Multiple sequence alignment - TraesCS7A01G443000

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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 TraesCS7A01G443000 chr7A 100.000 2773 0 0 1 2773 637337920 637335148 0.000000e+00 5121
1 TraesCS7A01G443000 chr7A 84.079 1162 114 23 587 1702 637037116 637035980 0.000000e+00 1055
2 TraesCS7A01G443000 chr7A 80.444 946 114 47 890 1801 637157987 637157079 0.000000e+00 656
3 TraesCS7A01G443000 chr7A 84.967 612 69 11 1097 1702 636919475 636918881 1.420000e-167 599
4 TraesCS7A01G443000 chr7A 81.178 611 71 21 890 1473 637078058 637077465 4.210000e-123 451
5 TraesCS7A01G443000 chr7A 85.246 122 16 2 2053 2174 200511785 200511904 1.040000e-24 124
6 TraesCS7A01G443000 chr7D 88.709 1913 166 26 355 2239 551929186 551927296 0.000000e+00 2290
7 TraesCS7A01G443000 chr7D 87.182 944 76 22 887 1811 551809216 551808299 0.000000e+00 1031
8 TraesCS7A01G443000 chr7D 82.903 930 103 32 901 1801 551000452 550999550 0.000000e+00 785
9 TraesCS7A01G443000 chr7D 84.325 689 70 18 587 1246 551115043 551114364 8.370000e-180 640
10 TraesCS7A01G443000 chr7D 87.707 423 30 10 1281 1702 551114374 551113973 8.990000e-130 473
11 TraesCS7A01G443000 chr7D 85.124 121 16 1 2053 2173 386719308 386719190 3.750000e-24 122
12 TraesCS7A01G443000 chr7D 82.836 134 18 4 2039 2171 31591329 31591200 6.280000e-22 115
13 TraesCS7A01G443000 chr7B 81.812 1479 192 41 362 1818 596783188 596781765 0.000000e+00 1170
14 TraesCS7A01G443000 chr7B 86.174 745 73 18 972 1702 595882196 595881468 0.000000e+00 778
15 TraesCS7A01G443000 chr7B 81.158 950 104 43 890 1797 596539080 596538164 0.000000e+00 693
16 TraesCS7A01G443000 chr7B 80.942 955 104 47 890 1801 596516244 596515325 0.000000e+00 684
17 TraesCS7A01G443000 chr7B 91.576 368 24 5 1433 1800 596680324 596679964 4.120000e-138 501
18 TraesCS7A01G443000 chr7B 88.701 354 39 1 1 354 596783717 596783365 5.490000e-117 431
19 TraesCS7A01G443000 chr7B 79.107 627 85 27 1184 1797 595993706 595993113 9.310000e-105 390
20 TraesCS7A01G443000 chr7B 87.651 332 36 3 2416 2745 596781449 596781121 5.600000e-102 381
21 TraesCS7A01G443000 chr6D 87.190 242 31 0 1 242 432676807 432676566 2.720000e-70 276
22 TraesCS7A01G443000 chr6A 86.777 242 32 0 1 242 578706504 578706263 1.270000e-68 270
23 TraesCS7A01G443000 chr1B 76.923 390 50 29 478 834 30402427 30402809 4.720000e-43 185
24 TraesCS7A01G443000 chr2B 86.179 123 15 1 2049 2171 709798766 709798646 6.230000e-27 132
25 TraesCS7A01G443000 chr2B 83.333 126 19 2 2048 2173 371166329 371166206 6.280000e-22 115
26 TraesCS7A01G443000 chr3B 85.246 122 16 1 2053 2174 201343458 201343577 1.040000e-24 124
27 TraesCS7A01G443000 chr2A 84.677 124 16 2 2048 2171 739282663 739282543 1.350000e-23 121
28 TraesCS7A01G443000 chr1D 85.000 120 16 1 2053 2172 453060033 453059916 1.350000e-23 121


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 TraesCS7A01G443000 chr7A 637335148 637337920 2772 True 5121.000000 5121 100.000000 1 2773 1 chr7A.!!$R5 2772
1 TraesCS7A01G443000 chr7A 637035980 637037116 1136 True 1055.000000 1055 84.079000 587 1702 1 chr7A.!!$R2 1115
2 TraesCS7A01G443000 chr7A 637157079 637157987 908 True 656.000000 656 80.444000 890 1801 1 chr7A.!!$R4 911
3 TraesCS7A01G443000 chr7A 636918881 636919475 594 True 599.000000 599 84.967000 1097 1702 1 chr7A.!!$R1 605
4 TraesCS7A01G443000 chr7A 637077465 637078058 593 True 451.000000 451 81.178000 890 1473 1 chr7A.!!$R3 583
5 TraesCS7A01G443000 chr7D 551927296 551929186 1890 True 2290.000000 2290 88.709000 355 2239 1 chr7D.!!$R5 1884
6 TraesCS7A01G443000 chr7D 551808299 551809216 917 True 1031.000000 1031 87.182000 887 1811 1 chr7D.!!$R4 924
7 TraesCS7A01G443000 chr7D 550999550 551000452 902 True 785.000000 785 82.903000 901 1801 1 chr7D.!!$R3 900
8 TraesCS7A01G443000 chr7D 551113973 551115043 1070 True 556.500000 640 86.016000 587 1702 2 chr7D.!!$R6 1115
9 TraesCS7A01G443000 chr7B 595881468 595882196 728 True 778.000000 778 86.174000 972 1702 1 chr7B.!!$R1 730
10 TraesCS7A01G443000 chr7B 596538164 596539080 916 True 693.000000 693 81.158000 890 1797 1 chr7B.!!$R4 907
11 TraesCS7A01G443000 chr7B 596515325 596516244 919 True 684.000000 684 80.942000 890 1801 1 chr7B.!!$R3 911
12 TraesCS7A01G443000 chr7B 596781121 596783717 2596 True 660.666667 1170 86.054667 1 2745 3 chr7B.!!$R6 2744
13 TraesCS7A01G443000 chr7B 595993113 595993706 593 True 390.000000 390 79.107000 1184 1797 1 chr7B.!!$R2 613

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
242 243 0.035739 ACGATTGGCAAGTACGGGTT 59.964 50.0 21.26 0.0 0.0 4.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1979 2394 0.179163 GCTATTTTCCTGTGGCGCAC 60.179 55.0 10.83 6.37 34.56 5.34 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
28 29 6.839124 AATCCACAAGCTAAATCACATGAA 57.161 33.333 0.00 0.00 0.00 2.57
30 31 5.069318 TCCACAAGCTAAATCACATGAACA 58.931 37.500 0.00 0.00 0.00 3.18
34 35 7.306749 CCACAAGCTAAATCACATGAACAAAAC 60.307 37.037 0.00 0.00 0.00 2.43
46 47 3.636679 TGAACAAAACCAGGTGGAATCA 58.363 40.909 2.10 0.00 38.94 2.57
60 61 3.934579 GTGGAATCAAACCAATGCAATCC 59.065 43.478 0.00 0.00 39.22 3.01
72 73 5.104193 ACCAATGCAATCCAGACTAAGATCT 60.104 40.000 0.00 0.00 0.00 2.75
76 77 6.798427 TGCAATCCAGACTAAGATCTAACT 57.202 37.500 0.00 0.00 0.00 2.24
94 95 9.543018 GATCTAACTGTAAACGGAAAAATGAAG 57.457 33.333 0.00 0.00 0.00 3.02
96 97 9.111613 TCTAACTGTAAACGGAAAAATGAAGAA 57.888 29.630 0.00 0.00 0.00 2.52
119 120 6.645790 AATGAAGCAATCAAGAAGAGTTGT 57.354 33.333 0.00 0.00 42.54 3.32
129 130 5.245531 TCAAGAAGAGTTGTCACAACAGTT 58.754 37.500 22.66 14.42 36.57 3.16
130 131 5.122239 TCAAGAAGAGTTGTCACAACAGTTG 59.878 40.000 22.66 15.91 36.57 3.16
138 139 2.171659 TGTCACAACAGTTGGCTAGGAA 59.828 45.455 17.76 0.00 34.12 3.36
160 161 4.445452 AAGCAAAGCAACATACCTGATG 57.555 40.909 0.00 0.00 41.79 3.07
166 167 3.411415 GCAACATACCTGATGCTCAAC 57.589 47.619 1.19 0.00 45.03 3.18
182 183 2.810852 CTCAACTTTGTGGCTCTCCTTC 59.189 50.000 0.00 0.00 0.00 3.46
184 185 0.603975 ACTTTGTGGCTCTCCTTCGC 60.604 55.000 0.00 0.00 0.00 4.70
185 186 0.321122 CTTTGTGGCTCTCCTTCGCT 60.321 55.000 0.00 0.00 0.00 4.93
198 199 4.586421 TCTCCTTCGCTCTACATGATGAAT 59.414 41.667 0.00 0.00 0.00 2.57
208 209 5.544650 TCTACATGATGAATGCGATGTGAT 58.455 37.500 0.00 0.00 40.22 3.06
212 213 6.839033 ACATGATGAATGCGATGTGATATTC 58.161 36.000 0.00 0.00 40.22 1.75
237 238 1.803334 TGGTCACGATTGGCAAGTAC 58.197 50.000 5.96 0.00 0.00 2.73
238 239 0.719465 GGTCACGATTGGCAAGTACG 59.281 55.000 17.73 17.73 0.00 3.67
242 243 0.035739 ACGATTGGCAAGTACGGGTT 59.964 50.000 21.26 0.00 0.00 4.11
243 244 0.446222 CGATTGGCAAGTACGGGTTG 59.554 55.000 5.96 0.00 0.00 3.77
244 245 1.816074 GATTGGCAAGTACGGGTTGA 58.184 50.000 5.96 0.00 0.00 3.18
246 247 0.535553 TTGGCAAGTACGGGTTGACC 60.536 55.000 0.00 0.00 31.22 4.02
247 248 1.071814 GGCAAGTACGGGTTGACCA 59.928 57.895 2.12 0.00 40.22 4.02
250 251 1.467342 GCAAGTACGGGTTGACCATTC 59.533 52.381 2.12 0.00 40.22 2.67
251 252 2.773487 CAAGTACGGGTTGACCATTCA 58.227 47.619 2.12 0.00 40.22 2.57
305 306 6.634805 TCATCAGTTCTAGTGAATGAAGGAC 58.365 40.000 3.85 0.00 34.40 3.85
324 325 3.997021 GGACGTCTTTGAACATGACTCAT 59.003 43.478 16.46 0.00 0.00 2.90
326 327 5.348418 ACGTCTTTGAACATGACTCATTG 57.652 39.130 0.00 0.00 0.00 2.82
329 330 4.913924 GTCTTTGAACATGACTCATTGCAC 59.086 41.667 0.00 0.00 0.00 4.57
341 342 5.414144 TGACTCATTGCACGGAATCAAATAA 59.586 36.000 0.00 0.00 0.00 1.40
343 344 4.657055 TCATTGCACGGAATCAAATAACG 58.343 39.130 0.00 0.00 0.00 3.18
351 352 5.732647 CACGGAATCAAATAACGACATCAAC 59.267 40.000 0.00 0.00 0.00 3.18
395 565 4.899239 CGTGCGGAGATGGGGCTC 62.899 72.222 0.00 0.00 0.00 4.70
429 599 2.283529 ATGAACCAGAGTCGCCGGT 61.284 57.895 1.90 0.00 33.32 5.28
431 601 2.342648 AACCAGAGTCGCCGGTTC 59.657 61.111 1.90 0.00 38.69 3.62
432 602 2.504274 AACCAGAGTCGCCGGTTCA 61.504 57.895 1.90 0.00 38.69 3.18
435 605 2.915659 AGAGTCGCCGGTTCACCA 60.916 61.111 1.90 0.00 35.14 4.17
466 641 2.602676 GGGCTACCAAGGACCTGCA 61.603 63.158 0.00 0.00 36.50 4.41
467 642 1.078143 GGCTACCAAGGACCTGCAG 60.078 63.158 6.78 6.78 0.00 4.41
476 651 1.305718 GGACCTGCAGGAGAGAGGT 60.306 63.158 39.19 16.11 43.06 3.85
490 665 3.318313 AGAGAGGTGAAAGGGTTTGAGA 58.682 45.455 0.00 0.00 0.00 3.27
516 691 2.541999 CGAGCTATCGTGGGAGAAAGAC 60.542 54.545 0.00 0.00 44.09 3.01
524 699 0.620556 TGGGAGAAAGACAGATGGGC 59.379 55.000 0.00 0.00 0.00 5.36
566 741 0.904649 CAGACAGATAGGGTGCACCA 59.095 55.000 35.78 18.49 43.89 4.17
567 742 0.905357 AGACAGATAGGGTGCACCAC 59.095 55.000 35.78 24.52 43.89 4.16
594 769 1.550524 GATCAATCGATCCATCCCCGA 59.449 52.381 0.00 0.00 42.03 5.14
613 788 2.954989 CGAATCATCCTCTCACCTCTCA 59.045 50.000 0.00 0.00 0.00 3.27
618 793 0.400594 TCCTCTCACCTCTCACGTGA 59.599 55.000 18.88 18.88 37.91 4.35
626 801 2.050714 TCTCACGTGACGCCGAAC 60.051 61.111 15.76 0.00 0.00 3.95
636 811 3.702048 CGCCGAACCCCCTTCTCA 61.702 66.667 0.00 0.00 0.00 3.27
646 821 1.834263 CCCCCTTCTCATTTCTCTCGT 59.166 52.381 0.00 0.00 0.00 4.18
650 825 3.131223 CCCTTCTCATTTCTCTCGTAGCA 59.869 47.826 0.00 0.00 0.00 3.49
701 879 1.344065 TTCCTTCGTGAGGGTTAGCA 58.656 50.000 7.56 0.00 46.31 3.49
715 899 0.251916 TTAGCAACCGGGTGGATCAG 59.748 55.000 23.69 0.00 39.21 2.90
835 1019 3.772932 TCGAACGCATAATCTAACGGTT 58.227 40.909 0.00 0.00 0.00 4.44
859 1043 5.817296 TGAAAACGCTGATATAGTGAAGCAT 59.183 36.000 0.00 0.00 39.30 3.79
884 1068 5.925509 TCAGTTTAGGCTCAGTTTTACTGT 58.074 37.500 6.71 0.00 46.03 3.55
885 1069 5.758296 TCAGTTTAGGCTCAGTTTTACTGTG 59.242 40.000 6.71 5.76 46.03 3.66
916 1121 7.956328 ACCCTAAAAGATTAAGATTTGGACC 57.044 36.000 0.00 0.00 0.00 4.46
938 1143 6.731467 ACCATATAAAACATCAGACAACCCT 58.269 36.000 0.00 0.00 0.00 4.34
943 1148 1.296392 CATCAGACAACCCTCCGCA 59.704 57.895 0.00 0.00 0.00 5.69
966 1171 0.537188 TCCTCTCGAGTGCCCAAATC 59.463 55.000 13.13 0.00 0.00 2.17
996 1217 2.348998 CACTCCCACAGTGCCTCC 59.651 66.667 0.00 0.00 46.30 4.30
1371 1676 3.885521 GAGGCCGTACGTCCTCCG 61.886 72.222 30.26 8.27 42.30 4.63
1415 1721 5.756195 ATGCATTCACCACACACATATAC 57.244 39.130 0.00 0.00 0.00 1.47
1472 1780 3.393089 AATATGCAGGTAGAGAAGGCG 57.607 47.619 0.00 0.00 0.00 5.52
1586 1894 1.511305 CGTCGAGGTGGTATGCTGT 59.489 57.895 0.00 0.00 0.00 4.40
1635 1951 1.592223 CTGACCGAGTTCCTGGACC 59.408 63.158 0.00 0.00 0.00 4.46
1762 2108 2.750712 ACTCCTCGAGTAGCTTGTCTTC 59.249 50.000 12.31 0.00 41.51 2.87
1791 2140 8.726870 TTTTTAACGAAGGTATTATCTCCCTG 57.273 34.615 0.00 0.00 0.00 4.45
1848 2262 1.180029 CTGTTTGGATTGGAGCCCTG 58.820 55.000 0.00 0.00 0.00 4.45
1865 2279 1.180029 CTGGACTGCCCATCCAAAAG 58.820 55.000 2.67 0.00 45.67 2.27
1889 2303 2.034999 GTTCATTGACCGGGCCCA 59.965 61.111 24.92 0.53 0.00 5.36
1907 2321 1.451028 AGGCTTTCTCGCTGATGGC 60.451 57.895 0.00 0.00 37.64 4.40
1961 2376 8.319146 TCTCGGTTCCTTTAGTTCAATTCTAAT 58.681 33.333 0.00 0.00 0.00 1.73
1962 2377 8.263940 TCGGTTCCTTTAGTTCAATTCTAATG 57.736 34.615 0.00 0.00 0.00 1.90
1964 2379 8.175716 CGGTTCCTTTAGTTCAATTCTAATGAC 58.824 37.037 0.00 0.00 0.00 3.06
1991 2406 1.904287 AAAAATAGTGCGCCACAGGA 58.096 45.000 4.18 0.00 36.74 3.86
1994 2409 1.904287 AATAGTGCGCCACAGGAAAA 58.096 45.000 4.18 0.00 36.74 2.29
1995 2410 2.128771 ATAGTGCGCCACAGGAAAAT 57.871 45.000 4.18 0.00 36.74 1.82
1996 2411 2.772077 TAGTGCGCCACAGGAAAATA 57.228 45.000 4.18 0.00 36.74 1.40
1999 2414 1.062525 GCGCCACAGGAAAATAGCG 59.937 57.895 0.00 0.00 45.91 4.26
2000 2415 1.644786 GCGCCACAGGAAAATAGCGT 61.645 55.000 0.00 0.00 45.00 5.07
2001 2416 0.373716 CGCCACAGGAAAATAGCGTC 59.626 55.000 0.00 0.00 38.81 5.19
2003 2418 1.006832 CCACAGGAAAATAGCGTCGG 58.993 55.000 0.00 0.00 0.00 4.79
2015 2430 4.870221 ATAGCGTCGGTTTAAAATCCAC 57.130 40.909 0.65 0.00 0.00 4.02
2016 2431 1.808343 AGCGTCGGTTTAAAATCCACC 59.192 47.619 0.00 0.00 0.00 4.61
2017 2432 1.808343 GCGTCGGTTTAAAATCCACCT 59.192 47.619 0.00 0.00 0.00 4.00
2020 2435 4.223659 CGTCGGTTTAAAATCCACCTTTG 58.776 43.478 0.00 0.00 0.00 2.77
2064 2479 5.753921 GCTATAGCATGTTACTTCCTTCGTT 59.246 40.000 20.01 0.00 41.59 3.85
2065 2480 6.074249 GCTATAGCATGTTACTTCCTTCGTTC 60.074 42.308 20.01 0.00 41.59 3.95
2066 2481 4.002906 AGCATGTTACTTCCTTCGTTCA 57.997 40.909 0.00 0.00 0.00 3.18
2067 2482 3.997021 AGCATGTTACTTCCTTCGTTCAG 59.003 43.478 0.00 0.00 0.00 3.02
2147 2566 8.087750 TCCATTTTTATCCATTTCTGTGACAAC 58.912 33.333 0.00 0.00 0.00 3.32
2158 2577 7.925483 CCATTTCTGTGACAACTAATTTTGGAA 59.075 33.333 0.00 0.00 0.00 3.53
2162 2581 4.586841 TGTGACAACTAATTTTGGAAGGGG 59.413 41.667 0.00 0.00 0.00 4.79
2192 2612 8.622948 AGTATATCGCACTATAGCATGCTATA 57.377 34.615 34.39 34.39 39.65 1.31
2196 2616 5.778862 TCGCACTATAGCATGCTATAAACA 58.221 37.500 35.33 22.54 39.94 2.83
2199 2619 6.401474 CGCACTATAGCATGCTATAAACAAGG 60.401 42.308 35.33 27.30 39.94 3.61
2200 2620 6.621596 GCACTATAGCATGCTATAAACAAGGC 60.622 42.308 35.33 27.86 39.94 4.35
2202 2622 7.120285 CACTATAGCATGCTATAAACAAGGCAT 59.880 37.037 35.33 18.80 44.77 4.40
2239 2659 6.808704 TGATATAACGATCTATTGCTCAGCAC 59.191 38.462 0.00 0.00 38.71 4.40
2240 2660 2.967599 ACGATCTATTGCTCAGCACA 57.032 45.000 0.00 0.00 38.71 4.57
2241 2661 2.544685 ACGATCTATTGCTCAGCACAC 58.455 47.619 0.00 0.00 38.71 3.82
2242 2662 2.167281 ACGATCTATTGCTCAGCACACT 59.833 45.455 0.00 0.00 38.71 3.55
2243 2663 3.381590 ACGATCTATTGCTCAGCACACTA 59.618 43.478 0.00 0.00 38.71 2.74
2244 2664 3.733224 CGATCTATTGCTCAGCACACTAC 59.267 47.826 0.00 0.00 38.71 2.73
2245 2665 4.686972 GATCTATTGCTCAGCACACTACA 58.313 43.478 0.00 0.00 38.71 2.74
2246 2666 4.115401 TCTATTGCTCAGCACACTACAG 57.885 45.455 0.00 0.00 38.71 2.74
2247 2667 1.446907 ATTGCTCAGCACACTACAGC 58.553 50.000 0.00 0.00 38.71 4.40
2248 2668 0.106521 TTGCTCAGCACACTACAGCA 59.893 50.000 0.00 0.00 38.71 4.41
2249 2669 0.322648 TGCTCAGCACACTACAGCAT 59.677 50.000 0.00 0.00 36.53 3.79
2250 2670 0.725686 GCTCAGCACACTACAGCATG 59.274 55.000 0.00 0.00 46.00 4.06
2251 2671 0.725686 CTCAGCACACTACAGCATGC 59.274 55.000 10.51 10.51 42.53 4.06
2253 2673 1.550072 TCAGCACACTACAGCATGCTA 59.450 47.619 22.19 4.69 46.49 3.49
2254 2674 2.169144 TCAGCACACTACAGCATGCTAT 59.831 45.455 22.19 12.95 46.49 2.97
2255 2675 2.941064 CAGCACACTACAGCATGCTATT 59.059 45.455 22.19 13.09 46.49 1.73
2256 2676 4.122046 CAGCACACTACAGCATGCTATTA 58.878 43.478 22.19 13.56 46.49 0.98
2257 2677 4.210746 CAGCACACTACAGCATGCTATTAG 59.789 45.833 22.19 23.60 46.49 1.73
2258 2678 3.496130 GCACACTACAGCATGCTATTAGG 59.504 47.826 27.31 20.98 42.53 2.69
2259 2679 4.060900 CACACTACAGCATGCTATTAGGG 58.939 47.826 25.86 25.86 42.53 3.53
2260 2680 3.071602 ACACTACAGCATGCTATTAGGGG 59.928 47.826 28.72 23.23 42.53 4.79
2261 2681 2.039084 ACTACAGCATGCTATTAGGGGC 59.961 50.000 27.31 0.00 42.53 5.80
2262 2682 0.250467 ACAGCATGCTATTAGGGGCG 60.250 55.000 22.19 7.14 42.53 6.13
2263 2683 0.250467 CAGCATGCTATTAGGGGCGT 60.250 55.000 22.19 0.00 0.00 5.68
2264 2684 0.035458 AGCATGCTATTAGGGGCGTC 59.965 55.000 21.21 0.00 0.00 5.19
2265 2685 0.250295 GCATGCTATTAGGGGCGTCA 60.250 55.000 11.37 0.00 0.00 4.35
2266 2686 1.611673 GCATGCTATTAGGGGCGTCAT 60.612 52.381 11.37 0.00 0.00 3.06
2267 2687 2.354704 GCATGCTATTAGGGGCGTCATA 60.355 50.000 11.37 0.00 0.00 2.15
2268 2688 3.525537 CATGCTATTAGGGGCGTCATAG 58.474 50.000 0.00 0.00 0.00 2.23
2269 2689 1.275291 TGCTATTAGGGGCGTCATAGC 59.725 52.381 9.48 9.48 43.01 2.97
2270 2690 1.736032 GCTATTAGGGGCGTCATAGCG 60.736 57.143 1.86 0.00 35.95 4.26
2280 2700 2.645628 CGTCATAGCGCGCTATTTTT 57.354 45.000 42.55 26.07 37.16 1.94
2318 2738 1.299541 AACTGTTGGCGAGTTGTCAG 58.700 50.000 0.00 0.00 32.30 3.51
2319 2739 0.532862 ACTGTTGGCGAGTTGTCAGG 60.533 55.000 0.00 0.00 30.83 3.86
2323 2743 1.701031 TTGGCGAGTTGTCAGGGGAA 61.701 55.000 0.00 0.00 30.83 3.97
2325 2745 0.322546 GGCGAGTTGTCAGGGGAAAT 60.323 55.000 0.00 0.00 0.00 2.17
2329 2749 3.694566 GCGAGTTGTCAGGGGAAATAATT 59.305 43.478 0.00 0.00 0.00 1.40
2332 2752 5.163754 CGAGTTGTCAGGGGAAATAATTGTC 60.164 44.000 0.00 0.00 0.00 3.18
2333 2753 5.892348 AGTTGTCAGGGGAAATAATTGTCT 58.108 37.500 0.00 0.00 0.00 3.41
2340 2760 4.651045 AGGGGAAATAATTGTCTGCCAATC 59.349 41.667 0.00 0.00 43.04 2.67
2358 2778 4.024556 CCAATCATTTGGCTCATCTACGTC 60.025 45.833 0.00 0.00 45.71 4.34
2360 2780 3.785486 TCATTTGGCTCATCTACGTCTG 58.215 45.455 0.00 0.00 0.00 3.51
2361 2781 3.447229 TCATTTGGCTCATCTACGTCTGA 59.553 43.478 0.00 0.00 0.00 3.27
2363 2783 1.834188 TGGCTCATCTACGTCTGACA 58.166 50.000 8.73 0.00 0.00 3.58
2364 2784 1.745653 TGGCTCATCTACGTCTGACAG 59.254 52.381 8.73 0.00 0.00 3.51
2365 2785 1.066303 GGCTCATCTACGTCTGACAGG 59.934 57.143 8.73 0.00 0.00 4.00
2366 2786 1.066303 GCTCATCTACGTCTGACAGGG 59.934 57.143 8.73 0.00 0.00 4.45
2367 2787 1.066303 CTCATCTACGTCTGACAGGGC 59.934 57.143 8.73 0.00 0.00 5.19
2368 2788 0.248661 CATCTACGTCTGACAGGGCG 60.249 60.000 8.73 15.33 0.00 6.13
2369 2789 1.384989 ATCTACGTCTGACAGGGCGG 61.385 60.000 19.13 7.41 0.00 6.13
2370 2790 3.064987 CTACGTCTGACAGGGCGGG 62.065 68.421 19.13 10.89 0.00 6.13
2374 2794 4.974438 TCTGACAGGGCGGGGGTT 62.974 66.667 1.81 0.00 0.00 4.11
2375 2795 4.722700 CTGACAGGGCGGGGGTTG 62.723 72.222 0.00 0.00 0.00 3.77
2382 2802 2.372074 GGGCGGGGGTTGTCTGATA 61.372 63.158 0.00 0.00 0.00 2.15
2390 2810 5.354234 GCGGGGGTTGTCTGATATATATTTG 59.646 44.000 0.00 0.00 0.00 2.32
2399 2819 8.272545 TGTCTGATATATATTTGCCTGATTGC 57.727 34.615 0.00 0.00 0.00 3.56
2403 2823 7.977904 TGATATATATTTGCCTGATTGCGAAG 58.022 34.615 0.00 0.00 38.01 3.79
2404 2824 7.823799 TGATATATATTTGCCTGATTGCGAAGA 59.176 33.333 0.00 0.00 38.01 2.87
2434 2867 7.661230 GTGCAACACATGGATGGAGATCCTA 62.661 48.000 0.00 0.00 42.59 2.94
2467 2900 1.960953 GCCCCGTTTCTAGAGGAGAGT 60.961 57.143 0.00 0.00 34.93 3.24
2472 2905 3.008330 CGTTTCTAGAGGAGAGTTCGGA 58.992 50.000 0.00 0.00 34.93 4.55
2474 2907 3.715638 TTCTAGAGGAGAGTTCGGACA 57.284 47.619 0.00 0.00 34.93 4.02
2502 2936 4.640201 TGCAAACAAGTTATATGCCTCTCC 59.360 41.667 5.84 0.00 36.20 3.71
2503 2937 4.036852 GCAAACAAGTTATATGCCTCTCCC 59.963 45.833 0.00 0.00 0.00 4.30
2518 2952 2.177594 CTCCCCAGCGTCTTTCTGCT 62.178 60.000 0.00 0.00 43.58 4.24
2555 2989 4.278419 AGAAACGAGTCTTCCCCATTTTTG 59.722 41.667 0.00 0.00 0.00 2.44
2563 2997 3.361174 CCCATTTTTGGGCGACGT 58.639 55.556 0.00 0.00 42.99 4.34
2574 3008 2.126031 GCGACGTCTCCAACTCCC 60.126 66.667 14.70 0.00 0.00 4.30
2578 3012 0.244178 GACGTCTCCAACTCCCAGAC 59.756 60.000 8.70 0.00 34.36 3.51
2585 3019 0.252742 CCAACTCCCAGACCTAGGGT 60.253 60.000 14.81 0.00 46.82 4.34
2607 3041 2.209315 ACCCATGTTTGCCTGGTGC 61.209 57.895 0.00 0.00 41.77 5.01
2617 3051 0.749818 TGCCTGGTGCGAACAAAAGA 60.750 50.000 0.00 0.00 45.60 2.52
2627 3061 4.451096 GTGCGAACAAAAGATTAGAGGTGA 59.549 41.667 0.00 0.00 0.00 4.02
2628 3062 5.122396 GTGCGAACAAAAGATTAGAGGTGAT 59.878 40.000 0.00 0.00 0.00 3.06
2629 3063 5.351465 TGCGAACAAAAGATTAGAGGTGATC 59.649 40.000 0.00 0.00 0.00 2.92
2636 3070 7.671398 ACAAAAGATTAGAGGTGATCCACATTT 59.329 33.333 0.00 0.00 35.86 2.32
2662 3097 0.323957 GAAGTAGTTGCCTCCCCGTT 59.676 55.000 0.00 0.00 0.00 4.44
2665 3100 1.017701 GTAGTTGCCTCCCCGTTTCG 61.018 60.000 0.00 0.00 0.00 3.46
2668 3103 3.540367 TTGCCTCCCCGTTTCGTCC 62.540 63.158 0.00 0.00 0.00 4.79
2676 3111 0.893447 CCCGTTTCGTCCTCCTACTT 59.107 55.000 0.00 0.00 0.00 2.24
2686 3121 4.701171 TCGTCCTCCTACTTTTCTTCTCTC 59.299 45.833 0.00 0.00 0.00 3.20
2691 3126 3.515901 TCCTACTTTTCTTCTCTCTGGCC 59.484 47.826 0.00 0.00 0.00 5.36
2705 3140 3.768757 TCTCTGGCCCATTTGTTATTTGG 59.231 43.478 0.00 0.00 0.00 3.28
2706 3141 2.235898 TCTGGCCCATTTGTTATTTGGC 59.764 45.455 0.00 0.00 38.16 4.52
2725 3160 1.206849 GCTTCTAGCTGCAAGAGAGGT 59.793 52.381 1.02 0.00 38.45 3.85
2731 3166 1.082690 GCTGCAAGAGAGGTAACTGC 58.917 55.000 0.00 0.00 44.12 4.40
2734 3169 2.934364 CTGCAAGAGAGGTAACTGCCAG 60.934 54.545 0.00 0.00 44.12 4.85
2752 3187 1.826720 CAGGATGGTTTTGGTGATGGG 59.173 52.381 0.00 0.00 0.00 4.00
2753 3188 0.536724 GGATGGTTTTGGTGATGGGC 59.463 55.000 0.00 0.00 0.00 5.36
2754 3189 0.173255 GATGGTTTTGGTGATGGGCG 59.827 55.000 0.00 0.00 0.00 6.13
2755 3190 0.251564 ATGGTTTTGGTGATGGGCGA 60.252 50.000 0.00 0.00 0.00 5.54
2756 3191 0.251564 TGGTTTTGGTGATGGGCGAT 60.252 50.000 0.00 0.00 0.00 4.58
2757 3192 1.004862 TGGTTTTGGTGATGGGCGATA 59.995 47.619 0.00 0.00 0.00 2.92
2758 3193 1.676006 GGTTTTGGTGATGGGCGATAG 59.324 52.381 0.00 0.00 0.00 2.08
2759 3194 1.676006 GTTTTGGTGATGGGCGATAGG 59.324 52.381 0.00 0.00 0.00 2.57
2760 3195 1.208706 TTTGGTGATGGGCGATAGGA 58.791 50.000 0.00 0.00 0.00 2.94
2761 3196 1.434188 TTGGTGATGGGCGATAGGAT 58.566 50.000 0.00 0.00 0.00 3.24
2762 3197 0.976641 TGGTGATGGGCGATAGGATC 59.023 55.000 0.00 0.00 0.00 3.36
2772 3207 1.073964 CGATAGGATCGCAATGCTGG 58.926 55.000 2.94 0.00 46.55 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 6.642131 CACCTGGTTTTGTTCATGTGATTTAG 59.358 38.462 0.00 0.00 33.41 1.85
28 29 3.133901 GGTTTGATTCCACCTGGTTTTGT 59.866 43.478 0.00 0.00 36.34 2.83
30 31 3.379452 TGGTTTGATTCCACCTGGTTTT 58.621 40.909 0.00 0.00 36.34 2.43
34 35 2.354003 GCATTGGTTTGATTCCACCTGG 60.354 50.000 0.00 0.00 34.45 4.45
46 47 5.324409 TCTTAGTCTGGATTGCATTGGTTT 58.676 37.500 0.00 0.00 0.00 3.27
60 61 7.759465 TCCGTTTACAGTTAGATCTTAGTCTG 58.241 38.462 0.00 7.47 0.00 3.51
76 77 9.243637 CTTCATTTCTTCATTTTTCCGTTTACA 57.756 29.630 0.00 0.00 0.00 2.41
94 95 7.144000 ACAACTCTTCTTGATTGCTTCATTTC 58.856 34.615 0.00 0.00 33.34 2.17
96 97 6.263842 TGACAACTCTTCTTGATTGCTTCATT 59.736 34.615 0.00 0.00 33.34 2.57
119 120 3.569194 TTTCCTAGCCAACTGTTGTGA 57.431 42.857 18.38 5.14 0.00 3.58
129 130 1.993956 TGCTTTGCTTTTCCTAGCCA 58.006 45.000 0.00 0.00 40.49 4.75
130 131 2.035832 TGTTGCTTTGCTTTTCCTAGCC 59.964 45.455 0.00 0.00 40.49 3.93
138 139 4.813027 CATCAGGTATGTTGCTTTGCTTT 58.187 39.130 0.00 0.00 0.00 3.51
160 161 0.877743 GGAGAGCCACAAAGTTGAGC 59.122 55.000 0.00 0.77 0.00 4.26
163 164 1.532868 CGAAGGAGAGCCACAAAGTTG 59.467 52.381 0.00 0.00 36.29 3.16
166 167 0.321122 AGCGAAGGAGAGCCACAAAG 60.321 55.000 0.00 0.00 36.29 2.77
182 183 2.397549 TCGCATTCATCATGTAGAGCG 58.602 47.619 13.38 13.38 44.66 5.03
184 185 4.986659 TCACATCGCATTCATCATGTAGAG 59.013 41.667 0.00 0.00 34.98 2.43
185 186 4.947645 TCACATCGCATTCATCATGTAGA 58.052 39.130 0.00 0.00 34.98 2.59
208 209 4.441792 CCAATCGTGACCATCAGTGAATA 58.558 43.478 0.00 0.00 0.00 1.75
212 213 0.729116 GCCAATCGTGACCATCAGTG 59.271 55.000 0.00 0.00 0.00 3.66
224 225 0.446222 CAACCCGTACTTGCCAATCG 59.554 55.000 0.00 0.00 0.00 3.34
237 238 0.523072 CAGCTTGAATGGTCAACCCG 59.477 55.000 0.00 0.00 38.88 5.28
238 239 1.270550 CACAGCTTGAATGGTCAACCC 59.729 52.381 0.00 0.00 38.88 4.11
242 243 2.040145 TCATCCACAGCTTGAATGGTCA 59.960 45.455 3.63 0.00 34.89 4.02
243 244 2.715046 TCATCCACAGCTTGAATGGTC 58.285 47.619 3.63 0.00 34.89 4.02
244 245 2.885135 TCATCCACAGCTTGAATGGT 57.115 45.000 3.63 0.00 34.89 3.55
247 248 5.733620 AAACATTCATCCACAGCTTGAAT 57.266 34.783 5.00 5.00 39.92 2.57
250 251 3.916172 CGAAAACATTCATCCACAGCTTG 59.084 43.478 0.00 0.00 0.00 4.01
251 252 3.820467 TCGAAAACATTCATCCACAGCTT 59.180 39.130 0.00 0.00 0.00 3.74
255 256 3.694072 GGGATCGAAAACATTCATCCACA 59.306 43.478 15.44 0.00 33.85 4.17
305 306 4.153986 GCAATGAGTCATGTTCAAAGACG 58.846 43.478 6.34 0.00 37.36 4.18
324 325 3.498777 TGTCGTTATTTGATTCCGTGCAA 59.501 39.130 0.00 0.00 0.00 4.08
326 327 3.733024 TGTCGTTATTTGATTCCGTGC 57.267 42.857 0.00 0.00 0.00 5.34
329 330 6.106877 AGTTGATGTCGTTATTTGATTCCG 57.893 37.500 0.00 0.00 0.00 4.30
341 342 0.109086 CTCGCAGGAGTTGATGTCGT 60.109 55.000 0.00 0.00 35.48 4.34
343 344 1.474478 TCTCTCGCAGGAGTTGATGTC 59.526 52.381 3.39 0.00 41.26 3.06
351 352 2.091541 ACTCTCTTTCTCTCGCAGGAG 58.908 52.381 0.00 0.00 41.89 3.69
395 565 1.503091 CATGTCGCCACCACATGTG 59.497 57.895 19.31 19.31 44.18 3.21
466 641 2.373502 CAAACCCTTTCACCTCTCTCCT 59.626 50.000 0.00 0.00 0.00 3.69
467 642 2.372172 TCAAACCCTTTCACCTCTCTCC 59.628 50.000 0.00 0.00 0.00 3.71
476 651 2.038426 TCGCTCATCTCAAACCCTTTCA 59.962 45.455 0.00 0.00 0.00 2.69
594 769 2.692557 CGTGAGAGGTGAGAGGATGATT 59.307 50.000 0.00 0.00 0.00 2.57
618 793 3.703127 GAGAAGGGGGTTCGGCGT 61.703 66.667 6.85 0.00 40.49 5.68
626 801 1.834263 ACGAGAGAAATGAGAAGGGGG 59.166 52.381 0.00 0.00 0.00 5.40
646 821 1.080093 CGGAACTGCTCGGTTGCTA 60.080 57.895 10.56 0.00 35.80 3.49
650 825 1.594293 CACACGGAACTGCTCGGTT 60.594 57.895 0.00 0.00 35.53 4.44
701 879 3.728373 GGCCTGATCCACCCGGTT 61.728 66.667 0.00 0.00 0.00 4.44
728 912 2.496817 GGCCGCTACTCTGGTGAG 59.503 66.667 0.00 0.00 45.43 3.51
731 915 0.689745 TAATGGGCCGCTACTCTGGT 60.690 55.000 0.00 0.00 0.00 4.00
771 955 3.120321 TCGTTTCAGCCACAATGTACT 57.880 42.857 0.00 0.00 0.00 2.73
835 1019 5.175127 TGCTTCACTATATCAGCGTTTTCA 58.825 37.500 0.00 0.00 34.82 2.69
850 1034 3.262915 AGCCTAAACTGAGATGCTTCACT 59.737 43.478 2.07 0.00 0.00 3.41
855 1039 2.836981 ACTGAGCCTAAACTGAGATGCT 59.163 45.455 0.00 0.00 0.00 3.79
856 1040 3.258971 ACTGAGCCTAAACTGAGATGC 57.741 47.619 0.00 0.00 0.00 3.91
859 1043 6.420913 AGTAAAACTGAGCCTAAACTGAGA 57.579 37.500 0.00 0.00 0.00 3.27
916 1121 6.017934 CGGAGGGTTGTCTGATGTTTTATATG 60.018 42.308 0.00 0.00 0.00 1.78
938 1143 4.710167 TCGAGAGGACGGTGCGGA 62.710 66.667 0.00 0.00 0.00 5.54
943 1148 3.063084 GGCACTCGAGAGGACGGT 61.063 66.667 21.68 0.00 0.00 4.83
996 1217 0.110419 TTTGCGAGTTCGGCATTTCG 60.110 50.000 3.50 0.00 40.23 3.46
1065 1307 4.617486 CGCGCGCGGTACTCCATA 62.617 66.667 43.28 0.00 35.56 2.74
1393 1698 4.273235 CGTATATGTGTGTGGTGAATGCAT 59.727 41.667 0.00 0.00 0.00 3.96
1415 1721 8.487970 CAATTATTACTACTCCTACAACATGCG 58.512 37.037 0.00 0.00 0.00 4.73
1586 1894 1.591703 GATCGGTGACTCCTGCACA 59.408 57.895 0.00 0.00 37.99 4.57
1635 1951 0.796312 CCGAACCGGTTTCTCACATG 59.204 55.000 23.22 4.28 42.73 3.21
1783 2132 9.878737 ATTTGATTAATGAATTCTCAGGGAGAT 57.121 29.630 7.05 0.00 38.56 2.75
1818 2169 1.069596 CCAAACAGCCCAAACCTGC 59.930 57.895 0.00 0.00 33.65 4.85
1848 2262 1.923356 TTCTTTTGGATGGGCAGTCC 58.077 50.000 0.82 0.82 36.26 3.85
1865 2279 2.673893 GCCCGGTCAATGAACCAATTTC 60.674 50.000 0.00 0.00 39.43 2.17
1889 2303 1.451028 GCCATCAGCGAGAAAGCCT 60.451 57.895 0.00 0.00 38.01 4.58
1907 2321 0.951558 GGCGCACCCATAATTAGTGG 59.048 55.000 10.83 6.32 36.47 4.00
1939 2354 9.232473 AGTCATTAGAATTGAACTAAAGGAACC 57.768 33.333 0.00 0.00 34.28 3.62
1972 2387 1.904287 TCCTGTGGCGCACTATTTTT 58.096 45.000 10.83 0.00 35.11 1.94
1973 2388 1.904287 TTCCTGTGGCGCACTATTTT 58.096 45.000 10.83 0.00 35.11 1.82
1974 2389 1.904287 TTTCCTGTGGCGCACTATTT 58.096 45.000 10.83 0.00 35.11 1.40
1977 2392 2.627945 CTATTTTCCTGTGGCGCACTA 58.372 47.619 10.83 0.00 35.11 2.74
1979 2394 0.179163 GCTATTTTCCTGTGGCGCAC 60.179 55.000 10.83 6.37 34.56 5.34
1980 2395 1.643868 CGCTATTTTCCTGTGGCGCA 61.644 55.000 10.83 0.00 36.46 6.09
1981 2396 1.062525 CGCTATTTTCCTGTGGCGC 59.937 57.895 0.00 0.00 36.46 6.53
1982 2397 0.373716 GACGCTATTTTCCTGTGGCG 59.626 55.000 0.00 0.00 46.47 5.69
1983 2398 0.373716 CGACGCTATTTTCCTGTGGC 59.626 55.000 0.00 0.00 0.00 5.01
1984 2399 1.006832 CCGACGCTATTTTCCTGTGG 58.993 55.000 0.00 0.00 0.00 4.17
1985 2400 1.722011 ACCGACGCTATTTTCCTGTG 58.278 50.000 0.00 0.00 0.00 3.66
1987 2402 4.932268 TTAAACCGACGCTATTTTCCTG 57.068 40.909 0.00 0.00 0.00 3.86
1989 2404 5.740569 GGATTTTAAACCGACGCTATTTTCC 59.259 40.000 0.00 0.00 0.00 3.13
1990 2405 6.249893 GTGGATTTTAAACCGACGCTATTTTC 59.750 38.462 0.00 0.00 0.00 2.29
1991 2406 6.088173 GTGGATTTTAAACCGACGCTATTTT 58.912 36.000 0.00 0.00 0.00 1.82
1994 2409 3.624410 GGTGGATTTTAAACCGACGCTAT 59.376 43.478 0.00 0.00 0.00 2.97
1995 2410 3.002102 GGTGGATTTTAAACCGACGCTA 58.998 45.455 0.00 0.00 0.00 4.26
1996 2411 1.808343 GGTGGATTTTAAACCGACGCT 59.192 47.619 0.00 0.00 0.00 5.07
2015 2430 9.084164 GCACGATTATATATAGTACACCAAAGG 57.916 37.037 0.00 0.00 0.00 3.11
2016 2431 9.856488 AGCACGATTATATATAGTACACCAAAG 57.144 33.333 0.00 0.00 0.00 2.77
2051 2466 7.929785 ACAAGTAATTCTGAACGAAGGAAGTAA 59.070 33.333 0.00 0.00 34.56 2.24
2061 2476 9.694520 CATTTATCTGACAAGTAATTCTGAACG 57.305 33.333 0.00 0.00 0.00 3.95
2122 2541 8.090214 AGTTGTCACAGAAATGGATAAAAATGG 58.910 33.333 0.00 0.00 0.00 3.16
2136 2555 6.040391 CCCTTCCAAAATTAGTTGTCACAGAA 59.960 38.462 0.00 0.00 0.00 3.02
2147 2566 3.269643 ACTCCCTCCCCTTCCAAAATTAG 59.730 47.826 0.00 0.00 0.00 1.73
2154 2573 2.225293 CGATATACTCCCTCCCCTTCCA 60.225 54.545 0.00 0.00 0.00 3.53
2155 2574 2.458620 CGATATACTCCCTCCCCTTCC 58.541 57.143 0.00 0.00 0.00 3.46
2158 2577 0.784495 TGCGATATACTCCCTCCCCT 59.216 55.000 0.00 0.00 0.00 4.79
2162 2581 4.882427 TGCTATAGTGCGATATACTCCCTC 59.118 45.833 0.84 0.00 35.36 4.30
2215 2635 6.808704 TGTGCTGAGCAATAGATCGTTATATC 59.191 38.462 9.51 0.00 41.47 1.63
2221 2641 2.167281 AGTGTGCTGAGCAATAGATCGT 59.833 45.455 9.51 0.00 41.47 3.73
2222 2642 2.819115 AGTGTGCTGAGCAATAGATCG 58.181 47.619 9.51 0.00 41.47 3.69
2239 2659 3.668447 CCCCTAATAGCATGCTGTAGTG 58.332 50.000 30.42 19.83 0.00 2.74
2240 2660 2.039084 GCCCCTAATAGCATGCTGTAGT 59.961 50.000 30.42 13.11 0.00 2.73
2241 2661 2.704572 GCCCCTAATAGCATGCTGTAG 58.295 52.381 30.42 26.29 0.00 2.74
2242 2662 1.001974 CGCCCCTAATAGCATGCTGTA 59.998 52.381 30.42 19.50 0.00 2.74
2243 2663 0.250467 CGCCCCTAATAGCATGCTGT 60.250 55.000 30.42 21.59 0.00 4.40
2244 2664 0.250467 ACGCCCCTAATAGCATGCTG 60.250 55.000 30.42 13.11 0.00 4.41
2245 2665 0.035458 GACGCCCCTAATAGCATGCT 59.965 55.000 25.99 25.99 0.00 3.79
2246 2666 0.250295 TGACGCCCCTAATAGCATGC 60.250 55.000 10.51 10.51 0.00 4.06
2247 2667 2.479566 ATGACGCCCCTAATAGCATG 57.520 50.000 0.00 0.00 0.00 4.06
2248 2668 2.093447 GCTATGACGCCCCTAATAGCAT 60.093 50.000 8.29 0.00 44.44 3.79
2249 2669 1.275291 GCTATGACGCCCCTAATAGCA 59.725 52.381 8.29 0.00 44.44 3.49
2250 2670 1.736032 CGCTATGACGCCCCTAATAGC 60.736 57.143 3.91 3.91 42.57 2.97
2251 2671 2.279582 CGCTATGACGCCCCTAATAG 57.720 55.000 0.00 0.00 0.00 1.73
2261 2681 2.645628 AAAAATAGCGCGCTATGACG 57.354 45.000 44.20 0.00 39.03 4.35
2278 2698 8.257306 ACAGTTTGGCTTAGAATTTCTCAAAAA 58.743 29.630 1.27 0.00 0.00 1.94
2279 2699 7.781056 ACAGTTTGGCTTAGAATTTCTCAAAA 58.219 30.769 1.27 0.00 0.00 2.44
2280 2700 7.346751 ACAGTTTGGCTTAGAATTTCTCAAA 57.653 32.000 1.27 4.76 0.00 2.69
2281 2701 6.959639 ACAGTTTGGCTTAGAATTTCTCAA 57.040 33.333 1.27 0.00 0.00 3.02
2282 2702 6.239008 CCAACAGTTTGGCTTAGAATTTCTCA 60.239 38.462 1.27 0.00 46.09 3.27
2283 2703 6.152379 CCAACAGTTTGGCTTAGAATTTCTC 58.848 40.000 1.27 0.00 46.09 2.87
2284 2704 6.089249 CCAACAGTTTGGCTTAGAATTTCT 57.911 37.500 4.03 4.03 46.09 2.52
2301 2721 1.230635 CCCTGACAACTCGCCAACAG 61.231 60.000 0.00 0.00 0.00 3.16
2308 2728 4.700213 ACAATTATTTCCCCTGACAACTCG 59.300 41.667 0.00 0.00 0.00 4.18
2340 2760 3.553511 GTCAGACGTAGATGAGCCAAATG 59.446 47.826 0.00 0.00 0.00 2.32
2349 2769 0.248661 CGCCCTGTCAGACGTAGATG 60.249 60.000 0.00 0.00 0.00 2.90
2350 2770 1.384989 CCGCCCTGTCAGACGTAGAT 61.385 60.000 0.00 0.00 0.00 1.98
2351 2771 2.044555 CCGCCCTGTCAGACGTAGA 61.045 63.158 0.00 0.00 0.00 2.59
2358 2778 4.722700 CAACCCCCGCCCTGTCAG 62.723 72.222 0.00 0.00 0.00 3.51
2360 2780 4.717313 GACAACCCCCGCCCTGTC 62.717 72.222 0.00 0.00 0.00 3.51
2363 2783 2.833151 TATCAGACAACCCCCGCCCT 62.833 60.000 0.00 0.00 0.00 5.19
2364 2784 1.705997 ATATCAGACAACCCCCGCCC 61.706 60.000 0.00 0.00 0.00 6.13
2365 2785 1.053424 TATATCAGACAACCCCCGCC 58.947 55.000 0.00 0.00 0.00 6.13
2366 2786 4.755266 ATATATATCAGACAACCCCCGC 57.245 45.455 0.00 0.00 0.00 6.13
2367 2787 5.354234 GCAAATATATATCAGACAACCCCCG 59.646 44.000 0.00 0.00 0.00 5.73
2368 2788 5.652452 GGCAAATATATATCAGACAACCCCC 59.348 44.000 0.00 0.00 0.00 5.40
2369 2789 6.375455 CAGGCAAATATATATCAGACAACCCC 59.625 42.308 0.00 0.00 0.00 4.95
2370 2790 7.168219 TCAGGCAAATATATATCAGACAACCC 58.832 38.462 0.00 0.00 0.00 4.11
2371 2791 8.798859 ATCAGGCAAATATATATCAGACAACC 57.201 34.615 0.00 0.00 0.00 3.77
2373 2793 8.733458 GCAATCAGGCAAATATATATCAGACAA 58.267 33.333 0.00 0.00 0.00 3.18
2374 2794 7.064966 CGCAATCAGGCAAATATATATCAGACA 59.935 37.037 0.00 0.00 0.00 3.41
2375 2795 7.278646 TCGCAATCAGGCAAATATATATCAGAC 59.721 37.037 0.00 0.00 0.00 3.51
2378 2798 7.823799 TCTTCGCAATCAGGCAAATATATATCA 59.176 33.333 0.00 0.00 0.00 2.15
2382 2802 5.106396 GCTCTTCGCAATCAGGCAAATATAT 60.106 40.000 0.00 0.00 38.92 0.86
2398 2818 0.040157 TGTTGCACAATGCTCTTCGC 60.040 50.000 2.02 0.00 45.31 4.70
2399 2819 1.002576 TGTGTTGCACAATGCTCTTCG 60.003 47.619 2.02 0.00 45.31 3.79
2411 2831 2.646930 GATCTCCATCCATGTGTTGCA 58.353 47.619 0.00 0.00 0.00 4.08
2449 2882 2.097791 CGAACTCTCCTCTAGAAACGGG 59.902 54.545 0.00 0.00 32.46 5.28
2450 2883 2.097791 CCGAACTCTCCTCTAGAAACGG 59.902 54.545 0.00 0.00 37.64 4.44
2455 2888 3.546724 CATGTCCGAACTCTCCTCTAGA 58.453 50.000 0.00 0.00 0.00 2.43
2467 2900 1.393603 TGTTTGCAACCATGTCCGAA 58.606 45.000 0.00 0.00 0.00 4.30
2472 2905 5.868801 GCATATAACTTGTTTGCAACCATGT 59.131 36.000 9.34 9.34 33.58 3.21
2474 2907 5.187576 AGGCATATAACTTGTTTGCAACCAT 59.812 36.000 0.00 0.00 35.04 3.55
2502 2936 1.743252 GGAGCAGAAAGACGCTGGG 60.743 63.158 0.00 0.00 38.99 4.45
2503 2937 0.392193 ATGGAGCAGAAAGACGCTGG 60.392 55.000 0.00 0.00 38.99 4.85
2518 2952 3.437213 TCGTTTCTAGGTCAGGAATGGA 58.563 45.455 0.00 0.00 30.49 3.41
2555 2989 2.126031 GAGTTGGAGACGTCGCCC 60.126 66.667 31.74 24.98 34.71 6.13
2558 2992 1.213013 CTGGGAGTTGGAGACGTCG 59.787 63.158 10.46 0.00 0.00 5.12
2561 2995 0.900647 AGGTCTGGGAGTTGGAGACG 60.901 60.000 0.00 0.00 37.57 4.18
2563 2997 1.007238 CCTAGGTCTGGGAGTTGGAGA 59.993 57.143 0.00 0.00 32.26 3.71
2584 3018 1.270252 CCAGGCAAACATGGGTGAAAC 60.270 52.381 0.00 0.00 32.63 2.78
2585 3019 1.047002 CCAGGCAAACATGGGTGAAA 58.953 50.000 0.00 0.00 32.63 2.69
2596 3030 0.532573 TTTTGTTCGCACCAGGCAAA 59.467 45.000 0.00 0.00 45.17 3.68
2607 3041 5.874810 TGGATCACCTCTAATCTTTTGTTCG 59.125 40.000 0.00 0.00 37.04 3.95
2611 3045 7.636150 AATGTGGATCACCTCTAATCTTTTG 57.364 36.000 0.00 0.00 37.04 2.44
2612 3046 7.671398 ACAAATGTGGATCACCTCTAATCTTTT 59.329 33.333 0.00 0.00 37.04 2.27
2617 3051 6.350445 GCAAACAAATGTGGATCACCTCTAAT 60.350 38.462 0.00 0.00 37.04 1.73
2627 3061 4.518970 ACTACTTCGCAAACAAATGTGGAT 59.481 37.500 0.00 0.00 0.00 3.41
2628 3062 3.880490 ACTACTTCGCAAACAAATGTGGA 59.120 39.130 0.00 0.00 0.00 4.02
2629 3063 4.223320 ACTACTTCGCAAACAAATGTGG 57.777 40.909 0.00 0.00 0.00 4.17
2662 3097 5.078256 AGAGAAGAAAAGTAGGAGGACGAA 58.922 41.667 0.00 0.00 0.00 3.85
2665 3100 5.105513 CCAGAGAGAAGAAAAGTAGGAGGAC 60.106 48.000 0.00 0.00 0.00 3.85
2668 3103 4.382577 GGCCAGAGAGAAGAAAAGTAGGAG 60.383 50.000 0.00 0.00 0.00 3.69
2676 3111 3.181429 ACAAATGGGCCAGAGAGAAGAAA 60.181 43.478 13.78 0.00 0.00 2.52
2686 3121 2.236893 AGCCAAATAACAAATGGGCCAG 59.763 45.455 13.78 0.00 42.29 4.85
2691 3126 6.038356 CAGCTAGAAGCCAAATAACAAATGG 58.962 40.000 0.00 0.00 43.77 3.16
2705 3140 1.206849 ACCTCTCTTGCAGCTAGAAGC 59.793 52.381 7.99 0.00 42.84 3.86
2706 3141 4.159506 AGTTACCTCTCTTGCAGCTAGAAG 59.840 45.833 7.99 8.11 0.00 2.85
2725 3160 2.158385 ACCAAAACCATCCTGGCAGTTA 60.158 45.455 14.43 1.05 42.67 2.24
2731 3166 1.826720 CCATCACCAAAACCATCCTGG 59.173 52.381 0.00 0.00 45.02 4.45
2734 3169 0.536724 GCCCATCACCAAAACCATCC 59.463 55.000 0.00 0.00 0.00 3.51
2745 3180 3.425578 CGATCCTATCGCCCATCAC 57.574 57.895 0.00 0.00 46.55 3.06


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

AutoCloner maintained by Alex Coulton.