Multiple sequence alignment - TraesCS7A01G382000

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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 TraesCS7A01G382000 chr7A 100.000 3524 0 0 1 3524 556507462 556503939 0.000000e+00 6508
1 TraesCS7A01G382000 chr7D 88.127 2173 129 58 1 2097 489723130 489721011 0.000000e+00 2464
2 TraesCS7A01G382000 chr7D 91.115 574 47 2 2952 3524 489719614 489719044 0.000000e+00 774
3 TraesCS7A01G382000 chr7D 84.430 745 64 24 2230 2965 489720368 489719667 0.000000e+00 686
4 TraesCS7A01G382000 chr7D 88.636 88 6 2 2106 2192 489720451 489720367 1.730000e-18 104
5 TraesCS7A01G382000 chr7B 86.237 2187 157 57 1 2097 518389875 518387743 0.000000e+00 2239
6 TraesCS7A01G382000 chr7B 86.431 877 61 27 2106 2965 518387597 518386762 0.000000e+00 907
7 TraesCS7A01G382000 chr7B 91.304 575 45 3 2952 3524 518386707 518386136 0.000000e+00 780
8 TraesCS7A01G382000 chr6B 87.615 218 24 1 1542 1756 223571472 223571255 2.100000e-62 250
9 TraesCS7A01G382000 chr6A 87.156 218 25 1 1542 1756 155224781 155224998 9.770000e-61 244
10 TraesCS7A01G382000 chr6D 86.099 223 27 2 1542 1760 125246960 125246738 1.640000e-58 237


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 TraesCS7A01G382000 chr7A 556503939 556507462 3523 True 6508.000000 6508 100.000000 1 3524 1 chr7A.!!$R1 3523
1 TraesCS7A01G382000 chr7D 489719044 489723130 4086 True 1007.000000 2464 88.077000 1 3524 4 chr7D.!!$R1 3523
2 TraesCS7A01G382000 chr7B 518386136 518389875 3739 True 1308.666667 2239 87.990667 1 3524 3 chr7B.!!$R1 3523

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
243 257 0.035056 AGAATCCCAAGGGCGAAGTG 60.035 55.0 0.0 0.0 34.68 3.16 F
1328 1431 0.034896 TGAAGGAGGAGCGGTTCAAC 59.965 55.0 0.0 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2226 2891 1.041437 AGTAGCTACATTCGGAGGGC 58.959 55.0 25.28 0.0 0.0 5.19 R
3316 4059 0.036388 TGGACCATGAGCTTTCGACC 60.036 55.0 0.00 0.0 0.0 4.79 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
180 194 0.897863 CCCTCCTCCTATCTCCTGCG 60.898 65.000 0.00 0.00 0.00 5.18
233 247 0.618458 CCAGACCCGAAGAATCCCAA 59.382 55.000 0.00 0.00 0.00 4.12
242 256 0.698818 AAGAATCCCAAGGGCGAAGT 59.301 50.000 0.00 0.00 34.68 3.01
243 257 0.035056 AGAATCCCAAGGGCGAAGTG 60.035 55.000 0.00 0.00 34.68 3.16
264 278 2.422945 GGGAAAAATATCGCACCTCCCT 60.423 50.000 0.00 0.00 38.42 4.20
360 401 2.045280 CCCCTGCTCTATCCACTCG 58.955 63.158 0.00 0.00 0.00 4.18
366 407 1.028905 GCTCTATCCACTCGCAGTCT 58.971 55.000 0.00 0.00 0.00 3.24
390 432 1.353103 CTGATTGATTCCGCGTGGC 59.647 57.895 11.05 0.00 34.14 5.01
468 510 0.881796 GCAGGTTTCTTTCTTCCGGG 59.118 55.000 0.00 0.00 0.00 5.73
486 528 0.582005 GGTAGACGATGATTTGGCGC 59.418 55.000 0.00 0.00 0.00 6.53
487 529 1.571919 GTAGACGATGATTTGGCGCT 58.428 50.000 7.64 0.00 0.00 5.92
607 657 4.454678 TGCCTGTGCCTAGATTCTTTATG 58.545 43.478 0.00 0.00 36.33 1.90
634 694 5.570206 CGTTAATTAGTGCTGTCAAGTACGA 59.430 40.000 0.00 0.00 43.23 3.43
655 715 1.465387 TCTTGTTGTTTGTTGTCGCGT 59.535 42.857 5.77 0.00 0.00 6.01
694 754 2.740981 CACTGCTGATTTCCTCACTGTC 59.259 50.000 0.00 0.00 0.00 3.51
699 759 3.376546 GCTGATTTCCTCACTGTCCATTC 59.623 47.826 0.00 0.00 0.00 2.67
702 762 4.018141 TGATTTCCTCACTGTCCATTCCAT 60.018 41.667 0.00 0.00 0.00 3.41
710 770 6.183361 CCTCACTGTCCATTCCATATTCAGTA 60.183 42.308 0.00 0.00 34.11 2.74
732 814 6.713903 AGTATGATTAGCTGATTGGTTGATGG 59.286 38.462 0.00 0.00 0.00 3.51
734 816 4.641541 TGATTAGCTGATTGGTTGATGGTG 59.358 41.667 0.00 0.00 0.00 4.17
748 830 3.009026 TGATGGTGGTGACGATGAAATG 58.991 45.455 0.00 0.00 0.00 2.32
760 849 3.056250 ACGATGAAATGCTGAGTGAGAGT 60.056 43.478 0.00 0.00 0.00 3.24
762 851 3.325293 TGAAATGCTGAGTGAGAGTCC 57.675 47.619 0.00 0.00 0.00 3.85
826 923 2.619177 GACTCTGAATGCGGTAGCTAGA 59.381 50.000 0.00 0.00 45.42 2.43
838 935 4.569341 GCTAGAGGCGAGCATAGC 57.431 61.111 0.00 9.33 39.84 2.97
849 946 1.406069 CGAGCATAGCTTGGTTCTGGT 60.406 52.381 0.00 0.00 39.88 4.00
856 953 5.068723 GCATAGCTTGGTTCTGGTACTACTA 59.931 44.000 0.00 0.00 0.00 1.82
857 954 6.505272 CATAGCTTGGTTCTGGTACTACTAC 58.495 44.000 0.00 0.00 0.00 2.73
858 955 4.675038 AGCTTGGTTCTGGTACTACTACT 58.325 43.478 0.00 0.00 0.00 2.57
859 956 5.085219 AGCTTGGTTCTGGTACTACTACTT 58.915 41.667 0.00 0.00 0.00 2.24
860 957 5.047235 AGCTTGGTTCTGGTACTACTACTTG 60.047 44.000 0.00 0.00 0.00 3.16
868 965 6.429151 TCTGGTACTACTACTTGGCAGAATA 58.571 40.000 0.00 0.00 0.00 1.75
879 976 9.224267 ACTACTTGGCAGAATATTATAATGCAG 57.776 33.333 8.28 1.86 38.63 4.41
905 1002 3.008375 AGCAGTCACCAAAGCTTGAGATA 59.992 43.478 0.00 0.00 32.52 1.98
938 1040 3.947910 ATGGTTCATTTTCAGGTGCTG 57.052 42.857 0.00 0.00 0.00 4.41
947 1049 2.169832 TTCAGGTGCTGCTACTGTTC 57.830 50.000 18.59 0.00 34.02 3.18
949 1051 1.374758 AGGTGCTGCTACTGTTCGC 60.375 57.895 0.00 0.00 0.00 4.70
957 1059 1.464608 TGCTACTGTTCGCTCATTTGC 59.535 47.619 0.00 0.00 0.00 3.68
958 1060 1.734465 GCTACTGTTCGCTCATTTGCT 59.266 47.619 0.00 0.00 0.00 3.91
959 1061 2.222908 GCTACTGTTCGCTCATTTGCTC 60.223 50.000 0.00 0.00 0.00 4.26
960 1062 2.175878 ACTGTTCGCTCATTTGCTCT 57.824 45.000 0.00 0.00 0.00 4.09
961 1063 1.802960 ACTGTTCGCTCATTTGCTCTG 59.197 47.619 0.00 0.00 0.00 3.35
962 1064 1.802960 CTGTTCGCTCATTTGCTCTGT 59.197 47.619 0.00 0.00 0.00 3.41
963 1065 2.995939 CTGTTCGCTCATTTGCTCTGTA 59.004 45.455 0.00 0.00 0.00 2.74
964 1066 3.599343 TGTTCGCTCATTTGCTCTGTAT 58.401 40.909 0.00 0.00 0.00 2.29
965 1067 3.618594 TGTTCGCTCATTTGCTCTGTATC 59.381 43.478 0.00 0.00 0.00 2.24
966 1068 2.826428 TCGCTCATTTGCTCTGTATCC 58.174 47.619 0.00 0.00 0.00 2.59
983 1085 1.601759 CCAGTTGTGGGCACTGAGG 60.602 63.158 4.41 0.00 40.67 3.86
984 1086 1.601759 CAGTTGTGGGCACTGAGGG 60.602 63.158 0.00 0.00 33.65 4.30
985 1087 1.770110 AGTTGTGGGCACTGAGGGA 60.770 57.895 0.00 0.00 0.00 4.20
986 1088 1.150536 GTTGTGGGCACTGAGGGAA 59.849 57.895 0.00 0.00 0.00 3.97
987 1089 1.150536 TTGTGGGCACTGAGGGAAC 59.849 57.895 0.00 0.00 0.00 3.62
1027 1129 4.973055 TGTTTGGACGCCCCGACG 62.973 66.667 0.00 0.00 37.93 5.12
1127 1229 3.985925 ACTTCGGTCAAGTCGTTCAATAC 59.014 43.478 0.00 0.00 42.07 1.89
1146 1248 9.793259 TTCAATACTATTATCATGAAGTTCCCC 57.207 33.333 0.00 0.00 0.00 4.81
1240 1342 7.307989 GCTCTTTGTGTGCTAGTCATTTTTCTA 60.308 37.037 0.00 0.00 32.89 2.10
1241 1343 8.621532 TCTTTGTGTGCTAGTCATTTTTCTAT 57.378 30.769 0.00 0.00 0.00 1.98
1277 1379 6.649141 AGTTCATAGCTAACGAATTGTGACAA 59.351 34.615 0.00 0.00 32.00 3.18
1279 1381 7.234187 TCATAGCTAACGAATTGTGACAATC 57.766 36.000 11.70 4.70 0.00 2.67
1283 1385 5.065218 AGCTAACGAATTGTGACAATCATCC 59.935 40.000 11.70 1.25 0.00 3.51
1289 1391 7.327975 ACGAATTGTGACAATCATCCTACTTA 58.672 34.615 11.70 0.00 0.00 2.24
1323 1426 3.967987 AGTTATAATGAAGGAGGAGCGGT 59.032 43.478 0.00 0.00 0.00 5.68
1328 1431 0.034896 TGAAGGAGGAGCGGTTCAAC 59.965 55.000 0.00 0.00 0.00 3.18
1362 1465 8.328758 TGATATCTGAACCCTTGTTTCACTTAT 58.671 33.333 3.98 0.00 33.97 1.73
1363 1466 9.178758 GATATCTGAACCCTTGTTTCACTTATT 57.821 33.333 0.00 0.00 33.97 1.40
1364 1467 6.633500 TCTGAACCCTTGTTTCACTTATTG 57.367 37.500 0.00 0.00 33.97 1.90
1365 1468 6.126409 TCTGAACCCTTGTTTCACTTATTGT 58.874 36.000 0.00 0.00 33.97 2.71
1366 1469 6.605594 TCTGAACCCTTGTTTCACTTATTGTT 59.394 34.615 0.00 0.00 33.97 2.83
1367 1470 6.801575 TGAACCCTTGTTTCACTTATTGTTC 58.198 36.000 0.00 0.00 33.97 3.18
1368 1471 6.605594 TGAACCCTTGTTTCACTTATTGTTCT 59.394 34.615 0.00 0.00 33.97 3.01
1369 1472 7.123547 TGAACCCTTGTTTCACTTATTGTTCTT 59.876 33.333 0.00 0.00 33.97 2.52
1370 1473 6.805713 ACCCTTGTTTCACTTATTGTTCTTG 58.194 36.000 0.00 0.00 0.00 3.02
1371 1474 6.379988 ACCCTTGTTTCACTTATTGTTCTTGT 59.620 34.615 0.00 0.00 0.00 3.16
1372 1475 6.918022 CCCTTGTTTCACTTATTGTTCTTGTC 59.082 38.462 0.00 0.00 0.00 3.18
1373 1476 7.416213 CCCTTGTTTCACTTATTGTTCTTGTCA 60.416 37.037 0.00 0.00 0.00 3.58
1374 1477 7.645340 CCTTGTTTCACTTATTGTTCTTGTCAG 59.355 37.037 0.00 0.00 0.00 3.51
1412 1515 2.224079 AGTGATGTTTTACAGTGCAGCG 59.776 45.455 0.00 0.00 0.00 5.18
1415 1518 2.242047 TGTTTTACAGTGCAGCGGTA 57.758 45.000 0.00 0.00 0.00 4.02
1431 1534 2.029649 GCGGTACCTATGCGGAAGAATA 60.030 50.000 10.90 0.00 36.31 1.75
1492 1595 9.754382 ACAAGCATAATTTATCTAGGCATTTTG 57.246 29.630 0.00 0.00 0.00 2.44
1520 1623 7.230510 TGCTTTTTGTGTAACTAACAGATCCAT 59.769 33.333 0.00 0.00 39.29 3.41
1528 1631 7.549488 GTGTAACTAACAGATCCATAACTTGCT 59.451 37.037 0.00 0.00 39.29 3.91
1532 1635 3.535561 ACAGATCCATAACTTGCTTCCG 58.464 45.455 0.00 0.00 0.00 4.30
1585 1688 7.484324 GTGAAATTGATAAAGAAGAGCTGAAGC 59.516 37.037 0.00 0.00 42.49 3.86
1590 1693 5.942236 TGATAAAGAAGAGCTGAAGCATTGT 59.058 36.000 4.90 0.00 45.16 2.71
1627 1733 7.153985 GGAAATCTCATTCACAGAGGAGATAG 58.846 42.308 11.25 0.00 44.13 2.08
1629 1735 3.894427 TCTCATTCACAGAGGAGATAGGC 59.106 47.826 0.00 0.00 31.82 3.93
1644 1750 3.640967 AGATAGGCGATCTCTTTGAAGCT 59.359 43.478 4.10 0.00 41.37 3.74
1726 1832 6.763135 CCTTGTTTATCTTCTCAATGATCCGA 59.237 38.462 0.00 0.00 0.00 4.55
1771 1877 7.611855 CCTTCATTCTTTATACACTGTTTCCCT 59.388 37.037 0.00 0.00 0.00 4.20
1860 1966 6.491403 ACTTCTGCATTCAGTTCCTGTTTTAT 59.509 34.615 0.00 0.00 41.10 1.40
1871 1977 7.524863 TCAGTTCCTGTTTTATGTCTCGTACAT 60.525 37.037 10.25 10.25 41.05 2.29
1887 1993 8.269424 GTCTCGTACATTAATTATGCAAGAGTG 58.731 37.037 0.00 0.00 37.81 3.51
2009 2116 3.069729 AGAATAAGGACGGGTATGTGAGC 59.930 47.826 0.00 0.00 0.00 4.26
2091 2198 6.201517 CGTATAGCCATGAAAAGATTTGGTG 58.798 40.000 0.00 0.00 0.00 4.17
2097 2204 5.279156 GCCATGAAAAGATTTGGTGAGTTCT 60.279 40.000 0.00 0.00 0.00 3.01
2099 2206 6.385033 CATGAAAAGATTTGGTGAGTTCTCC 58.615 40.000 0.00 0.00 0.00 3.71
2100 2207 5.445069 TGAAAAGATTTGGTGAGTTCTCCA 58.555 37.500 0.00 0.00 37.70 3.86
2101 2208 5.532406 TGAAAAGATTTGGTGAGTTCTCCAG 59.468 40.000 3.45 0.00 40.19 3.86
2102 2209 4.713792 AAGATTTGGTGAGTTCTCCAGT 57.286 40.909 3.45 0.00 40.19 4.00
2104 2211 4.646572 AGATTTGGTGAGTTCTCCAGTTC 58.353 43.478 3.45 5.21 40.19 3.01
2134 2792 6.935741 TGACTAGCTCTCTAATCTCTGTTC 57.064 41.667 0.00 0.00 0.00 3.18
2171 2830 1.906757 GACTCTGCACTCATGAGTCG 58.093 55.000 25.58 20.11 44.42 4.18
2207 2866 8.855110 TGAAGAAAACTAAATATGCACAGGAAA 58.145 29.630 0.00 0.00 0.00 3.13
2222 2881 1.615392 AGGAAAATGCTTGACACTGCC 59.385 47.619 0.00 0.00 0.00 4.85
2226 2891 1.518056 AATGCTTGACACTGCCACCG 61.518 55.000 0.00 0.00 0.00 4.94
2257 2922 4.456280 TGTAGCTACTTGATGTCACCTG 57.544 45.455 23.84 0.00 0.00 4.00
2259 2924 3.601443 AGCTACTTGATGTCACCTGTC 57.399 47.619 0.00 0.00 0.00 3.51
2343 3008 5.679638 GCTGCGGAATCCAAAACTGATAATT 60.680 40.000 0.00 0.00 0.00 1.40
2361 3026 8.703604 TGATAATTTGCACTGTTAGTCTAGAC 57.296 34.615 15.41 15.41 0.00 2.59
2362 3027 8.531982 TGATAATTTGCACTGTTAGTCTAGACT 58.468 33.333 27.72 27.72 45.02 3.24
2365 3030 7.704578 ATTTGCACTGTTAGTCTAGACTAGA 57.295 36.000 27.17 18.70 43.92 2.43
2366 3031 7.520451 TTTGCACTGTTAGTCTAGACTAGAA 57.480 36.000 27.17 19.62 43.92 2.10
2367 3032 6.745159 TGCACTGTTAGTCTAGACTAGAAG 57.255 41.667 27.17 26.98 43.92 2.85
2368 3033 6.239396 TGCACTGTTAGTCTAGACTAGAAGT 58.761 40.000 27.71 27.71 43.92 3.01
2371 3036 7.094720 GCACTGTTAGTCTAGACTAGAAGTTCA 60.095 40.741 29.33 21.21 43.92 3.18
2373 3038 9.523168 ACTGTTAGTCTAGACTAGAAGTTCATT 57.477 33.333 27.71 15.14 43.92 2.57
2389 3054 9.159364 AGAAGTTCATTTTATCCGGTAACTAAC 57.841 33.333 0.00 0.00 0.00 2.34
2466 3131 4.645136 GGGATGGTTACCTTCAAGGAATTC 59.355 45.833 11.59 0.00 37.67 2.17
2496 3161 0.325296 TCACTCGCTGGGTAGGGATT 60.325 55.000 0.00 0.00 43.85 3.01
2505 3170 1.286553 TGGGTAGGGATTGGCGAAAAT 59.713 47.619 0.00 0.00 0.00 1.82
2589 3256 4.494484 GTTGCATGGTGGTTTTATCTTCC 58.506 43.478 0.00 0.00 0.00 3.46
2591 3258 3.763360 TGCATGGTGGTTTTATCTTCCTG 59.237 43.478 0.00 0.00 0.00 3.86
2593 3260 4.220602 GCATGGTGGTTTTATCTTCCTGTT 59.779 41.667 0.00 0.00 0.00 3.16
2594 3261 5.417580 GCATGGTGGTTTTATCTTCCTGTTA 59.582 40.000 0.00 0.00 0.00 2.41
2595 3262 6.071616 GCATGGTGGTTTTATCTTCCTGTTAA 60.072 38.462 0.00 0.00 0.00 2.01
2597 3264 9.184523 CATGGTGGTTTTATCTTCCTGTTAATA 57.815 33.333 0.00 0.00 0.00 0.98
2598 3265 8.801882 TGGTGGTTTTATCTTCCTGTTAATAG 57.198 34.615 0.00 0.00 0.00 1.73
2599 3266 8.387813 TGGTGGTTTTATCTTCCTGTTAATAGT 58.612 33.333 0.00 0.00 0.00 2.12
2600 3267 8.674607 GGTGGTTTTATCTTCCTGTTAATAGTG 58.325 37.037 0.00 0.00 0.00 2.74
2601 3268 9.444600 GTGGTTTTATCTTCCTGTTAATAGTGA 57.555 33.333 0.00 0.00 0.00 3.41
2602 3269 9.444600 TGGTTTTATCTTCCTGTTAATAGTGAC 57.555 33.333 0.00 0.00 0.00 3.67
2603 3270 9.668497 GGTTTTATCTTCCTGTTAATAGTGACT 57.332 33.333 0.00 0.00 0.00 3.41
2605 3272 9.582431 TTTTATCTTCCTGTTAATAGTGACTCG 57.418 33.333 0.00 0.00 0.00 4.18
2606 3273 5.578005 TCTTCCTGTTAATAGTGACTCGG 57.422 43.478 0.00 0.00 0.00 4.63
2607 3274 3.795623 TCCTGTTAATAGTGACTCGGC 57.204 47.619 0.00 0.00 0.00 5.54
2608 3275 3.093814 TCCTGTTAATAGTGACTCGGCA 58.906 45.455 0.00 0.00 0.00 5.69
2609 3276 3.704566 TCCTGTTAATAGTGACTCGGCAT 59.295 43.478 0.00 0.00 0.00 4.40
2610 3277 3.804325 CCTGTTAATAGTGACTCGGCATG 59.196 47.826 0.00 0.00 0.00 4.06
2611 3278 4.433615 CTGTTAATAGTGACTCGGCATGT 58.566 43.478 0.00 0.00 0.00 3.21
2612 3279 4.827692 TGTTAATAGTGACTCGGCATGTT 58.172 39.130 0.00 0.00 0.00 2.71
2613 3280 4.868171 TGTTAATAGTGACTCGGCATGTTC 59.132 41.667 0.00 0.00 0.00 3.18
2614 3281 2.604046 ATAGTGACTCGGCATGTTCC 57.396 50.000 0.00 0.00 0.00 3.62
2615 3282 1.262417 TAGTGACTCGGCATGTTCCA 58.738 50.000 0.00 0.00 0.00 3.53
2651 3318 5.221621 TGACATGTCTGAACACCTGTATCAA 60.222 40.000 25.55 0.00 38.48 2.57
2666 3333 5.276461 TGTATCAAACAGTGTCTGTGACT 57.724 39.130 0.00 0.00 44.62 3.41
2679 3346 2.029844 GTGACTGCTTCGCCTCCAC 61.030 63.158 0.00 0.00 0.00 4.02
2699 3366 3.059257 CACTGCGCAAGTTATGTTGTGTA 60.059 43.478 13.05 0.00 39.64 2.90
2700 3367 3.562141 ACTGCGCAAGTTATGTTGTGTAA 59.438 39.130 13.05 0.00 39.64 2.41
2701 3368 4.140518 TGCGCAAGTTATGTTGTGTAAG 57.859 40.909 8.16 0.00 39.64 2.34
2702 3369 2.908626 GCGCAAGTTATGTTGTGTAAGC 59.091 45.455 0.30 0.00 39.64 3.09
2705 3372 4.973051 CGCAAGTTATGTTGTGTAAGCAAA 59.027 37.500 0.00 0.00 33.96 3.68
2707 3374 6.143758 CGCAAGTTATGTTGTGTAAGCAAAAT 59.856 34.615 0.00 0.00 33.96 1.82
2709 3376 9.139174 GCAAGTTATGTTGTGTAAGCAAAATAT 57.861 29.630 0.00 0.00 31.03 1.28
2716 3383 8.346476 TGTTGTGTAAGCAAAATATTGACAAC 57.654 30.769 0.00 0.00 43.03 3.32
2717 3384 7.976175 TGTTGTGTAAGCAAAATATTGACAACA 59.024 29.630 15.75 15.75 46.17 3.33
2718 3385 8.977505 GTTGTGTAAGCAAAATATTGACAACAT 58.022 29.630 0.00 0.00 42.68 2.71
2719 3386 9.539825 TTGTGTAAGCAAAATATTGACAACATT 57.460 25.926 0.00 0.00 38.94 2.71
2720 3387 8.976471 TGTGTAAGCAAAATATTGACAACATTG 58.024 29.630 0.00 0.00 38.94 2.82
2721 3388 9.190858 GTGTAAGCAAAATATTGACAACATTGA 57.809 29.630 0.00 0.00 38.94 2.57
2722 3389 9.755804 TGTAAGCAAAATATTGACAACATTGAA 57.244 25.926 0.00 0.00 38.94 2.69
2726 3393 8.938906 AGCAAAATATTGACAACATTGAAATCC 58.061 29.630 0.00 0.00 38.94 3.01
2727 3394 8.177013 GCAAAATATTGACAACATTGAAATCCC 58.823 33.333 0.00 0.00 38.94 3.85
2728 3395 8.382130 CAAAATATTGACAACATTGAAATCCCG 58.618 33.333 0.00 0.00 38.94 5.14
2729 3396 6.773976 ATATTGACAACATTGAAATCCCGT 57.226 33.333 0.00 0.00 0.00 5.28
2730 3397 3.913548 TGACAACATTGAAATCCCGTG 57.086 42.857 0.00 0.00 0.00 4.94
2731 3398 3.218453 TGACAACATTGAAATCCCGTGT 58.782 40.909 0.00 0.00 0.00 4.49
2732 3399 3.252215 TGACAACATTGAAATCCCGTGTC 59.748 43.478 0.00 0.00 0.00 3.67
2733 3400 3.486383 ACAACATTGAAATCCCGTGTCT 58.514 40.909 0.00 0.00 0.00 3.41
2734 3401 4.647611 ACAACATTGAAATCCCGTGTCTA 58.352 39.130 0.00 0.00 0.00 2.59
2735 3402 5.067273 ACAACATTGAAATCCCGTGTCTAA 58.933 37.500 0.00 0.00 0.00 2.10
2736 3403 5.710099 ACAACATTGAAATCCCGTGTCTAAT 59.290 36.000 0.00 0.00 0.00 1.73
2737 3404 6.128007 ACAACATTGAAATCCCGTGTCTAATC 60.128 38.462 0.00 0.00 0.00 1.75
2738 3405 5.496556 ACATTGAAATCCCGTGTCTAATCA 58.503 37.500 0.00 0.00 0.00 2.57
2745 3412 0.245539 CCGTGTCTAATCACCCGTGT 59.754 55.000 0.00 0.00 35.18 4.49
2747 3414 2.094597 CCGTGTCTAATCACCCGTGTTA 60.095 50.000 0.00 0.00 35.18 2.41
2789 3456 7.601886 GCTTATACTAGTTGACATGCATCATCT 59.398 37.037 0.00 0.94 33.98 2.90
2795 3462 9.650539 ACTAGTTGACATGCATCATCTTATATC 57.349 33.333 0.00 0.00 32.25 1.63
2805 3472 8.266363 TGCATCATCTTATATCCATGCCTATA 57.734 34.615 0.00 0.00 36.59 1.31
2835 3502 7.365741 CAACAGATTGTGAAATCAGTTTAGCT 58.634 34.615 6.52 0.00 36.97 3.32
2839 3506 7.119699 CAGATTGTGAAATCAGTTTAGCTACCA 59.880 37.037 0.00 0.00 0.00 3.25
2855 3522 0.541863 ACCAGATACCGAGCCCAAAG 59.458 55.000 0.00 0.00 0.00 2.77
2866 3535 0.250901 AGCCCAAAGTCACGCAATCT 60.251 50.000 0.00 0.00 0.00 2.40
2884 3553 3.153369 TCTGAAGCCCAATAACAGCAA 57.847 42.857 0.00 0.00 0.00 3.91
2892 3561 3.510719 CCCAATAACAGCAATTTCACCG 58.489 45.455 0.00 0.00 0.00 4.94
2901 3570 2.095059 AGCAATTTCACCGTGATGAAGC 60.095 45.455 1.09 5.38 39.68 3.86
2902 3571 2.095059 GCAATTTCACCGTGATGAAGCT 60.095 45.455 1.09 0.00 39.68 3.74
2903 3572 3.751621 CAATTTCACCGTGATGAAGCTC 58.248 45.455 1.09 0.00 39.68 4.09
2904 3573 2.839486 TTTCACCGTGATGAAGCTCT 57.161 45.000 1.09 0.00 39.68 4.09
2905 3574 3.953712 TTTCACCGTGATGAAGCTCTA 57.046 42.857 1.09 0.00 39.68 2.43
2906 3575 3.510388 TTCACCGTGATGAAGCTCTAG 57.490 47.619 1.09 0.00 33.62 2.43
2907 3576 2.723273 TCACCGTGATGAAGCTCTAGA 58.277 47.619 0.00 0.00 0.00 2.43
2908 3577 3.291584 TCACCGTGATGAAGCTCTAGAT 58.708 45.455 0.00 0.00 0.00 1.98
2909 3578 3.316588 TCACCGTGATGAAGCTCTAGATC 59.683 47.826 0.00 0.00 0.00 2.75
2910 3579 2.292016 ACCGTGATGAAGCTCTAGATCG 59.708 50.000 0.00 0.00 0.00 3.69
2912 3581 3.243234 CCGTGATGAAGCTCTAGATCGTT 60.243 47.826 0.00 0.00 0.00 3.85
2917 3590 6.920758 GTGATGAAGCTCTAGATCGTTACATT 59.079 38.462 0.00 0.00 0.00 2.71
2950 3623 9.213777 TGTTAGAATATTATGGAACCTCTGACT 57.786 33.333 0.00 0.00 0.00 3.41
2966 3707 5.991606 CCTCTGACTGAATAAACACAAGTGA 59.008 40.000 7.28 0.00 0.00 3.41
2989 3731 4.061596 TGCAATACAACACACATCGAAGA 58.938 39.130 0.00 0.00 45.75 2.87
3006 3748 3.679639 CGAAGACATGGTCCACATCATCA 60.680 47.826 0.00 0.00 37.84 3.07
3012 3754 3.616956 TGGTCCACATCATCAACTCTC 57.383 47.619 0.00 0.00 0.00 3.20
3018 3760 6.351371 GGTCCACATCATCAACTCTCTTCTAA 60.351 42.308 0.00 0.00 0.00 2.10
3027 3770 9.035890 TCATCAACTCTCTTCTAAGACCAATAA 57.964 33.333 0.00 0.00 0.00 1.40
3034 3777 9.403583 CTCTCTTCTAAGACCAATAACTCTACT 57.596 37.037 0.00 0.00 0.00 2.57
3042 3785 7.106439 AGACCAATAACTCTACTGACTGATG 57.894 40.000 0.00 0.00 0.00 3.07
3076 3819 7.621428 AGTGAATCCTAATCAAACATCACTG 57.379 36.000 4.46 0.00 43.20 3.66
3079 3822 4.574674 TCCTAATCAAACATCACTGCCT 57.425 40.909 0.00 0.00 0.00 4.75
3081 3824 4.019411 TCCTAATCAAACATCACTGCCTGA 60.019 41.667 0.00 0.00 0.00 3.86
3094 3837 2.170166 CTGCCTGAGCCATTGGTAAAA 58.830 47.619 4.26 0.00 38.69 1.52
3146 3889 4.457496 CAGATCGCCCTGTGCCGT 62.457 66.667 0.00 0.00 36.24 5.68
3162 3905 0.456221 CCGTATGAGAACACCGAGCT 59.544 55.000 0.00 0.00 0.00 4.09
3163 3906 1.135083 CCGTATGAGAACACCGAGCTT 60.135 52.381 0.00 0.00 0.00 3.74
3164 3907 2.186076 CGTATGAGAACACCGAGCTTC 58.814 52.381 0.00 0.00 0.00 3.86
3169 3912 1.271102 GAGAACACCGAGCTTCTCAGT 59.729 52.381 6.06 0.00 41.41 3.41
3178 3921 2.473540 CGAGCTTCTCAGTTGCAAATCG 60.474 50.000 0.00 0.00 0.00 3.34
3216 3959 2.355108 CCGGAATGATGTGAGGAAGTGT 60.355 50.000 0.00 0.00 0.00 3.55
3252 3995 1.980772 GGCCAAGGCTGTTGCTGAT 60.981 57.895 11.40 0.00 41.60 2.90
3253 3996 1.214589 GCCAAGGCTGTTGCTGATG 59.785 57.895 3.29 0.00 39.59 3.07
3299 4042 1.698532 TGTTTAGGAGGTAACCGGCAA 59.301 47.619 0.00 0.00 34.73 4.52
3316 4059 0.881118 CAACACAACTGGAATCCGGG 59.119 55.000 13.43 1.70 33.40 5.73
3324 4067 0.462047 CTGGAATCCGGGGTCGAAAG 60.462 60.000 0.00 0.00 39.00 2.62
3329 4072 1.338136 ATCCGGGGTCGAAAGCTCAT 61.338 55.000 0.00 0.00 39.00 2.90
3349 4092 1.194781 GGTCCAAGGAGAGGCAGTCA 61.195 60.000 0.00 0.00 0.00 3.41
3379 4122 1.462670 GAAAGAACCTTGAGCAGCTCG 59.537 52.381 17.81 6.10 32.35 5.03
3394 4137 0.603569 GCTCGTCTGTTCCTTCCAGA 59.396 55.000 0.00 0.00 36.63 3.86
3409 4152 0.396435 CCAGACCACCACTTGCAGTA 59.604 55.000 0.00 0.00 0.00 2.74
3415 4158 1.599797 ACCACTTGCAGTAACGGCC 60.600 57.895 0.00 0.00 0.00 6.13
3429 4172 2.674754 GGCCTTGTCCCGGAATGA 59.325 61.111 0.73 0.00 0.00 2.57
3444 4187 0.909610 AATGAGGGCTCCGAGGTCAA 60.910 55.000 0.00 0.00 0.00 3.18
3445 4188 1.617947 ATGAGGGCTCCGAGGTCAAC 61.618 60.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.911769 TAGGTGGCTCTGTGAATGGG 59.088 55.000 0.00 0.00 0.00 4.00
180 194 1.336887 GGGAAGCTTTTCCTTTTCGGC 60.337 52.381 0.00 0.00 40.90 5.54
233 247 2.891191 TATTTTTCCCACTTCGCCCT 57.109 45.000 0.00 0.00 0.00 5.19
242 256 2.650322 GGAGGTGCGATATTTTTCCCA 58.350 47.619 0.00 0.00 0.00 4.37
243 257 1.954382 GGGAGGTGCGATATTTTTCCC 59.046 52.381 0.00 0.00 36.35 3.97
304 345 3.858868 GAAGCCGGCGATGCGGATA 62.859 63.158 23.20 0.00 0.00 2.59
360 401 0.620556 TCAATCAGGGGGAAGACTGC 59.379 55.000 0.00 0.00 34.76 4.40
366 407 0.106719 GCGGAATCAATCAGGGGGAA 60.107 55.000 0.00 0.00 0.00 3.97
390 432 2.357517 AGACCAGCCGCAAGAACG 60.358 61.111 0.00 0.00 43.02 3.95
468 510 1.571919 AGCGCCAAATCATCGTCTAC 58.428 50.000 2.29 0.00 0.00 2.59
486 528 2.510874 CTCAGTTGAGTTCTCGCGTAG 58.489 52.381 5.77 2.22 37.40 3.51
487 529 1.401148 GCTCAGTTGAGTTCTCGCGTA 60.401 52.381 5.77 0.00 43.85 4.42
607 657 6.224420 ACTTGACAGCACTAATTAACGAAC 57.776 37.500 0.00 0.00 0.00 3.95
619 669 3.318017 ACAAGATCGTACTTGACAGCAC 58.682 45.455 22.86 0.00 46.85 4.40
634 694 2.096819 ACGCGACAACAAACAACAAGAT 59.903 40.909 15.93 0.00 0.00 2.40
694 754 8.890718 CAGCTAATCATACTGAATATGGAATGG 58.109 37.037 0.00 0.00 41.10 3.16
699 759 8.890718 CCAATCAGCTAATCATACTGAATATGG 58.109 37.037 0.00 0.00 43.23 2.74
702 762 9.276590 CAACCAATCAGCTAATCATACTGAATA 57.723 33.333 0.00 0.00 43.23 1.75
710 770 5.301045 CACCATCAACCAATCAGCTAATCAT 59.699 40.000 0.00 0.00 0.00 2.45
725 807 2.093306 TCATCGTCACCACCATCAAC 57.907 50.000 0.00 0.00 0.00 3.18
732 814 2.076100 TCAGCATTTCATCGTCACCAC 58.924 47.619 0.00 0.00 0.00 4.16
734 816 2.094894 CACTCAGCATTTCATCGTCACC 59.905 50.000 0.00 0.00 0.00 4.02
748 830 1.892474 AGAACAGGACTCTCACTCAGC 59.108 52.381 0.00 0.00 0.00 4.26
760 849 3.812156 TTTCACACGAGAAGAACAGGA 57.188 42.857 0.00 0.00 0.00 3.86
762 851 5.718649 TCTTTTTCACACGAGAAGAACAG 57.281 39.130 0.00 0.00 0.00 3.16
803 892 1.135915 AGCTACCGCATTCAGAGTCAG 59.864 52.381 0.00 0.00 39.10 3.51
826 923 0.462759 GAACCAAGCTATGCTCGCCT 60.463 55.000 0.00 0.00 38.25 5.52
838 935 5.721232 CCAAGTAGTAGTACCAGAACCAAG 58.279 45.833 4.02 0.00 0.00 3.61
856 953 7.720957 TCACTGCATTATAATATTCTGCCAAGT 59.279 33.333 0.00 0.00 31.89 3.16
857 954 8.102800 TCACTGCATTATAATATTCTGCCAAG 57.897 34.615 0.00 0.00 31.89 3.61
858 955 8.462589 TTCACTGCATTATAATATTCTGCCAA 57.537 30.769 0.00 0.00 31.89 4.52
859 956 7.308770 GCTTCACTGCATTATAATATTCTGCCA 60.309 37.037 0.00 0.00 31.89 4.92
860 957 7.025963 GCTTCACTGCATTATAATATTCTGCC 58.974 38.462 0.00 0.00 31.89 4.85
889 986 5.064452 GTCTGTCATATCTCAAGCTTTGGTG 59.936 44.000 0.00 0.00 0.00 4.17
905 1002 7.448161 TGAAAATGAACCATAGTTGTCTGTCAT 59.552 33.333 0.00 0.00 35.94 3.06
938 1040 1.734465 AGCAAATGAGCGAACAGTAGC 59.266 47.619 0.00 0.00 40.15 3.58
947 1049 2.554142 TGGATACAGAGCAAATGAGCG 58.446 47.619 0.00 0.00 46.17 5.03
961 1063 1.003118 TCAGTGCCCACAACTGGATAC 59.997 52.381 3.91 0.00 40.55 2.24
962 1064 1.278985 CTCAGTGCCCACAACTGGATA 59.721 52.381 3.91 0.00 40.55 2.59
963 1065 0.037303 CTCAGTGCCCACAACTGGAT 59.963 55.000 3.91 0.00 40.55 3.41
964 1066 1.451504 CTCAGTGCCCACAACTGGA 59.548 57.895 3.91 0.00 40.55 3.86
965 1067 1.601759 CCTCAGTGCCCACAACTGG 60.602 63.158 3.91 0.00 37.29 4.00
966 1068 1.601759 CCCTCAGTGCCCACAACTG 60.602 63.158 0.82 0.00 0.00 3.16
983 1085 0.524862 CATGCCAGCACTTCAGTTCC 59.475 55.000 0.00 0.00 0.00 3.62
984 1086 0.524862 CCATGCCAGCACTTCAGTTC 59.475 55.000 0.00 0.00 0.00 3.01
985 1087 0.896940 CCCATGCCAGCACTTCAGTT 60.897 55.000 0.00 0.00 0.00 3.16
986 1088 1.303888 CCCATGCCAGCACTTCAGT 60.304 57.895 0.00 0.00 0.00 3.41
987 1089 1.001764 TCCCATGCCAGCACTTCAG 60.002 57.895 0.00 0.00 0.00 3.02
1037 1139 3.348554 TTCATGCCATGCGAGCCCT 62.349 57.895 0.00 0.00 0.00 5.19
1127 1229 8.292448 CGATTTTGGGGAACTTCATGATAATAG 58.708 37.037 0.00 0.00 0.00 1.73
1146 1248 1.394917 CTCAAGCCCTCGTCGATTTTG 59.605 52.381 0.00 0.00 0.00 2.44
1240 1342 7.707035 CGTTAGCTATGAACTTAGAAGGACAAT 59.293 37.037 0.00 0.00 0.00 2.71
1241 1343 7.033791 CGTTAGCTATGAACTTAGAAGGACAA 58.966 38.462 0.00 0.00 0.00 3.18
1264 1366 5.734720 AGTAGGATGATTGTCACAATTCGT 58.265 37.500 4.04 3.74 0.00 3.85
1297 1399 6.226787 CGCTCCTCCTTCATTATAACTTCAT 58.773 40.000 0.00 0.00 0.00 2.57
1328 1431 7.605449 ACAAGGGTTCAGATATCAACAATTTG 58.395 34.615 5.32 9.17 0.00 2.32
1344 1447 7.039313 AGAACAATAAGTGAAACAAGGGTTC 57.961 36.000 0.00 0.00 41.43 3.62
1345 1448 7.093509 ACAAGAACAATAAGTGAAACAAGGGTT 60.094 33.333 0.00 0.00 41.43 4.11
1346 1449 6.379988 ACAAGAACAATAAGTGAAACAAGGGT 59.620 34.615 0.00 0.00 41.43 4.34
1347 1450 6.805713 ACAAGAACAATAAGTGAAACAAGGG 58.194 36.000 0.00 0.00 41.43 3.95
1348 1451 7.479980 TGACAAGAACAATAAGTGAAACAAGG 58.520 34.615 0.00 0.00 41.43 3.61
1362 1465 6.653320 ACTCAACAGTTTACTGACAAGAACAA 59.347 34.615 16.31 0.00 46.59 2.83
1363 1466 6.170506 ACTCAACAGTTTACTGACAAGAACA 58.829 36.000 16.31 0.00 46.59 3.18
1364 1467 6.663944 ACTCAACAGTTTACTGACAAGAAC 57.336 37.500 16.31 0.00 46.59 3.01
1365 1468 6.876789 TGAACTCAACAGTTTACTGACAAGAA 59.123 34.615 16.31 1.09 46.59 2.52
1366 1469 6.403049 TGAACTCAACAGTTTACTGACAAGA 58.597 36.000 16.31 7.31 46.59 3.02
1367 1470 6.662414 TGAACTCAACAGTTTACTGACAAG 57.338 37.500 16.31 11.25 46.59 3.16
1368 1471 6.653320 ACTTGAACTCAACAGTTTACTGACAA 59.347 34.615 16.31 9.00 46.59 3.18
1369 1472 6.092122 CACTTGAACTCAACAGTTTACTGACA 59.908 38.462 16.31 0.00 46.59 3.58
1370 1473 6.312918 TCACTTGAACTCAACAGTTTACTGAC 59.687 38.462 16.31 0.84 46.59 3.51
1371 1474 6.403049 TCACTTGAACTCAACAGTTTACTGA 58.597 36.000 16.31 0.00 46.59 3.41
1372 1475 6.662414 TCACTTGAACTCAACAGTTTACTG 57.338 37.500 8.29 8.29 43.37 2.74
1373 1476 6.823689 ACATCACTTGAACTCAACAGTTTACT 59.176 34.615 0.00 0.00 43.37 2.24
1374 1477 7.016361 ACATCACTTGAACTCAACAGTTTAC 57.984 36.000 0.00 0.00 43.37 2.01
1412 1515 4.557205 CAGTATTCTTCCGCATAGGTACC 58.443 47.826 2.73 2.73 41.99 3.34
1415 1518 2.434336 TGCAGTATTCTTCCGCATAGGT 59.566 45.455 0.00 0.00 41.99 3.08
1431 1534 8.076178 GTCAGTTAATATTTGTCAAAGTGCAGT 58.924 33.333 4.03 0.00 0.00 4.40
1492 1595 7.378728 GGATCTGTTAGTTACACAAAAAGCAAC 59.621 37.037 0.00 0.00 32.10 4.17
1520 1623 3.070446 TGAGAAAGGTCGGAAGCAAGTTA 59.930 43.478 0.00 0.00 0.00 2.24
1528 1631 3.832490 TCTTCATCTGAGAAAGGTCGGAA 59.168 43.478 0.00 0.00 35.44 4.30
1532 1635 5.738909 TGGAATCTTCATCTGAGAAAGGTC 58.261 41.667 0.00 0.00 0.00 3.85
1585 1688 6.453092 AGATTTCCAGCTTCTGAAAACAATG 58.547 36.000 6.85 0.00 32.44 2.82
1590 1693 6.491062 TGAATGAGATTTCCAGCTTCTGAAAA 59.509 34.615 6.85 0.00 32.44 2.29
1627 1733 1.202121 GCAAGCTTCAAAGAGATCGCC 60.202 52.381 0.00 0.00 0.00 5.54
1629 1735 1.995484 TCGCAAGCTTCAAAGAGATCG 59.005 47.619 0.00 0.00 37.18 3.69
1644 1750 5.048782 GCCCATATCTTCATTTATGTCGCAA 60.049 40.000 0.00 0.00 0.00 4.85
1813 1919 9.827411 GAAGTTTGTGAATACCATCTAAGAAAC 57.173 33.333 0.00 0.00 0.00 2.78
1860 1966 7.979537 ACTCTTGCATAATTAATGTACGAGACA 59.020 33.333 13.67 0.00 44.32 3.41
1908 2014 7.182026 TCCTAATCCCATCTTTGTCTTCTGTTA 59.818 37.037 0.00 0.00 0.00 2.41
2009 2116 5.830000 TTGCTTGAATCATCTCATCCTTG 57.170 39.130 0.00 0.00 0.00 3.61
2091 2198 7.913674 AGTCATTTTATGAACTGGAGAACTC 57.086 36.000 0.00 0.00 41.69 3.01
2097 2204 7.124901 AGAGAGCTAGTCATTTTATGAACTGGA 59.875 37.037 0.00 0.00 41.69 3.86
2099 2206 9.809096 TTAGAGAGCTAGTCATTTTATGAACTG 57.191 33.333 0.00 0.00 41.69 3.16
2146 2804 2.366590 TCATGAGTGCAGAGTCAACAGT 59.633 45.455 0.00 0.00 35.11 3.55
2147 2805 2.994578 CTCATGAGTGCAGAGTCAACAG 59.005 50.000 14.95 0.00 35.11 3.16
2148 2806 2.366590 ACTCATGAGTGCAGAGTCAACA 59.633 45.455 27.37 0.00 38.13 3.33
2158 2817 2.575694 AGATGACGACTCATGAGTGC 57.424 50.000 32.50 20.86 42.66 4.40
2207 2866 1.518056 CGGTGGCAGTGTCAAGCATT 61.518 55.000 0.00 0.00 0.00 3.56
2222 2881 1.227263 CTACATTCGGAGGGCGGTG 60.227 63.158 0.00 0.00 0.00 4.94
2226 2891 1.041437 AGTAGCTACATTCGGAGGGC 58.959 55.000 25.28 0.00 0.00 5.19
2232 2897 4.504461 GGTGACATCAAGTAGCTACATTCG 59.496 45.833 25.28 11.80 0.00 3.34
2257 2922 2.284263 TCACAGATGATGCTGTCGAC 57.716 50.000 9.11 9.11 45.54 4.20
2259 2924 2.340337 TGTTCACAGATGATGCTGTCG 58.660 47.619 0.00 0.00 45.54 4.35
2343 3008 6.715718 ACTTCTAGTCTAGACTAACAGTGCAA 59.284 38.462 27.78 13.93 42.72 4.08
2361 3026 8.943909 AGTTACCGGATAAAATGAACTTCTAG 57.056 34.615 9.46 0.00 0.00 2.43
2363 3028 9.159364 GTTAGTTACCGGATAAAATGAACTTCT 57.841 33.333 9.46 0.00 0.00 2.85
2364 3029 8.112449 CGTTAGTTACCGGATAAAATGAACTTC 58.888 37.037 9.46 1.68 0.00 3.01
2365 3030 7.603784 ACGTTAGTTACCGGATAAAATGAACTT 59.396 33.333 9.46 0.00 0.00 2.66
2366 3031 7.099120 ACGTTAGTTACCGGATAAAATGAACT 58.901 34.615 9.46 6.72 0.00 3.01
2367 3032 7.294676 ACGTTAGTTACCGGATAAAATGAAC 57.705 36.000 9.46 0.83 0.00 3.18
2371 3036 9.860898 GGATATACGTTAGTTACCGGATAAAAT 57.139 33.333 9.46 0.81 33.87 1.82
2373 3038 8.402798 TGGATATACGTTAGTTACCGGATAAA 57.597 34.615 9.46 0.00 33.87 1.40
2378 3043 7.951530 AAAATGGATATACGTTAGTTACCGG 57.048 36.000 0.00 0.00 0.00 5.28
2466 3131 0.877071 AGCGAGTGAATGCAAACAGG 59.123 50.000 0.00 0.00 0.00 4.00
2496 3161 1.011968 CGTCGTCCTCATTTTCGCCA 61.012 55.000 0.00 0.00 0.00 5.69
2505 3170 2.731027 CGTTCATTCATCGTCGTCCTCA 60.731 50.000 0.00 0.00 0.00 3.86
2589 3256 4.433615 ACATGCCGAGTCACTATTAACAG 58.566 43.478 0.00 0.00 0.00 3.16
2591 3258 4.270325 GGAACATGCCGAGTCACTATTAAC 59.730 45.833 0.00 0.00 0.00 2.01
2593 3260 3.449377 TGGAACATGCCGAGTCACTATTA 59.551 43.478 0.00 0.00 0.00 0.98
2594 3261 2.236146 TGGAACATGCCGAGTCACTATT 59.764 45.455 0.00 0.00 0.00 1.73
2595 3262 1.831106 TGGAACATGCCGAGTCACTAT 59.169 47.619 0.00 0.00 0.00 2.12
2597 3264 0.396435 TTGGAACATGCCGAGTCACT 59.604 50.000 0.00 0.00 39.30 3.41
2598 3265 1.234821 TTTGGAACATGCCGAGTCAC 58.765 50.000 0.00 0.00 39.30 3.67
2599 3266 2.198827 ATTTGGAACATGCCGAGTCA 57.801 45.000 0.00 0.00 39.30 3.41
2600 3267 3.531538 TCTATTTGGAACATGCCGAGTC 58.468 45.455 0.00 0.00 39.30 3.36
2601 3268 3.627395 TCTATTTGGAACATGCCGAGT 57.373 42.857 0.00 0.00 39.30 4.18
2602 3269 4.576053 TCATTCTATTTGGAACATGCCGAG 59.424 41.667 0.00 0.00 39.30 4.63
2603 3270 4.335315 GTCATTCTATTTGGAACATGCCGA 59.665 41.667 0.00 0.00 39.30 5.54
2604 3271 4.336433 AGTCATTCTATTTGGAACATGCCG 59.664 41.667 0.00 0.00 39.30 5.69
2605 3272 5.357878 TCAGTCATTCTATTTGGAACATGCC 59.642 40.000 0.00 0.00 39.30 4.40
2606 3273 6.127925 TGTCAGTCATTCTATTTGGAACATGC 60.128 38.462 0.00 0.00 39.30 4.06
2607 3274 7.381766 TGTCAGTCATTCTATTTGGAACATG 57.618 36.000 0.00 0.00 39.30 3.21
2608 3275 7.613022 ACATGTCAGTCATTCTATTTGGAACAT 59.387 33.333 0.00 0.00 33.83 2.71
2609 3276 6.942005 ACATGTCAGTCATTCTATTTGGAACA 59.058 34.615 0.00 0.00 34.09 3.18
2610 3277 7.335422 AGACATGTCAGTCATTCTATTTGGAAC 59.665 37.037 27.02 0.00 40.98 3.62
2611 3278 7.335171 CAGACATGTCAGTCATTCTATTTGGAA 59.665 37.037 27.02 0.00 40.98 3.53
2612 3279 6.820152 CAGACATGTCAGTCATTCTATTTGGA 59.180 38.462 27.02 0.00 40.98 3.53
2613 3280 6.820152 TCAGACATGTCAGTCATTCTATTTGG 59.180 38.462 27.02 0.00 40.98 3.28
2614 3281 7.838771 TCAGACATGTCAGTCATTCTATTTG 57.161 36.000 27.02 11.82 40.98 2.32
2615 3282 7.879677 TGTTCAGACATGTCAGTCATTCTATTT 59.120 33.333 27.02 0.00 40.98 1.40
2651 3318 2.555199 GAAGCAGTCACAGACACTGTT 58.445 47.619 1.46 0.00 42.59 3.16
2679 3346 2.686558 ACACAACATAACTTGCGCAG 57.313 45.000 11.31 7.81 0.00 5.18
2683 3350 6.820470 TTTTGCTTACACAACATAACTTGC 57.180 33.333 0.00 0.00 0.00 4.01
2700 3367 8.938906 GGATTTCAATGTTGTCAATATTTTGCT 58.061 29.630 4.91 0.00 32.61 3.91
2701 3368 8.177013 GGGATTTCAATGTTGTCAATATTTTGC 58.823 33.333 4.91 0.00 32.61 3.68
2702 3369 8.382130 CGGGATTTCAATGTTGTCAATATTTTG 58.618 33.333 4.91 0.00 0.00 2.44
2705 3372 7.035004 CACGGGATTTCAATGTTGTCAATATT 58.965 34.615 1.95 1.95 0.00 1.28
2707 3374 5.475220 ACACGGGATTTCAATGTTGTCAATA 59.525 36.000 0.00 0.00 0.00 1.90
2709 3376 3.634448 ACACGGGATTTCAATGTTGTCAA 59.366 39.130 0.00 0.00 0.00 3.18
2710 3377 3.218453 ACACGGGATTTCAATGTTGTCA 58.782 40.909 0.00 0.00 0.00 3.58
2711 3378 3.502211 AGACACGGGATTTCAATGTTGTC 59.498 43.478 0.00 0.00 0.00 3.18
2712 3379 3.486383 AGACACGGGATTTCAATGTTGT 58.514 40.909 0.00 0.00 0.00 3.32
2713 3380 5.621197 TTAGACACGGGATTTCAATGTTG 57.379 39.130 0.00 0.00 0.00 3.33
2714 3381 5.943416 TGATTAGACACGGGATTTCAATGTT 59.057 36.000 0.00 0.00 0.00 2.71
2715 3382 5.354234 GTGATTAGACACGGGATTTCAATGT 59.646 40.000 0.00 0.00 0.00 2.71
2716 3383 5.220854 GGTGATTAGACACGGGATTTCAATG 60.221 44.000 0.00 0.00 41.12 2.82
2717 3384 4.881850 GGTGATTAGACACGGGATTTCAAT 59.118 41.667 0.00 0.00 41.12 2.57
2718 3385 4.258543 GGTGATTAGACACGGGATTTCAA 58.741 43.478 0.00 0.00 41.12 2.69
2719 3386 3.370103 GGGTGATTAGACACGGGATTTCA 60.370 47.826 0.00 0.00 41.12 2.69
2720 3387 3.203716 GGGTGATTAGACACGGGATTTC 58.796 50.000 0.00 0.00 41.12 2.17
2721 3388 2.419574 CGGGTGATTAGACACGGGATTT 60.420 50.000 0.00 0.00 39.16 2.17
2722 3389 1.138266 CGGGTGATTAGACACGGGATT 59.862 52.381 0.00 0.00 39.16 3.01
2723 3390 0.750850 CGGGTGATTAGACACGGGAT 59.249 55.000 0.00 0.00 39.16 3.85
2724 3391 2.195389 CGGGTGATTAGACACGGGA 58.805 57.895 0.00 0.00 39.16 5.14
2725 3392 4.827481 CGGGTGATTAGACACGGG 57.173 61.111 0.00 0.00 39.16 5.28
2728 3395 6.072893 ACAAATTAACACGGGTGATTAGACAC 60.073 38.462 5.71 0.00 39.70 3.67
2729 3396 5.998981 ACAAATTAACACGGGTGATTAGACA 59.001 36.000 5.71 0.00 0.00 3.41
2730 3397 6.490566 ACAAATTAACACGGGTGATTAGAC 57.509 37.500 5.71 0.00 0.00 2.59
2731 3398 6.938030 AGAACAAATTAACACGGGTGATTAGA 59.062 34.615 5.71 0.00 0.00 2.10
2732 3399 7.141100 AGAACAAATTAACACGGGTGATTAG 57.859 36.000 5.71 0.00 0.00 1.73
2733 3400 7.364200 CAAGAACAAATTAACACGGGTGATTA 58.636 34.615 5.71 0.00 0.00 1.75
2734 3401 6.212955 CAAGAACAAATTAACACGGGTGATT 58.787 36.000 5.71 0.00 0.00 2.57
2735 3402 5.768317 CAAGAACAAATTAACACGGGTGAT 58.232 37.500 5.71 0.00 0.00 3.06
2736 3403 4.498345 GCAAGAACAAATTAACACGGGTGA 60.498 41.667 5.71 0.00 0.00 4.02
2737 3404 3.733727 GCAAGAACAAATTAACACGGGTG 59.266 43.478 0.00 0.00 0.00 4.61
2738 3405 3.549221 CGCAAGAACAAATTAACACGGGT 60.549 43.478 0.00 0.00 43.02 5.28
2745 3412 9.158233 AGTATAAGCTACGCAAGAACAAATTAA 57.842 29.630 0.00 0.00 43.62 1.40
2747 3414 7.611213 AGTATAAGCTACGCAAGAACAAATT 57.389 32.000 0.00 0.00 43.62 1.82
2772 3439 7.455891 TGGATATAAGATGATGCATGTCAACT 58.544 34.615 2.46 0.00 33.29 3.16
2781 3448 9.736414 AATATAGGCATGGATATAAGATGATGC 57.264 33.333 0.00 0.00 36.33 3.91
2789 3456 9.671279 CTGTTGTCAATATAGGCATGGATATAA 57.329 33.333 0.00 0.00 0.00 0.98
2795 3462 6.263842 ACAATCTGTTGTCAATATAGGCATGG 59.736 38.462 0.00 0.00 45.14 3.66
2805 3472 7.281040 ACTGATTTCACAATCTGTTGTCAAT 57.719 32.000 2.59 0.00 45.14 2.57
2833 3500 1.113517 TGGGCTCGGTATCTGGTAGC 61.114 60.000 0.00 0.00 0.00 3.58
2835 3502 1.760613 CTTTGGGCTCGGTATCTGGTA 59.239 52.381 0.00 0.00 0.00 3.25
2839 3506 1.207329 GTGACTTTGGGCTCGGTATCT 59.793 52.381 0.00 0.00 0.00 1.98
2855 3522 0.955428 TGGGCTTCAGATTGCGTGAC 60.955 55.000 0.00 0.00 0.00 3.67
2866 3535 4.282957 TGAAATTGCTGTTATTGGGCTTCA 59.717 37.500 0.00 0.00 0.00 3.02
2884 3553 3.340814 AGAGCTTCATCACGGTGAAAT 57.659 42.857 15.72 0.00 37.63 2.17
2892 3561 5.822278 TGTAACGATCTAGAGCTTCATCAC 58.178 41.667 6.41 0.00 0.00 3.06
2901 3570 9.737427 AACAGATTGTAATGTAACGATCTAGAG 57.263 33.333 0.00 0.00 45.10 2.43
2934 3607 7.606456 GTGTTTATTCAGTCAGAGGTTCCATAA 59.394 37.037 0.00 0.00 0.00 1.90
2935 3608 7.103641 GTGTTTATTCAGTCAGAGGTTCCATA 58.896 38.462 0.00 0.00 0.00 2.74
2941 3614 5.760253 CACTTGTGTTTATTCAGTCAGAGGT 59.240 40.000 0.00 0.00 0.00 3.85
2950 3623 7.880105 TGTATTGCATCACTTGTGTTTATTCA 58.120 30.769 0.46 0.00 0.00 2.57
2966 3707 4.694982 TCTTCGATGTGTGTTGTATTGCAT 59.305 37.500 0.00 0.00 0.00 3.96
2989 3731 3.265221 AGAGTTGATGATGTGGACCATGT 59.735 43.478 0.00 0.00 32.56 3.21
3006 3748 8.658840 AGAGTTATTGGTCTTAGAAGAGAGTT 57.341 34.615 0.00 0.00 35.32 3.01
3012 3754 8.962679 AGTCAGTAGAGTTATTGGTCTTAGAAG 58.037 37.037 0.00 0.00 0.00 2.85
3018 3760 6.097554 CCATCAGTCAGTAGAGTTATTGGTCT 59.902 42.308 0.00 0.00 0.00 3.85
3027 3770 6.191315 AGTTGTATCCATCAGTCAGTAGAGT 58.809 40.000 0.00 0.00 0.00 3.24
3034 3777 6.850752 TTCACTAGTTGTATCCATCAGTCA 57.149 37.500 0.00 0.00 0.00 3.41
3049 3792 8.543774 AGTGATGTTTGATTAGGATTCACTAGT 58.456 33.333 0.00 0.00 40.39 2.57
3054 3797 5.357878 GGCAGTGATGTTTGATTAGGATTCA 59.642 40.000 0.00 0.00 0.00 2.57
3058 3801 4.019411 TCAGGCAGTGATGTTTGATTAGGA 60.019 41.667 0.00 0.00 0.00 2.94
3076 3819 1.204704 GGTTTTACCAATGGCTCAGGC 59.795 52.381 0.00 0.00 38.42 4.85
3094 3837 0.994247 TGGATGCCAGTGAAGATGGT 59.006 50.000 0.00 0.00 40.17 3.55
3114 3857 2.650813 ATCTGGTTCATCGGCGGCTC 62.651 60.000 7.21 0.00 0.00 4.70
3146 3889 3.784701 GAGAAGCTCGGTGTTCTCATA 57.215 47.619 13.43 0.00 45.45 2.15
3162 3905 2.552315 GGTTCCGATTTGCAACTGAGAA 59.448 45.455 0.00 0.00 0.00 2.87
3163 3906 2.151202 GGTTCCGATTTGCAACTGAGA 58.849 47.619 0.00 0.00 0.00 3.27
3164 3907 1.200020 GGGTTCCGATTTGCAACTGAG 59.800 52.381 0.00 0.00 0.00 3.35
3178 3921 2.490685 GAGTCGAGCTCGGGTTCC 59.509 66.667 33.98 17.17 40.29 3.62
3193 3936 2.169352 ACTTCCTCACATCATTCCGGAG 59.831 50.000 3.34 0.00 0.00 4.63
3216 3959 0.878523 CCACGGAAACAGCGAGTTCA 60.879 55.000 0.00 0.00 40.26 3.18
3255 3998 1.767681 CCAGAGATAGCAAGAGGGCTT 59.232 52.381 0.00 0.00 42.71 4.35
3299 4042 1.378762 CCCCGGATTCCAGTTGTGT 59.621 57.895 0.73 0.00 0.00 3.72
3316 4059 0.036388 TGGACCATGAGCTTTCGACC 60.036 55.000 0.00 0.00 0.00 4.79
3324 4067 0.179936 CCTCTCCTTGGACCATGAGC 59.820 60.000 14.05 0.00 0.00 4.26
3329 4072 1.152030 ACTGCCTCTCCTTGGACCA 60.152 57.895 0.00 0.00 0.00 4.02
3349 4092 5.182760 GCTCAAGGTTCTTTCTTCACATGAT 59.817 40.000 0.00 0.00 0.00 2.45
3409 4152 2.902457 ATTCCGGGACAAGGCCGTT 61.902 57.895 0.00 0.00 0.00 4.44
3415 4158 1.452108 GCCCTCATTCCGGGACAAG 60.452 63.158 0.00 0.00 44.90 3.16
3429 4172 2.203788 TGTTGACCTCGGAGCCCT 60.204 61.111 0.00 0.00 0.00 5.19
3436 4179 1.004918 GACCCCAGTGTTGACCTCG 60.005 63.158 0.00 0.00 0.00 4.63
3444 4187 2.607750 AGCCATCGACCCCAGTGT 60.608 61.111 0.00 0.00 0.00 3.55
3445 4188 2.187946 GAGCCATCGACCCCAGTG 59.812 66.667 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.