004 1.160137 ATCTTCAGCCGCAAACAGTC 58.840 50.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.