Multiple sequence alignment - TraesCS5A01G241600

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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 TraesCS5A01G241600 chr5A 100.000 4250 0 0 1 4250 457263990 457268239 0.000000e+00 7849.0
1 TraesCS5A01G241600 chr5A 100.000 574 0 0 4601 5174 457268590 457269163 0.000000e+00 1061.0
2 TraesCS5A01G241600 chr5A 92.357 314 17 5 3348 3660 457187175 457187482 1.710000e-119 440.0
3 TraesCS5A01G241600 chr5A 91.279 172 14 1 1 171 398975239 398975410 3.120000e-57 233.0
4 TraesCS5A01G241600 chr5A 88.119 101 3 2 3655 3746 457203044 457203144 1.520000e-20 111.0
5 TraesCS5A01G241600 chr5D 96.217 2987 56 12 1277 4247 355041196 355044141 0.000000e+00 4837.0
6 TraesCS5A01G241600 chr5D 95.126 554 25 2 4621 5173 355044173 355044725 0.000000e+00 872.0
7 TraesCS5A01G241600 chr5D 90.977 665 29 20 482 1128 355040509 355041160 0.000000e+00 867.0
8 TraesCS5A01G241600 chr5D 89.842 443 41 3 12 451 355039702 355040143 2.700000e-157 566.0
9 TraesCS5A01G241600 chr5D 84.964 419 60 3 173 590 383742212 383742628 6.190000e-114 422.0
10 TraesCS5A01G241600 chr5D 85.600 125 16 2 1151 1273 374636169 374636293 4.200000e-26 130.0
11 TraesCS5A01G241600 chr4B 86.339 366 44 3 177 536 577009777 577010142 1.350000e-105 394.0
12 TraesCS5A01G241600 chr4B 87.574 169 19 2 4 171 438241160 438241327 1.470000e-45 195.0
13 TraesCS5A01G241600 chr4B 86.842 114 10 4 1157 1267 211973258 211973369 7.040000e-24 122.0
14 TraesCS5A01G241600 chr4B 100.000 31 0 0 593 623 404802451 404802481 2.010000e-04 58.4
15 TraesCS5A01G241600 chr6B 83.218 435 56 10 173 591 717911889 717911456 2.920000e-102 383.0
16 TraesCS5A01G241600 chr6B 87.861 173 19 1 1 171 44961456 44961284 8.780000e-48 202.0
17 TraesCS5A01G241600 chr6B 85.366 123 16 2 1151 1271 142439541 142439419 5.440000e-25 126.0
18 TraesCS5A01G241600 chr5B 90.476 294 15 6 3918 4211 548229253 548228973 4.890000e-100 375.0
19 TraesCS5A01G241600 chr5B 90.476 294 15 6 3918 4211 548233815 548233535 4.890000e-100 375.0
20 TraesCS5A01G241600 chr5B 88.372 172 19 1 1 171 656143043 656142872 6.790000e-49 206.0
21 TraesCS5A01G241600 chr5B 87.861 173 18 2 1 171 656149299 656149128 3.160000e-47 200.0
22 TraesCS5A01G241600 chr5B 94.000 50 1 1 3866 3915 548229461 548229508 2.000000e-09 75.0
23 TraesCS5A01G241600 chr5B 94.000 50 1 1 3866 3915 548234023 548234070 2.000000e-09 75.0
24 TraesCS5A01G241600 chr5B 97.222 36 1 0 1238 1273 238491958 238491993 1.560000e-05 62.1
25 TraesCS5A01G241600 chr5B 96.970 33 1 0 3929 3961 548229258 548229290 7.240000e-04 56.5
26 TraesCS5A01G241600 chr5B 96.970 33 1 0 3929 3961 548233820 548233852 7.240000e-04 56.5
27 TraesCS5A01G241600 chr1B 82.870 432 57 9 173 590 594063572 594063144 6.330000e-99 372.0
28 TraesCS5A01G241600 chr1B 86.508 126 15 1 1150 1273 297771688 297771563 2.510000e-28 137.0
29 TraesCS5A01G241600 chr1B 100.000 34 0 0 1197 1230 23985054 23985021 4.330000e-06 63.9
30 TraesCS5A01G241600 chr1B 100.000 29 0 0 595 623 678244776 678244804 3.000000e-03 54.7
31 TraesCS5A01G241600 chr3D 82.014 417 73 2 173 588 597140611 597140196 2.290000e-93 353.0
32 TraesCS5A01G241600 chr3D 88.095 168 19 1 5 171 283382047 283381880 1.140000e-46 198.0
33 TraesCS5A01G241600 chr3B 84.167 360 53 4 177 535 637532366 637532010 3.840000e-91 346.0
34 TraesCS5A01G241600 chr3B 84.000 125 18 2 1151 1273 176630770 176630894 9.100000e-23 119.0
35 TraesCS5A01G241600 chr2D 83.425 362 57 2 173 534 433685682 433686040 2.990000e-87 333.0
36 TraesCS5A01G241600 chr7B 83.196 363 55 6 177 536 703926282 703925923 1.390000e-85 327.0
37 TraesCS5A01G241600 chr7A 88.623 167 17 1 7 171 360655941 360655775 8.780000e-48 202.0
38 TraesCS5A01G241600 chr7D 87.931 174 16 4 1 171 608403529 608403358 3.160000e-47 200.0
39 TraesCS5A01G241600 chr7D 100.000 30 0 0 593 622 409475951 409475980 7.240000e-04 56.5
40 TraesCS5A01G241600 chr4A 85.714 133 16 3 1143 1273 724728157 724728288 2.510000e-28 137.0
41 TraesCS5A01G241600 chr4A 85.849 106 13 2 1167 1270 273818899 273819004 1.520000e-20 111.0
42 TraesCS5A01G241600 chr4A 86.364 88 10 2 1165 1250 501244617 501244704 1.530000e-15 95.3
43 TraesCS5A01G241600 chr2A 85.385 130 17 2 1146 1273 748213654 748213783 3.250000e-27 134.0
44 TraesCS5A01G241600 chr2A 84.127 126 16 4 1151 1273 62130960 62130836 9.100000e-23 119.0
45 TraesCS5A01G241600 chr1A 86.400 125 13 4 1150 1273 393470558 393470679 3.250000e-27 134.0
46 TraesCS5A01G241600 chr1A 80.800 125 18 2 1151 1270 514530936 514531059 5.520000e-15 93.5
47 TraesCS5A01G241600 chr2B 82.099 162 18 4 427 588 195681713 195681563 1.510000e-25 128.0
48 TraesCS5A01G241600 chr2B 83.200 125 19 2 1151 1273 769267719 769267595 4.230000e-21 113.0


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 TraesCS5A01G241600 chr5A 457263990 457269163 5173 False 4455.0 7849 100.0000 1 5174 2 chr5A.!!$F4 5173
1 TraesCS5A01G241600 chr5D 355039702 355044725 5023 False 1785.5 4837 93.0405 12 5173 4 chr5D.!!$F3 5161

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
266 269 0.675522 ATGGTAAGGTTTCGGTGCCG 60.676 55.000 3.94 3.94 41.35 5.69 F
404 407 0.702902 TCTAGGACCCCTTCGTCTGT 59.297 55.000 0.00 0.00 34.61 3.41 F
1270 1640 0.107361 AAGTATTTTCGGGCGGAGGG 60.107 55.000 0.00 0.00 0.00 4.30 F
1272 1642 0.532196 GTATTTTCGGGCGGAGGGAG 60.532 60.000 0.00 0.00 0.00 4.30 F
1402 1772 1.003718 CAAAGTCCAGGTCCCGTCC 60.004 63.158 0.00 0.00 0.00 4.79 F
3258 3629 0.877743 GCAACTCCAAGTTCCTGCTC 59.122 55.000 0.00 0.00 36.03 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1251 1621 0.107361 CCCTCCGCCCGAAAATACTT 60.107 55.0 0.00 0.00 0.00 2.24 R
1656 2027 0.179181 CCAAGCTACACGCATGCAAG 60.179 55.0 19.57 11.70 42.61 4.01 R
2317 2688 0.726256 GAGACGGACCAGTCGTAGTC 59.274 60.0 9.74 9.98 45.26 2.59 R
2742 3113 1.033574 ACCTCCTCCTTAGCGAATCG 58.966 55.0 0.00 0.00 0.00 3.34 R
3360 3746 0.542467 ATCCCACCAAATGCTGCACA 60.542 50.0 3.57 0.00 0.00 4.57 R
5098 5485 0.179097 CTCTTAGCGCTGTTCTCCCC 60.179 60.0 22.90 0.00 0.00 4.81 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
43 44 7.067494 GGCATTTGTACTCTGTTTGATAAGGAT 59.933 37.037 0.00 0.00 0.00 3.24
54 55 9.496873 TCTGTTTGATAAGGATTTTCTACGAAA 57.503 29.630 0.00 0.00 0.00 3.46
56 57 8.726988 TGTTTGATAAGGATTTTCTACGAAAGG 58.273 33.333 0.00 0.00 0.00 3.11
61 62 9.770503 GATAAGGATTTTCTACGAAAGGAAAAC 57.229 33.333 0.00 0.00 36.25 2.43
73 74 7.806149 ACGAAAGGAAAACAAGTAAAAACAG 57.194 32.000 0.00 0.00 0.00 3.16
175 178 5.309543 TCCAAGATTGATCATATAACCGGGT 59.690 40.000 6.32 0.00 0.00 5.28
188 191 0.830866 ACCGGGTATGGCTACTAGGC 60.831 60.000 6.32 2.59 41.77 3.93
194 197 3.935024 TGGCTACTAGGCAGACGG 58.065 61.111 8.23 0.00 46.47 4.79
199 202 1.380785 TACTAGGCAGACGGGTGGG 60.381 63.158 0.00 0.00 0.00 4.61
210 213 2.824880 CGGGTGGGGTGGAAAGTGA 61.825 63.158 0.00 0.00 0.00 3.41
250 253 2.880890 GGAGGAAAATGTGGATCGATGG 59.119 50.000 0.54 0.00 0.00 3.51
253 256 5.110814 AGGAAAATGTGGATCGATGGTAA 57.889 39.130 0.54 0.00 0.00 2.85
261 264 2.159014 TGGATCGATGGTAAGGTTTCGG 60.159 50.000 0.54 0.00 32.67 4.30
266 269 0.675522 ATGGTAAGGTTTCGGTGCCG 60.676 55.000 3.94 3.94 41.35 5.69
284 287 1.484356 CGCCGGTCGACTTAAATAGG 58.516 55.000 16.46 8.67 41.67 2.57
305 308 2.408835 GCAATGCAATACGCGGCT 59.591 55.556 12.47 0.00 46.97 5.52
345 348 3.117372 GTCATCGGTCCGACGGAT 58.883 61.111 21.53 14.18 39.18 4.18
363 366 0.965866 ATGAGACGAGCTTCGGACCA 60.966 55.000 9.75 5.11 45.59 4.02
404 407 0.702902 TCTAGGACCCCTTCGTCTGT 59.297 55.000 0.00 0.00 34.61 3.41
440 443 3.569210 CAGGCGCCCCCATATCCA 61.569 66.667 26.15 0.00 35.39 3.41
441 444 2.532715 AGGCGCCCCCATATCCAT 60.533 61.111 26.15 0.00 35.39 3.41
451 454 4.169856 GCCCCCATATCCATCCCATATTTA 59.830 45.833 0.00 0.00 0.00 1.40
452 455 5.341623 GCCCCCATATCCATCCCATATTTAA 60.342 44.000 0.00 0.00 0.00 1.52
453 456 6.376248 CCCCCATATCCATCCCATATTTAAG 58.624 44.000 0.00 0.00 0.00 1.85
454 457 5.835280 CCCCATATCCATCCCATATTTAAGC 59.165 44.000 0.00 0.00 0.00 3.09
455 458 6.355094 CCCCATATCCATCCCATATTTAAGCT 60.355 42.308 0.00 0.00 0.00 3.74
456 459 6.548622 CCCATATCCATCCCATATTTAAGCTG 59.451 42.308 0.00 0.00 0.00 4.24
457 460 6.548622 CCATATCCATCCCATATTTAAGCTGG 59.451 42.308 0.00 0.00 0.00 4.85
458 461 5.865977 ATCCATCCCATATTTAAGCTGGA 57.134 39.130 0.00 0.00 36.10 3.86
459 462 5.865977 TCCATCCCATATTTAAGCTGGAT 57.134 39.130 0.00 0.00 32.95 3.41
460 463 6.968400 TCCATCCCATATTTAAGCTGGATA 57.032 37.500 0.00 0.00 31.59 2.59
461 464 7.529534 TCCATCCCATATTTAAGCTGGATAT 57.470 36.000 0.00 0.00 31.59 1.63
462 465 7.348815 TCCATCCCATATTTAAGCTGGATATG 58.651 38.462 13.39 13.39 34.86 1.78
463 466 6.548622 CCATCCCATATTTAAGCTGGATATGG 59.451 42.308 23.62 23.62 46.41 2.74
466 469 5.203528 CCATATTTAAGCTGGATATGGGGG 58.796 45.833 23.21 8.75 44.56 5.40
503 841 1.302511 GTTTGAGGGCCGCTTGAGA 60.303 57.895 9.19 0.00 0.00 3.27
509 848 3.394836 GGCCGCTTGAGAGGTCCT 61.395 66.667 0.00 0.00 37.33 3.85
539 889 4.875713 AATCATGACCGGGCGGCC 62.876 66.667 20.04 20.04 39.32 6.13
556 906 1.461091 GCCCGTCCGGACATATGAGA 61.461 60.000 32.80 0.00 37.50 3.27
564 914 2.201732 CGGACATATGAGACGGGTTTG 58.798 52.381 10.38 0.00 0.00 2.93
566 916 3.195661 GGACATATGAGACGGGTTTGAC 58.804 50.000 10.38 0.00 0.00 3.18
574 924 2.358247 CGGGTTTGACAGGTCCGG 60.358 66.667 0.00 0.00 37.35 5.14
580 931 2.563702 GTTTGACAGGTCCGGTTGTAA 58.436 47.619 0.00 0.00 0.00 2.41
583 934 4.620589 TTGACAGGTCCGGTTGTAAATA 57.379 40.909 0.00 0.00 0.00 1.40
590 941 6.155737 ACAGGTCCGGTTGTAAATACTCTAAT 59.844 38.462 0.00 0.00 0.00 1.73
611 962 8.965819 TCTAATTATTTGCTCAACAGGCATTTA 58.034 29.630 0.00 0.00 39.54 1.40
619 970 8.845413 TTGCTCAACAGGCATTTATTTTTAAT 57.155 26.923 0.00 0.00 39.54 1.40
627 978 8.761689 ACAGGCATTTATTTTTAATCTCCATGT 58.238 29.630 0.00 0.00 0.00 3.21
655 1006 6.823497 TGTACTACTAGCACCAAAGAAAACT 58.177 36.000 0.00 0.00 0.00 2.66
666 1017 6.680378 GCACCAAAGAAAACTTTGAGCTCTTA 60.680 38.462 16.19 0.00 44.54 2.10
676 1027 6.214191 ACTTTGAGCTCTTATTCGATCTCA 57.786 37.500 16.19 0.00 35.17 3.27
677 1028 6.039616 ACTTTGAGCTCTTATTCGATCTCAC 58.960 40.000 16.19 0.00 36.30 3.51
696 1047 1.692519 ACGAAAAGTAGCAGACCCAGT 59.307 47.619 0.00 0.00 0.00 4.00
744 1095 1.867233 ACTTGCTTCACACAACTAGCG 59.133 47.619 0.00 0.00 36.43 4.26
761 1112 4.765856 ACTAGCGTCAGGAAAGTAAGAGAA 59.234 41.667 0.00 0.00 0.00 2.87
762 1113 4.810191 AGCGTCAGGAAAGTAAGAGAAT 57.190 40.909 0.00 0.00 0.00 2.40
763 1114 4.749976 AGCGTCAGGAAAGTAAGAGAATC 58.250 43.478 0.00 0.00 0.00 2.52
986 1342 5.728637 TTACACACTGATGACTGATGAGT 57.271 39.130 0.00 0.00 33.98 3.41
989 1345 4.222366 ACACACTGATGACTGATGAGTGAT 59.778 41.667 8.06 0.00 46.27 3.06
990 1346 4.567159 CACACTGATGACTGATGAGTGATG 59.433 45.833 8.06 0.70 46.27 3.07
991 1347 4.465305 ACACTGATGACTGATGAGTGATGA 59.535 41.667 8.06 0.00 46.27 2.92
992 1348 5.044558 CACTGATGACTGATGAGTGATGAG 58.955 45.833 0.00 0.00 46.27 2.90
993 1349 4.954826 ACTGATGACTGATGAGTGATGAGA 59.045 41.667 5.27 0.00 32.14 3.27
994 1350 5.599242 ACTGATGACTGATGAGTGATGAGAT 59.401 40.000 5.27 0.00 32.14 2.75
995 1351 6.776603 ACTGATGACTGATGAGTGATGAGATA 59.223 38.462 5.27 0.00 32.14 1.98
996 1352 6.979465 TGATGACTGATGAGTGATGAGATAC 58.021 40.000 0.00 0.00 30.16 2.24
997 1353 6.776603 TGATGACTGATGAGTGATGAGATACT 59.223 38.462 0.00 0.00 30.16 2.12
998 1354 7.941238 TGATGACTGATGAGTGATGAGATACTA 59.059 37.037 0.00 0.00 30.16 1.82
1074 1430 5.098211 GTGTGGAAATAAGAGAATGCTTGC 58.902 41.667 0.00 0.00 0.00 4.01
1102 1458 2.172483 ATCTGAAAGCTGCCGTCCGT 62.172 55.000 0.00 0.00 0.00 4.69
1105 1461 4.250305 AAAGCTGCCGTCCGTGGT 62.250 61.111 0.00 0.00 0.00 4.16
1116 1472 1.153061 TCCGTGGTCACTCTCTGGT 59.847 57.895 0.00 0.00 0.00 4.00
1128 1484 3.041946 ACTCTCTGGTCAAGTGGTCTTT 58.958 45.455 0.00 0.00 0.00 2.52
1131 1487 2.035961 CTCTGGTCAAGTGGTCTTTCGA 59.964 50.000 0.00 0.00 0.00 3.71
1139 1509 4.994852 TCAAGTGGTCTTTCGAATCGATTT 59.005 37.500 12.81 0.00 35.23 2.17
1151 1521 4.576053 TCGAATCGATTTCCTAACCTCGTA 59.424 41.667 12.81 0.00 33.10 3.43
1152 1522 4.674211 CGAATCGATTTCCTAACCTCGTAC 59.326 45.833 12.81 0.00 33.10 3.67
1153 1523 5.505324 CGAATCGATTTCCTAACCTCGTACT 60.505 44.000 12.81 0.00 33.10 2.73
1154 1524 4.889832 TCGATTTCCTAACCTCGTACTC 57.110 45.455 0.00 0.00 33.10 2.59
1155 1525 4.521146 TCGATTTCCTAACCTCGTACTCT 58.479 43.478 0.00 0.00 33.10 3.24
1156 1526 4.574013 TCGATTTCCTAACCTCGTACTCTC 59.426 45.833 0.00 0.00 33.10 3.20
1157 1527 4.575645 CGATTTCCTAACCTCGTACTCTCT 59.424 45.833 0.00 0.00 0.00 3.10
1158 1528 5.277442 CGATTTCCTAACCTCGTACTCTCTC 60.277 48.000 0.00 0.00 0.00 3.20
1159 1529 3.557228 TCCTAACCTCGTACTCTCTCC 57.443 52.381 0.00 0.00 0.00 3.71
1160 1530 2.172293 TCCTAACCTCGTACTCTCTCCC 59.828 54.545 0.00 0.00 0.00 4.30
1161 1531 2.173143 CCTAACCTCGTACTCTCTCCCT 59.827 54.545 0.00 0.00 0.00 4.20
1162 1532 2.903375 AACCTCGTACTCTCTCCCTT 57.097 50.000 0.00 0.00 0.00 3.95
1163 1533 2.423446 ACCTCGTACTCTCTCCCTTC 57.577 55.000 0.00 0.00 0.00 3.46
1164 1534 1.301423 CCTCGTACTCTCTCCCTTCG 58.699 60.000 0.00 0.00 0.00 3.79
1165 1535 1.134461 CCTCGTACTCTCTCCCTTCGA 60.134 57.143 0.00 0.00 0.00 3.71
1166 1536 2.630158 CTCGTACTCTCTCCCTTCGAA 58.370 52.381 0.00 0.00 0.00 3.71
1167 1537 3.008330 CTCGTACTCTCTCCCTTCGAAA 58.992 50.000 0.00 0.00 0.00 3.46
1168 1538 3.415212 TCGTACTCTCTCCCTTCGAAAA 58.585 45.455 0.00 0.00 0.00 2.29
1169 1539 4.015084 TCGTACTCTCTCCCTTCGAAAAT 58.985 43.478 0.00 0.00 0.00 1.82
1170 1540 5.188434 TCGTACTCTCTCCCTTCGAAAATA 58.812 41.667 0.00 0.00 0.00 1.40
1171 1541 5.065731 TCGTACTCTCTCCCTTCGAAAATAC 59.934 44.000 0.00 0.00 0.00 1.89
1172 1542 5.066246 CGTACTCTCTCCCTTCGAAAATACT 59.934 44.000 0.00 0.00 0.00 2.12
1173 1543 6.404513 CGTACTCTCTCCCTTCGAAAATACTT 60.405 42.308 0.00 0.00 0.00 2.24
1174 1544 7.201679 CGTACTCTCTCCCTTCGAAAATACTTA 60.202 40.741 0.00 0.00 0.00 2.24
1175 1545 7.663043 ACTCTCTCCCTTCGAAAATACTTAT 57.337 36.000 0.00 0.00 0.00 1.73
1176 1546 7.718525 ACTCTCTCCCTTCGAAAATACTTATC 58.281 38.462 0.00 0.00 0.00 1.75
1177 1547 7.342284 ACTCTCTCCCTTCGAAAATACTTATCA 59.658 37.037 0.00 0.00 0.00 2.15
1178 1548 8.251383 TCTCTCCCTTCGAAAATACTTATCAT 57.749 34.615 0.00 0.00 0.00 2.45
1179 1549 8.361139 TCTCTCCCTTCGAAAATACTTATCATC 58.639 37.037 0.00 0.00 0.00 2.92
1180 1550 8.018537 TCTCCCTTCGAAAATACTTATCATCA 57.981 34.615 0.00 0.00 0.00 3.07
1181 1551 8.482943 TCTCCCTTCGAAAATACTTATCATCAA 58.517 33.333 0.00 0.00 0.00 2.57
1182 1552 9.109393 CTCCCTTCGAAAATACTTATCATCAAA 57.891 33.333 0.00 0.00 0.00 2.69
1183 1553 9.456147 TCCCTTCGAAAATACTTATCATCAAAA 57.544 29.630 0.00 0.00 0.00 2.44
1264 1634 9.191995 CCATTTTAATGATAAGTATTTTCGGGC 57.808 33.333 4.07 0.00 38.70 6.13
1265 1635 8.901748 CATTTTAATGATAAGTATTTTCGGGCG 58.098 33.333 0.00 0.00 38.70 6.13
1266 1636 6.548441 TTAATGATAAGTATTTTCGGGCGG 57.452 37.500 0.00 0.00 0.00 6.13
1267 1637 3.823281 TGATAAGTATTTTCGGGCGGA 57.177 42.857 0.00 0.00 0.00 5.54
1268 1638 3.724374 TGATAAGTATTTTCGGGCGGAG 58.276 45.455 0.00 0.00 0.00 4.63
1269 1639 2.607631 TAAGTATTTTCGGGCGGAGG 57.392 50.000 0.00 0.00 0.00 4.30
1270 1640 0.107361 AAGTATTTTCGGGCGGAGGG 60.107 55.000 0.00 0.00 0.00 4.30
1271 1641 0.979187 AGTATTTTCGGGCGGAGGGA 60.979 55.000 0.00 0.00 0.00 4.20
1272 1642 0.532196 GTATTTTCGGGCGGAGGGAG 60.532 60.000 0.00 0.00 0.00 4.30
1273 1643 1.692173 TATTTTCGGGCGGAGGGAGG 61.692 60.000 0.00 0.00 0.00 4.30
1374 1744 4.093952 TCGTCGCGTCCGGTCTTC 62.094 66.667 17.84 0.00 34.56 2.87
1398 1768 2.763902 CCCCAAAGTCCAGGTCCC 59.236 66.667 0.00 0.00 0.00 4.46
1399 1769 2.351276 CCCAAAGTCCAGGTCCCG 59.649 66.667 0.00 0.00 0.00 5.14
1400 1770 2.526046 CCCAAAGTCCAGGTCCCGT 61.526 63.158 0.00 0.00 0.00 5.28
1402 1772 1.003718 CAAAGTCCAGGTCCCGTCC 60.004 63.158 0.00 0.00 0.00 4.79
1403 1773 1.152096 AAAGTCCAGGTCCCGTCCT 60.152 57.895 0.00 0.00 38.51 3.85
1609 1980 6.574350 AGACGCAAAAGATACTAGTAGCAAT 58.426 36.000 19.70 5.85 0.00 3.56
1610 1981 7.042335 AGACGCAAAAGATACTAGTAGCAATT 58.958 34.615 19.70 11.32 0.00 2.32
1611 1982 8.195436 AGACGCAAAAGATACTAGTAGCAATTA 58.805 33.333 19.70 0.00 0.00 1.40
1612 1983 8.712285 ACGCAAAAGATACTAGTAGCAATTAA 57.288 30.769 19.70 0.00 0.00 1.40
1613 1984 9.326413 ACGCAAAAGATACTAGTAGCAATTAAT 57.674 29.630 19.70 0.00 0.00 1.40
1614 1985 9.798885 CGCAAAAGATACTAGTAGCAATTAATC 57.201 33.333 19.70 5.52 0.00 1.75
1624 1995 9.765795 ACTAGTAGCAATTAATCTTAATCGCTT 57.234 29.630 12.04 0.87 39.63 4.68
1647 2018 3.118408 TGGTTAATCTAGCGGCATTGACT 60.118 43.478 1.45 0.00 0.00 3.41
1656 2027 3.403038 AGCGGCATTGACTAACCATATC 58.597 45.455 1.45 0.00 0.00 1.63
2101 2472 1.215382 CTCATGTTCCTGTCGGCGA 59.785 57.895 4.99 4.99 0.00 5.54
2190 2561 1.959226 GCGTGGCTTTGAAGACCGA 60.959 57.895 10.35 0.00 31.94 4.69
2351 2722 1.970114 TCTCCCGCGACGTCTTCTT 60.970 57.895 14.70 0.00 0.00 2.52
2391 2762 1.153369 CGATCCTTCCACGCCACAT 60.153 57.895 0.00 0.00 0.00 3.21
2457 2828 1.542915 TGCTACCAACGTCTCTACACC 59.457 52.381 0.00 0.00 0.00 4.16
2550 2921 1.746615 GGCGCTCTTCTTCATGGCA 60.747 57.895 7.64 0.00 0.00 4.92
2617 2988 3.736482 CTCGTAGGCGCCGTCACTC 62.736 68.421 23.20 8.06 38.14 3.51
2626 2997 2.575993 CCGTCACTCTGGAGGCAG 59.424 66.667 2.58 0.00 0.00 4.85
3031 3402 3.200593 CTGATCAGCAGCCGCCAC 61.201 66.667 10.38 0.00 37.90 5.01
3167 3538 3.744719 CGAGGCCTCCGACGACAA 61.745 66.667 27.20 0.00 32.43 3.18
3258 3629 0.877743 GCAACTCCAAGTTCCTGCTC 59.122 55.000 0.00 0.00 36.03 4.26
3297 3668 2.032681 ACCGCTCTTGTCAAGGCC 59.967 61.111 12.66 0.00 0.00 5.19
3537 3923 2.443952 TGGGGGCTCATCGTCGAT 60.444 61.111 0.75 0.75 0.00 3.59
3710 4096 2.447443 TGGACCTCACTAGTACTGCAG 58.553 52.381 13.48 13.48 0.00 4.41
3758 4144 1.966493 GCATACAAGTCGTGCGGGTG 61.966 60.000 0.00 0.00 0.00 4.61
3759 4145 1.740296 ATACAAGTCGTGCGGGTGC 60.740 57.895 0.00 0.00 43.20 5.01
3922 4308 6.603237 CACTTTCAGTTTGACAGTGTGATA 57.397 37.500 14.22 0.00 45.30 2.15
3971 4357 5.581126 ACAAATGTTTGACAGTGTGATGT 57.419 34.783 12.09 0.00 40.55 3.06
3978 4364 7.326968 TGTTTGACAGTGTGATGTTTGATAA 57.673 32.000 0.00 0.00 32.25 1.75
4047 4433 4.747108 CAGTTTCGTCAGAGAACAATCACT 59.253 41.667 0.00 0.00 0.00 3.41
4133 4519 5.040635 AGTTTGCATGTTTAAACTTCGGTG 58.959 37.500 18.72 10.60 42.67 4.94
4143 4529 6.766944 TGTTTAAACTTCGGTGGAACTATGAA 59.233 34.615 18.72 0.00 36.74 2.57
4151 4537 8.142551 ACTTCGGTGGAACTATGAAATATAGTC 58.857 37.037 0.00 0.00 34.04 2.59
4153 4539 6.263842 TCGGTGGAACTATGAAATATAGTCGT 59.736 38.462 0.00 0.00 34.04 4.34
4203 4589 2.430694 GGTTTTATTGATCTGGGTGCCC 59.569 50.000 0.00 0.00 0.00 5.36
4204 4590 3.365472 GTTTTATTGATCTGGGTGCCCT 58.635 45.455 8.91 0.00 36.94 5.19
4205 4591 4.532834 GTTTTATTGATCTGGGTGCCCTA 58.467 43.478 8.91 0.00 36.94 3.53
4206 4592 5.140454 GTTTTATTGATCTGGGTGCCCTAT 58.860 41.667 8.91 2.32 36.94 2.57
4207 4593 5.402054 TTTATTGATCTGGGTGCCCTATT 57.598 39.130 8.91 0.00 36.94 1.73
4208 4594 3.979501 ATTGATCTGGGTGCCCTATTT 57.020 42.857 8.91 0.00 36.94 1.40
4209 4595 3.756082 TTGATCTGGGTGCCCTATTTT 57.244 42.857 8.91 0.00 36.94 1.82
4210 4596 4.871871 TTGATCTGGGTGCCCTATTTTA 57.128 40.909 8.91 0.00 36.94 1.52
4235 4621 7.643123 ACTATTTTAGGGATGTTGTTGGAGAT 58.357 34.615 0.00 0.00 0.00 2.75
4242 4628 0.323302 TGTTGTTGGAGATGGCGCTA 59.677 50.000 7.64 0.00 0.00 4.26
4247 4633 0.975556 TTGGAGATGGCGCTACCTCA 60.976 55.000 17.84 0.98 40.22 3.86
4882 5268 9.823647 ATTATCTCTATCTTTCACACGAAACAT 57.176 29.630 0.00 0.00 36.19 2.71
4894 5280 1.404477 CGAAACATGTTTTCGCCCAC 58.596 50.000 24.02 9.21 43.52 4.61
4915 5301 7.632680 GCCCACCTTTATATGTAAAGCAACAAT 60.633 37.037 14.66 0.00 43.49 2.71
4934 5320 3.788227 ATTGAACTGAGTACAAGGCCA 57.212 42.857 5.01 0.00 0.00 5.36
4950 5336 5.126061 ACAAGGCCAAATGATACAAGATGAC 59.874 40.000 5.01 0.00 0.00 3.06
4952 5338 3.876914 GGCCAAATGATACAAGATGACGA 59.123 43.478 0.00 0.00 0.00 4.20
4970 5356 1.468054 CGAGCAGCCCTAAAACAATGC 60.468 52.381 0.00 0.00 0.00 3.56
5000 5386 0.104304 ATAACCGGATCACGCAGGAC 59.896 55.000 9.46 0.00 42.52 3.85
5001 5387 0.968901 TAACCGGATCACGCAGGACT 60.969 55.000 9.46 0.00 42.52 3.85
5014 5400 2.734606 CGCAGGACTCACGAAAATACAA 59.265 45.455 0.00 0.00 0.00 2.41
5048 5434 5.307196 AGAGCCTAGGAAAAACTGAGTACAA 59.693 40.000 14.75 0.00 0.00 2.41
5093 5479 3.157087 CCTAAGTTCCACAACATTGCCT 58.843 45.455 0.00 0.00 34.60 4.75
5098 5485 0.321564 TCCACAACATTGCCTCGAGG 60.322 55.000 27.83 27.83 38.53 4.63
5107 5494 2.683933 GCCTCGAGGGGGAGAACA 60.684 66.667 32.06 0.00 36.08 3.18
5109 5496 2.726351 CCTCGAGGGGGAGAACAGC 61.726 68.421 24.62 0.00 36.08 4.40
5134 5521 4.057428 GTCACCGCAGCCGAGTCT 62.057 66.667 0.00 0.00 36.29 3.24
5135 5522 3.749064 TCACCGCAGCCGAGTCTC 61.749 66.667 0.00 0.00 36.29 3.36
5137 5524 3.303135 ACCGCAGCCGAGTCTCAA 61.303 61.111 0.00 0.00 36.29 3.02
5173 5560 1.302511 CCTGAACCCCAACACGAGG 60.303 63.158 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.671251 GCCACGAAACATTTGGGTGA 59.329 50.000 0.00 0.00 0.00 4.02
1 2 0.387202 TGCCACGAAACATTTGGGTG 59.613 50.000 0.00 0.00 0.00 4.61
2 3 1.337118 ATGCCACGAAACATTTGGGT 58.663 45.000 0.00 0.00 0.00 4.51
3 4 2.453983 AATGCCACGAAACATTTGGG 57.546 45.000 0.00 0.00 32.67 4.12
6 7 5.009610 AGAGTACAAATGCCACGAAACATTT 59.990 36.000 0.00 7.96 45.03 2.32
7 8 4.518970 AGAGTACAAATGCCACGAAACATT 59.481 37.500 0.00 0.00 38.11 2.71
8 9 4.072131 AGAGTACAAATGCCACGAAACAT 58.928 39.130 0.00 0.00 0.00 2.71
9 10 3.249799 CAGAGTACAAATGCCACGAAACA 59.750 43.478 0.00 0.00 0.00 2.83
10 11 3.250040 ACAGAGTACAAATGCCACGAAAC 59.750 43.478 0.00 0.00 0.00 2.78
25 26 9.582431 CGTAGAAAATCCTTATCAAACAGAGTA 57.418 33.333 0.00 0.00 0.00 2.59
49 50 6.309494 GCTGTTTTTACTTGTTTTCCTTTCGT 59.691 34.615 0.00 0.00 0.00 3.85
54 55 6.589907 CAGTTGCTGTTTTTACTTGTTTTCCT 59.410 34.615 0.00 0.00 0.00 3.36
56 57 6.672118 GCCAGTTGCTGTTTTTACTTGTTTTC 60.672 38.462 0.00 0.00 36.87 2.29
61 62 3.551485 GTGCCAGTTGCTGTTTTTACTTG 59.449 43.478 0.00 0.00 42.00 3.16
73 74 1.593196 TAGTGACAAGTGCCAGTTGC 58.407 50.000 12.14 6.05 41.77 4.17
146 149 8.786898 CGGTTATATGATCAATCTTGGATGTTT 58.213 33.333 0.00 0.00 0.00 2.83
175 178 1.617322 CCGTCTGCCTAGTAGCCATA 58.383 55.000 0.00 0.00 0.00 2.74
188 191 2.748058 CTTTCCACCCCACCCGTCTG 62.748 65.000 0.00 0.00 0.00 3.51
189 192 2.448931 TTTCCACCCCACCCGTCT 60.449 61.111 0.00 0.00 0.00 4.18
194 197 1.599797 CGTCACTTTCCACCCCACC 60.600 63.158 0.00 0.00 0.00 4.61
199 202 3.047877 CCGCCGTCACTTTCCACC 61.048 66.667 0.00 0.00 0.00 4.61
223 226 1.032114 CCACATTTTCCTCCTCCCGC 61.032 60.000 0.00 0.00 0.00 6.13
225 228 2.746472 CGATCCACATTTTCCTCCTCCC 60.746 54.545 0.00 0.00 0.00 4.30
226 229 2.170607 TCGATCCACATTTTCCTCCTCC 59.829 50.000 0.00 0.00 0.00 4.30
250 253 2.683859 GGCGGCACCGAAACCTTAC 61.684 63.158 14.43 0.00 42.83 2.34
266 269 1.215244 GCCTATTTAAGTCGACCGGC 58.785 55.000 13.01 9.19 0.00 6.13
284 287 2.655044 GCGTATTGCATTGCCCGC 60.655 61.111 6.12 10.72 45.45 6.13
332 335 2.110967 GTCTCATCCGTCGGACCGA 61.111 63.158 18.08 13.88 32.98 4.69
345 348 1.602605 TGGTCCGAAGCTCGTCTCA 60.603 57.895 0.00 0.00 38.40 3.27
363 366 1.520600 GAAACGCCATCAAACCCGGT 61.521 55.000 0.00 0.00 0.00 5.28
388 391 1.609794 GGACAGACGAAGGGGTCCT 60.610 63.158 0.00 0.00 44.99 3.85
421 424 4.351054 GATATGGGGGCGCCTGGG 62.351 72.222 28.56 0.00 0.00 4.45
424 427 2.532715 ATGGATATGGGGGCGCCT 60.533 61.111 28.56 9.11 0.00 5.52
427 430 1.574526 ATGGGATGGATATGGGGGCG 61.575 60.000 0.00 0.00 0.00 6.13
428 431 1.607225 TATGGGATGGATATGGGGGC 58.393 55.000 0.00 0.00 0.00 5.80
429 432 4.905566 AAATATGGGATGGATATGGGGG 57.094 45.455 0.00 0.00 0.00 5.40
464 467 4.394712 CTGACTGACCGGCACCCC 62.395 72.222 0.00 0.00 0.00 4.95
465 468 4.394712 CCTGACTGACCGGCACCC 62.395 72.222 0.00 0.00 0.00 4.61
466 469 4.394712 CCCTGACTGACCGGCACC 62.395 72.222 0.00 0.00 0.00 5.01
470 473 3.530910 AAACGCCCTGACTGACCGG 62.531 63.158 0.00 0.00 0.00 5.28
471 474 2.030562 AAACGCCCTGACTGACCG 59.969 61.111 0.00 0.00 0.00 4.79
472 475 0.951040 CTCAAACGCCCTGACTGACC 60.951 60.000 0.00 0.00 0.00 4.02
473 476 0.951040 CCTCAAACGCCCTGACTGAC 60.951 60.000 0.00 0.00 0.00 3.51
474 477 1.371183 CCTCAAACGCCCTGACTGA 59.629 57.895 0.00 0.00 0.00 3.41
475 478 1.672356 CCCTCAAACGCCCTGACTG 60.672 63.158 0.00 0.00 0.00 3.51
476 479 2.750350 CCCTCAAACGCCCTGACT 59.250 61.111 0.00 0.00 0.00 3.41
477 480 3.056328 GCCCTCAAACGCCCTGAC 61.056 66.667 0.00 0.00 0.00 3.51
478 481 4.344865 GGCCCTCAAACGCCCTGA 62.345 66.667 0.00 0.00 39.39 3.86
497 835 1.552792 GACCCAGAAGGACCTCTCAAG 59.447 57.143 0.00 0.00 39.89 3.02
539 889 0.040336 CGTCTCATATGTCCGGACGG 60.040 60.000 28.70 17.82 43.69 4.79
540 890 0.040336 CCGTCTCATATGTCCGGACG 60.040 60.000 28.70 22.61 45.92 4.79
542 892 0.106369 ACCCGTCTCATATGTCCGGA 60.106 55.000 22.85 0.00 41.08 5.14
549 899 2.838202 ACCTGTCAAACCCGTCTCATAT 59.162 45.455 0.00 0.00 0.00 1.78
556 906 2.424302 CGGACCTGTCAAACCCGT 59.576 61.111 0.00 0.00 35.83 5.28
564 914 4.081807 AGAGTATTTACAACCGGACCTGTC 60.082 45.833 9.46 0.00 0.00 3.51
566 916 4.467198 AGAGTATTTACAACCGGACCTG 57.533 45.455 9.46 4.75 0.00 4.00
580 931 8.624776 GCCTGTTGAGCAAATAATTAGAGTATT 58.375 33.333 0.00 0.00 0.00 1.89
583 934 5.945784 TGCCTGTTGAGCAAATAATTAGAGT 59.054 36.000 0.00 0.00 37.28 3.24
590 941 8.845413 AAAATAAATGCCTGTTGAGCAAATAA 57.155 26.923 0.00 0.00 44.83 1.40
611 962 8.297470 AGTACATGCACATGGAGATTAAAAAT 57.703 30.769 14.73 0.00 42.91 1.82
619 970 4.038042 GCTAGTAGTACATGCACATGGAGA 59.962 45.833 14.73 0.00 42.91 3.71
627 978 4.221924 TCTTTGGTGCTAGTAGTACATGCA 59.778 41.667 18.55 13.76 32.12 3.96
666 1017 4.744570 TGCTACTTTTCGTGAGATCGAAT 58.255 39.130 2.57 0.00 46.55 3.34
676 1027 1.692519 ACTGGGTCTGCTACTTTTCGT 59.307 47.619 0.00 0.00 0.00 3.85
677 1028 2.338500 GACTGGGTCTGCTACTTTTCG 58.662 52.381 0.00 0.00 0.00 3.46
696 1047 2.545113 GCGTGTCAGTAGTTGTCTTGGA 60.545 50.000 0.00 0.00 0.00 3.53
744 1095 6.883744 AGGATGATTCTCTTACTTTCCTGAC 58.116 40.000 0.00 0.00 0.00 3.51
761 1112 4.624843 CGGCTCCTGCATTATTAGGATGAT 60.625 45.833 0.00 0.00 41.96 2.45
762 1113 3.306989 CGGCTCCTGCATTATTAGGATGA 60.307 47.826 0.00 0.00 41.96 2.92
763 1114 3.005554 CGGCTCCTGCATTATTAGGATG 58.994 50.000 0.00 0.00 41.96 3.51
959 1315 6.591448 TCATCAGTCATCAGTGTGTAAATCAC 59.409 38.462 0.00 0.00 46.31 3.06
1030 1386 1.160137 CTCTTTCCACCAAAGCCTCG 58.840 55.000 0.00 0.00 41.38 4.63
1074 1430 1.201647 CAGCTTTCAGATGGGCACAAG 59.798 52.381 0.00 0.00 0.00 3.16
1102 1458 1.688735 CACTTGACCAGAGAGTGACCA 59.311 52.381 0.00 0.00 42.54 4.02
1105 1461 1.964223 GACCACTTGACCAGAGAGTGA 59.036 52.381 4.43 0.00 42.54 3.41
1116 1472 3.653539 TCGATTCGAAAGACCACTTGA 57.346 42.857 6.24 0.00 41.84 3.02
1128 1484 3.379372 ACGAGGTTAGGAAATCGATTCGA 59.621 43.478 11.83 11.73 39.05 3.71
1131 1487 5.593502 AGAGTACGAGGTTAGGAAATCGATT 59.406 40.000 4.39 4.39 38.50 3.34
1139 1509 2.172293 GGGAGAGAGTACGAGGTTAGGA 59.828 54.545 0.00 0.00 0.00 2.94
1151 1521 7.342284 TGATAAGTATTTTCGAAGGGAGAGAGT 59.658 37.037 0.00 0.00 0.00 3.24
1152 1522 7.717568 TGATAAGTATTTTCGAAGGGAGAGAG 58.282 38.462 0.00 0.00 0.00 3.20
1153 1523 7.655521 TGATAAGTATTTTCGAAGGGAGAGA 57.344 36.000 0.00 0.00 0.00 3.10
1154 1524 8.144478 TGATGATAAGTATTTTCGAAGGGAGAG 58.856 37.037 0.00 0.00 0.00 3.20
1155 1525 8.018537 TGATGATAAGTATTTTCGAAGGGAGA 57.981 34.615 0.00 0.00 0.00 3.71
1156 1526 8.662781 TTGATGATAAGTATTTTCGAAGGGAG 57.337 34.615 0.00 0.00 0.00 4.30
1157 1527 9.456147 TTTTGATGATAAGTATTTTCGAAGGGA 57.544 29.630 0.00 0.00 0.00 4.20
1238 1608 9.191995 GCCCGAAAATACTTATCATTAAAATGG 57.808 33.333 3.00 0.00 37.03 3.16
1239 1609 8.901748 CGCCCGAAAATACTTATCATTAAAATG 58.098 33.333 0.00 0.00 37.75 2.32
1240 1610 8.079809 CCGCCCGAAAATACTTATCATTAAAAT 58.920 33.333 0.00 0.00 0.00 1.82
1241 1611 7.282675 TCCGCCCGAAAATACTTATCATTAAAA 59.717 33.333 0.00 0.00 0.00 1.52
1242 1612 6.766944 TCCGCCCGAAAATACTTATCATTAAA 59.233 34.615 0.00 0.00 0.00 1.52
1243 1613 6.289834 TCCGCCCGAAAATACTTATCATTAA 58.710 36.000 0.00 0.00 0.00 1.40
1244 1614 5.856156 TCCGCCCGAAAATACTTATCATTA 58.144 37.500 0.00 0.00 0.00 1.90
1245 1615 4.710324 TCCGCCCGAAAATACTTATCATT 58.290 39.130 0.00 0.00 0.00 2.57
1246 1616 4.315803 CTCCGCCCGAAAATACTTATCAT 58.684 43.478 0.00 0.00 0.00 2.45
1247 1617 3.493699 CCTCCGCCCGAAAATACTTATCA 60.494 47.826 0.00 0.00 0.00 2.15
1248 1618 3.064931 CCTCCGCCCGAAAATACTTATC 58.935 50.000 0.00 0.00 0.00 1.75
1249 1619 2.224450 CCCTCCGCCCGAAAATACTTAT 60.224 50.000 0.00 0.00 0.00 1.73
1250 1620 1.139455 CCCTCCGCCCGAAAATACTTA 59.861 52.381 0.00 0.00 0.00 2.24
1251 1621 0.107361 CCCTCCGCCCGAAAATACTT 60.107 55.000 0.00 0.00 0.00 2.24
1252 1622 0.979187 TCCCTCCGCCCGAAAATACT 60.979 55.000 0.00 0.00 0.00 2.12
1253 1623 0.532196 CTCCCTCCGCCCGAAAATAC 60.532 60.000 0.00 0.00 0.00 1.89
1254 1624 1.692173 CCTCCCTCCGCCCGAAAATA 61.692 60.000 0.00 0.00 0.00 1.40
1255 1625 2.590092 CTCCCTCCGCCCGAAAAT 59.410 61.111 0.00 0.00 0.00 1.82
1256 1626 3.712907 CCTCCCTCCGCCCGAAAA 61.713 66.667 0.00 0.00 0.00 2.29
1261 1631 4.153330 TACTCCCTCCCTCCGCCC 62.153 72.222 0.00 0.00 0.00 6.13
1262 1632 2.838693 GTACTCCCTCCCTCCGCC 60.839 72.222 0.00 0.00 0.00 6.13
1263 1633 3.217743 CGTACTCCCTCCCTCCGC 61.218 72.222 0.00 0.00 0.00 5.54
1264 1634 0.682209 TTTCGTACTCCCTCCCTCCG 60.682 60.000 0.00 0.00 0.00 4.63
1265 1635 1.790818 ATTTCGTACTCCCTCCCTCC 58.209 55.000 0.00 0.00 0.00 4.30
1266 1636 3.532542 CAAATTTCGTACTCCCTCCCTC 58.467 50.000 0.00 0.00 0.00 4.30
1267 1637 2.355818 GCAAATTTCGTACTCCCTCCCT 60.356 50.000 0.00 0.00 0.00 4.20
1268 1638 2.014857 GCAAATTTCGTACTCCCTCCC 58.985 52.381 0.00 0.00 0.00 4.30
1269 1639 2.987232 AGCAAATTTCGTACTCCCTCC 58.013 47.619 0.00 0.00 0.00 4.30
1270 1640 4.093556 CAGAAGCAAATTTCGTACTCCCTC 59.906 45.833 0.00 0.00 32.33 4.30
1271 1641 4.003648 CAGAAGCAAATTTCGTACTCCCT 58.996 43.478 0.00 0.00 32.33 4.20
1272 1642 3.426292 GCAGAAGCAAATTTCGTACTCCC 60.426 47.826 0.00 0.00 41.58 4.30
1273 1643 3.437049 AGCAGAAGCAAATTTCGTACTCC 59.563 43.478 0.00 0.00 45.49 3.85
1274 1644 4.436183 GGAGCAGAAGCAAATTTCGTACTC 60.436 45.833 0.00 0.00 45.49 2.59
1275 1645 3.437049 GGAGCAGAAGCAAATTTCGTACT 59.563 43.478 0.00 0.00 45.49 2.73
1276 1646 3.188460 TGGAGCAGAAGCAAATTTCGTAC 59.812 43.478 0.00 0.00 45.49 3.67
1277 1647 3.407698 TGGAGCAGAAGCAAATTTCGTA 58.592 40.909 0.00 0.00 45.49 3.43
1304 1674 0.674534 AGTCGTCAAGTCCACACCTC 59.325 55.000 0.00 0.00 0.00 3.85
1374 1744 1.251251 CTGGACTTTGGGGCTTCAAG 58.749 55.000 0.00 0.00 0.00 3.02
1398 1768 6.817641 AGTATACGAGATAGGTAATCAGGACG 59.182 42.308 0.00 0.00 37.03 4.79
1399 1769 9.316730 CTAGTATACGAGATAGGTAATCAGGAC 57.683 40.741 7.17 0.00 37.03 3.85
1400 1770 9.044646 ACTAGTATACGAGATAGGTAATCAGGA 57.955 37.037 18.55 0.00 37.03 3.86
1487 1858 9.898152 TCTTCTTCTTCTTCTTCTTTTTCTTCT 57.102 29.630 0.00 0.00 0.00 2.85
1494 1865 9.844257 TCATTCTTCTTCTTCTTCTTCTTCTTT 57.156 29.630 0.00 0.00 0.00 2.52
1517 1888 4.646040 TCATTTTCATCGGCCTCATTTCAT 59.354 37.500 0.00 0.00 0.00 2.57
1611 1982 8.560374 GCTAGATTAACCAAAGCGATTAAGATT 58.440 33.333 0.00 0.00 0.00 2.40
1612 1983 8.089115 GCTAGATTAACCAAAGCGATTAAGAT 57.911 34.615 0.00 0.00 0.00 2.40
1613 1984 7.478520 GCTAGATTAACCAAAGCGATTAAGA 57.521 36.000 0.00 0.00 0.00 2.10
1624 1995 3.625764 GTCAATGCCGCTAGATTAACCAA 59.374 43.478 0.00 0.00 0.00 3.67
1635 2006 3.071602 AGATATGGTTAGTCAATGCCGCT 59.928 43.478 0.00 0.00 0.00 5.52
1647 2018 3.540617 ACACGCATGCAAGATATGGTTA 58.459 40.909 19.57 0.00 0.00 2.85
1656 2027 0.179181 CCAAGCTACACGCATGCAAG 60.179 55.000 19.57 11.70 42.61 4.01
1947 2318 1.209261 TGCATGGAGAAAGCCGTGATA 59.791 47.619 6.79 0.00 45.81 2.15
2101 2472 1.519455 GCTCGCCGTACTTGATGCT 60.519 57.895 0.00 0.00 0.00 3.79
2150 2521 1.078143 AACTCCTTCATGAGCCGCC 60.078 57.895 0.00 0.00 35.72 6.13
2317 2688 0.726256 GAGACGGACCAGTCGTAGTC 59.274 60.000 9.74 9.98 45.26 2.59
2351 2722 1.077169 TCTGCTTGGAGTAGAGGTCCA 59.923 52.381 0.00 0.00 42.62 4.02
2550 2921 1.449070 GCCGTAGCCGCTTTTACCT 60.449 57.895 0.00 0.00 0.00 3.08
2593 2964 3.188786 GGCGCCTACGAGCAACAG 61.189 66.667 22.15 0.00 43.93 3.16
2626 2997 2.295885 CATGGACATGAAGAAGGAGGC 58.704 52.381 6.44 0.00 41.20 4.70
2635 3006 1.678728 GCGGGAGAACATGGACATGAA 60.679 52.381 18.38 0.00 41.20 2.57
2742 3113 1.033574 ACCTCCTCCTTAGCGAATCG 58.966 55.000 0.00 0.00 0.00 3.34
3031 3402 1.218585 CTGACAGGCTGAGGCTCTG 59.781 63.158 23.66 16.45 40.25 3.35
3161 3532 4.142469 GCCTGCTAATAATGGTTTTGTCGT 60.142 41.667 0.00 0.00 0.00 4.34
3258 3629 2.745884 TCATCACCGGCTTTGCGG 60.746 61.111 0.00 0.00 0.00 5.69
3297 3668 4.812476 TGTTCATCTCGCCGCCCG 62.812 66.667 0.00 0.00 38.61 6.13
3360 3746 0.542467 ATCCCACCAAATGCTGCACA 60.542 50.000 3.57 0.00 0.00 4.57
3406 3792 1.069765 CCGGCACTGTGTCTGAACT 59.930 57.895 11.02 0.00 0.00 3.01
3407 3793 2.607892 GCCGGCACTGTGTCTGAAC 61.608 63.158 24.80 0.82 0.00 3.18
3408 3794 2.280797 GCCGGCACTGTGTCTGAA 60.281 61.111 24.80 0.00 0.00 3.02
3537 3923 1.903294 GAGCATCTCCAGCCAGACA 59.097 57.895 0.00 0.00 0.00 3.41
3710 4096 1.017177 TTCAGGATACGCGTGCAACC 61.017 55.000 24.59 18.38 46.39 3.77
3880 4266 1.001293 TGACGAATCTGAAGCAGCTGT 59.999 47.619 16.64 0.00 0.00 4.40
3881 4267 1.392853 GTGACGAATCTGAAGCAGCTG 59.607 52.381 10.11 10.11 0.00 4.24
3882 4268 1.274728 AGTGACGAATCTGAAGCAGCT 59.725 47.619 0.00 0.00 0.00 4.24
3919 4305 9.370126 CCGACGAAACTGAATTTATCAAATATC 57.630 33.333 0.00 0.00 37.67 1.63
3922 4308 7.333423 TCTCCGACGAAACTGAATTTATCAAAT 59.667 33.333 0.00 0.00 37.67 2.32
3978 4364 9.151471 CTTTGAAGAATCTGAAATTGCAATCAT 57.849 29.630 13.38 4.80 0.00 2.45
4047 4433 9.836864 ATGCTAGTATATCAATCAAGTTCAACA 57.163 29.630 0.00 0.00 0.00 3.33
4206 4592 9.589461 TCCAACAACATCCCTAAAATAGTAAAA 57.411 29.630 0.00 0.00 0.00 1.52
4207 4593 9.238368 CTCCAACAACATCCCTAAAATAGTAAA 57.762 33.333 0.00 0.00 0.00 2.01
4208 4594 8.607713 TCTCCAACAACATCCCTAAAATAGTAA 58.392 33.333 0.00 0.00 0.00 2.24
4209 4595 8.153221 TCTCCAACAACATCCCTAAAATAGTA 57.847 34.615 0.00 0.00 0.00 1.82
4210 4596 7.027874 TCTCCAACAACATCCCTAAAATAGT 57.972 36.000 0.00 0.00 0.00 2.12
4618 5004 9.541143 GGAGTAAAAAGAATTGACCATGAAAAA 57.459 29.630 0.00 0.00 0.00 1.94
4619 5005 8.700051 TGGAGTAAAAAGAATTGACCATGAAAA 58.300 29.630 0.00 0.00 0.00 2.29
4685 5071 2.945008 ACAACATATCACATTGAGGGCG 59.055 45.455 0.00 0.00 0.00 6.13
4802 5188 2.629051 ACTCTAGTACAAATTGGCGGC 58.371 47.619 0.00 0.00 0.00 6.53
4864 5250 6.848800 CGAAAACATGTTTCGTGTGAAAGATA 59.151 34.615 23.47 0.00 43.85 1.98
4882 5268 4.337145 ACATATAAAGGTGGGCGAAAACA 58.663 39.130 0.00 0.00 0.00 2.83
4889 5275 5.126384 TGTTGCTTTACATATAAAGGTGGGC 59.874 40.000 5.67 0.00 45.15 5.36
4915 5301 3.569194 TTGGCCTTGTACTCAGTTCAA 57.431 42.857 3.32 0.00 0.00 2.69
4934 5320 4.272018 GCTGCTCGTCATCTTGTATCATTT 59.728 41.667 0.00 0.00 0.00 2.32
4950 5336 1.468054 GCATTGTTTTAGGGCTGCTCG 60.468 52.381 0.00 0.00 0.00 5.03
4952 5338 0.897621 GGCATTGTTTTAGGGCTGCT 59.102 50.000 0.00 0.00 0.00 4.24
4970 5356 0.973632 TCCGGTTATCATGGGATCGG 59.026 55.000 0.00 8.64 38.88 4.18
5000 5386 9.020813 TCTCTTTCGATATTGTATTTTCGTGAG 57.979 33.333 0.00 0.00 33.52 3.51
5001 5387 8.920509 TCTCTTTCGATATTGTATTTTCGTGA 57.079 30.769 0.00 0.00 33.52 4.35
5014 5400 6.732896 TTTTCCTAGGCTCTCTTTCGATAT 57.267 37.500 2.96 0.00 0.00 1.63
5036 5422 1.856597 GCGTGACGTTGTACTCAGTTT 59.143 47.619 6.91 0.00 0.00 2.66
5048 5434 0.685458 ATAGGGGGTTAGCGTGACGT 60.685 55.000 6.91 0.00 0.00 4.34
5093 5479 3.068691 CGCTGTTCTCCCCCTCGA 61.069 66.667 0.00 0.00 0.00 4.04
5098 5485 0.179097 CTCTTAGCGCTGTTCTCCCC 60.179 60.000 22.90 0.00 0.00 4.81
5109 5496 2.161486 GCTGCGGTGACTCTTAGCG 61.161 63.158 0.00 0.00 41.52 4.26
5134 5521 3.386402 GGGTGAAAACCTTTGTCCATTGA 59.614 43.478 0.00 0.00 0.00 2.57
5135 5522 3.387699 AGGGTGAAAACCTTTGTCCATTG 59.612 43.478 0.00 0.00 33.64 2.82
5137 5524 2.965147 CAGGGTGAAAACCTTTGTCCAT 59.035 45.455 0.00 0.00 35.78 3.41


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

AutoCloner maintained by Alex Coulton.