Multiple sequence alignment - TraesCS2B01G273200

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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 TraesCS2B01G273200 chr2B 100.000 4830 0 0 1 4830 374267778 374262949 0.000000e+00 8920.0
1 TraesCS2B01G273200 chr2B 84.810 79 9 2 1565 1640 47534648 47534570 5.180000e-10 76.8
2 TraesCS2B01G273200 chr2D 95.245 3239 88 19 1639 4830 306347968 306344749 0.000000e+00 5068.0
3 TraesCS2B01G273200 chr2D 86.483 1598 141 35 1 1566 306349521 306347967 0.000000e+00 1685.0
4 TraesCS2B01G273200 chr2D 80.934 257 45 4 97 349 360045157 360045413 2.950000e-47 200.0
5 TraesCS2B01G273200 chr2A 94.070 2226 84 19 2625 4830 385451363 385449166 0.000000e+00 3336.0
6 TraesCS2B01G273200 chr2A 91.615 966 34 14 1639 2591 385452287 385451356 0.000000e+00 1291.0
7 TraesCS2B01G273200 chr2A 92.825 446 20 3 1123 1566 385452721 385452286 1.900000e-178 636.0
8 TraesCS2B01G273200 chr7B 84.188 234 28 9 137 364 357649514 357649284 8.140000e-53 219.0
9 TraesCS2B01G273200 chr7B 94.737 38 0 2 1553 1590 663402225 663402260 1.880000e-04 58.4
10 TraesCS2B01G273200 chr7D 83.556 225 28 9 146 364 310987765 310987544 8.200000e-48 202.0
11 TraesCS2B01G273200 chr1A 82.278 79 13 1 1563 1641 530602367 530602290 3.120000e-07 67.6
12 TraesCS2B01G273200 chr4A 81.319 91 6 2 1560 1640 679672781 679672692 4.040000e-06 63.9
13 TraesCS2B01G273200 chr5B 80.220 91 6 7 1562 1641 77644626 77644715 1.880000e-04 58.4
14 TraesCS2B01G273200 chr5B 100.000 31 0 0 1561 1591 386559271 386559241 1.880000e-04 58.4
15 TraesCS2B01G273200 chr6D 100.000 30 0 0 1561 1590 324817545 324817574 6.750000e-04 56.5
16 TraesCS2B01G273200 chr7A 86.275 51 5 2 1563 1612 162041809 162041858 2.000000e-03 54.7
17 TraesCS2B01G273200 chr6A 86.000 50 5 2 1563 1611 473616619 473616571 9.000000e-03 52.8


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 TraesCS2B01G273200 chr2B 374262949 374267778 4829 True 8920.000000 8920 100.000000 1 4830 1 chr2B.!!$R2 4829
1 TraesCS2B01G273200 chr2D 306344749 306349521 4772 True 3376.500000 5068 90.864000 1 4830 2 chr2D.!!$R1 4829
2 TraesCS2B01G273200 chr2A 385449166 385452721 3555 True 1754.333333 3336 92.836667 1123 4830 3 chr2A.!!$R1 3707

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
998 1042 0.030235 GGTCCAAACGCCAGTTTCAC 59.970 55.0 0.00 0.0 46.73 3.18 F
1697 1758 0.181587 TTGCTGGTCACTTTCCCGAA 59.818 50.0 0.00 0.0 0.00 4.30 F
3434 3542 0.538287 AACCTGAAGGCTTGGCTGAC 60.538 55.0 3.46 0.0 39.32 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1800 1861 0.037447 AAGCAAAGGAGGGACAGAGC 59.963 55.0 0.0 0.0 0.00 4.09 R
3623 3731 1.160137 AGAAGAAATGCTCACGCCAC 58.840 50.0 0.0 0.0 34.43 5.01 R
4426 4537 0.905357 CCCCCTCGTTCAAGTCTGAT 59.095 55.0 0.0 0.0 0.00 2.90 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
74 75 1.407989 GGAGTTCAAGGCCTCCATCAG 60.408 57.143 5.23 0.00 45.47 2.90
117 118 4.676799 TCAAGACCTCCTCTTCCTCTTA 57.323 45.455 0.00 0.00 37.08 2.10
134 135 4.889995 CCTCTTATGAATTTGGGGAAGACC 59.110 45.833 0.00 0.00 39.11 3.85
135 136 5.509498 CTCTTATGAATTTGGGGAAGACCA 58.491 41.667 0.00 0.00 42.91 4.02
153 154 4.407296 AGACCACATCCAAGACCTTATCTC 59.593 45.833 0.00 0.00 36.27 2.75
162 163 4.547671 CAAGACCTTATCTCCCTAGTGGA 58.452 47.826 0.71 0.71 42.41 4.02
165 168 5.793967 AGACCTTATCTCCCTAGTGGATTT 58.206 41.667 0.98 0.00 44.07 2.17
197 200 8.272659 ACTTACCCTAATACTTATTCCCCTTC 57.727 38.462 0.00 0.00 0.00 3.46
222 225 4.578516 TGTTTGTGGATCTTGTGGTACTTG 59.421 41.667 0.00 0.00 0.00 3.16
223 226 4.431416 TTGTGGATCTTGTGGTACTTGT 57.569 40.909 0.00 0.00 0.00 3.16
267 270 5.637809 CATGTGTGATTGGATCTTGTCTTG 58.362 41.667 0.00 0.00 0.00 3.02
268 271 4.971939 TGTGTGATTGGATCTTGTCTTGA 58.028 39.130 0.00 0.00 0.00 3.02
282 285 2.092429 TGTCTTGAAGTGCTTGTTCCCT 60.092 45.455 0.00 0.00 0.00 4.20
286 289 1.408702 TGAAGTGCTTGTTCCCTTTGC 59.591 47.619 0.00 0.00 0.00 3.68
305 308 1.069636 GCGCTCTTGTTTGTTCCTCTG 60.070 52.381 0.00 0.00 0.00 3.35
306 309 2.483876 CGCTCTTGTTTGTTCCTCTGA 58.516 47.619 0.00 0.00 0.00 3.27
307 310 3.070018 CGCTCTTGTTTGTTCCTCTGAT 58.930 45.455 0.00 0.00 0.00 2.90
308 311 3.124297 CGCTCTTGTTTGTTCCTCTGATC 59.876 47.826 0.00 0.00 0.00 2.92
309 312 4.322567 GCTCTTGTTTGTTCCTCTGATCT 58.677 43.478 0.00 0.00 0.00 2.75
320 324 5.362143 TGTTCCTCTGATCTATCTCCAAGTG 59.638 44.000 0.00 0.00 0.00 3.16
332 336 3.754965 TCTCCAAGTGTGAAAGATTGGG 58.245 45.455 3.19 0.00 42.05 4.12
335 339 1.962807 CAAGTGTGAAAGATTGGGCCA 59.037 47.619 0.00 0.00 0.00 5.36
337 341 1.145738 AGTGTGAAAGATTGGGCCACT 59.854 47.619 5.23 0.00 0.00 4.00
342 346 2.039216 TGAAAGATTGGGCCACTTACGA 59.961 45.455 5.23 0.00 0.00 3.43
350 354 0.605589 GGCCACTTACGACTTTGCCT 60.606 55.000 0.00 0.00 34.61 4.75
357 361 4.688879 CACTTACGACTTTGCCTTACATCA 59.311 41.667 0.00 0.00 0.00 3.07
358 362 5.351465 CACTTACGACTTTGCCTTACATCAT 59.649 40.000 0.00 0.00 0.00 2.45
359 363 6.533723 CACTTACGACTTTGCCTTACATCATA 59.466 38.462 0.00 0.00 0.00 2.15
402 406 3.283684 CAACGAGGGCGCAACCAA 61.284 61.111 10.83 0.00 42.05 3.67
411 415 4.389576 CGCAACCAAGCCACGCTC 62.390 66.667 0.00 0.00 38.25 5.03
444 448 0.030773 TCGATCACGAGCCACATAGC 59.969 55.000 0.00 0.00 43.81 2.97
470 474 1.676529 ACTCCTCATCGGTATGTGTCG 59.323 52.381 0.00 0.00 34.50 4.35
475 479 0.385751 CATCGGTATGTGTCGCCTCT 59.614 55.000 0.00 0.00 0.00 3.69
480 484 1.469940 GGTATGTGTCGCCTCTGTGAG 60.470 57.143 0.00 0.00 0.00 3.51
510 514 2.244651 GCTGCTGTTGGTCGTCGTT 61.245 57.895 0.00 0.00 0.00 3.85
511 515 1.853319 CTGCTGTTGGTCGTCGTTC 59.147 57.895 0.00 0.00 0.00 3.95
520 524 3.347168 TCGTCGTTCGAGGAGCAA 58.653 55.556 12.41 0.00 44.01 3.91
530 534 1.073897 GAGGAGCAAAGCACCACCT 59.926 57.895 8.14 0.00 41.64 4.00
537 541 0.111253 CAAAGCACCACCTCCTCCTT 59.889 55.000 0.00 0.00 0.00 3.36
544 548 0.461961 CCACCTCCTCCTTCATCGAC 59.538 60.000 0.00 0.00 0.00 4.20
549 553 1.066908 CTCCTCCTTCATCGACAGAGC 59.933 57.143 0.00 0.00 0.00 4.09
567 571 2.446848 CGGTGGAGGATGATGGCCT 61.447 63.158 3.32 0.00 38.81 5.19
568 572 1.925888 GGTGGAGGATGATGGCCTT 59.074 57.895 3.32 0.00 35.44 4.35
570 574 0.548031 GTGGAGGATGATGGCCTTGA 59.452 55.000 3.32 0.00 35.44 3.02
574 578 2.107901 GGAGGATGATGGCCTTGAAGAT 59.892 50.000 3.32 0.00 35.44 2.40
577 581 2.486191 GGATGATGGCCTTGAAGATCGT 60.486 50.000 3.32 0.00 0.00 3.73
583 587 1.696832 GCCTTGAAGATCGTGGACGC 61.697 60.000 0.00 0.00 39.60 5.19
585 589 0.456142 CTTGAAGATCGTGGACGCGA 60.456 55.000 15.93 10.54 45.32 5.87
592 596 2.279186 CGTGGACGCGATGCCATA 60.279 61.111 15.93 0.00 36.41 2.74
617 621 0.106967 GAGCTCCCTTTGGATCCACC 60.107 60.000 15.91 0.00 40.80 4.61
618 622 1.076705 GCTCCCTTTGGATCCACCC 60.077 63.158 15.91 0.00 40.80 4.61
622 626 1.449601 CCTTTGGATCCACCCGTCG 60.450 63.158 15.91 0.00 38.00 5.12
645 649 0.895530 CCGAGAACTAGCCCTTGTCA 59.104 55.000 0.00 0.00 0.00 3.58
684 716 0.256464 GGTCGAGGAGAGGAGAGGAA 59.744 60.000 0.00 0.00 0.00 3.36
686 718 2.021457 GTCGAGGAGAGGAGAGGAAAG 58.979 57.143 0.00 0.00 0.00 2.62
691 723 2.244769 AGGAGAGGAGAGGAAAGGAGAG 59.755 54.545 0.00 0.00 0.00 3.20
692 724 2.666317 GAGAGGAGAGGAAAGGAGAGG 58.334 57.143 0.00 0.00 0.00 3.69
702 734 0.325671 AAAGGAGAGGCGAGGATGGA 60.326 55.000 0.00 0.00 0.00 3.41
711 743 1.945354 GCGAGGATGGAGTTGGTCGA 61.945 60.000 0.00 0.00 0.00 4.20
775 807 0.796312 CTTCAATGTAGCGCAACGGT 59.204 50.000 11.47 0.00 41.50 4.83
794 826 2.641305 GTCAGAGTAGGCTTCTCGGTA 58.359 52.381 17.77 5.41 37.07 4.02
795 827 2.614983 GTCAGAGTAGGCTTCTCGGTAG 59.385 54.545 17.77 9.38 37.07 3.18
796 828 1.335496 CAGAGTAGGCTTCTCGGTAGC 59.665 57.143 14.42 0.00 37.07 3.58
813 845 4.142687 CGGTAGCCTTGTGAACATTAAAGG 60.143 45.833 0.00 0.00 41.81 3.11
814 846 4.157840 GGTAGCCTTGTGAACATTAAAGGG 59.842 45.833 12.38 0.00 39.70 3.95
816 848 2.353704 GCCTTGTGAACATTAAAGGGGC 60.354 50.000 12.38 0.00 39.70 5.80
820 852 2.290387 TGTGAACATTAAAGGGGCGCTA 60.290 45.455 7.64 0.00 0.00 4.26
833 865 3.142393 CGCTACCCTCCCATCCAG 58.858 66.667 0.00 0.00 0.00 3.86
840 872 1.553690 CCCTCCCATCCAGTCACGTT 61.554 60.000 0.00 0.00 0.00 3.99
850 882 3.402110 TCCAGTCACGTTCGTCTAACTA 58.598 45.455 0.00 0.00 35.81 2.24
862 894 2.190981 GTCTAACTACCATTCACGCCG 58.809 52.381 0.00 0.00 0.00 6.46
865 897 1.886886 AACTACCATTCACGCCGTTT 58.113 45.000 0.00 0.00 0.00 3.60
874 906 2.157834 TCACGCCGTTTAGTCACATT 57.842 45.000 0.00 0.00 0.00 2.71
878 910 2.066262 CGCCGTTTAGTCACATTCACT 58.934 47.619 0.00 0.00 0.00 3.41
882 914 4.927425 GCCGTTTAGTCACATTCACTCTAA 59.073 41.667 0.00 0.00 0.00 2.10
913 945 3.548802 GCATGAATGCGCAAAAACG 57.451 47.368 17.11 4.44 44.67 3.60
914 946 1.059173 GCATGAATGCGCAAAAACGA 58.941 45.000 17.11 0.00 44.67 3.85
915 947 1.655099 GCATGAATGCGCAAAAACGAT 59.345 42.857 17.11 0.00 44.67 3.73
916 948 2.284627 GCATGAATGCGCAAAAACGATC 60.285 45.455 17.11 5.09 44.67 3.69
918 950 2.583739 TGAATGCGCAAAAACGATCAG 58.416 42.857 17.11 0.00 34.06 2.90
919 951 1.318491 GAATGCGCAAAAACGATCAGC 59.682 47.619 17.11 0.00 34.06 4.26
921 953 3.352536 CGCAAAAACGATCAGCGC 58.647 55.556 0.00 0.00 46.04 5.92
922 954 2.479782 CGCAAAAACGATCAGCGCG 61.480 57.895 0.00 0.00 46.04 6.86
923 955 2.145905 GCAAAAACGATCAGCGCGG 61.146 57.895 8.83 0.00 46.04 6.46
984 1016 1.885157 CCTACGTAACGCAGGTCCA 59.115 57.895 0.00 0.00 35.84 4.02
993 1025 2.594592 GCAGGTCCAAACGCCAGT 60.595 61.111 0.00 0.00 0.00 4.00
996 1040 0.310854 CAGGTCCAAACGCCAGTTTC 59.689 55.000 0.00 0.00 46.73 2.78
998 1042 0.030235 GGTCCAAACGCCAGTTTCAC 59.970 55.000 0.00 0.00 46.73 3.18
1009 1053 1.011333 CAGTTTCACGTCCGGTTTGT 58.989 50.000 0.00 0.00 0.00 2.83
1012 1056 1.096386 TTTCACGTCCGGTTTGTGGG 61.096 55.000 18.52 1.40 34.43 4.61
1020 1064 1.202782 TCCGGTTTGTGGGAATTCGAA 60.203 47.619 0.00 0.00 0.00 3.71
1021 1065 1.816224 CCGGTTTGTGGGAATTCGAAT 59.184 47.619 4.39 4.39 0.00 3.34
1022 1066 2.415357 CCGGTTTGTGGGAATTCGAATG 60.415 50.000 12.25 0.00 0.00 2.67
1023 1067 2.227865 CGGTTTGTGGGAATTCGAATGT 59.772 45.455 12.25 1.91 0.00 2.71
1026 1070 4.399978 GTTTGTGGGAATTCGAATGTACG 58.600 43.478 12.25 0.00 0.00 3.67
1027 1071 2.623535 TGTGGGAATTCGAATGTACGG 58.376 47.619 12.25 0.00 0.00 4.02
1028 1072 2.234168 TGTGGGAATTCGAATGTACGGA 59.766 45.455 12.25 0.00 0.00 4.69
1029 1073 2.606272 GTGGGAATTCGAATGTACGGAC 59.394 50.000 12.25 0.00 0.00 4.79
1030 1074 2.234168 TGGGAATTCGAATGTACGGACA 59.766 45.455 12.25 1.10 40.72 4.02
1031 1075 2.864343 GGGAATTCGAATGTACGGACAG 59.136 50.000 12.25 0.00 39.50 3.51
1032 1076 2.864343 GGAATTCGAATGTACGGACAGG 59.136 50.000 12.25 0.00 39.50 4.00
1033 1077 3.518590 GAATTCGAATGTACGGACAGGT 58.481 45.455 12.25 0.00 39.50 4.00
1034 1078 2.642139 TTCGAATGTACGGACAGGTC 57.358 50.000 6.62 5.35 39.50 3.85
1035 1079 0.813184 TCGAATGTACGGACAGGTCC 59.187 55.000 6.62 8.44 46.18 4.46
1045 1089 2.842462 ACAGGTCCGCACTGTCCA 60.842 61.111 0.00 0.00 45.50 4.02
1046 1090 2.357517 CAGGTCCGCACTGTCCAC 60.358 66.667 0.00 0.00 0.00 4.02
1047 1091 2.842462 AGGTCCGCACTGTCCACA 60.842 61.111 0.00 0.00 0.00 4.17
1048 1092 2.665185 GGTCCGCACTGTCCACAC 60.665 66.667 0.00 0.00 0.00 3.82
1049 1093 3.036084 GTCCGCACTGTCCACACG 61.036 66.667 0.00 0.00 0.00 4.49
1071 1115 0.868602 TAGCGGCGTTTCTATGCGTC 60.869 55.000 9.37 0.00 37.15 5.19
1090 1134 0.319900 CGGAGATGCCCTAACCATCG 60.320 60.000 0.00 0.00 42.92 3.84
1104 1148 3.842923 ATCGCGTGGCCTCCTCAG 61.843 66.667 5.77 0.00 0.00 3.35
1116 1160 1.613630 TCCTCAGGTCAGGGAAGCC 60.614 63.158 0.00 0.00 33.81 4.35
1120 1164 2.526873 AGGTCAGGGAAGCCGTGT 60.527 61.111 6.11 0.00 39.97 4.49
1152 1196 2.654863 CTCCAACCAAACACACTTCCT 58.345 47.619 0.00 0.00 0.00 3.36
1164 1208 0.321122 CACTTCCTGCAGGTCTCCAC 60.321 60.000 31.58 0.00 36.34 4.02
1165 1209 0.472734 ACTTCCTGCAGGTCTCCACT 60.473 55.000 31.58 6.35 36.34 4.00
1186 1230 1.693606 CAAAATTTGGTCAGGGTGGCT 59.306 47.619 0.00 0.00 0.00 4.75
1187 1231 1.341080 AAATTTGGTCAGGGTGGCTG 58.659 50.000 0.00 0.00 0.00 4.85
1188 1232 0.542702 AATTTGGTCAGGGTGGCTGG 60.543 55.000 0.00 0.00 0.00 4.85
1189 1233 3.808218 TTTGGTCAGGGTGGCTGGC 62.808 63.158 0.00 0.00 0.00 4.85
1191 1235 4.284550 GGTCAGGGTGGCTGGCAA 62.285 66.667 5.14 0.00 0.00 4.52
1192 1236 2.985847 GTCAGGGTGGCTGGCAAC 60.986 66.667 11.29 11.29 0.00 4.17
1193 1237 4.284550 TCAGGGTGGCTGGCAACC 62.285 66.667 29.22 29.22 39.31 3.77
1194 1238 4.601794 CAGGGTGGCTGGCAACCA 62.602 66.667 35.75 5.29 41.80 3.67
1195 1239 3.831637 AGGGTGGCTGGCAACCAA 61.832 61.111 35.75 0.00 41.80 3.67
1196 1240 2.841988 GGGTGGCTGGCAACCAAA 60.842 61.111 31.03 0.00 41.80 3.28
1197 1241 2.421314 GGTGGCTGGCAACCAAAC 59.579 61.111 11.93 4.13 39.80 2.93
1198 1242 2.430610 GGTGGCTGGCAACCAAACA 61.431 57.895 11.93 0.00 39.80 2.83
1199 1243 1.067916 GTGGCTGGCAACCAAACAG 59.932 57.895 11.93 0.00 39.39 3.16
1204 1248 3.549730 GGCAACCAAACAGCCCTT 58.450 55.556 0.00 0.00 42.58 3.95
1205 1249 1.367471 GGCAACCAAACAGCCCTTC 59.633 57.895 0.00 0.00 42.58 3.46
1206 1250 1.115326 GGCAACCAAACAGCCCTTCT 61.115 55.000 0.00 0.00 42.58 2.85
1207 1251 0.752658 GCAACCAAACAGCCCTTCTT 59.247 50.000 0.00 0.00 0.00 2.52
1225 1284 7.588512 CCCTTCTTCAAACATAGTTTCAGAAG 58.411 38.462 21.10 21.10 37.04 2.85
1227 1286 8.624776 CCTTCTTCAAACATAGTTTCAGAAGTT 58.375 33.333 23.40 0.00 36.01 2.66
1252 1311 1.891919 GAAGGTGCAGGCGTGACAA 60.892 57.895 11.29 0.00 0.00 3.18
1406 1465 0.850883 TGATTTCCCTTGGGCCCTCT 60.851 55.000 25.70 0.00 0.00 3.69
1417 1476 3.151022 GCCCTCTCCTCGACTGGG 61.151 72.222 0.00 0.00 40.74 4.45
1444 1503 2.364317 TTCGCTCCCCTCTCCAGG 60.364 66.667 0.00 0.00 39.98 4.45
1551 1610 6.502138 TCCTCCAATTCCAAAGGTAATGATT 58.498 36.000 0.00 0.00 0.00 2.57
1563 1624 7.148018 CCAAAGGTAATGATTTGCATAGTCAGT 60.148 37.037 0.00 0.00 35.78 3.41
1564 1625 7.944729 AAGGTAATGATTTGCATAGTCAGTT 57.055 32.000 0.00 0.00 35.78 3.16
1565 1626 9.461312 AAAGGTAATGATTTGCATAGTCAGTTA 57.539 29.630 0.00 0.00 35.78 2.24
1566 1627 8.438676 AGGTAATGATTTGCATAGTCAGTTAC 57.561 34.615 0.00 4.38 35.78 2.50
1567 1628 8.267894 AGGTAATGATTTGCATAGTCAGTTACT 58.732 33.333 16.63 0.00 42.62 2.24
1568 1629 8.552034 GGTAATGATTTGCATAGTCAGTTACTC 58.448 37.037 16.63 10.42 39.80 2.59
1569 1630 7.559590 AATGATTTGCATAGTCAGTTACTCC 57.440 36.000 0.00 0.00 39.80 3.85
1570 1631 5.428253 TGATTTGCATAGTCAGTTACTCCC 58.572 41.667 0.00 0.00 39.80 4.30
1571 1632 5.189736 TGATTTGCATAGTCAGTTACTCCCT 59.810 40.000 0.00 0.00 39.80 4.20
1572 1633 4.737855 TTGCATAGTCAGTTACTCCCTC 57.262 45.455 0.00 0.00 39.80 4.30
1573 1634 3.031736 TGCATAGTCAGTTACTCCCTCC 58.968 50.000 0.00 0.00 39.80 4.30
1574 1635 2.034812 GCATAGTCAGTTACTCCCTCCG 59.965 54.545 0.00 0.00 39.80 4.63
1575 1636 3.288964 CATAGTCAGTTACTCCCTCCGT 58.711 50.000 0.00 0.00 39.80 4.69
1576 1637 2.305858 AGTCAGTTACTCCCTCCGTT 57.694 50.000 0.00 0.00 30.33 4.44
1577 1638 2.606378 AGTCAGTTACTCCCTCCGTTT 58.394 47.619 0.00 0.00 30.33 3.60
1578 1639 2.561858 AGTCAGTTACTCCCTCCGTTTC 59.438 50.000 0.00 0.00 30.33 2.78
1579 1640 2.298163 GTCAGTTACTCCCTCCGTTTCA 59.702 50.000 0.00 0.00 0.00 2.69
1580 1641 2.967201 TCAGTTACTCCCTCCGTTTCAA 59.033 45.455 0.00 0.00 0.00 2.69
1581 1642 3.388676 TCAGTTACTCCCTCCGTTTCAAA 59.611 43.478 0.00 0.00 0.00 2.69
1582 1643 4.131596 CAGTTACTCCCTCCGTTTCAAAA 58.868 43.478 0.00 0.00 0.00 2.44
1583 1644 4.760204 CAGTTACTCCCTCCGTTTCAAAAT 59.240 41.667 0.00 0.00 0.00 1.82
1584 1645 5.935789 CAGTTACTCCCTCCGTTTCAAAATA 59.064 40.000 0.00 0.00 0.00 1.40
1585 1646 6.092259 CAGTTACTCCCTCCGTTTCAAAATAG 59.908 42.308 0.00 0.00 0.00 1.73
1586 1647 4.903045 ACTCCCTCCGTTTCAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
1587 1648 5.437191 ACTCCCTCCGTTTCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
1588 1649 5.186198 ACTCCCTCCGTTTCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
1589 1650 5.045869 ACTCCCTCCGTTTCAAAATAGATGA 60.046 40.000 0.00 0.00 0.00 2.92
1590 1651 6.001449 TCCCTCCGTTTCAAAATAGATGAT 57.999 37.500 0.00 0.00 0.00 2.45
1591 1652 7.131907 TCCCTCCGTTTCAAAATAGATGATA 57.868 36.000 0.00 0.00 0.00 2.15
1592 1653 7.745717 TCCCTCCGTTTCAAAATAGATGATAT 58.254 34.615 0.00 0.00 0.00 1.63
1593 1654 8.876181 TCCCTCCGTTTCAAAATAGATGATATA 58.124 33.333 0.00 0.00 0.00 0.86
1594 1655 9.502091 CCCTCCGTTTCAAAATAGATGATATAA 57.498 33.333 0.00 0.00 0.00 0.98
1632 1693 9.391006 AGTTAAATCATCTTATTTTGGTAGCGA 57.609 29.630 0.00 0.00 31.63 4.93
1633 1694 9.651718 GTTAAATCATCTTATTTTGGTAGCGAG 57.348 33.333 0.00 0.00 31.63 5.03
1634 1695 6.867662 AATCATCTTATTTTGGTAGCGAGG 57.132 37.500 0.00 0.00 0.00 4.63
1635 1696 4.703897 TCATCTTATTTTGGTAGCGAGGG 58.296 43.478 0.00 0.00 0.00 4.30
1636 1697 4.407621 TCATCTTATTTTGGTAGCGAGGGA 59.592 41.667 0.00 0.00 0.00 4.20
1637 1698 4.402056 TCTTATTTTGGTAGCGAGGGAG 57.598 45.455 0.00 0.00 0.00 4.30
1667 1728 1.489560 AAGGGTTCCGACCTCCCAAG 61.490 60.000 0.00 0.00 45.75 3.61
1697 1758 0.181587 TTGCTGGTCACTTTCCCGAA 59.818 50.000 0.00 0.00 0.00 4.30
1732 1793 2.252535 AGGAATTGGGGGTGGAAATG 57.747 50.000 0.00 0.00 0.00 2.32
1733 1794 1.721691 AGGAATTGGGGGTGGAAATGA 59.278 47.619 0.00 0.00 0.00 2.57
1734 1795 2.113414 AGGAATTGGGGGTGGAAATGAA 59.887 45.455 0.00 0.00 0.00 2.57
1735 1796 2.909662 GGAATTGGGGGTGGAAATGAAA 59.090 45.455 0.00 0.00 0.00 2.69
1736 1797 3.523157 GGAATTGGGGGTGGAAATGAAAT 59.477 43.478 0.00 0.00 0.00 2.17
1737 1798 4.384098 GGAATTGGGGGTGGAAATGAAATC 60.384 45.833 0.00 0.00 0.00 2.17
1738 1799 3.266477 TTGGGGGTGGAAATGAAATCA 57.734 42.857 0.00 0.00 0.00 2.57
1770 1831 4.714308 TGCTTTTATCCCCCAACATTTAGG 59.286 41.667 0.00 0.00 0.00 2.69
1800 1861 1.924731 TATGTCGATCTAGGCCCTGG 58.075 55.000 0.00 0.00 0.00 4.45
1828 1889 2.494059 CCTCCTTTGCTTGTTCGAGAA 58.506 47.619 0.00 0.00 0.00 2.87
1830 1891 3.126000 CCTCCTTTGCTTGTTCGAGAATC 59.874 47.826 0.00 0.00 0.00 2.52
1886 1947 2.262915 CCACGCTGGACTGGACTC 59.737 66.667 0.00 0.00 40.96 3.36
1963 2026 5.941948 AACTTCAGTTGGCAACTATGTAC 57.058 39.130 30.72 3.63 40.46 2.90
2110 2186 2.421073 CCATGTGATCGACAGTGCAATT 59.579 45.455 0.00 0.00 38.23 2.32
2141 2217 1.542547 GCGTCATGTTCCCGGGATATT 60.543 52.381 27.48 9.07 0.00 1.28
2146 2222 2.721425 TGTTCCCGGGATATTTGTCC 57.279 50.000 27.48 5.56 37.56 4.02
2167 2244 5.064834 GTCCTTTGTATTTAGCCTTCCTTCG 59.935 44.000 0.00 0.00 0.00 3.79
2198 2275 5.422214 AACAGAGAAATACCTACACCTGG 57.578 43.478 0.00 0.00 0.00 4.45
2204 2281 4.794067 AGAAATACCTACACCTGGGGAATT 59.206 41.667 1.10 0.00 0.00 2.17
2213 2290 6.546034 CCTACACCTGGGGAATTACTTTAATG 59.454 42.308 1.10 0.00 0.00 1.90
2466 2544 2.038557 GGACAGTAAGAAGCCACTGGAA 59.961 50.000 0.00 0.00 45.22 3.53
2502 2580 7.746703 AGAATATTAAGGAGCGTAGGGAAATT 58.253 34.615 0.00 0.00 0.00 1.82
2903 2982 2.174363 TATCCATCCTGAAGCATGCG 57.826 50.000 13.01 0.00 0.00 4.73
2976 3055 2.111384 TGGAGGAGGTAGAGAACATGC 58.889 52.381 0.00 0.00 0.00 4.06
2999 3078 3.633986 AGAAGGTGAAGAAGGTTGCAAAG 59.366 43.478 0.00 0.00 0.00 2.77
3053 3132 4.760530 TCTGGTGATACTGGGAAAGATG 57.239 45.455 0.00 0.00 0.00 2.90
3095 3174 8.759481 AGAACTGAGATGACAGATATGACTAA 57.241 34.615 0.00 0.00 40.63 2.24
3134 3213 6.403878 TGGAGTAGCAGAGTAACATTTTACC 58.596 40.000 0.00 0.00 38.79 2.85
3324 3403 5.855045 ACTGTTTCCTTGGTTAGTAGTCTG 58.145 41.667 0.00 0.00 0.00 3.51
3344 3423 0.829333 TGTGCCATTTGTGGTGCTTT 59.171 45.000 0.00 0.00 0.00 3.51
3366 3447 2.744741 GTTAGAACCTGCAAGAGAAGCC 59.255 50.000 0.00 0.00 34.07 4.35
3434 3542 0.538287 AACCTGAAGGCTTGGCTGAC 60.538 55.000 3.46 0.00 39.32 3.51
3548 3656 6.158598 TGCAATACTTGGAGAAGAATTTTGC 58.841 36.000 0.00 0.00 35.77 3.68
3591 3699 1.400846 GAAGCATGGACAGCTGTGATG 59.599 52.381 27.27 24.47 42.53 3.07
3623 3731 9.155053 GTAACGTTTTTCACTGAATCTTACTTG 57.845 33.333 5.91 0.00 0.00 3.16
3651 3759 6.860124 CGTGAGCATTTCTTCTTTTGAAAAG 58.140 36.000 11.30 11.30 38.07 2.27
3654 3762 5.059161 AGCATTTCTTCTTTTGAAAAGGGC 58.941 37.500 16.79 9.57 38.07 5.19
3662 3770 4.633651 TTCTTTTGAAAAGGGCTTCCCTCT 60.634 41.667 16.79 0.00 42.41 3.69
3673 3781 5.521906 GGGCTTCCCTCTAATTCAAATTC 57.478 43.478 0.00 0.00 41.34 2.17
3674 3782 4.956075 GGGCTTCCCTCTAATTCAAATTCA 59.044 41.667 0.00 0.00 41.34 2.57
3680 3790 8.884124 TTCCCTCTAATTCAAATTCAGTGAAT 57.116 30.769 12.75 12.75 45.47 2.57
3689 3799 6.024552 TCAAATTCAGTGAATAAGTTGGCC 57.975 37.500 18.56 0.00 31.46 5.36
3723 3834 7.013834 TCCCCTTCTAAAAGAAATTTGCCTTA 58.986 34.615 0.00 0.00 33.19 2.69
3732 3843 7.544804 AAAGAAATTTGCCTTATCTTCCACT 57.455 32.000 0.00 0.00 30.43 4.00
3808 3919 4.325972 TGATAAGCACTGCTGTCAAATCA 58.674 39.130 14.05 10.94 39.62 2.57
3859 3970 9.387257 TCTATATGAAACTACAGAAGTGACGTA 57.613 33.333 0.00 0.00 38.88 3.57
4165 4276 7.178274 AGCTAGATTGATGAAAGATCCTCGTAT 59.822 37.037 0.00 0.00 0.00 3.06
4344 4455 2.273179 CCCAGTCGGTCAGGTCGAA 61.273 63.158 0.00 0.00 38.42 3.71
4417 4528 1.007038 CAGCAGCGCAACACCAAAT 60.007 52.632 11.47 0.00 0.00 2.32
4426 4537 1.265635 GCAACACCAAATGCGTAGACA 59.734 47.619 0.00 0.00 32.17 3.41
4648 4759 3.687698 CACGGTCGAAATGGAGGTAATTT 59.312 43.478 0.00 0.00 0.00 1.82
4669 4780 2.260869 GCCACGTGCCACATCAACT 61.261 57.895 10.91 0.00 0.00 3.16
4763 4874 7.219484 AGACACAAGAAGGTTGAATTAATGG 57.781 36.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 8.098912 TCCCTCTTTAGTTTTAGTCCAACATAC 58.901 37.037 0.00 0.00 0.00 2.39
7 8 7.997773 AATCCCTCTTTAGTTTTAGTCCAAC 57.002 36.000 0.00 0.00 0.00 3.77
15 16 6.950619 AGATGAGCAAATCCCTCTTTAGTTTT 59.049 34.615 0.00 0.00 0.00 2.43
20 21 7.379059 TGATAGATGAGCAAATCCCTCTTTA 57.621 36.000 0.00 0.00 0.00 1.85
74 75 1.886422 ATCCCTTGGGACTCTTCTCC 58.114 55.000 11.04 0.00 0.00 3.71
117 118 3.541242 TGTGGTCTTCCCCAAATTCAT 57.459 42.857 0.00 0.00 35.92 2.57
134 135 3.713764 AGGGAGATAAGGTCTTGGATGTG 59.286 47.826 0.00 0.00 37.29 3.21
135 136 4.014273 AGGGAGATAAGGTCTTGGATGT 57.986 45.455 0.00 0.00 37.29 3.06
138 139 4.547671 CACTAGGGAGATAAGGTCTTGGA 58.452 47.826 0.00 0.00 37.29 3.53
153 154 4.576330 AGTTCTTCCAAATCCACTAGGG 57.424 45.455 0.00 0.00 34.83 3.53
190 193 2.716424 AGATCCACAAACAAGAAGGGGA 59.284 45.455 0.00 0.00 0.00 4.81
197 200 4.821805 AGTACCACAAGATCCACAAACAAG 59.178 41.667 0.00 0.00 0.00 3.16
222 225 3.367395 GCCCTCTTTAAGCAAATCCACAC 60.367 47.826 0.00 0.00 0.00 3.82
223 226 2.825532 GCCCTCTTTAAGCAAATCCACA 59.174 45.455 0.00 0.00 0.00 4.17
267 270 1.600413 CGCAAAGGGAACAAGCACTTC 60.600 52.381 0.00 0.00 29.54 3.01
268 271 0.385390 CGCAAAGGGAACAAGCACTT 59.615 50.000 0.00 0.00 31.53 3.16
282 285 1.748493 AGGAACAAACAAGAGCGCAAA 59.252 42.857 11.47 0.00 0.00 3.68
286 289 2.483876 TCAGAGGAACAAACAAGAGCG 58.516 47.619 0.00 0.00 0.00 5.03
305 308 7.226325 CCAATCTTTCACACTTGGAGATAGATC 59.774 40.741 0.00 0.00 40.48 2.75
306 309 7.052873 CCAATCTTTCACACTTGGAGATAGAT 58.947 38.462 0.00 0.00 40.48 1.98
307 310 6.409704 CCAATCTTTCACACTTGGAGATAGA 58.590 40.000 0.00 0.00 40.48 1.98
308 311 5.587844 CCCAATCTTTCACACTTGGAGATAG 59.412 44.000 1.83 0.00 40.48 2.08
309 312 5.500234 CCCAATCTTTCACACTTGGAGATA 58.500 41.667 1.83 0.00 40.48 1.98
320 324 2.161609 CGTAAGTGGCCCAATCTTTCAC 59.838 50.000 0.00 0.00 0.00 3.18
332 336 1.235724 AAGGCAAAGTCGTAAGTGGC 58.764 50.000 0.00 0.00 35.76 5.01
335 339 4.890088 TGATGTAAGGCAAAGTCGTAAGT 58.110 39.130 0.00 0.00 39.48 2.24
337 341 5.522460 GCTATGATGTAAGGCAAAGTCGTAA 59.478 40.000 0.00 0.00 0.00 3.18
342 346 5.365021 AGAGCTATGATGTAAGGCAAAGT 57.635 39.130 0.00 0.00 0.00 2.66
372 376 3.642503 CGTTGCCCCACCCCTACA 61.643 66.667 0.00 0.00 0.00 2.74
414 418 1.134530 CGTGATCGAGAAGTCGCACC 61.135 60.000 0.00 0.00 46.39 5.01
416 420 2.168054 TCGTGATCGAGAAGTCGCA 58.832 52.632 0.00 0.00 46.39 5.10
437 441 3.548745 TGAGGAGTTCCATGCTATGTG 57.451 47.619 0.28 0.00 38.89 3.21
438 442 3.244009 CGATGAGGAGTTCCATGCTATGT 60.244 47.826 0.28 0.00 38.89 2.29
443 447 0.179000 ACCGATGAGGAGTTCCATGC 59.821 55.000 0.28 0.00 45.00 4.06
444 448 3.070159 ACATACCGATGAGGAGTTCCATG 59.930 47.826 0.28 0.00 45.00 3.66
492 496 2.159272 GAACGACGACCAACAGCAGC 62.159 60.000 0.00 0.00 0.00 5.25
510 514 1.301716 GTGGTGCTTTGCTCCTCGA 60.302 57.895 11.18 0.00 42.02 4.04
511 515 2.328099 GGTGGTGCTTTGCTCCTCG 61.328 63.158 11.18 0.00 42.02 4.63
520 524 0.768221 TGAAGGAGGAGGTGGTGCTT 60.768 55.000 0.00 0.00 0.00 3.91
530 534 1.107114 GCTCTGTCGATGAAGGAGGA 58.893 55.000 0.00 0.00 0.00 3.71
537 541 1.657751 CTCCACCGCTCTGTCGATGA 61.658 60.000 0.00 0.00 0.00 2.92
544 548 0.249784 CATCATCCTCCACCGCTCTG 60.250 60.000 0.00 0.00 0.00 3.35
549 553 1.987807 AAGGCCATCATCCTCCACCG 61.988 60.000 5.01 0.00 32.45 4.94
567 571 1.582461 TCGCGTCCACGATCTTCAA 59.418 52.632 5.77 0.00 43.02 2.69
568 572 3.270000 TCGCGTCCACGATCTTCA 58.730 55.556 5.77 0.00 43.02 3.02
577 581 1.522806 GGTTATGGCATCGCGTCCA 60.523 57.895 16.79 16.79 36.70 4.02
583 587 1.961277 GCTCCGGGTTATGGCATCG 60.961 63.158 1.65 0.51 0.00 3.84
585 589 1.451936 GAGCTCCGGGTTATGGCAT 59.548 57.895 4.88 4.88 0.00 4.40
592 596 2.757077 CAAAGGGAGCTCCGGGTT 59.243 61.111 26.36 16.26 41.52 4.11
618 622 4.170062 TAGTTCTCGGCGCCGACG 62.170 66.667 45.37 36.48 44.01 5.12
622 626 4.893601 GGGCTAGTTCTCGGCGCC 62.894 72.222 19.07 19.07 39.98 6.53
625 629 0.460459 GACAAGGGCTAGTTCTCGGC 60.460 60.000 0.00 0.00 0.00 5.54
630 634 1.623811 TCTGGTGACAAGGGCTAGTTC 59.376 52.381 0.00 0.00 42.06 3.01
636 640 0.179018 ACAAGTCTGGTGACAAGGGC 60.179 55.000 0.00 0.00 45.20 5.19
645 649 0.687354 AAGCGATGGACAAGTCTGGT 59.313 50.000 0.00 0.00 0.00 4.00
684 716 0.758685 CTCCATCCTCGCCTCTCCTT 60.759 60.000 0.00 0.00 0.00 3.36
686 718 1.045911 AACTCCATCCTCGCCTCTCC 61.046 60.000 0.00 0.00 0.00 3.71
691 723 1.153349 GACCAACTCCATCCTCGCC 60.153 63.158 0.00 0.00 0.00 5.54
692 724 1.519455 CGACCAACTCCATCCTCGC 60.519 63.158 0.00 0.00 0.00 5.03
702 734 1.376424 CAGGCTGCATCGACCAACT 60.376 57.895 0.00 0.00 0.00 3.16
736 768 1.074775 GACATTGGCCACCTGACCA 59.925 57.895 19.01 0.00 0.00 4.02
772 804 0.378962 CGAGAAGCCTACTCTGACCG 59.621 60.000 0.00 0.00 32.87 4.79
775 807 2.920524 CTACCGAGAAGCCTACTCTGA 58.079 52.381 0.00 0.00 32.87 3.27
794 826 3.165071 CCCCTTTAATGTTCACAAGGCT 58.835 45.455 0.00 0.00 35.37 4.58
795 827 2.353704 GCCCCTTTAATGTTCACAAGGC 60.354 50.000 0.00 0.00 35.37 4.35
796 828 2.094752 CGCCCCTTTAATGTTCACAAGG 60.095 50.000 0.00 0.00 36.32 3.61
798 830 1.271102 GCGCCCCTTTAATGTTCACAA 59.729 47.619 0.00 0.00 0.00 3.33
799 831 0.885196 GCGCCCCTTTAATGTTCACA 59.115 50.000 0.00 0.00 0.00 3.58
800 832 1.173913 AGCGCCCCTTTAATGTTCAC 58.826 50.000 2.29 0.00 0.00 3.18
814 846 3.942439 GGATGGGAGGGTAGCGCC 61.942 72.222 2.29 0.00 0.00 6.53
816 848 1.749334 GACTGGATGGGAGGGTAGCG 61.749 65.000 0.00 0.00 0.00 4.26
820 852 1.990060 CGTGACTGGATGGGAGGGT 60.990 63.158 0.00 0.00 0.00 4.34
824 856 1.183030 ACGAACGTGACTGGATGGGA 61.183 55.000 0.00 0.00 0.00 4.37
825 857 0.736325 GACGAACGTGACTGGATGGG 60.736 60.000 4.19 0.00 0.00 4.00
833 865 3.542712 TGGTAGTTAGACGAACGTGAC 57.457 47.619 4.19 1.31 43.37 3.67
840 872 2.159338 GGCGTGAATGGTAGTTAGACGA 60.159 50.000 0.00 0.00 0.00 4.20
850 882 1.270412 TGACTAAACGGCGTGAATGGT 60.270 47.619 15.70 11.48 0.00 3.55
862 894 6.365247 TCGCTTTAGAGTGAATGTGACTAAAC 59.635 38.462 0.00 0.00 39.36 2.01
865 897 5.414765 TCTCGCTTTAGAGTGAATGTGACTA 59.585 40.000 0.00 0.00 41.58 2.59
878 910 1.153823 GCCGCACTCTCGCTTTAGA 60.154 57.895 0.00 0.00 0.00 2.10
882 914 2.786539 TTCATGCCGCACTCTCGCTT 62.787 55.000 0.00 0.00 0.00 4.68
905 937 2.145905 CCGCGCTGATCGTTTTTGC 61.146 57.895 5.56 0.00 41.07 3.68
921 953 3.744719 TCCTCGTTGCTCGTCCCG 61.745 66.667 2.39 0.00 40.80 5.14
922 954 1.310933 TAGTCCTCGTTGCTCGTCCC 61.311 60.000 2.39 0.00 40.80 4.46
923 955 0.739561 ATAGTCCTCGTTGCTCGTCC 59.260 55.000 2.39 0.00 40.80 4.79
929 961 1.369625 CCAACCATAGTCCTCGTTGC 58.630 55.000 0.00 0.00 35.38 4.17
933 965 1.146263 GCCCCAACCATAGTCCTCG 59.854 63.158 0.00 0.00 0.00 4.63
973 1005 3.284449 GGCGTTTGGACCTGCGTT 61.284 61.111 0.00 0.00 0.00 4.84
974 1006 4.555709 TGGCGTTTGGACCTGCGT 62.556 61.111 0.00 0.00 0.00 5.24
977 1009 0.310854 GAAACTGGCGTTTGGACCTG 59.689 55.000 11.15 0.00 43.09 4.00
984 1016 1.768112 CGGACGTGAAACTGGCGTTT 61.768 55.000 0.00 7.07 45.58 3.60
993 1025 1.096386 CCCACAAACCGGACGTGAAA 61.096 55.000 9.46 0.00 32.23 2.69
996 1040 0.887387 ATTCCCACAAACCGGACGTG 60.887 55.000 9.46 12.12 0.00 4.49
998 1042 0.519961 GAATTCCCACAAACCGGACG 59.480 55.000 9.46 0.00 0.00 4.79
1009 1053 2.234168 TGTCCGTACATTCGAATTCCCA 59.766 45.455 8.21 0.00 0.00 4.37
1012 1056 3.518590 ACCTGTCCGTACATTCGAATTC 58.481 45.455 8.21 0.00 34.37 2.17
1028 1072 2.842462 TGGACAGTGCGGACCTGT 60.842 61.111 2.38 7.66 45.52 4.00
1029 1073 2.357517 GTGGACAGTGCGGACCTG 60.358 66.667 2.38 4.19 36.01 4.00
1030 1074 2.842462 TGTGGACAGTGCGGACCT 60.842 61.111 2.38 0.00 0.00 3.85
1031 1075 2.665185 GTGTGGACAGTGCGGACC 60.665 66.667 2.38 0.00 0.00 4.46
1032 1076 3.036084 CGTGTGGACAGTGCGGAC 61.036 66.667 0.00 0.00 0.00 4.79
1033 1077 2.581208 AAACGTGTGGACAGTGCGGA 62.581 55.000 0.00 0.00 0.00 5.54
1034 1078 0.876777 TAAACGTGTGGACAGTGCGG 60.877 55.000 0.00 0.00 0.00 5.69
1035 1079 0.506932 CTAAACGTGTGGACAGTGCG 59.493 55.000 0.00 0.00 0.00 5.34
1036 1080 0.234884 GCTAAACGTGTGGACAGTGC 59.765 55.000 0.00 0.00 0.00 4.40
1037 1081 0.506932 CGCTAAACGTGTGGACAGTG 59.493 55.000 0.00 0.00 36.87 3.66
1038 1082 0.599204 CCGCTAAACGTGTGGACAGT 60.599 55.000 0.00 0.00 41.42 3.55
1039 1083 1.897398 GCCGCTAAACGTGTGGACAG 61.897 60.000 8.06 0.00 41.42 3.51
1040 1084 1.957186 GCCGCTAAACGTGTGGACA 60.957 57.895 8.06 0.00 41.42 4.02
1041 1085 2.858158 GCCGCTAAACGTGTGGAC 59.142 61.111 8.06 0.00 41.42 4.02
1042 1086 2.735478 CGCCGCTAAACGTGTGGA 60.735 61.111 8.06 0.00 41.42 4.02
1043 1087 2.108344 AAACGCCGCTAAACGTGTGG 62.108 55.000 0.00 0.00 42.68 4.17
1044 1088 0.720173 GAAACGCCGCTAAACGTGTG 60.720 55.000 0.00 0.00 42.68 3.82
1045 1089 0.877213 AGAAACGCCGCTAAACGTGT 60.877 50.000 0.00 0.00 42.68 4.49
1046 1090 1.062258 TAGAAACGCCGCTAAACGTG 58.938 50.000 0.00 0.00 42.68 4.49
1047 1091 1.657094 CATAGAAACGCCGCTAAACGT 59.343 47.619 0.00 0.00 46.07 3.99
1048 1092 1.591394 GCATAGAAACGCCGCTAAACG 60.591 52.381 0.00 0.00 43.15 3.60
1049 1093 1.591394 CGCATAGAAACGCCGCTAAAC 60.591 52.381 0.00 0.00 0.00 2.01
1071 1115 0.319900 CGATGGTTAGGGCATCTCCG 60.320 60.000 0.00 0.00 34.94 4.63
1090 1134 4.459089 GACCTGAGGAGGCCACGC 62.459 72.222 4.99 0.00 44.33 5.34
1104 1148 0.391263 CTTACACGGCTTCCCTGACC 60.391 60.000 0.00 0.00 0.00 4.02
1116 1160 0.741221 GGAGGCCTGAAGCTTACACG 60.741 60.000 12.00 0.00 43.05 4.49
1120 1164 0.328258 GGTTGGAGGCCTGAAGCTTA 59.672 55.000 12.00 0.00 43.05 3.09
1152 1196 2.957402 ATTTTGAGTGGAGACCTGCA 57.043 45.000 0.00 0.00 0.00 4.41
1164 1208 2.289010 GCCACCCTGACCAAATTTTGAG 60.289 50.000 10.72 3.78 0.00 3.02
1165 1209 1.691434 GCCACCCTGACCAAATTTTGA 59.309 47.619 10.72 0.00 0.00 2.69
1187 1231 1.115326 AGAAGGGCTGTTTGGTTGCC 61.115 55.000 0.00 0.00 45.42 4.52
1188 1232 0.752658 AAGAAGGGCTGTTTGGTTGC 59.247 50.000 0.00 0.00 0.00 4.17
1189 1233 2.031120 TGAAGAAGGGCTGTTTGGTTG 58.969 47.619 0.00 0.00 0.00 3.77
1190 1234 2.452600 TGAAGAAGGGCTGTTTGGTT 57.547 45.000 0.00 0.00 0.00 3.67
1191 1235 2.430694 GTTTGAAGAAGGGCTGTTTGGT 59.569 45.455 0.00 0.00 0.00 3.67
1192 1236 2.430332 TGTTTGAAGAAGGGCTGTTTGG 59.570 45.455 0.00 0.00 0.00 3.28
1193 1237 3.799281 TGTTTGAAGAAGGGCTGTTTG 57.201 42.857 0.00 0.00 0.00 2.93
1194 1238 5.140454 ACTATGTTTGAAGAAGGGCTGTTT 58.860 37.500 0.00 0.00 0.00 2.83
1195 1239 4.729868 ACTATGTTTGAAGAAGGGCTGTT 58.270 39.130 0.00 0.00 0.00 3.16
1196 1240 4.373156 ACTATGTTTGAAGAAGGGCTGT 57.627 40.909 0.00 0.00 0.00 4.40
1197 1241 5.241506 TGAAACTATGTTTGAAGAAGGGCTG 59.758 40.000 0.10 0.00 0.00 4.85
1198 1242 5.385198 TGAAACTATGTTTGAAGAAGGGCT 58.615 37.500 0.10 0.00 0.00 5.19
1199 1243 5.473504 TCTGAAACTATGTTTGAAGAAGGGC 59.526 40.000 0.10 0.00 0.00 5.19
1200 1244 7.229506 ACTTCTGAAACTATGTTTGAAGAAGGG 59.770 37.037 27.02 16.54 42.25 3.95
1201 1245 8.159344 ACTTCTGAAACTATGTTTGAAGAAGG 57.841 34.615 27.02 18.30 42.25 3.46
1203 1247 9.787532 CAAACTTCTGAAACTATGTTTGAAGAA 57.212 29.630 19.33 16.53 43.70 2.52
1204 1248 8.956426 ACAAACTTCTGAAACTATGTTTGAAGA 58.044 29.630 25.81 12.27 43.70 2.87
1206 1250 9.997482 GTACAAACTTCTGAAACTATGTTTGAA 57.003 29.630 25.81 0.00 43.70 2.69
1207 1251 8.617809 GGTACAAACTTCTGAAACTATGTTTGA 58.382 33.333 25.81 14.18 43.70 2.69
1225 1284 0.872388 CCTGCACCTTCGGTACAAAC 59.128 55.000 0.00 0.00 32.11 2.93
1227 1286 1.302192 GCCTGCACCTTCGGTACAA 60.302 57.895 0.00 0.00 32.11 2.41
1551 1610 3.451178 GGAGGGAGTAACTGACTATGCAA 59.549 47.826 0.00 0.00 39.06 4.08
1563 1624 6.363167 TCTATTTTGAAACGGAGGGAGTAA 57.637 37.500 0.00 0.00 0.00 2.24
1564 1625 6.155565 TCATCTATTTTGAAACGGAGGGAGTA 59.844 38.462 0.00 0.00 0.00 2.59
1565 1626 4.903045 TCTATTTTGAAACGGAGGGAGT 57.097 40.909 0.00 0.00 0.00 3.85
1566 1627 5.428253 TCATCTATTTTGAAACGGAGGGAG 58.572 41.667 0.00 0.00 0.00 4.30
1567 1628 5.429681 TCATCTATTTTGAAACGGAGGGA 57.570 39.130 0.00 0.00 0.00 4.20
1568 1629 7.986085 ATATCATCTATTTTGAAACGGAGGG 57.014 36.000 0.00 0.00 0.00 4.30
1606 1667 9.391006 TCGCTACCAAAATAAGATGATTTAACT 57.609 29.630 0.00 0.00 0.00 2.24
1607 1668 9.651718 CTCGCTACCAAAATAAGATGATTTAAC 57.348 33.333 0.00 0.00 0.00 2.01
1608 1669 8.836413 CCTCGCTACCAAAATAAGATGATTTAA 58.164 33.333 0.00 0.00 0.00 1.52
1609 1670 7.444183 CCCTCGCTACCAAAATAAGATGATTTA 59.556 37.037 0.00 0.00 0.00 1.40
1610 1671 6.263168 CCCTCGCTACCAAAATAAGATGATTT 59.737 38.462 0.00 0.00 0.00 2.17
1611 1672 5.765182 CCCTCGCTACCAAAATAAGATGATT 59.235 40.000 0.00 0.00 0.00 2.57
1612 1673 5.071788 TCCCTCGCTACCAAAATAAGATGAT 59.928 40.000 0.00 0.00 0.00 2.45
1613 1674 4.407621 TCCCTCGCTACCAAAATAAGATGA 59.592 41.667 0.00 0.00 0.00 2.92
1614 1675 4.703897 TCCCTCGCTACCAAAATAAGATG 58.296 43.478 0.00 0.00 0.00 2.90
1615 1676 4.409247 ACTCCCTCGCTACCAAAATAAGAT 59.591 41.667 0.00 0.00 0.00 2.40
1616 1677 3.773119 ACTCCCTCGCTACCAAAATAAGA 59.227 43.478 0.00 0.00 0.00 2.10
1617 1678 4.138487 ACTCCCTCGCTACCAAAATAAG 57.862 45.455 0.00 0.00 0.00 1.73
1618 1679 4.957954 TCTACTCCCTCGCTACCAAAATAA 59.042 41.667 0.00 0.00 0.00 1.40
1619 1680 4.539726 TCTACTCCCTCGCTACCAAAATA 58.460 43.478 0.00 0.00 0.00 1.40
1620 1681 3.371965 TCTACTCCCTCGCTACCAAAAT 58.628 45.455 0.00 0.00 0.00 1.82
1621 1682 2.811410 TCTACTCCCTCGCTACCAAAA 58.189 47.619 0.00 0.00 0.00 2.44
1622 1683 2.519771 TCTACTCCCTCGCTACCAAA 57.480 50.000 0.00 0.00 0.00 3.28
1623 1684 2.519771 TTCTACTCCCTCGCTACCAA 57.480 50.000 0.00 0.00 0.00 3.67
1624 1685 2.519771 TTTCTACTCCCTCGCTACCA 57.480 50.000 0.00 0.00 0.00 3.25
1625 1686 3.022406 TCTTTTCTACTCCCTCGCTACC 58.978 50.000 0.00 0.00 0.00 3.18
1626 1687 4.715527 TTCTTTTCTACTCCCTCGCTAC 57.284 45.455 0.00 0.00 0.00 3.58
1627 1688 5.337330 CCTTTTCTTTTCTACTCCCTCGCTA 60.337 44.000 0.00 0.00 0.00 4.26
1628 1689 4.563786 CCTTTTCTTTTCTACTCCCTCGCT 60.564 45.833 0.00 0.00 0.00 4.93
1629 1690 3.685272 CCTTTTCTTTTCTACTCCCTCGC 59.315 47.826 0.00 0.00 0.00 5.03
1630 1691 4.254492 CCCTTTTCTTTTCTACTCCCTCG 58.746 47.826 0.00 0.00 0.00 4.63
1631 1692 5.244189 ACCCTTTTCTTTTCTACTCCCTC 57.756 43.478 0.00 0.00 0.00 4.30
1632 1693 5.457778 GGAACCCTTTTCTTTTCTACTCCCT 60.458 44.000 0.00 0.00 0.00 4.20
1633 1694 4.765856 GGAACCCTTTTCTTTTCTACTCCC 59.234 45.833 0.00 0.00 0.00 4.30
1634 1695 4.454847 CGGAACCCTTTTCTTTTCTACTCC 59.545 45.833 0.00 0.00 0.00 3.85
1635 1696 5.178996 GTCGGAACCCTTTTCTTTTCTACTC 59.821 44.000 0.00 0.00 0.00 2.59
1636 1697 5.061853 GTCGGAACCCTTTTCTTTTCTACT 58.938 41.667 0.00 0.00 0.00 2.57
1637 1698 4.214971 GGTCGGAACCCTTTTCTTTTCTAC 59.785 45.833 0.00 0.00 39.93 2.59
1697 1758 3.453059 TTCCTTCTAACCTCTCCGAGT 57.547 47.619 0.00 0.00 0.00 4.18
1732 1793 7.964559 GGGATAAAAGCAAAAGCAAATGATTTC 59.035 33.333 0.00 0.00 34.37 2.17
1733 1794 7.094248 GGGGATAAAAGCAAAAGCAAATGATTT 60.094 33.333 0.00 0.00 36.78 2.17
1734 1795 6.375174 GGGGATAAAAGCAAAAGCAAATGATT 59.625 34.615 0.00 0.00 0.00 2.57
1735 1796 5.882000 GGGGATAAAAGCAAAAGCAAATGAT 59.118 36.000 0.00 0.00 0.00 2.45
1736 1797 5.244755 GGGGATAAAAGCAAAAGCAAATGA 58.755 37.500 0.00 0.00 0.00 2.57
1737 1798 4.395854 GGGGGATAAAAGCAAAAGCAAATG 59.604 41.667 0.00 0.00 0.00 2.32
1738 1799 4.042684 TGGGGGATAAAAGCAAAAGCAAAT 59.957 37.500 0.00 0.00 0.00 2.32
1740 1801 2.975489 TGGGGGATAAAAGCAAAAGCAA 59.025 40.909 0.00 0.00 0.00 3.91
1741 1802 2.614259 TGGGGGATAAAAGCAAAAGCA 58.386 42.857 0.00 0.00 0.00 3.91
1742 1803 3.244387 TGTTGGGGGATAAAAGCAAAAGC 60.244 43.478 0.00 0.00 0.00 3.51
1743 1804 4.615588 TGTTGGGGGATAAAAGCAAAAG 57.384 40.909 0.00 0.00 0.00 2.27
1744 1805 5.574970 AATGTTGGGGGATAAAAGCAAAA 57.425 34.783 0.00 0.00 0.00 2.44
1745 1806 5.574970 AAATGTTGGGGGATAAAAGCAAA 57.425 34.783 0.00 0.00 0.00 3.68
1746 1807 5.188751 CCTAAATGTTGGGGGATAAAAGCAA 59.811 40.000 0.00 0.00 0.00 3.91
1747 1808 4.714308 CCTAAATGTTGGGGGATAAAAGCA 59.286 41.667 0.00 0.00 0.00 3.91
1748 1809 4.100963 CCCTAAATGTTGGGGGATAAAAGC 59.899 45.833 1.54 0.00 46.99 3.51
1749 1810 5.869649 CCCTAAATGTTGGGGGATAAAAG 57.130 43.478 1.54 0.00 46.99 2.27
1770 1831 2.900546 AGATCGACATATCTCCCAACCC 59.099 50.000 0.00 0.00 30.09 4.11
1800 1861 0.037447 AAGCAAAGGAGGGACAGAGC 59.963 55.000 0.00 0.00 0.00 4.09
1832 1893 9.852091 GCAGATAAAAGAAATGAAATCAAGTCT 57.148 29.630 0.00 0.00 0.00 3.24
1833 1894 9.630098 TGCAGATAAAAGAAATGAAATCAAGTC 57.370 29.630 0.00 0.00 0.00 3.01
1834 1895 9.985730 TTGCAGATAAAAGAAATGAAATCAAGT 57.014 25.926 0.00 0.00 0.00 3.16
1886 1947 4.681483 GCAAGAAATTCAAGGGTTTTCGAG 59.319 41.667 0.00 0.00 35.14 4.04
1956 2017 6.945938 AGCTACACTGAAGGTAGTACATAG 57.054 41.667 2.06 0.00 40.24 2.23
1961 2024 5.138276 CCCATAGCTACACTGAAGGTAGTA 58.862 45.833 0.00 0.00 40.24 1.82
1962 2025 3.961408 CCCATAGCTACACTGAAGGTAGT 59.039 47.826 0.00 0.00 40.24 2.73
1963 2026 3.322254 CCCCATAGCTACACTGAAGGTAG 59.678 52.174 0.00 0.00 40.89 3.18
2141 2217 5.887754 AGGAAGGCTAAATACAAAGGACAA 58.112 37.500 0.00 0.00 0.00 3.18
2146 2222 6.737254 TTCGAAGGAAGGCTAAATACAAAG 57.263 37.500 0.00 0.00 0.00 2.77
2167 2244 4.767409 AGGTATTTCTCTGTTTGGCCTTTC 59.233 41.667 3.32 0.00 0.00 2.62
2177 2254 3.775316 CCCAGGTGTAGGTATTTCTCTGT 59.225 47.826 0.00 0.00 0.00 3.41
2198 2275 8.197439 AGCTACATTTGCATTAAAGTAATTCCC 58.803 33.333 0.00 0.00 0.00 3.97
2204 2281 7.606073 TCAGACAGCTACATTTGCATTAAAGTA 59.394 33.333 0.00 0.00 0.00 2.24
2213 2290 4.397417 AGGAAATCAGACAGCTACATTTGC 59.603 41.667 0.00 0.00 30.43 3.68
2466 2544 7.227512 CGCTCCTTAATATTCTTTTCCATGTCT 59.772 37.037 0.00 0.00 0.00 3.41
2502 2580 4.191544 AGTCATGCAGCGCTTTCTTTATA 58.808 39.130 7.50 0.00 0.00 0.98
2903 2982 2.766229 GCCTCCTCCACCTCCTCC 60.766 72.222 0.00 0.00 0.00 4.30
2976 3055 2.575532 TGCAACCTTCTTCACCTTCTG 58.424 47.619 0.00 0.00 0.00 3.02
3053 3132 7.656137 TCTCAGTTCTACACAAAACCAATCTAC 59.344 37.037 0.00 0.00 0.00 2.59
3095 3174 1.912043 ACTCCAAATACCAGCTCAGCT 59.088 47.619 0.00 0.00 40.77 4.24
3134 3213 5.755813 CACACAGAGAGAAACCAAGAAATG 58.244 41.667 0.00 0.00 0.00 2.32
3344 3423 3.403038 GCTTCTCTTGCAGGTTCTAACA 58.597 45.455 0.00 0.00 0.00 2.41
3366 3447 4.836825 TCCTATCACTTGGCTTTCTCTTG 58.163 43.478 0.00 0.00 0.00 3.02
3434 3542 3.836365 AACCCCCAACACATCTTTTTG 57.164 42.857 0.00 0.00 0.00 2.44
3591 3699 2.551032 CAGTGAAAAACGTTACCCTCCC 59.449 50.000 0.00 0.00 0.00 4.30
3623 3731 1.160137 AGAAGAAATGCTCACGCCAC 58.840 50.000 0.00 0.00 34.43 5.01
3634 3742 6.291377 GGAAGCCCTTTTCAAAAGAAGAAAT 58.709 36.000 11.73 0.00 35.17 2.17
3651 3759 4.956075 TGAATTTGAATTAGAGGGAAGCCC 59.044 41.667 0.00 0.00 45.90 5.19
3654 3762 7.928307 TCACTGAATTTGAATTAGAGGGAAG 57.072 36.000 0.00 0.00 0.00 3.46
3662 3770 9.638239 GCCAACTTATTCACTGAATTTGAATTA 57.362 29.630 9.57 0.94 40.12 1.40
3669 3777 4.415596 TGGGCCAACTTATTCACTGAATT 58.584 39.130 2.13 0.00 33.95 2.17
3670 3778 4.019174 CTGGGCCAACTTATTCACTGAAT 58.981 43.478 8.04 9.26 36.20 2.57
3671 3779 3.073798 TCTGGGCCAACTTATTCACTGAA 59.926 43.478 8.04 0.00 0.00 3.02
3672 3780 2.642311 TCTGGGCCAACTTATTCACTGA 59.358 45.455 8.04 0.00 0.00 3.41
3673 3781 3.071874 TCTGGGCCAACTTATTCACTG 57.928 47.619 8.04 0.00 0.00 3.66
3674 3782 4.263905 TGAATCTGGGCCAACTTATTCACT 60.264 41.667 20.54 0.00 30.59 3.41
3680 3790 2.091885 GGGATGAATCTGGGCCAACTTA 60.092 50.000 8.04 0.00 0.00 2.24
3689 3799 6.006275 TCTTTTAGAAGGGGATGAATCTGG 57.994 41.667 0.00 0.00 33.56 3.86
3831 3942 7.858382 CGTCACTTCTGTAGTTTCATATAGAGG 59.142 40.741 0.00 0.00 33.85 3.69
3859 3970 2.231478 CCTGTCAAGTGTACTGATCCGT 59.769 50.000 0.00 0.00 0.00 4.69
4165 4276 1.204146 GGCCTGGGATCAAGTCTGTA 58.796 55.000 0.00 0.00 0.00 2.74
4417 4528 3.575630 GTTCAAGTCTGATGTCTACGCA 58.424 45.455 0.00 0.00 0.00 5.24
4426 4537 0.905357 CCCCCTCGTTCAAGTCTGAT 59.095 55.000 0.00 0.00 0.00 2.90
4763 4874 9.213799 CCTCCTCATTCTATAAACTTATTGAGC 57.786 37.037 0.00 0.00 29.32 4.26


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

AutoCloner maintained by Alex Coulton.