Multiple sequence alignment - TraesCS2A01G010800

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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 TraesCS2A01G010800 chr2A 100.000 2597 0 0 1 2597 4112715 4115311 0.000000e+00 4796.0
1 TraesCS2A01G010800 chr2A 78.182 385 38 22 1527 1869 16945574 16945954 1.220000e-48 204.0
2 TraesCS2A01G010800 chr2A 79.268 164 27 7 511 672 497693702 497693860 9.830000e-20 108.0
3 TraesCS2A01G010800 chr2B 86.821 736 69 12 152 869 5995274 5994549 0.000000e+00 797.0
4 TraesCS2A01G010800 chr2B 92.683 328 24 0 1868 2195 713749772 713750099 8.410000e-130 473.0
5 TraesCS2A01G010800 chr2B 85.606 396 24 11 1501 1868 691405181 691404791 4.050000e-103 385.0
6 TraesCS2A01G010800 chr2B 80.070 286 28 14 2206 2476 71197115 71196844 4.410000e-43 185.0
7 TraesCS2A01G010800 chr2B 88.514 148 14 3 866 1011 691406133 691405987 2.660000e-40 176.0
8 TraesCS2A01G010800 chr2B 94.000 50 3 0 1191 1240 691405913 691405864 2.770000e-10 76.8
9 TraesCS2A01G010800 chr2B 97.222 36 1 0 1487 1522 776315037 776315002 7.760000e-06 62.1
10 TraesCS2A01G010800 chr2D 90.231 563 41 6 10 569 5469556 5469005 0.000000e+00 723.0
11 TraesCS2A01G010800 chr2D 87.532 385 44 2 485 869 5469005 5468625 2.370000e-120 442.0
12 TraesCS2A01G010800 chr2D 81.551 374 24 8 1535 1868 119783857 119784225 1.530000e-67 267.0
13 TraesCS2A01G010800 chr2D 80.423 189 31 4 1 183 23495274 23495462 3.480000e-29 139.0
14 TraesCS2A01G010800 chr2D 79.775 178 30 5 438 614 43279139 43279311 9.760000e-25 124.0
15 TraesCS2A01G010800 chr5A 97.067 341 10 0 1868 2208 362790463 362790123 2.240000e-160 575.0
16 TraesCS2A01G010800 chr5A 79.467 375 41 17 2206 2563 576616514 576616159 1.550000e-57 233.0
17 TraesCS2A01G010800 chr5A 90.833 120 9 2 865 982 282413780 282413899 2.670000e-35 159.0
18 TraesCS2A01G010800 chr7D 92.386 394 27 3 2207 2597 213056744 213056351 2.260000e-155 558.0
19 TraesCS2A01G010800 chr7D 90.549 328 17 7 1868 2195 13182580 13182893 3.090000e-114 422.0
20 TraesCS2A01G010800 chr7D 90.244 328 18 7 1868 2195 206013496 206013809 1.440000e-112 416.0
21 TraesCS2A01G010800 chr7D 89.394 330 19 9 1868 2195 438377292 438377607 4.030000e-108 401.0
22 TraesCS2A01G010800 chr7D 89.933 149 13 2 875 1022 204881267 204881414 9.490000e-45 191.0
23 TraesCS2A01G010800 chr7D 75.234 428 83 13 252 670 4239921 4240334 5.710000e-42 182.0
24 TraesCS2A01G010800 chr7D 74.468 376 65 21 252 614 262740404 262740761 1.620000e-27 134.0
25 TraesCS2A01G010800 chr7D 74.803 254 54 7 420 672 161136552 161136796 3.530000e-19 106.0
26 TraesCS2A01G010800 chr7D 85.714 70 8 1 2207 2276 269702145 269702078 3.580000e-09 73.1
27 TraesCS2A01G010800 chr3A 93.716 366 23 0 1028 1393 67123852 67124217 1.360000e-152 549.0
28 TraesCS2A01G010800 chr3A 96.838 253 8 0 1869 2121 423493054 423493306 8.590000e-115 424.0
29 TraesCS2A01G010800 chr3A 97.753 89 2 0 2117 2205 423493786 423493874 1.240000e-33 154.0
30 TraesCS2A01G010800 chr3D 93.443 366 24 0 1028 1393 58107788 58108153 6.320000e-151 544.0
31 TraesCS2A01G010800 chr3D 74.930 359 76 10 314 670 498946722 498946376 4.480000e-33 152.0
32 TraesCS2A01G010800 chr3D 74.483 290 49 19 387 670 43900325 43900055 4.570000e-18 102.0
33 TraesCS2A01G010800 chr3B 91.117 394 31 4 2207 2597 573475145 573475537 4.920000e-147 531.0
34 TraesCS2A01G010800 chr3B 92.623 366 27 0 1028 1393 91147506 91147871 6.370000e-146 527.0
35 TraesCS2A01G010800 chr3B 89.526 401 24 9 2206 2593 561749211 561748816 2.320000e-135 492.0
36 TraesCS2A01G010800 chr3B 84.324 185 26 3 2208 2390 803575823 803575640 7.390000e-41 178.0
37 TraesCS2A01G010800 chr3B 82.759 116 17 3 864 978 605028523 605028636 1.640000e-17 100.0
38 TraesCS2A01G010800 chr5D 92.643 367 24 3 2234 2597 292676941 292676575 2.290000e-145 525.0
39 TraesCS2A01G010800 chr5D 86.104 403 21 9 1412 1788 80220718 80221111 4.030000e-108 401.0
40 TraesCS2A01G010800 chr5D 79.134 508 33 22 1419 1867 533551433 533551926 1.520000e-72 283.0
41 TraesCS2A01G010800 chr1B 95.122 328 16 0 1868 2195 470904830 470904503 3.830000e-143 518.0
42 TraesCS2A01G010800 chr5B 92.988 328 23 0 1868 2195 306510357 306510684 1.810000e-131 479.0
43 TraesCS2A01G010800 chr5B 80.588 510 37 24 1417 1868 621056993 621056488 1.150000e-88 337.0
44 TraesCS2A01G010800 chr1D 85.200 500 28 10 1412 1866 478801477 478800979 3.030000e-129 472.0
45 TraesCS2A01G010800 chr1D 77.179 390 38 18 1527 1868 221299700 221300086 2.050000e-41 180.0
46 TraesCS2A01G010800 chr1D 95.283 106 4 1 865 969 478801629 478801524 1.600000e-37 167.0
47 TraesCS2A01G010800 chr1D 97.619 42 1 0 1480 1521 221299500 221299541 3.580000e-09 73.1
48 TraesCS2A01G010800 chr6D 91.159 328 15 9 1868 2195 386960003 386959690 1.430000e-117 433.0
49 TraesCS2A01G010800 chr6D 79.058 191 31 3 1 182 366982455 366982645 3.510000e-24 122.0
50 TraesCS2A01G010800 chr6D 84.545 110 16 1 865 973 27034217 27034326 9.830000e-20 108.0
51 TraesCS2A01G010800 chr6D 97.619 42 1 0 1487 1528 43038787 43038746 3.580000e-09 73.1
52 TraesCS2A01G010800 chr7B 87.000 400 24 13 2203 2597 238108960 238108584 2.390000e-115 425.0
53 TraesCS2A01G010800 chr7B 85.786 401 25 13 2206 2597 238110092 238109715 1.870000e-106 396.0
54 TraesCS2A01G010800 chr7B 81.609 174 27 3 445 617 134211841 134212010 3.480000e-29 139.0
55 TraesCS2A01G010800 chr7B 78.261 138 24 5 536 672 448796506 448796374 1.660000e-12 84.2
56 TraesCS2A01G010800 chr7B 94.118 51 2 1 2204 2253 123310218 123310168 2.770000e-10 76.8
57 TraesCS2A01G010800 chr6A 80.214 374 38 17 2207 2563 55016528 55016882 5.550000e-62 248.0
58 TraesCS2A01G010800 chr6A 91.129 124 11 0 1485 1608 438036833 438036956 4.440000e-38 169.0
59 TraesCS2A01G010800 chr6A 78.857 175 32 3 438 611 108938922 108939092 2.110000e-21 113.0
60 TraesCS2A01G010800 chr6A 83.784 111 16 2 869 978 104399906 104399797 1.270000e-18 104.0
61 TraesCS2A01G010800 chr4D 85.606 132 16 3 6 135 448175537 448175407 4.510000e-28 135.0
62 TraesCS2A01G010800 chr1A 86.992 123 12 3 862 983 90456962 90457081 4.510000e-28 135.0
63 TraesCS2A01G010800 chr1A 79.885 174 22 8 21 183 441747853 441747682 5.870000e-22 115.0
64 TraesCS2A01G010800 chrUn 85.000 120 14 4 865 981 129541880 129541762 4.540000e-23 119.0
65 TraesCS2A01G010800 chr6B 95.833 48 2 0 2206 2253 603328491 603328538 7.710000e-11 78.7
66 TraesCS2A01G010800 chr6B 95.745 47 2 0 2207 2253 603328142 603328188 2.770000e-10 76.8


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 TraesCS2A01G010800 chr2A 4112715 4115311 2596 False 4796.0 4796 100.000000 1 2597 1 chr2A.!!$F1 2596
1 TraesCS2A01G010800 chr2B 5994549 5995274 725 True 797.0 797 86.821000 152 869 1 chr2B.!!$R1 717
2 TraesCS2A01G010800 chr2B 691404791 691406133 1342 True 212.6 385 89.373333 866 1868 3 chr2B.!!$R4 1002
3 TraesCS2A01G010800 chr2D 5468625 5469556 931 True 582.5 723 88.881500 10 869 2 chr2D.!!$R1 859
4 TraesCS2A01G010800 chr3A 423493054 423493874 820 False 289.0 424 97.295500 1869 2205 2 chr3A.!!$F2 336
5 TraesCS2A01G010800 chr5B 621056488 621056993 505 True 337.0 337 80.588000 1417 1868 1 chr5B.!!$R1 451
6 TraesCS2A01G010800 chr1D 478800979 478801629 650 True 319.5 472 90.241500 865 1866 2 chr1D.!!$R1 1001
7 TraesCS2A01G010800 chr7B 238108584 238110092 1508 True 410.5 425 86.393000 2203 2597 2 chr7B.!!$R3 394

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
591 700 0.035739 ACTGTAATTTGGGTCGGCGT 59.964 50.0 6.85 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2048 2771 0.035056 AATGGCCAAGTCGAGGAAGG 60.035 55.0 10.96 0.0 0.0 3.46 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
25 26 5.412904 ACCCGAATTTGCAAAACTTTGAAAA 59.587 32.000 17.19 10.11 46.55 2.29
26 27 5.964751 CCCGAATTTGCAAAACTTTGAAAAG 59.035 36.000 17.19 1.22 45.92 2.27
77 78 7.479980 TCTGAAATTTGGACACAACAAACTAG 58.520 34.615 0.00 0.00 40.25 2.57
116 117 7.713942 AGCTTCTTGCAAAATTTCAGAGAAAAT 59.286 29.630 0.00 0.00 45.94 1.82
130 131 8.704849 TTCAGAGAAAATTAACATCCAAGGAA 57.295 30.769 0.00 0.00 0.00 3.36
166 167 7.754069 TTACTTCTCAAACATTGCACAAAAG 57.246 32.000 0.00 0.00 0.00 2.27
280 287 2.813179 GCGGCGCTACCATCTTGTG 61.813 63.158 26.86 0.00 39.03 3.33
375 382 4.003788 CGTCAAGGGTCGGCTGGT 62.004 66.667 0.00 0.00 0.00 4.00
385 392 2.034066 CGGCTGGTTGTCCATGGT 59.966 61.111 12.58 0.00 43.43 3.55
396 424 2.124983 CCATGGTGAGCGGGAGTG 60.125 66.667 2.57 0.00 0.00 3.51
397 425 2.124983 CATGGTGAGCGGGAGTGG 60.125 66.667 0.00 0.00 0.00 4.00
398 426 3.402681 ATGGTGAGCGGGAGTGGG 61.403 66.667 0.00 0.00 0.00 4.61
442 470 2.677968 AAAATGGGGGTGGCTGTGCT 62.678 55.000 0.00 0.00 0.00 4.40
503 531 0.442310 CGCGTCCATTTCGTGTCAAT 59.558 50.000 0.00 0.00 34.71 2.57
577 605 4.916983 AAAAAGCAGATGCACAACTGTA 57.083 36.364 7.68 0.00 45.16 2.74
578 606 4.916983 AAAAGCAGATGCACAACTGTAA 57.083 36.364 7.68 0.00 45.16 2.41
591 700 0.035739 ACTGTAATTTGGGTCGGCGT 59.964 50.000 6.85 0.00 0.00 5.68
618 727 2.206750 CCGACTTTTCTGTCCGTTTCA 58.793 47.619 0.00 0.00 33.70 2.69
625 734 1.961793 TCTGTCCGTTTCAACCCAAG 58.038 50.000 0.00 0.00 0.00 3.61
721 830 4.891168 ACATATGCAAGCATCATCAAGGAA 59.109 37.500 11.32 0.00 37.82 3.36
726 835 5.653507 TGCAAGCATCATCAAGGAAATAAC 58.346 37.500 0.00 0.00 0.00 1.89
816 925 1.270839 ACATAGCCTTGCAGAACACGT 60.271 47.619 0.00 0.00 0.00 4.49
834 943 4.328712 ACACGTTTTTGGTCTGAATTTTGC 59.671 37.500 0.00 0.00 0.00 3.68
877 986 6.519243 AATCCCCCTGATCTTAGAGCATCTC 61.519 48.000 0.00 0.00 38.78 2.75
894 1003 3.710722 CCAGCCGTTGAGCCCTCT 61.711 66.667 0.00 0.00 0.00 3.69
994 1105 1.077265 CCAAGCCCCACCTTGATGT 59.923 57.895 3.65 0.00 43.79 3.06
995 1106 0.331278 CCAAGCCCCACCTTGATGTA 59.669 55.000 3.65 0.00 43.79 2.29
1014 1125 2.969238 CCGATGGCGCAGGTGATC 60.969 66.667 10.83 1.09 35.83 2.92
1015 1126 2.107750 CGATGGCGCAGGTGATCT 59.892 61.111 10.83 0.00 0.00 2.75
1016 1127 1.522355 CGATGGCGCAGGTGATCTT 60.522 57.895 10.83 0.00 0.00 2.40
1017 1128 1.769098 CGATGGCGCAGGTGATCTTG 61.769 60.000 10.83 0.00 0.00 3.02
1018 1129 0.745845 GATGGCGCAGGTGATCTTGT 60.746 55.000 10.83 0.00 0.00 3.16
1019 1130 1.028330 ATGGCGCAGGTGATCTTGTG 61.028 55.000 10.83 0.00 34.89 3.33
1020 1131 2.401766 GGCGCAGGTGATCTTGTGG 61.402 63.158 10.83 0.00 32.88 4.17
1021 1132 2.401766 GCGCAGGTGATCTTGTGGG 61.402 63.158 0.30 0.00 32.88 4.61
1022 1133 2.401766 CGCAGGTGATCTTGTGGGC 61.402 63.158 0.00 0.00 0.00 5.36
1023 1134 2.048603 GCAGGTGATCTTGTGGGCC 61.049 63.158 0.00 0.00 0.00 5.80
1024 1135 1.746615 CAGGTGATCTTGTGGGCCG 60.747 63.158 0.00 0.00 0.00 6.13
1025 1136 1.918293 AGGTGATCTTGTGGGCCGA 60.918 57.895 0.00 0.00 0.00 5.54
1026 1137 1.224592 GGTGATCTTGTGGGCCGAT 59.775 57.895 0.00 0.00 0.00 4.18
1027 1138 1.097547 GGTGATCTTGTGGGCCGATG 61.098 60.000 0.00 0.00 0.00 3.84
1028 1139 1.097547 GTGATCTTGTGGGCCGATGG 61.098 60.000 0.00 0.00 0.00 3.51
1045 1156 2.755876 GCAGCCTAGCCCCAAACC 60.756 66.667 0.00 0.00 0.00 3.27
1087 1198 1.070134 CCAAGTTCTTCGAGTGGTGGA 59.930 52.381 0.00 0.00 0.00 4.02
1088 1199 2.289694 CCAAGTTCTTCGAGTGGTGGAT 60.290 50.000 0.00 0.00 0.00 3.41
1089 1200 2.996621 CAAGTTCTTCGAGTGGTGGATC 59.003 50.000 0.00 0.00 0.00 3.36
1090 1201 2.530701 AGTTCTTCGAGTGGTGGATCT 58.469 47.619 0.00 0.00 0.00 2.75
1091 1202 2.900546 AGTTCTTCGAGTGGTGGATCTT 59.099 45.455 0.00 0.00 0.00 2.40
1092 1203 2.996621 GTTCTTCGAGTGGTGGATCTTG 59.003 50.000 0.00 0.00 0.00 3.02
1093 1204 1.550524 TCTTCGAGTGGTGGATCTTGG 59.449 52.381 0.00 0.00 0.00 3.61
1094 1205 1.550524 CTTCGAGTGGTGGATCTTGGA 59.449 52.381 0.00 0.00 0.00 3.53
1097 1208 0.615331 GAGTGGTGGATCTTGGAGCA 59.385 55.000 0.00 0.00 0.00 4.26
1098 1209 0.617413 AGTGGTGGATCTTGGAGCAG 59.383 55.000 0.00 0.00 0.00 4.24
1099 1210 0.326264 GTGGTGGATCTTGGAGCAGT 59.674 55.000 0.00 0.00 0.00 4.40
1101 1212 0.107459 GGTGGATCTTGGAGCAGTCC 60.107 60.000 0.00 0.00 44.24 3.85
1103 1214 1.144936 GGATCTTGGAGCAGTCCCG 59.855 63.158 0.00 0.00 43.15 5.14
1104 1215 1.617947 GGATCTTGGAGCAGTCCCGT 61.618 60.000 0.00 0.00 43.15 5.28
1105 1216 0.460987 GATCTTGGAGCAGTCCCGTG 60.461 60.000 0.00 0.00 43.15 4.94
1106 1217 0.904865 ATCTTGGAGCAGTCCCGTGA 60.905 55.000 0.00 0.00 43.15 4.35
1107 1218 1.374758 CTTGGAGCAGTCCCGTGAC 60.375 63.158 0.00 0.00 43.15 3.67
1120 1231 4.090057 GTGACTTGGCCGCGCTTC 62.090 66.667 5.56 0.00 0.00 3.86
1180 1291 4.773117 GCCTCGTCGACCGTGTCC 62.773 72.222 10.58 0.00 37.94 4.02
1183 1294 2.281002 TCGTCGACCGTGTCCTCA 60.281 61.111 10.58 0.00 37.94 3.86
1184 1295 2.176055 CGTCGACCGTGTCCTCAG 59.824 66.667 10.58 0.00 0.00 3.35
1185 1296 2.126424 GTCGACCGTGTCCTCAGC 60.126 66.667 3.51 0.00 0.00 4.26
1186 1297 3.371063 TCGACCGTGTCCTCAGCC 61.371 66.667 0.00 0.00 0.00 4.85
1187 1298 3.680786 CGACCGTGTCCTCAGCCA 61.681 66.667 0.00 0.00 0.00 4.75
1188 1299 2.048127 GACCGTGTCCTCAGCCAC 60.048 66.667 0.00 0.00 0.00 5.01
1189 1300 2.842462 ACCGTGTCCTCAGCCACA 60.842 61.111 0.00 0.00 0.00 4.17
1193 1304 1.069090 GTGTCCTCAGCCACAACGA 59.931 57.895 0.00 0.00 0.00 3.85
1244 1355 4.498520 CGCCGACGTGCTCCTCAT 62.499 66.667 0.00 0.00 33.53 2.90
1245 1356 2.887568 GCCGACGTGCTCCTCATG 60.888 66.667 0.00 0.00 37.70 3.07
1247 1358 1.079819 CCGACGTGCTCCTCATGTT 60.080 57.895 0.00 0.00 44.52 2.71
1248 1359 1.078759 CCGACGTGCTCCTCATGTTC 61.079 60.000 0.00 0.00 44.52 3.18
1249 1360 1.406219 CGACGTGCTCCTCATGTTCG 61.406 60.000 0.00 0.00 44.52 3.95
1250 1361 1.687494 GACGTGCTCCTCATGTTCGC 61.687 60.000 0.00 0.00 44.52 4.70
1251 1362 2.792290 CGTGCTCCTCATGTTCGCG 61.792 63.158 0.00 0.00 0.00 5.87
1252 1363 2.815211 TGCTCCTCATGTTCGCGC 60.815 61.111 0.00 0.00 0.00 6.86
1253 1364 3.567797 GCTCCTCATGTTCGCGCC 61.568 66.667 0.00 0.00 0.00 6.53
1254 1365 2.892425 CTCCTCATGTTCGCGCCC 60.892 66.667 0.00 0.00 0.00 6.13
1255 1366 3.376935 CTCCTCATGTTCGCGCCCT 62.377 63.158 0.00 0.00 0.00 5.19
1256 1367 2.892425 CCTCATGTTCGCGCCCTC 60.892 66.667 0.00 0.00 0.00 4.30
1257 1368 3.257561 CTCATGTTCGCGCCCTCG 61.258 66.667 0.00 0.00 39.07 4.63
1258 1369 3.989698 CTCATGTTCGCGCCCTCGT 62.990 63.158 0.00 0.00 38.14 4.18
1259 1370 3.853330 CATGTTCGCGCCCTCGTG 61.853 66.667 0.00 0.00 46.68 4.35
1262 1373 4.814294 GTTCGCGCCCTCGTGGAT 62.814 66.667 0.00 0.00 45.48 3.41
1263 1374 4.508128 TTCGCGCCCTCGTGGATC 62.508 66.667 0.00 0.00 45.48 3.36
1265 1376 4.933064 CGCGCCCTCGTGGATCTC 62.933 72.222 4.76 0.00 42.06 2.75
1266 1377 4.593864 GCGCCCTCGTGGATCTCC 62.594 72.222 4.76 0.00 38.14 3.71
1267 1378 4.271816 CGCCCTCGTGGATCTCCG 62.272 72.222 4.76 0.00 39.43 4.63
1268 1379 3.148279 GCCCTCGTGGATCTCCGT 61.148 66.667 4.76 0.00 39.43 4.69
1269 1380 3.121019 CCCTCGTGGATCTCCGTC 58.879 66.667 4.76 0.00 39.43 4.79
1270 1381 1.753078 CCCTCGTGGATCTCCGTCA 60.753 63.158 4.76 0.00 39.43 4.35
1271 1382 1.433879 CCTCGTGGATCTCCGTCAC 59.566 63.158 0.00 0.00 39.43 3.67
1272 1383 1.433879 CTCGTGGATCTCCGTCACC 59.566 63.158 0.00 0.00 39.43 4.02
1273 1384 2.102357 CGTGGATCTCCGTCACCG 59.898 66.667 0.00 0.00 39.43 4.94
1274 1385 2.404186 CGTGGATCTCCGTCACCGA 61.404 63.158 0.00 0.00 39.43 4.69
1275 1386 1.433879 GTGGATCTCCGTCACCGAG 59.566 63.158 0.00 0.00 39.43 4.63
1276 1387 1.030488 GTGGATCTCCGTCACCGAGA 61.030 60.000 0.00 0.00 39.43 4.04
1277 1388 0.748367 TGGATCTCCGTCACCGAGAG 60.748 60.000 2.23 0.00 39.43 3.20
1278 1389 1.357334 GATCTCCGTCACCGAGAGC 59.643 63.158 2.23 0.00 33.86 4.09
1279 1390 2.065906 GATCTCCGTCACCGAGAGCC 62.066 65.000 0.34 0.00 33.86 4.70
1280 1391 2.559922 ATCTCCGTCACCGAGAGCCT 62.560 60.000 2.23 0.00 33.86 4.58
1281 1392 2.750637 TCCGTCACCGAGAGCCTC 60.751 66.667 0.00 0.00 35.63 4.70
1282 1393 2.752238 CCGTCACCGAGAGCCTCT 60.752 66.667 0.00 0.00 35.63 3.69
1283 1394 1.451567 CCGTCACCGAGAGCCTCTA 60.452 63.158 0.00 0.00 35.63 2.43
1284 1395 1.716826 CCGTCACCGAGAGCCTCTAC 61.717 65.000 0.00 0.00 35.63 2.59
1285 1396 1.716826 CGTCACCGAGAGCCTCTACC 61.717 65.000 0.00 0.00 35.63 3.18
1286 1397 0.394625 GTCACCGAGAGCCTCTACCT 60.395 60.000 0.00 0.00 0.00 3.08
1287 1398 0.107116 TCACCGAGAGCCTCTACCTC 60.107 60.000 0.00 0.00 0.00 3.85
1288 1399 0.106918 CACCGAGAGCCTCTACCTCT 60.107 60.000 0.00 0.00 42.12 3.69
1289 1400 0.106918 ACCGAGAGCCTCTACCTCTG 60.107 60.000 0.00 0.00 39.66 3.35
1290 1401 0.821711 CCGAGAGCCTCTACCTCTGG 60.822 65.000 0.00 0.00 39.66 3.86
1291 1402 0.106918 CGAGAGCCTCTACCTCTGGT 60.107 60.000 0.00 0.00 39.66 4.00
1292 1403 1.398692 GAGAGCCTCTACCTCTGGTG 58.601 60.000 0.00 0.00 39.66 4.17
1293 1404 0.686112 AGAGCCTCTACCTCTGGTGC 60.686 60.000 0.00 0.00 38.21 5.01
1294 1405 2.010582 GAGCCTCTACCTCTGGTGCG 62.011 65.000 0.00 0.00 36.19 5.34
1295 1406 3.082579 GCCTCTACCTCTGGTGCGG 62.083 68.421 0.00 0.00 36.19 5.69
1296 1407 2.496817 CTCTACCTCTGGTGCGGC 59.503 66.667 0.00 0.00 36.19 6.53
1297 1408 3.417275 CTCTACCTCTGGTGCGGCG 62.417 68.421 0.51 0.51 36.19 6.46
1298 1409 4.514577 CTACCTCTGGTGCGGCGG 62.515 72.222 9.78 0.00 36.19 6.13
1322 1433 4.100084 CCCCACTGCAGCGATCCA 62.100 66.667 15.27 0.00 0.00 3.41
1323 1434 2.513204 CCCACTGCAGCGATCCAG 60.513 66.667 15.27 0.00 35.26 3.86
1324 1435 3.200593 CCACTGCAGCGATCCAGC 61.201 66.667 15.27 0.00 32.37 4.85
1333 1444 3.603144 GCGATCCAGCTGCTCTATT 57.397 52.632 8.66 0.00 0.00 1.73
1334 1445 1.427435 GCGATCCAGCTGCTCTATTC 58.573 55.000 8.66 0.00 0.00 1.75
1335 1446 1.938926 GCGATCCAGCTGCTCTATTCC 60.939 57.143 8.66 0.00 0.00 3.01
1336 1447 1.342496 CGATCCAGCTGCTCTATTCCA 59.658 52.381 8.66 0.00 0.00 3.53
1337 1448 2.224137 CGATCCAGCTGCTCTATTCCAA 60.224 50.000 8.66 0.00 0.00 3.53
1338 1449 2.996249 TCCAGCTGCTCTATTCCAAG 57.004 50.000 8.66 0.00 0.00 3.61
1339 1450 2.191400 TCCAGCTGCTCTATTCCAAGT 58.809 47.619 8.66 0.00 0.00 3.16
1340 1451 2.169352 TCCAGCTGCTCTATTCCAAGTC 59.831 50.000 8.66 0.00 0.00 3.01
1341 1452 2.559440 CAGCTGCTCTATTCCAAGTCC 58.441 52.381 0.00 0.00 0.00 3.85
1342 1453 1.137872 AGCTGCTCTATTCCAAGTCCG 59.862 52.381 0.00 0.00 0.00 4.79
1343 1454 1.808133 GCTGCTCTATTCCAAGTCCGG 60.808 57.143 0.00 0.00 0.00 5.14
1344 1455 0.178068 TGCTCTATTCCAAGTCCGGC 59.822 55.000 0.00 0.00 0.00 6.13
1345 1456 0.876342 GCTCTATTCCAAGTCCGGCG 60.876 60.000 0.00 0.00 0.00 6.46
1346 1457 0.460311 CTCTATTCCAAGTCCGGCGT 59.540 55.000 6.01 0.00 0.00 5.68
1347 1458 0.174845 TCTATTCCAAGTCCGGCGTG 59.825 55.000 6.01 0.11 0.00 5.34
1348 1459 1.429148 CTATTCCAAGTCCGGCGTGC 61.429 60.000 6.01 0.00 0.00 5.34
1349 1460 2.173758 TATTCCAAGTCCGGCGTGCA 62.174 55.000 6.01 0.00 0.00 4.57
1410 1545 4.815108 TCCGCCGAGCAGCTCCTA 62.815 66.667 17.16 0.00 0.00 2.94
1668 2359 4.553330 AAGACGAGAAGAGAGAGAGAGT 57.447 45.455 0.00 0.00 0.00 3.24
1730 2438 1.375013 GTGGGCCTTTGCATGCAAG 60.375 57.895 30.25 21.70 40.13 4.01
1744 2452 2.388232 GCAAGAACGAATCGCCGGT 61.388 57.895 1.90 0.00 0.00 5.28
1789 2498 4.233558 GCTTGGGGTGGGGTTGGT 62.234 66.667 0.00 0.00 0.00 3.67
2025 2748 6.156429 ACCTTCCCTCGATAAAATACTCTTGT 59.844 38.462 0.00 0.00 0.00 3.16
2048 2771 5.627780 GTCGTGACTTTCTCTTTCTCTCTTC 59.372 44.000 0.00 0.00 0.00 2.87
2049 2772 4.920927 CGTGACTTTCTCTTTCTCTCTTCC 59.079 45.833 0.00 0.00 0.00 3.46
2062 2785 2.165437 CTCTCTTCCTTCCTCGACTTGG 59.835 54.545 0.00 0.00 0.00 3.61
2094 2817 0.727398 GTACGCAAGCTCCAACATCC 59.273 55.000 0.00 0.00 45.62 3.51
2121 2844 1.433534 CTCTGTTTTCGGTCCTCAGC 58.566 55.000 0.00 0.00 0.00 4.26
2195 3402 3.047877 GCCGCCAGTACGTGCTTT 61.048 61.111 2.37 0.00 0.00 3.51
2205 3412 3.741344 CAGTACGTGCTTTACTTCTGCTT 59.259 43.478 2.37 0.00 0.00 3.91
2206 3413 4.921515 CAGTACGTGCTTTACTTCTGCTTA 59.078 41.667 2.37 0.00 0.00 3.09
2207 3414 5.577164 CAGTACGTGCTTTACTTCTGCTTAT 59.423 40.000 2.37 0.00 0.00 1.73
2208 3415 5.805994 AGTACGTGCTTTACTTCTGCTTATC 59.194 40.000 0.00 0.00 0.00 1.75
2209 3416 4.822026 ACGTGCTTTACTTCTGCTTATCT 58.178 39.130 0.00 0.00 0.00 1.98
2216 3423 9.137459 TGCTTTACTTCTGCTTATCTCTACTAT 57.863 33.333 0.00 0.00 0.00 2.12
2253 3460 1.318158 TTCCGTCTCCCCTCTTACGC 61.318 60.000 0.00 0.00 34.13 4.42
2281 3488 1.334243 CCTTCGTCCATCCTCTCGTAC 59.666 57.143 0.00 0.00 0.00 3.67
2284 3491 0.304098 CGTCCATCCTCTCGTACGAC 59.696 60.000 15.28 0.56 32.35 4.34
2289 3496 2.222886 CATCCTCTCGTACGACCTCAT 58.777 52.381 15.28 1.55 0.00 2.90
2296 3503 0.666913 CGTACGACCTCATACCCCTG 59.333 60.000 10.44 0.00 0.00 4.45
2297 3504 0.388294 GTACGACCTCATACCCCTGC 59.612 60.000 0.00 0.00 0.00 4.85
2314 3521 1.200020 CTGCGCCGATTTTCTTTCCTT 59.800 47.619 4.18 0.00 0.00 3.36
2319 4640 2.423892 GCCGATTTTCTTTCCTTCCTCC 59.576 50.000 0.00 0.00 0.00 4.30
2320 4641 3.686016 CCGATTTTCTTTCCTTCCTCCA 58.314 45.455 0.00 0.00 0.00 3.86
2338 4659 5.045140 TCCTCCACCGATTTTCTTTCCTATT 60.045 40.000 0.00 0.00 0.00 1.73
2353 4674 1.496429 CCTATTGGGCTGGTTCCATCT 59.504 52.381 0.00 0.00 33.82 2.90
2377 4698 6.059484 TGATTCCCTCAATTAATCCCGTAAC 58.941 40.000 0.00 0.00 0.00 2.50
2436 4758 3.714391 GTGACTCACGTAGTTTCCTGTT 58.286 45.455 0.00 0.00 41.61 3.16
2440 4762 5.292589 TGACTCACGTAGTTTCCTGTTTTTC 59.707 40.000 0.00 0.00 41.61 2.29
2458 4780 0.112412 TCTTCCTTCCAAACCTGCCC 59.888 55.000 0.00 0.00 0.00 5.36
2461 4783 1.681229 TCCTTCCAAACCTGCCCTAT 58.319 50.000 0.00 0.00 0.00 2.57
2472 4794 1.681793 CCTGCCCTATCCGATATACCG 59.318 57.143 0.00 0.00 0.00 4.02
2482 4804 2.282674 ATATACCGGCCCGCTCGA 60.283 61.111 0.00 0.00 0.00 4.04
2484 4806 1.664321 ATATACCGGCCCGCTCGATC 61.664 60.000 0.00 0.00 0.00 3.69
2501 4823 1.468914 GATCCCCGTCTTTTCTTGTGC 59.531 52.381 0.00 0.00 0.00 4.57
2519 4841 0.872021 GCCGTCGTGGAAGATGCTAG 60.872 60.000 0.51 0.00 42.00 3.42
2526 4848 2.690497 CGTGGAAGATGCTAGGAGAGAA 59.310 50.000 0.00 0.00 0.00 2.87
2557 4881 2.581953 GAGAGAAGAGCAGCCGCG 60.582 66.667 0.00 0.00 45.49 6.46
2561 4885 4.443266 GAAGAGCAGCCGCGGTCT 62.443 66.667 28.70 21.17 45.40 3.85
2576 4900 4.662961 TCTGTGTGCAGGCGACCG 62.663 66.667 0.00 0.00 42.78 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.868077 TCAAAGTTTTGCAAATTCGGGTG 59.132 39.130 13.65 7.16 38.05 4.61
2 3 5.476752 TTTCAAAGTTTTGCAAATTCGGG 57.523 34.783 13.65 3.67 38.05 5.14
4 5 7.904461 ACATCTTTTCAAAGTTTTGCAAATTCG 59.096 29.630 13.65 0.00 33.96 3.34
5 6 9.002080 CACATCTTTTCAAAGTTTTGCAAATTC 57.998 29.630 13.65 9.52 33.96 2.17
6 7 8.728833 TCACATCTTTTCAAAGTTTTGCAAATT 58.271 25.926 13.65 2.09 33.96 1.82
7 8 8.266392 TCACATCTTTTCAAAGTTTTGCAAAT 57.734 26.923 13.65 0.00 33.96 2.32
8 9 7.664082 TCACATCTTTTCAAAGTTTTGCAAA 57.336 28.000 8.05 8.05 38.05 3.68
9 10 7.846644 ATCACATCTTTTCAAAGTTTTGCAA 57.153 28.000 0.00 0.00 38.05 4.08
10 11 8.939201 TTATCACATCTTTTCAAAGTTTTGCA 57.061 26.923 0.00 0.00 38.05 4.08
65 66 8.854979 TCAAACATTTGATCTAGTTTGTTGTG 57.145 30.769 20.98 13.11 46.52 3.33
77 78 5.224888 TGCAAGAAGCTCAAACATTTGATC 58.775 37.500 7.48 4.02 45.26 2.92
293 300 2.046285 CGCCTCCGCCAAAGGAAAT 61.046 57.895 0.00 0.00 40.25 2.17
330 337 2.764128 CCTTGCCTCCCTCGCCTA 60.764 66.667 0.00 0.00 0.00 3.93
373 380 2.040544 CCGCTCACCATGGACAACC 61.041 63.158 21.47 1.39 0.00 3.77
375 382 2.184020 CTCCCGCTCACCATGGACAA 62.184 60.000 21.47 1.73 0.00 3.18
423 451 2.216331 GCACAGCCACCCCCATTTT 61.216 57.895 0.00 0.00 0.00 1.82
483 511 0.876777 TTGACACGAAATGGACGCGT 60.877 50.000 13.85 13.85 39.04 6.01
490 518 2.787723 GCGTAGGCATTGACACGAAATG 60.788 50.000 15.56 0.00 39.62 2.32
491 519 1.396996 GCGTAGGCATTGACACGAAAT 59.603 47.619 15.56 0.00 39.62 2.17
513 541 2.837498 GGCATAAATTTGGGCCACATC 58.163 47.619 22.73 0.00 45.70 3.06
534 562 4.473520 CGCCTGCCGACCCATTCT 62.474 66.667 0.00 0.00 40.02 2.40
541 569 2.548295 TTTTTGTCCGCCTGCCGAC 61.548 57.895 4.04 4.04 40.02 4.79
569 597 1.883926 GCCGACCCAAATTACAGTTGT 59.116 47.619 0.00 0.00 0.00 3.32
571 599 1.161843 CGCCGACCCAAATTACAGTT 58.838 50.000 0.00 0.00 0.00 3.16
572 600 0.035739 ACGCCGACCCAAATTACAGT 59.964 50.000 0.00 0.00 0.00 3.55
574 602 0.250381 ACACGCCGACCCAAATTACA 60.250 50.000 0.00 0.00 0.00 2.41
577 605 1.657556 CAACACGCCGACCCAAATT 59.342 52.632 0.00 0.00 0.00 1.82
578 606 2.265182 CCAACACGCCGACCCAAAT 61.265 57.895 0.00 0.00 0.00 2.32
591 700 0.106918 ACAGAAAAGTCGGCCCAACA 60.107 50.000 0.00 0.00 0.00 3.33
641 750 1.336440 TCCAACGTGCCAACTCATTTG 59.664 47.619 0.00 0.00 34.63 2.32
657 766 9.513906 TGTGTATCTCATTTAGAACAATTCCAA 57.486 29.630 0.00 0.00 37.89 3.53
721 830 7.226441 TCTAGCCATCATATGTTGCTGTTATT 58.774 34.615 19.49 3.11 31.65 1.40
726 835 6.570672 AAATCTAGCCATCATATGTTGCTG 57.429 37.500 19.49 12.67 31.65 4.41
808 917 5.576447 AATTCAGACCAAAAACGTGTTCT 57.424 34.783 0.00 0.00 0.00 3.01
816 925 3.308323 GCGTGCAAAATTCAGACCAAAAA 59.692 39.130 0.00 0.00 0.00 1.94
827 936 2.472816 CCAAAGACAGCGTGCAAAATT 58.527 42.857 0.00 0.00 0.00 1.82
834 943 1.165907 TGGAAGCCAAAGACAGCGTG 61.166 55.000 0.00 0.00 0.00 5.34
877 986 2.303549 CTAGAGGGCTCAACGGCTGG 62.304 65.000 0.00 0.00 38.46 4.85
930 1040 0.783206 TCCCAGGGCCAAAATCTTCA 59.217 50.000 6.18 0.00 0.00 3.02
1004 1115 2.401766 GCCCACAAGATCACCTGCG 61.402 63.158 0.00 0.00 0.00 5.18
1007 1118 1.274703 ATCGGCCCACAAGATCACCT 61.275 55.000 0.00 0.00 0.00 4.00
1011 1122 2.189499 GCCATCGGCCCACAAGATC 61.189 63.158 0.00 0.00 44.06 2.75
1012 1123 2.124151 GCCATCGGCCCACAAGAT 60.124 61.111 0.00 0.00 44.06 2.40
1028 1139 2.755876 GGTTTGGGGCTAGGCTGC 60.756 66.667 16.80 0.00 0.00 5.25
1029 1140 2.043953 GGGTTTGGGGCTAGGCTG 60.044 66.667 16.80 0.00 0.00 4.85
1030 1141 3.347590 GGGGTTTGGGGCTAGGCT 61.348 66.667 16.80 0.00 0.00 4.58
1031 1142 4.815108 CGGGGTTTGGGGCTAGGC 62.815 72.222 8.00 8.00 0.00 3.93
1065 1176 0.600255 ACCACTCGAAGAACTTGGCG 60.600 55.000 0.00 0.00 35.19 5.69
1068 1179 2.526304 TCCACCACTCGAAGAACTTG 57.474 50.000 0.00 0.00 34.09 3.16
1087 1198 0.904865 TCACGGGACTGCTCCAAGAT 60.905 55.000 0.00 0.00 38.52 2.40
1088 1199 1.533033 TCACGGGACTGCTCCAAGA 60.533 57.895 0.00 0.00 38.52 3.02
1089 1200 1.374758 GTCACGGGACTGCTCCAAG 60.375 63.158 11.49 0.00 40.99 3.61
1090 1201 2.741092 GTCACGGGACTGCTCCAA 59.259 61.111 11.49 0.00 40.99 3.53
1103 1214 4.090057 GAAGCGCGGCCAAGTCAC 62.090 66.667 8.83 0.00 0.00 3.67
1168 1279 2.126424 GCTGAGGACACGGTCGAC 60.126 66.667 7.13 7.13 32.65 4.20
1169 1280 3.371063 GGCTGAGGACACGGTCGA 61.371 66.667 0.00 0.00 32.65 4.20
1178 1289 2.343758 GCTCGTTGTGGCTGAGGA 59.656 61.111 0.00 0.00 0.00 3.71
1180 1291 0.038251 TAGTGCTCGTTGTGGCTGAG 60.038 55.000 0.00 0.00 0.00 3.35
1183 1294 1.067776 GTAGTAGTGCTCGTTGTGGCT 60.068 52.381 0.00 0.00 0.00 4.75
1184 1295 1.347320 GTAGTAGTGCTCGTTGTGGC 58.653 55.000 0.00 0.00 0.00 5.01
1185 1296 1.731424 CGGTAGTAGTGCTCGTTGTGG 60.731 57.143 0.00 0.00 0.00 4.17
1186 1297 1.614385 CGGTAGTAGTGCTCGTTGTG 58.386 55.000 0.00 0.00 0.00 3.33
1187 1298 0.109412 GCGGTAGTAGTGCTCGTTGT 60.109 55.000 0.00 0.00 0.00 3.32
1188 1299 1.132199 CGCGGTAGTAGTGCTCGTTG 61.132 60.000 0.00 0.00 0.00 4.10
1189 1300 1.136147 CGCGGTAGTAGTGCTCGTT 59.864 57.895 0.00 0.00 0.00 3.85
1193 1304 2.558554 CTTGGCGCGGTAGTAGTGCT 62.559 60.000 8.83 0.00 43.87 4.40
1231 1342 1.687494 GCGAACATGAGGAGCACGTC 61.687 60.000 0.00 0.00 0.00 4.34
1236 1347 3.567797 GGCGCGAACATGAGGAGC 61.568 66.667 12.10 0.96 0.00 4.70
1237 1348 2.892425 GGGCGCGAACATGAGGAG 60.892 66.667 12.10 0.00 0.00 3.69
1238 1349 3.371097 GAGGGCGCGAACATGAGGA 62.371 63.158 12.10 0.00 0.00 3.71
1239 1350 2.892425 GAGGGCGCGAACATGAGG 60.892 66.667 12.10 0.00 0.00 3.86
1240 1351 3.257561 CGAGGGCGCGAACATGAG 61.258 66.667 12.10 0.00 0.00 2.90
1241 1352 4.063967 ACGAGGGCGCGAACATGA 62.064 61.111 12.10 0.00 42.48 3.07
1242 1353 3.853330 CACGAGGGCGCGAACATG 61.853 66.667 12.10 0.00 42.48 3.21
1245 1356 4.814294 ATCCACGAGGGCGCGAAC 62.814 66.667 12.10 0.11 42.48 3.95
1246 1357 4.508128 GATCCACGAGGGCGCGAA 62.508 66.667 12.10 0.00 42.48 4.70
1248 1359 4.933064 GAGATCCACGAGGGCGCG 62.933 72.222 0.00 0.00 42.48 6.86
1249 1360 4.593864 GGAGATCCACGAGGGCGC 62.594 72.222 0.00 0.00 42.48 6.53
1250 1361 4.271816 CGGAGATCCACGAGGGCG 62.272 72.222 0.00 0.00 44.79 6.13
1251 1362 3.140225 GACGGAGATCCACGAGGGC 62.140 68.421 12.86 0.00 36.21 5.19
1252 1363 1.753078 TGACGGAGATCCACGAGGG 60.753 63.158 12.86 0.00 35.14 4.30
1253 1364 1.433879 GTGACGGAGATCCACGAGG 59.566 63.158 12.86 0.00 35.14 4.63
1254 1365 1.433879 GGTGACGGAGATCCACGAG 59.566 63.158 12.86 0.00 35.14 4.18
1255 1366 3.599584 GGTGACGGAGATCCACGA 58.400 61.111 12.86 0.00 35.14 4.35
1267 1378 0.394625 AGGTAGAGGCTCTCGGTGAC 60.395 60.000 22.53 13.06 35.36 3.67
1268 1379 0.107116 GAGGTAGAGGCTCTCGGTGA 60.107 60.000 22.53 0.00 35.36 4.02
1269 1380 0.106918 AGAGGTAGAGGCTCTCGGTG 60.107 60.000 22.53 0.00 35.36 4.94
1270 1381 0.106918 CAGAGGTAGAGGCTCTCGGT 60.107 60.000 22.53 6.19 35.36 4.69
1271 1382 0.821711 CCAGAGGTAGAGGCTCTCGG 60.822 65.000 22.53 7.46 35.36 4.63
1272 1383 0.106918 ACCAGAGGTAGAGGCTCTCG 60.107 60.000 22.53 3.81 35.36 4.04
1273 1384 1.398692 CACCAGAGGTAGAGGCTCTC 58.601 60.000 22.53 12.48 32.11 3.20
1274 1385 0.686112 GCACCAGAGGTAGAGGCTCT 60.686 60.000 22.48 22.48 32.11 4.09
1275 1386 1.819905 GCACCAGAGGTAGAGGCTC 59.180 63.158 6.34 6.34 32.11 4.70
1276 1387 2.055042 CGCACCAGAGGTAGAGGCT 61.055 63.158 0.00 0.00 32.11 4.58
1277 1388 2.496817 CGCACCAGAGGTAGAGGC 59.503 66.667 0.00 0.00 32.11 4.70
1278 1389 3.082579 GCCGCACCAGAGGTAGAGG 62.083 68.421 0.00 0.00 37.01 3.69
1279 1390 2.496817 GCCGCACCAGAGGTAGAG 59.503 66.667 0.00 0.00 37.01 2.43
1280 1391 3.449227 CGCCGCACCAGAGGTAGA 61.449 66.667 0.00 0.00 37.01 2.59
1281 1392 4.514577 CCGCCGCACCAGAGGTAG 62.515 72.222 0.00 0.00 37.01 3.18
1305 1416 4.100084 TGGATCGCTGCAGTGGGG 62.100 66.667 26.23 8.49 0.00 4.96
1306 1417 2.513204 CTGGATCGCTGCAGTGGG 60.513 66.667 26.23 10.99 36.19 4.61
1307 1418 3.200593 GCTGGATCGCTGCAGTGG 61.201 66.667 26.23 13.53 42.43 4.00
1308 1419 2.125229 AGCTGGATCGCTGCAGTG 60.125 61.111 21.43 21.43 42.43 3.66
1314 1425 1.000731 GAATAGAGCAGCTGGATCGCT 59.999 52.381 17.12 5.36 41.90 4.93
1315 1426 1.427435 GAATAGAGCAGCTGGATCGC 58.573 55.000 17.12 0.00 36.90 4.58
1316 1427 1.342496 TGGAATAGAGCAGCTGGATCG 59.658 52.381 17.12 0.00 36.90 3.69
1317 1428 3.181456 ACTTGGAATAGAGCAGCTGGATC 60.181 47.826 17.12 4.54 0.00 3.36
1318 1429 2.776536 ACTTGGAATAGAGCAGCTGGAT 59.223 45.455 17.12 0.00 0.00 3.41
1319 1430 2.169352 GACTTGGAATAGAGCAGCTGGA 59.831 50.000 17.12 0.00 0.00 3.86
1320 1431 2.559440 GACTTGGAATAGAGCAGCTGG 58.441 52.381 17.12 0.00 0.00 4.85
1321 1432 2.559440 GGACTTGGAATAGAGCAGCTG 58.441 52.381 10.11 10.11 0.00 4.24
1322 1433 1.137872 CGGACTTGGAATAGAGCAGCT 59.862 52.381 0.00 0.00 0.00 4.24
1323 1434 1.576356 CGGACTTGGAATAGAGCAGC 58.424 55.000 0.00 0.00 0.00 5.25
1324 1435 1.808133 GCCGGACTTGGAATAGAGCAG 60.808 57.143 5.05 0.00 0.00 4.24
1325 1436 0.178068 GCCGGACTTGGAATAGAGCA 59.822 55.000 5.05 0.00 0.00 4.26
1326 1437 0.876342 CGCCGGACTTGGAATAGAGC 60.876 60.000 5.05 0.00 0.00 4.09
1327 1438 0.460311 ACGCCGGACTTGGAATAGAG 59.540 55.000 5.05 0.00 0.00 2.43
1328 1439 0.174845 CACGCCGGACTTGGAATAGA 59.825 55.000 5.05 0.00 0.00 1.98
1329 1440 1.429148 GCACGCCGGACTTGGAATAG 61.429 60.000 5.05 0.00 0.00 1.73
1330 1441 1.448893 GCACGCCGGACTTGGAATA 60.449 57.895 5.05 0.00 0.00 1.75
1331 1442 2.746277 GCACGCCGGACTTGGAAT 60.746 61.111 5.05 0.00 0.00 3.01
1332 1443 4.243008 TGCACGCCGGACTTGGAA 62.243 61.111 5.05 0.00 0.00 3.53
1333 1444 4.680237 CTGCACGCCGGACTTGGA 62.680 66.667 5.05 0.49 0.00 3.53
1344 1455 3.978723 CTGGGACTCGAGCTGCACG 62.979 68.421 13.61 13.28 0.00 5.34
1345 1456 2.125753 CTGGGACTCGAGCTGCAC 60.126 66.667 13.61 3.93 0.00 4.57
1346 1457 4.074526 GCTGGGACTCGAGCTGCA 62.075 66.667 13.61 0.00 40.84 4.41
1608 2287 2.665000 CTCGCCCTCTGCTTTCCA 59.335 61.111 0.00 0.00 38.05 3.53
1611 2302 4.767255 CCGCTCGCCCTCTGCTTT 62.767 66.667 0.00 0.00 38.05 3.51
1668 2359 2.658268 CTGACACACACGAGCGCA 60.658 61.111 11.47 0.00 0.00 6.09
1730 2438 3.861263 GGCACCGGCGATTCGTTC 61.861 66.667 9.30 0.00 42.47 3.95
1773 2482 1.076014 GTACCAACCCCACCCCAAG 59.924 63.158 0.00 0.00 0.00 3.61
1817 2540 4.640690 AGTCCCCACTCACGCCCT 62.641 66.667 0.00 0.00 0.00 5.19
1840 2563 1.083489 CTTTTTCATCGCCGGCACTA 58.917 50.000 28.98 11.85 0.00 2.74
1851 2574 4.706962 GGCTAATCAGGACCACTTTTTCAT 59.293 41.667 0.00 0.00 0.00 2.57
2025 2748 5.278561 GGAAGAGAGAAAGAGAAAGTCACGA 60.279 44.000 0.00 0.00 0.00 4.35
2048 2771 0.035056 AATGGCCAAGTCGAGGAAGG 60.035 55.000 10.96 0.00 0.00 3.46
2049 2772 1.089920 CAATGGCCAAGTCGAGGAAG 58.910 55.000 10.96 0.00 0.00 3.46
2062 2785 2.171725 GCGTACCGTCTCCAATGGC 61.172 63.158 0.00 0.00 37.59 4.40
2081 2804 2.357569 GGAGGAATGGATGTTGGAGCTT 60.358 50.000 0.00 0.00 0.00 3.74
2082 2805 1.213926 GGAGGAATGGATGTTGGAGCT 59.786 52.381 0.00 0.00 0.00 4.09
2094 2817 3.003480 GACCGAAAACAGAGGAGGAATG 58.997 50.000 0.00 0.00 0.00 2.67
2121 2844 0.810031 CGAGTAATGGCGTTGAGGGG 60.810 60.000 1.27 0.00 0.00 4.79
2206 3413 9.522804 CTTGCGTTTCTTTTAGATAGTAGAGAT 57.477 33.333 0.00 0.00 0.00 2.75
2207 3414 7.974501 CCTTGCGTTTCTTTTAGATAGTAGAGA 59.025 37.037 0.00 0.00 0.00 3.10
2208 3415 7.760340 ACCTTGCGTTTCTTTTAGATAGTAGAG 59.240 37.037 0.00 0.00 0.00 2.43
2209 3416 7.609056 ACCTTGCGTTTCTTTTAGATAGTAGA 58.391 34.615 0.00 0.00 0.00 2.59
2216 3423 3.249080 CGGAACCTTGCGTTTCTTTTAGA 59.751 43.478 0.00 0.00 37.24 2.10
2228 3435 2.046217 GGGGAGACGGAACCTTGC 60.046 66.667 0.00 0.00 0.00 4.01
2265 3472 0.304098 GTCGTACGAGAGGATGGACG 59.696 60.000 20.18 0.00 0.00 4.79
2281 3488 2.417516 CGCAGGGGTATGAGGTCG 59.582 66.667 0.00 0.00 0.00 4.79
2284 3491 4.609018 CGGCGCAGGGGTATGAGG 62.609 72.222 10.83 0.00 0.00 3.86
2289 3496 1.450669 GAAAATCGGCGCAGGGGTA 60.451 57.895 10.83 0.00 0.00 3.69
2296 3503 1.467543 GGAAGGAAAGAAAATCGGCGC 60.468 52.381 0.00 0.00 0.00 6.53
2297 3504 2.084546 AGGAAGGAAAGAAAATCGGCG 58.915 47.619 0.00 0.00 0.00 6.46
2314 3521 2.642807 AGGAAAGAAAATCGGTGGAGGA 59.357 45.455 0.00 0.00 0.00 3.71
2319 4640 4.440112 GCCCAATAGGAAAGAAAATCGGTG 60.440 45.833 0.00 0.00 38.24 4.94
2320 4641 3.699538 GCCCAATAGGAAAGAAAATCGGT 59.300 43.478 0.00 0.00 38.24 4.69
2338 4659 1.002069 AATCAGATGGAACCAGCCCA 58.998 50.000 5.45 0.00 38.19 5.36
2353 4674 4.788925 ACGGGATTAATTGAGGGAATCA 57.211 40.909 0.00 0.00 35.62 2.57
2377 4698 6.785337 ACGGGATTTTTAGGGGAAAATTAG 57.215 37.500 0.00 0.00 38.85 1.73
2436 4758 2.698274 GGCAGGTTTGGAAGGAAGAAAA 59.302 45.455 0.00 0.00 0.00 2.29
2440 4762 0.113190 AGGGCAGGTTTGGAAGGAAG 59.887 55.000 0.00 0.00 0.00 3.46
2482 4804 1.534729 GCACAAGAAAAGACGGGGAT 58.465 50.000 0.00 0.00 0.00 3.85
2484 4806 1.852067 CGGCACAAGAAAAGACGGGG 61.852 60.000 0.00 0.00 0.00 5.73
2501 4823 0.249073 CCTAGCATCTTCCACGACGG 60.249 60.000 0.00 0.00 0.00 4.79
2519 4841 1.135915 TGCTCTCGCTCATTTCTCTCC 59.864 52.381 0.00 0.00 36.97 3.71
2526 4848 1.761449 TCTCTCTGCTCTCGCTCATT 58.239 50.000 0.00 0.00 36.97 2.57
2545 4869 4.749310 CAGACCGCGGCTGCTCTT 62.749 66.667 28.58 2.52 39.65 2.85
2576 4900 4.785453 CTGCAGGGTCCCTTCGCC 62.785 72.222 8.08 0.00 0.00 5.54
2578 4902 4.785453 GGCTGCAGGGTCCCTTCG 62.785 72.222 17.12 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.