Multiple sequence alignment - TraesCS1D01G122100

Loading Multiple Alignment...

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 TraesCS1D01G122100 chr1D 100.000 7678 0 0 1 7678 122766518 122774195 0.000000e+00 14179.0
1 TraesCS1D01G122100 chr1A 96.214 5098 131 30 901 5959 134943448 134948522 0.000000e+00 8288.0
2 TraesCS1D01G122100 chr1A 95.711 956 30 2 5959 6904 134948582 134949536 0.000000e+00 1528.0
3 TraesCS1D01G122100 chr1A 91.603 786 36 13 6898 7678 134951145 134951905 0.000000e+00 1059.0
4 TraesCS1D01G122100 chr1A 91.520 684 47 9 1 674 134942364 134943046 0.000000e+00 931.0
5 TraesCS1D01G122100 chr1B 96.859 2515 53 11 3471 5959 186799240 186801754 0.000000e+00 4183.0
6 TraesCS1D01G122100 chr1B 96.386 1356 29 6 2150 3486 186797523 186798877 0.000000e+00 2215.0
7 TraesCS1D01G122100 chr1B 94.548 1339 34 20 801 2111 186796196 186797523 0.000000e+00 2032.0
8 TraesCS1D01G122100 chr1B 93.638 1226 53 9 5959 7161 186801814 186803037 0.000000e+00 1808.0
9 TraesCS1D01G122100 chr1B 92.754 345 18 3 7116 7457 186803029 186803369 6.920000e-135 492.0
10 TraesCS1D01G122100 chr1B 86.728 437 34 11 222 637 186788671 186789104 1.510000e-126 464.0
11 TraesCS1D01G122100 chr1B 93.304 224 15 0 1 224 186777387 186777610 1.600000e-86 331.0
12 TraesCS1D01G122100 chr1B 82.622 328 48 5 7124 7443 237575431 237575757 1.630000e-71 281.0
13 TraesCS1D01G122100 chr1B 94.318 88 4 1 3566 3652 669035882 669035969 4.830000e-27 134.0
14 TraesCS1D01G122100 chrUn 83.742 449 61 9 7187 7627 380809329 380809773 1.540000e-111 414.0
15 TraesCS1D01G122100 chr4D 83.742 449 61 9 7187 7627 438786016 438786460 1.540000e-111 414.0
16 TraesCS1D01G122100 chr4D 93.333 90 6 0 3568 3657 266952288 266952377 4.830000e-27 134.0
17 TraesCS1D01G122100 chr4D 94.253 87 5 0 3565 3651 291470249 291470163 4.830000e-27 134.0
18 TraesCS1D01G122100 chr2B 83.218 435 61 11 7249 7674 770494501 770494932 9.340000e-104 388.0
19 TraesCS1D01G122100 chr2B 87.029 239 28 3 559 794 213260069 213260307 4.570000e-67 267.0
20 TraesCS1D01G122100 chr4A 82.522 452 64 10 7185 7627 28246701 28247146 4.350000e-102 383.0
21 TraesCS1D01G122100 chr4A 86.831 243 29 3 558 797 631371718 631371476 1.270000e-67 268.0
22 TraesCS1D01G122100 chr4A 81.690 284 45 6 557 837 701953149 701952870 5.990000e-56 230.0
23 TraesCS1D01G122100 chr4A 76.923 364 75 9 7314 7674 572847099 572847456 1.690000e-46 198.0
24 TraesCS1D01G122100 chr4A 94.286 35 1 1 6098 6132 709048629 709048596 1.400000e-02 52.8
25 TraesCS1D01G122100 chr4B 78.510 577 92 21 7112 7678 419647434 419646880 4.410000e-92 350.0
26 TraesCS1D01G122100 chr4B 85.981 321 41 3 7358 7675 631167048 631167367 2.650000e-89 340.0
27 TraesCS1D01G122100 chr4B 94.253 87 5 0 3566 3652 144280465 144280551 4.830000e-27 134.0
28 TraesCS1D01G122100 chr7D 85.489 317 39 5 7358 7667 319794796 319794480 2.670000e-84 324.0
29 TraesCS1D01G122100 chr6D 89.177 231 22 3 559 787 454889536 454889307 1.260000e-72 285.0
30 TraesCS1D01G122100 chr6D 88.745 231 23 3 559 787 454923091 454922862 5.870000e-71 279.0
31 TraesCS1D01G122100 chr2A 87.083 240 28 3 558 794 409644292 409644053 1.270000e-67 268.0
32 TraesCS1D01G122100 chr3D 86.555 238 31 1 559 796 26154721 26154957 2.130000e-65 261.0
33 TraesCS1D01G122100 chr3D 92.391 92 6 1 3561 3652 76229518 76229428 6.250000e-26 130.0
34 TraesCS1D01G122100 chr3A 86.611 239 29 3 559 794 111839796 111840034 2.130000e-65 261.0
35 TraesCS1D01G122100 chr3A 100.000 28 0 0 6104 6131 44635994 44635967 1.400000e-02 52.8
36 TraesCS1D01G122100 chr2D 83.392 283 34 9 559 833 569088861 569089138 4.600000e-62 250.0
37 TraesCS1D01G122100 chr2D 94.382 89 4 1 3568 3655 102881862 102881950 1.340000e-27 135.0
38 TraesCS1D01G122100 chr3B 95.349 86 4 0 3568 3653 277085658 277085743 3.740000e-28 137.0
39 TraesCS1D01G122100 chr6B 87.356 87 11 0 7589 7675 47263681 47263595 4.900000e-17 100.0
40 TraesCS1D01G122100 chr7A 94.444 36 1 1 6098 6133 25522311 25522345 4.000000e-03 54.7


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 TraesCS1D01G122100 chr1D 122766518 122774195 7677 False 14179.0 14179 100.000 1 7678 1 chr1D.!!$F1 7677
1 TraesCS1D01G122100 chr1A 134942364 134951905 9541 False 2951.5 8288 93.762 1 7678 4 chr1A.!!$F1 7677
2 TraesCS1D01G122100 chr1B 186796196 186803369 7173 False 2146.0 4183 94.837 801 7457 5 chr1B.!!$F5 6656
3 TraesCS1D01G122100 chr4B 419646880 419647434 554 True 350.0 350 78.510 7112 7678 1 chr4B.!!$R1 566

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
437 446 0.108585 ACACAAGCCAATGTCGACCT 59.891 50.000 14.12 0.0 0.00 3.85 F
1534 1771 0.107312 GCTGTCATGCATCTCCACCT 60.107 55.000 0.00 0.0 0.00 4.00 F
1602 1842 0.914417 ATATGACCCTATGCCCCGGG 60.914 60.000 15.80 15.8 46.26 5.73 F
1656 1896 2.165030 CCTGCCCTTGTGATGAATGTTC 59.835 50.000 0.00 0.0 0.00 3.18 F
2132 2413 2.284754 TCAGTAATGTGGCCTTTGCA 57.715 45.000 3.32 0.0 40.13 4.08 F
3773 4459 1.069049 GTCACCAAGCAAAACATGGCT 59.931 47.619 0.00 0.0 41.01 4.75 F
5215 5919 2.301346 GCCAATCTTAGTCCATGGGTG 58.699 52.381 13.02 0.0 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2158 2439 0.038166 GACAAGGCATCCAGGGTGAA 59.962 55.000 2.88 0.0 0.00 3.18 R
3487 4171 3.249559 GCAGCTAAGGATATTGTGAGCAC 59.750 47.826 0.00 0.0 32.28 4.40 R
3505 4189 3.728845 TCGATCCTATACTTTTGGCAGC 58.271 45.455 0.00 0.0 0.00 5.25 R
3624 4310 2.811431 CTGCGTCCCAAAATGTAAGACA 59.189 45.455 0.00 0.0 0.00 3.41 R
3787 4473 6.893583 ACTTGCTCCAGATGTTTAGTCATAT 58.106 36.000 0.00 0.0 0.00 1.78 R
5231 5935 0.609957 CAGCATGCTTCAACCCAGGA 60.610 55.000 19.98 0.0 0.00 3.86 R
6755 7555 0.320374 CAGCCAAAGTAGGACACGGA 59.680 55.000 0.00 0.0 0.00 4.69 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
27 28 4.157120 CCGTGGGGCTAACTCCGG 62.157 72.222 0.00 0.00 0.00 5.14
60 62 2.103373 TGGAGAAATCAGAGGAGGACG 58.897 52.381 0.00 0.00 0.00 4.79
93 95 2.174969 GTCGTGCAAACACCGGTGA 61.175 57.895 40.21 15.74 44.40 4.02
96 98 1.083489 CGTGCAAACACCGGTGATAT 58.917 50.000 40.21 22.29 44.40 1.63
123 125 4.501058 GGATTCCCTAACGCGAGATAACTT 60.501 45.833 15.93 0.00 0.00 2.66
144 146 8.458573 AACTTGACAACCATGTGAGTTATAAA 57.541 30.769 0.00 0.00 40.74 1.40
147 149 7.667043 TGACAACCATGTGAGTTATAAAGAC 57.333 36.000 0.00 0.00 40.74 3.01
166 168 3.056536 AGACGTGCTTGGCGATCATATAT 60.057 43.478 0.00 0.00 0.00 0.86
174 176 5.412594 GCTTGGCGATCATATATCAGGAAAA 59.587 40.000 0.00 0.00 0.00 2.29
219 221 0.609131 CGCTCTGGTGGTGGGAAAAT 60.609 55.000 0.00 0.00 0.00 1.82
224 226 3.758554 CTCTGGTGGTGGGAAAATAACTG 59.241 47.826 0.00 0.00 0.00 3.16
233 235 3.842732 GGAAAATAACTGTCCCAACGG 57.157 47.619 0.00 0.00 37.81 4.44
248 250 2.623889 CCAACGGTAGGAGAGATAGTGG 59.376 54.545 0.00 0.00 0.00 4.00
267 269 2.164338 GGCAACATAAGGGTTTTCCGA 58.836 47.619 0.00 0.00 41.82 4.55
297 299 1.002868 CTGGAGCAACAGGTGGAGG 60.003 63.158 0.10 0.00 34.84 4.30
303 305 1.986413 CAACAGGTGGAGGGAGGAG 59.014 63.158 0.00 0.00 0.00 3.69
307 309 1.864559 AGGTGGAGGGAGGAGACCT 60.865 63.158 0.00 0.00 42.18 3.85
337 339 2.111043 ACCAACAGTGACTGGCGG 59.889 61.111 17.92 17.80 36.03 6.13
338 340 2.669569 CCAACAGTGACTGGCGGG 60.670 66.667 17.92 10.93 35.51 6.13
342 344 2.047844 CAGTGACTGGCGGGTGAG 60.048 66.667 4.28 0.00 0.00 3.51
344 346 1.610673 AGTGACTGGCGGGTGAGAT 60.611 57.895 0.00 0.00 0.00 2.75
369 378 0.252927 AAAGTGAGAGAGGGGGAGGG 60.253 60.000 0.00 0.00 0.00 4.30
371 380 1.156322 AGTGAGAGAGGGGGAGGGAA 61.156 60.000 0.00 0.00 0.00 3.97
388 397 1.229951 AAGGAGGGGGAGATGTGCA 60.230 57.895 0.00 0.00 0.00 4.57
392 401 0.466922 GAGGGGGAGATGTGCAATGG 60.467 60.000 0.00 0.00 0.00 3.16
394 403 0.753111 GGGGGAGATGTGCAATGGAC 60.753 60.000 0.00 0.00 0.00 4.02
437 446 0.108585 ACACAAGCCAATGTCGACCT 59.891 50.000 14.12 0.00 0.00 3.85
452 462 2.038426 TCGACCTGTGTCATCCATTTGT 59.962 45.455 0.00 0.00 41.85 2.83
468 478 2.015736 TTGTTGTTTTGCGGCAATGT 57.984 40.000 17.19 0.00 0.00 2.71
479 489 1.722011 CGGCAATGTACGGATATCCC 58.278 55.000 16.36 2.87 0.00 3.85
484 494 4.243270 GCAATGTACGGATATCCCACTAC 58.757 47.826 16.36 12.66 34.14 2.73
545 555 7.741785 TGTCTAGGTTTATCTCAGGTCAAAAA 58.258 34.615 0.00 0.00 0.00 1.94
593 604 4.661222 TGCTTGAATGGTTAGATGGACAA 58.339 39.130 0.00 0.00 0.00 3.18
607 618 5.513233 AGATGGACAATGGTATTTTCAGCT 58.487 37.500 0.00 0.00 0.00 4.24
608 619 5.591877 AGATGGACAATGGTATTTTCAGCTC 59.408 40.000 0.00 0.00 0.00 4.09
625 636 1.059913 CTCACCAGGGTTCAAGTCCT 58.940 55.000 0.00 0.00 0.00 3.85
656 667 7.874940 TCGCATTTATCCTGGATTTATTTCAG 58.125 34.615 15.55 1.04 0.00 3.02
666 677 5.901552 TGGATTTATTTCAGAATTTCCGGC 58.098 37.500 0.00 0.00 0.00 6.13
674 685 1.297598 GAATTTCCGGCGATGCACG 60.298 57.895 9.30 0.00 45.66 5.34
675 686 1.977594 GAATTTCCGGCGATGCACGT 61.978 55.000 9.30 0.00 44.60 4.49
676 687 1.582610 AATTTCCGGCGATGCACGTT 61.583 50.000 9.30 0.00 44.60 3.99
677 688 1.977594 ATTTCCGGCGATGCACGTTC 61.978 55.000 9.30 0.00 44.60 3.95
678 689 3.867700 TTCCGGCGATGCACGTTCA 62.868 57.895 9.30 0.00 44.60 3.18
679 690 3.853330 CCGGCGATGCACGTTCAG 61.853 66.667 9.30 0.00 44.60 3.02
680 691 3.112075 CGGCGATGCACGTTCAGT 61.112 61.111 0.00 0.00 44.60 3.41
690 701 2.005188 CACGTTCAGTGCGAGAAAAC 57.995 50.000 0.00 0.00 44.72 2.43
691 702 0.575390 ACGTTCAGTGCGAGAAAACG 59.425 50.000 10.05 10.05 45.90 3.60
692 703 0.575390 CGTTCAGTGCGAGAAAACGT 59.425 50.000 4.79 0.00 38.24 3.99
693 704 1.005347 CGTTCAGTGCGAGAAAACGTT 60.005 47.619 0.00 0.00 38.24 3.99
694 705 2.625828 GTTCAGTGCGAGAAAACGTTC 58.374 47.619 0.00 0.00 35.59 3.95
695 706 1.214367 TCAGTGCGAGAAAACGTTCC 58.786 50.000 0.00 0.00 33.92 3.62
696 707 0.234884 CAGTGCGAGAAAACGTTCCC 59.765 55.000 0.00 0.00 33.92 3.97
697 708 1.203313 GTGCGAGAAAACGTTCCCG 59.797 57.895 0.00 4.29 37.97 5.14
706 717 4.950744 ACGTTCCCGTCAACTACG 57.049 55.556 0.00 0.00 46.28 3.51
729 740 2.159338 GGCATCTACGGTGACTTCGTAA 60.159 50.000 0.00 0.00 41.62 3.18
765 776 2.010582 GCCGGCTCAGTCTCTCGAAT 62.011 60.000 22.15 0.00 0.00 3.34
771 782 2.796304 CTCAGTCTCTCGAATGTGCTC 58.204 52.381 0.00 0.00 36.65 4.26
777 788 3.316588 GTCTCTCGAATGTGCTCATAGGA 59.683 47.826 0.93 2.09 33.49 2.94
782 793 3.511540 TCGAATGTGCTCATAGGATAGGG 59.488 47.826 0.93 0.00 33.49 3.53
806 817 3.374058 GTGTGTTGTGTATATGAGCACCC 59.626 47.826 0.00 0.00 34.94 4.61
824 835 1.201647 CCCGTGTCTCTGTATTGACGT 59.798 52.381 0.00 0.00 36.10 4.34
895 1103 2.946990 ACGATTTGTCCGACTTGGTTTT 59.053 40.909 0.00 0.00 39.52 2.43
964 1198 2.154074 ACCCCTTCTGAACGGGCTT 61.154 57.895 20.28 3.69 40.86 4.35
965 1199 0.838987 ACCCCTTCTGAACGGGCTTA 60.839 55.000 20.28 0.00 40.86 3.09
1038 1272 0.804933 CTCACGCCGTAACCTAAGCC 60.805 60.000 0.00 0.00 0.00 4.35
1060 1294 1.064825 GTTTTCCTCCTCCACCTCCA 58.935 55.000 0.00 0.00 0.00 3.86
1061 1295 1.064825 TTTTCCTCCTCCACCTCCAC 58.935 55.000 0.00 0.00 0.00 4.02
1062 1296 0.840722 TTTCCTCCTCCACCTCCACC 60.841 60.000 0.00 0.00 0.00 4.61
1063 1297 1.751143 TTCCTCCTCCACCTCCACCT 61.751 60.000 0.00 0.00 0.00 4.00
1064 1298 1.687493 CCTCCTCCACCTCCACCTC 60.687 68.421 0.00 0.00 0.00 3.85
1065 1299 1.687493 CTCCTCCACCTCCACCTCC 60.687 68.421 0.00 0.00 0.00 4.30
1395 1630 0.400670 AGATGGGTAAGGGAGGAGGC 60.401 60.000 0.00 0.00 0.00 4.70
1459 1694 1.535437 GCGTGTTGATCTACCTACCCG 60.535 57.143 4.82 1.56 0.00 5.28
1534 1771 0.107312 GCTGTCATGCATCTCCACCT 60.107 55.000 0.00 0.00 0.00 4.00
1551 1788 2.026822 CACCTGAGCCTGTACCTCAAAT 60.027 50.000 2.55 0.00 38.73 2.32
1602 1842 0.914417 ATATGACCCTATGCCCCGGG 60.914 60.000 15.80 15.80 46.26 5.73
1636 1876 5.148651 ACCGATGGAGTAGTATTTATGCC 57.851 43.478 0.00 0.00 0.00 4.40
1656 1896 2.165030 CCTGCCCTTGTGATGAATGTTC 59.835 50.000 0.00 0.00 0.00 3.18
1898 2138 5.882557 GGTTTCCTGATATGTTGATGTCAGT 59.117 40.000 0.00 0.00 43.14 3.41
2111 2392 9.620259 ATTTCCTATTATTCTTGTGAGTTCCTC 57.380 33.333 0.00 0.00 0.00 3.71
2114 2395 8.478877 TCCTATTATTCTTGTGAGTTCCTCTTC 58.521 37.037 0.00 0.00 0.00 2.87
2115 2396 8.260818 CCTATTATTCTTGTGAGTTCCTCTTCA 58.739 37.037 0.00 0.00 0.00 3.02
2116 2397 9.311916 CTATTATTCTTGTGAGTTCCTCTTCAG 57.688 37.037 0.00 0.00 0.00 3.02
2117 2398 5.559148 ATTCTTGTGAGTTCCTCTTCAGT 57.441 39.130 0.00 0.00 0.00 3.41
2118 2399 6.672266 ATTCTTGTGAGTTCCTCTTCAGTA 57.328 37.500 0.00 0.00 0.00 2.74
2119 2400 6.479972 TTCTTGTGAGTTCCTCTTCAGTAA 57.520 37.500 0.00 0.00 0.00 2.24
2120 2401 6.672266 TCTTGTGAGTTCCTCTTCAGTAAT 57.328 37.500 0.00 0.00 0.00 1.89
2121 2402 6.459066 TCTTGTGAGTTCCTCTTCAGTAATG 58.541 40.000 0.00 0.00 0.00 1.90
2122 2403 5.808366 TGTGAGTTCCTCTTCAGTAATGT 57.192 39.130 0.00 0.00 0.00 2.71
2123 2404 5.541845 TGTGAGTTCCTCTTCAGTAATGTG 58.458 41.667 0.00 0.00 0.00 3.21
2124 2405 4.932200 GTGAGTTCCTCTTCAGTAATGTGG 59.068 45.833 0.00 0.00 0.00 4.17
2125 2406 3.935828 GAGTTCCTCTTCAGTAATGTGGC 59.064 47.826 0.00 0.00 0.00 5.01
2126 2407 3.010420 GTTCCTCTTCAGTAATGTGGCC 58.990 50.000 0.00 0.00 0.00 5.36
2127 2408 2.551270 TCCTCTTCAGTAATGTGGCCT 58.449 47.619 3.32 0.00 0.00 5.19
2128 2409 2.912956 TCCTCTTCAGTAATGTGGCCTT 59.087 45.455 3.32 0.00 0.00 4.35
2129 2410 3.330701 TCCTCTTCAGTAATGTGGCCTTT 59.669 43.478 3.32 0.00 0.00 3.11
2130 2411 3.441572 CCTCTTCAGTAATGTGGCCTTTG 59.558 47.826 3.32 0.00 0.00 2.77
2131 2412 2.819608 TCTTCAGTAATGTGGCCTTTGC 59.180 45.455 3.32 0.00 0.00 3.68
2132 2413 2.284754 TCAGTAATGTGGCCTTTGCA 57.715 45.000 3.32 0.00 40.13 4.08
2133 2414 2.806434 TCAGTAATGTGGCCTTTGCAT 58.194 42.857 3.32 0.25 40.13 3.96
2134 2415 3.164268 TCAGTAATGTGGCCTTTGCATT 58.836 40.909 3.32 11.80 40.13 3.56
2135 2416 3.193267 TCAGTAATGTGGCCTTTGCATTC 59.807 43.478 3.32 4.77 40.13 2.67
2136 2417 3.194116 CAGTAATGTGGCCTTTGCATTCT 59.806 43.478 3.32 6.66 40.13 2.40
2137 2418 3.834231 AGTAATGTGGCCTTTGCATTCTT 59.166 39.130 3.32 0.00 40.13 2.52
2138 2419 3.775261 AATGTGGCCTTTGCATTCTTT 57.225 38.095 3.32 0.00 40.13 2.52
2139 2420 3.775261 ATGTGGCCTTTGCATTCTTTT 57.225 38.095 3.32 0.00 40.13 2.27
2140 2421 3.110447 TGTGGCCTTTGCATTCTTTTC 57.890 42.857 3.32 0.00 40.13 2.29
2141 2422 2.699846 TGTGGCCTTTGCATTCTTTTCT 59.300 40.909 3.32 0.00 40.13 2.52
2142 2423 3.243839 TGTGGCCTTTGCATTCTTTTCTC 60.244 43.478 3.32 0.00 40.13 2.87
2143 2424 3.006217 GTGGCCTTTGCATTCTTTTCTCT 59.994 43.478 3.32 0.00 40.13 3.10
2144 2425 3.642848 TGGCCTTTGCATTCTTTTCTCTT 59.357 39.130 3.32 0.00 40.13 2.85
2145 2426 4.101430 TGGCCTTTGCATTCTTTTCTCTTT 59.899 37.500 3.32 0.00 40.13 2.52
2146 2427 5.059161 GGCCTTTGCATTCTTTTCTCTTTT 58.941 37.500 0.00 0.00 40.13 2.27
2147 2428 5.528690 GGCCTTTGCATTCTTTTCTCTTTTT 59.471 36.000 0.00 0.00 40.13 1.94
2188 2469 3.118261 GGATGCCTTGTCCTGATAGTTCA 60.118 47.826 0.00 0.00 32.85 3.18
2238 2519 6.310941 TGGGATTATTGACTTCCTTGTTGAA 58.689 36.000 0.00 0.00 0.00 2.69
2749 3046 6.379703 TGCCTAACAAATGTTGGCTATACATT 59.620 34.615 25.67 7.18 45.49 2.71
2794 3091 4.819630 TCTCATTGTTAGTTGCTTCCGTTT 59.180 37.500 0.00 0.00 0.00 3.60
2823 3120 8.980481 TCATTCATCCTAATTTACTTCTTCCC 57.020 34.615 0.00 0.00 0.00 3.97
2840 3137 8.606830 ACTTCTTCCCACTTCTAGACATTATTT 58.393 33.333 0.00 0.00 0.00 1.40
2841 3138 8.792830 TTCTTCCCACTTCTAGACATTATTTG 57.207 34.615 0.00 0.00 0.00 2.32
3181 3487 8.456471 ACTAACCAAACAAAGTTTCAGTTAGTC 58.544 33.333 24.50 0.00 42.91 2.59
3245 3551 3.964688 CTCCTTAACCAAACAACCCCTTT 59.035 43.478 0.00 0.00 0.00 3.11
3362 3668 4.025730 CCGTCATACATACATTGTGACAGC 60.026 45.833 0.00 0.00 39.48 4.40
3505 4189 6.573434 TGTGTAGTGCTCACAATATCCTTAG 58.427 40.000 2.63 0.00 41.83 2.18
3525 4209 3.733337 AGCTGCCAAAAGTATAGGATCG 58.267 45.455 0.00 0.00 0.00 3.69
3773 4459 1.069049 GTCACCAAGCAAAACATGGCT 59.931 47.619 0.00 0.00 41.01 4.75
3776 4462 3.577848 TCACCAAGCAAAACATGGCTAAT 59.422 39.130 0.00 0.00 41.01 1.73
4217 4912 6.418057 TTGGACCAGCAATCTTAATTTTGT 57.582 33.333 0.00 0.00 0.00 2.83
4247 4942 8.385898 TGTTTAAACTGATATTCGTTTGAGGT 57.614 30.769 18.72 0.00 35.25 3.85
4262 4957 5.281727 GTTTGAGGTTGTTGAAGATGAACC 58.718 41.667 0.00 0.00 38.54 3.62
4859 5560 7.041187 TGTAACTAAATAGAAGACGTTTGCG 57.959 36.000 0.00 0.00 44.93 4.85
5011 5714 5.948842 ACAGGTGGGTGTTTACTTAGAAAT 58.051 37.500 0.00 0.00 0.00 2.17
5013 5716 4.765339 AGGTGGGTGTTTACTTAGAAATGC 59.235 41.667 0.00 0.00 0.00 3.56
5026 5729 7.693969 ACTTAGAAATGCTTCTGTTGCTATT 57.306 32.000 0.00 0.00 42.11 1.73
5030 5733 6.752168 AGAAATGCTTCTGTTGCTATTTTGT 58.248 32.000 0.00 0.00 40.54 2.83
5125 5828 3.764434 TGTTCCTGTTTTGCACCTAAACA 59.236 39.130 13.13 13.13 41.69 2.83
5212 5916 3.819337 CTCATGCCAATCTTAGTCCATGG 59.181 47.826 4.97 4.97 32.96 3.66
5215 5919 2.301346 GCCAATCTTAGTCCATGGGTG 58.699 52.381 13.02 0.00 0.00 4.61
5231 5935 2.849943 TGGGTGTAAATCAGCTGGGTAT 59.150 45.455 15.13 0.00 43.26 2.73
5398 6110 8.040132 ACCAAAATGTGAAGTTCTTTTTCATCA 58.960 29.630 4.17 0.00 36.96 3.07
5413 6125 9.184062 TCTTTTTCATCATTTGAAGTTTCGATG 57.816 29.630 0.00 0.00 44.90 3.84
5550 6262 3.073798 TCATAGAGCAAAGTGGTGGGAAA 59.926 43.478 0.00 0.00 0.00 3.13
5573 6285 1.691976 CCCTGAACGCCTGGTATGATA 59.308 52.381 0.00 0.00 32.48 2.15
5914 6644 2.529780 TTTTGTGCAGGAAGGCATTG 57.470 45.000 0.00 0.00 46.92 2.82
5960 6750 7.120579 TGAAACAATTGGCATACAGGTTAGTAG 59.879 37.037 10.83 0.00 0.00 2.57
5966 6756 5.730550 TGGCATACAGGTTAGTAGAAACAG 58.269 41.667 0.00 0.00 0.00 3.16
5987 6777 1.378762 GCTGGGCTTTGGAGTGGTA 59.621 57.895 0.00 0.00 0.00 3.25
6084 6874 3.151542 AGTTACTCCCTCCATCCCATT 57.848 47.619 0.00 0.00 0.00 3.16
6088 6878 6.026186 AGTTACTCCCTCCATCCCATTATAG 58.974 44.000 0.00 0.00 0.00 1.31
6089 6879 3.808189 ACTCCCTCCATCCCATTATAGG 58.192 50.000 0.00 0.00 0.00 2.57
6091 6881 3.777522 CTCCCTCCATCCCATTATAGGAC 59.222 52.174 0.00 0.00 35.85 3.85
6093 6883 3.521126 CCCTCCATCCCATTATAGGACAG 59.479 52.174 0.00 0.00 35.85 3.51
6101 6891 5.765510 TCCCATTATAGGACAGTGCAAAAT 58.234 37.500 0.00 0.00 0.00 1.82
6403 7203 5.021033 TGTTTTGTAGGTCCAACTCGTTA 57.979 39.130 0.00 0.00 0.00 3.18
6485 7285 5.892348 AGTGGAACATTGTAAAGGGAGATT 58.108 37.500 0.00 0.00 44.52 2.40
6764 7564 0.602905 CGAAAAGGCTTCCGTGTCCT 60.603 55.000 0.00 0.00 0.00 3.85
6777 7577 2.167693 CCGTGTCCTACTTTGGCTGATA 59.832 50.000 0.00 0.00 0.00 2.15
6842 7642 6.913170 TGATTTTGTTTGCTCTACCTGATTC 58.087 36.000 0.00 0.00 0.00 2.52
6909 9324 7.174082 GCTAATTTAACTGTTAGCTTCAGACG 58.826 38.462 20.35 1.64 45.75 4.18
6934 9349 5.079689 AGATTTGATGTGAATGCATGCAA 57.920 34.783 26.68 8.17 0.00 4.08
6983 9398 3.551863 CCTTAGAGCAACTCTAGCGGATG 60.552 52.174 12.92 0.00 42.92 3.51
7023 9438 7.223584 ACAAGGGCTGCTTGTAAATTATTTTT 58.776 30.769 7.28 0.00 42.46 1.94
7047 9462 4.322725 CGGTATTCTGATATAAGGGCTGCA 60.323 45.833 0.50 0.00 0.00 4.41
7051 9466 5.823861 TTCTGATATAAGGGCTGCATGTA 57.176 39.130 0.50 0.00 0.00 2.29
7059 9474 9.196552 GATATAAGGGCTGCATGTAAAATTTTC 57.803 33.333 6.72 0.37 0.00 2.29
7085 9501 2.556287 CGTGAGGCCTTCGCAAAC 59.444 61.111 6.77 0.00 36.04 2.93
7086 9502 2.250939 CGTGAGGCCTTCGCAAACA 61.251 57.895 6.77 0.00 36.04 2.83
7087 9503 1.781025 CGTGAGGCCTTCGCAAACAA 61.781 55.000 6.77 0.00 36.04 2.83
7089 9505 0.383949 TGAGGCCTTCGCAAACAAAC 59.616 50.000 6.77 0.00 36.38 2.93
7090 9506 0.668535 GAGGCCTTCGCAAACAAACT 59.331 50.000 6.77 0.00 36.38 2.66
7131 9559 4.209080 CGGAAACTTGTCCTGCAAAATTTC 59.791 41.667 0.00 0.00 39.30 2.17
7180 9645 3.823330 CGAAGGCCTCGCGGTACT 61.823 66.667 17.59 0.00 41.49 2.73
7212 9677 2.560105 AGGAGCTTTGCAAATTCCTGAC 59.440 45.455 30.04 15.61 36.92 3.51
7218 9683 4.446719 GCTTTGCAAATTCCTGACTTTCAG 59.553 41.667 13.23 0.00 43.91 3.02
7494 9969 3.751698 ACCGTTCTCAATCTTTTGGTAGC 59.248 43.478 0.00 0.00 33.44 3.58
7519 9994 7.468220 GCTGTCAAGAAATGCATTGATCTCATA 60.468 37.037 13.82 1.85 37.72 2.15
7531 10006 3.657610 TGATCTCATATGTGTCCCTGGT 58.342 45.455 1.90 0.00 0.00 4.00
7598 10073 5.703978 TCAAATCTCTCTCATCCTCGATC 57.296 43.478 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.832608 GCCGGAGTTAGCCCCACG 62.833 72.222 5.05 0.00 0.00 4.94
27 28 1.205460 TTCTCCACCCCCACCTAAGC 61.205 60.000 0.00 0.00 0.00 3.09
60 62 1.101331 ACGACCCTTCTCACGGTATC 58.899 55.000 0.00 0.00 30.56 2.24
93 95 5.479375 TCTCGCGTTAGGGAATCCTTTATAT 59.521 40.000 5.77 0.00 41.56 0.86
96 98 3.025978 TCTCGCGTTAGGGAATCCTTTA 58.974 45.455 5.77 0.00 41.56 1.85
123 125 6.367695 CGTCTTTATAACTCACATGGTTGTCA 59.632 38.462 0.00 0.00 32.34 3.58
144 146 0.459899 TATGATCGCCAAGCACGTCT 59.540 50.000 0.00 0.00 0.00 4.18
147 149 3.253230 TGATATATGATCGCCAAGCACG 58.747 45.455 0.00 0.00 0.00 5.34
166 168 4.900684 TGGTCGTGATACATTTTTCCTGA 58.099 39.130 0.00 0.00 0.00 3.86
219 221 2.173519 CTCCTACCGTTGGGACAGTTA 58.826 52.381 0.00 0.00 42.39 2.24
224 226 1.777941 ATCTCTCCTACCGTTGGGAC 58.222 55.000 0.00 0.00 36.97 4.46
233 235 4.946478 ATGTTGCCACTATCTCTCCTAC 57.054 45.455 0.00 0.00 0.00 3.18
248 250 2.094906 GGTCGGAAAACCCTTATGTTGC 60.095 50.000 0.00 0.00 32.82 4.17
325 327 1.892819 ATCTCACCCGCCAGTCACTG 61.893 60.000 0.00 0.00 0.00 3.66
331 333 2.821366 GCACATCTCACCCGCCAG 60.821 66.667 0.00 0.00 0.00 4.85
337 339 1.808945 CTCACTTTGGCACATCTCACC 59.191 52.381 0.00 0.00 39.30 4.02
338 340 2.740981 CTCTCACTTTGGCACATCTCAC 59.259 50.000 0.00 0.00 39.30 3.51
342 344 2.354259 CCTCTCTCACTTTGGCACATC 58.646 52.381 0.00 0.00 39.30 3.06
344 346 0.397941 CCCTCTCTCACTTTGGCACA 59.602 55.000 0.00 0.00 0.00 4.57
369 378 1.274703 TGCACATCTCCCCCTCCTTC 61.275 60.000 0.00 0.00 0.00 3.46
371 380 0.625683 ATTGCACATCTCCCCCTCCT 60.626 55.000 0.00 0.00 0.00 3.69
437 446 4.569966 GCAAAACAACAAATGGATGACACA 59.430 37.500 0.00 0.00 0.00 3.72
452 462 1.600663 CCGTACATTGCCGCAAAACAA 60.601 47.619 10.42 0.00 0.00 2.83
577 588 8.608185 AAAATACCATTGTCCATCTAACCATT 57.392 30.769 0.00 0.00 0.00 3.16
580 591 7.639113 TGAAAATACCATTGTCCATCTAACC 57.361 36.000 0.00 0.00 0.00 2.85
586 597 5.126061 GTGAGCTGAAAATACCATTGTCCAT 59.874 40.000 0.00 0.00 0.00 3.41
593 604 3.624777 CCTGGTGAGCTGAAAATACCAT 58.375 45.455 0.00 0.00 40.34 3.55
607 618 0.764890 CAGGACTTGAACCCTGGTGA 59.235 55.000 0.00 0.00 44.68 4.02
608 619 3.329300 CAGGACTTGAACCCTGGTG 57.671 57.895 0.00 0.00 44.68 4.17
625 636 5.745312 ATCCAGGATAAATGCGAGTATCA 57.255 39.130 0.00 0.00 33.17 2.15
656 667 1.297598 CGTGCATCGCCGGAAATTC 60.298 57.895 5.05 0.00 0.00 2.17
674 685 2.599142 GGAACGTTTTCTCGCACTGAAC 60.599 50.000 0.46 0.00 31.71 3.18
675 686 1.595794 GGAACGTTTTCTCGCACTGAA 59.404 47.619 0.46 0.00 31.71 3.02
676 687 1.214367 GGAACGTTTTCTCGCACTGA 58.786 50.000 0.46 0.00 31.71 3.41
677 688 0.234884 GGGAACGTTTTCTCGCACTG 59.765 55.000 0.46 0.00 31.71 3.66
678 689 2.613390 GGGAACGTTTTCTCGCACT 58.387 52.632 0.46 0.00 31.71 4.40
697 708 2.541178 CCGTAGATGCCTCGTAGTTGAC 60.541 54.545 0.00 0.00 0.00 3.18
698 709 1.674441 CCGTAGATGCCTCGTAGTTGA 59.326 52.381 0.00 0.00 0.00 3.18
699 710 1.404391 ACCGTAGATGCCTCGTAGTTG 59.596 52.381 0.00 0.00 0.00 3.16
700 711 1.404391 CACCGTAGATGCCTCGTAGTT 59.596 52.381 0.00 0.00 0.00 2.24
701 712 1.022735 CACCGTAGATGCCTCGTAGT 58.977 55.000 0.00 0.00 0.00 2.73
702 713 1.002684 GTCACCGTAGATGCCTCGTAG 60.003 57.143 0.00 0.00 0.00 3.51
703 714 1.019673 GTCACCGTAGATGCCTCGTA 58.980 55.000 0.00 0.00 0.00 3.43
704 715 0.680280 AGTCACCGTAGATGCCTCGT 60.680 55.000 0.00 0.00 0.00 4.18
705 716 0.456221 AAGTCACCGTAGATGCCTCG 59.544 55.000 0.00 0.00 0.00 4.63
706 717 1.534175 CGAAGTCACCGTAGATGCCTC 60.534 57.143 0.00 0.00 0.00 4.70
707 718 0.456221 CGAAGTCACCGTAGATGCCT 59.544 55.000 0.00 0.00 0.00 4.75
708 719 0.172803 ACGAAGTCACCGTAGATGCC 59.827 55.000 0.00 0.00 29.74 4.40
709 720 2.838386 TACGAAGTCACCGTAGATGC 57.162 50.000 0.00 0.00 43.93 3.91
710 721 6.034591 AGATTTTACGAAGTCACCGTAGATG 58.965 40.000 0.00 0.00 43.93 2.90
711 722 6.127814 TGAGATTTTACGAAGTCACCGTAGAT 60.128 38.462 0.00 0.00 43.93 1.98
712 723 5.181811 TGAGATTTTACGAAGTCACCGTAGA 59.818 40.000 0.00 0.00 43.93 2.59
713 724 5.396484 TGAGATTTTACGAAGTCACCGTAG 58.604 41.667 0.00 0.00 43.93 3.51
714 725 5.375417 TGAGATTTTACGAAGTCACCGTA 57.625 39.130 0.00 0.00 43.93 4.02
715 726 4.247267 TGAGATTTTACGAAGTCACCGT 57.753 40.909 0.00 0.00 43.93 4.83
729 740 3.755378 GCCGGCATATCATCTTGAGATTT 59.245 43.478 24.80 0.00 31.21 2.17
765 776 2.700371 CACACCCTATCCTATGAGCACA 59.300 50.000 0.00 0.00 0.00 4.57
771 782 4.191544 CACAACACACACCCTATCCTATG 58.808 47.826 0.00 0.00 0.00 2.23
777 788 6.553953 TCATATACACAACACACACCCTAT 57.446 37.500 0.00 0.00 0.00 2.57
782 793 4.142902 GGTGCTCATATACACAACACACAC 60.143 45.833 0.00 0.00 38.57 3.82
806 817 6.442487 TTTAAACGTCAATACAGAGACACG 57.558 37.500 0.00 0.00 34.48 4.49
846 862 6.971726 AAATATCGGGGGAAAAGATAAACC 57.028 37.500 0.00 0.00 31.61 3.27
895 1103 3.514645 GGGCAAACTCGATACGTCTAAA 58.485 45.455 0.00 0.00 0.00 1.85
898 1106 0.175073 GGGGCAAACTCGATACGTCT 59.825 55.000 0.00 0.00 0.00 4.18
899 1107 1.143969 CGGGGCAAACTCGATACGTC 61.144 60.000 0.00 0.00 0.00 4.34
964 1198 0.122435 ATGGAGGGGGTGGAAAGGTA 59.878 55.000 0.00 0.00 0.00 3.08
965 1199 0.780090 AATGGAGGGGGTGGAAAGGT 60.780 55.000 0.00 0.00 0.00 3.50
1038 1272 1.003696 GAGGTGGAGGAGGAAAACCTG 59.996 57.143 0.00 0.00 41.33 4.00
1060 1294 3.717294 GGTGATGCCGGTGGAGGT 61.717 66.667 1.90 0.00 0.00 3.85
1061 1295 3.391665 GAGGTGATGCCGGTGGAGG 62.392 68.421 1.90 0.00 43.70 4.30
1062 1296 2.187946 GAGGTGATGCCGGTGGAG 59.812 66.667 1.90 0.00 43.70 3.86
1063 1297 3.770040 CGAGGTGATGCCGGTGGA 61.770 66.667 1.90 0.00 43.70 4.02
1064 1298 4.838152 CCGAGGTGATGCCGGTGG 62.838 72.222 1.90 0.00 43.70 4.61
1065 1299 3.770040 TCCGAGGTGATGCCGGTG 61.770 66.667 1.90 0.00 43.40 4.94
1459 1694 4.888239 TCAGGAGTACATGGCTAAGACTAC 59.112 45.833 0.00 0.00 0.00 2.73
1534 1771 4.202461 ACTTCAATTTGAGGTACAGGCTCA 60.202 41.667 12.01 0.00 34.78 4.26
1602 1842 1.070134 TCCATCGGTAATACCAGCTGC 59.930 52.381 8.66 0.00 38.47 5.25
1636 1876 2.159476 CGAACATTCATCACAAGGGCAG 60.159 50.000 0.00 0.00 0.00 4.85
1656 1896 3.005554 GGGCATCACATCCAAGATATCG 58.994 50.000 0.00 0.00 0.00 2.92
1754 1994 7.286087 TCATGCTGGATCAAAATATTACTTGCT 59.714 33.333 0.00 0.00 0.00 3.91
1821 2061 4.023291 GTTTCTATTCTGAAATGGGGCCA 58.977 43.478 4.39 0.00 38.09 5.36
1826 2066 8.680001 TCATCACATGTTTCTATTCTGAAATGG 58.320 33.333 0.00 0.00 38.09 3.16
1898 2138 6.469410 ACAGAATCCGTAGAAAACATACCAA 58.531 36.000 0.00 0.00 0.00 3.67
1967 2207 2.870411 ACGGCAAAAGACAGTTCTGTAC 59.130 45.455 5.40 0.85 29.98 2.90
1975 2215 6.607689 TCATAATGTTTACGGCAAAAGACAG 58.392 36.000 0.00 0.00 0.00 3.51
2111 2392 2.557924 TGCAAAGGCCACATTACTGAAG 59.442 45.455 5.01 0.00 40.13 3.02
2114 2395 3.194116 AGAATGCAAAGGCCACATTACTG 59.806 43.478 5.01 0.00 40.13 2.74
2115 2396 3.434309 AGAATGCAAAGGCCACATTACT 58.566 40.909 5.01 6.30 40.13 2.24
2116 2397 3.874392 AGAATGCAAAGGCCACATTAC 57.126 42.857 5.01 4.28 40.13 1.89
2117 2398 4.888326 AAAGAATGCAAAGGCCACATTA 57.112 36.364 5.01 0.00 40.13 1.90
2118 2399 3.775261 AAAGAATGCAAAGGCCACATT 57.225 38.095 5.01 9.33 40.13 2.71
2119 2400 3.325716 AGAAAAGAATGCAAAGGCCACAT 59.674 39.130 5.01 0.00 40.13 3.21
2120 2401 2.699846 AGAAAAGAATGCAAAGGCCACA 59.300 40.909 5.01 0.00 40.13 4.17
2121 2402 3.006217 AGAGAAAAGAATGCAAAGGCCAC 59.994 43.478 5.01 0.00 40.13 5.01
2122 2403 3.233507 AGAGAAAAGAATGCAAAGGCCA 58.766 40.909 5.01 0.00 40.13 5.36
2123 2404 3.949842 AGAGAAAAGAATGCAAAGGCC 57.050 42.857 0.00 0.00 40.13 5.19
2124 2405 6.609237 AAAAAGAGAAAAGAATGCAAAGGC 57.391 33.333 0.00 0.00 41.68 4.35
2154 2435 0.329596 AGGCATCCAGGGTGAAGAAC 59.670 55.000 2.88 0.00 0.00 3.01
2155 2436 1.075601 AAGGCATCCAGGGTGAAGAA 58.924 50.000 2.88 0.00 0.00 2.52
2156 2437 0.329261 CAAGGCATCCAGGGTGAAGA 59.671 55.000 2.88 0.00 0.00 2.87
2157 2438 0.038744 ACAAGGCATCCAGGGTGAAG 59.961 55.000 2.88 0.00 0.00 3.02
2158 2439 0.038166 GACAAGGCATCCAGGGTGAA 59.962 55.000 2.88 0.00 0.00 3.18
2159 2440 1.685224 GACAAGGCATCCAGGGTGA 59.315 57.895 2.88 0.00 0.00 4.02
2160 2441 1.379044 GGACAAGGCATCCAGGGTG 60.379 63.158 0.00 0.00 36.15 4.61
2161 2442 1.542375 AGGACAAGGCATCCAGGGT 60.542 57.895 5.42 0.00 38.86 4.34
2162 2443 1.077212 CAGGACAAGGCATCCAGGG 60.077 63.158 5.42 0.00 38.86 4.45
2163 2444 0.549950 ATCAGGACAAGGCATCCAGG 59.450 55.000 5.42 0.00 38.86 4.45
2164 2445 2.437281 ACTATCAGGACAAGGCATCCAG 59.563 50.000 5.42 0.00 38.86 3.86
2188 2469 5.939764 TCATACCAGCTTCTCACACTAAT 57.060 39.130 0.00 0.00 0.00 1.73
2336 2625 9.802039 AATTTTACTTTAGGACAACAGGACATA 57.198 29.630 0.00 0.00 0.00 2.29
2749 3046 7.069455 TGAGAGTGCAATATTTACTACAGGCTA 59.931 37.037 0.00 0.00 0.00 3.93
2768 3065 4.143030 CGGAAGCAACTAACAATGAGAGTG 60.143 45.833 0.00 0.00 0.00 3.51
2823 3120 7.488150 TCAGCGTACAAATAATGTCTAGAAGTG 59.512 37.037 0.00 0.00 42.70 3.16
3181 3487 6.112994 TGCATAAATATGTGTACGGTTGTG 57.887 37.500 2.63 0.00 36.11 3.33
3245 3551 5.131977 AGTGACATGGGCTAACATAATACCA 59.868 40.000 0.00 0.00 0.00 3.25
3252 3558 3.507233 CACAAAGTGACATGGGCTAACAT 59.493 43.478 0.00 0.00 35.23 2.71
3362 3668 5.519722 ACTCCTGCAAAAACATTAAGAACG 58.480 37.500 0.00 0.00 0.00 3.95
3487 4171 3.249559 GCAGCTAAGGATATTGTGAGCAC 59.750 47.826 0.00 0.00 32.28 4.40
3505 4189 3.728845 TCGATCCTATACTTTTGGCAGC 58.271 45.455 0.00 0.00 0.00 5.25
3525 4209 7.001073 AGTAGAAATAATGGGGAAAGCAGATC 58.999 38.462 0.00 0.00 0.00 2.75
3624 4310 2.811431 CTGCGTCCCAAAATGTAAGACA 59.189 45.455 0.00 0.00 0.00 3.41
3787 4473 6.893583 ACTTGCTCCAGATGTTTAGTCATAT 58.106 36.000 0.00 0.00 0.00 1.78
4247 4942 2.105821 ACTCCCGGTTCATCTTCAACAA 59.894 45.455 0.00 0.00 0.00 2.83
4262 4957 4.584327 ACAATTTGGAAGAAAACTCCCG 57.416 40.909 0.78 0.00 31.32 5.14
4633 5329 9.332502 TGCACACTTAACAAAGTTAATAGAGAA 57.667 29.630 3.13 0.00 0.00 2.87
4893 5594 4.960469 ACCTCCGGAACTAAATATCAGACA 59.040 41.667 5.23 0.00 0.00 3.41
4894 5595 5.532664 ACCTCCGGAACTAAATATCAGAC 57.467 43.478 5.23 0.00 0.00 3.51
4896 5597 6.651975 ACTACCTCCGGAACTAAATATCAG 57.348 41.667 5.23 0.00 0.00 2.90
4898 5599 7.757941 ACTACTACCTCCGGAACTAAATATC 57.242 40.000 5.23 0.00 0.00 1.63
4899 5600 8.544687 AAACTACTACCTCCGGAACTAAATAT 57.455 34.615 5.23 0.00 0.00 1.28
4900 5601 7.961326 AAACTACTACCTCCGGAACTAAATA 57.039 36.000 5.23 0.00 0.00 1.40
5001 5704 8.792830 AATAGCAACAGAAGCATTTCTAAGTA 57.207 30.769 0.00 0.00 41.71 2.24
5011 5714 4.584325 AGGAACAAAATAGCAACAGAAGCA 59.416 37.500 0.00 0.00 0.00 3.91
5013 5716 8.424274 AAAAAGGAACAAAATAGCAACAGAAG 57.576 30.769 0.00 0.00 0.00 2.85
5026 5729 5.927115 ACAACGCAAACTAAAAAGGAACAAA 59.073 32.000 0.00 0.00 0.00 2.83
5030 5733 5.710984 TGAACAACGCAAACTAAAAAGGAA 58.289 33.333 0.00 0.00 0.00 3.36
5125 5828 6.349611 GGAGACAGCATTTATCACACAATTGT 60.350 38.462 4.92 4.92 35.84 2.71
5144 5847 3.557054 GGTTATGTGCAACTCAGGAGACA 60.557 47.826 2.79 0.00 38.04 3.41
5212 5916 3.136626 AGGATACCCAGCTGATTTACACC 59.863 47.826 17.39 9.47 33.88 4.16
5215 5919 3.496870 CCCAGGATACCCAGCTGATTTAC 60.497 52.174 17.39 3.47 33.88 2.01
5231 5935 0.609957 CAGCATGCTTCAACCCAGGA 60.610 55.000 19.98 0.00 0.00 3.86
5392 6104 7.390440 AGGTACATCGAAACTTCAAATGATGAA 59.610 33.333 6.98 0.00 45.71 2.57
5413 6125 7.562135 TCACCATACTGAAGGAATAAAGGTAC 58.438 38.462 0.00 0.00 0.00 3.34
5550 6262 0.617820 ATACCAGGCGTTCAGGGAGT 60.618 55.000 0.00 0.00 0.00 3.85
5573 6285 9.424319 CAACGATTCTACCATATATGCTTTAGT 57.576 33.333 7.24 2.36 0.00 2.24
5811 6540 7.340999 TCAGTAAGCACCAACAGATATACTACA 59.659 37.037 0.00 0.00 0.00 2.74
5914 6644 1.009829 AATCGCTTCGCTGATGGTTC 58.990 50.000 0.00 0.00 0.00 3.62
5960 6750 0.032540 CAAAGCCCAGCACCTGTTTC 59.967 55.000 0.00 0.00 0.00 2.78
5966 6756 2.116125 ACTCCAAAGCCCAGCACC 59.884 61.111 0.00 0.00 0.00 5.01
6014 6804 7.158099 ACTTGTTTTATAAAGGGACAGCATC 57.842 36.000 0.00 0.00 0.00 3.91
6084 6874 8.264347 TGTAAGATCATTTTGCACTGTCCTATA 58.736 33.333 0.00 0.00 0.00 1.31
6088 6878 5.627499 TGTAAGATCATTTTGCACTGTCC 57.373 39.130 0.00 0.00 0.00 4.02
6091 6881 9.888878 CCTATAATGTAAGATCATTTTGCACTG 57.111 33.333 0.00 0.00 38.68 3.66
6093 6883 9.884465 GTCCTATAATGTAAGATCATTTTGCAC 57.116 33.333 0.00 0.00 38.68 4.57
6101 6891 7.535738 TCCCTCTGTCCTATAATGTAAGATCA 58.464 38.462 0.00 0.00 0.00 2.92
6403 7203 6.438763 CGAAGAAAATTAGTTGGCAGACTTT 58.561 36.000 7.46 0.00 0.00 2.66
6485 7285 7.336931 GGACTCTTTACATTTTATCCAGCAAGA 59.663 37.037 0.00 0.00 0.00 3.02
6755 7555 0.320374 CAGCCAAAGTAGGACACGGA 59.680 55.000 0.00 0.00 0.00 4.69
6764 7564 4.252971 GCTCGGTATATCAGCCAAAGTA 57.747 45.455 0.00 0.00 0.00 2.24
6777 7577 1.760192 AACAGTCGTAGGCTCGGTAT 58.240 50.000 0.00 0.00 40.46 2.73
6842 7642 9.334693 GCAGATCAAACAAACACTAAAATAGAG 57.665 33.333 0.00 0.00 0.00 2.43
6904 7704 5.510674 GCATTCACATCAAATCTTTCGTCTG 59.489 40.000 0.00 0.00 0.00 3.51
6909 9324 5.579119 TGCATGCATTCACATCAAATCTTTC 59.421 36.000 18.46 0.00 0.00 2.62
6934 9349 2.185004 ACTTCCTTGCGTATGCTGTT 57.815 45.000 8.69 0.00 43.34 3.16
6940 9355 3.133542 GGGGTAGTAACTTCCTTGCGTAT 59.866 47.826 0.00 0.00 0.00 3.06
6983 9398 3.065925 GCCCTTGTATCAGATTTGTGAGC 59.934 47.826 0.00 0.00 0.00 4.26
7023 9438 4.081642 GCAGCCCTTATATCAGAATACCGA 60.082 45.833 0.00 0.00 0.00 4.69
7047 9462 4.456566 ACGGTACCGCAGAAAATTTTACAT 59.543 37.500 33.62 5.61 44.19 2.29
7051 9466 2.879646 TCACGGTACCGCAGAAAATTTT 59.120 40.909 33.62 7.61 44.19 1.82
7059 9474 4.814294 GGCCTCACGGTACCGCAG 62.814 72.222 33.62 26.89 44.19 5.18
7081 9497 5.799681 ATTTTGCAGGACAAGTTTGTTTG 57.200 34.783 0.00 3.17 42.43 2.93
7082 9498 6.816134 AAATTTTGCAGGACAAGTTTGTTT 57.184 29.167 0.00 0.00 42.43 2.83
7084 9500 6.035542 CGTAAAATTTTGCAGGACAAGTTTGT 59.964 34.615 17.50 0.00 45.65 2.83
7085 9501 6.410038 CGTAAAATTTTGCAGGACAAGTTTG 58.590 36.000 17.50 0.00 40.06 2.93
7086 9502 5.522097 CCGTAAAATTTTGCAGGACAAGTTT 59.478 36.000 17.50 0.00 40.06 2.66
7087 9503 5.047188 CCGTAAAATTTTGCAGGACAAGTT 58.953 37.500 17.50 0.00 40.06 2.66
7089 9505 4.865776 TCCGTAAAATTTTGCAGGACAAG 58.134 39.130 20.06 5.23 40.06 3.16
7090 9506 4.920640 TCCGTAAAATTTTGCAGGACAA 57.079 36.364 20.06 6.91 36.13 3.18
7131 9559 6.055588 ACAAATCCTATAAACTCATCCCGTG 58.944 40.000 0.00 0.00 0.00 4.94
7180 9645 2.607771 GCAAAGCTCCTGAAAATTCGCA 60.608 45.455 0.02 0.00 0.00 5.10
7416 9891 2.502947 AGCATCAGTGGCAACTCTATGA 59.497 45.455 14.70 0.87 38.65 2.15
7494 9969 6.190954 TGAGATCAATGCATTTCTTGACAG 57.809 37.500 9.83 0.00 34.43 3.51
7519 9994 0.912486 GAAGCCTACCAGGGACACAT 59.088 55.000 0.00 0.00 35.37 3.21
7531 10006 0.901114 TGGTAGCCGTGTGAAGCCTA 60.901 55.000 0.00 0.00 0.00 3.93
7654 10129 1.219124 GGTCATGCTCGCTTCTGGA 59.781 57.895 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.