Multiple sequence alignment - TraesCS5D01G222600

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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 TraesCS5D01G222600 chr5D 100.000 2701 0 0 1 2701 330122237 330119537 0.000000e+00 4988
1 TraesCS5D01G222600 chr5D 93.798 258 14 1 586 843 477398234 477398489 1.170000e-103 387
2 TraesCS5D01G222600 chr5B 90.171 1465 75 40 841 2282 383209437 383208019 0.000000e+00 1844
3 TraesCS5D01G222600 chr5B 91.935 310 20 3 2377 2685 383208008 383207703 1.920000e-116 429
4 TraesCS5D01G222600 chr5B 95.652 92 4 0 2283 2374 480300129 480300220 6.030000e-32 148
5 TraesCS5D01G222600 chr5A 91.588 1272 52 22 840 2081 426709024 426710270 0.000000e+00 1705
6 TraesCS5D01G222600 chr5A 92.014 576 26 8 1 573 687684171 687684729 0.000000e+00 791
7 TraesCS5D01G222600 chr5A 89.826 344 22 11 2366 2700 426710430 426710769 1.920000e-116 429
8 TraesCS5D01G222600 chr4B 93.586 343 12 7 259 597 648319450 648319786 1.120000e-138 503
9 TraesCS5D01G222600 chr4B 94.656 262 14 0 1 262 648318982 648319243 9.000000e-110 407
10 TraesCS5D01G222600 chr4D 93.793 290 18 0 1 290 503263622 503263911 1.150000e-118 436
11 TraesCS5D01G222600 chr4D 92.776 263 18 1 578 840 82734258 82733997 1.960000e-101 379
12 TraesCS5D01G222600 chr4D 93.182 220 11 3 354 573 503264297 503264512 1.210000e-83 320
13 TraesCS5D01G222600 chr3D 95.367 259 10 1 582 840 319867459 319867715 6.960000e-111 411
14 TraesCS5D01G222600 chr3D 93.822 259 14 1 582 840 319866754 319866498 3.260000e-104 388
15 TraesCS5D01G222600 chr7D 93.822 259 14 1 582 840 55248152 55248408 3.260000e-104 388
16 TraesCS5D01G222600 chr7D 92.748 262 18 1 581 842 9824538 9824798 7.060000e-101 377
17 TraesCS5D01G222600 chr1D 93.725 255 14 1 586 840 405082427 405082679 5.460000e-102 381
18 TraesCS5D01G222600 chr6D 92.720 261 17 1 584 844 79935792 79935534 2.540000e-100 375
19 TraesCS5D01G222600 chrUn 92.015 263 19 1 578 840 335167265 335167005 4.250000e-98 368


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 TraesCS5D01G222600 chr5D 330119537 330122237 2700 True 4988.0 4988 100.0000 1 2701 1 chr5D.!!$R1 2700
1 TraesCS5D01G222600 chr5B 383207703 383209437 1734 True 1136.5 1844 91.0530 841 2685 2 chr5B.!!$R1 1844
2 TraesCS5D01G222600 chr5A 426709024 426710769 1745 False 1067.0 1705 90.7070 840 2700 2 chr5A.!!$F2 1860
3 TraesCS5D01G222600 chr5A 687684171 687684729 558 False 791.0 791 92.0140 1 573 1 chr5A.!!$F1 572
4 TraesCS5D01G222600 chr4B 648318982 648319786 804 False 455.0 503 94.1210 1 597 2 chr4B.!!$F1 596
5 TraesCS5D01G222600 chr4D 503263622 503264512 890 False 378.0 436 93.4875 1 573 2 chr4D.!!$F1 572

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
801 1336 0.105224 TGTGGTAGTTGTGTGGGACG 59.895 55.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2322 2928 0.03601 CAGCTTTGGACGGTGGAGAT 60.036 55.0 0.0 0.0 0.0 2.75 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
19 20 2.202570 GCGTCGATGGCGTACTGT 60.203 61.111 6.79 0.00 38.98 3.55
22 23 0.316772 CGTCGATGGCGTACTGTAGG 60.317 60.000 0.00 3.25 38.98 3.18
25 26 1.299926 GATGGCGTACTGTAGGGCG 60.300 63.158 23.14 9.98 41.36 6.13
31 32 3.142838 TACTGTAGGGCGGCGACC 61.143 66.667 28.04 28.04 0.00 4.79
188 189 2.721859 CATCGATCTGCGGTCCGA 59.278 61.111 17.49 12.70 41.33 4.55
207 208 2.371259 GGGAGGAGGTGGAGAAGCC 61.371 68.421 0.00 0.00 37.10 4.35
365 898 1.542547 GGTCCTCATGGTTGTTGTCGT 60.543 52.381 0.00 0.00 34.23 4.34
574 1109 1.401148 CGGATATTCCACTCGCGGTAG 60.401 57.143 6.13 0.00 35.91 3.18
608 1143 2.124320 CCCCACCTGGCATAACGG 60.124 66.667 0.00 0.00 0.00 4.44
609 1144 2.674754 CCCACCTGGCATAACGGT 59.325 61.111 0.00 0.00 0.00 4.83
610 1145 1.451387 CCCACCTGGCATAACGGTC 60.451 63.158 0.00 0.00 0.00 4.79
611 1146 1.298340 CCACCTGGCATAACGGTCA 59.702 57.895 0.00 0.00 0.00 4.02
612 1147 0.322098 CCACCTGGCATAACGGTCAA 60.322 55.000 0.00 0.00 0.00 3.18
613 1148 0.802494 CACCTGGCATAACGGTCAAC 59.198 55.000 0.00 0.00 0.00 3.18
614 1149 0.690762 ACCTGGCATAACGGTCAACT 59.309 50.000 0.00 0.00 0.00 3.16
615 1150 1.073284 ACCTGGCATAACGGTCAACTT 59.927 47.619 0.00 0.00 0.00 2.66
616 1151 2.303600 ACCTGGCATAACGGTCAACTTA 59.696 45.455 0.00 0.00 0.00 2.24
617 1152 3.244630 ACCTGGCATAACGGTCAACTTAA 60.245 43.478 0.00 0.00 0.00 1.85
618 1153 3.126343 CCTGGCATAACGGTCAACTTAAC 59.874 47.826 0.00 0.00 0.00 2.01
619 1154 2.737783 TGGCATAACGGTCAACTTAACG 59.262 45.455 0.00 0.00 0.00 3.18
620 1155 2.094734 GGCATAACGGTCAACTTAACGG 59.905 50.000 0.00 0.00 0.00 4.44
621 1156 2.738314 GCATAACGGTCAACTTAACGGT 59.262 45.455 0.00 0.00 0.00 4.83
622 1157 3.181527 GCATAACGGTCAACTTAACGGTC 60.182 47.826 0.00 0.00 30.82 4.79
623 1158 2.600470 AACGGTCAACTTAACGGTCA 57.400 45.000 0.00 0.00 30.82 4.02
624 1159 2.600470 ACGGTCAACTTAACGGTCAA 57.400 45.000 0.00 0.00 0.00 3.18
625 1160 2.903798 ACGGTCAACTTAACGGTCAAA 58.096 42.857 0.00 0.00 0.00 2.69
626 1161 3.269178 ACGGTCAACTTAACGGTCAAAA 58.731 40.909 0.00 0.00 0.00 2.44
627 1162 3.878699 ACGGTCAACTTAACGGTCAAAAT 59.121 39.130 0.00 0.00 0.00 1.82
628 1163 5.055812 ACGGTCAACTTAACGGTCAAAATA 58.944 37.500 0.00 0.00 0.00 1.40
629 1164 5.526846 ACGGTCAACTTAACGGTCAAAATAA 59.473 36.000 0.00 0.00 0.00 1.40
630 1165 6.038050 ACGGTCAACTTAACGGTCAAAATAAA 59.962 34.615 0.00 0.00 0.00 1.40
631 1166 6.357766 CGGTCAACTTAACGGTCAAAATAAAC 59.642 38.462 0.00 0.00 0.00 2.01
632 1167 7.194962 GGTCAACTTAACGGTCAAAATAAACA 58.805 34.615 0.00 0.00 0.00 2.83
633 1168 7.377662 GGTCAACTTAACGGTCAAAATAAACAG 59.622 37.037 0.00 0.00 0.00 3.16
634 1169 8.124199 GTCAACTTAACGGTCAAAATAAACAGA 58.876 33.333 0.00 0.00 0.00 3.41
635 1170 8.339714 TCAACTTAACGGTCAAAATAAACAGAG 58.660 33.333 0.00 0.00 0.00 3.35
636 1171 7.797038 ACTTAACGGTCAAAATAAACAGAGT 57.203 32.000 0.00 0.00 0.00 3.24
637 1172 8.217131 ACTTAACGGTCAAAATAAACAGAGTT 57.783 30.769 0.00 0.00 0.00 3.01
638 1173 8.126700 ACTTAACGGTCAAAATAAACAGAGTTG 58.873 33.333 0.00 0.00 0.00 3.16
639 1174 6.687081 AACGGTCAAAATAAACAGAGTTGA 57.313 33.333 0.00 0.00 0.00 3.18
640 1175 6.056428 ACGGTCAAAATAAACAGAGTTGAC 57.944 37.500 6.34 6.34 44.66 3.18
641 1176 5.820947 ACGGTCAAAATAAACAGAGTTGACT 59.179 36.000 12.91 0.00 44.73 3.41
642 1177 6.136071 CGGTCAAAATAAACAGAGTTGACTG 58.864 40.000 12.91 10.86 44.73 3.51
648 1183 3.248029 CAGAGTTGACTGTGCCGC 58.752 61.111 0.00 0.00 30.35 6.53
649 1184 2.031163 AGAGTTGACTGTGCCGCC 59.969 61.111 0.00 0.00 0.00 6.13
650 1185 2.280797 GAGTTGACTGTGCCGCCA 60.281 61.111 0.00 0.00 0.00 5.69
651 1186 2.591715 AGTTGACTGTGCCGCCAC 60.592 61.111 0.00 0.00 42.40 5.01
652 1187 4.012895 GTTGACTGTGCCGCCACG 62.013 66.667 0.00 0.00 45.04 4.94
653 1188 4.539083 TTGACTGTGCCGCCACGT 62.539 61.111 0.00 0.00 45.04 4.49
654 1189 4.961511 TGACTGTGCCGCCACGTC 62.962 66.667 12.31 12.31 45.04 4.34
655 1190 4.961511 GACTGTGCCGCCACGTCA 62.962 66.667 13.68 0.00 45.04 4.35
663 1198 4.308458 CGCCACGTCACCCCTGAA 62.308 66.667 0.00 0.00 0.00 3.02
664 1199 2.358737 GCCACGTCACCCCTGAAG 60.359 66.667 0.00 0.00 32.55 3.02
665 1200 2.347490 CCACGTCACCCCTGAAGG 59.653 66.667 0.00 0.00 30.67 3.46
682 1217 4.028490 GGTGGGTCCCGCATGTCA 62.028 66.667 23.12 0.00 35.42 3.58
683 1218 2.272146 GTGGGTCCCGCATGTCAT 59.728 61.111 17.13 0.00 33.65 3.06
684 1219 1.524961 GTGGGTCCCGCATGTCATA 59.475 57.895 17.13 0.00 33.65 2.15
685 1220 0.107410 GTGGGTCCCGCATGTCATAA 60.107 55.000 17.13 0.00 33.65 1.90
686 1221 0.621082 TGGGTCCCGCATGTCATAAA 59.379 50.000 2.65 0.00 0.00 1.40
687 1222 1.021968 GGGTCCCGCATGTCATAAAC 58.978 55.000 0.00 0.00 0.00 2.01
688 1223 0.655733 GGTCCCGCATGTCATAAACG 59.344 55.000 0.00 0.00 0.00 3.60
689 1224 1.365699 GTCCCGCATGTCATAAACGT 58.634 50.000 0.00 0.00 0.00 3.99
690 1225 1.062002 GTCCCGCATGTCATAAACGTG 59.938 52.381 0.00 0.00 46.01 4.49
691 1226 1.083489 CCCGCATGTCATAAACGTGT 58.917 50.000 0.00 0.00 45.19 4.49
692 1227 1.466950 CCCGCATGTCATAAACGTGTT 59.533 47.619 0.00 0.00 45.19 3.32
693 1228 2.095466 CCCGCATGTCATAAACGTGTTT 60.095 45.455 3.21 3.21 45.19 2.83
694 1229 3.125487 CCCGCATGTCATAAACGTGTTTA 59.875 43.478 7.58 7.58 45.19 2.01
695 1230 4.378563 CCCGCATGTCATAAACGTGTTTAA 60.379 41.667 9.06 0.00 45.19 1.52
696 1231 5.147865 CCGCATGTCATAAACGTGTTTAAA 58.852 37.500 9.06 0.00 45.19 1.52
697 1232 5.797934 CCGCATGTCATAAACGTGTTTAAAT 59.202 36.000 9.06 0.00 45.19 1.40
698 1233 6.021782 CCGCATGTCATAAACGTGTTTAAATC 60.022 38.462 9.06 4.08 45.19 2.17
699 1234 6.521477 CGCATGTCATAAACGTGTTTAAATCA 59.479 34.615 9.06 8.58 45.19 2.57
700 1235 7.218014 CGCATGTCATAAACGTGTTTAAATCAT 59.782 33.333 9.06 10.08 45.19 2.45
701 1236 8.523464 GCATGTCATAAACGTGTTTAAATCATC 58.477 33.333 9.06 5.65 45.19 2.92
702 1237 9.773328 CATGTCATAAACGTGTTTAAATCATCT 57.227 29.630 9.06 0.00 39.62 2.90
708 1243 9.763465 ATAAACGTGTTTAAATCATCTAAACCG 57.237 29.630 9.06 11.36 38.11 4.44
709 1244 6.173191 ACGTGTTTAAATCATCTAAACCGG 57.827 37.500 0.00 0.00 38.11 5.28
710 1245 5.702209 ACGTGTTTAAATCATCTAAACCGGT 59.298 36.000 0.00 0.00 38.11 5.28
711 1246 6.128472 ACGTGTTTAAATCATCTAAACCGGTC 60.128 38.462 8.04 0.00 38.11 4.79
712 1247 6.128499 CGTGTTTAAATCATCTAAACCGGTCA 60.128 38.462 8.04 0.00 38.11 4.02
713 1248 7.413657 CGTGTTTAAATCATCTAAACCGGTCAT 60.414 37.037 8.04 2.07 38.11 3.06
714 1249 8.241367 GTGTTTAAATCATCTAAACCGGTCATT 58.759 33.333 8.04 1.06 38.11 2.57
715 1250 8.798402 TGTTTAAATCATCTAAACCGGTCATTT 58.202 29.630 8.04 0.13 38.11 2.32
716 1251 9.634163 GTTTAAATCATCTAAACCGGTCATTTT 57.366 29.630 8.04 0.00 34.54 1.82
797 1332 4.909696 TTTGAATGTGGTAGTTGTGTGG 57.090 40.909 0.00 0.00 0.00 4.17
798 1333 2.857483 TGAATGTGGTAGTTGTGTGGG 58.143 47.619 0.00 0.00 0.00 4.61
799 1334 2.439880 TGAATGTGGTAGTTGTGTGGGA 59.560 45.455 0.00 0.00 0.00 4.37
800 1335 2.561478 ATGTGGTAGTTGTGTGGGAC 57.439 50.000 0.00 0.00 0.00 4.46
801 1336 0.105224 TGTGGTAGTTGTGTGGGACG 59.895 55.000 0.00 0.00 0.00 4.79
802 1337 0.390124 GTGGTAGTTGTGTGGGACGA 59.610 55.000 0.00 0.00 0.00 4.20
803 1338 0.390124 TGGTAGTTGTGTGGGACGAC 59.610 55.000 0.00 0.00 39.09 4.34
804 1339 0.390124 GGTAGTTGTGTGGGACGACA 59.610 55.000 0.00 0.00 41.07 4.35
805 1340 1.202557 GGTAGTTGTGTGGGACGACAA 60.203 52.381 0.00 0.00 41.07 3.18
807 1342 2.019337 GTTGTGTGGGACGACAACC 58.981 57.895 0.00 0.00 44.07 3.77
808 1343 1.153127 TTGTGTGGGACGACAACCC 60.153 57.895 0.00 0.00 46.87 4.11
809 1344 2.281276 GTGTGGGACGACAACCCC 60.281 66.667 0.00 0.00 46.21 4.95
810 1345 2.446994 TGTGGGACGACAACCCCT 60.447 61.111 0.00 0.00 46.21 4.79
811 1346 1.152290 TGTGGGACGACAACCCCTA 60.152 57.895 0.00 0.00 46.21 3.53
812 1347 0.763604 TGTGGGACGACAACCCCTAA 60.764 55.000 0.00 0.00 46.21 2.69
813 1348 0.616891 GTGGGACGACAACCCCTAAT 59.383 55.000 0.00 0.00 46.21 1.73
814 1349 0.616371 TGGGACGACAACCCCTAATG 59.384 55.000 0.00 0.00 46.21 1.90
815 1350 0.616891 GGGACGACAACCCCTAATGT 59.383 55.000 0.00 0.00 41.38 2.71
816 1351 1.677820 GGGACGACAACCCCTAATGTG 60.678 57.143 0.00 0.00 41.38 3.21
817 1352 1.677820 GGACGACAACCCCTAATGTGG 60.678 57.143 0.00 0.00 0.00 4.17
818 1353 1.002773 GACGACAACCCCTAATGTGGT 59.997 52.381 0.00 0.00 40.51 4.16
819 1354 2.234414 GACGACAACCCCTAATGTGGTA 59.766 50.000 0.00 0.00 38.39 3.25
820 1355 2.235402 ACGACAACCCCTAATGTGGTAG 59.765 50.000 0.00 0.00 36.84 3.18
821 1356 2.235402 CGACAACCCCTAATGTGGTAGT 59.765 50.000 0.00 0.00 33.52 2.73
822 1357 3.307199 CGACAACCCCTAATGTGGTAGTT 60.307 47.826 0.00 0.00 33.52 2.24
823 1358 4.659115 GACAACCCCTAATGTGGTAGTTT 58.341 43.478 0.00 0.00 33.52 2.66
824 1359 5.069518 ACAACCCCTAATGTGGTAGTTTT 57.930 39.130 0.00 0.00 33.52 2.43
825 1360 5.460416 ACAACCCCTAATGTGGTAGTTTTT 58.540 37.500 0.00 0.00 33.52 1.94
892 1440 4.501714 CACCATGCCATGCACCGC 62.502 66.667 0.00 0.00 43.04 5.68
968 1516 3.834056 CCTCCCCTCCGCCTCCTA 61.834 72.222 0.00 0.00 0.00 2.94
1021 1571 0.032017 AGTCATCCCTACGCCTCCTT 60.032 55.000 0.00 0.00 0.00 3.36
1056 1606 1.290134 ACCCCAAGAACATCCTCTCC 58.710 55.000 0.00 0.00 0.00 3.71
1057 1607 1.289160 CCCCAAGAACATCCTCTCCA 58.711 55.000 0.00 0.00 0.00 3.86
1059 1609 2.158696 CCCCAAGAACATCCTCTCCATC 60.159 54.545 0.00 0.00 0.00 3.51
1060 1610 2.776536 CCCAAGAACATCCTCTCCATCT 59.223 50.000 0.00 0.00 0.00 2.90
1061 1611 3.181456 CCCAAGAACATCCTCTCCATCTC 60.181 52.174 0.00 0.00 0.00 2.75
1145 1695 2.899044 CTCGTCGAGCCGGATCTCC 61.899 68.421 19.08 6.78 0.00 3.71
1641 2214 9.617053 AAGCTAGGGGTAGAGTTGTAATATAAT 57.383 33.333 0.00 0.00 0.00 1.28
1646 2219 7.038048 GGGGTAGAGTTGTAATATAATACGCC 58.962 42.308 0.00 0.00 37.68 5.68
1648 2221 7.758528 GGGTAGAGTTGTAATATAATACGCCTG 59.241 40.741 0.00 0.00 0.00 4.85
1651 2224 7.948357 AGAGTTGTAATATAATACGCCTGTCA 58.052 34.615 0.00 0.00 0.00 3.58
1661 2234 4.030452 GCCTGTCAAGCGTGCACC 62.030 66.667 12.15 4.10 0.00 5.01
1662 2235 3.716006 CCTGTCAAGCGTGCACCG 61.716 66.667 12.15 7.80 40.40 4.94
1663 2236 2.661537 CTGTCAAGCGTGCACCGA 60.662 61.111 12.15 0.00 39.56 4.69
1664 2237 2.661537 TGTCAAGCGTGCACCGAG 60.662 61.111 12.15 0.00 39.56 4.63
1665 2238 3.414700 GTCAAGCGTGCACCGAGG 61.415 66.667 12.15 0.00 39.56 4.63
1666 2239 4.680237 TCAAGCGTGCACCGAGGG 62.680 66.667 12.15 0.00 39.56 4.30
1738 2319 1.472026 CGTTCGTGGTAATTCGGGGAT 60.472 52.381 0.00 0.00 0.00 3.85
1745 2326 3.813724 GTGGTAATTCGGGGATTAGCTTC 59.186 47.826 9.59 0.00 39.51 3.86
1778 2359 1.202222 CGCCCAAGAATGATGCTGTTC 60.202 52.381 0.00 0.00 0.00 3.18
1920 2502 2.032894 GCATCCACGTACATTTCCATCG 60.033 50.000 0.00 0.00 0.00 3.84
1937 2541 1.939974 TCGGTGTATGCAAGCTCATC 58.060 50.000 0.00 0.00 0.00 2.92
1951 2555 1.000731 GCTCATCTCCTTCTGGGATCG 59.999 57.143 0.00 0.00 44.15 3.69
1960 2564 3.578716 TCCTTCTGGGATCGATACATTCC 59.421 47.826 10.45 1.17 39.58 3.01
1964 2568 5.215252 TCTGGGATCGATACATTCCTTTC 57.785 43.478 10.45 0.00 0.00 2.62
1965 2569 3.990092 TGGGATCGATACATTCCTTTCG 58.010 45.455 10.45 0.00 0.00 3.46
2069 2673 1.194772 GCCGACAAAACTGCTACAGAC 59.805 52.381 0.78 0.00 35.18 3.51
2121 2725 3.884693 TGCAGTGCTTCATCTTCTTTCAA 59.115 39.130 17.60 0.00 0.00 2.69
2137 2741 4.755123 TCTTTCAACAAAGTAGCTGGTAGC 59.245 41.667 0.00 0.00 40.16 3.58
2138 2742 4.377431 CTTTCAACAAAGTAGCTGGTAGCG 60.377 45.833 0.00 0.00 39.28 4.26
2154 2758 2.376808 AGCGGAATGTCAAGACAGAG 57.623 50.000 8.99 1.75 45.48 3.35
2167 2773 3.037431 AGACAGAGTTGATGTGAGCAC 57.963 47.619 0.00 0.00 0.00 4.40
2183 2789 1.005340 GCACAGCTGAATCTCTTCCG 58.995 55.000 23.35 0.00 0.00 4.30
2191 2797 0.464554 GAATCTCTTCCGGGGCCAAG 60.465 60.000 4.39 0.00 0.00 3.61
2202 2808 1.957877 CGGGGCCAAGAGTAACAAAAA 59.042 47.619 4.39 0.00 0.00 1.94
2219 2825 5.058490 ACAAAAACCCAATCAAGAATGCTG 58.942 37.500 0.00 0.00 0.00 4.41
2224 2830 3.094572 CCCAATCAAGAATGCTGAAGGT 58.905 45.455 0.00 0.00 0.00 3.50
2243 2849 1.459455 TTGGCGTTGGTGGGACAATG 61.459 55.000 0.00 0.00 44.16 2.82
2253 2859 0.612744 TGGGACAATGATCTCGTGCA 59.387 50.000 0.00 0.00 31.92 4.57
2271 2877 2.948979 TGCAGTTTACAAAGTCCCACAG 59.051 45.455 0.00 0.00 0.00 3.66
2282 2888 1.689273 AGTCCCACAGAGACAAGACAC 59.311 52.381 0.00 0.00 36.68 3.67
2283 2889 0.673985 TCCCACAGAGACAAGACACG 59.326 55.000 0.00 0.00 0.00 4.49
2284 2890 0.673985 CCCACAGAGACAAGACACGA 59.326 55.000 0.00 0.00 0.00 4.35
2285 2891 1.273606 CCCACAGAGACAAGACACGAT 59.726 52.381 0.00 0.00 0.00 3.73
2286 2892 2.492088 CCCACAGAGACAAGACACGATA 59.508 50.000 0.00 0.00 0.00 2.92
2287 2893 3.056821 CCCACAGAGACAAGACACGATAA 60.057 47.826 0.00 0.00 0.00 1.75
2288 2894 4.556233 CCACAGAGACAAGACACGATAAA 58.444 43.478 0.00 0.00 0.00 1.40
2290 2896 4.090642 CACAGAGACAAGACACGATAAAGC 59.909 45.833 0.00 0.00 0.00 3.51
2292 2898 3.258372 AGAGACAAGACACGATAAAGCCA 59.742 43.478 0.00 0.00 0.00 4.75
2293 2899 4.081420 AGAGACAAGACACGATAAAGCCAT 60.081 41.667 0.00 0.00 0.00 4.40
2294 2900 4.579869 AGACAAGACACGATAAAGCCATT 58.420 39.130 0.00 0.00 0.00 3.16
2295 2901 5.003804 AGACAAGACACGATAAAGCCATTT 58.996 37.500 0.00 0.00 0.00 2.32
2296 2902 6.170506 AGACAAGACACGATAAAGCCATTTA 58.829 36.000 0.00 0.00 35.41 1.40
2297 2903 6.092259 AGACAAGACACGATAAAGCCATTTAC 59.908 38.462 0.00 0.00 33.78 2.01
2298 2904 5.703592 ACAAGACACGATAAAGCCATTTACA 59.296 36.000 0.00 0.00 33.78 2.41
2299 2905 6.374333 ACAAGACACGATAAAGCCATTTACAT 59.626 34.615 0.00 0.00 33.78 2.29
2300 2906 7.094377 ACAAGACACGATAAAGCCATTTACATT 60.094 33.333 0.00 0.00 33.78 2.71
2301 2907 7.016361 AGACACGATAAAGCCATTTACATTC 57.984 36.000 0.00 0.00 33.78 2.67
2302 2908 5.806286 ACACGATAAAGCCATTTACATTCG 58.194 37.500 0.00 0.00 37.13 3.34
2303 2909 4.670621 CACGATAAAGCCATTTACATTCGC 59.329 41.667 0.00 0.00 35.67 4.70
2304 2910 3.900116 CGATAAAGCCATTTACATTCGCG 59.100 43.478 0.00 0.00 33.78 5.87
2305 2911 4.551990 CGATAAAGCCATTTACATTCGCGT 60.552 41.667 5.77 0.00 33.78 6.01
2306 2912 3.569250 AAAGCCATTTACATTCGCGTT 57.431 38.095 5.77 0.00 0.00 4.84
2307 2913 2.825086 AGCCATTTACATTCGCGTTC 57.175 45.000 5.77 0.00 0.00 3.95
2308 2914 1.400494 AGCCATTTACATTCGCGTTCC 59.600 47.619 5.77 0.00 0.00 3.62
2309 2915 1.131504 GCCATTTACATTCGCGTTCCA 59.868 47.619 5.77 0.00 0.00 3.53
2310 2916 2.223479 GCCATTTACATTCGCGTTCCAT 60.223 45.455 5.77 0.00 0.00 3.41
2311 2917 3.617669 CCATTTACATTCGCGTTCCATC 58.382 45.455 5.77 0.00 0.00 3.51
2312 2918 3.548014 CCATTTACATTCGCGTTCCATCC 60.548 47.826 5.77 0.00 0.00 3.51
2313 2919 2.388310 TTACATTCGCGTTCCATCCA 57.612 45.000 5.77 0.00 0.00 3.41
2314 2920 1.647346 TACATTCGCGTTCCATCCAC 58.353 50.000 5.77 0.00 0.00 4.02
2315 2921 0.321210 ACATTCGCGTTCCATCCACA 60.321 50.000 5.77 0.00 0.00 4.17
2316 2922 0.374758 CATTCGCGTTCCATCCACAG 59.625 55.000 5.77 0.00 0.00 3.66
2317 2923 1.369091 ATTCGCGTTCCATCCACAGC 61.369 55.000 5.77 0.00 0.00 4.40
2318 2924 3.853330 CGCGTTCCATCCACAGCG 61.853 66.667 0.00 0.00 41.56 5.18
2319 2925 4.166011 GCGTTCCATCCACAGCGC 62.166 66.667 0.00 0.00 38.15 5.92
2320 2926 3.499737 CGTTCCATCCACAGCGCC 61.500 66.667 2.29 0.00 0.00 6.53
2321 2927 2.045926 GTTCCATCCACAGCGCCT 60.046 61.111 2.29 0.00 0.00 5.52
2322 2928 1.220749 GTTCCATCCACAGCGCCTA 59.779 57.895 2.29 0.00 0.00 3.93
2323 2929 0.179045 GTTCCATCCACAGCGCCTAT 60.179 55.000 2.29 0.00 0.00 2.57
2324 2930 0.106708 TTCCATCCACAGCGCCTATC 59.893 55.000 2.29 0.00 0.00 2.08
2325 2931 0.760567 TCCATCCACAGCGCCTATCT 60.761 55.000 2.29 0.00 0.00 1.98
2326 2932 0.320247 CCATCCACAGCGCCTATCTC 60.320 60.000 2.29 0.00 0.00 2.75
2327 2933 0.320247 CATCCACAGCGCCTATCTCC 60.320 60.000 2.29 0.00 0.00 3.71
2328 2934 0.760567 ATCCACAGCGCCTATCTCCA 60.761 55.000 2.29 0.00 0.00 3.86
2329 2935 1.227380 CCACAGCGCCTATCTCCAC 60.227 63.158 2.29 0.00 0.00 4.02
2330 2936 1.227380 CACAGCGCCTATCTCCACC 60.227 63.158 2.29 0.00 0.00 4.61
2331 2937 2.028190 CAGCGCCTATCTCCACCG 59.972 66.667 2.29 0.00 0.00 4.94
2332 2938 2.442272 AGCGCCTATCTCCACCGT 60.442 61.111 2.29 0.00 0.00 4.83
2333 2939 2.027751 GCGCCTATCTCCACCGTC 59.972 66.667 0.00 0.00 0.00 4.79
2334 2940 2.728817 CGCCTATCTCCACCGTCC 59.271 66.667 0.00 0.00 0.00 4.79
2335 2941 2.125326 CGCCTATCTCCACCGTCCA 61.125 63.158 0.00 0.00 0.00 4.02
2336 2942 1.672854 CGCCTATCTCCACCGTCCAA 61.673 60.000 0.00 0.00 0.00 3.53
2337 2943 0.539986 GCCTATCTCCACCGTCCAAA 59.460 55.000 0.00 0.00 0.00 3.28
2338 2944 1.473434 GCCTATCTCCACCGTCCAAAG 60.473 57.143 0.00 0.00 0.00 2.77
2339 2945 1.473434 CCTATCTCCACCGTCCAAAGC 60.473 57.143 0.00 0.00 0.00 3.51
2340 2946 1.482593 CTATCTCCACCGTCCAAAGCT 59.517 52.381 0.00 0.00 0.00 3.74
2341 2947 0.036010 ATCTCCACCGTCCAAAGCTG 60.036 55.000 0.00 0.00 0.00 4.24
2342 2948 2.281484 TCCACCGTCCAAAGCTGC 60.281 61.111 0.00 0.00 0.00 5.25
2343 2949 2.281761 CCACCGTCCAAAGCTGCT 60.282 61.111 0.00 0.00 0.00 4.24
2344 2950 2.328099 CCACCGTCCAAAGCTGCTC 61.328 63.158 1.00 0.00 0.00 4.26
2345 2951 1.597854 CACCGTCCAAAGCTGCTCA 60.598 57.895 1.00 0.00 0.00 4.26
2346 2952 1.148273 ACCGTCCAAAGCTGCTCAA 59.852 52.632 1.00 0.00 0.00 3.02
2347 2953 0.886490 ACCGTCCAAAGCTGCTCAAG 60.886 55.000 1.00 0.00 0.00 3.02
2348 2954 0.603707 CCGTCCAAAGCTGCTCAAGA 60.604 55.000 1.00 0.00 0.00 3.02
2349 2955 1.446907 CGTCCAAAGCTGCTCAAGAT 58.553 50.000 1.00 0.00 0.00 2.40
2350 2956 1.396301 CGTCCAAAGCTGCTCAAGATC 59.604 52.381 1.00 0.00 0.00 2.75
2351 2957 1.396301 GTCCAAAGCTGCTCAAGATCG 59.604 52.381 1.00 0.00 0.00 3.69
2352 2958 1.276138 TCCAAAGCTGCTCAAGATCGA 59.724 47.619 1.00 0.00 0.00 3.59
2353 2959 2.079158 CCAAAGCTGCTCAAGATCGAA 58.921 47.619 1.00 0.00 0.00 3.71
2354 2960 2.485426 CCAAAGCTGCTCAAGATCGAAA 59.515 45.455 1.00 0.00 0.00 3.46
2355 2961 3.425892 CCAAAGCTGCTCAAGATCGAAAG 60.426 47.826 1.00 0.00 0.00 2.62
2370 2976 4.934075 TCGAAAGATGCATGTGAGAAAG 57.066 40.909 2.46 0.00 33.31 2.62
2371 2977 3.125829 TCGAAAGATGCATGTGAGAAAGC 59.874 43.478 2.46 0.00 33.31 3.51
2372 2978 3.126514 CGAAAGATGCATGTGAGAAAGCT 59.873 43.478 2.46 0.00 0.00 3.74
2503 3112 2.328099 CCGAAGCAGCACCAAGACC 61.328 63.158 0.00 0.00 0.00 3.85
2511 3120 1.270550 CAGCACCAAGACCCATCAAAC 59.729 52.381 0.00 0.00 0.00 2.93
2527 3137 1.106351 AAACACTGGTCGCCATGCAA 61.106 50.000 0.00 0.00 30.82 4.08
2528 3138 1.106351 AACACTGGTCGCCATGCAAA 61.106 50.000 0.00 0.00 30.82 3.68
2529 3139 0.895100 ACACTGGTCGCCATGCAAAT 60.895 50.000 0.00 0.00 30.82 2.32
2530 3140 0.244450 CACTGGTCGCCATGCAAATT 59.756 50.000 0.00 0.00 30.82 1.82
2531 3141 0.527565 ACTGGTCGCCATGCAAATTC 59.472 50.000 0.00 0.00 30.82 2.17
2534 3144 2.423185 CTGGTCGCCATGCAAATTCTAA 59.577 45.455 0.00 0.00 30.82 2.10
2594 3204 1.209019 GTGCAGAGTCAGATGATGGGT 59.791 52.381 0.00 0.00 0.00 4.51
2595 3205 1.208776 TGCAGAGTCAGATGATGGGTG 59.791 52.381 0.00 0.00 0.00 4.61
2630 3241 1.341285 CCAATTCCTGGCTGTCATGGA 60.341 52.381 0.00 0.00 38.76 3.41
2636 3249 0.747283 CTGGCTGTCATGGAGCTTCC 60.747 60.000 14.82 0.00 36.63 3.46
2700 3313 0.463833 ATGCTTAGTAACGGGCCTGC 60.464 55.000 12.89 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 2.434359 GCAGACTCGTTTCCCCCG 60.434 66.667 0.00 0.00 0.00 5.73
130 131 2.592861 GGCCAGATGGATGTCGCC 60.593 66.667 2.18 0.00 37.39 5.54
188 189 1.306568 GCTTCTCCACCTCCTCCCT 60.307 63.158 0.00 0.00 0.00 4.20
343 554 0.250727 ACAACAACCATGAGGACCCG 60.251 55.000 0.00 0.00 38.69 5.28
345 556 1.156736 CGACAACAACCATGAGGACC 58.843 55.000 0.00 0.00 38.69 4.46
352 885 0.821711 CCCACCACGACAACAACCAT 60.822 55.000 0.00 0.00 0.00 3.55
365 898 4.715130 CGTCCCCTCCTCCCACCA 62.715 72.222 0.00 0.00 0.00 4.17
507 1041 4.189580 CCCGATCCCCACGCCATT 62.190 66.667 0.00 0.00 0.00 3.16
597 1132 3.181524 CGTTAAGTTGACCGTTATGCCAG 60.182 47.826 0.00 0.00 0.00 4.85
598 1133 2.737783 CGTTAAGTTGACCGTTATGCCA 59.262 45.455 0.00 0.00 0.00 4.92
599 1134 2.094734 CCGTTAAGTTGACCGTTATGCC 59.905 50.000 0.00 0.00 0.00 4.40
600 1135 2.738314 ACCGTTAAGTTGACCGTTATGC 59.262 45.455 0.00 0.00 0.00 3.14
601 1136 3.989167 TGACCGTTAAGTTGACCGTTATG 59.011 43.478 0.00 0.00 0.00 1.90
602 1137 4.255833 TGACCGTTAAGTTGACCGTTAT 57.744 40.909 0.00 0.00 0.00 1.89
603 1138 3.724508 TGACCGTTAAGTTGACCGTTA 57.275 42.857 0.00 0.00 0.00 3.18
604 1139 2.600470 TGACCGTTAAGTTGACCGTT 57.400 45.000 0.00 0.00 0.00 4.44
605 1140 2.600470 TTGACCGTTAAGTTGACCGT 57.400 45.000 0.00 0.00 0.00 4.83
606 1141 3.948196 TTTTGACCGTTAAGTTGACCG 57.052 42.857 0.00 0.00 0.00 4.79
607 1142 7.194962 TGTTTATTTTGACCGTTAAGTTGACC 58.805 34.615 0.00 0.00 0.00 4.02
608 1143 8.124199 TCTGTTTATTTTGACCGTTAAGTTGAC 58.876 33.333 0.00 0.00 0.00 3.18
609 1144 8.211116 TCTGTTTATTTTGACCGTTAAGTTGA 57.789 30.769 0.00 0.00 0.00 3.18
610 1145 8.126700 ACTCTGTTTATTTTGACCGTTAAGTTG 58.873 33.333 0.00 0.00 0.00 3.16
611 1146 8.217131 ACTCTGTTTATTTTGACCGTTAAGTT 57.783 30.769 0.00 0.00 0.00 2.66
612 1147 7.797038 ACTCTGTTTATTTTGACCGTTAAGT 57.203 32.000 0.00 0.00 0.00 2.24
613 1148 8.339714 TCAACTCTGTTTATTTTGACCGTTAAG 58.660 33.333 0.00 0.00 0.00 1.85
614 1149 8.124199 GTCAACTCTGTTTATTTTGACCGTTAA 58.876 33.333 0.00 0.00 40.01 2.01
615 1150 7.496591 AGTCAACTCTGTTTATTTTGACCGTTA 59.503 33.333 8.72 0.00 44.69 3.18
616 1151 6.317893 AGTCAACTCTGTTTATTTTGACCGTT 59.682 34.615 8.72 0.00 44.69 4.44
617 1152 5.820947 AGTCAACTCTGTTTATTTTGACCGT 59.179 36.000 8.72 0.00 44.69 4.83
618 1153 6.136071 CAGTCAACTCTGTTTATTTTGACCG 58.864 40.000 8.72 0.00 44.69 4.79
619 1154 6.912591 CACAGTCAACTCTGTTTATTTTGACC 59.087 38.462 8.72 0.00 44.92 4.02
620 1155 6.414987 GCACAGTCAACTCTGTTTATTTTGAC 59.585 38.462 4.90 4.90 44.92 3.18
621 1156 6.459573 GGCACAGTCAACTCTGTTTATTTTGA 60.460 38.462 0.00 0.00 44.92 2.69
622 1157 5.687285 GGCACAGTCAACTCTGTTTATTTTG 59.313 40.000 0.00 0.00 44.92 2.44
623 1158 5.505654 CGGCACAGTCAACTCTGTTTATTTT 60.506 40.000 0.00 0.00 44.92 1.82
624 1159 4.024048 CGGCACAGTCAACTCTGTTTATTT 60.024 41.667 0.00 0.00 44.92 1.40
625 1160 3.498397 CGGCACAGTCAACTCTGTTTATT 59.502 43.478 0.00 0.00 44.92 1.40
626 1161 3.067106 CGGCACAGTCAACTCTGTTTAT 58.933 45.455 0.00 0.00 44.92 1.40
627 1162 2.479837 CGGCACAGTCAACTCTGTTTA 58.520 47.619 0.00 0.00 44.92 2.01
628 1163 1.299541 CGGCACAGTCAACTCTGTTT 58.700 50.000 0.00 0.00 44.92 2.83
629 1164 1.160329 GCGGCACAGTCAACTCTGTT 61.160 55.000 0.00 0.00 44.92 3.16
631 1166 2.320587 GGCGGCACAGTCAACTCTG 61.321 63.158 3.07 0.00 40.80 3.35
632 1167 2.031163 GGCGGCACAGTCAACTCT 59.969 61.111 3.07 0.00 0.00 3.24
633 1168 2.280797 TGGCGGCACAGTCAACTC 60.281 61.111 7.97 0.00 0.00 3.01
634 1169 2.591715 GTGGCGGCACAGTCAACT 60.592 61.111 34.40 0.00 0.00 3.16
635 1170 4.012895 CGTGGCGGCACAGTCAAC 62.013 66.667 36.79 12.80 0.00 3.18
636 1171 4.539083 ACGTGGCGGCACAGTCAA 62.539 61.111 36.79 0.09 0.00 3.18
637 1172 4.961511 GACGTGGCGGCACAGTCA 62.962 66.667 36.89 10.51 33.63 3.41
638 1173 4.961511 TGACGTGGCGGCACAGTC 62.962 66.667 36.13 36.13 41.22 3.51
646 1181 4.308458 TTCAGGGGTGACGTGGCG 62.308 66.667 0.00 0.00 35.71 5.69
647 1182 2.358737 CTTCAGGGGTGACGTGGC 60.359 66.667 0.00 0.00 35.71 5.01
648 1183 2.347490 CCTTCAGGGGTGACGTGG 59.653 66.667 0.00 0.00 35.71 4.94
665 1200 1.978455 TATGACATGCGGGACCCACC 61.978 60.000 12.15 0.76 38.08 4.61
666 1201 0.107410 TTATGACATGCGGGACCCAC 60.107 55.000 12.15 0.13 0.00 4.61
667 1202 0.621082 TTTATGACATGCGGGACCCA 59.379 50.000 12.15 0.00 0.00 4.51
668 1203 1.021968 GTTTATGACATGCGGGACCC 58.978 55.000 0.00 0.00 0.00 4.46
669 1204 0.655733 CGTTTATGACATGCGGGACC 59.344 55.000 0.00 0.00 0.00 4.46
670 1205 1.062002 CACGTTTATGACATGCGGGAC 59.938 52.381 0.00 0.00 0.00 4.46
671 1206 1.338294 ACACGTTTATGACATGCGGGA 60.338 47.619 14.86 0.00 0.00 5.14
672 1207 1.083489 ACACGTTTATGACATGCGGG 58.917 50.000 0.00 4.08 0.00 6.13
673 1208 2.892373 AACACGTTTATGACATGCGG 57.108 45.000 0.00 0.00 0.00 5.69
674 1209 6.521477 TGATTTAAACACGTTTATGACATGCG 59.479 34.615 3.35 3.03 35.27 4.73
675 1210 7.789341 TGATTTAAACACGTTTATGACATGC 57.211 32.000 3.35 0.00 35.27 4.06
676 1211 9.773328 AGATGATTTAAACACGTTTATGACATG 57.227 29.630 14.53 0.00 35.27 3.21
682 1217 9.763465 CGGTTTAGATGATTTAAACACGTTTAT 57.237 29.630 17.05 0.00 40.87 1.40
683 1218 8.229137 CCGGTTTAGATGATTTAAACACGTTTA 58.771 33.333 17.05 0.00 40.87 2.01
684 1219 7.079475 CCGGTTTAGATGATTTAAACACGTTT 58.921 34.615 17.05 0.22 40.87 3.60
685 1220 6.205270 ACCGGTTTAGATGATTTAAACACGTT 59.795 34.615 17.05 7.11 40.87 3.99
686 1221 5.702209 ACCGGTTTAGATGATTTAAACACGT 59.298 36.000 17.05 10.67 40.87 4.49
687 1222 6.128499 TGACCGGTTTAGATGATTTAAACACG 60.128 38.462 9.42 16.24 40.87 4.49
688 1223 7.136289 TGACCGGTTTAGATGATTTAAACAC 57.864 36.000 9.42 8.24 40.87 3.32
689 1224 7.931578 ATGACCGGTTTAGATGATTTAAACA 57.068 32.000 9.42 0.00 40.87 2.83
690 1225 9.634163 AAAATGACCGGTTTAGATGATTTAAAC 57.366 29.630 9.42 9.41 39.26 2.01
774 1309 5.394663 CCCACACAACTACCACATTCAAAAA 60.395 40.000 0.00 0.00 0.00 1.94
775 1310 4.098654 CCCACACAACTACCACATTCAAAA 59.901 41.667 0.00 0.00 0.00 2.44
776 1311 3.634448 CCCACACAACTACCACATTCAAA 59.366 43.478 0.00 0.00 0.00 2.69
777 1312 3.117851 TCCCACACAACTACCACATTCAA 60.118 43.478 0.00 0.00 0.00 2.69
778 1313 2.439880 TCCCACACAACTACCACATTCA 59.560 45.455 0.00 0.00 0.00 2.57
779 1314 2.812011 GTCCCACACAACTACCACATTC 59.188 50.000 0.00 0.00 0.00 2.67
780 1315 2.808933 CGTCCCACACAACTACCACATT 60.809 50.000 0.00 0.00 0.00 2.71
781 1316 1.270625 CGTCCCACACAACTACCACAT 60.271 52.381 0.00 0.00 0.00 3.21
782 1317 0.105224 CGTCCCACACAACTACCACA 59.895 55.000 0.00 0.00 0.00 4.17
783 1318 0.390124 TCGTCCCACACAACTACCAC 59.610 55.000 0.00 0.00 0.00 4.16
784 1319 0.390124 GTCGTCCCACACAACTACCA 59.610 55.000 0.00 0.00 0.00 3.25
785 1320 0.390124 TGTCGTCCCACACAACTACC 59.610 55.000 0.00 0.00 0.00 3.18
786 1321 1.862827 GTTGTCGTCCCACACAACTAC 59.137 52.381 7.96 0.00 45.97 2.73
787 1322 2.228138 GTTGTCGTCCCACACAACTA 57.772 50.000 7.96 0.00 45.97 2.24
788 1323 3.074594 GTTGTCGTCCCACACAACT 57.925 52.632 7.96 0.00 45.97 3.16
790 1325 1.153127 GGGTTGTCGTCCCACACAA 60.153 57.895 0.00 0.00 44.05 3.33
791 1326 2.506962 GGGTTGTCGTCCCACACA 59.493 61.111 0.00 0.00 44.05 3.72
792 1327 1.474332 TAGGGGTTGTCGTCCCACAC 61.474 60.000 3.37 0.00 46.26 3.82
793 1328 0.763604 TTAGGGGTTGTCGTCCCACA 60.764 55.000 3.37 0.00 46.26 4.17
794 1329 0.616891 ATTAGGGGTTGTCGTCCCAC 59.383 55.000 3.37 0.00 46.26 4.61
795 1330 0.616371 CATTAGGGGTTGTCGTCCCA 59.384 55.000 3.37 0.00 46.26 4.37
796 1331 0.616891 ACATTAGGGGTTGTCGTCCC 59.383 55.000 0.00 0.00 43.90 4.46
797 1332 1.677820 CCACATTAGGGGTTGTCGTCC 60.678 57.143 0.00 0.00 0.00 4.79
798 1333 1.002773 ACCACATTAGGGGTTGTCGTC 59.997 52.381 0.00 0.00 32.12 4.20
799 1334 1.061546 ACCACATTAGGGGTTGTCGT 58.938 50.000 0.00 0.00 32.12 4.34
800 1335 2.235402 ACTACCACATTAGGGGTTGTCG 59.765 50.000 0.00 0.00 38.47 4.35
801 1336 3.994931 ACTACCACATTAGGGGTTGTC 57.005 47.619 0.00 0.00 38.47 3.18
802 1337 4.734843 AAACTACCACATTAGGGGTTGT 57.265 40.909 0.00 0.00 43.37 3.32
824 1359 6.044404 AGAGGAGAGGGAGTATTTGACAAAAA 59.956 38.462 4.41 0.00 0.00 1.94
825 1360 5.548056 AGAGGAGAGGGAGTATTTGACAAAA 59.452 40.000 4.41 0.00 0.00 2.44
826 1361 5.094387 AGAGGAGAGGGAGTATTTGACAAA 58.906 41.667 2.48 2.48 0.00 2.83
827 1362 4.689062 AGAGGAGAGGGAGTATTTGACAA 58.311 43.478 0.00 0.00 0.00 3.18
828 1363 4.282496 GAGAGGAGAGGGAGTATTTGACA 58.718 47.826 0.00 0.00 0.00 3.58
829 1364 3.639561 GGAGAGGAGAGGGAGTATTTGAC 59.360 52.174 0.00 0.00 0.00 3.18
830 1365 3.533907 AGGAGAGGAGAGGGAGTATTTGA 59.466 47.826 0.00 0.00 0.00 2.69
831 1366 3.895041 GAGGAGAGGAGAGGGAGTATTTG 59.105 52.174 0.00 0.00 0.00 2.32
832 1367 3.116900 GGAGGAGAGGAGAGGGAGTATTT 60.117 52.174 0.00 0.00 0.00 1.40
833 1368 2.449345 GGAGGAGAGGAGAGGGAGTATT 59.551 54.545 0.00 0.00 0.00 1.89
834 1369 2.070573 GGAGGAGAGGAGAGGGAGTAT 58.929 57.143 0.00 0.00 0.00 2.12
835 1370 1.275061 TGGAGGAGAGGAGAGGGAGTA 60.275 57.143 0.00 0.00 0.00 2.59
836 1371 0.553862 TGGAGGAGAGGAGAGGGAGT 60.554 60.000 0.00 0.00 0.00 3.85
837 1372 0.185901 CTGGAGGAGAGGAGAGGGAG 59.814 65.000 0.00 0.00 0.00 4.30
838 1373 1.292941 CCTGGAGGAGAGGAGAGGGA 61.293 65.000 0.00 0.00 37.39 4.20
892 1440 4.029809 GGGTCAAGGTGTCGGGGG 62.030 72.222 0.00 0.00 0.00 5.40
964 1512 5.044328 AGGTGGCGAGAGGTTATATATAGGA 60.044 44.000 0.00 0.00 0.00 2.94
967 1515 5.198965 GGAGGTGGCGAGAGGTTATATATA 58.801 45.833 0.00 0.00 0.00 0.86
968 1516 4.024670 GGAGGTGGCGAGAGGTTATATAT 58.975 47.826 0.00 0.00 0.00 0.86
1021 1571 1.346722 GGGGTTCAGTCGGAAAGAGAA 59.653 52.381 0.00 0.00 37.23 2.87
1056 1606 3.468770 CCATTGGAAGCAGAGAGAGATG 58.531 50.000 0.00 0.00 0.00 2.90
1057 1607 2.158784 GCCATTGGAAGCAGAGAGAGAT 60.159 50.000 6.95 0.00 0.00 2.75
1059 1609 1.666054 GCCATTGGAAGCAGAGAGAG 58.334 55.000 6.95 0.00 0.00 3.20
1060 1610 0.107993 CGCCATTGGAAGCAGAGAGA 60.108 55.000 6.95 0.00 0.00 3.10
1061 1611 0.107993 TCGCCATTGGAAGCAGAGAG 60.108 55.000 6.95 0.00 0.00 3.20
1277 1845 3.530104 CGCGACTTGCCGACGTAC 61.530 66.667 0.00 0.00 42.08 3.67
1552 2124 4.749310 ACTCTGGCGAGCTTGGCG 62.749 66.667 21.60 16.03 41.09 5.69
1553 2125 2.359230 AACTCTGGCGAGCTTGGC 60.359 61.111 20.47 20.47 41.09 4.52
1646 2219 2.661537 TCGGTGCACGCTTGACAG 60.662 61.111 11.45 0.00 43.86 3.51
1648 2221 3.414700 CCTCGGTGCACGCTTGAC 61.415 66.667 11.45 0.00 43.86 3.18
1658 2231 4.778415 CTCACGTCGCCCTCGGTG 62.778 72.222 0.00 0.00 36.13 4.94
1660 2233 4.778415 CACTCACGTCGCCCTCGG 62.778 72.222 0.00 0.00 36.13 4.63
1661 2234 4.778415 CCACTCACGTCGCCCTCG 62.778 72.222 0.00 0.00 0.00 4.63
1662 2235 4.436998 CCCACTCACGTCGCCCTC 62.437 72.222 0.00 0.00 0.00 4.30
1663 2236 3.873679 TACCCACTCACGTCGCCCT 62.874 63.158 0.00 0.00 0.00 5.19
1664 2237 2.234913 ATTACCCACTCACGTCGCCC 62.235 60.000 0.00 0.00 0.00 6.13
1665 2238 0.390735 AATTACCCACTCACGTCGCC 60.391 55.000 0.00 0.00 0.00 5.54
1666 2239 2.282701 TAATTACCCACTCACGTCGC 57.717 50.000 0.00 0.00 0.00 5.19
1667 2240 3.841643 ACTTAATTACCCACTCACGTCG 58.158 45.455 0.00 0.00 0.00 5.12
1668 2241 4.992951 ACAACTTAATTACCCACTCACGTC 59.007 41.667 0.00 0.00 0.00 4.34
1669 2242 4.753107 CACAACTTAATTACCCACTCACGT 59.247 41.667 0.00 0.00 0.00 4.49
1670 2243 4.753107 ACACAACTTAATTACCCACTCACG 59.247 41.667 0.00 0.00 0.00 4.35
1671 2244 5.529800 ACACACAACTTAATTACCCACTCAC 59.470 40.000 0.00 0.00 0.00 3.51
1672 2245 5.529430 CACACACAACTTAATTACCCACTCA 59.471 40.000 0.00 0.00 0.00 3.41
1673 2246 5.048991 CCACACACAACTTAATTACCCACTC 60.049 44.000 0.00 0.00 0.00 3.51
1678 2251 7.448748 AATCTCCACACACAACTTAATTACC 57.551 36.000 0.00 0.00 0.00 2.85
1688 2261 8.356657 CAAGGTTAAATAAATCTCCACACACAA 58.643 33.333 0.00 0.00 0.00 3.33
1778 2359 5.397360 AGGGAAATTGATTAATAGCCCCAG 58.603 41.667 13.55 0.00 39.11 4.45
1920 2502 2.158842 AGGAGATGAGCTTGCATACACC 60.159 50.000 0.00 0.00 0.00 4.16
1951 2555 7.713073 AGGAAAGAGATTCGAAAGGAATGTATC 59.287 37.037 0.00 0.00 45.33 2.24
2019 2623 1.133637 TGCCTTCAACTACCAGCCAAA 60.134 47.619 0.00 0.00 0.00 3.28
2069 2673 6.564709 TTTTCTCCTGTCAATGACATCTTG 57.435 37.500 17.10 4.99 41.94 3.02
2121 2725 1.263356 TCCGCTACCAGCTACTTTGT 58.737 50.000 0.00 0.00 39.60 2.83
2137 2741 3.653344 TCAACTCTGTCTTGACATTCCG 58.347 45.455 3.79 0.00 0.00 4.30
2138 2742 4.999950 ACATCAACTCTGTCTTGACATTCC 59.000 41.667 3.79 0.00 30.46 3.01
2154 2758 1.516161 TCAGCTGTGCTCACATCAAC 58.484 50.000 14.67 0.00 41.01 3.18
2167 2773 0.179062 CCCCGGAAGAGATTCAGCTG 60.179 60.000 7.63 7.63 0.00 4.24
2183 2789 2.036733 GGTTTTTGTTACTCTTGGCCCC 59.963 50.000 0.00 0.00 0.00 5.80
2191 2797 7.095649 GCATTCTTGATTGGGTTTTTGTTACTC 60.096 37.037 0.00 0.00 0.00 2.59
2202 2808 3.094572 CCTTCAGCATTCTTGATTGGGT 58.905 45.455 0.00 0.00 0.00 4.51
2219 2825 2.561037 CCCACCAACGCCAACCTTC 61.561 63.158 0.00 0.00 0.00 3.46
2224 2830 1.152652 ATTGTCCCACCAACGCCAA 60.153 52.632 0.00 0.00 0.00 4.52
2243 2849 4.143094 GGACTTTGTAAACTGCACGAGATC 60.143 45.833 0.00 0.00 0.00 2.75
2253 2859 4.163458 TGTCTCTGTGGGACTTTGTAAACT 59.837 41.667 0.00 0.00 35.04 2.66
2271 2877 3.585862 TGGCTTTATCGTGTCTTGTCTC 58.414 45.455 0.00 0.00 0.00 3.36
2282 2888 3.900116 CGCGAATGTAAATGGCTTTATCG 59.100 43.478 0.00 0.00 33.28 2.92
2283 2889 4.844267 ACGCGAATGTAAATGGCTTTATC 58.156 39.130 15.93 0.00 0.00 1.75
2284 2890 4.893424 ACGCGAATGTAAATGGCTTTAT 57.107 36.364 15.93 0.00 0.00 1.40
2285 2891 4.437659 GGAACGCGAATGTAAATGGCTTTA 60.438 41.667 15.93 0.00 0.00 1.85
2286 2892 3.498082 GAACGCGAATGTAAATGGCTTT 58.502 40.909 15.93 0.00 0.00 3.51
2287 2893 2.159435 GGAACGCGAATGTAAATGGCTT 60.159 45.455 15.93 0.00 0.00 4.35
2288 2894 1.400494 GGAACGCGAATGTAAATGGCT 59.600 47.619 15.93 0.00 0.00 4.75
2290 2896 3.548014 GGATGGAACGCGAATGTAAATGG 60.548 47.826 15.93 0.00 0.00 3.16
2292 2898 3.064820 GTGGATGGAACGCGAATGTAAAT 59.935 43.478 15.93 0.00 0.00 1.40
2293 2899 2.417239 GTGGATGGAACGCGAATGTAAA 59.583 45.455 15.93 0.00 0.00 2.01
2294 2900 2.004017 GTGGATGGAACGCGAATGTAA 58.996 47.619 15.93 0.00 0.00 2.41
2295 2901 1.066787 TGTGGATGGAACGCGAATGTA 60.067 47.619 15.93 0.00 0.00 2.29
2296 2902 0.321210 TGTGGATGGAACGCGAATGT 60.321 50.000 15.93 0.00 0.00 2.71
2297 2903 0.374758 CTGTGGATGGAACGCGAATG 59.625 55.000 15.93 0.00 0.00 2.67
2298 2904 1.369091 GCTGTGGATGGAACGCGAAT 61.369 55.000 15.93 0.00 0.00 3.34
2299 2905 2.032634 GCTGTGGATGGAACGCGAA 61.033 57.895 15.93 0.00 0.00 4.70
2300 2906 2.434185 GCTGTGGATGGAACGCGA 60.434 61.111 15.93 0.00 0.00 5.87
2301 2907 3.853330 CGCTGTGGATGGAACGCG 61.853 66.667 3.53 3.53 35.50 6.01
2302 2908 4.166011 GCGCTGTGGATGGAACGC 62.166 66.667 0.00 0.00 39.49 4.84
2303 2909 2.572095 TAGGCGCTGTGGATGGAACG 62.572 60.000 7.64 0.00 0.00 3.95
2304 2910 0.179045 ATAGGCGCTGTGGATGGAAC 60.179 55.000 7.64 0.00 0.00 3.62
2305 2911 0.106708 GATAGGCGCTGTGGATGGAA 59.893 55.000 7.64 0.00 0.00 3.53
2306 2912 0.760567 AGATAGGCGCTGTGGATGGA 60.761 55.000 7.64 0.00 0.00 3.41
2307 2913 0.320247 GAGATAGGCGCTGTGGATGG 60.320 60.000 7.64 0.00 0.00 3.51
2308 2914 0.320247 GGAGATAGGCGCTGTGGATG 60.320 60.000 7.64 0.00 0.00 3.51
2309 2915 0.760567 TGGAGATAGGCGCTGTGGAT 60.761 55.000 7.64 0.00 0.00 3.41
2310 2916 1.381191 TGGAGATAGGCGCTGTGGA 60.381 57.895 7.64 0.00 0.00 4.02
2311 2917 1.227380 GTGGAGATAGGCGCTGTGG 60.227 63.158 7.64 0.00 0.00 4.17
2312 2918 1.227380 GGTGGAGATAGGCGCTGTG 60.227 63.158 7.64 0.00 0.00 3.66
2313 2919 2.786495 CGGTGGAGATAGGCGCTGT 61.786 63.158 7.64 0.00 0.00 4.40
2314 2920 2.028190 CGGTGGAGATAGGCGCTG 59.972 66.667 7.64 0.00 0.00 5.18
2315 2921 2.442272 ACGGTGGAGATAGGCGCT 60.442 61.111 7.64 0.00 0.00 5.92
2316 2922 2.027751 GACGGTGGAGATAGGCGC 59.972 66.667 0.00 0.00 0.00 6.53
2317 2923 1.672854 TTGGACGGTGGAGATAGGCG 61.673 60.000 0.00 0.00 0.00 5.52
2318 2924 0.539986 TTTGGACGGTGGAGATAGGC 59.460 55.000 0.00 0.00 0.00 3.93
2319 2925 1.473434 GCTTTGGACGGTGGAGATAGG 60.473 57.143 0.00 0.00 0.00 2.57
2320 2926 1.482593 AGCTTTGGACGGTGGAGATAG 59.517 52.381 0.00 0.00 0.00 2.08
2321 2927 1.207089 CAGCTTTGGACGGTGGAGATA 59.793 52.381 0.00 0.00 0.00 1.98
2322 2928 0.036010 CAGCTTTGGACGGTGGAGAT 60.036 55.000 0.00 0.00 0.00 2.75
2323 2929 1.371183 CAGCTTTGGACGGTGGAGA 59.629 57.895 0.00 0.00 0.00 3.71
2324 2930 2.328099 GCAGCTTTGGACGGTGGAG 61.328 63.158 0.00 0.00 0.00 3.86
2325 2931 2.281484 GCAGCTTTGGACGGTGGA 60.281 61.111 0.00 0.00 0.00 4.02
2326 2932 2.281761 AGCAGCTTTGGACGGTGG 60.282 61.111 0.00 0.00 0.00 4.61
2327 2933 1.165907 TTGAGCAGCTTTGGACGGTG 61.166 55.000 0.00 0.00 0.00 4.94
2328 2934 0.886490 CTTGAGCAGCTTTGGACGGT 60.886 55.000 0.00 0.00 0.00 4.83
2329 2935 0.603707 TCTTGAGCAGCTTTGGACGG 60.604 55.000 0.00 0.00 0.00 4.79
2330 2936 1.396301 GATCTTGAGCAGCTTTGGACG 59.604 52.381 0.00 0.00 0.00 4.79
2331 2937 1.396301 CGATCTTGAGCAGCTTTGGAC 59.604 52.381 0.00 0.00 0.00 4.02
2332 2938 1.276138 TCGATCTTGAGCAGCTTTGGA 59.724 47.619 0.00 0.00 0.00 3.53
2333 2939 1.730501 TCGATCTTGAGCAGCTTTGG 58.269 50.000 0.00 0.00 0.00 3.28
2334 2940 3.434641 TCTTTCGATCTTGAGCAGCTTTG 59.565 43.478 0.00 0.00 0.00 2.77
2335 2941 3.668447 TCTTTCGATCTTGAGCAGCTTT 58.332 40.909 0.00 0.00 0.00 3.51
2336 2942 3.325293 TCTTTCGATCTTGAGCAGCTT 57.675 42.857 0.00 0.00 0.00 3.74
2337 2943 3.196463 CATCTTTCGATCTTGAGCAGCT 58.804 45.455 0.00 0.00 0.00 4.24
2338 2944 2.286301 GCATCTTTCGATCTTGAGCAGC 60.286 50.000 0.00 0.00 0.00 5.25
2339 2945 2.934553 TGCATCTTTCGATCTTGAGCAG 59.065 45.455 0.00 0.00 0.00 4.24
2340 2946 2.976589 TGCATCTTTCGATCTTGAGCA 58.023 42.857 0.00 0.00 0.00 4.26
2341 2947 3.311871 ACATGCATCTTTCGATCTTGAGC 59.688 43.478 0.00 0.00 0.00 4.26
2342 2948 4.569564 TCACATGCATCTTTCGATCTTGAG 59.430 41.667 0.00 0.00 0.00 3.02
2343 2949 4.506758 TCACATGCATCTTTCGATCTTGA 58.493 39.130 0.00 0.00 0.00 3.02
2344 2950 4.569564 TCTCACATGCATCTTTCGATCTTG 59.430 41.667 0.00 0.00 0.00 3.02
2345 2951 4.763073 TCTCACATGCATCTTTCGATCTT 58.237 39.130 0.00 0.00 0.00 2.40
2346 2952 4.397481 TCTCACATGCATCTTTCGATCT 57.603 40.909 0.00 0.00 0.00 2.75
2347 2953 5.475273 TTTCTCACATGCATCTTTCGATC 57.525 39.130 0.00 0.00 0.00 3.69
2348 2954 4.201891 GCTTTCTCACATGCATCTTTCGAT 60.202 41.667 0.00 0.00 0.00 3.59
2349 2955 3.125829 GCTTTCTCACATGCATCTTTCGA 59.874 43.478 0.00 0.00 0.00 3.71
2350 2956 3.126514 AGCTTTCTCACATGCATCTTTCG 59.873 43.478 0.00 0.00 0.00 3.46
2351 2957 4.082895 ACAGCTTTCTCACATGCATCTTTC 60.083 41.667 0.00 0.00 0.00 2.62
2352 2958 3.825014 ACAGCTTTCTCACATGCATCTTT 59.175 39.130 0.00 0.00 0.00 2.52
2353 2959 3.190744 CACAGCTTTCTCACATGCATCTT 59.809 43.478 0.00 0.00 0.00 2.40
2354 2960 2.747989 CACAGCTTTCTCACATGCATCT 59.252 45.455 0.00 0.00 0.00 2.90
2355 2961 2.159421 CCACAGCTTTCTCACATGCATC 60.159 50.000 0.00 0.00 0.00 3.91
2356 2962 1.816835 CCACAGCTTTCTCACATGCAT 59.183 47.619 0.00 0.00 0.00 3.96
2357 2963 1.241165 CCACAGCTTTCTCACATGCA 58.759 50.000 0.00 0.00 0.00 3.96
2358 2964 0.524862 CCCACAGCTTTCTCACATGC 59.475 55.000 0.00 0.00 0.00 4.06
2359 2965 1.808945 GACCCACAGCTTTCTCACATG 59.191 52.381 0.00 0.00 0.00 3.21
2360 2966 1.609061 CGACCCACAGCTTTCTCACAT 60.609 52.381 0.00 0.00 0.00 3.21
2361 2967 0.249868 CGACCCACAGCTTTCTCACA 60.250 55.000 0.00 0.00 0.00 3.58
2362 2968 0.249911 ACGACCCACAGCTTTCTCAC 60.250 55.000 0.00 0.00 0.00 3.51
2363 2969 0.468226 AACGACCCACAGCTTTCTCA 59.532 50.000 0.00 0.00 0.00 3.27
2364 2970 1.149148 GAACGACCCACAGCTTTCTC 58.851 55.000 0.00 0.00 0.00 2.87
2365 2971 0.468226 TGAACGACCCACAGCTTTCT 59.532 50.000 0.00 0.00 0.00 2.52
2366 2972 1.305201 TTGAACGACCCACAGCTTTC 58.695 50.000 0.00 0.00 0.00 2.62
2367 2973 1.757682 TTTGAACGACCCACAGCTTT 58.242 45.000 0.00 0.00 0.00 3.51
2368 2974 1.757682 TTTTGAACGACCCACAGCTT 58.242 45.000 0.00 0.00 0.00 3.74
2369 2975 1.404035 GTTTTTGAACGACCCACAGCT 59.596 47.619 0.00 0.00 0.00 4.24
2370 2976 1.133407 TGTTTTTGAACGACCCACAGC 59.867 47.619 0.00 0.00 0.00 4.40
2371 2977 3.434637 CTTGTTTTTGAACGACCCACAG 58.565 45.455 0.00 0.00 0.00 3.66
2372 2978 2.416162 GCTTGTTTTTGAACGACCCACA 60.416 45.455 0.00 0.00 0.00 4.17
2472 3079 1.517257 CTTCGGCGACTAGGCTGTG 60.517 63.158 10.16 0.00 44.22 3.66
2503 3112 0.888736 TGGCGACCAGTGTTTGATGG 60.889 55.000 0.00 0.00 42.60 3.51
2511 3120 0.244450 AATTTGCATGGCGACCAGTG 59.756 50.000 4.90 4.92 36.75 3.66
2527 3137 8.953665 ACCCTCTGATTGGATTAGATTAGAATT 58.046 33.333 0.85 0.00 0.00 2.17
2528 3138 8.517323 ACCCTCTGATTGGATTAGATTAGAAT 57.483 34.615 0.85 0.00 0.00 2.40
2529 3139 7.937700 ACCCTCTGATTGGATTAGATTAGAA 57.062 36.000 0.85 0.00 0.00 2.10
2530 3140 7.937700 AACCCTCTGATTGGATTAGATTAGA 57.062 36.000 0.85 0.00 0.00 2.10
2531 3141 8.986929 AAAACCCTCTGATTGGATTAGATTAG 57.013 34.615 0.85 0.00 0.00 1.73
2534 3144 8.560903 ACTTAAAACCCTCTGATTGGATTAGAT 58.439 33.333 0.85 0.00 0.00 1.98
2548 3158 6.073385 CGAACTTCCACTTACTTAAAACCCTC 60.073 42.308 0.00 0.00 0.00 4.30
2630 3241 4.148079 CAAAGGGAAGAGAAAAGGAAGCT 58.852 43.478 0.00 0.00 0.00 3.74
2636 3249 3.575687 ACCATGCAAAGGGAAGAGAAAAG 59.424 43.478 12.59 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.