Multiple sequence alignment - TraesCS7D01G456400

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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 TraesCS7D01G456400 chr7D 100.000 3112 0 0 1 3112 575150680 575147569 0.000000e+00 5747.0
1 TraesCS7D01G456400 chr7D 90.265 1058 67 19 958 1995 574874726 574875767 0.000000e+00 1351.0
2 TraesCS7D01G456400 chr7D 87.325 1144 66 21 882 1998 575074570 575073479 0.000000e+00 1236.0
3 TraesCS7D01G456400 chr7D 86.555 1138 87 27 958 2035 574925523 574924392 0.000000e+00 1194.0
4 TraesCS7D01G456400 chr7D 88.518 958 76 15 883 1820 575218260 575217317 0.000000e+00 1129.0
5 TraesCS7D01G456400 chr7D 83.962 530 63 15 1 526 575075769 575075258 3.610000e-134 488.0
6 TraesCS7D01G456400 chr7D 86.376 367 38 9 521 882 575218738 575218379 1.050000e-104 390.0
7 TraesCS7D01G456400 chr7D 77.954 694 68 33 2367 2999 575072918 575072249 3.820000e-94 355.0
8 TraesCS7D01G456400 chr7D 89.046 283 21 5 2393 2669 575214017 575213739 2.970000e-90 342.0
9 TraesCS7D01G456400 chr7D 84.000 325 36 9 521 837 575075197 575074881 6.520000e-77 298.0
10 TraesCS7D01G456400 chr7D 93.793 145 9 0 2045 2189 574876789 574876933 5.230000e-53 219.0
11 TraesCS7D01G456400 chr7D 85.714 168 12 6 2367 2523 574877417 574877583 1.920000e-37 167.0
12 TraesCS7D01G456400 chr7D 82.234 197 17 6 2848 3042 575213581 575213401 1.490000e-33 154.0
13 TraesCS7D01G456400 chr7D 80.874 183 17 9 2486 2655 575010421 575010244 9.060000e-26 128.0
14 TraesCS7D01G456400 chr7D 84.545 110 7 1 2031 2140 575073066 575072967 1.970000e-17 100.0
15 TraesCS7D01G456400 chr7D 90.000 70 3 1 2528 2597 574860918 574860983 1.540000e-13 87.9
16 TraesCS7D01G456400 chr7D 84.091 88 6 2 2541 2624 574877677 574877760 9.250000e-11 78.7
17 TraesCS7D01G456400 chr7D 77.778 135 19 8 558 688 175641050 175640923 4.300000e-09 73.1
18 TraesCS7D01G456400 chr7D 95.455 44 2 0 404 447 14641744 14641787 1.550000e-08 71.3
19 TraesCS7D01G456400 chr7B 89.304 1337 95 27 684 1997 636433610 636432299 0.000000e+00 1633.0
20 TraesCS7D01G456400 chr7B 89.756 1064 81 13 956 1995 635300854 635301913 0.000000e+00 1336.0
21 TraesCS7D01G456400 chr7B 90.651 845 58 10 1175 1998 635749106 635748262 0.000000e+00 1103.0
22 TraesCS7D01G456400 chr7B 93.636 220 7 4 1786 1998 635935518 635935299 3.870000e-84 322.0
23 TraesCS7D01G456400 chr7B 79.518 415 47 21 143 526 635943004 635942597 8.560000e-66 261.0
24 TraesCS7D01G456400 chr7B 80.442 317 27 18 2808 3112 636429407 636429114 3.140000e-50 209.0
25 TraesCS7D01G456400 chr7B 80.178 338 15 17 1735 2035 635065582 635065904 4.070000e-49 206.0
26 TraesCS7D01G456400 chr7B 91.818 110 9 0 2069 2178 635739051 635738942 1.490000e-33 154.0
27 TraesCS7D01G456400 chr7B 83.146 178 10 8 1866 2035 635171322 635171487 8.990000e-31 145.0
28 TraesCS7D01G456400 chr7B 91.892 74 6 0 1708 1781 635940556 635940483 1.530000e-18 104.0
29 TraesCS7D01G456400 chr7B 93.846 65 4 0 2413 2477 635934203 635934139 7.100000e-17 99.0
30 TraesCS7D01G456400 chr7B 85.106 94 14 0 2390 2483 636430763 636430670 2.550000e-16 97.1
31 TraesCS7D01G456400 chr7B 90.000 70 3 1 2528 2597 635018506 635018571 1.540000e-13 87.9
32 TraesCS7D01G456400 chr7B 94.231 52 3 0 2626 2677 635718483 635718432 2.570000e-11 80.5
33 TraesCS7D01G456400 chr7B 85.484 62 9 0 462 523 744002103 744002042 7.200000e-07 65.8
34 TraesCS7D01G456400 chr7A 90.447 984 76 8 883 1866 664699113 664700078 0.000000e+00 1280.0
35 TraesCS7D01G456400 chr7A 87.832 978 77 19 1077 2035 664781187 664780233 0.000000e+00 1109.0
36 TraesCS7D01G456400 chr7A 85.018 1088 95 37 958 1995 664602987 664604056 0.000000e+00 1044.0
37 TraesCS7D01G456400 chr7A 90.406 271 19 2 2414 2677 665116158 665115888 1.780000e-92 350.0
38 TraesCS7D01G456400 chr7A 83.908 261 27 11 2521 2774 664869563 664869311 5.190000e-58 235.0
39 TraesCS7D01G456400 chr7A 86.957 161 14 1 2959 3112 664868628 664868468 1.150000e-39 174.0
40 TraesCS7D01G456400 chr7A 81.743 241 15 11 2808 3039 665115761 665115541 1.150000e-39 174.0
41 TraesCS7D01G456400 chr7A 82.456 171 21 2 2041 2203 664777469 664777300 1.160000e-29 141.0
42 TraesCS7D01G456400 chr7A 91.250 80 4 1 1006 1082 664781447 664781368 4.240000e-19 106.0
43 TraesCS7D01G456400 chr7A 84.906 106 10 4 2812 2913 664868879 664868776 5.490000e-18 102.0
44 TraesCS7D01G456400 chr7A 79.874 159 11 5 2532 2669 664896681 664896523 2.550000e-16 97.1
45 TraesCS7D01G456400 chr3A 92.771 166 12 0 2194 2359 478426329 478426494 1.120000e-59 241.0
46 TraesCS7D01G456400 chr3A 93.210 162 11 0 2196 2357 200806136 200806297 4.010000e-59 239.0
47 TraesCS7D01G456400 chr3A 87.500 64 8 0 462 525 474969579 474969642 1.200000e-09 75.0
48 TraesCS7D01G456400 chr3A 94.595 37 2 0 578 614 481876996 481877032 1.210000e-04 58.4
49 TraesCS7D01G456400 chr3B 91.860 172 12 1 2188 2357 183601257 183601086 4.010000e-59 239.0
50 TraesCS7D01G456400 chr3B 90.217 184 16 2 2176 2357 540175112 540174929 4.010000e-59 239.0
51 TraesCS7D01G456400 chr3B 85.915 71 8 2 462 530 55101392 55101322 1.200000e-09 75.0
52 TraesCS7D01G456400 chr3B 76.471 153 21 11 568 715 94499318 94499460 5.570000e-08 69.4
53 TraesCS7D01G456400 chr5A 92.169 166 13 0 2194 2359 114649457 114649292 5.190000e-58 235.0
54 TraesCS7D01G456400 chr5A 90.741 54 5 0 406 459 657427545 657427492 4.300000e-09 73.1
55 TraesCS7D01G456400 chr5A 90.196 51 5 0 406 456 689893571 689893621 2.000000e-07 67.6
56 TraesCS7D01G456400 chr4B 91.765 170 13 1 2196 2365 483266379 483266547 5.190000e-58 235.0
57 TraesCS7D01G456400 chr4B 90.000 50 5 0 406 455 571608080 571608031 7.200000e-07 65.8
58 TraesCS7D01G456400 chr3D 92.169 166 13 0 2194 2359 410670226 410670061 5.190000e-58 235.0
59 TraesCS7D01G456400 chr3D 88.525 61 6 1 463 523 355892848 355892907 4.300000e-09 73.1
60 TraesCS7D01G456400 chr3D 90.385 52 5 0 405 456 612730067 612730118 5.570000e-08 69.4
61 TraesCS7D01G456400 chr2D 92.121 165 13 0 2193 2357 305515033 305514869 1.870000e-57 233.0
62 TraesCS7D01G456400 chr2D 78.667 150 20 11 579 726 421794825 421794686 4.270000e-14 89.8
63 TraesCS7D01G456400 chr2D 87.097 62 4 4 462 523 526380471 526380528 2.000000e-07 67.6
64 TraesCS7D01G456400 chr2B 89.773 176 17 1 2194 2369 659017214 659017040 1.120000e-54 224.0
65 TraesCS7D01G456400 chr1B 90.141 71 5 2 462 530 137141580 137141510 1.190000e-14 91.6
66 TraesCS7D01G456400 chr6D 79.389 131 16 5 578 704 9355458 9355335 7.150000e-12 82.4
67 TraesCS7D01G456400 chr2A 90.323 62 6 0 462 523 744542878 744542939 7.150000e-12 82.4
68 TraesCS7D01G456400 chr2A 90.741 54 5 0 402 455 23885342 23885395 4.300000e-09 73.1
69 TraesCS7D01G456400 chr2A 87.931 58 6 1 402 459 1492795 1492851 2.000000e-07 67.6
70 TraesCS7D01G456400 chr4A 78.014 141 22 5 567 704 514080011 514080145 2.570000e-11 80.5
71 TraesCS7D01G456400 chr4A 92.593 54 4 0 463 516 694865886 694865939 9.250000e-11 78.7
72 TraesCS7D01G456400 chr6A 83.721 86 7 6 570 654 63566322 63566401 1.200000e-09 75.0
73 TraesCS7D01G456400 chr5D 90.385 52 5 0 404 455 214709356 214709305 5.570000e-08 69.4
74 TraesCS7D01G456400 chrUn 97.297 37 1 0 578 614 373420142 373420106 2.590000e-06 63.9


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 TraesCS7D01G456400 chr7D 575147569 575150680 3111 True 5747.000000 5747 100.000000 1 3112 1 chr7D.!!$R4 3111
1 TraesCS7D01G456400 chr7D 574924392 574925523 1131 True 1194.000000 1194 86.555000 958 2035 1 chr7D.!!$R2 1077
2 TraesCS7D01G456400 chr7D 575213401 575218738 5337 True 503.750000 1129 86.543500 521 3042 4 chr7D.!!$R6 2521
3 TraesCS7D01G456400 chr7D 575072249 575075769 3520 True 495.400000 1236 83.557200 1 2999 5 chr7D.!!$R5 2998
4 TraesCS7D01G456400 chr7D 574874726 574877760 3034 False 453.925000 1351 88.465750 958 2624 4 chr7D.!!$F3 1666
5 TraesCS7D01G456400 chr7B 635300854 635301913 1059 False 1336.000000 1336 89.756000 956 1995 1 chr7B.!!$F4 1039
6 TraesCS7D01G456400 chr7B 635748262 635749106 844 True 1103.000000 1103 90.651000 1175 1998 1 chr7B.!!$R3 823
7 TraesCS7D01G456400 chr7B 636429114 636433610 4496 True 646.366667 1633 84.950667 684 3112 3 chr7B.!!$R7 2428
8 TraesCS7D01G456400 chr7B 635934139 635935518 1379 True 210.500000 322 93.741000 1786 2477 2 chr7B.!!$R5 691
9 TraesCS7D01G456400 chr7A 664699113 664700078 965 False 1280.000000 1280 90.447000 883 1866 1 chr7A.!!$F2 983
10 TraesCS7D01G456400 chr7A 664602987 664604056 1069 False 1044.000000 1044 85.018000 958 1995 1 chr7A.!!$F1 1037
11 TraesCS7D01G456400 chr7A 664777300 664781447 4147 True 452.000000 1109 87.179333 1006 2203 3 chr7A.!!$R2 1197
12 TraesCS7D01G456400 chr7A 665115541 665116158 617 True 262.000000 350 86.074500 2414 3039 2 chr7A.!!$R4 625

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
106 107 0.108585 GGGAGGACAAGACTGTTGCA 59.891 55.0 0.0 0.0 35.30 4.08 F
479 481 0.240411 GCGACTACGAAGGTGTCTGT 59.760 55.0 0.0 0.0 42.66 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1322 2003 0.518764 CGAAGAACGAGGACGACGAG 60.519 60.0 0.0 0.0 45.77 4.18 R
2381 10460 1.084370 GCACTGGACGGACACTATGC 61.084 60.0 0.0 0.0 0.00 3.14 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
62 63 1.495584 GAAGTCCTTGCGCGACAACA 61.496 55.000 12.10 0.00 33.68 3.33
72 73 0.650476 CGCGACAACAAACACGACAG 60.650 55.000 0.00 0.00 0.00 3.51
93 94 0.994050 TCGAGAGGATGAGGGGAGGA 60.994 60.000 0.00 0.00 0.00 3.71
95 96 0.263172 GAGAGGATGAGGGGAGGACA 59.737 60.000 0.00 0.00 0.00 4.02
100 101 1.623834 GGATGAGGGGAGGACAAGACT 60.624 57.143 0.00 0.00 0.00 3.24
103 104 1.353091 GAGGGGAGGACAAGACTGTT 58.647 55.000 0.00 0.00 35.30 3.16
105 106 0.606673 GGGGAGGACAAGACTGTTGC 60.607 60.000 0.00 0.00 35.30 4.17
106 107 0.108585 GGGAGGACAAGACTGTTGCA 59.891 55.000 0.00 0.00 35.30 4.08
107 108 1.517242 GGAGGACAAGACTGTTGCAG 58.483 55.000 0.00 0.00 35.30 4.41
108 109 1.517242 GAGGACAAGACTGTTGCAGG 58.483 55.000 1.08 0.00 35.30 4.85
109 110 1.070758 GAGGACAAGACTGTTGCAGGA 59.929 52.381 1.08 0.00 35.30 3.86
110 111 1.071385 AGGACAAGACTGTTGCAGGAG 59.929 52.381 1.08 0.00 35.30 3.69
111 112 0.871057 GACAAGACTGTTGCAGGAGC 59.129 55.000 1.08 0.00 35.30 4.70
112 113 0.882042 ACAAGACTGTTGCAGGAGCG 60.882 55.000 1.08 0.00 46.23 5.03
113 114 1.963338 AAGACTGTTGCAGGAGCGC 60.963 57.895 0.00 0.00 46.23 5.92
114 115 3.426568 GACTGTTGCAGGAGCGCC 61.427 66.667 2.29 0.00 46.23 6.53
122 123 3.506096 CAGGAGCGCCGTCGTCTA 61.506 66.667 2.29 0.00 39.96 2.59
123 124 3.507009 AGGAGCGCCGTCGTCTAC 61.507 66.667 2.29 0.00 39.96 2.59
124 125 3.807538 GGAGCGCCGTCGTCTACA 61.808 66.667 2.29 0.00 38.14 2.74
157 159 0.391130 GACGGTTGGCATGTGCTAGA 60.391 55.000 4.84 0.00 41.70 2.43
158 160 0.253044 ACGGTTGGCATGTGCTAGAT 59.747 50.000 4.84 0.00 41.70 1.98
160 162 1.743431 CGGTTGGCATGTGCTAGATCA 60.743 52.381 4.84 0.00 41.70 2.92
197 199 3.153919 TGAAGTGGAATAGTGTTTGCCC 58.846 45.455 0.00 0.00 0.00 5.36
198 200 2.969821 AGTGGAATAGTGTTTGCCCA 57.030 45.000 0.00 0.00 0.00 5.36
209 211 2.890945 GTGTTTGCCCATTAGAGTTGGT 59.109 45.455 0.00 0.00 31.99 3.67
220 222 5.011125 CCATTAGAGTTGGTAGATGATCCGT 59.989 44.000 0.00 0.00 0.00 4.69
252 254 4.390603 CGACCTTGATACAATGGTTCGAAA 59.609 41.667 0.00 0.00 32.30 3.46
267 269 6.106673 TGGTTCGAAAAGAAGTGGATAGATC 58.893 40.000 0.00 0.00 39.95 2.75
270 272 5.822278 TCGAAAAGAAGTGGATAGATCGAG 58.178 41.667 0.00 0.00 33.46 4.04
271 273 5.357314 TCGAAAAGAAGTGGATAGATCGAGT 59.643 40.000 0.00 0.00 33.46 4.18
285 287 3.375299 AGATCGAGTAGGCACAAAAATGC 59.625 43.478 0.00 0.00 45.34 3.56
286 288 2.778299 TCGAGTAGGCACAAAAATGCT 58.222 42.857 0.00 0.00 45.38 3.79
289 291 3.914364 CGAGTAGGCACAAAAATGCTTTC 59.086 43.478 0.00 0.00 45.38 2.62
290 292 3.900941 AGTAGGCACAAAAATGCTTTCG 58.099 40.909 0.00 0.00 45.38 3.46
292 294 1.686052 AGGCACAAAAATGCTTTCGGA 59.314 42.857 0.00 0.00 45.38 4.55
293 295 1.792367 GGCACAAAAATGCTTTCGGAC 59.208 47.619 0.00 0.00 45.38 4.79
297 299 1.969256 CAAAAATGCTTTCGGACGACG 59.031 47.619 0.00 0.00 46.11 5.12
307 309 4.353437 GGACGACGAACGCCTGGT 62.353 66.667 0.00 0.00 46.94 4.00
315 317 1.652563 GAACGCCTGGTCGCTTTTT 59.347 52.632 9.82 0.00 0.00 1.94
398 400 9.486857 GGTAAGTATTCGCTAAAAGAATGAAAC 57.513 33.333 2.12 0.00 38.61 2.78
403 405 9.144085 GTATTCGCTAAAAGAATGAAACATACG 57.856 33.333 2.12 0.00 38.61 3.06
404 406 6.954616 TCGCTAAAAGAATGAAACATACGA 57.045 33.333 0.00 0.00 0.00 3.43
405 407 6.989437 TCGCTAAAAGAATGAAACATACGAG 58.011 36.000 0.00 0.00 0.00 4.18
412 414 7.687941 AAGAATGAAACATACGAGAACCAAT 57.312 32.000 0.00 0.00 0.00 3.16
415 417 8.258007 AGAATGAAACATACGAGAACCAATCTA 58.742 33.333 0.00 0.00 38.96 1.98
441 443 3.248024 TGGATGGTTAGAAGGACAGTGT 58.752 45.455 0.00 0.00 0.00 3.55
442 444 3.650942 TGGATGGTTAGAAGGACAGTGTT 59.349 43.478 0.00 0.00 0.00 3.32
446 448 5.416271 TGGTTAGAAGGACAGTGTTATCC 57.584 43.478 0.00 0.00 34.98 2.59
447 449 4.841813 TGGTTAGAAGGACAGTGTTATCCA 59.158 41.667 0.00 0.00 37.47 3.41
448 450 5.176592 GGTTAGAAGGACAGTGTTATCCAC 58.823 45.833 0.00 0.00 44.89 4.02
459 461 4.546829 GTGTTATCCACAACCCACTAGA 57.453 45.455 0.00 0.00 43.92 2.43
460 462 4.504858 GTGTTATCCACAACCCACTAGAG 58.495 47.826 0.00 0.00 43.92 2.43
462 464 0.537188 ATCCACAACCCACTAGAGCG 59.463 55.000 0.00 0.00 0.00 5.03
473 475 2.008329 CACTAGAGCGACTACGAAGGT 58.992 52.381 0.00 0.00 42.66 3.50
479 481 0.240411 GCGACTACGAAGGTGTCTGT 59.760 55.000 0.00 0.00 42.66 3.41
485 487 0.959553 ACGAAGGTGTCTGTGACGAT 59.040 50.000 0.00 0.00 34.95 3.73
488 490 2.408704 CGAAGGTGTCTGTGACGATTTC 59.591 50.000 0.00 0.00 34.95 2.17
509 511 5.973651 TCGTCAATCTCAAGATAATGTGC 57.026 39.130 0.00 0.00 33.73 4.57
514 516 0.947244 CTCAAGATAATGTGCCGGCC 59.053 55.000 26.77 16.24 0.00 6.13
523 525 4.500116 GTGCCGGCCGAGTCTCTC 62.500 72.222 30.73 7.14 0.00 3.20
538 606 0.375454 CTCTCGAGTGCCTACGTCTG 59.625 60.000 13.13 0.00 0.00 3.51
591 659 9.396022 ACTATTCCCTGTGTTCACAAATATAAG 57.604 33.333 7.07 4.44 0.00 1.73
594 662 7.864108 TCCCTGTGTTCACAAATATAAGATG 57.136 36.000 7.07 0.00 0.00 2.90
597 665 8.184192 CCCTGTGTTCACAAATATAAGATGTTC 58.816 37.037 7.07 0.00 0.00 3.18
626 694 4.848562 TCCAATATGTGCTAGGACTACG 57.151 45.455 15.92 0.11 0.00 3.51
630 698 5.241064 CCAATATGTGCTAGGACTACGTACT 59.759 44.000 15.92 0.00 0.00 2.73
638 706 5.352569 TGCTAGGACTACGTACTAACTGAAC 59.647 44.000 0.00 0.00 27.51 3.18
682 752 6.307031 TGTGTGTATGTACATTTGGTTCAC 57.693 37.500 14.77 14.12 38.63 3.18
718 795 8.561738 ACCAACTTATAGTATTTGTGAACAGG 57.438 34.615 0.00 0.00 0.00 4.00
721 798 7.504926 ACTTATAGTATTTGTGAACAGGGGA 57.495 36.000 0.00 0.00 0.00 4.81
727 804 3.935818 TTTGTGAACAGGGGAAGTACA 57.064 42.857 0.00 0.00 0.00 2.90
754 831 3.090952 TGCAAAATGAAGGAACCAACG 57.909 42.857 0.00 0.00 0.00 4.10
771 848 1.604604 ACGATCCCCAACTGTTTGTG 58.395 50.000 0.00 0.00 0.00 3.33
776 853 0.318120 CCCCAACTGTTTGTGATGGC 59.682 55.000 0.00 0.00 0.00 4.40
782 859 5.511202 CCCAACTGTTTGTGATGGCTTTAAT 60.511 40.000 0.00 0.00 0.00 1.40
878 1227 3.797256 CGCCAAGTTAGTCTCGATTTAGG 59.203 47.826 0.00 0.00 0.00 2.69
983 1451 6.152661 ACATTCCATTCCGAGCAAAGAATTTA 59.847 34.615 0.00 0.00 35.03 1.40
1178 1856 0.734253 CGCTTCCAAGTCTCGAGGTG 60.734 60.000 13.56 8.52 0.00 4.00
1217 1895 1.136147 CAGCAACATGAAGCGCCTC 59.864 57.895 2.29 0.00 35.48 4.70
1627 2308 1.783031 GCCGCGCTCTACTACTAGCA 61.783 60.000 5.56 0.00 38.70 3.49
1647 2340 2.434774 GCCCTTCCCCGTTTCACT 59.565 61.111 0.00 0.00 0.00 3.41
1692 2390 1.337635 GCGTGATTGGAAATTTGCCCA 60.338 47.619 7.27 0.69 0.00 5.36
2017 2810 6.038356 GGCTGTGAAATGGATGATTTTGTAG 58.962 40.000 0.00 0.00 34.18 2.74
2035 7944 3.957497 TGTAGTGCAAAAGTTTGGTCCAT 59.043 39.130 5.95 0.00 38.57 3.41
2054 7963 6.127310 GGTCCATATACACTGTGAAGAGAGTT 60.127 42.308 15.86 0.00 0.00 3.01
2075 7984 2.239400 TCGTCCAGATAGCACATAGGG 58.761 52.381 0.00 0.00 0.00 3.53
2076 7985 1.273606 CGTCCAGATAGCACATAGGGG 59.726 57.143 0.00 0.00 0.00 4.79
2114 8137 0.742281 CTCCAAGCAGGTGTCATCGG 60.742 60.000 0.00 0.00 39.02 4.18
2172 8203 3.018856 TGCTGATATGCCAGAACTTTGG 58.981 45.455 0.00 0.00 41.35 3.28
2197 10017 8.178313 GGAGAAATTGTATTGCTTCAGAACTAC 58.822 37.037 0.00 0.00 0.00 2.73
2200 10020 7.617041 AATTGTATTGCTTCAGAACTACTCC 57.383 36.000 0.00 0.00 0.00 3.85
2201 10021 5.086104 TGTATTGCTTCAGAACTACTCCC 57.914 43.478 0.00 0.00 0.00 4.30
2202 10022 4.777896 TGTATTGCTTCAGAACTACTCCCT 59.222 41.667 0.00 0.00 0.00 4.20
2203 10023 3.963428 TTGCTTCAGAACTACTCCCTC 57.037 47.619 0.00 0.00 0.00 4.30
2205 10025 1.135333 GCTTCAGAACTACTCCCTCCG 59.865 57.143 0.00 0.00 0.00 4.63
2209 10029 1.477295 CAGAACTACTCCCTCCGTTCC 59.523 57.143 0.00 0.00 37.15 3.62
2210 10030 1.358445 AGAACTACTCCCTCCGTTCCT 59.642 52.381 0.00 0.00 37.15 3.36
2211 10031 2.579860 AGAACTACTCCCTCCGTTCCTA 59.420 50.000 0.00 0.00 37.15 2.94
2212 10032 3.011032 AGAACTACTCCCTCCGTTCCTAA 59.989 47.826 0.00 0.00 37.15 2.69
2213 10033 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
2214 10034 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
2215 10035 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
2216 10036 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
2217 10037 6.856757 ACTACTCCCTCCGTTCCTAAATATA 58.143 40.000 0.00 0.00 0.00 0.86
2218 10038 7.300658 ACTACTCCCTCCGTTCCTAAATATAA 58.699 38.462 0.00 0.00 0.00 0.98
2219 10039 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
2220 10040 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
2221 10041 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
2222 10042 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
2223 10043 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
2224 10044 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
2225 10045 8.645110 CCCTCCGTTCCTAAATATAAGTCTTTA 58.355 37.037 0.00 0.00 0.00 1.85
2226 10046 9.473640 CCTCCGTTCCTAAATATAAGTCTTTAC 57.526 37.037 0.00 0.00 0.00 2.01
2243 10063 9.702253 AAGTCTTTACAGAGATTCTACTATGGA 57.298 33.333 0.00 0.00 34.01 3.41
2244 10064 9.127277 AGTCTTTACAGAGATTCTACTATGGAC 57.873 37.037 0.00 0.00 34.01 4.02
2245 10065 9.127277 GTCTTTACAGAGATTCTACTATGGACT 57.873 37.037 0.00 0.00 34.01 3.85
2248 10068 9.916360 TTTACAGAGATTCTACTATGGACTACA 57.084 33.333 0.00 0.00 34.01 2.74
2251 10071 9.509956 ACAGAGATTCTACTATGGACTACATAC 57.490 37.037 0.00 0.00 41.03 2.39
2252 10072 8.661257 CAGAGATTCTACTATGGACTACATACG 58.339 40.741 0.00 0.00 41.03 3.06
2253 10073 8.377034 AGAGATTCTACTATGGACTACATACGT 58.623 37.037 0.00 0.00 41.03 3.57
2254 10074 9.650539 GAGATTCTACTATGGACTACATACGTA 57.349 37.037 0.00 0.00 41.03 3.57
2268 10088 7.520119 CTACATACGTAGCAAAATGAGTGAA 57.480 36.000 0.08 0.00 38.84 3.18
2269 10089 6.985188 ACATACGTAGCAAAATGAGTGAAT 57.015 33.333 0.08 0.00 0.00 2.57
2270 10090 7.005062 ACATACGTAGCAAAATGAGTGAATC 57.995 36.000 0.08 0.00 0.00 2.52
2271 10091 6.818644 ACATACGTAGCAAAATGAGTGAATCT 59.181 34.615 0.08 0.00 0.00 2.40
2272 10092 7.979537 ACATACGTAGCAAAATGAGTGAATCTA 59.020 33.333 0.08 0.00 0.00 1.98
2273 10093 6.648725 ACGTAGCAAAATGAGTGAATCTAC 57.351 37.500 0.00 0.00 0.00 2.59
2274 10094 5.581085 ACGTAGCAAAATGAGTGAATCTACC 59.419 40.000 0.00 0.00 0.00 3.18
2275 10095 5.006746 CGTAGCAAAATGAGTGAATCTACCC 59.993 44.000 0.00 0.00 0.00 3.69
2276 10096 5.184892 AGCAAAATGAGTGAATCTACCCT 57.815 39.130 0.00 0.00 0.00 4.34
2277 10097 5.189180 AGCAAAATGAGTGAATCTACCCTC 58.811 41.667 0.00 0.00 0.00 4.30
2278 10098 5.045286 AGCAAAATGAGTGAATCTACCCTCT 60.045 40.000 0.00 0.00 0.00 3.69
2279 10099 6.156949 AGCAAAATGAGTGAATCTACCCTCTA 59.843 38.462 0.00 0.00 0.00 2.43
2280 10100 6.823689 GCAAAATGAGTGAATCTACCCTCTAA 59.176 38.462 0.00 0.00 0.00 2.10
2281 10101 7.336931 GCAAAATGAGTGAATCTACCCTCTAAA 59.663 37.037 0.00 0.00 0.00 1.85
2282 10102 9.231297 CAAAATGAGTGAATCTACCCTCTAAAA 57.769 33.333 0.00 0.00 0.00 1.52
2283 10103 9.981460 AAAATGAGTGAATCTACCCTCTAAAAT 57.019 29.630 0.00 0.00 0.00 1.82
2284 10104 8.970859 AATGAGTGAATCTACCCTCTAAAATG 57.029 34.615 0.00 0.00 0.00 2.32
2285 10105 6.349300 TGAGTGAATCTACCCTCTAAAATGC 58.651 40.000 0.00 0.00 0.00 3.56
2286 10106 6.070251 TGAGTGAATCTACCCTCTAAAATGCA 60.070 38.462 0.00 0.00 0.00 3.96
2287 10107 6.904626 AGTGAATCTACCCTCTAAAATGCAT 58.095 36.000 0.00 0.00 0.00 3.96
2288 10108 6.995091 AGTGAATCTACCCTCTAAAATGCATC 59.005 38.462 0.00 0.00 0.00 3.91
2289 10109 6.995091 GTGAATCTACCCTCTAAAATGCATCT 59.005 38.462 0.00 0.00 0.00 2.90
2290 10110 8.150945 GTGAATCTACCCTCTAAAATGCATCTA 58.849 37.037 0.00 0.00 0.00 1.98
2291 10111 8.884323 TGAATCTACCCTCTAAAATGCATCTAT 58.116 33.333 0.00 0.00 0.00 1.98
2310 10130 9.689976 GCATCTATATACATCTGTATGTGATCC 57.310 37.037 12.10 1.90 45.99 3.36
2318 10138 9.981460 ATACATCTGTATGTGATCCATAGTAGA 57.019 33.333 2.10 13.96 45.99 2.59
2319 10139 8.712228 ACATCTGTATGTGATCCATAGTAGAA 57.288 34.615 14.78 6.35 44.79 2.10
2320 10140 9.319060 ACATCTGTATGTGATCCATAGTAGAAT 57.681 33.333 14.78 8.81 44.79 2.40
2321 10141 9.800433 CATCTGTATGTGATCCATAGTAGAATC 57.200 37.037 14.78 0.00 36.71 2.52
2322 10142 9.766754 ATCTGTATGTGATCCATAGTAGAATCT 57.233 33.333 14.78 0.00 36.71 2.40
2355 10175 9.495382 AGACTTATATTTAGAAACAGAGGGAGT 57.505 33.333 0.00 0.00 0.00 3.85
2361 10181 6.742559 TTTAGAAACAGAGGGAGTAGTTGT 57.257 37.500 0.00 0.00 0.00 3.32
2362 10182 4.608948 AGAAACAGAGGGAGTAGTTGTG 57.391 45.455 0.00 0.00 0.00 3.33
2363 10183 3.967987 AGAAACAGAGGGAGTAGTTGTGT 59.032 43.478 0.00 0.00 0.00 3.72
2405 10484 0.388649 GTGTCCGTCCAGTGCTGTAG 60.389 60.000 0.00 0.00 0.00 2.74
2477 10557 2.664916 CAGCCAAACACAACTGTATGC 58.335 47.619 0.00 0.00 0.00 3.14
2569 11612 1.966451 CGCTTTCGGTTGGGCTTCT 60.966 57.895 0.00 0.00 0.00 2.85
2570 11613 1.581447 GCTTTCGGTTGGGCTTCTG 59.419 57.895 0.00 0.00 0.00 3.02
2614 11665 1.067142 GTGAGTAGGCAACGACATGGA 60.067 52.381 0.00 0.00 45.76 3.41
2689 11750 1.741770 GGCGGTGCCTGTCAGTTAG 60.742 63.158 0.00 0.00 46.69 2.34
2690 11751 1.004918 GCGGTGCCTGTCAGTTAGT 60.005 57.895 0.00 0.00 0.00 2.24
2692 11753 0.389948 CGGTGCCTGTCAGTTAGTCC 60.390 60.000 0.00 0.00 0.00 3.85
2693 11754 0.685097 GGTGCCTGTCAGTTAGTCCA 59.315 55.000 0.00 0.00 0.00 4.02
2695 11756 2.350522 GTGCCTGTCAGTTAGTCCATG 58.649 52.381 0.00 0.00 0.00 3.66
2696 11757 1.977854 TGCCTGTCAGTTAGTCCATGT 59.022 47.619 0.00 0.00 0.00 3.21
2697 11758 3.056107 GTGCCTGTCAGTTAGTCCATGTA 60.056 47.826 0.00 0.00 0.00 2.29
2698 11759 3.056107 TGCCTGTCAGTTAGTCCATGTAC 60.056 47.826 0.00 0.00 0.00 2.90
2699 11760 3.679083 GCCTGTCAGTTAGTCCATGTACC 60.679 52.174 0.00 0.00 0.00 3.34
2700 11761 3.118738 CCTGTCAGTTAGTCCATGTACCC 60.119 52.174 0.00 0.00 0.00 3.69
2701 11762 2.835764 TGTCAGTTAGTCCATGTACCCC 59.164 50.000 0.00 0.00 0.00 4.95
2702 11763 2.104967 TCAGTTAGTCCATGTACCCCG 58.895 52.381 0.00 0.00 0.00 5.73
2703 11764 2.104967 CAGTTAGTCCATGTACCCCGA 58.895 52.381 0.00 0.00 0.00 5.14
2760 11841 4.815108 GGCGTTCCCATGGACCCC 62.815 72.222 15.22 1.96 0.00 4.95
2776 11874 1.376037 CCCGAGGCCAGAAGAACAC 60.376 63.158 5.01 0.00 0.00 3.32
2777 11875 1.738099 CCGAGGCCAGAAGAACACG 60.738 63.158 5.01 0.00 0.00 4.49
2778 11876 1.006102 CGAGGCCAGAAGAACACGT 60.006 57.895 5.01 0.00 0.00 4.49
2780 11878 1.711206 GAGGCCAGAAGAACACGTAC 58.289 55.000 5.01 0.00 0.00 3.67
2784 11882 2.490903 GGCCAGAAGAACACGTACTCTA 59.509 50.000 0.00 0.00 0.00 2.43
2786 11884 3.427773 GCCAGAAGAACACGTACTCTAGG 60.428 52.174 0.00 0.00 0.00 3.02
2787 11885 4.008330 CCAGAAGAACACGTACTCTAGGA 58.992 47.826 0.00 0.00 0.00 2.94
2788 11886 4.458295 CCAGAAGAACACGTACTCTAGGAA 59.542 45.833 0.00 0.00 0.00 3.36
2791 11909 7.148120 CCAGAAGAACACGTACTCTAGGAATAA 60.148 40.741 0.00 0.00 0.00 1.40
2844 11980 4.395854 TGTAATACGTACGGATCGGCATAT 59.604 41.667 21.06 1.76 35.23 1.78
2851 11987 1.338973 ACGGATCGGCATATGTACGTT 59.661 47.619 17.33 11.62 0.00 3.99
2852 11988 1.719246 CGGATCGGCATATGTACGTTG 59.281 52.381 17.33 0.00 0.00 4.10
2853 11989 2.750948 GGATCGGCATATGTACGTTGT 58.249 47.619 17.33 8.49 0.00 3.32
2854 11990 2.475111 GGATCGGCATATGTACGTTGTG 59.525 50.000 17.33 0.00 0.00 3.33
2855 11991 2.658373 TCGGCATATGTACGTTGTGT 57.342 45.000 17.33 0.00 0.00 3.72
2856 11992 2.263945 TCGGCATATGTACGTTGTGTG 58.736 47.619 17.33 0.00 0.00 3.82
2857 11993 1.996898 CGGCATATGTACGTTGTGTGT 59.003 47.619 4.29 0.00 0.00 3.72
2858 11994 3.119566 TCGGCATATGTACGTTGTGTGTA 60.120 43.478 17.33 0.00 0.00 2.90
2859 11995 3.000476 CGGCATATGTACGTTGTGTGTAC 60.000 47.826 4.29 0.00 41.97 2.90
2860 11996 3.000476 GGCATATGTACGTTGTGTGTACG 60.000 47.826 4.29 0.00 44.00 3.67
2861 11997 3.540744 GCATATGTACGTTGTGTGTACGC 60.541 47.826 4.29 0.00 44.00 4.42
2862 11998 1.054574 ATGTACGTTGTGTGTACGCG 58.945 50.000 3.53 3.53 44.00 6.01
2898 12042 0.318699 TCTTGCTTGTCTCCGTCACG 60.319 55.000 0.00 0.00 0.00 4.35
2938 12082 4.831307 GCGACGAGCCGACGATGT 62.831 66.667 19.11 0.00 46.01 3.06
2939 12083 2.648102 CGACGAGCCGACGATGTC 60.648 66.667 12.24 0.00 46.01 3.06
2977 12121 4.345859 ACGTAAATGACAGGTCCAAAGA 57.654 40.909 0.00 0.00 0.00 2.52
3044 12193 7.063074 ACGATATTGAAAGCGTAATATACTGGC 59.937 37.037 0.00 0.00 34.93 4.85
3048 12200 4.808895 TGAAAGCGTAATATACTGGCACTG 59.191 41.667 0.00 0.00 0.00 3.66
3093 12246 0.959867 CATCCATGTCGGCACAACCA 60.960 55.000 0.00 0.00 39.03 3.67
3094 12247 0.960364 ATCCATGTCGGCACAACCAC 60.960 55.000 0.00 0.00 39.03 4.16
3106 12259 2.618241 GCACAACCACACAAGAGATGAA 59.382 45.455 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.337071 TCGATATCCAGTTCTGGCGAC 59.663 52.381 13.44 0.00 0.00 5.19
24 25 3.808834 TCCCTCTAAGCTCCATCGATA 57.191 47.619 0.00 0.00 0.00 2.92
25 26 2.685106 TCCCTCTAAGCTCCATCGAT 57.315 50.000 0.00 0.00 0.00 3.59
53 54 0.650476 CTGTCGTGTTTGTTGTCGCG 60.650 55.000 0.00 0.00 38.63 5.87
72 73 1.036707 CTCCCCTCATCCTCTCGAAC 58.963 60.000 0.00 0.00 0.00 3.95
93 94 0.882042 CGCTCCTGCAACAGTCTTGT 60.882 55.000 0.00 0.00 39.87 3.16
95 96 1.963338 GCGCTCCTGCAACAGTCTT 60.963 57.895 0.00 0.00 39.64 3.01
105 106 3.506096 TAGACGACGGCGCTCCTG 61.506 66.667 12.58 0.00 42.48 3.86
106 107 3.507009 GTAGACGACGGCGCTCCT 61.507 66.667 12.58 8.53 42.48 3.69
107 108 3.736482 CTGTAGACGACGGCGCTCC 62.736 68.421 12.58 0.00 42.48 4.70
108 109 2.277373 CTGTAGACGACGGCGCTC 60.277 66.667 12.58 8.02 42.48 5.03
109 110 3.812019 CCTGTAGACGACGGCGCT 61.812 66.667 12.58 12.28 42.48 5.92
110 111 3.736482 CTCCTGTAGACGACGGCGC 62.736 68.421 12.58 3.05 42.48 6.53
111 112 2.403987 CTCCTGTAGACGACGGCG 59.596 66.667 10.39 10.39 44.79 6.46
112 113 2.799371 CCTCCTGTAGACGACGGC 59.201 66.667 0.00 0.00 32.45 5.68
113 114 2.799371 GCCTCCTGTAGACGACGG 59.201 66.667 0.00 0.00 0.00 4.79
114 115 2.403987 CGCCTCCTGTAGACGACG 59.596 66.667 0.00 0.00 0.00 5.12
115 116 1.716826 CTCCGCCTCCTGTAGACGAC 61.717 65.000 0.00 0.00 0.00 4.34
116 117 1.451567 CTCCGCCTCCTGTAGACGA 60.452 63.158 0.00 0.00 0.00 4.20
117 118 2.482333 CCTCCGCCTCCTGTAGACG 61.482 68.421 0.00 0.00 0.00 4.18
118 119 2.787567 GCCTCCGCCTCCTGTAGAC 61.788 68.421 0.00 0.00 0.00 2.59
119 120 2.442272 GCCTCCGCCTCCTGTAGA 60.442 66.667 0.00 0.00 0.00 2.59
120 121 2.759973 TGCCTCCGCCTCCTGTAG 60.760 66.667 0.00 0.00 0.00 2.74
121 122 2.759973 CTGCCTCCGCCTCCTGTA 60.760 66.667 0.00 0.00 0.00 2.74
122 123 4.704103 TCTGCCTCCGCCTCCTGT 62.704 66.667 0.00 0.00 0.00 4.00
123 124 4.154347 GTCTGCCTCCGCCTCCTG 62.154 72.222 0.00 0.00 0.00 3.86
157 159 2.026641 CATCCTTTGGTCGCCATTGAT 58.973 47.619 0.00 0.95 31.53 2.57
158 160 1.004161 TCATCCTTTGGTCGCCATTGA 59.996 47.619 0.00 0.00 31.53 2.57
160 162 2.094675 CTTCATCCTTTGGTCGCCATT 58.905 47.619 0.00 0.00 31.53 3.16
197 199 5.923114 CACGGATCATCTACCAACTCTAATG 59.077 44.000 0.00 0.00 0.00 1.90
198 200 5.598830 ACACGGATCATCTACCAACTCTAAT 59.401 40.000 0.00 0.00 0.00 1.73
220 222 2.296752 TGTATCAAGGTCGAACCGAACA 59.703 45.455 7.17 0.00 46.95 3.18
232 234 6.494893 TCTTTTCGAACCATTGTATCAAGG 57.505 37.500 0.00 0.00 0.00 3.61
252 254 4.521256 GCCTACTCGATCTATCCACTTCTT 59.479 45.833 0.00 0.00 0.00 2.52
267 269 3.559238 AAGCATTTTTGTGCCTACTCG 57.441 42.857 0.00 0.00 46.19 4.18
270 272 2.986479 CCGAAAGCATTTTTGTGCCTAC 59.014 45.455 0.00 0.00 46.19 3.18
271 273 2.887783 TCCGAAAGCATTTTTGTGCCTA 59.112 40.909 0.00 0.00 46.19 3.93
290 292 4.353437 ACCAGGCGTTCGTCGTCC 62.353 66.667 4.15 6.12 46.16 4.79
292 294 4.695231 CGACCAGGCGTTCGTCGT 62.695 66.667 14.53 0.00 43.29 4.34
297 299 1.652563 AAAAAGCGACCAGGCGTTC 59.347 52.632 0.00 0.00 33.50 3.95
298 300 3.836151 AAAAAGCGACCAGGCGTT 58.164 50.000 0.00 0.00 36.16 4.84
371 373 7.459394 TCATTCTTTTAGCGAATACTTACCG 57.541 36.000 0.00 0.00 30.40 4.02
391 393 8.830580 CATAGATTGGTTCTCGTATGTTTCATT 58.169 33.333 0.00 0.00 35.79 2.57
412 414 5.130477 GTCCTTCTAACCATCCAACCATAGA 59.870 44.000 0.00 0.00 0.00 1.98
415 417 3.591527 TGTCCTTCTAACCATCCAACCAT 59.408 43.478 0.00 0.00 0.00 3.55
422 424 6.049790 GGATAACACTGTCCTTCTAACCATC 58.950 44.000 0.00 0.00 30.25 3.51
424 426 4.841813 TGGATAACACTGTCCTTCTAACCA 59.158 41.667 0.00 0.00 34.00 3.67
425 427 5.176592 GTGGATAACACTGTCCTTCTAACC 58.823 45.833 0.00 0.00 46.72 2.85
441 443 2.167693 CGCTCTAGTGGGTTGTGGATAA 59.832 50.000 0.95 0.00 0.00 1.75
442 444 1.754803 CGCTCTAGTGGGTTGTGGATA 59.245 52.381 0.95 0.00 0.00 2.59
446 448 0.603569 AGTCGCTCTAGTGGGTTGTG 59.396 55.000 8.50 0.00 0.00 3.33
447 449 1.817447 GTAGTCGCTCTAGTGGGTTGT 59.183 52.381 8.50 0.00 0.00 3.32
448 450 1.202154 CGTAGTCGCTCTAGTGGGTTG 60.202 57.143 8.50 0.00 0.00 3.77
450 452 0.251354 TCGTAGTCGCTCTAGTGGGT 59.749 55.000 8.50 0.00 36.96 4.51
451 453 1.331138 CTTCGTAGTCGCTCTAGTGGG 59.669 57.143 2.63 2.63 36.96 4.61
458 460 0.803740 AGACACCTTCGTAGTCGCTC 59.196 55.000 0.00 0.00 37.36 5.03
459 461 0.522180 CAGACACCTTCGTAGTCGCT 59.478 55.000 0.00 0.00 37.36 4.93
460 462 0.240411 ACAGACACCTTCGTAGTCGC 59.760 55.000 0.00 0.00 37.36 5.19
462 464 2.664971 CGTCACAGACACCTTCGTAGTC 60.665 54.545 0.00 0.00 32.09 2.59
485 487 6.183360 GGCACATTATCTTGAGATTGACGAAA 60.183 38.462 0.00 0.00 36.05 3.46
488 490 4.318333 CGGCACATTATCTTGAGATTGACG 60.318 45.833 4.75 4.75 34.89 4.35
497 499 0.813610 TCGGCCGGCACATTATCTTG 60.814 55.000 30.85 4.03 0.00 3.02
503 505 3.665675 GAGACTCGGCCGGCACATT 62.666 63.158 30.85 9.48 0.00 2.71
523 525 2.159421 ACAATACAGACGTAGGCACTCG 60.159 50.000 0.00 0.00 41.75 4.18
558 626 9.575868 TTGTGAACACAGGGAATAGTATTTTTA 57.424 29.630 7.67 0.00 42.94 1.52
573 641 9.764870 CAGAACATCTTATATTTGTGAACACAG 57.235 33.333 7.67 0.00 42.94 3.66
575 643 8.946085 TCCAGAACATCTTATATTTGTGAACAC 58.054 33.333 0.00 0.00 0.00 3.32
606 674 4.585955 ACGTAGTCCTAGCACATATTGG 57.414 45.455 0.00 0.00 29.74 3.16
614 682 5.089970 TCAGTTAGTACGTAGTCCTAGCA 57.910 43.478 6.10 0.00 43.93 3.49
615 683 5.584251 AGTTCAGTTAGTACGTAGTCCTAGC 59.416 44.000 6.10 2.03 43.93 3.42
626 694 9.472361 TGTTTATTCACTCAGTTCAGTTAGTAC 57.528 33.333 0.00 0.00 0.00 2.73
630 698 8.201464 TCAGTGTTTATTCACTCAGTTCAGTTA 58.799 33.333 0.00 0.00 45.37 2.24
659 727 5.823045 TGTGAACCAAATGTACATACACACA 59.177 36.000 9.21 15.27 39.30 3.72
660 728 6.307031 TGTGAACCAAATGTACATACACAC 57.693 37.500 9.21 13.21 39.30 3.82
704 781 5.310451 TGTACTTCCCCTGTTCACAAATAC 58.690 41.667 0.00 0.00 0.00 1.89
705 782 5.570205 TGTACTTCCCCTGTTCACAAATA 57.430 39.130 0.00 0.00 0.00 1.40
706 783 4.447138 TGTACTTCCCCTGTTCACAAAT 57.553 40.909 0.00 0.00 0.00 2.32
716 793 3.571590 TGCAAACATTTGTACTTCCCCT 58.428 40.909 6.24 0.00 40.24 4.79
718 795 6.481644 TCATTTTGCAAACATTTGTACTTCCC 59.518 34.615 12.39 0.00 40.24 3.97
721 798 7.768120 TCCTTCATTTTGCAAACATTTGTACTT 59.232 29.630 12.39 0.00 40.24 2.24
727 804 5.884792 TGGTTCCTTCATTTTGCAAACATTT 59.115 32.000 12.39 0.00 0.00 2.32
754 831 2.493278 CCATCACAAACAGTTGGGGATC 59.507 50.000 1.94 0.00 38.80 3.36
771 848 6.454795 TGTCTTGTTCCAAATTAAAGCCATC 58.545 36.000 0.00 0.00 0.00 3.51
782 859 6.014755 TGCCATGAATAATGTCTTGTTCCAAA 60.015 34.615 0.00 0.00 33.02 3.28
857 934 4.804665 GTCCTAAATCGAGACTAACTTGGC 59.195 45.833 0.00 0.00 0.00 4.52
878 1227 3.906720 TGGCCCTGTTTCATACTAGTC 57.093 47.619 0.00 0.00 0.00 2.59
983 1451 7.439056 CCATTATTTTTCTCGCTTGGCATTTAT 59.561 33.333 0.00 0.00 0.00 1.40
1191 1869 1.131883 CTTCATGTTGCTGCTGCTACC 59.868 52.381 22.88 9.49 42.66 3.18
1193 1871 0.806868 GCTTCATGTTGCTGCTGCTA 59.193 50.000 17.00 6.36 40.48 3.49
1217 1895 3.522731 CGGGAGAGCCGTCTGAGG 61.523 72.222 0.00 0.00 30.97 3.86
1322 2003 0.518764 CGAAGAACGAGGACGACGAG 60.519 60.000 0.00 0.00 45.77 4.18
1627 2308 2.271173 GAAACGGGGAAGGGCGAT 59.729 61.111 0.00 0.00 0.00 4.58
1647 2340 3.760035 GGCAGCCGAACGAGGAGA 61.760 66.667 0.00 0.00 0.00 3.71
1692 2390 2.040544 CCGATTTGCCTTCGCCAGT 61.041 57.895 0.00 0.00 35.31 4.00
2017 2810 5.861787 GTGTATATGGACCAAACTTTTGCAC 59.138 40.000 0.00 0.00 36.86 4.57
2035 7944 6.349115 GGACGAAACTCTCTTCACAGTGTATA 60.349 42.308 0.00 0.00 0.00 1.47
2054 7963 2.628178 CCCTATGTGCTATCTGGACGAA 59.372 50.000 0.00 0.00 40.08 3.85
2075 7984 4.501743 GGAGAGAAAGTGATAACGATCCCC 60.502 50.000 0.00 0.00 0.00 4.81
2076 7985 4.099573 TGGAGAGAAAGTGATAACGATCCC 59.900 45.833 0.00 0.00 0.00 3.85
2114 8137 1.372582 TGCTCGAGGACAAATGATGC 58.627 50.000 15.58 0.00 0.00 3.91
2160 8191 4.590850 ACAATTTCTCCAAAGTTCTGGC 57.409 40.909 0.66 0.00 36.32 4.85
2172 8203 8.940952 AGTAGTTCTGAAGCAATACAATTTCTC 58.059 33.333 0.00 0.00 0.00 2.87
2197 10017 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
2200 10020 9.473640 GTAAAGACTTATATTTAGGAACGGAGG 57.526 37.037 0.00 0.00 0.00 4.30
2217 10037 9.702253 TCCATAGTAGAATCTCTGTAAAGACTT 57.298 33.333 0.00 0.00 0.00 3.01
2218 10038 9.127277 GTCCATAGTAGAATCTCTGTAAAGACT 57.873 37.037 0.00 0.00 0.00 3.24
2219 10039 9.127277 AGTCCATAGTAGAATCTCTGTAAAGAC 57.873 37.037 0.00 0.00 0.00 3.01
2222 10042 9.916360 TGTAGTCCATAGTAGAATCTCTGTAAA 57.084 33.333 0.00 0.00 0.00 2.01
2225 10045 9.509956 GTATGTAGTCCATAGTAGAATCTCTGT 57.490 37.037 0.00 0.00 36.71 3.41
2226 10046 8.661257 CGTATGTAGTCCATAGTAGAATCTCTG 58.339 40.741 0.00 0.00 36.71 3.35
2227 10047 8.377034 ACGTATGTAGTCCATAGTAGAATCTCT 58.623 37.037 0.00 0.00 36.71 3.10
2228 10048 8.550710 ACGTATGTAGTCCATAGTAGAATCTC 57.449 38.462 0.00 0.00 36.71 2.75
2229 10049 9.656040 CTACGTATGTAGTCCATAGTAGAATCT 57.344 37.037 13.15 0.00 42.61 2.40
2245 10065 7.979537 AGATTCACTCATTTTGCTACGTATGTA 59.020 33.333 0.00 0.00 0.00 2.29
2246 10066 6.818644 AGATTCACTCATTTTGCTACGTATGT 59.181 34.615 0.00 0.00 0.00 2.29
2247 10067 7.239166 AGATTCACTCATTTTGCTACGTATG 57.761 36.000 0.00 0.00 0.00 2.39
2248 10068 7.438459 GGTAGATTCACTCATTTTGCTACGTAT 59.562 37.037 0.00 0.00 0.00 3.06
2249 10069 6.755141 GGTAGATTCACTCATTTTGCTACGTA 59.245 38.462 0.00 0.00 0.00 3.57
2250 10070 5.581085 GGTAGATTCACTCATTTTGCTACGT 59.419 40.000 0.00 0.00 0.00 3.57
2251 10071 5.006746 GGGTAGATTCACTCATTTTGCTACG 59.993 44.000 0.00 0.00 0.00 3.51
2252 10072 6.116126 AGGGTAGATTCACTCATTTTGCTAC 58.884 40.000 0.00 0.00 0.00 3.58
2253 10073 6.156949 AGAGGGTAGATTCACTCATTTTGCTA 59.843 38.462 0.00 0.00 40.03 3.49
2254 10074 5.045286 AGAGGGTAGATTCACTCATTTTGCT 60.045 40.000 0.00 0.00 40.03 3.91
2255 10075 5.189180 AGAGGGTAGATTCACTCATTTTGC 58.811 41.667 0.00 0.00 40.03 3.68
2256 10076 8.792830 TTTAGAGGGTAGATTCACTCATTTTG 57.207 34.615 0.00 0.00 40.03 2.44
2257 10077 9.981460 ATTTTAGAGGGTAGATTCACTCATTTT 57.019 29.630 0.00 0.00 40.03 1.82
2258 10078 9.401058 CATTTTAGAGGGTAGATTCACTCATTT 57.599 33.333 0.00 0.00 40.03 2.32
2259 10079 7.500559 GCATTTTAGAGGGTAGATTCACTCATT 59.499 37.037 0.00 0.00 40.03 2.57
2260 10080 6.995091 GCATTTTAGAGGGTAGATTCACTCAT 59.005 38.462 0.00 0.00 40.03 2.90
2261 10081 6.070251 TGCATTTTAGAGGGTAGATTCACTCA 60.070 38.462 0.00 0.00 40.03 3.41
2262 10082 6.349300 TGCATTTTAGAGGGTAGATTCACTC 58.651 40.000 0.00 0.00 38.06 3.51
2263 10083 6.313519 TGCATTTTAGAGGGTAGATTCACT 57.686 37.500 0.00 0.00 0.00 3.41
2264 10084 6.995091 AGATGCATTTTAGAGGGTAGATTCAC 59.005 38.462 0.00 0.00 0.00 3.18
2265 10085 7.141758 AGATGCATTTTAGAGGGTAGATTCA 57.858 36.000 0.00 0.00 0.00 2.57
2284 10104 9.689976 GGATCACATACAGATGTATATAGATGC 57.310 37.037 5.21 9.87 44.82 3.91
2292 10112 9.981460 TCTACTATGGATCACATACAGATGTAT 57.019 33.333 0.00 0.00 44.82 2.29
2293 10113 9.807921 TTCTACTATGGATCACATACAGATGTA 57.192 33.333 0.00 0.00 44.82 2.29
2295 10115 9.800433 GATTCTACTATGGATCACATACAGATG 57.200 37.037 0.00 0.00 41.03 2.90
2296 10116 9.766754 AGATTCTACTATGGATCACATACAGAT 57.233 33.333 0.00 0.00 41.03 2.90
2329 10149 9.495382 ACTCCCTCTGTTTCTAAATATAAGTCT 57.505 33.333 0.00 0.00 0.00 3.24
2335 10155 9.047947 ACAACTACTCCCTCTGTTTCTAAATAT 57.952 33.333 0.00 0.00 0.00 1.28
2336 10156 8.311836 CACAACTACTCCCTCTGTTTCTAAATA 58.688 37.037 0.00 0.00 0.00 1.40
2337 10157 7.162082 CACAACTACTCCCTCTGTTTCTAAAT 58.838 38.462 0.00 0.00 0.00 1.40
2338 10158 6.099269 ACACAACTACTCCCTCTGTTTCTAAA 59.901 38.462 0.00 0.00 0.00 1.85
2339 10159 5.601313 ACACAACTACTCCCTCTGTTTCTAA 59.399 40.000 0.00 0.00 0.00 2.10
2340 10160 5.145564 ACACAACTACTCCCTCTGTTTCTA 58.854 41.667 0.00 0.00 0.00 2.10
2341 10161 3.967987 ACACAACTACTCCCTCTGTTTCT 59.032 43.478 0.00 0.00 0.00 2.52
2342 10162 4.338379 ACACAACTACTCCCTCTGTTTC 57.662 45.455 0.00 0.00 0.00 2.78
2343 10163 4.772886 AACACAACTACTCCCTCTGTTT 57.227 40.909 0.00 0.00 0.00 2.83
2344 10164 5.881923 TTAACACAACTACTCCCTCTGTT 57.118 39.130 0.00 0.00 0.00 3.16
2345 10165 5.881923 TTTAACACAACTACTCCCTCTGT 57.118 39.130 0.00 0.00 0.00 3.41
2371 10192 3.245797 CGGACACTATGCATCTAATCGG 58.754 50.000 0.19 0.00 0.00 4.18
2373 10194 4.238514 GGACGGACACTATGCATCTAATC 58.761 47.826 0.19 0.00 0.00 1.75
2381 10460 1.084370 GCACTGGACGGACACTATGC 61.084 60.000 0.00 0.00 0.00 3.14
2405 10484 3.571401 CCCAAATGGCTGATCTTGATACC 59.429 47.826 0.00 0.00 0.00 2.73
2493 11448 5.652744 ACTAACTAAAACAAGCACGACTG 57.347 39.130 0.00 0.00 0.00 3.51
2538 11572 2.486128 CGAAAGCGAGTGAATCAAACG 58.514 47.619 6.09 6.09 40.82 3.60
2569 11612 0.607489 GAGCAAAGCTTCTCCTGCCA 60.607 55.000 15.50 0.00 39.88 4.92
2570 11613 0.322366 AGAGCAAAGCTTCTCCTGCC 60.322 55.000 15.50 8.61 39.88 4.85
2614 11665 1.745115 TACAGTACGTACGCCGCCT 60.745 57.895 19.49 2.86 41.42 5.52
2689 11750 0.899720 TCAACTCGGGGTACATGGAC 59.100 55.000 0.00 0.00 0.00 4.02
2690 11751 1.874129 ATCAACTCGGGGTACATGGA 58.126 50.000 0.00 0.00 0.00 3.41
2692 11753 3.198068 CTGAATCAACTCGGGGTACATG 58.802 50.000 0.00 0.00 0.00 3.21
2693 11754 2.838202 ACTGAATCAACTCGGGGTACAT 59.162 45.455 0.00 0.00 0.00 2.29
2695 11756 2.734492 CGACTGAATCAACTCGGGGTAC 60.734 54.545 2.91 0.00 0.00 3.34
2696 11757 1.475280 CGACTGAATCAACTCGGGGTA 59.525 52.381 2.91 0.00 0.00 3.69
2697 11758 0.246635 CGACTGAATCAACTCGGGGT 59.753 55.000 2.91 0.00 0.00 4.95
2698 11759 1.084370 GCGACTGAATCAACTCGGGG 61.084 60.000 10.72 0.00 0.00 5.73
2699 11760 1.413767 CGCGACTGAATCAACTCGGG 61.414 60.000 0.00 10.94 33.56 5.14
2700 11761 1.413767 CCGCGACTGAATCAACTCGG 61.414 60.000 8.23 7.76 0.00 4.63
2701 11762 0.732880 ACCGCGACTGAATCAACTCG 60.733 55.000 8.23 5.82 0.00 4.18
2702 11763 0.716108 CACCGCGACTGAATCAACTC 59.284 55.000 8.23 0.00 0.00 3.01
2703 11764 0.670546 CCACCGCGACTGAATCAACT 60.671 55.000 8.23 0.00 0.00 3.16
2760 11841 0.242825 TACGTGTTCTTCTGGCCTCG 59.757 55.000 3.32 0.00 0.00 4.63
2776 11874 7.705214 AGTTAAGCACTTATTCCTAGAGTACG 58.295 38.462 0.00 0.00 27.32 3.67
2780 11878 9.522804 CACTTAGTTAAGCACTTATTCCTAGAG 57.477 37.037 0.00 0.00 36.88 2.43
2784 11882 7.180408 TCCTCACTTAGTTAAGCACTTATTCCT 59.820 37.037 0.00 0.00 36.88 3.36
2786 11884 8.773404 TTCCTCACTTAGTTAAGCACTTATTC 57.227 34.615 0.00 0.00 36.88 1.75
2791 11909 8.135382 TCTTATTCCTCACTTAGTTAAGCACT 57.865 34.615 0.00 0.00 39.87 4.40
2844 11980 1.538946 GCGCGTACACACAACGTACA 61.539 55.000 8.43 0.00 42.26 2.90
2898 12042 1.670406 CACTGTCACTGAGCTGGCC 60.670 63.158 0.00 0.00 0.00 5.36
2945 12089 2.606272 GTCATTTACGTTGGACCGATCC 59.394 50.000 0.00 0.00 46.48 3.36
2977 12121 0.461961 GTACTCCATCTCGGCAGCTT 59.538 55.000 0.00 0.00 33.14 3.74
3022 12171 7.170828 CAGTGCCAGTATATTACGCTTTCAATA 59.829 37.037 0.00 0.00 0.00 1.90
3028 12177 3.134081 ACCAGTGCCAGTATATTACGCTT 59.866 43.478 0.00 0.00 0.00 4.68
3066 12218 1.381522 CCGACATGGATGCAATGACA 58.618 50.000 3.89 0.00 42.00 3.58


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

AutoCloner maintained by Alex Coulton.