Multiple sequence alignment - TraesCS7D01G512000

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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 TraesCS7D01G512000 chr7D 100.000 3638 0 0 1 3638 613829121 613825484 0.000000e+00 6719.0
1 TraesCS7D01G512000 chr7D 90.349 1720 134 14 937 2640 613799301 613801004 0.000000e+00 2228.0
2 TraesCS7D01G512000 chr7D 84.706 425 54 3 2728 3144 74611232 74611653 7.270000e-112 414.0
3 TraesCS7D01G512000 chr7D 84.507 426 55 3 2728 3144 625558652 625559075 9.400000e-111 411.0
4 TraesCS7D01G512000 chr7D 95.349 43 2 0 3243 3285 613825823 613825781 6.520000e-08 69.4
5 TraesCS7D01G512000 chr7D 95.349 43 2 0 3299 3341 613825879 613825837 6.520000e-08 69.4
6 TraesCS7D01G512000 chr7B 92.375 2623 143 11 722 3316 705128231 705125638 0.000000e+00 3683.0
7 TraesCS7D01G512000 chr7B 88.337 1209 91 20 718 1905 705109763 705110942 0.000000e+00 1406.0
8 TraesCS7D01G512000 chr7B 89.970 658 61 4 1974 2630 705111041 705111694 0.000000e+00 845.0
9 TraesCS7D01G512000 chr7B 93.989 366 18 4 1 364 705198185 705197822 5.310000e-153 551.0
10 TraesCS7D01G512000 chr7B 94.077 287 17 0 3352 3638 705125252 705124966 1.550000e-118 436.0
11 TraesCS7D01G512000 chr7B 90.182 275 23 3 362 635 705197307 705197036 4.470000e-94 355.0
12 TraesCS7D01G512000 chr7B 80.000 200 29 6 3299 3491 632959968 632960163 1.760000e-28 137.0
13 TraesCS7D01G512000 chr7B 81.651 109 16 2 254 362 25399949 25399845 1.800000e-13 87.9
14 TraesCS7D01G512000 chr7B 78.992 119 23 2 3299 3416 705125711 705125594 3.010000e-11 80.5
15 TraesCS7D01G512000 chr7A 90.064 1731 137 15 932 2640 705678183 705679900 0.000000e+00 2211.0
16 TraesCS7D01G512000 chr7A 88.824 340 34 1 945 1284 705595165 705595500 7.270000e-112 414.0
17 TraesCS7D01G512000 chr5B 87.322 915 101 9 994 1905 586534240 586535142 0.000000e+00 1033.0
18 TraesCS7D01G512000 chr5B 86.676 683 76 7 1976 2658 586535342 586536009 0.000000e+00 743.0
19 TraesCS7D01G512000 chr5B 90.196 102 10 0 3145 3246 655624645 655624746 2.280000e-27 134.0
20 TraesCS7D01G512000 chr5B 90.698 86 8 0 3145 3230 622588662 622588747 8.250000e-22 115.0
21 TraesCS7D01G512000 chr5D 85.539 816 94 18 944 1743 478689807 478689000 0.000000e+00 832.0
22 TraesCS7D01G512000 chr5D 86.536 661 66 16 1978 2628 478598798 478599445 0.000000e+00 706.0
23 TraesCS7D01G512000 chr5D 87.454 542 65 2 1976 2517 478688988 478688450 3.990000e-174 621.0
24 TraesCS7D01G512000 chr5D 86.311 431 46 5 2724 3144 462017847 462018274 1.190000e-124 457.0
25 TraesCS7D01G512000 chr5D 85.981 214 26 3 1601 1812 478598282 478598493 3.660000e-55 226.0
26 TraesCS7D01G512000 chr2B 85.280 428 49 6 2728 3144 720014650 720015074 2.600000e-116 429.0
27 TraesCS7D01G512000 chr2B 76.704 807 167 15 1108 1902 764109529 764108732 2.600000e-116 429.0
28 TraesCS7D01G512000 chr6A 85.211 426 51 4 2728 3144 92350390 92349968 9.340000e-116 427.0
29 TraesCS7D01G512000 chr4A 85.176 425 53 2 2728 3144 494646844 494646422 9.340000e-116 427.0
30 TraesCS7D01G512000 chr1B 85.012 427 51 5 2728 3144 388404043 388403620 4.340000e-114 422.0
31 TraesCS7D01G512000 chr1B 88.000 100 12 0 223 322 148422324 148422225 6.380000e-23 119.0
32 TraesCS7D01G512000 chr2A 84.296 433 52 6 2724 3144 475885531 475885103 3.380000e-110 409.0
33 TraesCS7D01G512000 chr1A 78.009 673 117 19 1976 2646 560880239 560879596 9.470000e-106 394.0
34 TraesCS7D01G512000 chr3A 79.252 588 101 16 1108 1686 142878817 142879392 1.220000e-104 390.0
35 TraesCS7D01G512000 chr3A 87.255 102 13 0 3145 3246 491535032 491535133 2.300000e-22 117.0
36 TraesCS7D01G512000 chr4D 77.080 685 115 21 1958 2639 509136039 509136684 1.240000e-94 357.0
37 TraesCS7D01G512000 chrUn 90.196 102 10 0 3145 3246 309817615 309817716 2.280000e-27 134.0
38 TraesCS7D01G512000 chr3D 79.000 200 31 8 3299 3491 496792935 496792740 3.810000e-25 126.0
39 TraesCS7D01G512000 chr2D 79.000 200 31 8 3299 3491 97633584 97633389 3.810000e-25 126.0
40 TraesCS7D01G512000 chr1D 78.500 200 32 8 3299 3491 462390216 462390411 1.770000e-23 121.0
41 TraesCS7D01G512000 chr1D 78.000 200 33 8 3299 3491 426917684 426917489 8.250000e-22 115.0
42 TraesCS7D01G512000 chr6B 79.429 175 28 8 3368 3538 648222093 648222263 2.300000e-22 117.0
43 TraesCS7D01G512000 chr6B 82.857 105 15 2 3384 3485 37611039 37610935 1.390000e-14 91.6
44 TraesCS7D01G512000 chr5A 91.045 67 3 3 3432 3497 588405714 588405778 1.800000e-13 87.9
45 TraesCS7D01G512000 chr6D 78.862 123 13 9 245 362 427603739 427603853 1.810000e-08 71.3


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 TraesCS7D01G512000 chr7D 613825484 613829121 3637 True 2285.933333 6719 96.899333 1 3638 3 chr7D.!!$R1 3637
1 TraesCS7D01G512000 chr7D 613799301 613801004 1703 False 2228.000000 2228 90.349000 937 2640 1 chr7D.!!$F2 1703
2 TraesCS7D01G512000 chr7B 705124966 705128231 3265 True 1399.833333 3683 88.481333 722 3638 3 chr7B.!!$R2 2916
3 TraesCS7D01G512000 chr7B 705109763 705111694 1931 False 1125.500000 1406 89.153500 718 2630 2 chr7B.!!$F2 1912
4 TraesCS7D01G512000 chr7B 705197036 705198185 1149 True 453.000000 551 92.085500 1 635 2 chr7B.!!$R3 634
5 TraesCS7D01G512000 chr7A 705678183 705679900 1717 False 2211.000000 2211 90.064000 932 2640 1 chr7A.!!$F2 1708
6 TraesCS7D01G512000 chr5B 586534240 586536009 1769 False 888.000000 1033 86.999000 994 2658 2 chr5B.!!$F3 1664
7 TraesCS7D01G512000 chr5D 478688450 478689807 1357 True 726.500000 832 86.496500 944 2517 2 chr5D.!!$R1 1573
8 TraesCS7D01G512000 chr5D 478598282 478599445 1163 False 466.000000 706 86.258500 1601 2628 2 chr5D.!!$F2 1027
9 TraesCS7D01G512000 chr2B 764108732 764109529 797 True 429.000000 429 76.704000 1108 1902 1 chr2B.!!$R1 794
10 TraesCS7D01G512000 chr1A 560879596 560880239 643 True 394.000000 394 78.009000 1976 2646 1 chr1A.!!$R1 670
11 TraesCS7D01G512000 chr3A 142878817 142879392 575 False 390.000000 390 79.252000 1108 1686 1 chr3A.!!$F1 578
12 TraesCS7D01G512000 chr4D 509136039 509136684 645 False 357.000000 357 77.080000 1958 2639 1 chr4D.!!$F1 681

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
691 1212 0.026285 GTTACGCGGCATGCACTTAG 59.974 55.0 21.36 8.11 46.97 2.18 F
696 1217 0.028110 GCGGCATGCACTTAGCTTAC 59.972 55.0 21.36 0.00 45.94 2.34 F
893 1434 0.031178 ACGTAGGTCGCGTGTTCTTT 59.969 50.0 5.77 0.00 44.19 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2404 3208 0.326264 AATGGCAGGAGCTCGAAGTT 59.674 50.000 7.83 0.0 41.70 2.66 R
2538 3348 1.215647 GGTCATGTCGAACTCGGCT 59.784 57.895 5.21 0.0 45.41 5.52 R
2717 3528 0.041400 CGCACGCATCACAAACTGAA 60.041 50.000 0.00 0.0 30.60 3.02 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
29 32 0.532862 CCCACACAGAGGTCACACAC 60.533 60.000 0.00 0.00 0.00 3.82
38 41 3.908737 GGTCACACACCACTAGGAC 57.091 57.895 0.00 0.00 45.98 3.85
60 63 2.060383 TCAGAGGGGCTCATGGTCG 61.060 63.158 0.00 0.00 32.06 4.79
62 65 4.899239 GAGGGGCTCATGGTCGCG 62.899 72.222 0.00 0.00 37.57 5.87
78 81 2.972505 CGCGGTTTGTCCTGCACT 60.973 61.111 0.00 0.00 36.21 4.40
81 84 2.908073 CGGTTTGTCCTGCACTGCC 61.908 63.158 0.00 0.00 0.00 4.85
83 86 0.250727 GGTTTGTCCTGCACTGCCTA 60.251 55.000 0.00 0.00 0.00 3.93
206 209 2.553028 GGCCTGATTTGGAACTCTGTCA 60.553 50.000 0.00 0.00 0.00 3.58
219 222 5.278022 GGAACTCTGTCATGTTTTGGAACTC 60.278 44.000 0.00 0.00 36.70 3.01
297 300 2.291282 CCTCTGTGTGAGTAGTCCTCCT 60.291 54.545 0.00 0.00 41.11 3.69
299 302 3.157881 TCTGTGTGAGTAGTCCTCCTTG 58.842 50.000 0.00 0.00 39.65 3.61
316 319 6.043243 TCCTCCTTGGACTATGAATCCATAAC 59.957 42.308 0.00 0.00 45.71 1.89
321 324 7.875041 CCTTGGACTATGAATCCATAACAGTAG 59.125 40.741 0.00 0.00 45.71 2.57
323 326 5.864474 GGACTATGAATCCATAACAGTAGCG 59.136 44.000 0.00 0.00 35.06 4.26
364 367 6.151648 TCTCCCTTGTTCTTCATTGCAATAAG 59.848 38.462 12.53 15.01 0.00 1.73
365 368 5.185635 TCCCTTGTTCTTCATTGCAATAAGG 59.814 40.000 20.80 20.80 37.86 2.69
366 369 4.866486 CCTTGTTCTTCATTGCAATAAGGC 59.134 41.667 17.61 14.21 33.32 4.35
370 373 4.924305 TCTTCATTGCAATAAGGCCATC 57.076 40.909 12.53 0.00 0.00 3.51
372 375 4.710865 TCTTCATTGCAATAAGGCCATCAA 59.289 37.500 12.53 0.00 0.00 2.57
373 376 5.364446 TCTTCATTGCAATAAGGCCATCAAT 59.636 36.000 12.53 1.98 0.00 2.57
448 968 8.052141 TCCAACACCATTTTATCATAGATGACA 58.948 33.333 0.00 0.00 40.03 3.58
479 999 0.699399 AGGAGACGTCTTGAGGAGGA 59.301 55.000 21.08 0.00 34.32 3.71
493 1013 1.227973 GAGGATGGGGGCGATTCAC 60.228 63.158 0.00 0.00 0.00 3.18
506 1026 2.073816 CGATTCACCTGGTGTTGGTAC 58.926 52.381 25.15 11.47 35.80 3.34
521 1041 2.758327 TACGTCGATGCTGGGGCT 60.758 61.111 4.06 0.00 39.59 5.19
522 1042 3.076258 TACGTCGATGCTGGGGCTG 62.076 63.158 4.06 0.00 39.59 4.85
523 1043 4.147449 CGTCGATGCTGGGGCTGA 62.147 66.667 0.00 0.00 39.59 4.26
562 1083 6.069731 AGGCTAGAAAGTCTTTGGATCAAGAT 60.070 38.462 1.60 0.00 32.20 2.40
574 1095 2.880890 GGATCAAGATCCGAAACCATGG 59.119 50.000 11.19 11.19 46.84 3.66
576 1097 2.710377 TCAAGATCCGAAACCATGGTG 58.290 47.619 20.60 5.79 0.00 4.17
611 1132 3.764885 AAGAAATTACATGCGGCTGTC 57.235 42.857 0.00 0.00 0.00 3.51
620 1141 1.135139 CATGCGGCTGTCTAGTAGTGT 59.865 52.381 0.00 0.00 0.00 3.55
623 1144 0.377554 CGGCTGTCTAGTAGTGTCCG 59.622 60.000 0.00 3.30 0.00 4.79
629 1150 3.689347 TGTCTAGTAGTGTCCGCCTTAA 58.311 45.455 0.00 0.00 0.00 1.85
631 1152 4.708421 TGTCTAGTAGTGTCCGCCTTAAAT 59.292 41.667 0.00 0.00 0.00 1.40
635 1156 5.927281 AGTAGTGTCCGCCTTAAATCTTA 57.073 39.130 0.00 0.00 0.00 2.10
636 1157 6.290294 AGTAGTGTCCGCCTTAAATCTTAA 57.710 37.500 0.00 0.00 0.00 1.85
637 1158 6.885922 AGTAGTGTCCGCCTTAAATCTTAAT 58.114 36.000 0.00 0.00 0.00 1.40
638 1159 7.336396 AGTAGTGTCCGCCTTAAATCTTAATT 58.664 34.615 0.00 0.00 0.00 1.40
639 1160 8.480501 AGTAGTGTCCGCCTTAAATCTTAATTA 58.519 33.333 0.00 0.00 0.00 1.40
640 1161 7.549615 AGTGTCCGCCTTAAATCTTAATTAC 57.450 36.000 0.00 0.00 0.00 1.89
641 1162 7.107542 AGTGTCCGCCTTAAATCTTAATTACA 58.892 34.615 0.00 0.00 0.00 2.41
642 1163 7.773690 AGTGTCCGCCTTAAATCTTAATTACAT 59.226 33.333 0.00 0.00 0.00 2.29
643 1164 8.403236 GTGTCCGCCTTAAATCTTAATTACATT 58.597 33.333 0.00 0.00 0.00 2.71
644 1165 8.402472 TGTCCGCCTTAAATCTTAATTACATTG 58.598 33.333 0.00 0.00 0.00 2.82
645 1166 8.403236 GTCCGCCTTAAATCTTAATTACATTGT 58.597 33.333 0.00 0.00 0.00 2.71
646 1167 8.962679 TCCGCCTTAAATCTTAATTACATTGTT 58.037 29.630 0.00 0.00 0.00 2.83
677 1198 6.479095 TTTTTGGGTAATTACCTCGTTACG 57.521 37.500 29.26 0.00 45.72 3.18
678 1199 3.163630 TGGGTAATTACCTCGTTACGC 57.836 47.619 29.26 13.75 45.72 4.42
679 1200 2.119457 GGGTAATTACCTCGTTACGCG 58.881 52.381 29.26 3.53 45.72 6.01
680 1201 2.119457 GGTAATTACCTCGTTACGCGG 58.881 52.381 24.79 12.50 43.10 6.46
681 1202 1.518515 GTAATTACCTCGTTACGCGGC 59.481 52.381 14.02 0.00 41.72 6.53
682 1203 0.108709 AATTACCTCGTTACGCGGCA 60.109 50.000 14.02 0.00 41.72 5.69
683 1204 0.103572 ATTACCTCGTTACGCGGCAT 59.896 50.000 14.02 3.55 41.72 4.40
684 1205 0.802994 TTACCTCGTTACGCGGCATG 60.803 55.000 14.02 1.21 41.72 4.06
685 1206 3.925238 CCTCGTTACGCGGCATGC 61.925 66.667 12.47 9.90 41.72 4.06
686 1207 3.185365 CTCGTTACGCGGCATGCA 61.185 61.111 21.36 0.00 46.97 3.96
687 1208 3.420222 CTCGTTACGCGGCATGCAC 62.420 63.158 21.36 10.08 46.97 4.57
688 1209 3.487202 CGTTACGCGGCATGCACT 61.487 61.111 21.36 0.21 46.97 4.40
689 1210 2.867472 GTTACGCGGCATGCACTT 59.133 55.556 21.36 7.11 46.97 3.16
690 1211 1.688422 CGTTACGCGGCATGCACTTA 61.688 55.000 21.36 6.05 46.97 2.24
691 1212 0.026285 GTTACGCGGCATGCACTTAG 59.974 55.000 21.36 8.11 46.97 2.18
692 1213 1.701545 TTACGCGGCATGCACTTAGC 61.702 55.000 21.36 14.57 46.97 3.09
693 1214 2.572095 TACGCGGCATGCACTTAGCT 62.572 55.000 21.36 8.68 46.97 3.32
694 1215 2.753966 CGCGGCATGCACTTAGCTT 61.754 57.895 21.36 0.00 46.97 3.74
695 1216 1.428370 CGCGGCATGCACTTAGCTTA 61.428 55.000 21.36 0.00 46.97 3.09
696 1217 0.028110 GCGGCATGCACTTAGCTTAC 59.972 55.000 21.36 0.00 45.94 2.34
697 1218 1.368641 CGGCATGCACTTAGCTTACA 58.631 50.000 21.36 0.00 45.94 2.41
698 1219 1.062587 CGGCATGCACTTAGCTTACAC 59.937 52.381 21.36 0.00 45.94 2.90
699 1220 1.062587 GGCATGCACTTAGCTTACACG 59.937 52.381 21.36 0.00 45.94 4.49
700 1221 1.732259 GCATGCACTTAGCTTACACGT 59.268 47.619 14.21 0.00 45.94 4.49
701 1222 2.927477 GCATGCACTTAGCTTACACGTA 59.073 45.455 14.21 0.00 45.94 3.57
702 1223 3.369756 GCATGCACTTAGCTTACACGTAA 59.630 43.478 14.21 0.00 45.94 3.18
703 1224 4.034048 GCATGCACTTAGCTTACACGTAAT 59.966 41.667 14.21 0.00 45.94 1.89
704 1225 5.233476 GCATGCACTTAGCTTACACGTAATA 59.767 40.000 14.21 0.00 45.94 0.98
705 1226 6.237996 GCATGCACTTAGCTTACACGTAATAA 60.238 38.462 14.21 0.00 45.94 1.40
706 1227 6.636666 TGCACTTAGCTTACACGTAATAAC 57.363 37.500 0.00 0.00 45.94 1.89
748 1270 7.821652 TGGAGATGCTCTAAATTCGAGTATAG 58.178 38.462 7.83 0.00 34.61 1.31
751 1273 8.410673 AGATGCTCTAAATTCGAGTATAGGAA 57.589 34.615 7.83 0.00 34.61 3.36
853 1394 8.894768 AATAAGAGTCTTTTATCCATTCCTCG 57.105 34.615 11.40 0.00 0.00 4.63
870 1411 3.118920 TCCTCGACCGCATCTTTGATTTA 60.119 43.478 0.00 0.00 0.00 1.40
871 1412 3.001330 CCTCGACCGCATCTTTGATTTAC 59.999 47.826 0.00 0.00 0.00 2.01
872 1413 2.601314 TCGACCGCATCTTTGATTTACG 59.399 45.455 0.00 0.00 0.00 3.18
873 1414 2.347452 CGACCGCATCTTTGATTTACGT 59.653 45.455 0.00 0.00 0.00 3.57
874 1415 3.548668 CGACCGCATCTTTGATTTACGTA 59.451 43.478 0.00 0.00 0.00 3.57
875 1416 4.547587 CGACCGCATCTTTGATTTACGTAC 60.548 45.833 0.00 0.00 0.00 3.67
876 1417 3.305094 ACCGCATCTTTGATTTACGTACG 59.695 43.478 15.01 15.01 0.00 3.67
877 1418 3.305094 CCGCATCTTTGATTTACGTACGT 59.695 43.478 25.98 25.98 0.00 3.57
878 1419 4.500117 CCGCATCTTTGATTTACGTACGTA 59.500 41.667 23.60 23.60 0.00 3.57
879 1420 5.331309 CCGCATCTTTGATTTACGTACGTAG 60.331 44.000 25.56 15.62 31.71 3.51
880 1421 5.331309 CGCATCTTTGATTTACGTACGTAGG 60.331 44.000 25.56 13.47 31.71 3.18
881 1422 5.517770 GCATCTTTGATTTACGTACGTAGGT 59.482 40.000 25.56 22.91 31.71 3.08
882 1423 6.291479 GCATCTTTGATTTACGTACGTAGGTC 60.291 42.308 25.56 24.59 31.71 3.85
883 1424 5.323900 TCTTTGATTTACGTACGTAGGTCG 58.676 41.667 25.56 12.85 46.00 4.79
884 1425 3.051606 TGATTTACGTACGTAGGTCGC 57.948 47.619 25.56 15.59 44.19 5.19
885 1426 2.029815 GATTTACGTACGTAGGTCGCG 58.970 52.381 25.56 12.13 44.19 5.87
886 1427 0.793861 TTTACGTACGTAGGTCGCGT 59.206 50.000 25.56 17.08 45.11 6.01
887 1428 0.094558 TTACGTACGTAGGTCGCGTG 59.905 55.000 25.56 0.00 42.87 5.34
888 1429 1.011968 TACGTACGTAGGTCGCGTGT 61.012 55.000 23.60 1.20 42.87 4.49
889 1430 1.154413 CGTACGTAGGTCGCGTGTT 60.154 57.895 7.22 0.00 42.87 3.32
890 1431 1.122419 CGTACGTAGGTCGCGTGTTC 61.122 60.000 7.22 0.00 42.87 3.18
891 1432 0.166814 GTACGTAGGTCGCGTGTTCT 59.833 55.000 5.77 2.24 42.87 3.01
892 1433 0.874390 TACGTAGGTCGCGTGTTCTT 59.126 50.000 5.77 0.00 42.87 2.52
893 1434 0.031178 ACGTAGGTCGCGTGTTCTTT 59.969 50.000 5.77 0.00 44.19 2.52
894 1435 0.433492 CGTAGGTCGCGTGTTCTTTG 59.567 55.000 5.77 0.00 0.00 2.77
921 1462 1.535860 CCACGACAAGGTGCCAAAAAG 60.536 52.381 0.00 0.00 36.59 2.27
924 1465 1.606668 CGACAAGGTGCCAAAAAGCTA 59.393 47.619 0.00 0.00 0.00 3.32
927 1468 2.299867 ACAAGGTGCCAAAAAGCTATGG 59.700 45.455 8.40 8.40 39.80 2.74
964 1513 2.159421 ACCGCGCGTCTATATATGAAGG 60.159 50.000 29.95 10.25 0.00 3.46
977 1534 0.257039 ATGAAGGGGCACACTGATCC 59.743 55.000 0.00 0.00 0.00 3.36
982 1539 0.034186 GGGGCACACTGATCCATCAA 60.034 55.000 0.00 0.00 36.18 2.57
983 1540 1.410648 GGGGCACACTGATCCATCAAT 60.411 52.381 0.00 0.00 36.18 2.57
984 1541 1.679680 GGGCACACTGATCCATCAATG 59.320 52.381 0.00 0.00 39.70 2.82
985 1542 1.066605 GGCACACTGATCCATCAATGC 59.933 52.381 9.91 9.91 37.53 3.56
1018 1575 4.676986 CGAAAATGGAGGACATCGTCTACA 60.677 45.833 1.93 0.00 39.40 2.74
1071 1628 2.365105 CTAACCAGGCGGGGGAGA 60.365 66.667 8.94 0.00 42.91 3.71
2176 2971 1.888018 GTCATCCGGGAGACGTTCA 59.112 57.895 0.00 0.00 42.24 3.18
2699 3510 0.102300 TCTCGACGTACATGCATGGG 59.898 55.000 29.41 19.76 0.00 4.00
2704 3515 0.748005 ACGTACATGCATGGGGAAGC 60.748 55.000 29.41 11.80 0.00 3.86
2707 3518 0.463654 TACATGCATGGGGAAGCGAC 60.464 55.000 29.41 0.00 0.00 5.19
2715 3526 2.951458 GGGAAGCGACCCGTTTTG 59.049 61.111 5.56 0.00 40.49 2.44
2717 3528 1.895231 GGAAGCGACCCGTTTTGGT 60.895 57.895 0.00 0.00 42.79 3.67
2732 3543 2.772568 TTGGTTCAGTTTGTGATGCG 57.227 45.000 0.00 0.00 34.17 4.73
2735 3546 1.398595 GTTCAGTTTGTGATGCGTGC 58.601 50.000 0.00 0.00 34.17 5.34
2749 3560 1.067142 TGCGTGCGAGAGGAGTTAATT 60.067 47.619 0.00 0.00 0.00 1.40
2757 3568 6.421202 GTGCGAGAGGAGTTAATTATAAGTGG 59.579 42.308 0.00 0.00 0.00 4.00
2768 3579 7.893833 AGTTAATTATAAGTGGGAGGCTTGTTT 59.106 33.333 0.00 0.00 0.00 2.83
2770 3581 9.756571 TTAATTATAAGTGGGAGGCTTGTTTAA 57.243 29.630 0.00 0.00 0.00 1.52
2778 3589 5.710567 GTGGGAGGCTTGTTTAAGTAAGAAT 59.289 40.000 0.00 0.00 36.27 2.40
2780 3591 7.065923 GTGGGAGGCTTGTTTAAGTAAGAATAG 59.934 40.741 0.00 0.00 36.27 1.73
2783 3594 7.120726 GGAGGCTTGTTTAAGTAAGAATAGCAA 59.879 37.037 0.00 0.00 36.27 3.91
2794 3605 0.451783 GAATAGCAACCAAGCACCGG 59.548 55.000 0.00 0.00 36.85 5.28
2804 3615 3.050354 AAGCACCGGTCAACCCACA 62.050 57.895 2.59 0.00 0.00 4.17
2805 3616 2.282180 GCACCGGTCAACCCACAT 60.282 61.111 2.59 0.00 0.00 3.21
2852 3663 4.154015 ACGCGAATCAAAGAAACATGATGA 59.846 37.500 15.93 0.00 36.44 2.92
2868 3679 6.134055 ACATGATGAAGATGAATTCCCATGT 58.866 36.000 0.00 13.81 41.90 3.21
2872 3683 4.920999 TGAAGATGAATTCCCATGTGTCA 58.079 39.130 2.27 0.00 0.00 3.58
2911 3722 7.440198 ACTTACTATAAGATAAACTTCCGGCC 58.560 38.462 0.00 0.00 39.72 6.13
2921 3732 0.110486 ACTTCCGGCCTGTCATTTGT 59.890 50.000 0.00 0.00 0.00 2.83
2942 3753 6.687081 TGTTATAAAAAGGATTGGGCTACG 57.313 37.500 0.00 0.00 0.00 3.51
2943 3754 5.591067 TGTTATAAAAAGGATTGGGCTACGG 59.409 40.000 0.00 0.00 0.00 4.02
2951 3762 0.178068 ATTGGGCTACGGTACTGCAG 59.822 55.000 13.48 13.48 0.00 4.41
2956 3767 1.134907 GGCTACGGTACTGCAGCTTTA 60.135 52.381 23.16 0.00 34.41 1.85
3014 3825 8.910351 ATCTTGCTATCAAACTATTCCTTACC 57.090 34.615 0.00 0.00 0.00 2.85
3031 3842 6.880484 TCCTTACCGATAATTTCAGTGCTTA 58.120 36.000 0.00 0.00 0.00 3.09
3032 3843 6.759827 TCCTTACCGATAATTTCAGTGCTTAC 59.240 38.462 0.00 0.00 0.00 2.34
3066 3877 4.732784 TGCTGAAAACCGCTTATCATTTC 58.267 39.130 0.00 0.00 0.00 2.17
3068 3879 4.142381 GCTGAAAACCGCTTATCATTTCCT 60.142 41.667 0.00 0.00 30.80 3.36
3078 3889 4.886489 GCTTATCATTTCCTTCTGCTCCTT 59.114 41.667 0.00 0.00 0.00 3.36
3079 3890 5.221009 GCTTATCATTTCCTTCTGCTCCTTG 60.221 44.000 0.00 0.00 0.00 3.61
3090 3901 0.534203 TGCTCCTTGTTGGGTTCGAC 60.534 55.000 0.00 0.00 36.20 4.20
3104 3915 4.142534 TGGGTTCGACACTCTTACTTATCG 60.143 45.833 0.00 0.00 0.00 2.92
3109 3920 7.020010 GTTCGACACTCTTACTTATCGAAAGA 58.980 38.462 8.30 5.57 46.48 2.52
3161 3972 2.016318 TCATCGCCCTAAATGCAACTG 58.984 47.619 0.00 0.00 0.00 3.16
3176 3987 3.419915 GCAACTGCATGTCTTCAATACG 58.580 45.455 0.00 0.00 41.59 3.06
3178 3989 2.009774 ACTGCATGTCTTCAATACGGC 58.990 47.619 0.00 0.00 0.00 5.68
3187 3998 3.058224 GTCTTCAATACGGCTGCAACTTT 60.058 43.478 0.50 0.00 0.00 2.66
3188 3999 3.188460 TCTTCAATACGGCTGCAACTTTC 59.812 43.478 0.50 0.00 0.00 2.62
3206 4017 0.107831 TCCAGTGTTTTGTCGAGGGG 59.892 55.000 0.00 0.00 0.00 4.79
3220 4031 2.500098 TCGAGGGGAAGGAAGTTGTATG 59.500 50.000 0.00 0.00 0.00 2.39
3287 4117 5.918576 GGTTGCAACTTAGTGGTGTTTTATC 59.081 40.000 27.64 2.37 35.37 1.75
3288 4118 5.351233 TGCAACTTAGTGGTGTTTTATCG 57.649 39.130 0.00 0.00 35.37 2.92
3289 4119 5.057819 TGCAACTTAGTGGTGTTTTATCGA 58.942 37.500 0.00 0.00 35.37 3.59
3295 4125 4.884668 AGTGGTGTTTTATCGAAGGAGA 57.115 40.909 0.00 0.00 0.00 3.71
3296 4126 4.822026 AGTGGTGTTTTATCGAAGGAGAG 58.178 43.478 0.00 0.00 0.00 3.20
3301 4131 3.008594 TGTTTTATCGAAGGAGAGGGCAA 59.991 43.478 0.00 0.00 0.00 4.52
3302 4132 2.981859 TTATCGAAGGAGAGGGCAAC 57.018 50.000 0.00 0.00 0.00 4.17
3316 4146 2.240667 AGGGCAACTGCATGTCTTCTAT 59.759 45.455 3.76 0.00 44.36 1.98
3317 4147 2.357009 GGGCAACTGCATGTCTTCTATG 59.643 50.000 3.76 0.00 44.36 2.23
3318 4148 3.012518 GGCAACTGCATGTCTTCTATGT 58.987 45.455 3.76 0.00 44.36 2.29
3319 4149 3.181503 GGCAACTGCATGTCTTCTATGTG 60.182 47.826 3.76 0.00 44.36 3.21
3321 4151 3.988976 ACTGCATGTCTTCTATGTGGT 57.011 42.857 0.00 0.00 0.00 4.16
3323 4284 4.005650 ACTGCATGTCTTCTATGTGGTTG 58.994 43.478 0.00 0.00 0.00 3.77
3327 4288 4.726416 CATGTCTTCTATGTGGTTGCAAC 58.274 43.478 21.59 21.59 0.00 4.17
3330 4291 5.616270 TGTCTTCTATGTGGTTGCAACTTA 58.384 37.500 27.64 15.18 0.00 2.24
3334 4295 5.222079 TCTATGTGGTTGCAACTTAGTGA 57.778 39.130 27.64 16.00 30.93 3.41
3335 4296 4.994852 TCTATGTGGTTGCAACTTAGTGAC 59.005 41.667 27.64 14.90 30.93 3.67
3343 4304 4.688511 TGCAACTTAGTGACGTTTTGTT 57.311 36.364 0.00 0.00 0.00 2.83
3345 4306 3.789224 GCAACTTAGTGACGTTTTGTTGG 59.211 43.478 14.53 0.00 35.34 3.77
3347 4308 2.946990 ACTTAGTGACGTTTTGTTGGGG 59.053 45.455 0.00 0.00 0.00 4.96
3348 4309 2.713863 TAGTGACGTTTTGTTGGGGT 57.286 45.000 0.00 0.00 0.00 4.95
3350 4311 1.096416 GTGACGTTTTGTTGGGGTGA 58.904 50.000 0.00 0.00 0.00 4.02
3368 4548 2.771943 GTGAGGGGACAGTTCCATATCA 59.228 50.000 0.00 0.00 44.98 2.15
3369 4549 3.041211 TGAGGGGACAGTTCCATATCAG 58.959 50.000 0.00 0.00 44.98 2.90
3391 4571 3.674997 CCACTAGGCACACAACTACATT 58.325 45.455 0.00 0.00 0.00 2.71
3422 4602 3.935203 CGATTGCAACTCTATGGTGTCTT 59.065 43.478 0.00 0.00 35.37 3.01
3426 4606 5.222079 TGCAACTCTATGGTGTCTTGTTA 57.778 39.130 0.00 0.00 35.37 2.41
3433 4613 6.049955 TCTATGGTGTCTTGTTAAGAAGGG 57.950 41.667 12.06 0.00 39.67 3.95
3506 4686 2.309693 CAACTGCATGTGTTTAGTGCG 58.690 47.619 0.00 0.00 41.61 5.34
3529 4709 4.717233 TTGCAACTCTGTGATGTTTTGT 57.283 36.364 0.00 0.00 0.00 2.83
3530 4710 4.291540 TGCAACTCTGTGATGTTTTGTC 57.708 40.909 0.00 0.00 0.00 3.18
3538 4718 2.441375 TGTGATGTTTTGTCAGGGAGGA 59.559 45.455 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.598130 GTGTGACCTCTGTGTGGGC 60.598 63.158 0.00 0.00 0.00 5.36
13 14 0.178068 GTGGTGTGTGACCTCTGTGT 59.822 55.000 0.00 0.00 46.32 3.72
15 16 1.964223 CTAGTGGTGTGTGACCTCTGT 59.036 52.381 0.00 0.00 46.17 3.41
29 32 1.429825 CTCTGACGCGTCCTAGTGG 59.570 63.158 34.34 18.51 0.00 4.00
38 41 3.842923 ATGAGCCCCTCTGACGCG 61.843 66.667 3.53 3.53 0.00 6.01
60 63 4.683334 GTGCAGGACAAACCGCGC 62.683 66.667 0.00 0.00 44.74 6.86
62 65 2.639286 CAGTGCAGGACAAACCGC 59.361 61.111 0.00 0.00 44.74 5.68
66 69 2.584835 AATAGGCAGTGCAGGACAAA 57.415 45.000 18.61 0.00 0.00 2.83
78 81 2.489938 AGCGTCCAAAGAAATAGGCA 57.510 45.000 0.00 0.00 0.00 4.75
181 184 2.093447 AGAGTTCCAAATCAGGCCTACG 60.093 50.000 3.98 0.00 0.00 3.51
206 209 3.307480 CCTCCGGTAGAGTTCCAAAACAT 60.307 47.826 0.00 0.00 41.47 2.71
219 222 1.269998 GATGGATTCGTCCTCCGGTAG 59.730 57.143 0.00 0.00 35.41 3.18
299 302 5.864474 CGCTACTGTTATGGATTCATAGTCC 59.136 44.000 0.00 0.00 37.20 3.85
316 319 5.041951 GAGAGGTTATCATCTCGCTACTG 57.958 47.826 0.07 0.00 40.71 2.74
385 905 8.713737 ACCGAGGTTTGTAGAAAGTAATATTC 57.286 34.615 0.00 0.00 0.00 1.75
396 916 6.183360 CCTCCAAATATACCGAGGTTTGTAGA 60.183 42.308 0.00 0.00 37.67 2.59
436 956 5.012046 TCCCGCTTATTGTGTCATCTATGAT 59.988 40.000 0.00 0.00 39.30 2.45
442 962 2.158957 TCCTCCCGCTTATTGTGTCATC 60.159 50.000 0.00 0.00 0.00 2.92
448 968 0.460311 CGTCTCCTCCCGCTTATTGT 59.540 55.000 0.00 0.00 0.00 2.71
454 974 2.035940 AAGACGTCTCCTCCCGCT 59.964 61.111 20.33 0.00 0.00 5.52
457 977 0.323542 TCCTCAAGACGTCTCCTCCC 60.324 60.000 20.33 0.00 0.00 4.30
479 999 2.597340 CAGGTGAATCGCCCCCAT 59.403 61.111 9.54 0.00 33.99 4.00
493 1013 0.245539 ATCGACGTACCAACACCAGG 59.754 55.000 0.00 0.00 0.00 4.45
506 1026 4.147449 TCAGCCCCAGCATCGACG 62.147 66.667 0.00 0.00 43.56 5.12
521 1041 5.580998 TCTAGCCTTCTTCTTTCTACCTCA 58.419 41.667 0.00 0.00 0.00 3.86
522 1042 6.532988 TTCTAGCCTTCTTCTTTCTACCTC 57.467 41.667 0.00 0.00 0.00 3.85
523 1043 6.499000 ACTTTCTAGCCTTCTTCTTTCTACCT 59.501 38.462 0.00 0.00 0.00 3.08
562 1083 2.350057 TCAAACACCATGGTTTCGGA 57.650 45.000 16.84 8.33 38.86 4.55
565 1086 8.600449 TTAATCAAATCAAACACCATGGTTTC 57.400 30.769 16.84 0.00 38.86 2.78
566 1087 8.970859 TTTAATCAAATCAAACACCATGGTTT 57.029 26.923 16.84 6.07 41.44 3.27
602 1123 0.809385 GACACTACTAGACAGCCGCA 59.191 55.000 0.00 0.00 0.00 5.69
611 1132 5.517322 AGATTTAAGGCGGACACTACTAG 57.483 43.478 0.00 0.00 0.00 2.57
620 1141 8.514330 ACAATGTAATTAAGATTTAAGGCGGA 57.486 30.769 0.00 0.00 32.46 5.54
671 1192 1.688422 TAAGTGCATGCCGCGTAACG 61.688 55.000 16.68 0.00 46.97 3.18
672 1193 0.026285 CTAAGTGCATGCCGCGTAAC 59.974 55.000 16.68 5.26 46.97 2.50
673 1194 1.701545 GCTAAGTGCATGCCGCGTAA 61.702 55.000 16.68 0.00 46.97 3.18
674 1195 2.171079 GCTAAGTGCATGCCGCGTA 61.171 57.895 16.68 9.70 46.97 4.42
675 1196 3.499737 GCTAAGTGCATGCCGCGT 61.500 61.111 16.68 9.03 46.97 6.01
676 1197 1.428370 TAAGCTAAGTGCATGCCGCG 61.428 55.000 16.68 0.00 46.97 6.46
677 1198 0.028110 GTAAGCTAAGTGCATGCCGC 59.972 55.000 16.68 8.31 45.94 6.53
678 1199 1.062587 GTGTAAGCTAAGTGCATGCCG 59.937 52.381 16.68 0.00 45.94 5.69
679 1200 1.062587 CGTGTAAGCTAAGTGCATGCC 59.937 52.381 16.68 6.65 45.94 4.40
680 1201 1.732259 ACGTGTAAGCTAAGTGCATGC 59.268 47.619 11.82 11.82 45.94 4.06
681 1202 5.718649 ATTACGTGTAAGCTAAGTGCATG 57.281 39.130 0.00 0.00 45.94 4.06
682 1203 6.020121 CGTTATTACGTGTAAGCTAAGTGCAT 60.020 38.462 0.00 0.00 42.68 3.96
683 1204 5.286797 CGTTATTACGTGTAAGCTAAGTGCA 59.713 40.000 0.00 0.00 42.68 4.57
684 1205 5.711302 CGTTATTACGTGTAAGCTAAGTGC 58.289 41.667 0.00 0.00 42.72 4.40
697 1218 6.085555 AGATGATCATCCACGTTATTACGT 57.914 37.500 28.23 3.69 46.90 3.57
698 1219 8.587111 CAATAGATGATCATCCACGTTATTACG 58.413 37.037 28.23 12.42 44.63 3.18
699 1220 8.873830 CCAATAGATGATCATCCACGTTATTAC 58.126 37.037 28.23 3.55 38.58 1.89
700 1221 8.811994 TCCAATAGATGATCATCCACGTTATTA 58.188 33.333 28.23 14.09 38.58 0.98
701 1222 7.679783 TCCAATAGATGATCATCCACGTTATT 58.320 34.615 28.23 21.24 38.58 1.40
702 1223 7.179160 TCTCCAATAGATGATCATCCACGTTAT 59.821 37.037 28.23 17.36 38.58 1.89
703 1224 6.493458 TCTCCAATAGATGATCATCCACGTTA 59.507 38.462 28.23 16.02 38.58 3.18
704 1225 5.305386 TCTCCAATAGATGATCATCCACGTT 59.695 40.000 28.23 16.36 38.58 3.99
705 1226 4.835056 TCTCCAATAGATGATCATCCACGT 59.165 41.667 28.23 14.80 38.58 4.49
706 1227 5.397142 TCTCCAATAGATGATCATCCACG 57.603 43.478 28.23 15.96 38.58 4.94
748 1270 2.557056 CCCTTTCCGAAAAAGACCTTCC 59.443 50.000 10.67 0.00 0.00 3.46
751 1273 1.778484 TCCCCTTTCCGAAAAAGACCT 59.222 47.619 10.67 0.00 0.00 3.85
853 1394 4.547587 CGTACGTAAATCAAAGATGCGGTC 60.548 45.833 7.22 0.00 0.00 4.79
870 1411 1.841663 AACACGCGACCTACGTACGT 61.842 55.000 25.98 25.98 42.96 3.57
871 1412 1.122419 GAACACGCGACCTACGTACG 61.122 60.000 15.93 15.01 42.96 3.67
872 1413 0.166814 AGAACACGCGACCTACGTAC 59.833 55.000 15.93 0.00 42.96 3.67
873 1414 0.874390 AAGAACACGCGACCTACGTA 59.126 50.000 15.93 0.00 42.96 3.57
874 1415 0.031178 AAAGAACACGCGACCTACGT 59.969 50.000 15.93 0.00 46.42 3.57
875 1416 0.433492 CAAAGAACACGCGACCTACG 59.567 55.000 15.93 0.00 45.66 3.51
876 1417 1.191647 CACAAAGAACACGCGACCTAC 59.808 52.381 15.93 0.00 0.00 3.18
877 1418 1.493772 CACAAAGAACACGCGACCTA 58.506 50.000 15.93 0.00 0.00 3.08
878 1419 1.772063 GCACAAAGAACACGCGACCT 61.772 55.000 15.93 0.13 0.00 3.85
879 1420 1.368850 GCACAAAGAACACGCGACC 60.369 57.895 15.93 0.00 0.00 4.79
880 1421 0.383124 GAGCACAAAGAACACGCGAC 60.383 55.000 15.93 0.65 0.00 5.19
881 1422 0.808060 TGAGCACAAAGAACACGCGA 60.808 50.000 15.93 0.00 0.00 5.87
882 1423 0.654472 GTGAGCACAAAGAACACGCG 60.654 55.000 3.53 3.53 0.00 6.01
883 1424 0.317020 GGTGAGCACAAAGAACACGC 60.317 55.000 2.75 0.00 33.08 5.34
884 1425 1.013596 TGGTGAGCACAAAGAACACG 58.986 50.000 2.75 0.00 33.08 4.49
885 1426 1.268032 CGTGGTGAGCACAAAGAACAC 60.268 52.381 15.55 0.00 0.00 3.32
886 1427 1.013596 CGTGGTGAGCACAAAGAACA 58.986 50.000 15.55 0.00 0.00 3.18
887 1428 1.003866 GTCGTGGTGAGCACAAAGAAC 60.004 52.381 15.55 1.16 0.00 3.01
888 1429 1.295792 GTCGTGGTGAGCACAAAGAA 58.704 50.000 15.55 0.00 0.00 2.52
889 1430 0.176910 TGTCGTGGTGAGCACAAAGA 59.823 50.000 15.55 1.15 0.00 2.52
890 1431 1.003545 CTTGTCGTGGTGAGCACAAAG 60.004 52.381 15.55 10.77 0.00 2.77
891 1432 1.013596 CTTGTCGTGGTGAGCACAAA 58.986 50.000 15.55 5.15 0.00 2.83
892 1433 0.813610 CCTTGTCGTGGTGAGCACAA 60.814 55.000 15.55 0.92 0.00 3.33
893 1434 1.227527 CCTTGTCGTGGTGAGCACA 60.228 57.895 15.55 0.00 0.00 4.57
894 1435 1.227556 ACCTTGTCGTGGTGAGCAC 60.228 57.895 4.41 4.41 36.30 4.40
921 1462 1.525535 CTCCACTGGCAGCCATAGC 60.526 63.158 16.64 0.00 40.32 2.97
924 1465 1.200760 TACACTCCACTGGCAGCCAT 61.201 55.000 16.64 2.18 30.82 4.40
927 1468 1.376037 GGTACACTCCACTGGCAGC 60.376 63.158 15.89 0.00 0.00 5.25
934 1475 4.712425 ACGCGCGGTACACTCCAC 62.712 66.667 35.22 0.00 0.00 4.02
964 1513 1.679680 CATTGATGGATCAGTGTGCCC 59.320 52.381 4.41 0.00 39.02 5.36
983 1540 1.135053 CCATTTTCGTGATGCCATGCA 60.135 47.619 0.00 0.00 44.86 3.96
984 1541 1.134753 TCCATTTTCGTGATGCCATGC 59.865 47.619 0.00 0.00 0.00 4.06
985 1542 2.223641 CCTCCATTTTCGTGATGCCATG 60.224 50.000 0.00 0.00 0.00 3.66
1018 1575 2.770048 CCCGAGGGCCAGGAAGAT 60.770 66.667 18.18 0.00 0.00 2.40
1599 2164 4.394078 CGGAGGAACACGTCGCGA 62.394 66.667 3.71 3.71 0.00 5.87
2073 2868 2.972505 CGCCGCACCTCTGTTGTT 60.973 61.111 0.00 0.00 0.00 2.83
2379 3183 3.322466 CTGAAGTCCACCCCCGCT 61.322 66.667 0.00 0.00 0.00 5.52
2404 3208 0.326264 AATGGCAGGAGCTCGAAGTT 59.674 50.000 7.83 0.00 41.70 2.66
2463 3267 3.575351 GAGCTCCACGTTGGCGAGT 62.575 63.158 0.87 0.00 42.00 4.18
2538 3348 1.215647 GGTCATGTCGAACTCGGCT 59.784 57.895 5.21 0.00 45.41 5.52
2699 3510 1.449726 AACCAAAACGGGTCGCTTCC 61.450 55.000 0.00 0.00 41.32 3.46
2707 3518 2.164624 TCACAAACTGAACCAAAACGGG 59.835 45.455 0.00 0.00 40.22 5.28
2709 3520 3.242712 GCATCACAAACTGAACCAAAACG 59.757 43.478 0.00 0.00 30.60 3.60
2711 3522 3.119316 ACGCATCACAAACTGAACCAAAA 60.119 39.130 0.00 0.00 30.60 2.44
2715 3526 1.925946 GCACGCATCACAAACTGAACC 60.926 52.381 0.00 0.00 30.60 3.62
2717 3528 0.041400 CGCACGCATCACAAACTGAA 60.041 50.000 0.00 0.00 30.60 3.02
2732 3543 6.421202 CCACTTATAATTAACTCCTCTCGCAC 59.579 42.308 0.00 0.00 0.00 5.34
2735 3546 7.286215 TCCCACTTATAATTAACTCCTCTCG 57.714 40.000 0.00 0.00 0.00 4.04
2749 3560 6.382919 ACTTAAACAAGCCTCCCACTTATA 57.617 37.500 0.00 0.00 0.00 0.98
2757 3568 6.598064 TGCTATTCTTACTTAAACAAGCCTCC 59.402 38.462 0.00 0.00 0.00 4.30
2768 3579 5.646360 GGTGCTTGGTTGCTATTCTTACTTA 59.354 40.000 0.00 0.00 0.00 2.24
2770 3581 4.010349 GGTGCTTGGTTGCTATTCTTACT 58.990 43.478 0.00 0.00 0.00 2.24
2778 3589 1.302192 GACCGGTGCTTGGTTGCTA 60.302 57.895 14.63 0.00 40.63 3.49
2780 3591 2.485795 TTGACCGGTGCTTGGTTGC 61.486 57.895 14.63 0.00 40.63 4.17
2783 3594 2.203294 GGTTGACCGGTGCTTGGT 60.203 61.111 14.63 0.00 44.10 3.67
2824 3635 3.242478 TGTTTCTTTGATTCGCGTTCGTT 60.242 39.130 5.77 0.00 36.96 3.85
2830 3641 4.650985 TCATCATGTTTCTTTGATTCGCG 58.349 39.130 0.00 0.00 30.24 5.87
2832 3643 8.179615 TCATCTTCATCATGTTTCTTTGATTCG 58.820 33.333 0.00 0.00 30.24 3.34
2852 3663 7.959658 TTTATGACACATGGGAATTCATCTT 57.040 32.000 0.00 0.00 0.00 2.40
2891 3702 5.855045 ACAGGCCGGAAGTTTATCTTATAG 58.145 41.667 10.86 0.00 36.40 1.31
2893 3704 4.163458 TGACAGGCCGGAAGTTTATCTTAT 59.837 41.667 10.86 0.00 36.40 1.73
2900 3711 1.613437 CAAATGACAGGCCGGAAGTTT 59.387 47.619 10.86 4.21 0.00 2.66
2911 3722 9.369904 CCCAATCCTTTTTATAACAAATGACAG 57.630 33.333 0.00 0.00 0.00 3.51
2921 3732 5.757988 ACCGTAGCCCAATCCTTTTTATAA 58.242 37.500 0.00 0.00 0.00 0.98
2942 3753 6.483640 AGCAATAGTAATAAAGCTGCAGTACC 59.516 38.462 16.64 0.00 0.00 3.34
2943 3754 7.484035 AGCAATAGTAATAAAGCTGCAGTAC 57.516 36.000 16.64 8.62 0.00 2.73
3006 3817 5.741011 AGCACTGAAATTATCGGTAAGGAA 58.259 37.500 0.00 0.00 46.15 3.36
3007 3818 5.353394 AGCACTGAAATTATCGGTAAGGA 57.647 39.130 0.00 0.00 46.15 3.36
3009 3820 7.491372 TCTGTAAGCACTGAAATTATCGGTAAG 59.509 37.037 0.00 0.00 46.15 2.34
3011 3822 6.869695 TCTGTAAGCACTGAAATTATCGGTA 58.130 36.000 0.00 0.00 46.15 4.02
3031 3842 5.507315 CGGTTTTCAGCAAGGTATTTTCTGT 60.507 40.000 0.00 0.00 0.00 3.41
3032 3843 4.917415 CGGTTTTCAGCAAGGTATTTTCTG 59.083 41.667 0.00 0.00 0.00 3.02
3066 3877 0.111253 ACCCAACAAGGAGCAGAAGG 59.889 55.000 0.00 0.00 41.22 3.46
3068 3879 1.813862 CGAACCCAACAAGGAGCAGAA 60.814 52.381 0.00 0.00 41.22 3.02
3078 3889 2.696707 AGTAAGAGTGTCGAACCCAACA 59.303 45.455 0.00 0.00 0.00 3.33
3079 3890 3.382048 AGTAAGAGTGTCGAACCCAAC 57.618 47.619 0.00 0.00 0.00 3.77
3090 3901 8.173775 TCGTAGTTCTTTCGATAAGTAAGAGTG 58.826 37.037 0.00 0.00 37.51 3.51
3104 3915 9.623350 GTATAGGGTATCAATCGTAGTTCTTTC 57.377 37.037 0.00 0.00 0.00 2.62
3109 3920 8.358148 CACAAGTATAGGGTATCAATCGTAGTT 58.642 37.037 0.00 0.00 0.00 2.24
3161 3972 1.268234 GCAGCCGTATTGAAGACATGC 60.268 52.381 0.00 0.00 0.00 4.06
3174 3985 3.749981 CTGGAAAGTTGCAGCCGT 58.250 55.556 0.00 0.00 39.74 5.68
3187 3998 0.107831 CCCCTCGACAAAACACTGGA 59.892 55.000 0.00 0.00 0.00 3.86
3188 3999 0.107831 TCCCCTCGACAAAACACTGG 59.892 55.000 0.00 0.00 0.00 4.00
3206 4017 3.437049 GTGCCTGACATACAACTTCCTTC 59.563 47.826 0.00 0.00 0.00 3.46
3220 4031 1.738099 CGTGTGCCTAGTGCCTGAC 60.738 63.158 1.42 0.00 40.16 3.51
3287 4117 1.743252 GCAGTTGCCCTCTCCTTCG 60.743 63.158 0.00 0.00 34.31 3.79
3288 4118 0.034670 ATGCAGTTGCCCTCTCCTTC 60.035 55.000 1.06 0.00 41.18 3.46
3289 4119 0.323178 CATGCAGTTGCCCTCTCCTT 60.323 55.000 1.06 0.00 41.18 3.36
3295 4125 0.403271 AGAAGACATGCAGTTGCCCT 59.597 50.000 1.06 0.00 41.18 5.19
3296 4126 2.113860 TAGAAGACATGCAGTTGCCC 57.886 50.000 1.06 0.00 41.18 5.36
3301 4131 3.988976 ACCACATAGAAGACATGCAGT 57.011 42.857 0.00 0.00 0.00 4.40
3302 4132 3.181503 GCAACCACATAGAAGACATGCAG 60.182 47.826 0.00 0.00 0.00 4.41
3316 4146 1.937223 CGTCACTAAGTTGCAACCACA 59.063 47.619 25.62 10.28 0.00 4.17
3317 4147 1.937899 ACGTCACTAAGTTGCAACCAC 59.062 47.619 25.62 11.59 0.00 4.16
3318 4148 2.319136 ACGTCACTAAGTTGCAACCA 57.681 45.000 25.62 13.17 0.00 3.67
3319 4149 3.685836 AAACGTCACTAAGTTGCAACC 57.314 42.857 25.62 7.76 0.00 3.77
3321 4151 4.688511 ACAAAACGTCACTAAGTTGCAA 57.311 36.364 0.00 0.00 0.00 4.08
3323 4284 3.789224 CCAACAAAACGTCACTAAGTTGC 59.211 43.478 0.00 0.00 34.98 4.17
3327 4288 2.946990 ACCCCAACAAAACGTCACTAAG 59.053 45.455 0.00 0.00 0.00 2.18
3330 4291 1.099689 CACCCCAACAAAACGTCACT 58.900 50.000 0.00 0.00 0.00 3.41
3334 4295 0.753848 CCCTCACCCCAACAAAACGT 60.754 55.000 0.00 0.00 0.00 3.99
3335 4296 1.460273 CCCCTCACCCCAACAAAACG 61.460 60.000 0.00 0.00 0.00 3.60
3343 4304 1.846124 GAACTGTCCCCTCACCCCA 60.846 63.158 0.00 0.00 0.00 4.96
3345 4306 1.208165 ATGGAACTGTCCCCTCACCC 61.208 60.000 0.00 0.00 44.23 4.61
3347 4308 2.771943 TGATATGGAACTGTCCCCTCAC 59.228 50.000 1.74 0.00 44.23 3.51
3348 4309 3.041211 CTGATATGGAACTGTCCCCTCA 58.959 50.000 1.74 0.00 44.23 3.86
3350 4311 1.771255 GCTGATATGGAACTGTCCCCT 59.229 52.381 1.74 0.00 44.23 4.79
3387 4567 0.037419 GCAATCGGGGCAACAAATGT 60.037 50.000 0.00 0.00 39.74 2.71
3391 4571 3.862142 TTGCAATCGGGGCAACAA 58.138 50.000 0.00 0.00 45.57 2.83
3422 4602 4.202524 ACATGCAACTACCCCTTCTTAACA 60.203 41.667 0.00 0.00 0.00 2.41
3426 4606 2.644798 AGACATGCAACTACCCCTTCTT 59.355 45.455 0.00 0.00 0.00 2.52
3506 4686 5.284079 ACAAAACATCACAGAGTTGCAATC 58.716 37.500 0.59 1.43 0.00 2.67
3514 4694 3.743521 TCCCTGACAAAACATCACAGAG 58.256 45.455 0.00 0.00 0.00 3.35
3517 4697 2.441375 TCCTCCCTGACAAAACATCACA 59.559 45.455 0.00 0.00 0.00 3.58
3529 4709 3.397439 GCAGCTGCTCCTCCCTGA 61.397 66.667 31.33 0.00 38.21 3.86
3530 4710 3.045267 ATGCAGCTGCTCCTCCCTG 62.045 63.158 36.61 0.00 42.66 4.45
3538 4718 4.818546 CCTAGTTAAATACATGCAGCTGCT 59.181 41.667 36.61 21.18 42.66 4.24
3588 4768 2.867975 ACTAAACACCACGTAGTTGCAC 59.132 45.455 0.00 0.00 41.61 4.57
3597 4777 1.206371 CCCTCCCTACTAAACACCACG 59.794 57.143 0.00 0.00 0.00 4.94
3603 4783 4.524053 CAATTGTCCCCTCCCTACTAAAC 58.476 47.826 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.