Multiple sequence alignment - TraesCS2B01G176000

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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 TraesCS2B01G176000 chr2B 100.000 2097 0 0 1 2097 150986518 150984422 0.000000e+00 3873.0
1 TraesCS2B01G176000 chr2B 100.000 383 0 0 2293 2675 150984226 150983844 0.000000e+00 708.0
2 TraesCS2B01G176000 chr2B 89.808 520 36 9 1283 1791 150948353 150947840 0.000000e+00 651.0
3 TraesCS2B01G176000 chr2B 87.500 368 41 3 1283 1646 151627925 151627559 1.150000e-113 420.0
4 TraesCS2B01G176000 chr2B 92.771 83 6 0 1207 1289 30636963 30636881 1.300000e-23 121.0
5 TraesCS2B01G176000 chr2A 87.137 1205 72 27 1 1175 98896168 98897319 0.000000e+00 1290.0
6 TraesCS2B01G176000 chr2A 88.421 570 52 9 1283 1840 98908209 98908776 0.000000e+00 675.0
7 TraesCS2B01G176000 chr2A 87.356 522 52 7 1283 1791 98903312 98903832 1.070000e-163 586.0
8 TraesCS2B01G176000 chr2A 89.254 456 43 5 1640 2095 98898070 98898519 1.390000e-157 566.0
9 TraesCS2B01G176000 chr2A 86.141 368 46 3 1283 1646 99159568 99159202 2.500000e-105 392.0
10 TraesCS2B01G176000 chr2A 85.399 363 53 0 1284 1646 19914173 19914535 6.990000e-101 377.0
11 TraesCS2B01G176000 chr2A 87.209 258 26 2 1032 1289 98907887 98908137 1.210000e-73 287.0
12 TraesCS2B01G176000 chr2A 83.710 221 28 6 1071 1288 98903024 98903239 4.520000e-48 202.0
13 TraesCS2B01G176000 chr2A 92.771 83 6 0 1207 1289 19914018 19914100 1.300000e-23 121.0
14 TraesCS2B01G176000 chr2A 92.771 83 6 0 1207 1289 19928860 19928942 1.300000e-23 121.0
15 TraesCS2B01G176000 chr2A 100.000 33 0 0 135 167 35949827 35949795 8.000000e-06 62.1
16 TraesCS2B01G176000 chr2D 90.831 698 30 16 597 1289 99682867 99683535 0.000000e+00 904.0
17 TraesCS2B01G176000 chr2D 96.060 533 21 0 1283 1815 99683607 99684139 0.000000e+00 869.0
18 TraesCS2B01G176000 chr2D 93.206 471 19 6 1 463 99682362 99682827 0.000000e+00 680.0
19 TraesCS2B01G176000 chr2D 88.269 520 48 7 1283 1791 99703861 99704378 6.330000e-171 610.0
20 TraesCS2B01G176000 chr2D 87.500 368 41 3 1283 1646 99737105 99736739 1.150000e-113 420.0
21 TraesCS2B01G176000 chr2D 90.975 277 18 3 1815 2091 99690470 99690739 1.510000e-97 366.0
22 TraesCS2B01G176000 chr2D 90.547 201 16 2 2473 2672 626173950 626174148 2.040000e-66 263.0
23 TraesCS2B01G176000 chr2D 85.644 202 23 4 1089 1288 99703591 99703788 9.710000e-50 207.0
24 TraesCS2B01G176000 chr2D 81.517 211 26 12 2302 2506 626173731 626173934 7.660000e-36 161.0
25 TraesCS2B01G176000 chr4A 97.867 375 7 1 2302 2675 616614275 616613901 0.000000e+00 647.0
26 TraesCS2B01G176000 chr4A 97.872 376 5 2 2302 2675 665695511 665695137 0.000000e+00 647.0
27 TraesCS2B01G176000 chr5A 97.082 377 8 2 2302 2675 568057649 568058025 1.350000e-177 632.0
28 TraesCS2B01G176000 chr5A 87.736 106 9 4 177 280 444533245 444533142 1.300000e-23 121.0
29 TraesCS2B01G176000 chr7B 97.074 376 8 3 2301 2675 613624357 613623984 4.860000e-177 630.0
30 TraesCS2B01G176000 chr7B 90.196 102 8 2 178 278 44939653 44939553 6.010000e-27 132.0
31 TraesCS2B01G176000 chr7D 90.686 204 18 1 2473 2675 83748186 83747983 1.220000e-68 270.0
32 TraesCS2B01G176000 chr7D 79.268 246 17 10 2298 2536 39586857 39587075 9.980000e-30 141.0
33 TraesCS2B01G176000 chr7D 85.542 83 8 3 2431 2509 83748281 83748199 1.710000e-12 84.2
34 TraesCS2B01G176000 chr1D 91.500 200 12 3 2473 2671 362341392 362341197 1.220000e-68 270.0
35 TraesCS2B01G176000 chr1D 89.103 156 15 1 2302 2457 5248921 5249074 2.720000e-45 193.0
36 TraesCS2B01G176000 chr1D 80.841 214 28 11 2301 2509 362341610 362341405 3.570000e-34 156.0
37 TraesCS2B01G176000 chr1D 88.571 105 10 2 177 280 305226395 305226292 2.800000e-25 126.0
38 TraesCS2B01G176000 chr3B 91.339 127 10 1 2545 2670 64417051 64417177 3.540000e-39 172.0
39 TraesCS2B01G176000 chr3B 86.395 147 19 1 2524 2669 683361185 683361331 2.760000e-35 159.0
40 TraesCS2B01G176000 chr3B 89.691 97 8 2 177 272 654432402 654432497 3.620000e-24 122.0
41 TraesCS2B01G176000 chr3B 89.000 100 6 3 2302 2396 683361031 683361130 4.680000e-23 119.0
42 TraesCS2B01G176000 chr6B 90.385 104 8 2 178 280 537553940 537553838 4.650000e-28 135.0
43 TraesCS2B01G176000 chr3D 87.500 104 10 3 176 277 482857318 482857420 1.680000e-22 117.0
44 TraesCS2B01G176000 chrUn 91.566 83 7 0 1207 1289 24377304 24377222 6.050000e-22 115.0
45 TraesCS2B01G176000 chrUn 86.667 105 8 5 1187 1289 24365462 24365362 7.830000e-21 111.0
46 TraesCS2B01G176000 chr3A 86.538 104 12 2 178 280 514492542 514492440 2.180000e-21 113.0
47 TraesCS2B01G176000 chr1B 79.333 150 21 8 132 276 1733434 1733290 2.190000e-16 97.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G176000 chr2B 150983844 150986518 2674 True 2290.500000 3873 100.000000 1 2675 2 chr2B.!!$R4 2674
1 TraesCS2B01G176000 chr2B 150947840 150948353 513 True 651.000000 651 89.808000 1283 1791 1 chr2B.!!$R2 508
2 TraesCS2B01G176000 chr2A 98896168 98898519 2351 False 928.000000 1290 88.195500 1 2095 2 chr2A.!!$F3 2094
3 TraesCS2B01G176000 chr2A 98907887 98908776 889 False 481.000000 675 87.815000 1032 1840 2 chr2A.!!$F5 808
4 TraesCS2B01G176000 chr2A 98903024 98903832 808 False 394.000000 586 85.533000 1071 1791 2 chr2A.!!$F4 720
5 TraesCS2B01G176000 chr2A 19914018 19914535 517 False 249.000000 377 89.085000 1207 1646 2 chr2A.!!$F2 439
6 TraesCS2B01G176000 chr2D 99682362 99684139 1777 False 817.666667 904 93.365667 1 1815 3 chr2D.!!$F2 1814
7 TraesCS2B01G176000 chr2D 99703591 99704378 787 False 408.500000 610 86.956500 1089 1791 2 chr2D.!!$F3 702

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
278 293 1.617322 TCTGTGAACGAGGCAGTACT 58.383 50.0 0.0 0.0 0.0 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2014 2842 0.682855 CTCTTCTCCCTCACCGCTCT 60.683 60.0 0.0 0.0 0.0 4.09 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
69 70 4.678509 TGATTTAGTGAAATGGACGCAC 57.321 40.909 0.00 0.00 35.33 5.34
111 112 8.439971 AGAATATTGTTGGCTTGGTATGATCTA 58.560 33.333 0.00 0.00 0.00 1.98
142 144 5.347978 TCTAGGCCTTAAAAACTACTCCCT 58.652 41.667 12.58 0.00 0.00 4.20
204 218 5.277974 CGGACTGAAATGAGTGAACAAACAT 60.278 40.000 0.00 0.00 0.00 2.71
278 293 1.617322 TCTGTGAACGAGGCAGTACT 58.383 50.000 0.00 0.00 0.00 2.73
279 294 2.786777 TCTGTGAACGAGGCAGTACTA 58.213 47.619 0.00 0.00 0.00 1.82
280 295 2.486982 TCTGTGAACGAGGCAGTACTAC 59.513 50.000 0.00 0.00 0.00 2.73
281 296 2.488545 CTGTGAACGAGGCAGTACTACT 59.511 50.000 0.00 0.00 0.00 2.57
324 360 8.564509 ACTTATTTAATTTGCCATGCATTGTT 57.435 26.923 0.00 0.00 38.76 2.83
395 431 7.095774 CCGCGTAACATATATATATCCTTTGGC 60.096 40.741 4.92 2.68 0.00 4.52
450 486 5.163457 TGGTATGACTTTATCGTCAGCATCA 60.163 40.000 0.00 0.00 46.07 3.07
467 503 5.412594 CAGCATCAGCCTAAAAGAACACTTA 59.587 40.000 0.00 0.00 43.56 2.24
495 531 6.534436 TCACATGCATGCAATTTTATACAACC 59.466 34.615 26.68 0.00 0.00 3.77
496 532 6.313164 CACATGCATGCAATTTTATACAACCA 59.687 34.615 26.68 0.00 0.00 3.67
502 538 3.857093 GCAATTTTATACAACCACCTGCG 59.143 43.478 0.00 0.00 0.00 5.18
539 576 4.315803 TCCTTTGTCATTTCGGACTCTTC 58.684 43.478 0.00 0.00 38.61 2.87
558 595 2.225467 TCGTTCCATTGTGCATGTTGA 58.775 42.857 0.00 0.00 0.00 3.18
593 630 2.052237 GCGTTGTGTGCACCTTCG 60.052 61.111 15.69 14.35 0.00 3.79
667 707 5.007332 ACGAGGTGAGATTTACAACAACAAC 59.993 40.000 0.00 0.00 0.00 3.32
687 732 5.687285 ACAACAAAAACTTTCATGATCGAGC 59.313 36.000 0.00 0.00 0.00 5.03
694 739 7.938563 AAACTTTCATGATCGAGCTCTATAC 57.061 36.000 12.85 1.91 0.00 1.47
697 742 7.721402 ACTTTCATGATCGAGCTCTATACTTT 58.279 34.615 12.85 0.00 0.00 2.66
699 744 8.948631 TTTCATGATCGAGCTCTATACTTTTT 57.051 30.769 12.85 0.00 0.00 1.94
735 785 4.837896 AACAGAGTAGAAAGCAAAAGGC 57.162 40.909 0.00 0.00 45.30 4.35
802 852 5.883115 TGTTTAGGTCCAATGCGATAATGAA 59.117 36.000 0.00 0.00 0.00 2.57
813 863 5.456548 TGCGATAATGAAATCATGCCAAT 57.543 34.783 0.00 0.00 36.56 3.16
857 907 2.515290 TAGCGTCGATCTGCGGGA 60.515 61.111 0.00 0.00 41.33 5.14
990 1040 3.567797 GCGCATGCTCGAGTTCCC 61.568 66.667 17.13 0.00 38.39 3.97
991 1041 2.185350 CGCATGCTCGAGTTCCCT 59.815 61.111 17.13 0.00 0.00 4.20
992 1042 1.880340 CGCATGCTCGAGTTCCCTC 60.880 63.158 17.13 0.00 0.00 4.30
1021 1072 3.216147 ACACAACAGCAACAAGAACAC 57.784 42.857 0.00 0.00 0.00 3.32
1022 1073 2.094752 ACACAACAGCAACAAGAACACC 60.095 45.455 0.00 0.00 0.00 4.16
1023 1074 1.132262 ACAACAGCAACAAGAACACCG 59.868 47.619 0.00 0.00 0.00 4.94
1024 1075 1.400142 CAACAGCAACAAGAACACCGA 59.600 47.619 0.00 0.00 0.00 4.69
1025 1076 1.967319 ACAGCAACAAGAACACCGAT 58.033 45.000 0.00 0.00 0.00 4.18
1026 1077 1.873591 ACAGCAACAAGAACACCGATC 59.126 47.619 0.00 0.00 0.00 3.69
1027 1078 1.136252 CAGCAACAAGAACACCGATCG 60.136 52.381 8.51 8.51 0.00 3.69
1028 1079 0.865769 GCAACAAGAACACCGATCGT 59.134 50.000 15.09 0.00 0.00 3.73
1029 1080 1.136336 GCAACAAGAACACCGATCGTC 60.136 52.381 15.09 4.78 0.00 4.20
1030 1081 1.459592 CAACAAGAACACCGATCGTCC 59.540 52.381 15.09 0.00 0.00 4.79
1179 1231 1.841302 ATGTTCCTGCTCGCCTTGGA 61.841 55.000 0.00 0.00 0.00 3.53
1339 1469 2.603473 CTGGTCACGGAGGGGACA 60.603 66.667 0.00 0.00 37.61 4.02
1405 1535 6.041296 AGGGTTTCTACTTCTACGACAAGAAA 59.959 38.462 0.00 0.00 35.14 2.52
1408 1538 7.650903 GGTTTCTACTTCTACGACAAGAAAGAA 59.349 37.037 0.00 0.28 35.14 2.52
1420 1550 3.805422 ACAAGAAAGAATCGTACAACGCA 59.195 39.130 0.00 0.00 42.21 5.24
1774 2601 2.166821 TGGGCATGTGAATTTTGTGC 57.833 45.000 0.00 0.00 35.17 4.57
1780 2607 3.125658 GCATGTGAATTTTGTGCCATTCC 59.874 43.478 0.00 0.00 0.00 3.01
1810 2637 2.614983 TCACGCCCACAAGAGTTTTAAC 59.385 45.455 0.00 0.00 0.00 2.01
1830 2658 9.562583 TTTTAACCGTATGATGTTTTATTCTGC 57.437 29.630 0.00 0.00 0.00 4.26
1898 2726 6.639671 TTCTTTTGACAATTTGTTTCACCG 57.360 33.333 3.08 0.00 0.00 4.94
1906 2734 3.791973 ATTTGTTTCACCGCACAAGAA 57.208 38.095 0.00 0.00 34.43 2.52
1909 2737 3.791973 TGTTTCACCGCACAAGAATTT 57.208 38.095 0.00 0.00 0.00 1.82
1913 2741 5.517054 TGTTTCACCGCACAAGAATTTTAAC 59.483 36.000 0.00 0.00 0.00 2.01
1922 2750 5.621329 GCACAAGAATTTTAACCGTATGGCT 60.621 40.000 0.00 0.00 39.70 4.75
1923 2751 6.403855 GCACAAGAATTTTAACCGTATGGCTA 60.404 38.462 0.00 0.00 39.70 3.93
1940 2768 1.269778 GCTATCACTAGATGCGCCACA 60.270 52.381 4.18 0.00 35.67 4.17
2010 2838 1.070105 CGGGTCTCGGTGGTTTTCA 59.930 57.895 0.00 0.00 34.75 2.69
2043 2871 1.034292 GGGAGAAGAGCATTGTGCCC 61.034 60.000 0.00 0.00 46.52 5.36
2045 2873 0.034670 GAGAAGAGCATTGTGCCCCT 60.035 55.000 0.00 0.00 46.52 4.79
2050 2878 1.133976 AGAGCATTGTGCCCCTCATAC 60.134 52.381 0.00 0.00 46.52 2.39
2053 2881 0.552848 CATTGTGCCCCTCATACCCT 59.447 55.000 0.00 0.00 0.00 4.34
2061 2889 0.104462 CCCTCATACCCTCCCCATGA 60.104 60.000 0.00 0.00 0.00 3.07
2063 2891 1.132721 CCTCATACCCTCCCCATGAGA 60.133 57.143 11.40 0.00 45.58 3.27
2067 2895 1.586586 TACCCTCCCCATGAGACCGA 61.587 60.000 0.00 0.00 44.42 4.69
2068 2896 2.136878 CCCTCCCCATGAGACCGAG 61.137 68.421 0.00 0.00 44.42 4.63
2360 3188 2.442087 GGGCCCCCGAAATTGAGG 60.442 66.667 12.23 0.00 0.00 3.86
2365 3193 2.442087 CCCGAAATTGAGGGGCCC 60.442 66.667 17.12 17.12 43.90 5.80
2366 3194 2.442087 CCGAAATTGAGGGGCCCC 60.442 66.667 35.90 35.90 0.00 5.80
2367 3195 2.442087 CGAAATTGAGGGGCCCCC 60.442 66.667 38.68 28.05 45.90 5.40
2380 3208 4.619227 CCCCCACGTTCGTGTGCT 62.619 66.667 20.93 0.00 38.55 4.40
2381 3209 3.041940 CCCCACGTTCGTGTGCTC 61.042 66.667 20.93 0.00 38.55 4.26
2382 3210 2.029073 CCCACGTTCGTGTGCTCT 59.971 61.111 20.93 0.00 38.55 4.09
2383 3211 2.022129 CCCACGTTCGTGTGCTCTC 61.022 63.158 20.93 0.00 38.55 3.20
2384 3212 1.007271 CCACGTTCGTGTGCTCTCT 60.007 57.895 20.93 0.00 38.55 3.10
2385 3213 1.278172 CCACGTTCGTGTGCTCTCTG 61.278 60.000 20.93 2.85 38.55 3.35
2386 3214 0.595053 CACGTTCGTGTGCTCTCTGT 60.595 55.000 15.81 0.00 32.31 3.41
2387 3215 0.949397 ACGTTCGTGTGCTCTCTGTA 59.051 50.000 0.00 0.00 0.00 2.74
2388 3216 1.540267 ACGTTCGTGTGCTCTCTGTAT 59.460 47.619 0.00 0.00 0.00 2.29
2389 3217 2.177977 CGTTCGTGTGCTCTCTGTATC 58.822 52.381 0.00 0.00 0.00 2.24
2390 3218 2.531206 GTTCGTGTGCTCTCTGTATCC 58.469 52.381 0.00 0.00 0.00 2.59
2391 3219 1.834188 TCGTGTGCTCTCTGTATCCA 58.166 50.000 0.00 0.00 0.00 3.41
2392 3220 1.745653 TCGTGTGCTCTCTGTATCCAG 59.254 52.381 0.00 0.00 40.25 3.86
2393 3221 1.800655 CGTGTGCTCTCTGTATCCAGC 60.801 57.143 0.00 0.00 38.66 4.85
2394 3222 0.826715 TGTGCTCTCTGTATCCAGCC 59.173 55.000 0.00 0.00 38.66 4.85
2395 3223 0.105778 GTGCTCTCTGTATCCAGCCC 59.894 60.000 0.00 0.00 38.66 5.19
2396 3224 1.365633 GCTCTCTGTATCCAGCCCG 59.634 63.158 0.00 0.00 38.66 6.13
2397 3225 1.395826 GCTCTCTGTATCCAGCCCGT 61.396 60.000 0.00 0.00 38.66 5.28
2398 3226 0.387202 CTCTCTGTATCCAGCCCGTG 59.613 60.000 0.00 0.00 38.66 4.94
2399 3227 1.227380 CTCTGTATCCAGCCCGTGC 60.227 63.158 0.00 0.00 38.66 5.34
2400 3228 2.586079 CTGTATCCAGCCCGTGCG 60.586 66.667 0.00 0.00 44.33 5.34
2401 3229 4.830765 TGTATCCAGCCCGTGCGC 62.831 66.667 0.00 0.00 44.33 6.09
2402 3230 4.530857 GTATCCAGCCCGTGCGCT 62.531 66.667 9.73 0.00 44.33 5.92
2403 3231 4.221422 TATCCAGCCCGTGCGCTC 62.221 66.667 9.73 3.51 44.33 5.03
2407 3235 4.749310 CAGCCCGTGCGCTCTCTT 62.749 66.667 9.73 0.00 44.33 2.85
2408 3236 3.068691 AGCCCGTGCGCTCTCTTA 61.069 61.111 9.73 0.00 44.33 2.10
2409 3237 2.125673 GCCCGTGCGCTCTCTTAA 60.126 61.111 9.73 0.00 0.00 1.85
2410 3238 1.521681 GCCCGTGCGCTCTCTTAAT 60.522 57.895 9.73 0.00 0.00 1.40
2411 3239 1.491505 GCCCGTGCGCTCTCTTAATC 61.492 60.000 9.73 0.00 0.00 1.75
2412 3240 0.876342 CCCGTGCGCTCTCTTAATCC 60.876 60.000 9.73 0.00 0.00 3.01
2413 3241 0.179111 CCGTGCGCTCTCTTAATCCA 60.179 55.000 9.73 0.00 0.00 3.41
2414 3242 1.203928 CGTGCGCTCTCTTAATCCAG 58.796 55.000 9.73 0.00 0.00 3.86
2415 3243 0.933796 GTGCGCTCTCTTAATCCAGC 59.066 55.000 9.73 0.00 0.00 4.85
2416 3244 0.179073 TGCGCTCTCTTAATCCAGCC 60.179 55.000 9.73 0.00 0.00 4.85
2417 3245 0.882484 GCGCTCTCTTAATCCAGCCC 60.882 60.000 0.00 0.00 0.00 5.19
2418 3246 0.465705 CGCTCTCTTAATCCAGCCCA 59.534 55.000 0.00 0.00 0.00 5.36
2419 3247 1.071385 CGCTCTCTTAATCCAGCCCAT 59.929 52.381 0.00 0.00 0.00 4.00
2420 3248 2.502295 GCTCTCTTAATCCAGCCCATG 58.498 52.381 0.00 0.00 0.00 3.66
2421 3249 2.105477 GCTCTCTTAATCCAGCCCATGA 59.895 50.000 0.00 0.00 0.00 3.07
2422 3250 3.806507 GCTCTCTTAATCCAGCCCATGAG 60.807 52.174 0.00 0.00 0.00 2.90
2423 3251 3.645212 CTCTCTTAATCCAGCCCATGAGA 59.355 47.826 0.00 0.00 0.00 3.27
2424 3252 4.040047 TCTCTTAATCCAGCCCATGAGAA 58.960 43.478 0.00 0.00 0.00 2.87
2425 3253 4.474651 TCTCTTAATCCAGCCCATGAGAAA 59.525 41.667 0.00 0.00 0.00 2.52
2426 3254 5.044919 TCTCTTAATCCAGCCCATGAGAAAA 60.045 40.000 0.00 0.00 0.00 2.29
2427 3255 5.579047 TCTTAATCCAGCCCATGAGAAAAA 58.421 37.500 0.00 0.00 0.00 1.94
2447 3275 6.927933 AAAAACGATTCTCGCCTAATTTTG 57.072 33.333 0.00 0.00 45.12 2.44
2448 3276 5.873179 AAACGATTCTCGCCTAATTTTGA 57.127 34.783 0.00 0.00 45.12 2.69
2449 3277 6.436843 AAACGATTCTCGCCTAATTTTGAT 57.563 33.333 0.00 0.00 45.12 2.57
2450 3278 5.409643 ACGATTCTCGCCTAATTTTGATG 57.590 39.130 0.00 0.00 45.12 3.07
2451 3279 4.214437 CGATTCTCGCCTAATTTTGATGC 58.786 43.478 0.00 0.00 31.14 3.91
2452 3280 4.260743 CGATTCTCGCCTAATTTTGATGCA 60.261 41.667 0.00 0.00 31.14 3.96
2453 3281 5.581126 ATTCTCGCCTAATTTTGATGCAA 57.419 34.783 0.00 0.00 0.00 4.08
2454 3282 4.355543 TCTCGCCTAATTTTGATGCAAC 57.644 40.909 0.00 0.00 0.00 4.17
2455 3283 3.755905 TCTCGCCTAATTTTGATGCAACA 59.244 39.130 0.00 0.00 0.00 3.33
2456 3284 4.095410 TCGCCTAATTTTGATGCAACAG 57.905 40.909 0.00 0.00 0.00 3.16
2457 3285 2.599973 CGCCTAATTTTGATGCAACAGC 59.400 45.455 0.00 0.00 0.00 4.40
2458 3286 2.599973 GCCTAATTTTGATGCAACAGCG 59.400 45.455 0.00 0.00 0.00 5.18
2459 3287 3.673052 GCCTAATTTTGATGCAACAGCGA 60.673 43.478 0.00 0.00 0.00 4.93
2460 3288 4.484236 CCTAATTTTGATGCAACAGCGAA 58.516 39.130 0.00 0.00 0.00 4.70
2461 3289 4.324402 CCTAATTTTGATGCAACAGCGAAC 59.676 41.667 0.00 0.00 0.00 3.95
2462 3290 2.859526 TTTTGATGCAACAGCGAACA 57.140 40.000 0.00 0.00 0.00 3.18
2463 3291 3.367992 TTTTGATGCAACAGCGAACAT 57.632 38.095 0.00 0.00 0.00 2.71
2464 3292 3.367992 TTTGATGCAACAGCGAACATT 57.632 38.095 0.00 0.00 0.00 2.71
2465 3293 4.495911 TTTGATGCAACAGCGAACATTA 57.504 36.364 0.00 0.00 0.00 1.90
2466 3294 3.745332 TGATGCAACAGCGAACATTAG 57.255 42.857 0.00 0.00 0.00 1.73
2467 3295 2.159531 TGATGCAACAGCGAACATTAGC 60.160 45.455 0.00 0.00 0.00 3.09
2468 3296 1.522668 TGCAACAGCGAACATTAGCT 58.477 45.000 0.00 0.00 45.74 3.32
2473 3301 3.159298 AGCGAACATTAGCTGTGGG 57.841 52.632 0.00 0.00 42.82 4.61
2474 3302 1.026718 AGCGAACATTAGCTGTGGGC 61.027 55.000 0.00 1.49 42.82 5.36
2475 3303 1.305219 GCGAACATTAGCTGTGGGCA 61.305 55.000 0.00 0.00 44.79 5.36
2476 3304 1.164411 CGAACATTAGCTGTGGGCAA 58.836 50.000 0.00 0.00 44.79 4.52
2477 3305 1.131126 CGAACATTAGCTGTGGGCAAG 59.869 52.381 0.00 0.00 44.79 4.01
2478 3306 2.162681 GAACATTAGCTGTGGGCAAGT 58.837 47.619 0.00 0.00 44.79 3.16
2479 3307 3.343617 GAACATTAGCTGTGGGCAAGTA 58.656 45.455 0.00 0.00 44.79 2.24
2480 3308 3.433306 ACATTAGCTGTGGGCAAGTAA 57.567 42.857 0.00 0.00 44.79 2.24
2481 3309 3.761897 ACATTAGCTGTGGGCAAGTAAA 58.238 40.909 0.00 0.00 44.79 2.01
2482 3310 4.344104 ACATTAGCTGTGGGCAAGTAAAT 58.656 39.130 0.00 0.00 44.79 1.40
2483 3311 4.399303 ACATTAGCTGTGGGCAAGTAAATC 59.601 41.667 0.00 0.00 44.79 2.17
2484 3312 2.584835 AGCTGTGGGCAAGTAAATCA 57.415 45.000 0.00 0.00 44.79 2.57
2485 3313 2.440409 AGCTGTGGGCAAGTAAATCAG 58.560 47.619 0.00 0.00 44.79 2.90
2486 3314 1.135286 GCTGTGGGCAAGTAAATCAGC 60.135 52.381 0.00 0.00 41.35 4.26
2487 3315 1.131126 CTGTGGGCAAGTAAATCAGCG 59.869 52.381 0.00 0.00 0.00 5.18
2488 3316 1.271108 TGTGGGCAAGTAAATCAGCGA 60.271 47.619 0.00 0.00 0.00 4.93
2489 3317 2.017049 GTGGGCAAGTAAATCAGCGAT 58.983 47.619 0.00 0.00 0.00 4.58
2490 3318 2.423538 GTGGGCAAGTAAATCAGCGATT 59.576 45.455 0.00 0.00 33.25 3.34
2491 3319 3.625764 GTGGGCAAGTAAATCAGCGATTA 59.374 43.478 4.60 0.00 31.46 1.75
2492 3320 3.876914 TGGGCAAGTAAATCAGCGATTAG 59.123 43.478 4.60 0.00 31.46 1.73
2506 3334 4.474226 GCGATTAGCTAAATTGGTGGAG 57.526 45.455 10.85 0.00 44.04 3.86
2507 3335 3.877508 GCGATTAGCTAAATTGGTGGAGT 59.122 43.478 10.85 0.00 44.04 3.85
2508 3336 4.335594 GCGATTAGCTAAATTGGTGGAGTT 59.664 41.667 10.85 0.00 44.04 3.01
2509 3337 5.163652 GCGATTAGCTAAATTGGTGGAGTTT 60.164 40.000 10.85 0.00 44.04 2.66
2510 3338 6.487103 CGATTAGCTAAATTGGTGGAGTTTC 58.513 40.000 10.85 0.00 0.00 2.78
2511 3339 6.316390 CGATTAGCTAAATTGGTGGAGTTTCT 59.684 38.462 10.85 0.00 0.00 2.52
2512 3340 7.466050 CGATTAGCTAAATTGGTGGAGTTTCTC 60.466 40.741 10.85 0.00 0.00 2.87
2513 3341 4.985538 AGCTAAATTGGTGGAGTTTCTCA 58.014 39.130 0.00 0.00 31.08 3.27
2514 3342 5.385198 AGCTAAATTGGTGGAGTTTCTCAA 58.615 37.500 0.00 0.00 31.08 3.02
2515 3343 5.474876 AGCTAAATTGGTGGAGTTTCTCAAG 59.525 40.000 0.00 0.00 31.08 3.02
2516 3344 5.473504 GCTAAATTGGTGGAGTTTCTCAAGA 59.526 40.000 0.00 0.00 31.08 3.02
2517 3345 6.016276 GCTAAATTGGTGGAGTTTCTCAAGAA 60.016 38.462 0.00 0.00 31.08 2.52
2518 3346 6.790232 AAATTGGTGGAGTTTCTCAAGAAA 57.210 33.333 1.06 1.06 41.29 2.52
2519 3347 6.790232 AATTGGTGGAGTTTCTCAAGAAAA 57.210 33.333 6.76 0.00 44.58 2.29
2520 3348 6.790232 ATTGGTGGAGTTTCTCAAGAAAAA 57.210 33.333 6.76 0.00 44.58 1.94
2551 3379 3.719816 GTGGAACTTCCGTTTCCCT 57.280 52.632 3.28 0.00 40.17 4.20
2552 3380 1.520494 GTGGAACTTCCGTTTCCCTC 58.480 55.000 3.28 0.00 40.17 4.30
2553 3381 0.034337 TGGAACTTCCGTTTCCCTCG 59.966 55.000 3.28 0.00 40.17 4.63
2554 3382 1.296755 GGAACTTCCGTTTCCCTCGC 61.297 60.000 0.00 0.00 32.39 5.03
2555 3383 1.623973 GAACTTCCGTTTCCCTCGCG 61.624 60.000 0.00 0.00 32.39 5.87
2556 3384 3.488090 CTTCCGTTTCCCTCGCGC 61.488 66.667 0.00 0.00 0.00 6.86
2557 3385 4.302509 TTCCGTTTCCCTCGCGCA 62.303 61.111 8.75 0.00 0.00 6.09
2558 3386 4.735132 TCCGTTTCCCTCGCGCAG 62.735 66.667 8.75 3.84 0.00 5.18
2561 3389 3.119096 GTTTCCCTCGCGCAGGTC 61.119 66.667 19.93 7.89 41.51 3.85
2562 3390 4.388499 TTTCCCTCGCGCAGGTCC 62.388 66.667 19.93 0.00 41.51 4.46
2572 3400 3.945434 GCAGGTCCGCGCATGATG 61.945 66.667 8.75 0.54 0.00 3.07
2573 3401 2.202919 CAGGTCCGCGCATGATGA 60.203 61.111 8.75 0.00 0.00 2.92
2574 3402 2.202932 AGGTCCGCGCATGATGAC 60.203 61.111 8.75 0.69 0.00 3.06
2575 3403 2.511373 GGTCCGCGCATGATGACA 60.511 61.111 8.75 0.00 0.00 3.58
2576 3404 1.889105 GGTCCGCGCATGATGACAT 60.889 57.895 8.75 0.00 37.19 3.06
2588 3416 2.554142 TGATGACATGAGCAATCGACC 58.446 47.619 0.00 0.00 0.00 4.79
2589 3417 2.169144 TGATGACATGAGCAATCGACCT 59.831 45.455 0.00 0.00 0.00 3.85
2590 3418 3.384467 TGATGACATGAGCAATCGACCTA 59.616 43.478 0.00 0.00 0.00 3.08
2591 3419 3.443099 TGACATGAGCAATCGACCTAG 57.557 47.619 0.00 0.00 0.00 3.02
2592 3420 2.131183 GACATGAGCAATCGACCTAGC 58.869 52.381 0.00 0.00 0.00 3.42
2593 3421 1.135046 CATGAGCAATCGACCTAGCG 58.865 55.000 0.00 0.00 0.00 4.26
2594 3422 1.032794 ATGAGCAATCGACCTAGCGA 58.967 50.000 0.00 0.00 45.22 4.93
2595 3423 0.100682 TGAGCAATCGACCTAGCGAC 59.899 55.000 0.00 0.00 43.79 5.19
2596 3424 0.100682 GAGCAATCGACCTAGCGACA 59.899 55.000 0.00 0.00 43.79 4.35
2597 3425 0.747255 AGCAATCGACCTAGCGACAT 59.253 50.000 0.00 0.00 43.79 3.06
2598 3426 1.954382 AGCAATCGACCTAGCGACATA 59.046 47.619 0.00 0.00 43.79 2.29
2599 3427 2.558795 AGCAATCGACCTAGCGACATAT 59.441 45.455 0.00 0.00 43.79 1.78
2600 3428 2.917971 GCAATCGACCTAGCGACATATC 59.082 50.000 0.00 0.00 43.79 1.63
2601 3429 3.502920 CAATCGACCTAGCGACATATCC 58.497 50.000 0.00 0.00 43.79 2.59
2602 3430 1.531423 TCGACCTAGCGACATATCCC 58.469 55.000 0.00 0.00 35.01 3.85
2603 3431 0.168348 CGACCTAGCGACATATCCCG 59.832 60.000 0.00 0.00 0.00 5.14
2609 3437 3.642755 CGACATATCCCGCAAGCC 58.357 61.111 0.00 0.00 0.00 4.35
2610 3438 1.961277 CGACATATCCCGCAAGCCC 60.961 63.158 0.00 0.00 0.00 5.19
2611 3439 1.961277 GACATATCCCGCAAGCCCG 60.961 63.158 0.00 0.00 0.00 6.13
2612 3440 2.377628 GACATATCCCGCAAGCCCGA 62.378 60.000 0.00 0.00 0.00 5.14
2613 3441 1.669115 CATATCCCGCAAGCCCGAG 60.669 63.158 0.00 0.00 0.00 4.63
2614 3442 2.883828 ATATCCCGCAAGCCCGAGG 61.884 63.158 0.00 0.00 0.00 4.63
2641 3469 4.003788 CCGCCGACACAACCTCCT 62.004 66.667 0.00 0.00 0.00 3.69
2642 3470 2.432628 CGCCGACACAACCTCCTC 60.433 66.667 0.00 0.00 0.00 3.71
2643 3471 2.047179 GCCGACACAACCTCCTCC 60.047 66.667 0.00 0.00 0.00 4.30
2644 3472 2.663196 CCGACACAACCTCCTCCC 59.337 66.667 0.00 0.00 0.00 4.30
2645 3473 2.261671 CGACACAACCTCCTCCCG 59.738 66.667 0.00 0.00 0.00 5.14
2646 3474 2.047179 GACACAACCTCCTCCCGC 60.047 66.667 0.00 0.00 0.00 6.13
2647 3475 3.934391 GACACAACCTCCTCCCGCG 62.934 68.421 0.00 0.00 0.00 6.46
2648 3476 4.760047 CACAACCTCCTCCCGCGG 62.760 72.222 21.04 21.04 0.00 6.46
2664 3492 2.527875 GGAGGCCTCCCCGATGAT 60.528 66.667 38.25 0.00 43.94 2.45
2665 3493 2.150051 GGAGGCCTCCCCGATGATT 61.150 63.158 38.25 0.00 43.94 2.57
2666 3494 1.709994 GGAGGCCTCCCCGATGATTT 61.710 60.000 38.25 0.00 43.94 2.17
2667 3495 0.250510 GAGGCCTCCCCGATGATTTC 60.251 60.000 23.19 0.00 39.21 2.17
2668 3496 0.695803 AGGCCTCCCCGATGATTTCT 60.696 55.000 0.00 0.00 39.21 2.52
2669 3497 0.250510 GGCCTCCCCGATGATTTCTC 60.251 60.000 0.00 0.00 0.00 2.87
2670 3498 0.601311 GCCTCCCCGATGATTTCTCG 60.601 60.000 0.00 0.00 35.92 4.04
2671 3499 0.753262 CCTCCCCGATGATTTCTCGT 59.247 55.000 0.00 0.00 34.36 4.18
2672 3500 1.539065 CCTCCCCGATGATTTCTCGTG 60.539 57.143 0.00 0.00 34.36 4.35
2673 3501 0.179084 TCCCCGATGATTTCTCGTGC 60.179 55.000 0.00 0.00 34.36 5.34
2674 3502 0.461870 CCCCGATGATTTCTCGTGCA 60.462 55.000 0.00 0.00 34.36 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 2.812542 TTCTGATCACCGGCGTCACG 62.813 60.000 6.01 0.00 0.00 4.35
78 79 5.450965 CCAAGCCAACAATATTCTGATCACC 60.451 44.000 0.00 0.00 0.00 4.02
80 81 5.263599 ACCAAGCCAACAATATTCTGATCA 58.736 37.500 0.00 0.00 0.00 2.92
111 112 9.011095 GTAGTTTTTAAGGCCTAGAAGACAATT 57.989 33.333 5.16 0.00 0.00 2.32
169 172 8.755941 CACTCATTTCAGTCCGTATACAAATAG 58.244 37.037 3.32 2.81 0.00 1.73
175 178 6.097356 TGTTCACTCATTTCAGTCCGTATAC 58.903 40.000 0.00 0.00 0.00 1.47
178 181 4.594123 TGTTCACTCATTTCAGTCCGTA 57.406 40.909 0.00 0.00 0.00 4.02
180 183 4.035091 TGTTTGTTCACTCATTTCAGTCCG 59.965 41.667 0.00 0.00 0.00 4.79
182 185 7.865707 AGTATGTTTGTTCACTCATTTCAGTC 58.134 34.615 0.00 0.00 0.00 3.51
260 274 2.488545 AGTAGTACTGCCTCGTTCACAG 59.511 50.000 5.39 0.00 37.45 3.66
278 293 5.515106 AGTAAGGCCATGGCAAATTAAGTA 58.485 37.500 36.56 13.64 44.11 2.24
279 294 4.352893 AGTAAGGCCATGGCAAATTAAGT 58.647 39.130 36.56 18.52 44.11 2.24
280 295 5.343307 AAGTAAGGCCATGGCAAATTAAG 57.657 39.130 36.56 0.00 44.11 1.85
281 296 7.430760 AATAAGTAAGGCCATGGCAAATTAA 57.569 32.000 36.56 16.95 44.11 1.40
395 431 2.890311 ACTCTGATCGATTAGGCAGGAG 59.110 50.000 16.35 9.10 0.00 3.69
450 486 7.817418 TGTGAATTAAGTGTTCTTTTAGGCT 57.183 32.000 0.00 0.00 35.36 4.58
467 503 8.719560 TGTATAAAATTGCATGCATGTGAATT 57.280 26.923 26.79 24.42 0.00 2.17
495 531 5.390567 GGAGTAATACAACTTTTCGCAGGTG 60.391 44.000 0.00 0.00 37.52 4.00
496 532 4.694037 GGAGTAATACAACTTTTCGCAGGT 59.306 41.667 0.00 0.00 0.00 4.00
539 576 2.702898 TCAACATGCACAATGGAACG 57.297 45.000 0.00 0.00 40.94 3.95
558 595 8.286800 ACACAACGCGCATATATACATAAATTT 58.713 29.630 5.73 0.00 0.00 1.82
593 630 4.762251 AGTTTAATCCCAGTCTCTGCAAAC 59.238 41.667 0.00 0.00 0.00 2.93
667 707 5.936054 AGAGCTCGATCATGAAAGTTTTTG 58.064 37.500 8.37 0.00 0.00 2.44
735 785 2.967459 TGTCTGTACTTGCAATTGCG 57.033 45.000 24.58 14.19 45.83 4.85
802 852 9.224267 GACAGAGTATTATGTATTGGCATGATT 57.776 33.333 0.00 0.00 0.00 2.57
813 863 9.563898 CACAAACTTACGACAGAGTATTATGTA 57.436 33.333 0.00 0.00 0.00 2.29
822 872 3.361053 CGCTACACAAACTTACGACAGAG 59.639 47.826 0.00 0.00 0.00 3.35
824 874 3.047796 ACGCTACACAAACTTACGACAG 58.952 45.455 0.00 0.00 0.00 3.51
987 1037 0.104672 TTGTGTTGAGAGGGGAGGGA 60.105 55.000 0.00 0.00 0.00 4.20
988 1038 0.036875 GTTGTGTTGAGAGGGGAGGG 59.963 60.000 0.00 0.00 0.00 4.30
989 1039 0.764890 TGTTGTGTTGAGAGGGGAGG 59.235 55.000 0.00 0.00 0.00 4.30
990 1040 1.879796 GCTGTTGTGTTGAGAGGGGAG 60.880 57.143 0.00 0.00 0.00 4.30
991 1041 0.108585 GCTGTTGTGTTGAGAGGGGA 59.891 55.000 0.00 0.00 0.00 4.81
992 1042 0.179020 TGCTGTTGTGTTGAGAGGGG 60.179 55.000 0.00 0.00 0.00 4.79
1021 1072 0.037697 TGTGTTCTTGGGACGATCGG 60.038 55.000 20.98 0.00 0.00 4.18
1022 1073 1.726791 CTTGTGTTCTTGGGACGATCG 59.273 52.381 14.88 14.88 0.00 3.69
1023 1074 2.076863 CCTTGTGTTCTTGGGACGATC 58.923 52.381 0.00 0.00 0.00 3.69
1024 1075 1.420138 ACCTTGTGTTCTTGGGACGAT 59.580 47.619 0.00 0.00 0.00 3.73
1025 1076 0.834612 ACCTTGTGTTCTTGGGACGA 59.165 50.000 0.00 0.00 0.00 4.20
1026 1077 1.226746 GACCTTGTGTTCTTGGGACG 58.773 55.000 0.00 0.00 0.00 4.79
1027 1078 1.947456 GTGACCTTGTGTTCTTGGGAC 59.053 52.381 0.00 0.00 0.00 4.46
1028 1079 1.474320 CGTGACCTTGTGTTCTTGGGA 60.474 52.381 0.00 0.00 0.00 4.37
1029 1080 0.944386 CGTGACCTTGTGTTCTTGGG 59.056 55.000 0.00 0.00 0.00 4.12
1030 1081 1.867233 CTCGTGACCTTGTGTTCTTGG 59.133 52.381 0.00 0.00 0.00 3.61
1150 1202 1.639298 GCAGGAACATCACGAGCACC 61.639 60.000 0.00 0.00 0.00 5.01
1384 1514 9.408069 GATTCTTTCTTGTCGTAGAAGTAGAAA 57.592 33.333 11.79 0.00 39.69 2.52
1405 1535 2.380084 ACCATGCGTTGTACGATTCT 57.620 45.000 3.04 0.00 46.05 2.40
1408 1538 1.730064 GTGAACCATGCGTTGTACGAT 59.270 47.619 3.04 0.00 46.05 3.73
1420 1550 0.905357 CGAGGGAGAAGGTGAACCAT 59.095 55.000 1.62 0.00 38.89 3.55
1537 1667 2.390599 GCGCGCCATGAAGAAGTCA 61.391 57.895 23.24 0.00 41.67 3.41
1774 2601 2.097466 GGCGTGAAACATACAGGAATGG 59.903 50.000 0.00 0.00 35.74 3.16
1780 2607 1.518325 TGTGGGCGTGAAACATACAG 58.482 50.000 0.00 0.00 35.74 2.74
1810 2637 9.950680 AAATAAGCAGAATAAAACATCATACGG 57.049 29.630 0.00 0.00 0.00 4.02
1852 2680 9.832445 AGAAAAGTATCGACCATGTAAATGTAT 57.168 29.630 0.00 0.00 0.00 2.29
1895 2723 2.619646 ACGGTTAAAATTCTTGTGCGGT 59.380 40.909 0.00 0.00 0.00 5.68
1898 2726 4.561213 GCCATACGGTTAAAATTCTTGTGC 59.439 41.667 0.00 0.00 33.28 4.57
1906 2734 7.959175 TCTAGTGATAGCCATACGGTTAAAAT 58.041 34.615 0.00 0.00 30.94 1.82
1909 2737 6.571731 GCATCTAGTGATAGCCATACGGTTAA 60.572 42.308 0.00 0.00 30.94 2.01
1913 2741 3.732169 CGCATCTAGTGATAGCCATACGG 60.732 52.174 0.00 0.00 0.00 4.02
1922 2750 3.132111 TCTTTGTGGCGCATCTAGTGATA 59.868 43.478 10.83 0.00 0.00 2.15
1923 2751 2.093500 TCTTTGTGGCGCATCTAGTGAT 60.093 45.455 10.83 0.00 0.00 3.06
1940 2768 0.889994 TTGCGAGCATTGGCATCTTT 59.110 45.000 0.00 0.00 44.61 2.52
1972 2800 4.587189 CCGTTCGGATCTCGGGCC 62.587 72.222 5.19 0.00 40.49 5.80
1984 2812 2.412112 CCGAGACCCGATCCGTTC 59.588 66.667 0.00 0.00 41.76 3.95
1988 2816 1.896122 AAACCACCGAGACCCGATCC 61.896 60.000 0.00 0.00 41.76 3.36
1992 2820 1.070105 TGAAAACCACCGAGACCCG 59.930 57.895 0.00 0.00 38.18 5.28
2014 2842 0.682855 CTCTTCTCCCTCACCGCTCT 60.683 60.000 0.00 0.00 0.00 4.09
2043 2871 1.132721 TCTCATGGGGAGGGTATGAGG 60.133 57.143 12.05 0.00 44.88 3.86
2045 2873 1.414538 GGTCTCATGGGGAGGGTATGA 60.415 57.143 0.00 0.00 44.19 2.15
2050 2878 2.041922 TCGGTCTCATGGGGAGGG 60.042 66.667 0.00 0.00 44.19 4.30
2053 2881 1.753078 CGACTCGGTCTCATGGGGA 60.753 63.158 0.00 0.00 0.00 4.81
2063 2891 4.129737 CATGGGCGTCGACTCGGT 62.130 66.667 14.70 0.00 0.00 4.69
2067 2895 4.760047 GGTGCATGGGCGTCGACT 62.760 66.667 14.70 0.00 45.35 4.18
2078 2906 3.195002 CCGATCAACGCGGTGCAT 61.195 61.111 21.87 14.10 43.66 3.96
2343 3171 2.442087 CCTCAATTTCGGGGGCCC 60.442 66.667 15.76 15.76 0.00 5.80
2344 3172 2.442087 CCCTCAATTTCGGGGGCC 60.442 66.667 0.00 0.00 36.78 5.80
2348 3176 2.442087 GGGCCCCTCAATTTCGGG 60.442 66.667 12.23 2.34 40.29 5.14
2349 3177 2.442087 GGGGCCCCTCAATTTCGG 60.442 66.667 35.49 0.00 0.00 4.30
2350 3178 2.442087 GGGGGCCCCTCAATTTCG 60.442 66.667 39.92 0.00 41.34 3.46
2351 3179 1.685765 GTGGGGGCCCCTCAATTTC 60.686 63.158 40.43 21.98 45.70 2.17
2352 3180 2.449777 GTGGGGGCCCCTCAATTT 59.550 61.111 40.43 0.00 45.70 1.82
2353 3181 4.060667 CGTGGGGGCCCCTCAATT 62.061 66.667 40.43 0.00 45.70 2.32
2368 3196 0.949397 TACAGAGAGCACACGAACGT 59.051 50.000 0.00 0.00 0.00 3.99
2369 3197 2.177977 GATACAGAGAGCACACGAACG 58.822 52.381 0.00 0.00 0.00 3.95
2370 3198 2.094700 TGGATACAGAGAGCACACGAAC 60.095 50.000 0.00 0.00 46.17 3.95
2371 3199 2.167662 TGGATACAGAGAGCACACGAA 58.832 47.619 0.00 0.00 46.17 3.85
2372 3200 1.834188 TGGATACAGAGAGCACACGA 58.166 50.000 0.00 0.00 46.17 4.35
2385 3213 4.530857 AGCGCACGGGCTGGATAC 62.531 66.667 11.47 0.00 42.86 2.24
2386 3214 4.221422 GAGCGCACGGGCTGGATA 62.221 66.667 13.84 0.00 44.93 2.59
2390 3218 2.835701 TTAAGAGAGCGCACGGGCTG 62.836 60.000 13.84 1.91 44.93 4.85
2392 3220 1.491505 GATTAAGAGAGCGCACGGGC 61.492 60.000 11.47 0.00 0.00 6.13
2393 3221 0.876342 GGATTAAGAGAGCGCACGGG 60.876 60.000 11.47 0.00 0.00 5.28
2394 3222 0.179111 TGGATTAAGAGAGCGCACGG 60.179 55.000 11.47 0.00 0.00 4.94
2395 3223 1.203928 CTGGATTAAGAGAGCGCACG 58.796 55.000 11.47 0.00 0.00 5.34
2396 3224 0.933796 GCTGGATTAAGAGAGCGCAC 59.066 55.000 11.47 2.25 0.00 5.34
2397 3225 0.179073 GGCTGGATTAAGAGAGCGCA 60.179 55.000 11.47 0.00 31.89 6.09
2398 3226 0.882484 GGGCTGGATTAAGAGAGCGC 60.882 60.000 0.00 0.00 37.25 5.92
2399 3227 0.465705 TGGGCTGGATTAAGAGAGCG 59.534 55.000 0.00 0.00 31.89 5.03
2400 3228 2.105477 TCATGGGCTGGATTAAGAGAGC 59.895 50.000 0.00 0.00 0.00 4.09
2401 3229 3.645212 TCTCATGGGCTGGATTAAGAGAG 59.355 47.826 0.00 0.00 0.00 3.20
2402 3230 3.657610 TCTCATGGGCTGGATTAAGAGA 58.342 45.455 0.00 0.00 0.00 3.10
2403 3231 4.428294 TTCTCATGGGCTGGATTAAGAG 57.572 45.455 0.00 0.00 0.00 2.85
2404 3232 4.860802 TTTCTCATGGGCTGGATTAAGA 57.139 40.909 0.00 0.00 0.00 2.10
2405 3233 5.920193 TTTTTCTCATGGGCTGGATTAAG 57.080 39.130 0.00 0.00 0.00 1.85
2430 3258 5.173774 TGCATCAAAATTAGGCGAGAATC 57.826 39.130 0.00 0.00 0.00 2.52
2431 3259 5.105797 TGTTGCATCAAAATTAGGCGAGAAT 60.106 36.000 0.00 0.00 0.00 2.40
2432 3260 4.217334 TGTTGCATCAAAATTAGGCGAGAA 59.783 37.500 0.00 0.00 0.00 2.87
2433 3261 3.755905 TGTTGCATCAAAATTAGGCGAGA 59.244 39.130 0.00 0.00 0.00 4.04
2434 3262 4.095410 TGTTGCATCAAAATTAGGCGAG 57.905 40.909 0.00 0.00 0.00 5.03
2435 3263 3.673052 GCTGTTGCATCAAAATTAGGCGA 60.673 43.478 0.00 0.00 39.41 5.54
2436 3264 2.599973 GCTGTTGCATCAAAATTAGGCG 59.400 45.455 0.00 0.00 39.41 5.52
2437 3265 2.599973 CGCTGTTGCATCAAAATTAGGC 59.400 45.455 0.00 0.00 39.64 3.93
2438 3266 4.095410 TCGCTGTTGCATCAAAATTAGG 57.905 40.909 0.00 0.00 39.64 2.69
2439 3267 4.916831 TGTTCGCTGTTGCATCAAAATTAG 59.083 37.500 0.00 0.00 39.64 1.73
2440 3268 4.864633 TGTTCGCTGTTGCATCAAAATTA 58.135 34.783 0.00 0.00 39.64 1.40
2441 3269 3.715495 TGTTCGCTGTTGCATCAAAATT 58.285 36.364 0.00 0.00 39.64 1.82
2442 3270 3.367992 TGTTCGCTGTTGCATCAAAAT 57.632 38.095 0.00 0.00 39.64 1.82
2443 3271 2.859526 TGTTCGCTGTTGCATCAAAA 57.140 40.000 0.00 0.00 39.64 2.44
2444 3272 3.367992 AATGTTCGCTGTTGCATCAAA 57.632 38.095 0.00 0.00 39.64 2.69
2445 3273 3.670359 GCTAATGTTCGCTGTTGCATCAA 60.670 43.478 0.00 0.00 39.64 2.57
2446 3274 2.159531 GCTAATGTTCGCTGTTGCATCA 60.160 45.455 0.00 0.00 39.64 3.07
2447 3275 2.096496 AGCTAATGTTCGCTGTTGCATC 59.904 45.455 0.00 0.00 39.64 3.91
2448 3276 2.086869 AGCTAATGTTCGCTGTTGCAT 58.913 42.857 0.00 0.00 39.64 3.96
2449 3277 1.197492 CAGCTAATGTTCGCTGTTGCA 59.803 47.619 10.18 0.00 46.38 4.08
2450 3278 1.887320 CAGCTAATGTTCGCTGTTGC 58.113 50.000 10.18 0.00 46.38 4.17
2455 3283 1.026718 GCCCACAGCTAATGTTCGCT 61.027 55.000 0.00 0.00 41.41 4.93
2456 3284 1.305219 TGCCCACAGCTAATGTTCGC 61.305 55.000 0.00 0.00 41.41 4.70
2457 3285 1.131126 CTTGCCCACAGCTAATGTTCG 59.869 52.381 0.00 0.00 41.41 3.95
2458 3286 2.162681 ACTTGCCCACAGCTAATGTTC 58.837 47.619 0.00 0.00 41.41 3.18
2459 3287 2.292828 ACTTGCCCACAGCTAATGTT 57.707 45.000 0.00 0.00 41.41 2.71
2460 3288 3.433306 TTACTTGCCCACAGCTAATGT 57.567 42.857 0.00 0.00 45.43 2.71
2461 3289 4.398988 TGATTTACTTGCCCACAGCTAATG 59.601 41.667 0.00 0.00 44.23 1.90
2462 3290 4.599041 TGATTTACTTGCCCACAGCTAAT 58.401 39.130 0.00 0.00 44.23 1.73
2463 3291 4.009675 CTGATTTACTTGCCCACAGCTAA 58.990 43.478 0.00 0.00 44.23 3.09
2464 3292 3.609853 CTGATTTACTTGCCCACAGCTA 58.390 45.455 0.00 0.00 44.23 3.32
2465 3293 2.440409 CTGATTTACTTGCCCACAGCT 58.560 47.619 0.00 0.00 44.23 4.24
2466 3294 1.135286 GCTGATTTACTTGCCCACAGC 60.135 52.381 0.00 0.00 41.33 4.40
2467 3295 1.131126 CGCTGATTTACTTGCCCACAG 59.869 52.381 0.00 0.00 0.00 3.66
2468 3296 1.164411 CGCTGATTTACTTGCCCACA 58.836 50.000 0.00 0.00 0.00 4.17
2469 3297 1.448985 TCGCTGATTTACTTGCCCAC 58.551 50.000 0.00 0.00 0.00 4.61
2470 3298 2.418368 ATCGCTGATTTACTTGCCCA 57.582 45.000 0.00 0.00 0.00 5.36
2471 3299 3.304057 GCTAATCGCTGATTTACTTGCCC 60.304 47.826 8.65 0.00 33.95 5.36
2472 3300 3.878245 GCTAATCGCTGATTTACTTGCC 58.122 45.455 8.65 0.00 33.95 4.52
2485 3313 3.877508 ACTCCACCAATTTAGCTAATCGC 59.122 43.478 7.08 0.00 39.57 4.58
2486 3314 6.316390 AGAAACTCCACCAATTTAGCTAATCG 59.684 38.462 7.08 0.00 0.00 3.34
2487 3315 7.336931 TGAGAAACTCCACCAATTTAGCTAATC 59.663 37.037 7.08 0.00 0.00 1.75
2488 3316 7.175104 TGAGAAACTCCACCAATTTAGCTAAT 58.825 34.615 7.08 0.00 0.00 1.73
2489 3317 6.539173 TGAGAAACTCCACCAATTTAGCTAA 58.461 36.000 0.86 0.86 0.00 3.09
2490 3318 6.121776 TGAGAAACTCCACCAATTTAGCTA 57.878 37.500 0.00 0.00 0.00 3.32
2491 3319 4.985538 TGAGAAACTCCACCAATTTAGCT 58.014 39.130 0.00 0.00 0.00 3.32
2492 3320 5.473504 TCTTGAGAAACTCCACCAATTTAGC 59.526 40.000 0.00 0.00 0.00 3.09
2493 3321 7.510549 TTCTTGAGAAACTCCACCAATTTAG 57.489 36.000 0.00 0.00 0.00 1.85
2494 3322 7.889873 TTTCTTGAGAAACTCCACCAATTTA 57.110 32.000 2.16 0.00 38.94 1.40
2495 3323 6.790232 TTTCTTGAGAAACTCCACCAATTT 57.210 33.333 2.16 0.00 38.94 1.82
2496 3324 6.790232 TTTTCTTGAGAAACTCCACCAATT 57.210 33.333 5.71 0.00 43.01 2.32
2497 3325 6.790232 TTTTTCTTGAGAAACTCCACCAAT 57.210 33.333 5.71 0.00 43.01 3.16
2519 3347 7.013942 ACGGAAGTTCCACTAATTTAGCTTTTT 59.986 33.333 21.76 0.00 46.40 1.94
2520 3348 6.489022 ACGGAAGTTCCACTAATTTAGCTTTT 59.511 34.615 21.76 0.00 46.40 2.27
2521 3349 6.002082 ACGGAAGTTCCACTAATTTAGCTTT 58.998 36.000 21.76 0.00 46.40 3.51
2522 3350 5.557866 ACGGAAGTTCCACTAATTTAGCTT 58.442 37.500 21.76 0.00 46.40 3.74
2523 3351 5.161943 ACGGAAGTTCCACTAATTTAGCT 57.838 39.130 21.76 0.00 46.40 3.32
2539 3367 3.488090 GCGCGAGGGAAACGGAAG 61.488 66.667 12.10 0.00 0.00 3.46
2540 3368 4.302509 TGCGCGAGGGAAACGGAA 62.303 61.111 12.10 0.00 0.00 4.30
2541 3369 4.735132 CTGCGCGAGGGAAACGGA 62.735 66.667 12.10 0.00 0.00 4.69
2555 3383 3.945434 CATCATGCGCGGACCTGC 61.945 66.667 8.83 0.00 0.00 4.85
2556 3384 2.202919 TCATCATGCGCGGACCTG 60.203 61.111 8.83 0.38 0.00 4.00
2557 3385 2.202932 GTCATCATGCGCGGACCT 60.203 61.111 8.83 0.00 0.00 3.85
2558 3386 1.889105 ATGTCATCATGCGCGGACC 60.889 57.895 8.83 0.00 32.51 4.46
2559 3387 1.277739 CATGTCATCATGCGCGGAC 59.722 57.895 8.83 6.08 43.66 4.79
2560 3388 3.721851 CATGTCATCATGCGCGGA 58.278 55.556 8.83 5.00 43.66 5.54
2567 3395 3.136763 GGTCGATTGCTCATGTCATCAT 58.863 45.455 0.00 0.00 34.21 2.45
2568 3396 2.169144 AGGTCGATTGCTCATGTCATCA 59.831 45.455 0.00 0.00 0.00 3.07
2569 3397 2.831333 AGGTCGATTGCTCATGTCATC 58.169 47.619 0.00 0.00 0.00 2.92
2570 3398 2.996249 AGGTCGATTGCTCATGTCAT 57.004 45.000 0.00 0.00 0.00 3.06
2571 3399 2.481969 GCTAGGTCGATTGCTCATGTCA 60.482 50.000 0.00 0.00 0.00 3.58
2572 3400 2.131183 GCTAGGTCGATTGCTCATGTC 58.869 52.381 0.00 0.00 0.00 3.06
2573 3401 1.536922 CGCTAGGTCGATTGCTCATGT 60.537 52.381 0.00 0.00 0.00 3.21
2574 3402 1.135046 CGCTAGGTCGATTGCTCATG 58.865 55.000 0.00 0.00 0.00 3.07
2575 3403 1.032794 TCGCTAGGTCGATTGCTCAT 58.967 50.000 0.00 0.00 33.02 2.90
2576 3404 0.100682 GTCGCTAGGTCGATTGCTCA 59.899 55.000 0.00 0.00 40.84 4.26
2577 3405 0.100682 TGTCGCTAGGTCGATTGCTC 59.899 55.000 0.00 0.00 40.84 4.26
2578 3406 0.747255 ATGTCGCTAGGTCGATTGCT 59.253 50.000 0.00 0.00 40.84 3.91
2579 3407 2.417339 TATGTCGCTAGGTCGATTGC 57.583 50.000 0.00 0.00 40.84 3.56
2580 3408 3.502920 GGATATGTCGCTAGGTCGATTG 58.497 50.000 0.00 0.00 40.84 2.67
2581 3409 2.492484 GGGATATGTCGCTAGGTCGATT 59.508 50.000 0.00 0.00 40.84 3.34
2582 3410 2.093106 GGGATATGTCGCTAGGTCGAT 58.907 52.381 0.00 0.00 40.84 3.59
2583 3411 1.531423 GGGATATGTCGCTAGGTCGA 58.469 55.000 0.00 0.00 34.67 4.20
2584 3412 0.168348 CGGGATATGTCGCTAGGTCG 59.832 60.000 5.03 0.00 35.31 4.79
2592 3420 1.961277 GGGCTTGCGGGATATGTCG 60.961 63.158 0.00 0.00 0.00 4.35
2593 3421 1.961277 CGGGCTTGCGGGATATGTC 60.961 63.158 0.00 0.00 0.00 3.06
2594 3422 2.111043 CGGGCTTGCGGGATATGT 59.889 61.111 0.00 0.00 0.00 2.29
2595 3423 1.669115 CTCGGGCTTGCGGGATATG 60.669 63.158 0.00 0.00 0.00 1.78
2596 3424 2.743718 CTCGGGCTTGCGGGATAT 59.256 61.111 0.00 0.00 0.00 1.63
2597 3425 3.546543 CCTCGGGCTTGCGGGATA 61.547 66.667 0.00 0.00 0.00 2.59
2624 3452 3.934391 GAGGAGGTTGTGTCGGCGG 62.934 68.421 7.21 0.00 0.00 6.13
2625 3453 2.432628 GAGGAGGTTGTGTCGGCG 60.433 66.667 0.00 0.00 0.00 6.46
2626 3454 2.047179 GGAGGAGGTTGTGTCGGC 60.047 66.667 0.00 0.00 0.00 5.54
2627 3455 2.663196 GGGAGGAGGTTGTGTCGG 59.337 66.667 0.00 0.00 0.00 4.79
2628 3456 2.261671 CGGGAGGAGGTTGTGTCG 59.738 66.667 0.00 0.00 0.00 4.35
2629 3457 2.047179 GCGGGAGGAGGTTGTGTC 60.047 66.667 0.00 0.00 0.00 3.67
2630 3458 4.003788 CGCGGGAGGAGGTTGTGT 62.004 66.667 0.00 0.00 0.00 3.72
2631 3459 4.760047 CCGCGGGAGGAGGTTGTG 62.760 72.222 20.10 0.00 0.00 3.33
2648 3476 0.250510 GAAATCATCGGGGAGGCCTC 60.251 60.000 25.59 25.59 0.00 4.70
2649 3477 0.695803 AGAAATCATCGGGGAGGCCT 60.696 55.000 3.86 3.86 0.00 5.19
2650 3478 0.250510 GAGAAATCATCGGGGAGGCC 60.251 60.000 0.00 0.00 0.00 5.19
2651 3479 0.601311 CGAGAAATCATCGGGGAGGC 60.601 60.000 0.00 0.00 36.54 4.70
2652 3480 0.753262 ACGAGAAATCATCGGGGAGG 59.247 55.000 0.00 0.00 44.36 4.30
2653 3481 1.858091 CACGAGAAATCATCGGGGAG 58.142 55.000 0.00 0.00 44.36 4.30
2654 3482 0.179084 GCACGAGAAATCATCGGGGA 60.179 55.000 0.00 0.00 43.75 4.81
2655 3483 0.461870 TGCACGAGAAATCATCGGGG 60.462 55.000 0.00 0.00 43.75 5.73
2656 3484 3.064079 TGCACGAGAAATCATCGGG 57.936 52.632 0.00 0.00 46.29 5.14


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

AutoCloner maintained by Alex Coulton.