Multiple sequence alignment - TraesCS2D01G150700

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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 TraesCS2D01G150700 chr2D 100.000 5799 0 0 1 5799 93052795 93058593 0.000000e+00 10709
1 TraesCS2D01G150700 chr2D 98.851 87 1 0 1103 1189 93053983 93053897 7.780000e-34 156
2 TraesCS2D01G150700 chr2B 89.838 4438 291 78 1186 5543 144605660 144610017 0.000000e+00 5550
3 TraesCS2D01G150700 chr2B 87.556 1117 72 26 1 1093 144604547 144605620 0.000000e+00 1230
4 TraesCS2D01G150700 chr2B 92.885 253 15 2 5548 5799 144610143 144610393 1.190000e-96 364
5 TraesCS2D01G150700 chr2B 96.842 95 0 3 1099 1192 85695567 85695659 7.780000e-34 156
6 TraesCS2D01G150700 chr2A 92.876 3748 181 36 2068 5783 90743936 90747629 0.000000e+00 5363
7 TraesCS2D01G150700 chr2A 87.533 1131 75 29 1 1093 90741748 90742850 0.000000e+00 1247
8 TraesCS2D01G150700 chr2A 89.674 368 27 9 1189 1549 90742887 90743250 5.300000e-125 459
9 TraesCS2D01G150700 chr2A 88.728 346 32 3 1745 2083 90743556 90743901 3.230000e-112 416
10 TraesCS2D01G150700 chr2A 90.503 179 12 2 1556 1732 90743338 90743513 1.260000e-56 231
11 TraesCS2D01G150700 chr5B 94.059 101 3 3 1090 1189 470992268 470992366 3.620000e-32 150
12 TraesCS2D01G150700 chr5B 90.265 113 4 6 1085 1193 681344986 681345095 2.180000e-29 141
13 TraesCS2D01G150700 chr3D 93.269 104 3 3 1093 1194 239360673 239360774 3.620000e-32 150
14 TraesCS2D01G150700 chr3D 92.381 105 2 6 1088 1189 137515222 137515121 1.680000e-30 145
15 TraesCS2D01G150700 chr7B 94.000 100 3 3 1101 1199 11532902 11532999 1.300000e-31 148
16 TraesCS2D01G150700 chr4B 94.000 100 3 3 1103 1202 585819033 585819129 1.300000e-31 148
17 TraesCS2D01G150700 chr1D 95.745 94 1 3 1098 1190 440409671 440409762 1.300000e-31 148


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 TraesCS2D01G150700 chr2D 93052795 93058593 5798 False 10709.000000 10709 100.0000 1 5799 1 chr2D.!!$F1 5798
1 TraesCS2D01G150700 chr2B 144604547 144610393 5846 False 2381.333333 5550 90.0930 1 5799 3 chr2B.!!$F2 5798
2 TraesCS2D01G150700 chr2A 90741748 90747629 5881 False 1543.200000 5363 89.8628 1 5783 5 chr2A.!!$F1 5782

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
664 697 1.216710 CGCCGCTCTTCTCCTTCTT 59.783 57.895 0.00 0.0 0.00 2.52 F
1400 1459 0.038744 AAGCCTGTTGGGATGGTGAG 59.961 55.000 0.00 0.0 37.23 3.51 F
2304 2556 0.034186 TGCCTGGCTGGATTTAGGTG 60.034 55.000 21.03 0.0 38.35 4.00 F
2490 2742 1.483595 CCTGAGACTGTGAAGGGGCA 61.484 60.000 0.00 0.0 0.00 5.36 F
2925 3193 1.553248 AGGCATTGCACAGCATGAAAT 59.447 42.857 11.39 0.0 39.69 2.17 F
4181 4475 1.460504 TGTCGCCTGTTCGAGATACT 58.539 50.000 0.00 0.0 39.34 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2287 2539 0.034186 TGCACCTAAATCCAGCCAGG 60.034 55.000 0.00 0.00 39.47 4.45 R
2570 2830 0.459899 ACAACAGTGTCAGCGACTCA 59.540 50.000 0.00 0.00 29.49 3.41 R
3964 4242 0.968405 TGGTTTTCTGGAGCCATTGC 59.032 50.000 0.00 0.00 37.95 3.56 R
4173 4467 3.066064 ACTAGCAAGTGCAGAGTATCTCG 59.934 47.826 6.00 0.00 39.41 4.04 R
4514 4808 0.320050 TGAAGCAGACATACGTGGCA 59.680 50.000 0.00 0.00 35.06 4.92 R
5704 6147 0.034896 TTTCAGAAGCAGACCGGGTC 59.965 55.000 19.61 19.61 0.00 4.46 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 4.276926 GCAATCTTCAAAGGAACAGACACT 59.723 41.667 0.00 0.00 0.00 3.55
76 77 7.287005 TCCTGTTCATAACTACTCCGTATGAAT 59.713 37.037 8.19 0.00 38.75 2.57
110 118 7.194607 ACTAATGTTCTGAATGATAATGCGG 57.805 36.000 0.00 0.00 0.00 5.69
111 119 5.443185 AATGTTCTGAATGATAATGCGGG 57.557 39.130 0.00 0.00 0.00 6.13
186 195 2.685388 CAGCTAGCAGTCTAGTAGCACA 59.315 50.000 18.83 0.00 43.30 4.57
199 208 2.358898 AGTAGCACACCAACTGCAAAAG 59.641 45.455 0.00 0.00 37.08 2.27
200 209 1.473258 AGCACACCAACTGCAAAAGA 58.527 45.000 0.00 0.00 37.08 2.52
258 268 1.399440 CGCAGATGGATGTCAACTTGG 59.601 52.381 0.00 0.00 0.00 3.61
265 275 6.600822 CAGATGGATGTCAACTTGGTTAATCT 59.399 38.462 0.00 0.00 0.00 2.40
302 315 9.833182 GCTTAAATTAGATTATTCCAGCTTAGC 57.167 33.333 0.00 0.00 0.00 3.09
310 323 3.778954 ATTCCAGCTTAGCATCTACCC 57.221 47.619 7.07 0.00 0.00 3.69
319 332 4.579869 CTTAGCATCTACCCACACAAAGT 58.420 43.478 0.00 0.00 0.00 2.66
332 345 3.074412 ACACAAAGTAAATCTGAGGCGG 58.926 45.455 0.00 0.00 0.00 6.13
405 418 2.552599 TGCAACCTAAACGACCATCA 57.447 45.000 0.00 0.00 0.00 3.07
449 462 2.815211 CACGGGATCCACGCACAG 60.815 66.667 15.23 2.91 34.00 3.66
497 518 2.001803 CAGCATCAAAGGGGGAGGA 58.998 57.895 0.00 0.00 0.00 3.71
659 692 2.010582 ATCAGACGCCGCTCTTCTCC 62.011 60.000 0.00 0.00 0.00 3.71
660 693 2.361865 AGACGCCGCTCTTCTCCT 60.362 61.111 0.00 0.00 0.00 3.69
661 694 1.979693 AGACGCCGCTCTTCTCCTT 60.980 57.895 0.00 0.00 0.00 3.36
662 695 1.517475 GACGCCGCTCTTCTCCTTC 60.517 63.158 0.00 0.00 0.00 3.46
663 696 1.939769 GACGCCGCTCTTCTCCTTCT 61.940 60.000 0.00 0.00 0.00 2.85
664 697 1.216710 CGCCGCTCTTCTCCTTCTT 59.783 57.895 0.00 0.00 0.00 2.52
795 833 2.668632 GAATGACCGTCCTGCCCA 59.331 61.111 0.00 0.00 0.00 5.36
955 1004 2.364970 CACTTCCAATTTCCAACCTGCA 59.635 45.455 0.00 0.00 0.00 4.41
960 1009 1.342174 CAATTTCCAACCTGCAGCTGT 59.658 47.619 16.64 0.00 0.00 4.40
1093 1151 1.586154 CCGCAAGTAGGGGTTTGCTG 61.586 60.000 7.49 0.00 44.93 4.41
1095 1153 1.328279 GCAAGTAGGGGTTTGCTGTT 58.672 50.000 2.22 0.00 37.44 3.16
1096 1154 1.269723 GCAAGTAGGGGTTTGCTGTTC 59.730 52.381 2.22 0.00 37.44 3.18
1097 1155 2.863809 CAAGTAGGGGTTTGCTGTTCT 58.136 47.619 0.00 0.00 0.00 3.01
1098 1156 2.554032 CAAGTAGGGGTTTGCTGTTCTG 59.446 50.000 0.00 0.00 0.00 3.02
1099 1157 2.054799 AGTAGGGGTTTGCTGTTCTGA 58.945 47.619 0.00 0.00 0.00 3.27
1101 1159 1.915141 AGGGGTTTGCTGTTCTGATG 58.085 50.000 0.00 0.00 0.00 3.07
1107 1165 3.437049 GGTTTGCTGTTCTGATGTACTCC 59.563 47.826 0.00 0.00 0.00 3.85
1111 1169 2.159028 GCTGTTCTGATGTACTCCCTCC 60.159 54.545 0.00 0.00 0.00 4.30
1113 1171 2.291346 TGTTCTGATGTACTCCCTCCGA 60.291 50.000 0.00 0.00 0.00 4.55
1114 1172 2.959707 GTTCTGATGTACTCCCTCCGAT 59.040 50.000 0.00 0.00 0.00 4.18
1116 1174 3.223435 TCTGATGTACTCCCTCCGATTC 58.777 50.000 0.00 0.00 0.00 2.52
1119 1177 2.241281 TGTACTCCCTCCGATTCCAA 57.759 50.000 0.00 0.00 0.00 3.53
1120 1178 2.542550 TGTACTCCCTCCGATTCCAAA 58.457 47.619 0.00 0.00 0.00 3.28
1123 1181 4.717778 TGTACTCCCTCCGATTCCAAATTA 59.282 41.667 0.00 0.00 0.00 1.40
1126 1184 4.141688 ACTCCCTCCGATTCCAAATTACTC 60.142 45.833 0.00 0.00 0.00 2.59
1127 1185 3.131396 CCCTCCGATTCCAAATTACTCG 58.869 50.000 0.00 0.00 0.00 4.18
1129 1187 3.802685 CCTCCGATTCCAAATTACTCGTC 59.197 47.826 0.00 0.00 0.00 4.20
1131 1189 3.119388 TCCGATTCCAAATTACTCGTCGT 60.119 43.478 0.00 0.00 0.00 4.34
1132 1190 3.000078 CCGATTCCAAATTACTCGTCGTG 60.000 47.826 0.00 0.00 0.00 4.35
1134 1192 3.389925 TTCCAAATTACTCGTCGTGGT 57.610 42.857 0.00 0.00 0.00 4.16
1135 1193 3.389925 TCCAAATTACTCGTCGTGGTT 57.610 42.857 0.00 0.00 0.00 3.67
1137 1195 4.128643 TCCAAATTACTCGTCGTGGTTTT 58.871 39.130 0.00 0.00 0.00 2.43
1138 1196 5.295950 TCCAAATTACTCGTCGTGGTTTTA 58.704 37.500 0.00 0.00 0.00 1.52
1139 1197 5.406175 TCCAAATTACTCGTCGTGGTTTTAG 59.594 40.000 0.00 0.00 0.00 1.85
1140 1198 5.178067 CCAAATTACTCGTCGTGGTTTTAGT 59.822 40.000 0.00 0.00 0.00 2.24
1141 1199 6.293027 CCAAATTACTCGTCGTGGTTTTAGTT 60.293 38.462 0.00 0.00 0.00 2.24
1142 1200 6.457851 AATTACTCGTCGTGGTTTTAGTTC 57.542 37.500 0.00 0.00 0.00 3.01
1143 1201 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
1144 1202 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
1145 1203 4.374399 ACTCGTCGTGGTTTTAGTTCAAT 58.626 39.130 0.00 0.00 0.00 2.57
1146 1204 4.812626 ACTCGTCGTGGTTTTAGTTCAATT 59.187 37.500 0.00 0.00 0.00 2.32
1147 1205 5.295045 ACTCGTCGTGGTTTTAGTTCAATTT 59.705 36.000 0.00 0.00 0.00 1.82
1148 1206 5.503498 TCGTCGTGGTTTTAGTTCAATTTG 58.497 37.500 0.00 0.00 0.00 2.32
1149 1207 5.293814 TCGTCGTGGTTTTAGTTCAATTTGA 59.706 36.000 0.00 0.00 0.00 2.69
1150 1208 5.966503 CGTCGTGGTTTTAGTTCAATTTGAA 59.033 36.000 7.74 7.74 33.32 2.69
1164 1222 5.503498 TCAATTTGAACTAAAACCACGACG 58.497 37.500 0.00 0.00 0.00 5.12
1165 1223 5.293814 TCAATTTGAACTAAAACCACGACGA 59.706 36.000 0.00 0.00 0.00 4.20
1166 1224 4.782252 TTTGAACTAAAACCACGACGAG 57.218 40.909 0.00 0.00 0.00 4.18
1167 1225 3.441496 TGAACTAAAACCACGACGAGT 57.559 42.857 0.00 0.00 0.00 4.18
1168 1226 4.566545 TGAACTAAAACCACGACGAGTA 57.433 40.909 0.00 0.00 0.00 2.59
1169 1227 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
1170 1228 5.531634 TGAACTAAAACCACGACGAGTAAT 58.468 37.500 0.00 0.00 0.00 1.89
1171 1229 5.984926 TGAACTAAAACCACGACGAGTAATT 59.015 36.000 0.00 1.08 0.00 1.40
1172 1230 6.479660 TGAACTAAAACCACGACGAGTAATTT 59.520 34.615 0.00 0.34 0.00 1.82
1173 1231 6.219302 ACTAAAACCACGACGAGTAATTTG 57.781 37.500 0.00 2.39 0.00 2.32
1174 1232 4.477302 AAAACCACGACGAGTAATTTGG 57.523 40.909 0.00 0.00 0.00 3.28
1175 1233 3.389925 AACCACGACGAGTAATTTGGA 57.610 42.857 0.00 0.00 0.00 3.53
1176 1234 3.389925 ACCACGACGAGTAATTTGGAA 57.610 42.857 0.00 0.00 0.00 3.53
1177 1235 3.934068 ACCACGACGAGTAATTTGGAAT 58.066 40.909 0.00 0.00 0.00 3.01
1178 1236 3.930848 ACCACGACGAGTAATTTGGAATC 59.069 43.478 0.00 0.00 0.00 2.52
1179 1237 3.000078 CCACGACGAGTAATTTGGAATCG 60.000 47.826 0.00 0.00 39.22 3.34
1180 1238 3.000078 CACGACGAGTAATTTGGAATCGG 60.000 47.826 0.00 0.00 37.69 4.18
1181 1239 3.119388 ACGACGAGTAATTTGGAATCGGA 60.119 43.478 0.00 0.00 37.69 4.55
1182 1240 3.486108 CGACGAGTAATTTGGAATCGGAG 59.514 47.826 2.16 0.00 37.69 4.63
1183 1241 3.793559 ACGAGTAATTTGGAATCGGAGG 58.206 45.455 2.16 0.00 37.69 4.30
1184 1242 3.131396 CGAGTAATTTGGAATCGGAGGG 58.869 50.000 0.00 0.00 0.00 4.30
1217 1275 7.758076 TGAATTGAAAGCTTCTATGCTGATTTG 59.242 33.333 0.00 0.00 43.24 2.32
1322 1380 1.633945 CAGTTAGTGCCCCTACCCTTT 59.366 52.381 0.00 0.00 0.00 3.11
1377 1436 1.740718 GCTAGCTAAGCGAGGCAGTTT 60.741 52.381 7.70 0.00 42.53 2.66
1400 1459 0.038744 AAGCCTGTTGGGATGGTGAG 59.961 55.000 0.00 0.00 37.23 3.51
1407 1466 0.251297 TTGGGATGGTGAGTTGGCAG 60.251 55.000 0.00 0.00 0.00 4.85
1412 1471 2.674380 GGTGAGTTGGCAGCAGGG 60.674 66.667 3.63 0.00 36.35 4.45
1414 1473 3.177884 TGAGTTGGCAGCAGGGGT 61.178 61.111 3.63 0.00 0.00 4.95
1415 1474 2.360475 GAGTTGGCAGCAGGGGTC 60.360 66.667 3.63 0.00 0.00 4.46
1417 1476 1.538876 AGTTGGCAGCAGGGGTCTA 60.539 57.895 3.63 0.00 0.00 2.59
1427 1490 2.172679 GCAGGGGTCTATACTAGCTCC 58.827 57.143 0.00 0.00 0.00 4.70
1447 1511 8.312669 AGCTCCTTCTGTGTAAAATCTACTAT 57.687 34.615 0.00 0.00 0.00 2.12
1465 1529 2.743928 GAGCAGGGACAAGCGTGG 60.744 66.667 4.26 0.00 36.75 4.94
1466 1530 3.240134 GAGCAGGGACAAGCGTGGA 62.240 63.158 4.26 0.00 36.75 4.02
1467 1531 3.050275 GCAGGGACAAGCGTGGAC 61.050 66.667 4.26 0.00 0.00 4.02
1468 1532 2.425592 CAGGGACAAGCGTGGACA 59.574 61.111 4.26 0.00 0.00 4.02
1549 1616 4.447290 TGTGCTGCTCAAGTTAGTTACAA 58.553 39.130 1.33 0.00 0.00 2.41
1550 1617 5.063204 TGTGCTGCTCAAGTTAGTTACAAT 58.937 37.500 1.33 0.00 0.00 2.71
1554 1702 5.853282 GCTGCTCAAGTTAGTTACAATTGTG 59.147 40.000 21.42 0.96 0.00 3.33
1591 1739 2.362077 ACAAGTTGTTCAATCCAGCACC 59.638 45.455 1.64 0.00 0.00 5.01
1592 1740 1.238439 AGTTGTTCAATCCAGCACCG 58.762 50.000 0.00 0.00 0.00 4.94
1593 1741 0.951558 GTTGTTCAATCCAGCACCGT 59.048 50.000 0.00 0.00 0.00 4.83
1610 1761 1.952296 CCGTTCACGTAGTAGCCCTAT 59.048 52.381 0.00 0.00 41.61 2.57
1710 1864 6.546034 ACTGCCAGTTTGTTCTACTTGTTTAT 59.454 34.615 0.00 0.00 0.00 1.40
1712 1866 7.777095 TGCCAGTTTGTTCTACTTGTTTATTT 58.223 30.769 0.00 0.00 0.00 1.40
1721 1875 9.349713 TGTTCTACTTGTTTATTTGATGAGGTT 57.650 29.630 0.00 0.00 0.00 3.50
1734 1888 7.815840 TTTGATGAGGTTTTGATCACAAGTA 57.184 32.000 0.00 0.00 37.32 2.24
1767 1951 8.492748 CGTAATAACAGCCGTATCAATTGTAAT 58.507 33.333 5.13 0.00 0.00 1.89
1785 1969 5.768317 TGTAATTAGCTTGTTTCTGGTTGC 58.232 37.500 0.00 0.00 0.00 4.17
1813 2004 8.021396 CAGTTACAGCTTAGGTAAAATGTTTCC 58.979 37.037 0.00 0.00 32.94 3.13
1820 2011 6.350110 GCTTAGGTAAAATGTTTCCAGCATGA 60.350 38.462 0.00 0.00 39.69 3.07
1830 2021 6.587206 TGTTTCCAGCATGAAAATATGTCA 57.413 33.333 0.00 0.00 39.69 3.58
1867 2058 3.319122 GGGCATTGTCTTCTTGTTGTCTT 59.681 43.478 0.00 0.00 0.00 3.01
2074 2272 1.337823 GCGACTCTTACCCTTGCTTCA 60.338 52.381 0.00 0.00 0.00 3.02
2083 2331 1.425066 ACCCTTGCTTCATTCTGTCCA 59.575 47.619 0.00 0.00 0.00 4.02
2085 2333 2.686915 CCCTTGCTTCATTCTGTCCATC 59.313 50.000 0.00 0.00 0.00 3.51
2086 2334 3.349927 CCTTGCTTCATTCTGTCCATCA 58.650 45.455 0.00 0.00 0.00 3.07
2088 2336 4.202020 CCTTGCTTCATTCTGTCCATCATG 60.202 45.833 0.00 0.00 0.00 3.07
2122 2370 2.560504 CCAGAGGCATGTACGCAAATA 58.439 47.619 0.00 0.00 0.00 1.40
2282 2534 2.488545 AGTCTCGTGGTTAGCACACTAG 59.511 50.000 14.97 8.46 36.71 2.57
2287 2539 1.464997 GTGGTTAGCACACTAGCTTGC 59.535 52.381 9.85 7.89 43.70 4.01
2304 2556 0.034186 TGCCTGGCTGGATTTAGGTG 60.034 55.000 21.03 0.00 38.35 4.00
2346 2598 7.120285 CCCATATTACAGAGTGCCAGATATTTG 59.880 40.741 0.00 0.00 0.00 2.32
2351 2603 8.662781 TTACAGAGTGCCAGATATTTGTTATC 57.337 34.615 0.00 0.00 37.55 1.75
2384 2636 2.035321 CCGCCACCACTAACAAACATTT 59.965 45.455 0.00 0.00 0.00 2.32
2386 2638 3.305110 GCCACCACTAACAAACATTTCG 58.695 45.455 0.00 0.00 0.00 3.46
2387 2639 3.243267 GCCACCACTAACAAACATTTCGT 60.243 43.478 0.00 0.00 0.00 3.85
2490 2742 1.483595 CCTGAGACTGTGAAGGGGCA 61.484 60.000 0.00 0.00 0.00 5.36
2556 2816 4.320608 ACCGCATTCACTTCAAATTGTT 57.679 36.364 0.00 0.00 0.00 2.83
2574 2834 9.950680 CAAATTGTTATCTTACAAACACTGAGT 57.049 29.630 0.00 0.00 41.02 3.41
2576 2836 7.402811 TTGTTATCTTACAAACACTGAGTCG 57.597 36.000 0.00 0.00 35.43 4.18
2741 3001 5.688814 ATGATCTTGAGACTTCCACATGA 57.311 39.130 0.00 0.00 0.00 3.07
2921 3189 4.494811 CAGGCATTGCACAGCATG 57.505 55.556 11.39 9.41 46.00 4.06
2925 3193 1.553248 AGGCATTGCACAGCATGAAAT 59.447 42.857 11.39 0.00 39.69 2.17
2960 3228 3.243168 CCGGCAACAATCATCCAATGTAG 60.243 47.826 0.00 0.00 0.00 2.74
2966 3234 6.404623 GCAACAATCATCCAATGTAGTGCTAA 60.405 38.462 0.00 0.00 0.00 3.09
3235 3503 6.998074 TGGATCTGAACTGATACTTTTGTTGT 59.002 34.615 0.00 0.00 0.00 3.32
3433 3701 6.750148 TGCATATATCAATTGCTGCATTTCA 58.250 32.000 1.84 0.00 37.28 2.69
4034 4313 5.856126 TCCTTAAGTCTAAAATGCACACG 57.144 39.130 0.97 0.00 0.00 4.49
4062 4341 7.762159 TGTGATGCACTCGTACATAAAGATAAA 59.238 33.333 0.00 0.00 35.11 1.40
4168 4462 4.438744 CCATTCCTTTATCAGTTTGTCGCC 60.439 45.833 0.00 0.00 0.00 5.54
4173 4467 4.378459 CCTTTATCAGTTTGTCGCCTGTTC 60.378 45.833 0.00 0.00 0.00 3.18
4181 4475 1.460504 TGTCGCCTGTTCGAGATACT 58.539 50.000 0.00 0.00 39.34 2.12
4188 4482 2.425312 CCTGTTCGAGATACTCTGCACT 59.575 50.000 0.00 0.00 0.00 4.40
4223 4517 7.862512 TTTTCCTTGTGCAAAAATGATTCTT 57.137 28.000 0.00 0.00 0.00 2.52
4231 4525 6.260271 TGTGCAAAAATGATTCTTCAAATGCA 59.740 30.769 0.00 0.00 37.52 3.96
4239 4533 6.593268 TGATTCTTCAAATGCATTCCTGAA 57.407 33.333 20.16 20.16 0.00 3.02
4496 4790 6.605194 ACTCATACAAGTGAGATCTTAGAGCA 59.395 38.462 10.57 0.00 46.77 4.26
4514 4808 5.488341 AGAGCAACCGTGACACTTTAATAT 58.512 37.500 3.68 0.00 0.00 1.28
4520 4814 3.242284 CCGTGACACTTTAATATGCCACG 60.242 47.826 16.38 16.38 43.67 4.94
4574 4868 9.683069 ATTATGTTCTGCAACTAACTTTCTTTG 57.317 29.630 7.51 0.00 33.17 2.77
4617 4912 7.485913 CGCCAATTCCAGTATTAATGCATATTC 59.514 37.037 0.00 0.00 0.00 1.75
4723 5019 2.293399 AGCTGAAAAACGTGGAATGGTC 59.707 45.455 0.00 0.00 0.00 4.02
4881 5180 5.191722 TCCTATCAGGAAAGCCAATGTTACT 59.808 40.000 0.00 0.00 42.51 2.24
4968 5270 4.766891 CCATGGGAGAAAACAGTACAACAT 59.233 41.667 2.85 0.00 0.00 2.71
5018 5320 9.853555 TGATTGATTCAGCGTAAAATTTACATT 57.146 25.926 15.19 0.81 0.00 2.71
5023 5325 9.103048 GATTCAGCGTAAAATTTACATTATCCG 57.897 33.333 15.19 1.77 0.00 4.18
5024 5326 7.773864 TCAGCGTAAAATTTACATTATCCGA 57.226 32.000 15.19 0.46 0.00 4.55
5025 5327 7.623770 TCAGCGTAAAATTTACATTATCCGAC 58.376 34.615 15.19 0.00 0.00 4.79
5026 5328 6.568601 CAGCGTAAAATTTACATTATCCGACG 59.431 38.462 15.19 1.99 0.00 5.12
5073 5375 0.320374 AAGAAGCGATTCGGGTCACA 59.680 50.000 7.91 0.00 0.00 3.58
5075 5377 0.721718 GAAGCGATTCGGGTCACAAG 59.278 55.000 8.34 0.00 0.00 3.16
5076 5378 1.298859 AAGCGATTCGGGTCACAAGC 61.299 55.000 8.34 0.00 0.00 4.01
5077 5379 2.032634 GCGATTCGGGTCACAAGCA 61.033 57.895 8.34 0.00 0.00 3.91
5078 5380 1.369091 GCGATTCGGGTCACAAGCAT 61.369 55.000 8.34 0.00 0.00 3.79
5079 5381 0.652592 CGATTCGGGTCACAAGCATC 59.347 55.000 0.00 0.00 0.00 3.91
5085 5387 1.026182 GGGTCACAAGCATCGCATCA 61.026 55.000 0.00 0.00 0.00 3.07
5091 5393 0.654160 CAAGCATCGCATCACATCGT 59.346 50.000 0.00 0.00 0.00 3.73
5095 5397 0.923403 CATCGCATCACATCGTCGTT 59.077 50.000 0.00 0.00 0.00 3.85
5105 5407 3.427528 TCACATCGTCGTTACAGCTTTTC 59.572 43.478 0.00 0.00 0.00 2.29
5106 5408 2.735134 ACATCGTCGTTACAGCTTTTCC 59.265 45.455 0.00 0.00 0.00 3.13
5107 5409 1.787012 TCGTCGTTACAGCTTTTCCC 58.213 50.000 0.00 0.00 0.00 3.97
5108 5410 1.342174 TCGTCGTTACAGCTTTTCCCT 59.658 47.619 0.00 0.00 0.00 4.20
5109 5411 2.557924 TCGTCGTTACAGCTTTTCCCTA 59.442 45.455 0.00 0.00 0.00 3.53
5110 5412 2.921754 CGTCGTTACAGCTTTTCCCTAG 59.078 50.000 0.00 0.00 0.00 3.02
5114 5418 3.306502 CGTTACAGCTTTTCCCTAGACCA 60.307 47.826 0.00 0.00 0.00 4.02
5221 5525 6.255950 CAGTTGCATCATATGAACTTGACTG 58.744 40.000 9.99 14.97 32.34 3.51
5231 5535 2.435805 TGAACTTGACTGCTTGAGAGGT 59.564 45.455 0.00 0.00 0.00 3.85
5232 5536 2.540265 ACTTGACTGCTTGAGAGGTG 57.460 50.000 0.00 0.00 0.00 4.00
5233 5537 1.155042 CTTGACTGCTTGAGAGGTGC 58.845 55.000 0.00 0.00 0.00 5.01
5234 5538 0.761187 TTGACTGCTTGAGAGGTGCT 59.239 50.000 0.00 0.00 0.00 4.40
5269 5573 1.542987 GCCTGAAGATGCTCTGGATCC 60.543 57.143 4.20 4.20 36.74 3.36
5324 5629 2.430332 CACCAAAACCCACACTGAATGT 59.570 45.455 0.00 0.00 44.81 2.71
5411 5716 0.802494 ATGCGACGTGGATCCAAAAC 59.198 50.000 18.20 9.49 0.00 2.43
5415 5720 1.726791 CGACGTGGATCCAAAACTCTG 59.273 52.381 18.20 3.16 0.00 3.35
5418 5723 1.177401 GTGGATCCAAAACTCTGGGC 58.823 55.000 18.20 0.00 37.06 5.36
5447 5752 3.764466 CTGCTTCCTCGCCCTCGT 61.764 66.667 0.00 0.00 36.96 4.18
5449 5754 4.856607 GCTTCCTCGCCCTCGTCG 62.857 72.222 0.00 0.00 36.96 5.12
5450 5755 3.132139 CTTCCTCGCCCTCGTCGA 61.132 66.667 0.00 0.00 36.96 4.20
5451 5756 2.439701 TTCCTCGCCCTCGTCGAT 60.440 61.111 0.00 0.00 35.25 3.59
5490 5807 4.874521 TGCCCTAGTCAGCAGAGT 57.125 55.556 0.00 0.00 33.08 3.24
5564 6007 1.115930 TCTAGCTCGGAATCAGCCCC 61.116 60.000 0.00 0.00 37.63 5.80
5650 6093 1.001974 TCCTGTTGCTAACGCTGATGT 59.998 47.619 0.00 0.00 36.97 3.06
5668 6111 2.985847 GTTGCACTGGACCTGCCC 60.986 66.667 3.43 0.00 33.36 5.36
5728 6171 1.528586 CGGTCTGCTTCTGAAACAGTG 59.471 52.381 17.57 7.90 32.61 3.66
5766 6210 1.069204 TCGATTACAGGGAGATGCAGC 59.931 52.381 0.00 0.00 0.00 5.25
5775 6219 0.807667 GGAGATGCAGCCACGTACAG 60.808 60.000 0.00 0.00 0.00 2.74
5783 6227 2.100252 GCAGCCACGTACAGGAATAGTA 59.900 50.000 5.57 0.00 0.00 1.82
5785 6229 4.022589 GCAGCCACGTACAGGAATAGTATA 60.023 45.833 5.57 0.00 0.00 1.47
5787 6231 6.323266 CAGCCACGTACAGGAATAGTATATC 58.677 44.000 5.57 0.00 0.00 1.63
5788 6232 5.418209 AGCCACGTACAGGAATAGTATATCC 59.582 44.000 5.57 4.18 35.88 2.59
5789 6233 5.675575 GCCACGTACAGGAATAGTATATCCG 60.676 48.000 5.57 0.00 40.78 4.18
5791 6235 6.595326 CCACGTACAGGAATAGTATATCCGTA 59.405 42.308 0.00 7.91 40.78 4.02
5792 6236 7.281774 CCACGTACAGGAATAGTATATCCGTAT 59.718 40.741 0.00 0.00 40.78 3.06
5793 6237 8.121086 CACGTACAGGAATAGTATATCCGTATG 58.879 40.741 18.31 18.31 40.78 2.39
5794 6238 8.043113 ACGTACAGGAATAGTATATCCGTATGA 58.957 37.037 21.75 0.00 40.78 2.15
5798 6242 8.958506 ACAGGAATAGTATATCCGTATGAAGAC 58.041 37.037 6.00 0.00 40.78 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 1.974236 CAGGAGGAGTGTCTGTTCCTT 59.026 52.381 0.00 0.00 43.76 3.36
47 48 3.952323 CGGAGTAGTTATGAACAGGAGGA 59.048 47.826 0.00 0.00 0.00 3.71
100 101 4.516321 CACTTCAATGATCCCGCATTATCA 59.484 41.667 0.00 0.00 36.39 2.15
101 102 4.614535 GCACTTCAATGATCCCGCATTATC 60.615 45.833 0.00 0.00 36.39 1.75
108 116 1.452110 TGTGCACTTCAATGATCCCG 58.548 50.000 19.41 0.00 0.00 5.14
110 118 5.627499 TTAGTTGTGCACTTCAATGATCC 57.373 39.130 19.41 0.00 36.88 3.36
111 119 6.909357 GCTATTAGTTGTGCACTTCAATGATC 59.091 38.462 19.41 0.00 36.88 2.92
186 195 5.789643 ATGTTGTATCTTTTGCAGTTGGT 57.210 34.783 0.00 0.00 0.00 3.67
199 208 8.241367 AGAATCGGTTTTTACCAATGTTGTATC 58.759 33.333 0.00 0.00 0.00 2.24
200 209 8.117813 AGAATCGGTTTTTACCAATGTTGTAT 57.882 30.769 0.00 0.00 0.00 2.29
289 299 4.040461 GTGGGTAGATGCTAAGCTGGAATA 59.960 45.833 0.00 0.00 0.00 1.75
294 307 2.093500 TGTGTGGGTAGATGCTAAGCTG 60.093 50.000 0.00 0.00 0.00 4.24
302 315 6.878923 TCAGATTTACTTTGTGTGGGTAGATG 59.121 38.462 0.00 0.00 0.00 2.90
310 323 3.120199 CCGCCTCAGATTTACTTTGTGTG 60.120 47.826 0.00 0.00 0.00 3.82
319 332 2.504032 CCGGCCGCCTCAGATTTA 59.496 61.111 22.85 0.00 0.00 1.40
405 418 1.271840 TGCTTAGATCTTGGGCGGGT 61.272 55.000 0.00 0.00 0.00 5.28
447 460 2.434428 AGATGTTGCTTCTTGCTCCTG 58.566 47.619 0.00 0.00 43.37 3.86
449 462 2.680339 GGTAGATGTTGCTTCTTGCTCC 59.320 50.000 0.00 0.00 43.37 4.70
633 657 2.791927 CGGCGTCTGATCTCGTCA 59.208 61.111 0.00 0.00 35.05 4.35
686 719 3.033764 TGTGGAAGCGTCGCGTTC 61.034 61.111 12.30 14.81 0.00 3.95
795 833 1.133668 GGAACATTCTAGGGCTGGCAT 60.134 52.381 2.88 0.00 0.00 4.40
898 936 1.749258 GTTGGATTGGACCCTCGGC 60.749 63.158 0.00 0.00 0.00 5.54
1017 1066 4.816984 TCCTCCCGCTCCCTCGTC 62.817 72.222 0.00 0.00 0.00 4.20
1093 1151 2.376109 TCGGAGGGAGTACATCAGAAC 58.624 52.381 0.00 0.00 0.00 3.01
1095 1153 3.223435 GAATCGGAGGGAGTACATCAGA 58.777 50.000 0.00 0.00 0.00 3.27
1096 1154 2.297597 GGAATCGGAGGGAGTACATCAG 59.702 54.545 0.00 0.00 0.00 2.90
1097 1155 2.317040 GGAATCGGAGGGAGTACATCA 58.683 52.381 0.00 0.00 0.00 3.07
1098 1156 2.317040 TGGAATCGGAGGGAGTACATC 58.683 52.381 0.00 0.00 26.02 3.06
1099 1157 2.471815 TGGAATCGGAGGGAGTACAT 57.528 50.000 0.00 0.00 26.02 2.29
1101 1159 3.840124 ATTTGGAATCGGAGGGAGTAC 57.160 47.619 0.00 0.00 0.00 2.73
1107 1165 3.793559 ACGAGTAATTTGGAATCGGAGG 58.206 45.455 2.16 0.00 37.69 4.30
1111 1169 3.000078 CCACGACGAGTAATTTGGAATCG 60.000 47.826 0.00 0.00 39.22 3.34
1113 1171 3.934068 ACCACGACGAGTAATTTGGAAT 58.066 40.909 0.00 0.00 0.00 3.01
1114 1172 3.389925 ACCACGACGAGTAATTTGGAA 57.610 42.857 0.00 0.00 0.00 3.53
1116 1174 4.477302 AAAACCACGACGAGTAATTTGG 57.523 40.909 0.00 0.00 0.00 3.28
1119 1177 5.984926 TGAACTAAAACCACGACGAGTAATT 59.015 36.000 0.00 1.08 0.00 1.40
1120 1178 5.531634 TGAACTAAAACCACGACGAGTAAT 58.468 37.500 0.00 0.00 0.00 1.89
1123 1181 3.441496 TGAACTAAAACCACGACGAGT 57.559 42.857 0.00 0.00 0.00 4.18
1126 1184 5.503498 TCAAATTGAACTAAAACCACGACG 58.497 37.500 0.00 0.00 0.00 5.12
1140 1198 5.966503 CGTCGTGGTTTTAGTTCAAATTGAA 59.033 36.000 4.03 4.03 33.32 2.69
1141 1199 5.293814 TCGTCGTGGTTTTAGTTCAAATTGA 59.706 36.000 0.00 0.00 0.00 2.57
1142 1200 5.503498 TCGTCGTGGTTTTAGTTCAAATTG 58.497 37.500 0.00 0.00 0.00 2.32
1143 1201 5.295045 ACTCGTCGTGGTTTTAGTTCAAATT 59.705 36.000 0.00 0.00 0.00 1.82
1144 1202 4.812626 ACTCGTCGTGGTTTTAGTTCAAAT 59.187 37.500 0.00 0.00 0.00 2.32
1145 1203 4.183101 ACTCGTCGTGGTTTTAGTTCAAA 58.817 39.130 0.00 0.00 0.00 2.69
1146 1204 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
1147 1205 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
1148 1206 6.457851 AATTACTCGTCGTGGTTTTAGTTC 57.542 37.500 0.00 0.00 0.00 3.01
1149 1207 6.293027 CCAAATTACTCGTCGTGGTTTTAGTT 60.293 38.462 0.00 0.00 0.00 2.24
1150 1208 5.178067 CCAAATTACTCGTCGTGGTTTTAGT 59.822 40.000 0.00 0.00 0.00 2.24
1151 1209 5.406175 TCCAAATTACTCGTCGTGGTTTTAG 59.594 40.000 0.00 0.00 0.00 1.85
1152 1210 5.295950 TCCAAATTACTCGTCGTGGTTTTA 58.704 37.500 0.00 0.00 0.00 1.52
1153 1211 4.128643 TCCAAATTACTCGTCGTGGTTTT 58.871 39.130 0.00 0.00 0.00 2.43
1154 1212 3.731089 TCCAAATTACTCGTCGTGGTTT 58.269 40.909 0.00 0.00 0.00 3.27
1155 1213 3.389925 TCCAAATTACTCGTCGTGGTT 57.610 42.857 0.00 0.00 0.00 3.67
1156 1214 3.389925 TTCCAAATTACTCGTCGTGGT 57.610 42.857 0.00 0.00 0.00 4.16
1157 1215 3.000078 CGATTCCAAATTACTCGTCGTGG 60.000 47.826 0.00 0.00 0.00 4.94
1158 1216 3.000078 CCGATTCCAAATTACTCGTCGTG 60.000 47.826 0.00 0.00 0.00 4.35
1159 1217 3.119388 TCCGATTCCAAATTACTCGTCGT 60.119 43.478 0.00 0.00 0.00 4.34
1160 1218 3.441163 TCCGATTCCAAATTACTCGTCG 58.559 45.455 0.00 0.00 0.00 5.12
1161 1219 3.802685 CCTCCGATTCCAAATTACTCGTC 59.197 47.826 0.00 0.00 0.00 4.20
1162 1220 3.431766 CCCTCCGATTCCAAATTACTCGT 60.432 47.826 0.00 0.00 0.00 4.18
1163 1221 3.131396 CCCTCCGATTCCAAATTACTCG 58.869 50.000 0.00 0.00 0.00 4.18
1164 1222 4.141688 ACTCCCTCCGATTCCAAATTACTC 60.142 45.833 0.00 0.00 0.00 2.59
1165 1223 3.780850 ACTCCCTCCGATTCCAAATTACT 59.219 43.478 0.00 0.00 0.00 2.24
1166 1224 4.152284 ACTCCCTCCGATTCCAAATTAC 57.848 45.455 0.00 0.00 0.00 1.89
1167 1225 4.202326 GCTACTCCCTCCGATTCCAAATTA 60.202 45.833 0.00 0.00 0.00 1.40
1168 1226 3.433740 GCTACTCCCTCCGATTCCAAATT 60.434 47.826 0.00 0.00 0.00 1.82
1169 1227 2.104963 GCTACTCCCTCCGATTCCAAAT 59.895 50.000 0.00 0.00 0.00 2.32
1170 1228 1.485066 GCTACTCCCTCCGATTCCAAA 59.515 52.381 0.00 0.00 0.00 3.28
1171 1229 1.120530 GCTACTCCCTCCGATTCCAA 58.879 55.000 0.00 0.00 0.00 3.53
1172 1230 0.261991 AGCTACTCCCTCCGATTCCA 59.738 55.000 0.00 0.00 0.00 3.53
1173 1231 0.676736 CAGCTACTCCCTCCGATTCC 59.323 60.000 0.00 0.00 0.00 3.01
1174 1232 1.693627 TCAGCTACTCCCTCCGATTC 58.306 55.000 0.00 0.00 0.00 2.52
1175 1233 2.160721 TTCAGCTACTCCCTCCGATT 57.839 50.000 0.00 0.00 0.00 3.34
1176 1234 2.366916 CAATTCAGCTACTCCCTCCGAT 59.633 50.000 0.00 0.00 0.00 4.18
1177 1235 1.757118 CAATTCAGCTACTCCCTCCGA 59.243 52.381 0.00 0.00 0.00 4.55
1178 1236 1.757118 TCAATTCAGCTACTCCCTCCG 59.243 52.381 0.00 0.00 0.00 4.63
1179 1237 3.914426 TTCAATTCAGCTACTCCCTCC 57.086 47.619 0.00 0.00 0.00 4.30
1180 1238 3.625313 GCTTTCAATTCAGCTACTCCCTC 59.375 47.826 0.00 0.00 32.87 4.30
1181 1239 3.265479 AGCTTTCAATTCAGCTACTCCCT 59.735 43.478 2.11 0.00 44.86 4.20
1182 1240 3.615155 AGCTTTCAATTCAGCTACTCCC 58.385 45.455 2.11 0.00 44.86 4.30
1183 1241 4.940654 AGAAGCTTTCAATTCAGCTACTCC 59.059 41.667 0.00 0.00 46.01 3.85
1184 1242 7.629130 CATAGAAGCTTTCAATTCAGCTACTC 58.371 38.462 0.00 0.82 46.01 2.59
1217 1275 1.593265 CTGCCCAAATCCAGCAACC 59.407 57.895 0.00 0.00 35.79 3.77
1322 1380 1.999648 ACATTGGCAAGGAAGAAGCA 58.000 45.000 19.84 0.00 0.00 3.91
1377 1436 1.922447 ACCATCCCAACAGGCTTATCA 59.078 47.619 0.00 0.00 34.51 2.15
1400 1459 0.837272 TATAGACCCCTGCTGCCAAC 59.163 55.000 0.00 0.00 0.00 3.77
1407 1466 2.172679 GGAGCTAGTATAGACCCCTGC 58.827 57.143 0.00 0.00 42.77 4.85
1409 1468 3.991621 AGAAGGAGCTAGTATAGACCCCT 59.008 47.826 0.00 0.00 42.77 4.79
1412 1471 5.134661 ACACAGAAGGAGCTAGTATAGACC 58.865 45.833 0.00 0.00 42.77 3.85
1414 1473 8.818622 TTTTACACAGAAGGAGCTAGTATAGA 57.181 34.615 0.00 0.00 42.77 1.98
1415 1474 9.685828 GATTTTACACAGAAGGAGCTAGTATAG 57.314 37.037 0.00 0.00 43.09 1.31
1417 1476 8.312669 AGATTTTACACAGAAGGAGCTAGTAT 57.687 34.615 0.00 0.00 0.00 2.12
1427 1490 8.932945 TGCTCATAGTAGATTTTACACAGAAG 57.067 34.615 0.00 0.00 0.00 2.85
1447 1511 2.031012 CACGCTTGTCCCTGCTCA 59.969 61.111 0.00 0.00 0.00 4.26
1465 1529 5.047235 TGCTCTAAACTAAGGAACCTCTGTC 60.047 44.000 0.00 0.00 0.00 3.51
1466 1530 4.838986 TGCTCTAAACTAAGGAACCTCTGT 59.161 41.667 0.00 0.00 0.00 3.41
1467 1531 5.186021 TCTGCTCTAAACTAAGGAACCTCTG 59.814 44.000 0.00 0.00 0.00 3.35
1468 1532 5.334421 TCTGCTCTAAACTAAGGAACCTCT 58.666 41.667 0.00 0.00 0.00 3.69
1549 1616 6.125327 TGTAATTGTCGACACAAACACAAT 57.875 33.333 19.90 3.24 45.78 2.71
1550 1617 5.547181 TGTAATTGTCGACACAAACACAA 57.453 34.783 19.90 0.39 45.78 3.33
1554 1702 6.025280 ACAACTTGTAATTGTCGACACAAAC 58.975 36.000 19.90 16.01 45.78 2.93
1591 1739 6.486253 TTATATAGGGCTACTACGTGAACG 57.514 41.667 0.00 0.40 46.33 3.95
1592 1740 6.750963 GCATTATATAGGGCTACTACGTGAAC 59.249 42.308 0.00 0.00 33.70 3.18
1593 1741 6.662234 AGCATTATATAGGGCTACTACGTGAA 59.338 38.462 0.00 0.00 34.25 3.18
1649 1800 3.808726 GTGCAGCAATTCATTGACCAAAA 59.191 39.130 0.00 0.00 40.14 2.44
1689 1841 9.965824 ATCAAATAAACAAGTAGAACAAACTGG 57.034 29.630 0.00 0.00 0.00 4.00
1710 1864 6.713762 ACTTGTGATCAAAACCTCATCAAA 57.286 33.333 0.00 0.00 32.87 2.69
1712 1866 9.685276 ATTATACTTGTGATCAAAACCTCATCA 57.315 29.630 0.00 0.00 32.87 3.07
1734 1888 7.829725 TGATACGGCTGTTATTACGGTATTAT 58.170 34.615 1.99 0.00 32.95 1.28
1767 1951 1.001815 GCGCAACCAGAAACAAGCTAA 60.002 47.619 0.30 0.00 0.00 3.09
1769 1953 1.360192 GCGCAACCAGAAACAAGCT 59.640 52.632 0.30 0.00 0.00 3.74
1785 1969 5.121768 ACATTTTACCTAAGCTGTAACTGCG 59.878 40.000 0.00 0.00 33.59 5.18
1813 2004 6.185852 TGTCACTGACATATTTTCATGCTG 57.814 37.500 7.84 0.00 37.67 4.41
1830 2021 2.291209 TGCCCAAATCACATGTCACT 57.709 45.000 0.00 0.00 0.00 3.41
1867 2058 4.328536 ACACCCGTTTTTGCTACATATGA 58.671 39.130 10.38 0.00 0.00 2.15
1913 2110 1.203013 AGACAAGGTAAAAGTGGCCCC 60.203 52.381 0.00 0.00 0.00 5.80
2074 2272 6.805016 AGAAGTAGACATGATGGACAGAAT 57.195 37.500 0.00 0.00 0.00 2.40
2083 2331 5.204292 TCTGGCTGTAGAAGTAGACATGAT 58.796 41.667 0.00 0.00 30.16 2.45
2085 2333 4.202101 CCTCTGGCTGTAGAAGTAGACATG 60.202 50.000 0.00 0.00 30.16 3.21
2086 2334 3.957497 CCTCTGGCTGTAGAAGTAGACAT 59.043 47.826 0.00 0.00 30.16 3.06
2088 2336 2.100087 GCCTCTGGCTGTAGAAGTAGAC 59.900 54.545 0.73 0.00 46.69 2.59
2187 2435 5.355350 GTGTAGCATGGTCAGCTCTATTTTT 59.645 40.000 0.00 0.00 42.32 1.94
2188 2436 4.878397 GTGTAGCATGGTCAGCTCTATTTT 59.122 41.667 0.00 0.00 42.32 1.82
2196 2444 2.005451 CTTGAGTGTAGCATGGTCAGC 58.995 52.381 0.00 0.00 0.00 4.26
2282 2534 0.743097 CTAAATCCAGCCAGGCAAGC 59.257 55.000 15.80 0.00 37.29 4.01
2287 2539 0.034186 TGCACCTAAATCCAGCCAGG 60.034 55.000 0.00 0.00 39.47 4.45
2346 2598 2.287009 GGCGGCATGTTAAGCAGATAAC 60.287 50.000 3.07 0.00 36.52 1.89
2351 2603 1.137404 GTGGCGGCATGTTAAGCAG 59.863 57.895 17.19 0.00 0.00 4.24
2358 2610 1.674322 GTTAGTGGTGGCGGCATGT 60.674 57.895 17.19 2.56 0.00 3.21
2363 2615 1.243902 ATGTTTGTTAGTGGTGGCGG 58.756 50.000 0.00 0.00 0.00 6.13
2384 2636 0.746204 TCAGCTGCACCAAACAACGA 60.746 50.000 9.47 0.00 0.00 3.85
2386 2638 2.514205 AATCAGCTGCACCAAACAAC 57.486 45.000 9.47 0.00 0.00 3.32
2387 2639 3.825585 TCATAATCAGCTGCACCAAACAA 59.174 39.130 9.47 0.00 0.00 2.83
2490 2742 6.552350 CCCAGATCCCAACTCAATTAATGAAT 59.448 38.462 0.00 0.00 37.67 2.57
2536 2796 6.324819 AGATAACAATTTGAAGTGAATGCGG 58.675 36.000 2.79 0.00 0.00 5.69
2556 2816 5.048294 TCAGCGACTCAGTGTTTGTAAGATA 60.048 40.000 0.00 0.00 0.00 1.98
2569 2829 1.135046 CAACAGTGTCAGCGACTCAG 58.865 55.000 0.00 6.11 33.15 3.35
2570 2830 0.459899 ACAACAGTGTCAGCGACTCA 59.540 50.000 0.00 0.00 29.49 3.41
2571 2831 0.855349 CACAACAGTGTCAGCGACTC 59.145 55.000 0.00 6.49 35.07 3.36
2572 2832 0.459899 TCACAACAGTGTCAGCGACT 59.540 50.000 0.00 0.00 35.07 4.18
2573 2833 0.577269 GTCACAACAGTGTCAGCGAC 59.423 55.000 0.00 0.00 35.07 5.19
2574 2834 0.459899 AGTCACAACAGTGTCAGCGA 59.540 50.000 0.00 0.00 35.07 4.93
2575 2835 1.004610 CAAGTCACAACAGTGTCAGCG 60.005 52.381 0.00 0.00 35.07 5.18
2576 2836 1.268234 GCAAGTCACAACAGTGTCAGC 60.268 52.381 0.00 0.00 35.07 4.26
2724 2984 8.327941 TCTTAAAATCATGTGGAAGTCTCAAG 57.672 34.615 0.00 0.00 0.00 3.02
2916 3184 5.563475 CGGACAGACTGAAAAATTTCATGCT 60.563 40.000 10.08 6.86 45.26 3.79
2921 3189 3.004315 TGCCGGACAGACTGAAAAATTTC 59.996 43.478 5.05 0.00 37.69 2.17
2925 3193 1.673920 GTTGCCGGACAGACTGAAAAA 59.326 47.619 5.05 0.00 0.00 1.94
2960 3228 9.050601 AGTTCTAGCATTTGAAGATATTAGCAC 57.949 33.333 0.00 0.00 0.00 4.40
2993 3261 5.220719 GCATCATTCACGATCAATGAAGTCA 60.221 40.000 13.25 2.92 42.23 3.41
3235 3503 3.032017 GCTTCTCAGCAGTCAACACTA 57.968 47.619 0.00 0.00 46.49 2.74
3408 3676 6.866248 TGAAATGCAGCAATTGATATATGCAG 59.134 34.615 10.34 0.00 45.76 4.41
3433 3701 0.976641 TTCTGCGAGTCAAGGTCCAT 59.023 50.000 0.00 0.00 0.00 3.41
3951 4229 4.884164 GGAGCCATTGCAAGTACTTCTTAT 59.116 41.667 4.77 0.00 41.13 1.73
3964 4242 0.968405 TGGTTTTCTGGAGCCATTGC 59.032 50.000 0.00 0.00 37.95 3.56
4034 4313 5.748630 TCTTTATGTACGAGTGCATCACATC 59.251 40.000 9.95 0.00 37.16 3.06
4136 4430 3.705579 TGATAAAGGAATGGGCAACATGG 59.294 43.478 0.00 0.00 40.44 3.66
4173 4467 3.066064 ACTAGCAAGTGCAGAGTATCTCG 59.934 47.826 6.00 0.00 39.41 4.04
4181 4475 4.216257 GGAAAATGAACTAGCAAGTGCAGA 59.784 41.667 6.00 0.00 44.80 4.26
4188 4482 4.340666 TGCACAAGGAAAATGAACTAGCAA 59.659 37.500 0.00 0.00 0.00 3.91
4223 4517 8.750515 TTCTATATGTTCAGGAATGCATTTGA 57.249 30.769 14.33 11.47 0.00 2.69
4239 4533 4.594920 AGCCAGCCTGTACATTCTATATGT 59.405 41.667 0.00 0.00 36.13 2.29
4399 4693 5.116882 GGATAACCGGGCATAATATCTCAC 58.883 45.833 6.32 0.00 0.00 3.51
4496 4790 4.155280 GTGGCATATTAAAGTGTCACGGTT 59.845 41.667 11.00 0.00 40.58 4.44
4514 4808 0.320050 TGAAGCAGACATACGTGGCA 59.680 50.000 0.00 0.00 35.06 4.92
4520 4814 8.078596 AGACAGAAAAATTTGAAGCAGACATAC 58.921 33.333 0.00 0.00 0.00 2.39
4558 4852 6.330278 AGGACAAACAAAGAAAGTTAGTTGC 58.670 36.000 0.00 0.00 0.00 4.17
4574 4868 7.646526 GGAATTGGCGTAAATAATAGGACAAAC 59.353 37.037 1.13 0.23 34.53 2.93
4643 4939 6.071560 TCGAGGAGACAAGCATCTTAGTTAAA 60.072 38.462 0.00 0.00 0.00 1.52
4663 4959 1.620323 TCCATGCTGGTCATATCGAGG 59.380 52.381 0.00 0.00 39.03 4.63
4723 5019 2.178521 CCGTCCACTTCCTCGACG 59.821 66.667 2.01 2.01 46.79 5.12
5009 5311 2.803956 CGGCCGTCGGATAATGTAAATT 59.196 45.455 19.50 0.00 34.75 1.82
5010 5312 2.409975 CGGCCGTCGGATAATGTAAAT 58.590 47.619 19.50 0.00 34.75 1.40
5026 5328 3.837570 AAAAGGACCACGACCGGCC 62.838 63.158 0.00 0.00 0.00 6.13
5038 5340 5.296813 GCTTCTTGATTTAGCGAAAAGGA 57.703 39.130 0.00 0.00 0.00 3.36
5073 5375 0.933097 GACGATGTGATGCGATGCTT 59.067 50.000 0.00 0.00 0.00 3.91
5075 5377 1.200103 CGACGATGTGATGCGATGC 59.800 57.895 0.00 0.00 0.00 3.91
5076 5378 0.923403 AACGACGATGTGATGCGATG 59.077 50.000 0.00 0.00 0.00 3.84
5077 5379 2.117137 GTAACGACGATGTGATGCGAT 58.883 47.619 0.00 0.00 0.00 4.58
5078 5380 1.135632 TGTAACGACGATGTGATGCGA 60.136 47.619 0.00 0.00 0.00 5.10
5079 5381 1.252779 CTGTAACGACGATGTGATGCG 59.747 52.381 0.00 0.00 0.00 4.73
5085 5387 2.735134 GGAAAAGCTGTAACGACGATGT 59.265 45.455 0.00 0.00 0.00 3.06
5091 5393 3.056322 GGTCTAGGGAAAAGCTGTAACGA 60.056 47.826 0.00 0.00 0.00 3.85
5095 5397 4.362677 AGATGGTCTAGGGAAAAGCTGTA 58.637 43.478 0.00 0.00 0.00 2.74
5105 5407 5.394738 TGGTACTTGATAGATGGTCTAGGG 58.605 45.833 0.00 0.00 31.67 3.53
5106 5408 6.978674 TTGGTACTTGATAGATGGTCTAGG 57.021 41.667 0.00 0.00 31.67 3.02
5107 5409 8.183104 TCATTGGTACTTGATAGATGGTCTAG 57.817 38.462 0.00 0.00 31.67 2.43
5108 5410 8.004801 TCTCATTGGTACTTGATAGATGGTCTA 58.995 37.037 0.00 0.00 32.87 2.59
5109 5411 6.841229 TCTCATTGGTACTTGATAGATGGTCT 59.159 38.462 0.00 0.00 0.00 3.85
5110 5412 7.055667 TCTCATTGGTACTTGATAGATGGTC 57.944 40.000 0.00 0.00 0.00 4.02
5114 5418 7.290948 TGGTCATCTCATTGGTACTTGATAGAT 59.709 37.037 0.00 0.00 0.00 1.98
5221 5525 0.240411 CAAGCAAGCACCTCTCAAGC 59.760 55.000 0.00 0.00 0.00 4.01
5231 5535 2.732016 CCTGCAAGCAAGCAAGCA 59.268 55.556 10.24 10.24 45.13 3.91
5232 5536 2.048503 CCCTGCAAGCAAGCAAGC 60.049 61.111 4.63 0.00 45.13 4.01
5233 5537 2.048503 GCCCTGCAAGCAAGCAAG 60.049 61.111 10.74 0.00 45.13 4.01
5234 5538 3.618750 GGCCCTGCAAGCAAGCAA 61.619 61.111 15.76 0.00 45.13 3.91
5269 5573 3.136123 CAAGCACGAGCCCATGGG 61.136 66.667 27.87 27.87 43.56 4.00
5368 5673 2.353610 GGCAACTTGGCATGGGAGG 61.354 63.158 10.37 0.00 43.14 4.30
5398 5703 1.453155 CCCAGAGTTTTGGATCCACG 58.547 55.000 15.91 0.00 40.87 4.94
5418 5723 3.006247 GAGGAAGCAGGCTAAAGAACAG 58.994 50.000 0.00 0.00 0.00 3.16
5433 5738 2.005960 AATCGACGAGGGCGAGGAAG 62.006 60.000 3.01 0.00 41.49 3.46
5447 5752 4.051554 CGAGTTGTCGCGAATCGA 57.948 55.556 22.17 5.62 46.29 3.59
5490 5807 2.363795 CCTCCGTGACAGGGCCTA 60.364 66.667 5.28 0.00 0.00 3.93
5494 5811 1.966451 GTTTGCCTCCGTGACAGGG 60.966 63.158 7.92 7.92 0.00 4.45
5526 5848 5.507985 GCTAGAAGAAGAAAAGCAAAGCCAA 60.508 40.000 0.00 0.00 33.38 4.52
5527 5849 4.022849 GCTAGAAGAAGAAAAGCAAAGCCA 60.023 41.667 0.00 0.00 33.38 4.75
5650 6093 2.203337 GGCAGGTCCAGTGCAACA 60.203 61.111 5.54 0.00 43.12 3.33
5668 6111 2.325761 CGGTTTCGGATTATAGCGGAG 58.674 52.381 0.00 0.00 0.00 4.63
5699 6142 2.508586 GAAGCAGACCGGGTCCAGAC 62.509 65.000 23.21 10.45 32.18 3.51
5700 6143 2.203788 AAGCAGACCGGGTCCAGA 60.204 61.111 23.21 0.00 32.18 3.86
5704 6147 0.034896 TTTCAGAAGCAGACCGGGTC 59.965 55.000 19.61 19.61 0.00 4.46
5766 6210 5.413833 ACGGATATACTATTCCTGTACGTGG 59.586 44.000 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.