Multiple sequence alignment - TraesCS7A01G102500

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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 TraesCS7A01G102500 chr7A 100.000 3413 0 0 1 3413 62885075 62888487 0.000000e+00 6303.0
1 TraesCS7A01G102500 chr7A 75.243 618 113 31 130 727 423563650 423564247 1.220000e-64 257.0
2 TraesCS7A01G102500 chr7A 90.667 150 8 4 3140 3288 62888127 62888271 9.660000e-46 195.0
3 TraesCS7A01G102500 chr7A 90.667 150 8 4 3053 3197 62888214 62888362 9.660000e-46 195.0
4 TraesCS7A01G102500 chr7A 92.793 111 5 2 3256 3366 47019530 47019637 1.270000e-34 158.0
5 TraesCS7A01G102500 chr4A 92.180 1266 56 18 869 2101 675279325 675280580 0.000000e+00 1749.0
6 TraesCS7A01G102500 chr4A 87.528 906 75 12 2151 3051 675280593 675281465 0.000000e+00 1013.0
7 TraesCS7A01G102500 chr4A 87.595 524 59 6 2414 2936 675225578 675226096 1.350000e-168 603.0
8 TraesCS7A01G102500 chr4A 87.595 524 59 6 2414 2936 675293183 675293701 1.350000e-168 603.0
9 TraesCS7A01G102500 chr4A 93.750 192 10 1 869 1058 675221798 675221989 1.550000e-73 287.0
10 TraesCS7A01G102500 chr4A 88.991 218 24 0 3196 3413 675291739 675291956 1.560000e-68 270.0
11 TraesCS7A01G102500 chr4A 87.634 186 23 0 3228 3413 675224175 675224360 2.060000e-52 217.0
12 TraesCS7A01G102500 chr4A 89.744 117 11 1 3282 3398 675226724 675226839 7.630000e-32 148.0
13 TraesCS7A01G102500 chr4A 89.744 117 11 1 3282 3398 675295216 675295331 7.630000e-32 148.0
14 TraesCS7A01G102500 chrUn 92.212 1130 47 17 1003 2101 305776969 305778088 0.000000e+00 1561.0
15 TraesCS7A01G102500 chrUn 87.528 906 75 12 2151 3051 305778101 305778973 0.000000e+00 1013.0
16 TraesCS7A01G102500 chrUn 87.634 186 23 0 3228 3413 354341644 354341829 2.060000e-52 217.0
17 TraesCS7A01G102500 chrUn 89.744 117 11 1 3282 3398 330523580 330523695 7.630000e-32 148.0
18 TraesCS7A01G102500 chrUn 89.744 117 11 1 3282 3398 376008354 376008239 7.630000e-32 148.0
19 TraesCS7A01G102500 chrUn 83.077 130 14 5 1563 1684 323923205 323923076 1.000000e-20 111.0
20 TraesCS7A01G102500 chr7D 91.192 1124 68 20 355 1467 58623549 58624652 0.000000e+00 1498.0
21 TraesCS7A01G102500 chr7D 89.637 743 45 14 2314 3051 58625521 58626236 0.000000e+00 917.0
22 TraesCS7A01G102500 chr7D 89.297 626 50 11 1484 2101 58624757 58625373 0.000000e+00 769.0
23 TraesCS7A01G102500 chr7D 86.747 332 31 4 1 330 58623239 58623559 1.160000e-94 357.0
24 TraesCS7A01G102500 chr7D 75.563 622 134 11 130 741 376356318 376356931 1.200000e-74 291.0
25 TraesCS7A01G102500 chr7D 89.189 148 13 3 3257 3401 58626361 58626508 7.520000e-42 182.0
26 TraesCS7A01G102500 chr3B 73.276 580 136 16 134 703 70420446 70421016 9.660000e-46 195.0
27 TraesCS7A01G102500 chr3B 74.658 438 93 15 179 610 3265421 3264996 9.730000e-41 178.0
28 TraesCS7A01G102500 chr3B 70.978 634 158 23 133 752 70467061 70467682 9.940000e-26 128.0
29 TraesCS7A01G102500 chr6D 74.670 379 70 18 246 610 426334843 426334477 9.870000e-31 145.0
30 TraesCS7A01G102500 chr4D 74.847 326 60 16 181 503 65225223 65224917 9.940000e-26 128.0
31 TraesCS7A01G102500 chr4D 82.308 130 15 5 1563 1684 109929556 109929685 4.660000e-19 106.0
32 TraesCS7A01G102500 chr5A 72.326 430 104 14 160 581 3060572 3060150 1.660000e-23 121.0
33 TraesCS7A01G102500 chr5D 82.308 130 15 5 1563 1684 479354779 479354908 4.660000e-19 106.0
34 TraesCS7A01G102500 chr2B 82.308 130 15 5 1563 1684 463774337 463774208 4.660000e-19 106.0
35 TraesCS7A01G102500 chr2B 75.510 196 44 4 386 579 710331253 710331446 3.630000e-15 93.5
36 TraesCS7A01G102500 chr5B 76.064 188 39 5 425 610 410539635 410539452 3.630000e-15 93.5
37 TraesCS7A01G102500 chr5B 73.832 214 53 2 480 693 54508036 54508246 7.850000e-12 82.4
38 TraesCS7A01G102500 chr4B 84.000 100 12 2 186 284 95872656 95872560 3.630000e-15 93.5
39 TraesCS7A01G102500 chr3A 88.158 76 9 0 11 86 444676073 444675998 1.300000e-14 91.6
40 TraesCS7A01G102500 chr2D 93.443 61 4 0 11 71 459318912 459318852 1.300000e-14 91.6
41 TraesCS7A01G102500 chr6A 76.829 164 35 3 231 392 155250184 155250022 4.690000e-14 89.8
42 TraesCS7A01G102500 chr3D 72.696 293 71 8 160 447 56293526 56293814 4.690000e-14 89.8
43 TraesCS7A01G102500 chr3D 72.542 295 71 9 160 448 56307217 56307507 1.690000e-13 87.9


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 TraesCS7A01G102500 chr7A 62885075 62888487 3412 False 2231.000000 6303 93.778000 1 3413 3 chr7A.!!$F3 3412
1 TraesCS7A01G102500 chr7A 423563650 423564247 597 False 257.000000 257 75.243000 130 727 1 chr7A.!!$F2 597
2 TraesCS7A01G102500 chr4A 675279325 675281465 2140 False 1381.000000 1749 89.854000 869 3051 2 chr4A.!!$F2 2182
3 TraesCS7A01G102500 chr4A 675291739 675295331 3592 False 340.333333 603 88.776667 2414 3413 3 chr4A.!!$F3 999
4 TraesCS7A01G102500 chr4A 675221798 675226839 5041 False 313.750000 603 89.680750 869 3413 4 chr4A.!!$F1 2544
5 TraesCS7A01G102500 chrUn 305776969 305778973 2004 False 1287.000000 1561 89.870000 1003 3051 2 chrUn.!!$F3 2048
6 TraesCS7A01G102500 chr7D 58623239 58626508 3269 False 744.600000 1498 89.212400 1 3401 5 chr7D.!!$F2 3400
7 TraesCS7A01G102500 chr7D 376356318 376356931 613 False 291.000000 291 75.563000 130 741 1 chr7D.!!$F1 611

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
610 617 0.031314 CGATAGGTGAGCTGCGACAT 59.969 55.0 0.0 2.86 0.0 3.06 F
1380 1408 0.033405 TTCTCCCTGCCGTAGCTACT 60.033 55.0 21.2 0.00 40.8 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2373 3953 0.178767 CATGTTCCTCCTCGGCATCA 59.821 55.0 0.00 0.0 0.0 3.07 R
3014 7563 0.110678 ATCAGACCGGAGCGATCCTA 59.889 55.0 19.08 0.0 0.0 2.94 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
40 41 2.069165 AACTCCCCTCCAAGCACCAC 62.069 60.000 0.00 0.00 0.00 4.16
48 49 1.973281 CCAAGCACCACCAGCGAAT 60.973 57.895 0.00 0.00 37.01 3.34
49 50 1.503542 CAAGCACCACCAGCGAATC 59.496 57.895 0.00 0.00 37.01 2.52
50 51 1.675641 AAGCACCACCAGCGAATCC 60.676 57.895 0.00 0.00 37.01 3.01
65 66 0.464452 AATCCGTGGATTCGTCTCCC 59.536 55.000 8.33 0.00 40.44 4.30
66 67 0.397254 ATCCGTGGATTCGTCTCCCT 60.397 55.000 0.00 0.00 34.12 4.20
67 68 0.613853 TCCGTGGATTCGTCTCCCTT 60.614 55.000 4.03 0.00 34.12 3.95
68 69 0.179108 CCGTGGATTCGTCTCCCTTC 60.179 60.000 4.03 0.00 34.12 3.46
69 70 0.818296 CGTGGATTCGTCTCCCTTCT 59.182 55.000 4.03 0.00 34.12 2.85
70 71 1.469940 CGTGGATTCGTCTCCCTTCTG 60.470 57.143 4.03 0.00 34.12 3.02
71 72 1.550976 GTGGATTCGTCTCCCTTCTGT 59.449 52.381 4.03 0.00 34.12 3.41
80 81 1.187087 CTCCCTTCTGTCTACCGCTT 58.813 55.000 0.00 0.00 0.00 4.68
138 139 5.326900 TCAATTACCAACCCTTTTCCCTAC 58.673 41.667 0.00 0.00 0.00 3.18
179 180 2.833913 CCCTCCAAGCACCACCAGT 61.834 63.158 0.00 0.00 0.00 4.00
192 193 2.124983 CCAGTGAGCCCGTGGATG 60.125 66.667 0.00 0.00 32.60 3.51
193 194 2.665000 CAGTGAGCCCGTGGATGT 59.335 61.111 0.00 0.00 0.00 3.06
209 211 1.578215 ATGTGCCTCCTTCTGCCCAT 61.578 55.000 0.00 0.00 0.00 4.00
212 214 3.036429 GCCTCCTTCTGCCCATCGT 62.036 63.158 0.00 0.00 0.00 3.73
228 230 2.351276 GTTCCAGTGGCCGATGGT 59.649 61.111 21.90 0.00 37.84 3.55
240 242 0.676782 CCGATGGTGGGGTGAAGAAC 60.677 60.000 0.00 0.00 0.00 3.01
338 344 3.065371 CACACTCCTTTGTTGAGTTGGTC 59.935 47.826 0.00 0.00 41.02 4.02
343 349 2.623416 CCTTTGTTGAGTTGGTCTTCCC 59.377 50.000 0.00 0.00 0.00 3.97
357 363 1.676678 CTTCCCGGCTTCGATCCTCA 61.677 60.000 0.00 0.00 35.61 3.86
376 382 3.531538 TCATTTAGTTCGTCCATCTGGC 58.468 45.455 0.00 0.00 34.44 4.85
398 404 0.037326 AAATCGACAGAGCTTCGGCA 60.037 50.000 6.46 0.00 44.74 5.69
413 419 1.754803 TCGGCATACATTCCTCTCGTT 59.245 47.619 0.00 0.00 0.00 3.85
425 431 1.912371 CTCTCGTTTCTTTGGGGCGC 61.912 60.000 0.00 0.00 0.00 6.53
459 466 1.958715 CGTCATGCGTGGGTGACAA 60.959 57.895 5.98 0.00 43.74 3.18
465 472 2.594962 GCGTGGGTGACAACGAGTG 61.595 63.158 13.18 0.00 0.00 3.51
471 478 1.274167 GGGTGACAACGAGTGATGGTA 59.726 52.381 0.00 0.00 0.00 3.25
506 513 3.937079 GGTCGATTCAAGGGTTTAACGAT 59.063 43.478 0.00 0.00 0.00 3.73
508 515 4.390909 GTCGATTCAAGGGTTTAACGATGT 59.609 41.667 0.00 0.00 0.00 3.06
566 573 1.134367 CGCATGAAGACTTCCCGACTA 59.866 52.381 12.66 0.00 0.00 2.59
610 617 0.031314 CGATAGGTGAGCTGCGACAT 59.969 55.000 0.00 2.86 0.00 3.06
617 624 4.393155 AGCTGCGACATCGGCCAA 62.393 61.111 2.24 0.00 40.23 4.52
619 626 2.764314 GCTGCGACATCGGCCAATT 61.764 57.895 2.24 0.00 40.23 2.32
648 655 1.342496 GCCCTACCGGTAGTATTGGTC 59.658 57.143 33.97 20.85 37.20 4.02
653 660 3.683365 ACCGGTAGTATTGGTCGTTTT 57.317 42.857 4.49 0.00 0.00 2.43
660 667 3.143728 AGTATTGGTCGTTTTGTGGTCC 58.856 45.455 0.00 0.00 0.00 4.46
661 668 2.060050 ATTGGTCGTTTTGTGGTCCA 57.940 45.000 0.00 0.00 0.00 4.02
665 672 3.552875 TGGTCGTTTTGTGGTCCATAAA 58.447 40.909 9.56 9.56 0.00 1.40
731 743 9.751542 CTGATGAACTTTTATAAGAGATACGGT 57.248 33.333 9.85 0.00 35.30 4.83
736 748 8.421673 AACTTTTATAAGAGATACGGTTGCTC 57.578 34.615 9.85 0.00 35.30 4.26
740 752 9.444600 TTTTATAAGAGATACGGTTGCTCTTTT 57.555 29.630 21.96 18.14 44.22 2.27
742 754 3.863041 AGAGATACGGTTGCTCTTTTCC 58.137 45.455 6.63 0.00 35.59 3.13
746 758 4.455877 AGATACGGTTGCTCTTTTCCAAAG 59.544 41.667 0.00 0.00 0.00 2.77
766 778 9.161629 TCCAAAGAAAAAGAAGGAAATGTTTTC 57.838 29.630 0.00 0.00 38.09 2.29
772 784 8.662781 AAAAAGAAGGAAATGTTTTCTTAGGC 57.337 30.769 0.00 0.00 39.52 3.93
773 785 6.976934 AAGAAGGAAATGTTTTCTTAGGCA 57.023 33.333 0.00 0.00 38.88 4.75
774 786 6.976934 AGAAGGAAATGTTTTCTTAGGCAA 57.023 33.333 0.00 0.00 36.16 4.52
775 787 7.360113 AGAAGGAAATGTTTTCTTAGGCAAA 57.640 32.000 0.00 0.00 36.16 3.68
776 788 7.436933 AGAAGGAAATGTTTTCTTAGGCAAAG 58.563 34.615 0.00 0.00 36.16 2.77
777 789 6.976934 AGGAAATGTTTTCTTAGGCAAAGA 57.023 33.333 0.00 0.00 42.62 2.52
778 790 7.544804 AGGAAATGTTTTCTTAGGCAAAGAT 57.455 32.000 1.98 0.00 43.75 2.40
779 791 8.650143 AGGAAATGTTTTCTTAGGCAAAGATA 57.350 30.769 1.98 0.00 43.75 1.98
853 869 1.665766 ACGAATTTAACGCAACGCAC 58.334 45.000 0.00 0.00 0.00 5.34
1212 1236 3.478274 GCCTGGAGGGAGGAGCTG 61.478 72.222 0.00 0.00 34.69 4.24
1366 1394 3.502920 CGCAGTGATATACCGATTCTCC 58.497 50.000 0.00 0.00 0.00 3.71
1380 1408 0.033405 TTCTCCCTGCCGTAGCTACT 60.033 55.000 21.20 0.00 40.80 2.57
1381 1409 0.841961 TCTCCCTGCCGTAGCTACTA 59.158 55.000 21.20 7.17 40.80 1.82
1382 1410 0.953003 CTCCCTGCCGTAGCTACTAC 59.047 60.000 21.20 13.21 40.80 2.73
1396 1424 7.277981 CCGTAGCTACTACAGATTTGTCATTTT 59.722 37.037 21.20 0.00 36.83 1.82
1399 1427 8.854614 AGCTACTACAGATTTGTCATTTTTCT 57.145 30.769 0.00 0.00 38.76 2.52
1400 1428 8.940952 AGCTACTACAGATTTGTCATTTTTCTC 58.059 33.333 0.00 0.00 38.76 2.87
1437 1467 9.994432 GAACCTTCAGATTTATCACTACATTTG 57.006 33.333 0.00 0.00 0.00 2.32
1467 1497 3.196469 TGATGCTAGTCTGAACCTGAAGG 59.804 47.826 0.00 0.00 42.17 3.46
1553 1672 6.780457 AGCATGTTAAACCTGCATTTATCT 57.220 33.333 9.86 0.00 41.32 1.98
1596 1715 2.089980 AGAGATTGTGGCATTGCACTC 58.910 47.619 11.39 8.55 0.00 3.51
1617 1736 2.503331 CACATTTGGAGGTGCTGTGTA 58.497 47.619 0.00 0.00 34.07 2.90
1681 1800 1.742308 TTTAGGAGTTCAGGGCAGGT 58.258 50.000 0.00 0.00 0.00 4.00
1686 1805 0.393537 GAGTTCAGGGCAGGTGGATG 60.394 60.000 0.00 0.00 0.00 3.51
1687 1806 1.136329 AGTTCAGGGCAGGTGGATGT 61.136 55.000 0.00 0.00 0.00 3.06
1688 1807 0.962356 GTTCAGGGCAGGTGGATGTG 60.962 60.000 0.00 0.00 0.00 3.21
1689 1808 1.426251 TTCAGGGCAGGTGGATGTGT 61.426 55.000 0.00 0.00 0.00 3.72
1691 1810 0.392998 CAGGGCAGGTGGATGTGTAC 60.393 60.000 0.00 0.00 0.00 2.90
1693 1812 0.392998 GGGCAGGTGGATGTGTACTG 60.393 60.000 0.00 0.00 0.00 2.74
1694 1813 0.392998 GGCAGGTGGATGTGTACTGG 60.393 60.000 0.00 0.00 0.00 4.00
1717 1842 3.305720 ACTGGAACTGGAACTGTGTAGA 58.694 45.455 0.00 0.00 41.30 2.59
1758 1884 7.495279 TGTTATTATTTGGCTGGAATTTCATGC 59.505 33.333 0.00 1.95 0.00 4.06
1832 1959 3.451141 AGCTCGAAATGCTAGAAGAGG 57.549 47.619 0.00 0.00 39.21 3.69
1850 1977 2.154462 AGGTGCTTCACTGTATGCAAC 58.846 47.619 8.25 8.25 42.78 4.17
1864 1991 2.651135 TGCAACGCGTAGGTTATGTA 57.349 45.000 14.46 1.83 0.00 2.29
1987 2119 6.906157 AGTCTGATGATGGACAAAACAAAT 57.094 33.333 0.00 0.00 35.18 2.32
2049 2181 5.013079 TCAGTTGTGGATATTGTTGGACTCT 59.987 40.000 0.00 0.00 0.00 3.24
2076 2260 4.219070 TGTTGAAATTGAGCTGATCCCAAG 59.781 41.667 0.00 0.00 0.00 3.61
2101 2285 4.634199 ATGCCATAATTTGCATGTAAGGC 58.366 39.130 14.31 14.31 45.96 4.35
2110 2294 0.179129 GCATGTAAGGCCATGTGTGC 60.179 55.000 5.01 6.06 43.33 4.57
2112 2296 1.402968 CATGTAAGGCCATGTGTGCTC 59.597 52.381 5.01 0.00 37.91 4.26
2113 2297 0.692476 TGTAAGGCCATGTGTGCTCT 59.308 50.000 5.01 0.00 0.00 4.09
2114 2298 1.073763 TGTAAGGCCATGTGTGCTCTT 59.926 47.619 5.01 0.00 0.00 2.85
2115 2299 1.740025 GTAAGGCCATGTGTGCTCTTC 59.260 52.381 5.01 0.00 0.00 2.87
2116 2300 0.111061 AAGGCCATGTGTGCTCTTCA 59.889 50.000 5.01 0.00 0.00 3.02
2117 2301 0.607489 AGGCCATGTGTGCTCTTCAC 60.607 55.000 5.01 0.00 45.82 3.18
2118 2302 0.607489 GGCCATGTGTGCTCTTCACT 60.607 55.000 0.00 0.00 45.81 3.41
2119 2303 1.242076 GCCATGTGTGCTCTTCACTT 58.758 50.000 0.00 0.00 45.81 3.16
2120 2304 1.068748 GCCATGTGTGCTCTTCACTTG 60.069 52.381 0.00 0.00 45.81 3.16
2121 2305 1.538512 CCATGTGTGCTCTTCACTTGG 59.461 52.381 13.58 13.58 46.55 3.61
2122 2306 2.224606 CATGTGTGCTCTTCACTTGGT 58.775 47.619 0.00 0.00 45.81 3.67
2123 2307 1.667236 TGTGTGCTCTTCACTTGGTG 58.333 50.000 0.00 0.00 45.81 4.17
2124 2308 0.947244 GTGTGCTCTTCACTTGGTGG 59.053 55.000 0.00 0.00 45.81 4.61
2125 2309 0.546122 TGTGCTCTTCACTTGGTGGT 59.454 50.000 0.00 0.00 45.81 4.16
2126 2310 1.765904 TGTGCTCTTCACTTGGTGGTA 59.234 47.619 0.00 0.00 45.81 3.25
2127 2311 2.143925 GTGCTCTTCACTTGGTGGTAC 58.856 52.381 0.00 0.00 42.38 3.34
2128 2312 1.071699 TGCTCTTCACTTGGTGGTACC 59.928 52.381 4.43 4.43 39.22 3.34
2129 2313 1.939838 GCTCTTCACTTGGTGGTACCG 60.940 57.143 7.57 0.00 42.58 4.02
2130 2314 1.343465 CTCTTCACTTGGTGGTACCGT 59.657 52.381 7.57 0.00 42.58 4.83
2131 2315 2.559668 CTCTTCACTTGGTGGTACCGTA 59.440 50.000 7.57 0.00 42.58 4.02
2132 2316 2.297033 TCTTCACTTGGTGGTACCGTAC 59.703 50.000 7.57 0.00 42.58 3.67
2141 2325 2.204748 GGTACCGTACCCATGAGCA 58.795 57.895 15.95 0.00 43.18 4.26
2142 2326 0.756903 GGTACCGTACCCATGAGCAT 59.243 55.000 15.95 0.00 43.18 3.79
2143 2327 1.140252 GGTACCGTACCCATGAGCATT 59.860 52.381 15.95 0.00 43.18 3.56
2144 2328 2.420967 GGTACCGTACCCATGAGCATTT 60.421 50.000 15.95 0.00 43.18 2.32
2145 2329 1.750193 ACCGTACCCATGAGCATTTG 58.250 50.000 0.00 0.00 0.00 2.32
2146 2330 0.381801 CCGTACCCATGAGCATTTGC 59.618 55.000 0.00 0.00 42.49 3.68
2147 2331 0.381801 CGTACCCATGAGCATTTGCC 59.618 55.000 0.00 0.00 43.38 4.52
2148 2332 1.767759 GTACCCATGAGCATTTGCCT 58.232 50.000 0.00 0.00 43.38 4.75
2149 2333 2.102578 GTACCCATGAGCATTTGCCTT 58.897 47.619 0.00 0.00 43.38 4.35
2161 2345 3.243839 GCATTTGCCTTCCTTCTTGAACA 60.244 43.478 0.00 0.00 34.31 3.18
2169 2353 4.457257 CCTTCCTTCTTGAACAGTTGGATC 59.543 45.833 0.00 0.00 0.00 3.36
2179 2363 5.263599 TGAACAGTTGGATCATATTTGGCT 58.736 37.500 0.00 0.00 0.00 4.75
2180 2364 5.125900 TGAACAGTTGGATCATATTTGGCTG 59.874 40.000 0.00 0.00 0.00 4.85
2196 2380 0.524862 GCTGACAACCTCAAGGCATG 59.475 55.000 0.00 0.00 39.32 4.06
2205 2389 0.520404 CTCAAGGCATGACAGCACAC 59.480 55.000 0.00 0.00 35.83 3.82
2206 2390 0.179023 TCAAGGCATGACAGCACACA 60.179 50.000 0.00 0.00 35.83 3.72
2209 2393 0.037160 AGGCATGACAGCACACATCA 59.963 50.000 0.00 0.00 35.83 3.07
2222 2406 2.921121 CACACATCAATGCACATTGCTC 59.079 45.455 16.74 0.00 45.77 4.26
2223 2407 2.559231 ACACATCAATGCACATTGCTCA 59.441 40.909 16.74 2.63 45.77 4.26
2226 2410 3.006003 ACATCAATGCACATTGCTCACAA 59.994 39.130 16.74 1.30 45.77 3.33
2233 2417 3.119209 TGCACATTGCTCACAACAAAAGA 60.119 39.130 0.00 0.00 45.31 2.52
2235 2419 4.259930 GCACATTGCTCACAACAAAAGAAC 60.260 41.667 0.00 0.00 40.96 3.01
2237 2421 4.081752 ACATTGCTCACAACAAAAGAACCA 60.082 37.500 0.00 0.00 38.99 3.67
2242 2426 2.687935 TCACAACAAAAGAACCAGGAGC 59.312 45.455 0.00 0.00 0.00 4.70
2288 2472 4.357018 TGTCGAGCAGTTCTACATACTG 57.643 45.455 0.00 0.00 44.55 2.74
2289 2473 3.756963 TGTCGAGCAGTTCTACATACTGT 59.243 43.478 0.00 0.00 43.81 3.55
2290 2474 4.939439 TGTCGAGCAGTTCTACATACTGTA 59.061 41.667 0.00 0.00 43.81 2.74
2291 2475 5.589050 TGTCGAGCAGTTCTACATACTGTAT 59.411 40.000 0.00 0.00 43.81 2.29
2292 2476 6.095021 TGTCGAGCAGTTCTACATACTGTATT 59.905 38.462 0.00 0.00 43.81 1.89
2293 2477 6.973474 GTCGAGCAGTTCTACATACTGTATTT 59.027 38.462 0.00 0.00 43.81 1.40
2294 2478 7.488471 GTCGAGCAGTTCTACATACTGTATTTT 59.512 37.037 0.00 0.00 43.81 1.82
2295 2479 8.033038 TCGAGCAGTTCTACATACTGTATTTTT 58.967 33.333 0.00 0.00 43.81 1.94
2296 2480 9.297586 CGAGCAGTTCTACATACTGTATTTTTA 57.702 33.333 0.00 0.00 43.81 1.52
2373 3953 1.553706 CTTTTCAATCTGCAGGCCCT 58.446 50.000 15.13 0.00 0.00 5.19
2457 5708 3.446442 AATTGCAGAACTGGTCCAGAT 57.554 42.857 26.18 14.31 35.18 2.90
2510 5761 4.218200 TCCGTCGACCTAACATAAAGAACA 59.782 41.667 10.58 0.00 0.00 3.18
2511 5762 5.105635 TCCGTCGACCTAACATAAAGAACAT 60.106 40.000 10.58 0.00 0.00 2.71
2520 5771 7.824779 ACCTAACATAAAGAACATTGTCTCCTC 59.175 37.037 0.00 0.00 0.00 3.71
2551 5804 4.142403 TGTTTTATGCAGCTAATGGACAGC 60.142 41.667 0.00 0.00 39.41 4.40
2558 5811 0.179100 GCTAATGGACAGCGCTGAGA 60.179 55.000 42.03 24.63 0.00 3.27
2559 5812 1.740380 GCTAATGGACAGCGCTGAGAA 60.740 52.381 42.03 25.65 0.00 2.87
2579 5832 6.107901 AGAAAGTCTTGTGTAGAAGCTCAT 57.892 37.500 0.00 0.00 33.81 2.90
2580 5833 5.931146 AGAAAGTCTTGTGTAGAAGCTCATG 59.069 40.000 0.00 0.00 33.81 3.07
2600 5853 2.094803 TGTGTTGTTGTCCTTGCACTTG 60.095 45.455 0.00 0.00 0.00 3.16
2608 5861 5.769662 TGTTGTCCTTGCACTTGATATTTCT 59.230 36.000 0.00 0.00 0.00 2.52
2615 5868 6.183360 CCTTGCACTTGATATTTCTTACCTGG 60.183 42.308 0.00 0.00 0.00 4.45
2636 5890 4.142491 TGGATGTCTTCACACACAAACAAC 60.142 41.667 0.00 0.00 34.48 3.32
2698 5953 0.093705 GTTGTGTCGATTGCTCTCGC 59.906 55.000 0.00 1.33 38.52 5.03
2728 5983 4.584874 TCTGTTCTGTTGTGTTTCTTCCA 58.415 39.130 0.00 0.00 0.00 3.53
2761 6902 1.314730 GGAGACAAAAACCGAGCCAA 58.685 50.000 0.00 0.00 0.00 4.52
2813 6956 2.359900 GGTAACTCAGTTGGATGCTGG 58.640 52.381 0.00 0.00 34.89 4.85
2867 7010 5.435686 TCTCTTGGTACAGTAAATGGCAT 57.564 39.130 0.00 0.00 42.39 4.40
2908 7051 4.251268 GTTACCATAGTTCGCTCCACTTT 58.749 43.478 0.00 0.00 0.00 2.66
2986 7535 4.553323 TGAGAACTAGACGTTGCTTTACC 58.447 43.478 0.00 0.00 35.56 2.85
2990 7539 4.803098 ACTAGACGTTGCTTTACCAGAT 57.197 40.909 0.00 0.00 0.00 2.90
2991 7540 5.909621 ACTAGACGTTGCTTTACCAGATA 57.090 39.130 0.00 0.00 0.00 1.98
2992 7541 6.466885 ACTAGACGTTGCTTTACCAGATAT 57.533 37.500 0.00 0.00 0.00 1.63
3025 7592 1.938926 GCTGAAGCATAGGATCGCTCC 60.939 57.143 0.00 0.00 40.52 4.70
3035 7602 0.959553 GGATCGCTCCGGTCTGATTA 59.040 55.000 0.00 0.00 37.15 1.75
3039 7606 3.093717 TCGCTCCGGTCTGATTATTTC 57.906 47.619 0.00 0.00 0.00 2.17
3051 7618 6.316390 GGTCTGATTATTTCTTGTACTGTGGG 59.684 42.308 0.00 0.00 0.00 4.61
3053 7620 7.606456 GTCTGATTATTTCTTGTACTGTGGGAA 59.394 37.037 0.00 0.00 0.00 3.97
3055 7622 7.458397 TGATTATTTCTTGTACTGTGGGAACT 58.542 34.615 0.00 0.00 0.00 3.01
3058 7625 1.765904 TCTTGTACTGTGGGAACTGCA 59.234 47.619 0.00 0.00 0.00 4.41
3060 7627 2.949177 TGTACTGTGGGAACTGCATT 57.051 45.000 0.00 0.00 0.00 3.56
3061 7628 2.778299 TGTACTGTGGGAACTGCATTC 58.222 47.619 0.00 0.00 36.48 2.67
3062 7629 2.105649 TGTACTGTGGGAACTGCATTCA 59.894 45.455 9.92 0.00 39.30 2.57
3063 7630 1.609208 ACTGTGGGAACTGCATTCAC 58.391 50.000 9.92 7.42 41.61 3.18
3068 7635 2.227388 GTGGGAACTGCATTCACTTGAG 59.773 50.000 10.95 0.00 41.80 3.02
3069 7636 1.815003 GGGAACTGCATTCACTTGAGG 59.185 52.381 9.92 0.00 37.78 3.86
3071 7638 2.746362 GGAACTGCATTCACTTGAGGAG 59.254 50.000 9.92 0.00 39.30 3.69
3074 7641 4.298103 ACTGCATTCACTTGAGGAGATT 57.702 40.909 0.00 0.00 0.00 2.40
3075 7642 4.660168 ACTGCATTCACTTGAGGAGATTT 58.340 39.130 0.00 0.00 0.00 2.17
3076 7643 5.075493 ACTGCATTCACTTGAGGAGATTTT 58.925 37.500 0.00 0.00 0.00 1.82
3077 7644 5.048224 ACTGCATTCACTTGAGGAGATTTTG 60.048 40.000 0.00 0.00 0.00 2.44
3079 7646 4.381292 GCATTCACTTGAGGAGATTTTGGG 60.381 45.833 0.00 0.00 0.00 4.12
3080 7647 4.453480 TTCACTTGAGGAGATTTTGGGT 57.547 40.909 0.00 0.00 0.00 4.51
3081 7648 4.453480 TCACTTGAGGAGATTTTGGGTT 57.547 40.909 0.00 0.00 0.00 4.11
3082 7649 4.803452 TCACTTGAGGAGATTTTGGGTTT 58.197 39.130 0.00 0.00 0.00 3.27
3083 7650 4.584325 TCACTTGAGGAGATTTTGGGTTTG 59.416 41.667 0.00 0.00 0.00 2.93
3085 7652 4.584743 ACTTGAGGAGATTTTGGGTTTGAC 59.415 41.667 0.00 0.00 0.00 3.18
3088 7655 4.145052 GAGGAGATTTTGGGTTTGACAGT 58.855 43.478 0.00 0.00 0.00 3.55
3090 7657 5.892348 AGGAGATTTTGGGTTTGACAGTAT 58.108 37.500 0.00 0.00 0.00 2.12
3091 7658 6.314917 AGGAGATTTTGGGTTTGACAGTATT 58.685 36.000 0.00 0.00 0.00 1.89
3092 7659 6.782494 AGGAGATTTTGGGTTTGACAGTATTT 59.218 34.615 0.00 0.00 0.00 1.40
3094 7661 7.598869 GGAGATTTTGGGTTTGACAGTATTTTC 59.401 37.037 0.00 0.00 0.00 2.29
3095 7662 8.017418 AGATTTTGGGTTTGACAGTATTTTCA 57.983 30.769 0.00 0.00 0.00 2.69
3096 7663 8.143835 AGATTTTGGGTTTGACAGTATTTTCAG 58.856 33.333 0.00 0.00 0.00 3.02
3098 7665 7.595819 TTTGGGTTTGACAGTATTTTCAGAT 57.404 32.000 0.00 0.00 0.00 2.90
3100 7667 6.542821 TGGGTTTGACAGTATTTTCAGATCT 58.457 36.000 0.00 0.00 0.00 2.75
3123 7690 3.462483 AAAAACCATTCGTTTGGGGAC 57.538 42.857 10.41 0.00 44.09 4.46
3134 7701 1.268625 GTTTGGGGACGTCCAACATTC 59.731 52.381 34.40 21.58 45.48 2.67
3166 7733 5.951148 TGCATTTACTGATGGAGAATTTGGA 59.049 36.000 0.00 0.00 0.00 3.53
3170 7737 9.525409 CATTTACTGATGGAGAATTTGGATTTC 57.475 33.333 0.00 0.00 0.00 2.17
3171 7738 8.648698 TTTACTGATGGAGAATTTGGATTTCA 57.351 30.769 0.00 0.00 0.00 2.69
3172 7739 6.521151 ACTGATGGAGAATTTGGATTTCAC 57.479 37.500 0.00 0.00 0.00 3.18
3173 7740 6.012113 ACTGATGGAGAATTTGGATTTCACA 58.988 36.000 0.00 0.00 0.00 3.58
3174 7741 6.152323 ACTGATGGAGAATTTGGATTTCACAG 59.848 38.462 0.00 0.00 0.00 3.66
3175 7742 6.012113 TGATGGAGAATTTGGATTTCACAGT 58.988 36.000 0.00 0.00 0.00 3.55
3176 7743 7.174413 TGATGGAGAATTTGGATTTCACAGTA 58.826 34.615 0.00 0.00 0.00 2.74
3177 7744 7.835682 TGATGGAGAATTTGGATTTCACAGTAT 59.164 33.333 0.00 0.00 0.00 2.12
3178 7745 8.599624 ATGGAGAATTTGGATTTCACAGTATT 57.400 30.769 0.00 0.00 0.00 1.89
3179 7746 8.421249 TGGAGAATTTGGATTTCACAGTATTT 57.579 30.769 0.00 0.00 0.00 1.40
3180 7747 8.869109 TGGAGAATTTGGATTTCACAGTATTTT 58.131 29.630 0.00 0.00 0.00 1.82
3181 7748 9.710900 GGAGAATTTGGATTTCACAGTATTTTT 57.289 29.630 0.00 0.00 0.00 1.94
3187 7754 9.695526 TTTGGATTTCACAGTATTTTTCAGATG 57.304 29.630 0.00 0.00 0.00 2.90
3188 7755 8.408043 TGGATTTCACAGTATTTTTCAGATGT 57.592 30.769 0.00 0.00 0.00 3.06
3189 7756 9.513906 TGGATTTCACAGTATTTTTCAGATGTA 57.486 29.630 0.00 0.00 0.00 2.29
3213 7780 2.194201 AATCATTCGTTTGGGGACGT 57.806 45.000 0.00 0.00 43.23 4.34
3226 7793 0.036306 GGGACGTCCAACATTCCAGT 59.964 55.000 34.40 0.00 37.91 4.00
3244 7811 3.376234 CCAGTAACTGCATTCACTGATGG 59.624 47.826 18.29 3.86 40.67 3.51
3245 7812 3.376234 CAGTAACTGCATTCACTGATGGG 59.624 47.826 13.62 0.00 40.67 4.00
3246 7813 1.843368 AACTGCATTCACTGATGGGG 58.157 50.000 0.00 0.00 0.00 4.96
3247 7814 0.994247 ACTGCATTCACTGATGGGGA 59.006 50.000 0.00 0.00 0.00 4.81
3248 7815 1.355381 ACTGCATTCACTGATGGGGAA 59.645 47.619 0.00 0.00 0.00 3.97
3249 7816 2.024655 ACTGCATTCACTGATGGGGAAT 60.025 45.455 0.00 0.00 0.00 3.01
3250 7817 3.028850 CTGCATTCACTGATGGGGAATT 58.971 45.455 0.00 0.00 0.00 2.17
3251 7818 3.443052 TGCATTCACTGATGGGGAATTT 58.557 40.909 0.00 0.00 0.00 1.82
3252 7819 3.196039 TGCATTCACTGATGGGGAATTTG 59.804 43.478 0.00 0.00 0.00 2.32
3253 7820 3.431207 GCATTCACTGATGGGGAATTTGG 60.431 47.826 0.00 0.00 0.00 3.28
3254 7821 3.824001 TTCACTGATGGGGAATTTGGA 57.176 42.857 0.00 0.00 0.00 3.53
3255 7822 4.335735 TTCACTGATGGGGAATTTGGAT 57.664 40.909 0.00 0.00 0.00 3.41
3256 7823 4.335735 TCACTGATGGGGAATTTGGATT 57.664 40.909 0.00 0.00 0.00 3.01
3257 7824 4.686891 TCACTGATGGGGAATTTGGATTT 58.313 39.130 0.00 0.00 0.00 2.17
3258 7825 4.711355 TCACTGATGGGGAATTTGGATTTC 59.289 41.667 0.00 0.00 0.00 2.17
3259 7826 4.467082 CACTGATGGGGAATTTGGATTTCA 59.533 41.667 0.00 0.00 0.00 2.69
3260 7827 4.467438 ACTGATGGGGAATTTGGATTTCAC 59.533 41.667 0.00 0.00 0.00 3.18
3261 7828 4.423913 TGATGGGGAATTTGGATTTCACA 58.576 39.130 0.00 0.00 38.52 3.58
3262 7829 4.467082 TGATGGGGAATTTGGATTTCACAG 59.533 41.667 0.00 0.00 37.58 3.66
3263 7830 3.855668 TGGGGAATTTGGATTTCACAGT 58.144 40.909 0.00 0.00 28.90 3.55
3264 7831 5.004361 TGGGGAATTTGGATTTCACAGTA 57.996 39.130 0.00 0.00 28.90 2.74
3275 7842 9.695526 TTTGGATTTCACAGTATTTTTCAGATG 57.304 29.630 0.00 0.00 0.00 2.90
3278 7845 7.274250 GGATTTCACAGTATTTTTCAGATGTGC 59.726 37.037 0.00 0.00 38.29 4.57
3279 7846 5.281693 TCACAGTATTTTTCAGATGTGCG 57.718 39.130 0.00 0.00 38.29 5.34
3366 7934 1.622811 CCATCTGAGCTACATCCCCTC 59.377 57.143 0.00 0.00 0.00 4.30
3390 7958 7.082602 TCGATGTTAGCTTCCGTTAATCTATC 58.917 38.462 0.00 0.00 0.00 2.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 4.540153 AATCCACGGATTCGCTGG 57.460 55.556 5.44 8.28 40.44 4.85
48 49 0.613853 AAGGGAGACGAATCCACGGA 60.614 55.000 11.76 0.00 41.52 4.69
49 50 0.179108 GAAGGGAGACGAATCCACGG 60.179 60.000 11.76 0.00 41.52 4.94
50 51 0.818296 AGAAGGGAGACGAATCCACG 59.182 55.000 11.76 0.00 41.52 4.94
60 61 0.331954 AGCGGTAGACAGAAGGGAGA 59.668 55.000 0.00 0.00 0.00 3.71
61 62 1.135333 GAAGCGGTAGACAGAAGGGAG 59.865 57.143 0.00 0.00 0.00 4.30
62 63 1.183549 GAAGCGGTAGACAGAAGGGA 58.816 55.000 0.00 0.00 0.00 4.20
63 64 0.895530 TGAAGCGGTAGACAGAAGGG 59.104 55.000 0.00 0.00 0.00 3.95
64 65 2.743636 TTGAAGCGGTAGACAGAAGG 57.256 50.000 0.00 0.00 0.00 3.46
65 66 2.932614 CCATTGAAGCGGTAGACAGAAG 59.067 50.000 0.00 0.00 0.00 2.85
66 67 2.301870 ACCATTGAAGCGGTAGACAGAA 59.698 45.455 0.00 0.00 32.31 3.02
67 68 1.899814 ACCATTGAAGCGGTAGACAGA 59.100 47.619 0.00 0.00 32.31 3.41
68 69 2.386661 ACCATTGAAGCGGTAGACAG 57.613 50.000 0.00 0.00 32.31 3.51
69 70 2.037902 TCAACCATTGAAGCGGTAGACA 59.962 45.455 0.00 0.00 36.59 3.41
70 71 2.695359 TCAACCATTGAAGCGGTAGAC 58.305 47.619 0.00 0.00 36.59 2.59
71 72 3.627395 ATCAACCATTGAAGCGGTAGA 57.373 42.857 0.00 0.00 43.95 2.59
104 105 5.242838 GGGTTGGTAATTGATCAGAAACACA 59.757 40.000 0.00 0.00 0.00 3.72
107 108 6.590234 AAGGGTTGGTAATTGATCAGAAAC 57.410 37.500 0.00 0.00 0.00 2.78
113 114 5.023452 AGGGAAAAGGGTTGGTAATTGATC 58.977 41.667 0.00 0.00 0.00 2.92
138 139 5.875359 GGGAATTATAAACTCTAGCCATCGG 59.125 44.000 0.00 0.00 0.00 4.18
179 180 4.408821 GGCACATCCACGGGCTCA 62.409 66.667 0.00 0.00 34.01 4.26
192 193 1.452833 GATGGGCAGAAGGAGGCAC 60.453 63.158 0.00 0.00 0.00 5.01
193 194 3.001514 GATGGGCAGAAGGAGGCA 58.998 61.111 0.00 0.00 0.00 4.75
209 211 2.264480 CATCGGCCACTGGAACGA 59.736 61.111 15.07 15.07 37.82 3.85
212 214 2.350895 CACCATCGGCCACTGGAA 59.649 61.111 23.87 0.00 36.35 3.53
240 242 1.975407 CAAAGCAGAGGCACCAGGG 60.975 63.158 0.00 0.00 44.61 4.45
316 322 3.016736 ACCAACTCAACAAAGGAGTGTG 58.983 45.455 0.00 0.00 44.50 3.82
338 344 1.068250 GAGGATCGAAGCCGGGAAG 59.932 63.158 2.18 0.00 36.24 3.46
343 349 3.099267 ACTAAATGAGGATCGAAGCCG 57.901 47.619 0.00 0.00 38.61 5.52
357 363 2.919228 GGCCAGATGGACGAACTAAAT 58.081 47.619 2.18 0.00 37.39 1.40
376 382 0.917259 CGAAGCTCTGTCGATTTCGG 59.083 55.000 0.00 0.00 41.02 4.30
398 404 5.186198 CCCAAAGAAACGAGAGGAATGTAT 58.814 41.667 0.00 0.00 0.00 2.29
413 419 2.114488 TAACCTCGCGCCCCAAAGAA 62.114 55.000 0.00 0.00 0.00 2.52
465 472 4.804139 CGACCTAAAGTGTGTGATACCATC 59.196 45.833 0.00 0.00 0.00 3.51
471 478 5.147330 TGAATCGACCTAAAGTGTGTGAT 57.853 39.130 0.00 0.00 0.00 3.06
475 482 3.684788 CCCTTGAATCGACCTAAAGTGTG 59.315 47.826 0.00 0.00 0.00 3.82
476 483 3.326880 ACCCTTGAATCGACCTAAAGTGT 59.673 43.478 0.00 0.00 0.00 3.55
506 513 1.675310 CCTGGAGCCGCAATCAACA 60.675 57.895 0.00 0.00 0.00 3.33
508 515 2.045045 CCCTGGAGCCGCAATCAA 60.045 61.111 0.00 0.00 0.00 2.57
530 537 2.534903 GCGCGTGCCCTTTAGGATC 61.535 63.158 10.56 0.00 38.24 3.36
531 538 2.513897 GCGCGTGCCCTTTAGGAT 60.514 61.111 10.56 0.00 38.24 3.24
536 543 2.981560 CTTCATGCGCGTGCCCTTT 61.982 57.895 24.82 0.00 41.78 3.11
581 588 0.755698 TCACCTATCGGAGCCAGACC 60.756 60.000 0.00 0.00 0.00 3.85
583 590 3.117657 CTCACCTATCGGAGCCAGA 57.882 57.895 0.00 0.00 0.00 3.86
593 600 0.031314 CGATGTCGCAGCTCACCTAT 59.969 55.000 0.00 0.00 0.00 2.57
603 610 2.405805 CCAATTGGCCGATGTCGCA 61.406 57.895 12.53 0.00 38.18 5.10
629 636 1.610522 CGACCAATACTACCGGTAGGG 59.389 57.143 37.97 31.03 43.47 3.53
634 641 3.123959 CACAAAACGACCAATACTACCGG 59.876 47.826 0.00 0.00 0.00 5.28
648 655 6.256975 TCGAGATATTTATGGACCACAAAACG 59.743 38.462 1.23 4.39 0.00 3.60
653 660 6.419484 ACATCGAGATATTTATGGACCACA 57.581 37.500 0.00 0.00 0.00 4.17
740 752 9.161629 GAAAACATTTCCTTCTTTTTCTTTGGA 57.838 29.630 0.00 0.00 34.66 3.53
746 758 8.765219 GCCTAAGAAAACATTTCCTTCTTTTTC 58.235 33.333 1.98 0.00 39.50 2.29
751 763 6.976934 TTGCCTAAGAAAACATTTCCTTCT 57.023 33.333 0.00 0.00 0.00 2.85
755 767 9.875691 AATATCTTTGCCTAAGAAAACATTTCC 57.124 29.630 2.89 0.00 45.62 3.13
1038 1062 3.072468 TTCTCCGGGTTCGCCGAT 61.072 61.111 0.00 0.00 38.45 4.18
1366 1394 1.676746 TCTGTAGTAGCTACGGCAGG 58.323 55.000 31.36 20.95 41.58 4.85
1381 1409 9.874205 TTTTTCTGAGAAAAATGACAAATCTGT 57.126 25.926 24.62 0.00 38.98 3.41
1408 1438 9.965902 ATGTAGTGATAAATCTGAAGGTTCTTT 57.034 29.630 0.00 0.00 0.00 2.52
1414 1444 8.400947 CCACAAATGTAGTGATAAATCTGAAGG 58.599 37.037 0.00 0.00 39.30 3.46
1429 1459 2.026641 CATCAGCCCCCACAAATGTAG 58.973 52.381 0.00 0.00 0.00 2.74
1437 1467 1.147153 GACTAGCATCAGCCCCCAC 59.853 63.158 0.00 0.00 43.56 4.61
1467 1497 3.089284 ACCCCTACAAGCTAAAACATGC 58.911 45.455 0.00 0.00 0.00 4.06
1553 1672 8.584063 TCTGTAAATACACTATCCAGTACACA 57.416 34.615 0.00 0.00 32.21 3.72
1617 1736 3.165071 CAAACCCCTTTTGATGCCTACT 58.835 45.455 0.00 0.00 46.76 2.57
1681 1800 2.615391 TCCAGTTCCAGTACACATCCA 58.385 47.619 0.00 0.00 0.00 3.41
1686 1805 2.367567 TCCAGTTCCAGTTCCAGTACAC 59.632 50.000 0.00 0.00 0.00 2.90
1687 1806 2.684943 TCCAGTTCCAGTTCCAGTACA 58.315 47.619 0.00 0.00 0.00 2.90
1688 1807 3.071167 AGTTCCAGTTCCAGTTCCAGTAC 59.929 47.826 0.00 0.00 0.00 2.73
1689 1808 3.071023 CAGTTCCAGTTCCAGTTCCAGTA 59.929 47.826 0.00 0.00 0.00 2.74
1691 1810 2.158755 ACAGTTCCAGTTCCAGTTCCAG 60.159 50.000 0.00 0.00 0.00 3.86
1693 1812 2.222027 CACAGTTCCAGTTCCAGTTCC 58.778 52.381 0.00 0.00 0.00 3.62
1694 1813 2.919228 ACACAGTTCCAGTTCCAGTTC 58.081 47.619 0.00 0.00 0.00 3.01
1832 1959 1.725931 GCGTTGCATACAGTGAAGCAC 60.726 52.381 0.00 0.00 36.62 4.40
1850 1977 6.088173 TGCATATTAGTACATAACCTACGCG 58.912 40.000 3.53 3.53 0.00 6.01
1987 2119 4.367166 TGTAAATCCTGTGATCCTACCCA 58.633 43.478 0.00 0.00 0.00 4.51
2049 2181 4.456911 GGATCAGCTCAATTTCAACACAGA 59.543 41.667 0.00 0.00 0.00 3.41
2107 2291 3.128698 GGTACCACCAAGTGAAGAGCAC 61.129 54.545 7.15 0.00 42.24 4.40
2108 2292 1.071699 GGTACCACCAAGTGAAGAGCA 59.928 52.381 7.15 0.00 38.42 4.26
2109 2293 1.809684 GGTACCACCAAGTGAAGAGC 58.190 55.000 7.15 0.00 38.42 4.09
2110 2294 1.343465 ACGGTACCACCAAGTGAAGAG 59.657 52.381 13.54 0.00 38.47 2.85
2112 2296 2.680577 GTACGGTACCACCAAGTGAAG 58.319 52.381 13.54 0.00 38.47 3.02
2113 2297 2.818130 GTACGGTACCACCAAGTGAA 57.182 50.000 13.54 0.00 38.47 3.18
2124 2308 2.612212 CAAATGCTCATGGGTACGGTAC 59.388 50.000 9.82 9.82 0.00 3.34
2125 2309 2.912771 CAAATGCTCATGGGTACGGTA 58.087 47.619 0.00 0.00 0.00 4.02
2126 2310 1.750193 CAAATGCTCATGGGTACGGT 58.250 50.000 0.00 0.00 0.00 4.83
2127 2311 0.381801 GCAAATGCTCATGGGTACGG 59.618 55.000 0.00 0.00 38.21 4.02
2128 2312 0.381801 GGCAAATGCTCATGGGTACG 59.618 55.000 5.25 0.00 41.70 3.67
2129 2313 1.767759 AGGCAAATGCTCATGGGTAC 58.232 50.000 5.25 0.00 41.70 3.34
2130 2314 2.378038 GAAGGCAAATGCTCATGGGTA 58.622 47.619 5.25 0.00 41.70 3.69
2131 2315 1.188863 GAAGGCAAATGCTCATGGGT 58.811 50.000 5.25 0.00 41.70 4.51
2132 2316 0.462789 GGAAGGCAAATGCTCATGGG 59.537 55.000 5.25 0.00 41.70 4.00
2133 2317 1.481871 AGGAAGGCAAATGCTCATGG 58.518 50.000 5.25 0.00 41.70 3.66
2134 2318 2.758979 AGAAGGAAGGCAAATGCTCATG 59.241 45.455 5.25 0.00 41.70 3.07
2135 2319 3.097342 AGAAGGAAGGCAAATGCTCAT 57.903 42.857 5.25 0.00 41.70 2.90
2136 2320 2.559668 CAAGAAGGAAGGCAAATGCTCA 59.440 45.455 5.25 0.00 41.70 4.26
2137 2321 2.821969 TCAAGAAGGAAGGCAAATGCTC 59.178 45.455 5.25 0.00 41.70 4.26
2138 2322 2.880443 TCAAGAAGGAAGGCAAATGCT 58.120 42.857 5.25 0.00 41.70 3.79
2139 2323 3.243839 TGTTCAAGAAGGAAGGCAAATGC 60.244 43.478 0.00 0.00 41.14 3.56
2140 2324 4.038402 ACTGTTCAAGAAGGAAGGCAAATG 59.962 41.667 0.00 0.00 0.00 2.32
2141 2325 4.218312 ACTGTTCAAGAAGGAAGGCAAAT 58.782 39.130 0.00 0.00 0.00 2.32
2142 2326 3.631250 ACTGTTCAAGAAGGAAGGCAAA 58.369 40.909 0.00 0.00 0.00 3.68
2143 2327 3.297134 ACTGTTCAAGAAGGAAGGCAA 57.703 42.857 0.00 0.00 0.00 4.52
2144 2328 2.951642 CAACTGTTCAAGAAGGAAGGCA 59.048 45.455 0.00 0.00 0.00 4.75
2145 2329 2.294512 CCAACTGTTCAAGAAGGAAGGC 59.705 50.000 0.00 0.00 0.00 4.35
2146 2330 3.820557 TCCAACTGTTCAAGAAGGAAGG 58.179 45.455 0.00 0.00 32.12 3.46
2147 2331 5.065914 TGATCCAACTGTTCAAGAAGGAAG 58.934 41.667 0.00 0.00 36.46 3.46
2148 2332 5.047566 TGATCCAACTGTTCAAGAAGGAA 57.952 39.130 0.00 0.00 36.46 3.36
2149 2333 4.705110 TGATCCAACTGTTCAAGAAGGA 57.295 40.909 0.00 0.00 37.00 3.36
2161 2345 4.858850 TGTCAGCCAAATATGATCCAACT 58.141 39.130 0.00 0.00 0.00 3.16
2169 2353 4.142315 CCTTGAGGTTGTCAGCCAAATATG 60.142 45.833 8.59 0.00 36.21 1.78
2179 2363 1.142667 TGTCATGCCTTGAGGTTGTCA 59.857 47.619 0.00 0.00 34.17 3.58
2180 2364 1.808945 CTGTCATGCCTTGAGGTTGTC 59.191 52.381 0.00 0.00 34.17 3.18
2196 2380 1.267533 TGTGCATTGATGTGTGCTGTC 59.732 47.619 0.00 0.00 41.78 3.51
2205 2389 3.224884 TGTGAGCAATGTGCATTGATG 57.775 42.857 24.10 3.95 46.10 3.07
2222 2406 2.426738 TGCTCCTGGTTCTTTTGTTGTG 59.573 45.455 0.00 0.00 0.00 3.33
2223 2407 2.427095 GTGCTCCTGGTTCTTTTGTTGT 59.573 45.455 0.00 0.00 0.00 3.32
2226 2410 2.435372 TGTGCTCCTGGTTCTTTTGT 57.565 45.000 0.00 0.00 0.00 2.83
2233 2417 1.392589 CACTGTTTGTGCTCCTGGTT 58.607 50.000 0.00 0.00 40.06 3.67
2252 2436 2.964768 CTCGACAAAAACTAAACAGCGC 59.035 45.455 0.00 0.00 0.00 5.92
2259 2443 6.044046 TGTAGAACTGCTCGACAAAAACTAA 58.956 36.000 0.00 0.00 36.81 2.24
2267 2451 4.357018 CAGTATGTAGAACTGCTCGACA 57.643 45.455 0.00 0.00 42.90 4.35
2304 2488 9.755804 TGCATCAATAAATTTACAGTTGTCAAA 57.244 25.926 0.00 0.00 0.00 2.69
2305 2489 9.190858 GTGCATCAATAAATTTACAGTTGTCAA 57.809 29.630 0.00 0.00 0.00 3.18
2306 2490 7.812191 GGTGCATCAATAAATTTACAGTTGTCA 59.188 33.333 0.00 2.79 0.00 3.58
2307 2491 7.812191 TGGTGCATCAATAAATTTACAGTTGTC 59.188 33.333 0.00 0.69 0.00 3.18
2308 2492 7.665690 TGGTGCATCAATAAATTTACAGTTGT 58.334 30.769 0.00 0.00 0.00 3.32
2309 2493 8.597227 CATGGTGCATCAATAAATTTACAGTTG 58.403 33.333 2.42 2.12 0.00 3.16
2310 2494 7.765360 CCATGGTGCATCAATAAATTTACAGTT 59.235 33.333 2.42 0.00 0.00 3.16
2311 2495 7.267128 CCATGGTGCATCAATAAATTTACAGT 58.733 34.615 2.42 0.00 0.00 3.55
2312 2496 6.201425 GCCATGGTGCATCAATAAATTTACAG 59.799 38.462 14.67 0.00 0.00 2.74
2373 3953 0.178767 CATGTTCCTCCTCGGCATCA 59.821 55.000 0.00 0.00 0.00 3.07
2510 5761 2.125512 GCGCCACGAGGAGACAAT 60.126 61.111 6.84 0.00 36.74 2.71
2511 5762 3.303135 AGCGCCACGAGGAGACAA 61.303 61.111 2.29 0.00 36.74 3.18
2520 5771 0.794229 CTGCATAAAACAGCGCCACG 60.794 55.000 2.29 0.00 0.00 4.94
2546 5799 1.458827 CAAGACTTTCTCAGCGCTGTC 59.541 52.381 34.70 23.72 0.00 3.51
2551 5804 3.902150 TCTACACAAGACTTTCTCAGCG 58.098 45.455 0.00 0.00 0.00 5.18
2558 5811 5.468072 CACATGAGCTTCTACACAAGACTTT 59.532 40.000 0.00 0.00 32.51 2.66
2559 5812 4.993584 CACATGAGCTTCTACACAAGACTT 59.006 41.667 0.00 0.00 32.51 3.01
2579 5832 1.832883 AGTGCAAGGACAACAACACA 58.167 45.000 0.00 0.00 0.00 3.72
2580 5833 2.163412 TCAAGTGCAAGGACAACAACAC 59.837 45.455 0.00 0.00 0.00 3.32
2600 5853 7.987458 TGTGAAGACATCCAGGTAAGAAATATC 59.013 37.037 0.00 0.00 0.00 1.63
2608 5861 3.389656 TGTGTGTGAAGACATCCAGGTAA 59.610 43.478 0.00 0.00 33.63 2.85
2615 5868 5.235305 AGTTGTTTGTGTGTGAAGACATC 57.765 39.130 0.00 0.00 33.63 3.06
2636 5890 7.811653 TCAAACGAGAGCTATACATCTCATAG 58.188 38.462 9.17 0.00 41.71 2.23
2698 5953 5.567138 ACACAACAGAACAGAAAAAGAGG 57.433 39.130 0.00 0.00 0.00 3.69
2728 5983 0.540923 GTCTCCAATGCTGAGAGCCT 59.459 55.000 0.00 0.00 41.51 4.58
2761 6902 3.509184 GCTTTCCATTTCTTCAGGAGCTT 59.491 43.478 0.00 0.00 32.11 3.74
2813 6956 4.613031 GCGTGAGAAAAAGCTAAACATCAC 59.387 41.667 9.91 9.91 34.03 3.06
2898 7041 0.662374 CAAGCAAGCAAAGTGGAGCG 60.662 55.000 0.00 0.00 35.48 5.03
2908 7051 1.073722 CTCCCCTCACAAGCAAGCA 59.926 57.895 0.00 0.00 0.00 3.91
2986 7535 8.396390 GCTTCAGCAAATATCACCATATATCTG 58.604 37.037 0.00 0.00 41.59 2.90
3014 7563 0.110678 ATCAGACCGGAGCGATCCTA 59.889 55.000 19.08 0.00 0.00 2.94
3025 7592 6.036083 CCACAGTACAAGAAATAATCAGACCG 59.964 42.308 0.00 0.00 0.00 4.79
3035 7602 3.821033 GCAGTTCCCACAGTACAAGAAAT 59.179 43.478 0.00 0.00 0.00 2.17
3039 7606 2.254546 TGCAGTTCCCACAGTACAAG 57.745 50.000 0.00 0.00 0.00 3.16
3051 7618 3.668447 TCTCCTCAAGTGAATGCAGTTC 58.332 45.455 0.00 0.00 35.52 3.01
3053 7620 3.996921 ATCTCCTCAAGTGAATGCAGT 57.003 42.857 0.00 0.00 0.00 4.40
3055 7622 4.219070 CCAAAATCTCCTCAAGTGAATGCA 59.781 41.667 0.00 0.00 0.00 3.96
3058 7625 5.003096 ACCCAAAATCTCCTCAAGTGAAT 57.997 39.130 0.00 0.00 0.00 2.57
3060 7627 4.453480 AACCCAAAATCTCCTCAAGTGA 57.547 40.909 0.00 0.00 0.00 3.41
3061 7628 4.584325 TCAAACCCAAAATCTCCTCAAGTG 59.416 41.667 0.00 0.00 0.00 3.16
3062 7629 4.584743 GTCAAACCCAAAATCTCCTCAAGT 59.415 41.667 0.00 0.00 0.00 3.16
3063 7630 4.584325 TGTCAAACCCAAAATCTCCTCAAG 59.416 41.667 0.00 0.00 0.00 3.02
3068 7635 6.590234 AATACTGTCAAACCCAAAATCTCC 57.410 37.500 0.00 0.00 0.00 3.71
3069 7636 8.141268 TGAAAATACTGTCAAACCCAAAATCTC 58.859 33.333 0.00 0.00 0.00 2.75
3071 7638 8.141268 TCTGAAAATACTGTCAAACCCAAAATC 58.859 33.333 0.00 0.00 0.00 2.17
3074 7641 7.505585 AGATCTGAAAATACTGTCAAACCCAAA 59.494 33.333 0.00 0.00 0.00 3.28
3075 7642 7.004086 AGATCTGAAAATACTGTCAAACCCAA 58.996 34.615 0.00 0.00 0.00 4.12
3076 7643 6.542821 AGATCTGAAAATACTGTCAAACCCA 58.457 36.000 0.00 0.00 0.00 4.51
3077 7644 8.561738 TTAGATCTGAAAATACTGTCAAACCC 57.438 34.615 5.18 0.00 0.00 4.11
3104 7671 1.338655 CGTCCCCAAACGAATGGTTTT 59.661 47.619 9.73 0.00 46.52 2.43
3106 7673 0.179012 ACGTCCCCAAACGAATGGTT 60.179 50.000 3.16 0.00 45.37 3.67
3107 7674 0.604511 GACGTCCCCAAACGAATGGT 60.605 55.000 3.51 0.00 45.37 3.55
3122 7689 3.399330 CAGTTACTGGAATGTTGGACGT 58.601 45.455 4.14 0.00 0.00 4.34
3123 7690 2.159627 GCAGTTACTGGAATGTTGGACG 59.840 50.000 14.63 0.00 31.21 4.79
3153 7720 8.599624 AATACTGTGAAATCCAAATTCTCCAT 57.400 30.769 0.00 0.00 0.00 3.41
3211 7778 2.159627 GCAGTTACTGGAATGTTGGACG 59.840 50.000 14.63 0.00 31.21 4.79
3213 7780 3.500448 TGCAGTTACTGGAATGTTGGA 57.500 42.857 14.63 0.00 31.21 3.53
3226 7793 2.575735 TCCCCATCAGTGAATGCAGTTA 59.424 45.455 0.00 0.00 0.00 2.24
3244 7811 8.846943 AAAAATACTGTGAAATCCAAATTCCC 57.153 30.769 0.00 0.00 0.00 3.97
3245 7812 9.487790 TGAAAAATACTGTGAAATCCAAATTCC 57.512 29.630 0.00 0.00 0.00 3.01
3249 7816 9.695526 CATCTGAAAAATACTGTGAAATCCAAA 57.304 29.630 0.00 0.00 0.00 3.28
3250 7817 8.859090 ACATCTGAAAAATACTGTGAAATCCAA 58.141 29.630 0.00 0.00 0.00 3.53
3251 7818 8.298854 CACATCTGAAAAATACTGTGAAATCCA 58.701 33.333 0.24 0.00 36.89 3.41
3252 7819 7.274250 GCACATCTGAAAAATACTGTGAAATCC 59.726 37.037 8.93 0.00 36.89 3.01
3253 7820 7.007725 CGCACATCTGAAAAATACTGTGAAATC 59.992 37.037 8.93 0.00 36.89 2.17
3254 7821 6.803320 CGCACATCTGAAAAATACTGTGAAAT 59.197 34.615 8.93 0.00 36.89 2.17
3255 7822 6.017523 TCGCACATCTGAAAAATACTGTGAAA 60.018 34.615 8.93 0.00 36.89 2.69
3256 7823 5.468409 TCGCACATCTGAAAAATACTGTGAA 59.532 36.000 8.93 0.00 36.89 3.18
3257 7824 4.994217 TCGCACATCTGAAAAATACTGTGA 59.006 37.500 8.93 0.00 36.89 3.58
3258 7825 5.281693 TCGCACATCTGAAAAATACTGTG 57.718 39.130 1.91 1.91 37.60 3.66
3259 7826 5.940192 TTCGCACATCTGAAAAATACTGT 57.060 34.783 0.00 0.00 0.00 3.55
3260 7827 7.621832 TTTTTCGCACATCTGAAAAATACTG 57.378 32.000 8.34 0.00 44.61 2.74
3287 7854 3.449737 CGATACCCCACTTCTCCACTTAA 59.550 47.826 0.00 0.00 0.00 1.85
3291 7859 1.481871 TCGATACCCCACTTCTCCAC 58.518 55.000 0.00 0.00 0.00 4.02
3366 7934 7.085116 AGATAGATTAACGGAAGCTAACATCG 58.915 38.462 2.06 0.00 39.41 3.84


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

AutoCloner maintained by Alex Coulton.