Multiple sequence alignment - TraesCS3D01G041800

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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 TraesCS3D01G041800 chr3D 100.000 3723 0 0 1 3723 16031239 16034961 0.000000e+00 6876.0
1 TraesCS3D01G041800 chr3D 93.712 493 30 1 1983 2475 15996343 15995852 0.000000e+00 737.0
2 TraesCS3D01G041800 chr3D 96.078 51 2 0 2471 2521 15994709 15994659 2.380000e-12 84.2
3 TraesCS3D01G041800 chr3B 89.018 3433 214 79 417 3723 23182156 23185551 0.000000e+00 4100.0
4 TraesCS3D01G041800 chr3B 87.713 1058 78 31 2699 3723 23317307 23318345 0.000000e+00 1186.0
5 TraesCS3D01G041800 chr3B 87.127 536 44 19 2718 3231 23193560 23194092 5.360000e-163 584.0
6 TraesCS3D01G041800 chr3B 90.503 179 16 1 1 179 325804653 325804476 6.220000e-58 235.0
7 TraesCS3D01G041800 chr3B 82.474 194 26 6 3257 3447 23194176 23194364 2.980000e-36 163.0
8 TraesCS3D01G041800 chr3B 88.800 125 14 0 262 386 23182041 23182165 1.790000e-33 154.0
9 TraesCS3D01G041800 chr3B 91.398 93 8 0 171 263 23181855 23181947 1.090000e-25 128.0
10 TraesCS3D01G041800 chr3A 90.862 2900 166 53 417 3231 20337598 20334713 0.000000e+00 3795.0
11 TraesCS3D01G041800 chr3A 92.593 216 10 3 3513 3723 20334340 20334126 4.670000e-79 305.0
12 TraesCS3D01G041800 chr3A 82.684 231 22 12 174 386 20337819 20337589 4.910000e-44 189.0
13 TraesCS3D01G041800 chr1D 84.859 284 33 9 3257 3538 451533699 451533424 1.020000e-70 278.0
14 TraesCS3D01G041800 chr1D 92.398 171 13 0 1 171 410459721 410459551 1.030000e-60 244.0
15 TraesCS3D01G041800 chr1D 83.616 177 13 11 2866 3037 451534119 451533954 6.440000e-33 152.0
16 TraesCS3D01G041800 chr4D 91.860 172 14 0 1 172 37936588 37936759 1.340000e-59 241.0
17 TraesCS3D01G041800 chr2D 91.860 172 14 0 1 172 204112774 204112945 1.340000e-59 241.0
18 TraesCS3D01G041800 chr2D 91.429 175 15 0 1 175 458730615 458730441 1.340000e-59 241.0
19 TraesCS3D01G041800 chr7D 91.813 171 14 0 1 171 101582909 101582739 4.810000e-59 239.0
20 TraesCS3D01G041800 chr7B 92.262 168 13 0 1 168 598954867 598955034 4.810000e-59 239.0
21 TraesCS3D01G041800 chr7B 91.813 171 14 0 1 171 700360303 700360133 4.810000e-59 239.0
22 TraesCS3D01G041800 chr4A 91.813 171 14 0 1 171 111436276 111436106 4.810000e-59 239.0


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 TraesCS3D01G041800 chr3D 16031239 16034961 3722 False 6876.000000 6876 100.000000 1 3723 1 chr3D.!!$F1 3722
1 TraesCS3D01G041800 chr3D 15994659 15996343 1684 True 410.600000 737 94.895000 1983 2521 2 chr3D.!!$R1 538
2 TraesCS3D01G041800 chr3B 23181855 23185551 3696 False 1460.666667 4100 89.738667 171 3723 3 chr3B.!!$F2 3552
3 TraesCS3D01G041800 chr3B 23317307 23318345 1038 False 1186.000000 1186 87.713000 2699 3723 1 chr3B.!!$F1 1024
4 TraesCS3D01G041800 chr3B 23193560 23194364 804 False 373.500000 584 84.800500 2718 3447 2 chr3B.!!$F3 729
5 TraesCS3D01G041800 chr3A 20334126 20337819 3693 True 1429.666667 3795 88.713000 174 3723 3 chr3A.!!$R1 3549
6 TraesCS3D01G041800 chr1D 451533424 451534119 695 True 215.000000 278 84.237500 2866 3538 2 chr1D.!!$R2 672

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
427 523 0.178981 CCCCCGGATTCAATGCTCAT 60.179 55.0 0.73 0.0 0.0 2.90 F
714 822 0.461516 ATGCATCGTGAGCCAGTCTG 60.462 55.0 0.00 0.0 0.0 3.51 F
1180 1328 0.527385 CGTGCTTGTGTTTGGGGTTG 60.527 55.0 0.00 0.0 0.0 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1927 2078 1.006043 ACAGAGAGGGATCGGAGTTCA 59.994 52.381 0.00 0.00 0.0 3.18 R
1990 2146 1.260561 CCGGTAAACTGCATGCGTATC 59.739 52.381 14.09 2.15 0.0 2.24 R
2991 4363 0.390603 CATGGACGCCGAACACCTAA 60.391 55.000 0.00 0.00 0.0 2.69 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
49 50 7.967890 ATATCAAAATACGTCTCATGATGCA 57.032 32.000 13.79 0.00 32.64 3.96
50 51 6.872628 ATCAAAATACGTCTCATGATGCAT 57.127 33.333 0.00 0.00 32.64 3.96
51 52 6.291067 TCAAAATACGTCTCATGATGCATC 57.709 37.500 20.14 20.14 32.64 3.91
52 53 6.051074 TCAAAATACGTCTCATGATGCATCT 58.949 36.000 26.32 10.21 32.64 2.90
53 54 5.919272 AAATACGTCTCATGATGCATCTG 57.081 39.130 26.32 20.36 32.64 2.90
54 55 4.861102 ATACGTCTCATGATGCATCTGA 57.139 40.909 26.32 22.87 32.64 3.27
55 56 3.747854 ACGTCTCATGATGCATCTGAT 57.252 42.857 26.32 10.77 32.64 2.90
56 57 4.861102 ACGTCTCATGATGCATCTGATA 57.139 40.909 26.32 16.18 32.64 2.15
57 58 5.205759 ACGTCTCATGATGCATCTGATAA 57.794 39.130 26.32 14.60 32.64 1.75
58 59 5.791666 ACGTCTCATGATGCATCTGATAAT 58.208 37.500 26.32 9.30 32.64 1.28
59 60 6.928520 ACGTCTCATGATGCATCTGATAATA 58.071 36.000 26.32 5.68 32.64 0.98
60 61 7.554211 ACGTCTCATGATGCATCTGATAATAT 58.446 34.615 26.32 7.86 32.64 1.28
61 62 8.039538 ACGTCTCATGATGCATCTGATAATATT 58.960 33.333 26.32 8.16 32.64 1.28
62 63 8.328864 CGTCTCATGATGCATCTGATAATATTG 58.671 37.037 26.32 13.09 0.00 1.90
63 64 9.379791 GTCTCATGATGCATCTGATAATATTGA 57.620 33.333 26.32 14.75 0.00 2.57
123 124 6.772078 AGTTAGTCAAACTTCACAAAACTCG 58.228 36.000 0.00 0.00 46.61 4.18
124 125 6.592607 AGTTAGTCAAACTTCACAAAACTCGA 59.407 34.615 0.00 0.00 46.61 4.04
125 126 5.217895 AGTCAAACTTCACAAAACTCGAC 57.782 39.130 0.00 0.00 0.00 4.20
126 127 4.935808 AGTCAAACTTCACAAAACTCGACT 59.064 37.500 0.00 0.00 0.00 4.18
127 128 5.411669 AGTCAAACTTCACAAAACTCGACTT 59.588 36.000 0.00 0.00 0.00 3.01
128 129 6.072673 AGTCAAACTTCACAAAACTCGACTTT 60.073 34.615 0.00 0.00 0.00 2.66
129 130 6.032460 GTCAAACTTCACAAAACTCGACTTTG 59.968 38.462 11.82 11.82 39.26 2.77
130 131 5.873179 AACTTCACAAAACTCGACTTTGA 57.127 34.783 17.84 0.00 37.25 2.69
131 132 5.217895 ACTTCACAAAACTCGACTTTGAC 57.782 39.130 17.84 0.00 37.25 3.18
132 133 4.094442 ACTTCACAAAACTCGACTTTGACC 59.906 41.667 17.84 0.00 37.25 4.02
133 134 3.601435 TCACAAAACTCGACTTTGACCA 58.399 40.909 17.84 3.28 37.25 4.02
134 135 4.004314 TCACAAAACTCGACTTTGACCAA 58.996 39.130 17.84 0.00 37.25 3.67
135 136 4.456222 TCACAAAACTCGACTTTGACCAAA 59.544 37.500 17.84 0.00 37.25 3.28
136 137 4.557301 CACAAAACTCGACTTTGACCAAAC 59.443 41.667 17.84 0.00 37.25 2.93
137 138 4.102649 CAAAACTCGACTTTGACCAAACC 58.897 43.478 8.84 0.00 36.12 3.27
138 139 3.277142 AACTCGACTTTGACCAAACCT 57.723 42.857 0.00 0.00 0.00 3.50
139 140 3.277142 ACTCGACTTTGACCAAACCTT 57.723 42.857 0.00 0.00 0.00 3.50
140 141 4.411256 ACTCGACTTTGACCAAACCTTA 57.589 40.909 0.00 0.00 0.00 2.69
141 142 4.969484 ACTCGACTTTGACCAAACCTTAT 58.031 39.130 0.00 0.00 0.00 1.73
142 143 6.105397 ACTCGACTTTGACCAAACCTTATA 57.895 37.500 0.00 0.00 0.00 0.98
143 144 6.708285 ACTCGACTTTGACCAAACCTTATAT 58.292 36.000 0.00 0.00 0.00 0.86
144 145 6.594159 ACTCGACTTTGACCAAACCTTATATG 59.406 38.462 0.00 0.00 0.00 1.78
145 146 6.469410 TCGACTTTGACCAAACCTTATATGT 58.531 36.000 0.00 0.00 0.00 2.29
146 147 6.370442 TCGACTTTGACCAAACCTTATATGTG 59.630 38.462 0.00 0.00 0.00 3.21
147 148 6.403200 CGACTTTGACCAAACCTTATATGTGG 60.403 42.308 0.00 0.00 35.39 4.17
148 149 6.548321 ACTTTGACCAAACCTTATATGTGGA 58.452 36.000 0.00 0.00 33.39 4.02
149 150 6.433093 ACTTTGACCAAACCTTATATGTGGAC 59.567 38.462 0.00 0.00 33.39 4.02
150 151 5.772393 TGACCAAACCTTATATGTGGACT 57.228 39.130 0.00 0.00 33.39 3.85
151 152 6.877668 TGACCAAACCTTATATGTGGACTA 57.122 37.500 0.00 0.00 33.39 2.59
152 153 7.260387 TGACCAAACCTTATATGTGGACTAA 57.740 36.000 0.00 0.00 33.39 2.24
153 154 7.691213 TGACCAAACCTTATATGTGGACTAAA 58.309 34.615 0.00 0.00 33.39 1.85
154 155 8.164733 TGACCAAACCTTATATGTGGACTAAAA 58.835 33.333 0.00 0.00 33.39 1.52
155 156 8.943594 ACCAAACCTTATATGTGGACTAAAAA 57.056 30.769 0.00 0.00 33.39 1.94
156 157 9.020731 ACCAAACCTTATATGTGGACTAAAAAG 57.979 33.333 0.00 0.00 33.39 2.27
157 158 9.238368 CCAAACCTTATATGTGGACTAAAAAGA 57.762 33.333 3.28 0.00 0.00 2.52
161 162 9.239551 ACCTTATATGTGGACTAAAAAGAAACC 57.760 33.333 3.28 0.00 0.00 3.27
162 163 8.395633 CCTTATATGTGGACTAAAAAGAAACCG 58.604 37.037 0.00 0.00 0.00 4.44
163 164 9.158233 CTTATATGTGGACTAAAAAGAAACCGA 57.842 33.333 0.00 0.00 0.00 4.69
164 165 5.941948 ATGTGGACTAAAAAGAAACCGAG 57.058 39.130 0.00 0.00 0.00 4.63
165 166 4.131596 TGTGGACTAAAAAGAAACCGAGG 58.868 43.478 0.00 0.00 0.00 4.63
166 167 3.501062 GTGGACTAAAAAGAAACCGAGGG 59.499 47.826 0.00 0.00 0.00 4.30
167 168 3.391955 TGGACTAAAAAGAAACCGAGGGA 59.608 43.478 0.00 0.00 0.00 4.20
168 169 4.141436 TGGACTAAAAAGAAACCGAGGGAA 60.141 41.667 0.00 0.00 0.00 3.97
169 170 5.008331 GGACTAAAAAGAAACCGAGGGAAT 58.992 41.667 0.00 0.00 0.00 3.01
170 171 6.175471 GGACTAAAAAGAAACCGAGGGAATA 58.825 40.000 0.00 0.00 0.00 1.75
171 172 6.827251 GGACTAAAAAGAAACCGAGGGAATAT 59.173 38.462 0.00 0.00 0.00 1.28
172 173 7.201705 GGACTAAAAAGAAACCGAGGGAATATG 60.202 40.741 0.00 0.00 0.00 1.78
242 299 5.491070 TGTCTTGTCCTGATCAATAAGTGG 58.509 41.667 0.00 0.00 0.00 4.00
355 451 0.618458 GTGGTCCATGTGAGGCCTAA 59.382 55.000 4.42 0.00 0.00 2.69
360 456 3.477530 GTCCATGTGAGGCCTAAATACC 58.522 50.000 4.42 0.00 0.00 2.73
363 459 3.371487 CCATGTGAGGCCTAAATACCACA 60.371 47.826 21.09 21.09 38.63 4.17
386 482 3.944015 GGTACTCAATGCTTCAATGCTCT 59.056 43.478 0.00 0.00 0.00 4.09
388 484 5.105997 GGTACTCAATGCTTCAATGCTCTTT 60.106 40.000 0.00 0.00 0.00 2.52
389 485 5.464030 ACTCAATGCTTCAATGCTCTTTT 57.536 34.783 0.00 0.00 0.00 2.27
411 507 5.397553 TTTTGGAATAGGAGGATTACCCC 57.602 43.478 0.00 0.00 36.73 4.95
412 508 2.999928 TGGAATAGGAGGATTACCCCC 58.000 52.381 0.00 0.00 36.73 5.40
413 509 1.907255 GGAATAGGAGGATTACCCCCG 59.093 57.143 0.00 0.00 36.73 5.73
414 510 1.907255 GAATAGGAGGATTACCCCCGG 59.093 57.143 0.00 0.00 36.73 5.73
415 511 1.173425 ATAGGAGGATTACCCCCGGA 58.827 55.000 0.73 0.00 36.73 5.14
416 512 1.173425 TAGGAGGATTACCCCCGGAT 58.827 55.000 0.73 0.00 36.73 4.18
417 513 0.271005 AGGAGGATTACCCCCGGATT 59.729 55.000 0.73 0.00 36.73 3.01
418 514 0.691332 GGAGGATTACCCCCGGATTC 59.309 60.000 0.73 0.00 36.73 2.52
419 515 1.430992 GAGGATTACCCCCGGATTCA 58.569 55.000 0.73 0.00 36.73 2.57
420 516 1.772453 GAGGATTACCCCCGGATTCAA 59.228 52.381 0.73 0.00 36.73 2.69
421 517 2.375509 GAGGATTACCCCCGGATTCAAT 59.624 50.000 0.73 0.00 36.73 2.57
422 518 2.108250 AGGATTACCCCCGGATTCAATG 59.892 50.000 0.73 0.00 36.73 2.82
423 519 1.886542 GATTACCCCCGGATTCAATGC 59.113 52.381 0.73 0.00 0.00 3.56
424 520 0.923358 TTACCCCCGGATTCAATGCT 59.077 50.000 0.73 0.00 0.00 3.79
425 521 0.472471 TACCCCCGGATTCAATGCTC 59.528 55.000 0.73 0.00 0.00 4.26
426 522 1.227102 CCCCCGGATTCAATGCTCA 59.773 57.895 0.73 0.00 0.00 4.26
427 523 0.178981 CCCCCGGATTCAATGCTCAT 60.179 55.000 0.73 0.00 0.00 2.90
428 524 1.073763 CCCCCGGATTCAATGCTCATA 59.926 52.381 0.73 0.00 0.00 2.15
429 525 2.488891 CCCCCGGATTCAATGCTCATAA 60.489 50.000 0.73 0.00 0.00 1.90
430 526 2.816087 CCCCGGATTCAATGCTCATAAG 59.184 50.000 0.73 0.00 0.00 1.73
431 527 3.496692 CCCCGGATTCAATGCTCATAAGA 60.497 47.826 0.73 0.00 0.00 2.10
436 532 7.201679 CCCGGATTCAATGCTCATAAGAATATC 60.202 40.741 0.73 0.00 30.70 1.63
438 534 8.388853 CGGATTCAATGCTCATAAGAATATCTG 58.611 37.037 9.15 0.00 30.70 2.90
439 535 9.445878 GGATTCAATGCTCATAAGAATATCTGA 57.554 33.333 9.15 0.00 30.70 3.27
442 538 9.617523 TTCAATGCTCATAAGAATATCTGAACA 57.382 29.630 0.00 0.00 0.00 3.18
457 553 9.778993 AATATCTGAACATCTCGAAACATTTTG 57.221 29.630 0.00 0.00 0.00 2.44
465 561 3.882888 TCTCGAAACATTTTGGCTCACTT 59.117 39.130 0.00 0.00 0.00 3.16
497 598 1.818674 GAACGTTGCATCCCCTCAAAT 59.181 47.619 5.00 0.00 0.00 2.32
504 605 3.096092 TGCATCCCCTCAAATTTACCAC 58.904 45.455 0.00 0.00 0.00 4.16
507 608 3.343941 TCCCCTCAAATTTACCACGAG 57.656 47.619 0.00 0.00 0.00 4.18
541 642 2.771089 GAGCCTCACATGTTTCACTCA 58.229 47.619 0.00 0.00 0.00 3.41
552 657 6.750501 CACATGTTTCACTCATGATGAAATCC 59.249 38.462 23.77 17.02 45.27 3.01
555 660 5.352293 TGTTTCACTCATGATGAAATCCGAG 59.648 40.000 23.77 3.97 45.27 4.63
602 709 3.815401 AGCATCTGAATATTGTTACCGGC 59.185 43.478 0.00 0.00 0.00 6.13
714 822 0.461516 ATGCATCGTGAGCCAGTCTG 60.462 55.000 0.00 0.00 0.00 3.51
774 889 1.721926 GAAGTCCGAACTGAAGCGAAG 59.278 52.381 0.00 0.00 35.36 3.79
924 1045 2.499693 CTCCCTCTTCTCCTTCTTCCAC 59.500 54.545 0.00 0.00 0.00 4.02
925 1046 2.112691 TCCCTCTTCTCCTTCTTCCACT 59.887 50.000 0.00 0.00 0.00 4.00
937 1058 7.032598 TCCTTCTTCCACTTCCAGAAAATAT 57.967 36.000 0.00 0.00 0.00 1.28
964 1089 1.187087 GAGGAGGAGGAGAAAGCGAA 58.813 55.000 0.00 0.00 0.00 4.70
973 1098 2.879026 AGGAGAAAGCGAAAGAAACACC 59.121 45.455 0.00 0.00 0.00 4.16
974 1099 2.616842 GGAGAAAGCGAAAGAAACACCA 59.383 45.455 0.00 0.00 0.00 4.17
980 1117 1.940613 GCGAAAGAAACACCAGTGAGT 59.059 47.619 4.48 0.00 0.00 3.41
1005 1142 4.889856 CCGGCGATCGACATGGCA 62.890 66.667 23.01 0.00 42.43 4.92
1008 1145 3.993234 GCGATCGACATGGCAGCG 61.993 66.667 21.57 1.41 34.01 5.18
1083 1220 3.471244 GATGGAGCGGTCGGTCTCG 62.471 68.421 19.51 0.00 41.80 4.04
1166 1313 2.117156 GCTGATTCCATGGCGTGCT 61.117 57.895 6.96 0.00 0.00 4.40
1180 1328 0.527385 CGTGCTTGTGTTTGGGGTTG 60.527 55.000 0.00 0.00 0.00 3.77
1324 1475 2.163211 GCTTGCTCTGTTCTTGGAATCC 59.837 50.000 0.00 0.00 0.00 3.01
1327 1478 1.742268 GCTCTGTTCTTGGAATCCAGC 59.258 52.381 0.86 0.00 33.81 4.85
1338 1489 1.202417 GGAATCCAGCGTTCTGATCGA 60.202 52.381 11.97 0.00 42.95 3.59
1347 1498 1.257415 CGTTCTGATCGATTGCTCTGC 59.743 52.381 0.00 0.00 0.00 4.26
1355 1506 3.257469 TCGATTGCTCTGCTTCTTGAT 57.743 42.857 0.00 0.00 0.00 2.57
1356 1507 2.934553 TCGATTGCTCTGCTTCTTGATG 59.065 45.455 0.00 0.00 0.00 3.07
1357 1508 2.934553 CGATTGCTCTGCTTCTTGATGA 59.065 45.455 0.00 0.00 0.00 2.92
1482 1633 2.035442 GTTGAGGCTGGCGTTCCTC 61.035 63.158 11.19 11.19 46.95 3.71
1484 1635 2.347490 GAGGCTGGCGTTCCTCAA 59.653 61.111 12.69 0.00 46.24 3.02
1566 1717 2.278013 GTCATCCTCGTCGACGCC 60.278 66.667 32.19 10.00 39.60 5.68
1568 1719 3.872728 CATCCTCGTCGACGCCGA 61.873 66.667 32.19 26.93 43.35 5.54
1749 1900 4.760047 GTCGGCCTCACCATGCGT 62.760 66.667 0.00 0.00 39.03 5.24
1859 2010 4.893601 GGGAAGCTACGAGGGCGC 62.894 72.222 0.00 0.00 42.48 6.53
1884 2035 4.899239 GCCGAGGCCATGACCGAG 62.899 72.222 5.01 0.00 34.56 4.63
1902 2053 3.774702 GCCTTCAACGTCCGCGAC 61.775 66.667 8.23 2.72 42.00 5.19
1926 2077 2.174349 GGCGAACGTACGTCGACT 59.826 61.111 30.43 15.40 42.86 4.18
1927 2078 1.441016 GGCGAACGTACGTCGACTT 60.441 57.895 30.43 15.07 42.86 3.01
1938 2089 1.135746 ACGTCGACTTGAACTCCGATC 60.136 52.381 14.70 0.00 33.47 3.69
1949 2100 2.239681 ACTCCGATCCCTCTCTGTTT 57.760 50.000 0.00 0.00 0.00 2.83
1983 2139 1.225854 GAACTGCGCGTGCTCATTC 60.226 57.895 23.16 17.59 43.34 2.67
1985 2141 1.904852 AACTGCGCGTGCTCATTCTG 61.905 55.000 23.16 5.99 43.34 3.02
1989 2145 1.630244 GCGCGTGCTCATTCTGTCTT 61.630 55.000 15.02 0.00 38.39 3.01
1990 2146 0.094216 CGCGTGCTCATTCTGTCTTG 59.906 55.000 0.00 0.00 0.00 3.02
2004 2163 2.674852 CTGTCTTGATACGCATGCAGTT 59.325 45.455 19.57 3.42 0.00 3.16
2073 2232 0.618968 AGAAGATCGGCAAGGAGGGT 60.619 55.000 0.00 0.00 0.00 4.34
2166 2325 3.015095 GAAATGCTGCGCGCGATG 61.015 61.111 37.18 25.13 43.27 3.84
2512 3821 1.002888 AGCAACACATCCTCTGACCAG 59.997 52.381 0.00 0.00 0.00 4.00
2544 3854 2.159407 GCTCCTGAAAATGCTCTGCTTC 60.159 50.000 0.00 0.00 0.00 3.86
2548 3858 3.127203 CCTGAAAATGCTCTGCTTCTCTG 59.873 47.826 0.00 0.00 0.00 3.35
2549 3859 4.001652 CTGAAAATGCTCTGCTTCTCTGA 58.998 43.478 0.00 0.00 0.00 3.27
2550 3860 4.392047 TGAAAATGCTCTGCTTCTCTGAA 58.608 39.130 0.00 0.00 0.00 3.02
2551 3861 5.008331 TGAAAATGCTCTGCTTCTCTGAAT 58.992 37.500 0.00 0.00 0.00 2.57
2552 3862 5.475909 TGAAAATGCTCTGCTTCTCTGAATT 59.524 36.000 0.00 0.00 0.00 2.17
2553 3863 5.564048 AAATGCTCTGCTTCTCTGAATTC 57.436 39.130 0.00 0.00 0.00 2.17
2554 3864 3.977134 TGCTCTGCTTCTCTGAATTCT 57.023 42.857 7.05 0.00 0.00 2.40
2555 3865 3.597255 TGCTCTGCTTCTCTGAATTCTG 58.403 45.455 7.05 6.50 0.00 3.02
2556 3866 3.260128 TGCTCTGCTTCTCTGAATTCTGA 59.740 43.478 13.64 13.64 0.00 3.27
2558 3868 4.183101 CTCTGCTTCTCTGAATTCTGACC 58.817 47.826 10.68 2.00 0.00 4.02
2568 3892 4.827284 TCTGAATTCTGACCAAAACCTTCC 59.173 41.667 10.68 0.00 0.00 3.46
2632 3957 3.003173 CCGCTCTGGTTCCAGGGA 61.003 66.667 21.41 2.11 36.71 4.20
2800 4160 6.292923 TCTATCTACTCCTACTTCAGAGTGC 58.707 44.000 3.00 0.00 43.14 4.40
2832 4192 1.529865 GGTCAGTTAAGCCACACGAAC 59.470 52.381 0.00 0.00 0.00 3.95
2971 4337 8.046294 TGGTTTATTCGTATGCTTTGTTGTAT 57.954 30.769 0.00 0.00 0.00 2.29
2981 4347 7.477422 CGTATGCTTTGTTGTATGTTGTACTTC 59.523 37.037 0.00 0.00 0.00 3.01
2982 4348 6.935741 TGCTTTGTTGTATGTTGTACTTCT 57.064 33.333 0.00 0.00 0.00 2.85
2983 4349 6.724263 TGCTTTGTTGTATGTTGTACTTCTG 58.276 36.000 0.00 0.00 0.00 3.02
2991 4363 8.557029 GTTGTATGTTGTACTTCTGTTAAGCTT 58.443 33.333 3.48 3.48 0.00 3.74
3000 4382 6.862711 ACTTCTGTTAAGCTTTAGGTGTTC 57.137 37.500 3.20 0.00 0.00 3.18
3068 4451 5.243954 ACTTCACCTTTTTCTAGCATTTCCC 59.756 40.000 0.00 0.00 0.00 3.97
3204 4609 1.202758 TGTACAAGCACTCCAAGGTGG 60.203 52.381 0.00 0.00 39.43 4.61
3282 4745 8.177663 TCGAAGAAGAAATTTGAGATGCATTAC 58.822 33.333 0.00 0.00 0.00 1.89
3291 4756 8.566008 AATTTGAGATGCATTACGAAAATAGC 57.434 30.769 0.00 0.00 0.00 2.97
3292 4757 5.328886 TGAGATGCATTACGAAAATAGCG 57.671 39.130 0.00 0.00 0.00 4.26
3300 4765 6.015504 GCATTACGAAAATAGCGTATGATGG 58.984 40.000 0.00 0.00 42.90 3.51
3315 4783 6.458342 GCGTATGATGGAAAACCCTTTTAGAG 60.458 42.308 0.00 0.00 35.38 2.43
3410 4879 8.206325 AGATCAGATGTATAACAACAAAGCTG 57.794 34.615 0.00 0.00 32.02 4.24
3411 4880 6.182039 TCAGATGTATAACAACAAAGCTGC 57.818 37.500 0.00 0.00 32.09 5.25
3425 4895 5.669477 ACAAAGCTGCCTGTTTGATAAAAA 58.331 33.333 16.63 0.00 37.16 1.94
3581 5108 2.283145 ACAGAGCATGGAAGCAAAGT 57.717 45.000 0.00 0.00 36.85 2.66
3593 5120 4.637534 TGGAAGCAAAGTAGAGCATCATTC 59.362 41.667 0.00 0.00 37.82 2.67
3608 5135 4.026310 GCATCATTCATTCGTTCCAAATGC 60.026 41.667 0.00 0.00 34.73 3.56
3610 5137 3.438434 TCATTCATTCGTTCCAAATGCGA 59.562 39.130 0.00 0.00 34.73 5.10
3664 5208 3.718434 TGGAGGGTGCTAATGAAGATGAT 59.282 43.478 0.00 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 9.487790 TGCATCATGAGACGTATTTTGATATTA 57.512 29.630 0.09 0.00 0.00 0.98
24 25 8.382030 TGCATCATGAGACGTATTTTGATATT 57.618 30.769 0.09 0.00 0.00 1.28
25 26 7.967890 TGCATCATGAGACGTATTTTGATAT 57.032 32.000 0.09 0.00 0.00 1.63
26 27 7.874528 AGATGCATCATGAGACGTATTTTGATA 59.125 33.333 27.81 0.00 0.00 2.15
27 28 6.709397 AGATGCATCATGAGACGTATTTTGAT 59.291 34.615 27.81 0.00 0.00 2.57
28 29 6.018507 CAGATGCATCATGAGACGTATTTTGA 60.019 38.462 27.81 0.00 0.00 2.69
29 30 6.018507 TCAGATGCATCATGAGACGTATTTTG 60.019 38.462 27.81 12.15 0.00 2.44
30 31 6.051074 TCAGATGCATCATGAGACGTATTTT 58.949 36.000 27.81 0.00 0.00 1.82
31 32 5.604565 TCAGATGCATCATGAGACGTATTT 58.395 37.500 27.81 0.00 0.00 1.40
32 33 5.205759 TCAGATGCATCATGAGACGTATT 57.794 39.130 27.81 0.00 0.00 1.89
33 34 4.861102 TCAGATGCATCATGAGACGTAT 57.139 40.909 27.81 0.51 0.00 3.06
34 35 4.861102 ATCAGATGCATCATGAGACGTA 57.139 40.909 27.81 7.29 0.00 3.57
35 36 3.747854 ATCAGATGCATCATGAGACGT 57.252 42.857 27.81 10.72 0.00 4.34
36 37 8.328864 CAATATTATCAGATGCATCATGAGACG 58.671 37.037 27.81 7.61 0.00 4.18
37 38 9.379791 TCAATATTATCAGATGCATCATGAGAC 57.620 33.333 27.81 0.00 0.00 3.36
100 101 6.681599 GTCGAGTTTTGTGAAGTTTGACTAAC 59.318 38.462 0.00 0.00 36.99 2.34
101 102 6.592607 AGTCGAGTTTTGTGAAGTTTGACTAA 59.407 34.615 0.00 0.00 31.72 2.24
102 103 6.103997 AGTCGAGTTTTGTGAAGTTTGACTA 58.896 36.000 0.00 0.00 31.72 2.59
103 104 4.935808 AGTCGAGTTTTGTGAAGTTTGACT 59.064 37.500 0.00 0.00 0.00 3.41
104 105 5.217895 AGTCGAGTTTTGTGAAGTTTGAC 57.782 39.130 0.00 0.00 0.00 3.18
105 106 5.873179 AAGTCGAGTTTTGTGAAGTTTGA 57.127 34.783 0.00 0.00 0.00 2.69
106 107 6.032460 GTCAAAGTCGAGTTTTGTGAAGTTTG 59.968 38.462 15.54 1.90 36.97 2.93
107 108 6.084277 GTCAAAGTCGAGTTTTGTGAAGTTT 58.916 36.000 15.54 0.00 36.97 2.66
108 109 5.391629 GGTCAAAGTCGAGTTTTGTGAAGTT 60.392 40.000 15.54 0.00 36.97 2.66
109 110 4.094442 GGTCAAAGTCGAGTTTTGTGAAGT 59.906 41.667 15.54 0.00 36.97 3.01
110 111 4.094294 TGGTCAAAGTCGAGTTTTGTGAAG 59.906 41.667 15.54 4.04 36.97 3.02
111 112 4.004314 TGGTCAAAGTCGAGTTTTGTGAA 58.996 39.130 15.54 0.00 36.97 3.18
112 113 3.601435 TGGTCAAAGTCGAGTTTTGTGA 58.399 40.909 15.54 8.49 36.97 3.58
113 114 4.349663 TTGGTCAAAGTCGAGTTTTGTG 57.650 40.909 15.54 6.18 36.97 3.33
114 115 4.380128 GGTTTGGTCAAAGTCGAGTTTTGT 60.380 41.667 15.54 0.00 36.97 2.83
115 116 4.102649 GGTTTGGTCAAAGTCGAGTTTTG 58.897 43.478 15.54 14.37 36.98 2.44
116 117 4.014406 AGGTTTGGTCAAAGTCGAGTTTT 58.986 39.130 15.54 2.27 0.00 2.43
117 118 3.617284 AGGTTTGGTCAAAGTCGAGTTT 58.383 40.909 12.50 12.50 0.00 2.66
118 119 3.277142 AGGTTTGGTCAAAGTCGAGTT 57.723 42.857 0.00 0.00 0.00 3.01
119 120 3.277142 AAGGTTTGGTCAAAGTCGAGT 57.723 42.857 0.00 0.00 0.00 4.18
120 121 6.594159 ACATATAAGGTTTGGTCAAAGTCGAG 59.406 38.462 0.00 0.00 0.00 4.04
121 122 6.370442 CACATATAAGGTTTGGTCAAAGTCGA 59.630 38.462 0.00 0.00 0.00 4.20
122 123 6.403200 CCACATATAAGGTTTGGTCAAAGTCG 60.403 42.308 0.00 0.00 0.00 4.18
123 124 6.657541 TCCACATATAAGGTTTGGTCAAAGTC 59.342 38.462 0.00 0.00 0.00 3.01
124 125 6.433093 GTCCACATATAAGGTTTGGTCAAAGT 59.567 38.462 0.00 0.00 0.00 2.66
125 126 6.659242 AGTCCACATATAAGGTTTGGTCAAAG 59.341 38.462 0.00 0.00 0.00 2.77
126 127 6.548321 AGTCCACATATAAGGTTTGGTCAAA 58.452 36.000 0.00 0.00 0.00 2.69
127 128 6.134535 AGTCCACATATAAGGTTTGGTCAA 57.865 37.500 0.00 0.00 0.00 3.18
128 129 5.772393 AGTCCACATATAAGGTTTGGTCA 57.228 39.130 0.00 0.00 0.00 4.02
129 130 8.570068 TTTTAGTCCACATATAAGGTTTGGTC 57.430 34.615 0.00 0.00 0.00 4.02
130 131 8.943594 TTTTTAGTCCACATATAAGGTTTGGT 57.056 30.769 0.00 0.00 0.00 3.67
131 132 9.238368 TCTTTTTAGTCCACATATAAGGTTTGG 57.762 33.333 0.00 0.00 0.00 3.28
135 136 9.239551 GGTTTCTTTTTAGTCCACATATAAGGT 57.760 33.333 0.00 0.00 0.00 3.50
136 137 8.395633 CGGTTTCTTTTTAGTCCACATATAAGG 58.604 37.037 0.00 0.00 0.00 2.69
137 138 9.158233 TCGGTTTCTTTTTAGTCCACATATAAG 57.842 33.333 0.00 0.00 0.00 1.73
138 139 9.158233 CTCGGTTTCTTTTTAGTCCACATATAA 57.842 33.333 0.00 0.00 0.00 0.98
139 140 7.767198 CCTCGGTTTCTTTTTAGTCCACATATA 59.233 37.037 0.00 0.00 0.00 0.86
140 141 6.598064 CCTCGGTTTCTTTTTAGTCCACATAT 59.402 38.462 0.00 0.00 0.00 1.78
141 142 5.935789 CCTCGGTTTCTTTTTAGTCCACATA 59.064 40.000 0.00 0.00 0.00 2.29
142 143 4.760204 CCTCGGTTTCTTTTTAGTCCACAT 59.240 41.667 0.00 0.00 0.00 3.21
143 144 4.131596 CCTCGGTTTCTTTTTAGTCCACA 58.868 43.478 0.00 0.00 0.00 4.17
144 145 3.501062 CCCTCGGTTTCTTTTTAGTCCAC 59.499 47.826 0.00 0.00 0.00 4.02
145 146 3.391955 TCCCTCGGTTTCTTTTTAGTCCA 59.608 43.478 0.00 0.00 0.00 4.02
146 147 4.011966 TCCCTCGGTTTCTTTTTAGTCC 57.988 45.455 0.00 0.00 0.00 3.85
147 148 7.336176 ACATATTCCCTCGGTTTCTTTTTAGTC 59.664 37.037 0.00 0.00 0.00 2.59
148 149 7.120726 CACATATTCCCTCGGTTTCTTTTTAGT 59.879 37.037 0.00 0.00 0.00 2.24
149 150 7.335924 TCACATATTCCCTCGGTTTCTTTTTAG 59.664 37.037 0.00 0.00 0.00 1.85
150 151 7.169591 TCACATATTCCCTCGGTTTCTTTTTA 58.830 34.615 0.00 0.00 0.00 1.52
151 152 6.007703 TCACATATTCCCTCGGTTTCTTTTT 58.992 36.000 0.00 0.00 0.00 1.94
152 153 5.566469 TCACATATTCCCTCGGTTTCTTTT 58.434 37.500 0.00 0.00 0.00 2.27
153 154 5.174037 TCACATATTCCCTCGGTTTCTTT 57.826 39.130 0.00 0.00 0.00 2.52
154 155 4.837093 TCACATATTCCCTCGGTTTCTT 57.163 40.909 0.00 0.00 0.00 2.52
155 156 4.019681 TGTTCACATATTCCCTCGGTTTCT 60.020 41.667 0.00 0.00 0.00 2.52
156 157 4.258543 TGTTCACATATTCCCTCGGTTTC 58.741 43.478 0.00 0.00 0.00 2.78
157 158 4.295141 TGTTCACATATTCCCTCGGTTT 57.705 40.909 0.00 0.00 0.00 3.27
158 159 3.992943 TGTTCACATATTCCCTCGGTT 57.007 42.857 0.00 0.00 0.00 4.44
159 160 3.992943 TTGTTCACATATTCCCTCGGT 57.007 42.857 0.00 0.00 0.00 4.69
160 161 5.835113 AATTTGTTCACATATTCCCTCGG 57.165 39.130 0.00 0.00 0.00 4.63
161 162 8.458843 ACTTTAATTTGTTCACATATTCCCTCG 58.541 33.333 0.00 0.00 31.63 4.63
162 163 9.788960 GACTTTAATTTGTTCACATATTCCCTC 57.211 33.333 0.00 0.00 31.63 4.30
163 164 9.308000 TGACTTTAATTTGTTCACATATTCCCT 57.692 29.630 0.00 0.00 31.63 4.20
170 171 9.467258 CACTCAATGACTTTAATTTGTTCACAT 57.533 29.630 0.00 0.00 0.00 3.21
171 172 7.434897 GCACTCAATGACTTTAATTTGTTCACA 59.565 33.333 0.00 0.00 0.00 3.58
172 173 7.649306 AGCACTCAATGACTTTAATTTGTTCAC 59.351 33.333 0.00 0.00 0.00 3.18
212 213 3.580022 TGATCAGGACAAGACATGTGAGT 59.420 43.478 1.15 0.00 44.12 3.41
242 299 4.309933 TGACTCACATGTCTTGTCATGAC 58.690 43.478 19.27 19.27 45.41 3.06
274 370 8.147642 ACTCACTGACTTCAATTCTTTTGTAG 57.852 34.615 0.00 0.00 0.00 2.74
276 372 7.770897 AGTACTCACTGACTTCAATTCTTTTGT 59.229 33.333 0.00 0.00 32.25 2.83
283 379 5.455056 ACGAGTACTCACTGACTTCAATT 57.545 39.130 22.37 0.00 34.21 2.32
287 383 3.436015 TGCTACGAGTACTCACTGACTTC 59.564 47.826 22.37 3.88 34.21 3.01
290 386 3.623960 AGATGCTACGAGTACTCACTGAC 59.376 47.826 22.37 8.10 34.21 3.51
294 390 4.211794 GGTCTAGATGCTACGAGTACTCAC 59.788 50.000 22.37 9.10 0.00 3.51
355 451 4.844349 AGCATTGAGTACCTGTGGTATT 57.156 40.909 0.00 0.00 40.54 1.89
360 456 4.673580 GCATTGAAGCATTGAGTACCTGTG 60.674 45.833 0.00 0.00 0.00 3.66
363 459 3.944015 GAGCATTGAAGCATTGAGTACCT 59.056 43.478 0.00 0.00 36.85 3.08
388 484 5.773091 GGGGTAATCCTCCTATTCCAAAAA 58.227 41.667 0.00 0.00 35.33 1.94
389 485 5.397553 GGGGTAATCCTCCTATTCCAAAA 57.602 43.478 0.00 0.00 35.33 2.44
400 496 1.430992 TGAATCCGGGGGTAATCCTC 58.569 55.000 0.00 0.00 35.33 3.71
401 497 1.901648 TTGAATCCGGGGGTAATCCT 58.098 50.000 0.00 0.00 35.33 3.24
402 498 2.514803 CATTGAATCCGGGGGTAATCC 58.485 52.381 0.00 0.00 0.00 3.01
403 499 1.886542 GCATTGAATCCGGGGGTAATC 59.113 52.381 0.00 0.00 0.00 1.75
404 500 1.499007 AGCATTGAATCCGGGGGTAAT 59.501 47.619 0.00 0.00 0.00 1.89
405 501 0.923358 AGCATTGAATCCGGGGGTAA 59.077 50.000 0.00 0.00 0.00 2.85
406 502 0.472471 GAGCATTGAATCCGGGGGTA 59.528 55.000 0.00 0.00 0.00 3.69
407 503 1.227383 GAGCATTGAATCCGGGGGT 59.773 57.895 0.00 0.00 0.00 4.95
408 504 0.178981 ATGAGCATTGAATCCGGGGG 60.179 55.000 0.00 0.00 0.00 5.40
409 505 2.566833 TATGAGCATTGAATCCGGGG 57.433 50.000 0.00 0.00 0.00 5.73
410 506 3.743521 TCTTATGAGCATTGAATCCGGG 58.256 45.455 0.00 0.00 0.00 5.73
411 507 5.954296 ATTCTTATGAGCATTGAATCCGG 57.046 39.130 0.00 0.00 0.00 5.14
412 508 8.388853 CAGATATTCTTATGAGCATTGAATCCG 58.611 37.037 11.74 0.00 30.91 4.18
413 509 9.445878 TCAGATATTCTTATGAGCATTGAATCC 57.554 33.333 11.74 7.90 30.91 3.01
416 512 9.617523 TGTTCAGATATTCTTATGAGCATTGAA 57.382 29.630 0.00 0.00 29.49 2.69
417 513 9.788889 ATGTTCAGATATTCTTATGAGCATTGA 57.211 29.630 0.00 0.00 39.59 2.57
420 516 9.656040 GAGATGTTCAGATATTCTTATGAGCAT 57.344 33.333 3.50 3.50 43.47 3.79
421 517 7.811713 CGAGATGTTCAGATATTCTTATGAGCA 59.188 37.037 0.00 0.00 37.32 4.26
422 518 8.026026 TCGAGATGTTCAGATATTCTTATGAGC 58.974 37.037 0.00 0.00 0.00 4.26
423 519 9.905171 TTCGAGATGTTCAGATATTCTTATGAG 57.095 33.333 0.00 0.00 0.00 2.90
428 524 8.954950 ATGTTTCGAGATGTTCAGATATTCTT 57.045 30.769 0.00 0.00 0.00 2.52
429 525 8.954950 AATGTTTCGAGATGTTCAGATATTCT 57.045 30.769 0.00 0.00 0.00 2.40
430 526 9.994432 AAAATGTTTCGAGATGTTCAGATATTC 57.006 29.630 0.00 0.00 0.00 1.75
431 527 9.778993 CAAAATGTTTCGAGATGTTCAGATATT 57.221 29.630 0.00 0.00 0.00 1.28
436 532 4.618489 GCCAAAATGTTTCGAGATGTTCAG 59.382 41.667 0.00 0.00 0.00 3.02
438 534 4.798574 AGCCAAAATGTTTCGAGATGTTC 58.201 39.130 0.00 0.00 0.00 3.18
439 535 4.278170 TGAGCCAAAATGTTTCGAGATGTT 59.722 37.500 0.00 0.00 0.00 2.71
441 537 4.083110 AGTGAGCCAAAATGTTTCGAGATG 60.083 41.667 0.00 0.00 0.00 2.90
442 538 4.074970 AGTGAGCCAAAATGTTTCGAGAT 58.925 39.130 0.00 0.00 0.00 2.75
480 581 3.428862 GGTAAATTTGAGGGGATGCAACG 60.429 47.826 0.00 0.00 0.00 4.10
485 586 3.616219 TCGTGGTAAATTTGAGGGGATG 58.384 45.455 0.00 0.00 0.00 3.51
497 598 3.271729 TGACACTTTTGCTCGTGGTAAA 58.728 40.909 0.00 0.00 35.51 2.01
504 605 1.657538 GCTCGTTGACACTTTTGCTCG 60.658 52.381 0.00 0.00 0.00 5.03
507 608 0.663153 AGGCTCGTTGACACTTTTGC 59.337 50.000 0.00 0.00 0.00 3.68
541 642 4.959596 GCATATGCTCGGATTTCATCAT 57.040 40.909 20.64 0.00 38.21 2.45
555 660 4.858692 ACAAATGTGTTTTCGAGCATATGC 59.141 37.500 20.36 20.36 36.39 3.14
570 675 9.577110 AACAATATTCAGATGCTAACAAATGTG 57.423 29.630 0.00 0.00 0.00 3.21
633 741 4.143363 GGCGTACGCTTTCGGTGC 62.143 66.667 36.24 15.92 41.60 5.01
714 822 1.873591 GATGTAATGGCCCGATGTCAC 59.126 52.381 0.00 0.00 0.00 3.67
755 870 1.784525 CTTCGCTTCAGTTCGGACTT 58.215 50.000 0.00 0.00 32.54 3.01
756 871 0.667792 GCTTCGCTTCAGTTCGGACT 60.668 55.000 0.00 0.00 36.25 3.85
757 872 1.627550 GGCTTCGCTTCAGTTCGGAC 61.628 60.000 0.00 0.00 0.00 4.79
758 873 1.374252 GGCTTCGCTTCAGTTCGGA 60.374 57.895 0.00 0.00 0.00 4.55
759 874 0.951040 AAGGCTTCGCTTCAGTTCGG 60.951 55.000 0.00 0.00 0.00 4.30
760 875 0.440371 GAAGGCTTCGCTTCAGTTCG 59.560 55.000 12.12 0.00 0.00 3.95
761 876 1.802069 AGAAGGCTTCGCTTCAGTTC 58.198 50.000 20.78 0.00 34.02 3.01
774 889 1.611936 GGAAGGTGTGAGGAAGAAGGC 60.612 57.143 0.00 0.00 0.00 4.35
924 1045 5.577164 CCTCGGCGTATATATTTTCTGGAAG 59.423 44.000 6.85 0.00 0.00 3.46
925 1046 5.244402 TCCTCGGCGTATATATTTTCTGGAA 59.756 40.000 6.85 0.00 0.00 3.53
937 1058 0.036448 CTCCTCCTCCTCGGCGTATA 59.964 60.000 6.85 0.00 0.00 1.47
964 1089 2.548067 CCGCTACTCACTGGTGTTTCTT 60.548 50.000 0.53 0.00 0.00 2.52
1029 1166 3.379445 TCGGGGTCCTGCTCGAAC 61.379 66.667 0.00 0.00 0.00 3.95
1117 1254 3.367703 CCATGGATGAACAAGAACCAAGC 60.368 47.826 5.56 0.00 34.28 4.01
1166 1313 1.333636 CCCTGCAACCCCAAACACAA 61.334 55.000 0.00 0.00 0.00 3.33
1180 1328 3.866582 CCTCCCGGATCACCCTGC 61.867 72.222 0.73 0.00 0.00 4.85
1324 1475 1.257415 GAGCAATCGATCAGAACGCTG 59.743 52.381 0.00 0.00 39.56 5.18
1327 1478 1.257415 GCAGAGCAATCGATCAGAACG 59.743 52.381 0.00 0.00 0.00 3.95
1338 1489 3.632604 CCATCATCAAGAAGCAGAGCAAT 59.367 43.478 0.00 0.00 0.00 3.56
1347 1498 1.010350 GCGCGCCATCATCAAGAAG 60.010 57.895 23.24 0.00 0.00 2.85
1926 2077 2.103373 CAGAGAGGGATCGGAGTTCAA 58.897 52.381 0.00 0.00 0.00 2.69
1927 2078 1.006043 ACAGAGAGGGATCGGAGTTCA 59.994 52.381 0.00 0.00 0.00 3.18
1938 2089 3.149981 GTTCAGGGAAAAACAGAGAGGG 58.850 50.000 0.00 0.00 0.00 4.30
1949 2100 3.569701 GCAGTTCAGAATGTTCAGGGAAA 59.430 43.478 0.00 0.00 37.40 3.13
1983 2139 2.274437 ACTGCATGCGTATCAAGACAG 58.726 47.619 14.09 2.91 0.00 3.51
1985 2141 3.747099 AAACTGCATGCGTATCAAGAC 57.253 42.857 14.09 0.00 0.00 3.01
1989 2145 1.930503 CGGTAAACTGCATGCGTATCA 59.069 47.619 14.09 0.00 0.00 2.15
1990 2146 1.260561 CCGGTAAACTGCATGCGTATC 59.739 52.381 14.09 2.15 0.00 2.24
2004 2163 1.892338 CGGGTAGTGCTTCCGGTAA 59.108 57.895 0.00 0.00 40.07 2.85
2166 2325 3.272334 GTCATGCCGTCGCCCATC 61.272 66.667 0.00 0.00 0.00 3.51
2512 3821 5.648572 CATTTTCAGGAGCAGAAGGAATTC 58.351 41.667 0.00 0.00 0.00 2.17
2544 3854 5.048434 GGAAGGTTTTGGTCAGAATTCAGAG 60.048 44.000 8.44 0.00 0.00 3.35
2548 3858 5.073428 AGAGGAAGGTTTTGGTCAGAATTC 58.927 41.667 0.00 0.00 0.00 2.17
2549 3859 5.066913 AGAGGAAGGTTTTGGTCAGAATT 57.933 39.130 0.00 0.00 0.00 2.17
2550 3860 4.731313 AGAGGAAGGTTTTGGTCAGAAT 57.269 40.909 0.00 0.00 0.00 2.40
2551 3861 4.519906 AAGAGGAAGGTTTTGGTCAGAA 57.480 40.909 0.00 0.00 0.00 3.02
2552 3862 4.080015 TGAAAGAGGAAGGTTTTGGTCAGA 60.080 41.667 0.00 0.00 0.00 3.27
2553 3863 4.207165 TGAAAGAGGAAGGTTTTGGTCAG 58.793 43.478 0.00 0.00 0.00 3.51
2554 3864 4.080015 TCTGAAAGAGGAAGGTTTTGGTCA 60.080 41.667 0.00 0.00 38.67 4.02
2555 3865 4.461198 TCTGAAAGAGGAAGGTTTTGGTC 58.539 43.478 0.00 0.00 38.67 4.02
2556 3866 4.519906 TCTGAAAGAGGAAGGTTTTGGT 57.480 40.909 0.00 0.00 38.67 3.67
2776 4122 6.292923 GCACTCTGAAGTAGGAGTAGATAGA 58.707 44.000 0.00 0.00 40.33 1.98
2778 4124 5.057819 CGCACTCTGAAGTAGGAGTAGATA 58.942 45.833 0.00 0.00 40.33 1.98
2779 4125 3.880490 CGCACTCTGAAGTAGGAGTAGAT 59.120 47.826 0.00 0.00 40.33 1.98
2780 4126 3.271729 CGCACTCTGAAGTAGGAGTAGA 58.728 50.000 0.00 0.00 40.33 2.59
2781 4127 3.011119 ACGCACTCTGAAGTAGGAGTAG 58.989 50.000 0.00 0.00 40.33 2.57
2782 4128 2.747989 CACGCACTCTGAAGTAGGAGTA 59.252 50.000 0.00 0.00 40.33 2.59
2783 4129 1.542030 CACGCACTCTGAAGTAGGAGT 59.458 52.381 0.00 0.00 42.67 3.85
2784 4130 1.542030 ACACGCACTCTGAAGTAGGAG 59.458 52.381 0.00 0.00 33.25 3.69
2785 4131 1.269723 CACACGCACTCTGAAGTAGGA 59.730 52.381 0.00 0.00 33.25 2.94
2800 4160 1.651987 AACTGACCTGAACACACACG 58.348 50.000 0.00 0.00 0.00 4.49
2832 4192 2.735134 GTTCACCTAGTTGCCTTACACG 59.265 50.000 0.00 0.00 0.00 4.49
2911 4277 3.346101 GATCGATCGACCGCCTCT 58.654 61.111 22.06 1.65 0.00 3.69
2918 4284 7.959845 GAATTCCTTTCACTCGATCGATCGAC 61.960 46.154 38.89 23.44 42.68 4.20
2930 4296 8.082242 CGAATAAACCAAAGAATTCCTTTCACT 58.918 33.333 0.65 0.00 42.88 3.41
2931 4297 7.865889 ACGAATAAACCAAAGAATTCCTTTCAC 59.134 33.333 0.65 0.00 42.88 3.18
2932 4298 7.947282 ACGAATAAACCAAAGAATTCCTTTCA 58.053 30.769 0.65 0.00 42.88 2.69
2935 4301 7.973944 GCATACGAATAAACCAAAGAATTCCTT 59.026 33.333 0.65 0.00 36.47 3.36
2936 4302 7.339466 AGCATACGAATAAACCAAAGAATTCCT 59.661 33.333 0.65 0.00 0.00 3.36
2938 4304 8.911247 AAGCATACGAATAAACCAAAGAATTC 57.089 30.769 0.00 0.00 0.00 2.17
2971 4337 7.225931 CACCTAAAGCTTAACAGAAGTACAACA 59.774 37.037 0.00 0.00 0.00 3.33
2981 4347 3.120304 GCCGAACACCTAAAGCTTAACAG 60.120 47.826 0.00 0.00 0.00 3.16
2982 4348 2.809696 GCCGAACACCTAAAGCTTAACA 59.190 45.455 0.00 0.00 0.00 2.41
2983 4349 2.159747 CGCCGAACACCTAAAGCTTAAC 60.160 50.000 0.00 0.00 0.00 2.01
2991 4363 0.390603 CATGGACGCCGAACACCTAA 60.391 55.000 0.00 0.00 0.00 2.69
3020 4402 0.610785 ACCCCCAACATTACAAGCGG 60.611 55.000 0.00 0.00 0.00 5.52
3068 4451 6.435904 TGGAATTTACAAGACCCATAACTTGG 59.564 38.462 0.00 0.00 45.03 3.61
3106 4489 4.646960 CAAAAAGGCAAGTTTTTGTTCCG 58.353 39.130 16.77 0.00 45.91 4.30
3133 4517 7.382218 GGAAACCAAAGACAAGTATGATTGTTG 59.618 37.037 0.00 0.00 43.32 3.33
3204 4609 4.763793 AGCTGGTCAATATGTGCATTATCC 59.236 41.667 0.00 0.00 0.00 2.59
3254 4717 6.605849 TGCATCTCAAATTTCTTCTTCGAAG 58.394 36.000 19.35 19.35 0.00 3.79
3270 4733 4.808895 ACGCTATTTTCGTAATGCATCTCA 59.191 37.500 0.00 0.00 38.52 3.27
3282 4745 5.907391 GGTTTTCCATCATACGCTATTTTCG 59.093 40.000 0.00 0.00 40.31 3.46
3291 4756 6.821665 TCTCTAAAAGGGTTTTCCATCATACG 59.178 38.462 0.00 0.00 42.91 3.06
3292 4757 8.575649 TTCTCTAAAAGGGTTTTCCATCATAC 57.424 34.615 0.00 0.00 42.91 2.39
3315 4783 6.623767 GCCTGGATTTGTGTAGTCATCTTTTC 60.624 42.308 0.00 0.00 0.00 2.29
3329 4798 5.075493 GGATATGAATCTGCCTGGATTTGT 58.925 41.667 0.00 0.00 36.24 2.83
3410 4879 3.832490 AGGGTCCTTTTTATCAAACAGGC 59.168 43.478 0.00 0.00 0.00 4.85
3411 4880 4.321974 GCAGGGTCCTTTTTATCAAACAGG 60.322 45.833 0.00 0.00 0.00 4.00
3425 4895 0.555769 TTTGGTTTCTGCAGGGTCCT 59.444 50.000 15.13 0.00 0.00 3.85
3581 5108 5.022282 TGGAACGAATGAATGATGCTCTA 57.978 39.130 0.00 0.00 0.00 2.43
3593 5120 2.661195 GGTTTCGCATTTGGAACGAATG 59.339 45.455 5.12 5.12 44.37 2.67
3608 5135 6.419710 GGAATAGTTTTCTTTGTTGGGTTTCG 59.580 38.462 0.00 0.00 0.00 3.46
3610 5137 7.432148 AGGAATAGTTTTCTTTGTTGGGTTT 57.568 32.000 0.00 0.00 0.00 3.27
3664 5208 2.925724 AGTGTGAAACCAACGGATGAA 58.074 42.857 0.00 0.00 34.36 2.57


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

AutoCloner maintained by Alex Coulton.