Multiple sequence alignment - TraesCS2D01G313800

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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 TraesCS2D01G313800 chr2D 100.000 4229 0 0 1 4229 403477345 403481573 0.000000e+00 7810.0
1 TraesCS2D01G313800 chr2D 93.868 1060 40 7 3067 4104 83852750 83851694 0.000000e+00 1574.0
2 TraesCS2D01G313800 chr2D 92.877 1081 17 8 3068 4094 638306349 638307423 0.000000e+00 1515.0
3 TraesCS2D01G313800 chr2D 91.848 1055 34 13 3068 4091 48176283 48177316 0.000000e+00 1424.0
4 TraesCS2D01G313800 chr2D 92.857 266 18 1 1995 2260 403346825 403346561 6.630000e-103 385.0
5 TraesCS2D01G313800 chr2D 91.707 205 17 0 1674 1878 403347141 403346937 6.920000e-73 285.0
6 TraesCS2D01G313800 chr2D 84.774 243 33 4 1052 1292 403347824 403347584 1.520000e-59 241.0
7 TraesCS2D01G313800 chr2A 90.502 3085 186 61 1 3043 541774882 541777901 0.000000e+00 3975.0
8 TraesCS2D01G313800 chr2A 93.487 261 17 0 1995 2255 540849099 540848839 5.130000e-104 388.0
9 TraesCS2D01G313800 chr2A 91.707 205 17 0 1674 1878 540849415 540849211 6.920000e-73 285.0
10 TraesCS2D01G313800 chr2A 84.774 243 33 4 1052 1292 540850074 540849834 1.520000e-59 241.0
11 TraesCS2D01G313800 chr2A 92.308 52 4 0 4101 4152 772654050 772653999 1.630000e-09 75.0
12 TraesCS2D01G313800 chr2B 91.394 2324 109 38 1 2264 477572321 477574613 0.000000e+00 3099.0
13 TraesCS2D01G313800 chr2B 92.620 813 44 10 2262 3067 477574648 477575451 0.000000e+00 1155.0
14 TraesCS2D01G313800 chr2B 89.817 766 49 9 3062 3802 756550962 756551723 0.000000e+00 955.0
15 TraesCS2D01G313800 chr2B 88.941 425 39 4 3672 4094 756551630 756552048 6.270000e-143 518.0
16 TraesCS2D01G313800 chr2B 93.985 266 15 1 1995 2260 477528912 477528648 6.590000e-108 401.0
17 TraesCS2D01G313800 chr2B 87.789 303 36 1 3068 3370 143131048 143130747 1.870000e-93 353.0
18 TraesCS2D01G313800 chr2B 88.214 280 23 8 3825 4094 776688974 776689253 4.080000e-85 326.0
19 TraesCS2D01G313800 chr2B 91.707 205 17 0 1674 1878 477529207 477529003 6.920000e-73 285.0
20 TraesCS2D01G313800 chr2B 85.366 246 26 9 1052 1292 477529845 477529605 3.270000e-61 246.0
21 TraesCS2D01G313800 chr2B 86.364 66 9 0 4101 4166 14834389 14834324 5.870000e-09 73.1
22 TraesCS2D01G313800 chr1D 97.080 993 18 5 3068 4051 363855974 363854984 0.000000e+00 1663.0
23 TraesCS2D01G313800 chr1D 94.521 219 9 3 3068 3285 30247034 30246818 6.780000e-88 335.0
24 TraesCS2D01G313800 chr6D 92.871 1066 32 15 3068 4094 461655291 461656351 0.000000e+00 1507.0
25 TraesCS2D01G313800 chr6D 94.521 219 10 2 3067 3285 303525467 303525251 1.880000e-88 337.0
26 TraesCS2D01G313800 chr6D 87.189 281 26 5 3068 3341 380428100 380428377 1.140000e-80 311.0
27 TraesCS2D01G313800 chr4A 89.710 1069 64 10 3065 4094 733354673 733353612 0.000000e+00 1323.0
28 TraesCS2D01G313800 chr4A 86.235 1097 78 8 3068 4094 717726807 717725714 0.000000e+00 1122.0
29 TraesCS2D01G313800 chr4A 78.543 508 85 21 1099 1594 75215112 75214617 3.170000e-81 313.0
30 TraesCS2D01G313800 chr4A 91.556 225 17 2 1669 1892 574870428 574870205 4.110000e-80 309.0
31 TraesCS2D01G313800 chr4A 89.498 219 23 0 1669 1887 75214547 75214329 1.160000e-70 278.0
32 TraesCS2D01G313800 chr4A 87.273 220 26 2 1674 1892 641451881 641452099 2.520000e-62 250.0
33 TraesCS2D01G313800 chr4A 89.691 194 20 0 1099 1292 574872603 574872410 9.080000e-62 248.0
34 TraesCS2D01G313800 chr4A 89.175 194 21 0 1099 1292 641451293 641451486 4.220000e-60 243.0
35 TraesCS2D01G313800 chr3B 87.665 1062 92 27 3068 4094 452700954 452699897 0.000000e+00 1199.0
36 TraesCS2D01G313800 chr3B 89.175 194 21 0 1099 1292 9914572 9914765 4.220000e-60 243.0
37 TraesCS2D01G313800 chr5B 86.794 1098 72 14 3067 4094 281370154 281369060 0.000000e+00 1157.0
38 TraesCS2D01G313800 chr5B 84.801 1079 107 33 3068 4095 682507063 682508135 0.000000e+00 1031.0
39 TraesCS2D01G313800 chr5B 86.765 408 45 4 3253 3651 375611928 375612335 3.000000e-121 446.0
40 TraesCS2D01G313800 chr5B 92.222 270 20 1 3250 3519 184773322 184773054 8.580000e-102 381.0
41 TraesCS2D01G313800 chr5B 86.833 281 30 7 3820 4094 460968397 460968676 1.480000e-79 307.0
42 TraesCS2D01G313800 chr5B 88.265 196 23 0 1099 1294 670067937 670067742 7.070000e-58 235.0
43 TraesCS2D01G313800 chr4D 78.731 804 134 31 1099 1883 393635979 393636764 1.760000e-138 503.0
44 TraesCS2D01G313800 chr4D 92.692 260 17 2 1994 2252 28839749 28840007 1.440000e-99 374.0
45 TraesCS2D01G313800 chr4D 91.954 261 19 2 1994 2253 393636858 393637117 8.640000e-97 364.0
46 TraesCS2D01G313800 chr4D 90.310 258 18 6 3844 4095 26526872 26526616 8.760000e-87 331.0
47 TraesCS2D01G313800 chr4D 94.416 197 11 0 1672 1868 28839448 28839644 1.910000e-78 303.0
48 TraesCS2D01G313800 chr4D 89.175 194 20 1 1099 1292 28560244 28560436 1.520000e-59 241.0
49 TraesCS2D01G313800 chr4D 88.660 194 22 0 1099 1292 28837093 28837286 1.970000e-58 237.0
50 TraesCS2D01G313800 chr4D 94.595 37 2 0 4101 4137 467755814 467755850 1.640000e-04 58.4
51 TraesCS2D01G313800 chr4B 92.692 260 17 2 1994 2252 41012875 41013133 1.440000e-99 374.0
52 TraesCS2D01G313800 chr4B 92.337 261 18 2 1994 2253 483334259 483334000 1.860000e-98 370.0
53 TraesCS2D01G313800 chr4B 94.472 199 11 0 1670 1868 41012540 41012738 1.480000e-79 307.0
54 TraesCS2D01G313800 chr4B 88.584 219 25 0 1674 1892 483334557 483334339 2.510000e-67 267.0
55 TraesCS2D01G313800 chr4B 90.206 194 19 0 1099 1292 41010053 41010246 1.950000e-63 254.0
56 TraesCS2D01G313800 chr7A 93.722 223 13 1 3068 3290 727424944 727424723 2.440000e-87 333.0
57 TraesCS2D01G313800 chr3D 87.544 281 26 4 3068 3341 522158518 522158796 2.450000e-82 316.0
58 TraesCS2D01G313800 chr3D 89.362 188 20 0 1105 1292 7590682 7590869 1.970000e-58 237.0
59 TraesCS2D01G313800 chr6A 88.672 256 25 4 3841 4094 478916277 478916024 4.110000e-80 309.0
60 TraesCS2D01G313800 chr5D 86.447 273 32 5 3828 4096 217295413 217295142 1.150000e-75 294.0
61 TraesCS2D01G313800 chr5D 86.818 220 26 3 1674 1892 530825617 530825400 4.220000e-60 243.0
62 TraesCS2D01G313800 chr5D 88.265 196 23 0 1099 1294 530826185 530825990 7.070000e-58 235.0
63 TraesCS2D01G313800 chr5D 87.302 63 6 2 4105 4166 430065209 430065270 2.110000e-08 71.3
64 TraesCS2D01G313800 chr5A 86.598 194 26 0 1099 1292 494220291 494220484 9.210000e-52 215.0
65 TraesCS2D01G313800 chr5A 88.136 59 4 3 4110 4167 56320084 56320028 2.730000e-07 67.6
66 TraesCS2D01G313800 chrUn 79.487 156 25 7 329 482 336020994 336020844 2.080000e-18 104.0
67 TraesCS2D01G313800 chr7B 78.378 148 23 9 333 473 129663992 129663847 2.090000e-13 87.9
68 TraesCS2D01G313800 chr7D 88.060 67 6 2 4101 4166 595026497 595026562 1.260000e-10 78.7
69 TraesCS2D01G313800 chr3A 87.879 66 6 2 4101 4165 86601817 86601753 4.530000e-10 76.8
70 TraesCS2D01G313800 chr3A 86.667 60 7 1 4101 4159 12955980 12956039 9.810000e-07 65.8
71 TraesCS2D01G313800 chr1B 86.154 65 9 0 4101 4165 309925680 309925744 2.110000e-08 71.3


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 TraesCS2D01G313800 chr2D 403477345 403481573 4228 False 7810.000000 7810 100.000000 1 4229 1 chr2D.!!$F2 4228
1 TraesCS2D01G313800 chr2D 83851694 83852750 1056 True 1574.000000 1574 93.868000 3067 4104 1 chr2D.!!$R1 1037
2 TraesCS2D01G313800 chr2D 638306349 638307423 1074 False 1515.000000 1515 92.877000 3068 4094 1 chr2D.!!$F3 1026
3 TraesCS2D01G313800 chr2D 48176283 48177316 1033 False 1424.000000 1424 91.848000 3068 4091 1 chr2D.!!$F1 1023
4 TraesCS2D01G313800 chr2D 403346561 403347824 1263 True 303.666667 385 89.779333 1052 2260 3 chr2D.!!$R2 1208
5 TraesCS2D01G313800 chr2A 541774882 541777901 3019 False 3975.000000 3975 90.502000 1 3043 1 chr2A.!!$F1 3042
6 TraesCS2D01G313800 chr2A 540848839 540850074 1235 True 304.666667 388 89.989333 1052 2255 3 chr2A.!!$R2 1203
7 TraesCS2D01G313800 chr2B 477572321 477575451 3130 False 2127.000000 3099 92.007000 1 3067 2 chr2B.!!$F2 3066
8 TraesCS2D01G313800 chr2B 756550962 756552048 1086 False 736.500000 955 89.379000 3062 4094 2 chr2B.!!$F3 1032
9 TraesCS2D01G313800 chr2B 477528648 477529845 1197 True 310.666667 401 90.352667 1052 2260 3 chr2B.!!$R3 1208
10 TraesCS2D01G313800 chr1D 363854984 363855974 990 True 1663.000000 1663 97.080000 3068 4051 1 chr1D.!!$R2 983
11 TraesCS2D01G313800 chr6D 461655291 461656351 1060 False 1507.000000 1507 92.871000 3068 4094 1 chr6D.!!$F2 1026
12 TraesCS2D01G313800 chr4A 733353612 733354673 1061 True 1323.000000 1323 89.710000 3065 4094 1 chr4A.!!$R2 1029
13 TraesCS2D01G313800 chr4A 717725714 717726807 1093 True 1122.000000 1122 86.235000 3068 4094 1 chr4A.!!$R1 1026
14 TraesCS2D01G313800 chr4A 75214329 75215112 783 True 295.500000 313 84.020500 1099 1887 2 chr4A.!!$R3 788
15 TraesCS2D01G313800 chr4A 574870205 574872603 2398 True 278.500000 309 90.623500 1099 1892 2 chr4A.!!$R4 793
16 TraesCS2D01G313800 chr4A 641451293 641452099 806 False 246.500000 250 88.224000 1099 1892 2 chr4A.!!$F1 793
17 TraesCS2D01G313800 chr3B 452699897 452700954 1057 True 1199.000000 1199 87.665000 3068 4094 1 chr3B.!!$R1 1026
18 TraesCS2D01G313800 chr5B 281369060 281370154 1094 True 1157.000000 1157 86.794000 3067 4094 1 chr5B.!!$R2 1027
19 TraesCS2D01G313800 chr5B 682507063 682508135 1072 False 1031.000000 1031 84.801000 3068 4095 1 chr5B.!!$F3 1027
20 TraesCS2D01G313800 chr4D 393635979 393637117 1138 False 433.500000 503 85.342500 1099 2253 2 chr4D.!!$F4 1154
21 TraesCS2D01G313800 chr4D 28837093 28840007 2914 False 304.666667 374 91.922667 1099 2252 3 chr4D.!!$F3 1153
22 TraesCS2D01G313800 chr4B 483334000 483334557 557 True 318.500000 370 90.460500 1674 2253 2 chr4B.!!$R1 579
23 TraesCS2D01G313800 chr4B 41010053 41013133 3080 False 311.666667 374 92.456667 1099 2252 3 chr4B.!!$F1 1153
24 TraesCS2D01G313800 chr5D 530825400 530826185 785 True 239.000000 243 87.541500 1099 1892 2 chr5D.!!$R2 793

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
582 636 0.252284 ACTCCACGTCCCATTCTCCT 60.252 55.0 0.0 0.0 0.0 3.69 F
1557 4354 0.105039 GAGGGGAAGCCATACGACAG 59.895 60.0 0.0 0.0 0.0 3.51 F
2368 5292 0.326264 GATCTTGTGCAGGGTCCAGT 59.674 55.0 0.0 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2105 4992 1.301401 GTACTTGTGCCCGCTGACA 60.301 57.895 0.0 0.0 0.00 3.58 R
2997 5931 0.179037 GGCATAGCAGTCATCTGGCA 60.179 55.000 0.0 0.0 41.57 4.92 R
4149 7316 0.039180 TCCGTACTTCCTCTGCTCCA 59.961 55.000 0.0 0.0 0.00 3.86 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
127 131 2.680805 GCACTGTCTGCTTAGGCCAATA 60.681 50.000 5.01 0.00 43.33 1.90
167 171 3.446161 TCAACCCAGGTACGATAACAGAG 59.554 47.826 0.00 0.00 0.00 3.35
172 176 4.442706 CCAGGTACGATAACAGAGCAATT 58.557 43.478 0.00 0.00 0.00 2.32
187 191 1.581934 CAATTAGCCGATTCTCCGCA 58.418 50.000 0.00 0.00 0.00 5.69
195 199 1.135431 CCGATTCTCCGCAAAAATGCA 60.135 47.619 1.42 0.00 34.41 3.96
213 217 8.847444 AAAATGCATTTCTAATTCTAAGCTCG 57.153 30.769 24.28 0.00 0.00 5.03
217 221 8.887036 TGCATTTCTAATTCTAAGCTCGAATA 57.113 30.769 10.54 0.00 31.27 1.75
392 423 6.827586 AATAAGTTTTTGAGGCATCGGTTA 57.172 33.333 0.00 0.00 0.00 2.85
393 424 7.404671 AATAAGTTTTTGAGGCATCGGTTAT 57.595 32.000 0.00 0.00 0.00 1.89
394 425 4.701956 AGTTTTTGAGGCATCGGTTATG 57.298 40.909 0.00 0.00 38.74 1.90
398 429 5.461032 TTTTGAGGCATCGGTTATGTTTT 57.539 34.783 0.00 0.00 37.93 2.43
550 590 6.797454 AGCGGTTTTTGTTTTAGTATTCACA 58.203 32.000 0.00 0.00 0.00 3.58
563 603 3.818210 AGTATTCACACGGTGCATTTGAA 59.182 39.130 8.30 10.83 32.98 2.69
582 636 0.252284 ACTCCACGTCCCATTCTCCT 60.252 55.000 0.00 0.00 0.00 3.69
622 676 1.523758 GTGAATCGTGACAAAGCCCT 58.476 50.000 0.00 0.00 0.00 5.19
626 680 2.094762 ATCGTGACAAAGCCCTACAC 57.905 50.000 0.00 0.00 0.00 2.90
749 808 1.239968 GCAGTGGGAAGCAACAGAGG 61.240 60.000 0.00 0.00 0.00 3.69
755 814 0.322008 GGAAGCAACAGAGGTCCCAG 60.322 60.000 0.00 0.00 0.00 4.45
793 852 4.277515 ACTGAGATCAAGTAAAGCAGCA 57.722 40.909 0.00 0.00 0.00 4.41
889 948 1.594397 GGCAAGCAAAGCACAAGAAAC 59.406 47.619 0.00 0.00 0.00 2.78
938 997 8.586744 TGTATATATATGGTTCGTGTTGCCTAA 58.413 33.333 5.44 0.00 0.00 2.69
939 998 9.595823 GTATATATATGGTTCGTGTTGCCTAAT 57.404 33.333 5.44 0.00 0.00 1.73
940 999 6.801539 ATATATGGTTCGTGTTGCCTAATG 57.198 37.500 0.00 0.00 0.00 1.90
941 1000 1.529226 TGGTTCGTGTTGCCTAATGG 58.471 50.000 0.00 0.00 0.00 3.16
942 1001 1.072489 TGGTTCGTGTTGCCTAATGGA 59.928 47.619 0.00 0.00 34.57 3.41
943 1002 2.156098 GGTTCGTGTTGCCTAATGGAA 58.844 47.619 0.00 0.00 34.57 3.53
944 1003 2.095415 GGTTCGTGTTGCCTAATGGAAC 60.095 50.000 0.00 0.00 34.57 3.62
1014 1083 1.672356 AGGCATGGTTCTGACGCAC 60.672 57.895 0.00 0.00 0.00 5.34
1324 4086 3.627577 AGTGGCATTCCGATATGTGTTTC 59.372 43.478 0.00 0.00 34.14 2.78
1557 4354 0.105039 GAGGGGAAGCCATACGACAG 59.895 60.000 0.00 0.00 0.00 3.51
1615 4412 1.719608 CGATAGATAACGCGCGTACGT 60.720 52.381 37.93 23.72 45.03 3.57
1616 4413 2.470621 CGATAGATAACGCGCGTACGTA 60.471 50.000 37.93 25.22 42.75 3.57
1636 4439 4.629634 CGTACATTACCTGCTTCATCACAA 59.370 41.667 0.00 0.00 0.00 3.33
1642 4445 3.499338 ACCTGCTTCATCACAAATGGAA 58.501 40.909 0.00 0.00 0.00 3.53
1902 4764 0.514691 GAACAAGGTCTGCTTGCTCG 59.485 55.000 0.00 0.00 35.39 5.03
1908 4770 1.519719 GTCTGCTTGCTCGGATCCT 59.480 57.895 10.75 0.00 0.00 3.24
1983 4870 2.699576 TATGACGCGGCTGGCATCTC 62.700 60.000 15.80 0.00 43.84 2.75
1984 4871 4.521062 GACGCGGCTGGCATCTCT 62.521 66.667 12.47 0.00 43.84 3.10
1985 4872 4.087892 ACGCGGCTGGCATCTCTT 62.088 61.111 12.47 0.00 43.84 2.85
1986 4873 3.267860 CGCGGCTGGCATCTCTTC 61.268 66.667 0.00 0.00 43.84 2.87
2105 4992 1.741706 CCGCTTGTGAAGAGCATCAAT 59.258 47.619 0.00 0.00 40.13 2.57
2264 5151 4.138290 TCTCCAAAGGCACGAACATTTTA 58.862 39.130 0.00 0.00 0.00 1.52
2308 5232 6.251471 ACAGACAGAATCCCTGATTTGATTT 58.749 36.000 0.00 0.00 45.78 2.17
2312 5236 6.928520 ACAGAATCCCTGATTTGATTTTGTC 58.071 36.000 0.00 0.00 45.78 3.18
2319 5243 5.801947 CCCTGATTTGATTTTGTCATTCGAC 59.198 40.000 0.00 0.00 42.93 4.20
2324 5248 8.134261 TGATTTGATTTTGTCATTCGACTTCAA 58.866 29.630 0.00 0.00 43.06 2.69
2368 5292 0.326264 GATCTTGTGCAGGGTCCAGT 59.674 55.000 0.00 0.00 0.00 4.00
2392 5316 4.668576 AATCATCGCGCAATATTACCAG 57.331 40.909 8.75 0.00 0.00 4.00
2430 5354 6.801862 GGTTTCGAGGTACAAAATTCATGAAG 59.198 38.462 14.54 2.58 0.00 3.02
2445 5369 7.713734 ATTCATGAAGAAACCAATCATCAGT 57.286 32.000 14.54 0.00 40.22 3.41
2446 5370 7.528996 TTCATGAAGAAACCAATCATCAGTT 57.471 32.000 3.38 0.00 31.35 3.16
2451 5375 8.231692 TGAAGAAACCAATCATCAGTTTAACA 57.768 30.769 0.00 0.00 34.00 2.41
2453 5377 9.528018 GAAGAAACCAATCATCAGTTTAACAAA 57.472 29.630 0.00 0.00 34.00 2.83
2931 5865 0.898789 TCAGGGTCGTCAAGAGGGAC 60.899 60.000 0.00 0.00 34.42 4.46
2997 5931 0.833834 AGGGTGTGTGCTAGTCTGCT 60.834 55.000 0.00 0.00 0.00 4.24
3013 5947 0.835276 TGCTGCCAGATGACTGCTAT 59.165 50.000 0.00 0.00 42.25 2.97
3036 5970 1.394917 CTGCCGATTGTGCTACAGAAC 59.605 52.381 0.00 0.00 0.00 3.01
3047 5981 8.848474 ATTGTGCTACAGAACAAATTACTACT 57.152 30.769 6.87 0.00 45.87 2.57
3055 5989 5.875359 CAGAACAAATTACTACTCCCTCCAC 59.125 44.000 0.00 0.00 0.00 4.02
3061 5995 2.038329 TACTCCCTCCACCCCACG 59.962 66.667 0.00 0.00 0.00 4.94
3625 6654 3.731728 GGAGACCCATGGCTGGCA 61.732 66.667 6.09 6.31 41.64 4.92
4097 7264 8.644318 AGTAGTTTTATGCTATTTACTCCACG 57.356 34.615 0.00 0.00 0.00 4.94
4098 7265 6.920569 AGTTTTATGCTATTTACTCCACGG 57.079 37.500 0.00 0.00 0.00 4.94
4099 7266 5.296035 AGTTTTATGCTATTTACTCCACGGC 59.704 40.000 0.00 0.00 0.00 5.68
4100 7267 4.409718 TTATGCTATTTACTCCACGGCA 57.590 40.909 0.00 0.00 0.00 5.69
4101 7268 3.492102 ATGCTATTTACTCCACGGCAT 57.508 42.857 0.00 0.00 34.68 4.40
4103 7270 4.409718 TGCTATTTACTCCACGGCATAA 57.590 40.909 0.00 0.00 0.00 1.90
4104 7271 4.377021 TGCTATTTACTCCACGGCATAAG 58.623 43.478 0.00 0.00 0.00 1.73
4106 7273 5.221641 TGCTATTTACTCCACGGCATAAGAT 60.222 40.000 0.00 0.00 0.00 2.40
4107 7274 5.348997 GCTATTTACTCCACGGCATAAGATC 59.651 44.000 0.00 0.00 0.00 2.75
4108 7275 4.746535 TTTACTCCACGGCATAAGATCA 57.253 40.909 0.00 0.00 0.00 2.92
4109 7276 4.955811 TTACTCCACGGCATAAGATCAT 57.044 40.909 0.00 0.00 0.00 2.45
4110 7277 3.845781 ACTCCACGGCATAAGATCATT 57.154 42.857 0.00 0.00 0.00 2.57
4111 7278 4.156455 ACTCCACGGCATAAGATCATTT 57.844 40.909 0.00 0.00 0.00 2.32
4112 7279 4.526970 ACTCCACGGCATAAGATCATTTT 58.473 39.130 0.00 0.00 0.00 1.82
4113 7280 4.336433 ACTCCACGGCATAAGATCATTTTG 59.664 41.667 0.00 0.00 0.00 2.44
4114 7281 3.066621 TCCACGGCATAAGATCATTTTGC 59.933 43.478 0.00 3.96 0.00 3.68
4115 7282 3.181488 CCACGGCATAAGATCATTTTGCA 60.181 43.478 16.06 0.00 35.04 4.08
4116 7283 4.422840 CACGGCATAAGATCATTTTGCAA 58.577 39.130 16.06 0.00 35.04 4.08
4117 7284 4.501559 CACGGCATAAGATCATTTTGCAAG 59.498 41.667 16.06 12.94 35.04 4.01
4118 7285 4.158394 ACGGCATAAGATCATTTTGCAAGT 59.842 37.500 16.06 13.33 35.04 3.16
4119 7286 5.104374 CGGCATAAGATCATTTTGCAAGTT 58.896 37.500 16.06 0.00 35.04 2.66
4120 7287 5.005012 CGGCATAAGATCATTTTGCAAGTTG 59.995 40.000 16.06 0.00 35.04 3.16
4121 7288 5.870978 GGCATAAGATCATTTTGCAAGTTGT 59.129 36.000 16.06 0.00 35.04 3.32
4122 7289 6.369615 GGCATAAGATCATTTTGCAAGTTGTT 59.630 34.615 16.06 0.00 35.04 2.83
4123 7290 7.095102 GGCATAAGATCATTTTGCAAGTTGTTT 60.095 33.333 16.06 2.28 35.04 2.83
4124 7291 8.284693 GCATAAGATCATTTTGCAAGTTGTTTT 58.715 29.630 4.48 1.98 33.58 2.43
4127 7294 7.412137 AGATCATTTTGCAAGTTGTTTTAGC 57.588 32.000 4.48 0.00 0.00 3.09
4128 7295 7.212274 AGATCATTTTGCAAGTTGTTTTAGCT 58.788 30.769 4.48 0.00 0.00 3.32
4129 7296 7.712205 AGATCATTTTGCAAGTTGTTTTAGCTT 59.288 29.630 4.48 0.00 0.00 3.74
4130 7297 7.002816 TCATTTTGCAAGTTGTTTTAGCTTG 57.997 32.000 4.48 0.00 46.68 4.01
4137 7304 5.247340 CAAGTTGTTTTAGCTTGCAAAACG 58.753 37.500 15.21 0.00 44.91 3.60
4138 7305 4.490743 AGTTGTTTTAGCTTGCAAAACGT 58.509 34.783 15.21 3.91 44.91 3.99
4139 7306 4.926832 AGTTGTTTTAGCTTGCAAAACGTT 59.073 33.333 15.21 0.00 44.91 3.99
4140 7307 5.407084 AGTTGTTTTAGCTTGCAAAACGTTT 59.593 32.000 7.96 7.96 44.91 3.60
4141 7308 5.847670 TGTTTTAGCTTGCAAAACGTTTT 57.152 30.435 20.26 20.26 44.91 2.43
4142 7309 5.848786 TGTTTTAGCTTGCAAAACGTTTTC 58.151 33.333 22.90 17.08 44.91 2.29
4143 7310 5.405571 TGTTTTAGCTTGCAAAACGTTTTCA 59.594 32.000 22.90 19.17 44.91 2.69
4144 7311 6.091441 TGTTTTAGCTTGCAAAACGTTTTCAT 59.909 30.769 22.90 11.50 44.91 2.57
4145 7312 7.275779 TGTTTTAGCTTGCAAAACGTTTTCATA 59.724 29.630 22.90 9.75 44.91 2.15
4146 7313 7.938563 TTTAGCTTGCAAAACGTTTTCATAT 57.061 28.000 22.90 13.64 0.00 1.78
4147 7314 7.938563 TTAGCTTGCAAAACGTTTTCATATT 57.061 28.000 22.90 10.09 0.00 1.28
4148 7315 9.464714 TTTAGCTTGCAAAACGTTTTCATATTA 57.535 25.926 22.90 9.21 0.00 0.98
4149 7316 9.632807 TTAGCTTGCAAAACGTTTTCATATTAT 57.367 25.926 22.90 9.54 0.00 1.28
4150 7317 7.952339 AGCTTGCAAAACGTTTTCATATTATG 58.048 30.769 22.90 11.48 0.00 1.90
4151 7318 7.063308 AGCTTGCAAAACGTTTTCATATTATGG 59.937 33.333 22.90 9.98 0.00 2.74
4152 7319 7.062839 GCTTGCAAAACGTTTTCATATTATGGA 59.937 33.333 22.90 9.06 0.00 3.41
4153 7320 8.459521 TTGCAAAACGTTTTCATATTATGGAG 57.540 30.769 22.90 8.81 0.00 3.86
4154 7321 6.529829 TGCAAAACGTTTTCATATTATGGAGC 59.470 34.615 22.90 17.61 0.00 4.70
4155 7322 6.529829 GCAAAACGTTTTCATATTATGGAGCA 59.470 34.615 22.90 0.00 0.00 4.26
4156 7323 7.253750 GCAAAACGTTTTCATATTATGGAGCAG 60.254 37.037 22.90 7.62 0.00 4.24
4157 7324 7.624360 AAACGTTTTCATATTATGGAGCAGA 57.376 32.000 7.96 0.00 0.00 4.26
4158 7325 6.851222 ACGTTTTCATATTATGGAGCAGAG 57.149 37.500 3.89 0.00 0.00 3.35
4159 7326 5.760253 ACGTTTTCATATTATGGAGCAGAGG 59.240 40.000 3.89 0.00 0.00 3.69
4160 7327 5.991606 CGTTTTCATATTATGGAGCAGAGGA 59.008 40.000 3.89 0.00 0.00 3.71
4161 7328 6.483307 CGTTTTCATATTATGGAGCAGAGGAA 59.517 38.462 3.89 0.00 0.00 3.36
4162 7329 7.307632 CGTTTTCATATTATGGAGCAGAGGAAG 60.308 40.741 3.89 0.00 0.00 3.46
4163 7330 6.753913 TTCATATTATGGAGCAGAGGAAGT 57.246 37.500 3.89 0.00 0.00 3.01
4164 7331 7.855784 TTCATATTATGGAGCAGAGGAAGTA 57.144 36.000 3.89 0.00 0.00 2.24
4165 7332 7.233389 TCATATTATGGAGCAGAGGAAGTAC 57.767 40.000 3.89 0.00 0.00 2.73
4166 7333 4.592485 ATTATGGAGCAGAGGAAGTACG 57.408 45.455 0.00 0.00 0.00 3.67
4167 7334 1.115467 ATGGAGCAGAGGAAGTACGG 58.885 55.000 0.00 0.00 0.00 4.02
4168 7335 0.039180 TGGAGCAGAGGAAGTACGGA 59.961 55.000 0.00 0.00 0.00 4.69
4169 7336 1.183549 GGAGCAGAGGAAGTACGGAA 58.816 55.000 0.00 0.00 0.00 4.30
4170 7337 1.135053 GGAGCAGAGGAAGTACGGAAC 60.135 57.143 0.00 0.00 0.00 3.62
4171 7338 1.819903 GAGCAGAGGAAGTACGGAACT 59.180 52.381 0.00 0.00 41.49 3.01
4183 7350 6.777213 AAGTACGGAACTTCTGACTCATAT 57.223 37.500 4.52 0.00 45.64 1.78
4184 7351 7.876936 AAGTACGGAACTTCTGACTCATATA 57.123 36.000 4.52 0.00 45.64 0.86
4185 7352 7.876936 AGTACGGAACTTCTGACTCATATAA 57.123 36.000 4.52 0.00 33.35 0.98
4186 7353 8.289939 AGTACGGAACTTCTGACTCATATAAA 57.710 34.615 4.52 0.00 33.35 1.40
4187 7354 8.746530 AGTACGGAACTTCTGACTCATATAAAA 58.253 33.333 4.52 0.00 33.35 1.52
4188 7355 9.530633 GTACGGAACTTCTGACTCATATAAAAT 57.469 33.333 4.52 0.00 0.00 1.82
4189 7356 8.425577 ACGGAACTTCTGACTCATATAAAATG 57.574 34.615 4.52 0.00 0.00 2.32
4190 7357 7.011482 ACGGAACTTCTGACTCATATAAAATGC 59.989 37.037 4.52 0.00 0.00 3.56
4191 7358 7.225538 CGGAACTTCTGACTCATATAAAATGCT 59.774 37.037 0.00 0.00 0.00 3.79
4192 7359 8.341173 GGAACTTCTGACTCATATAAAATGCTG 58.659 37.037 0.00 0.00 0.00 4.41
4193 7360 7.798596 ACTTCTGACTCATATAAAATGCTGG 57.201 36.000 0.00 0.00 0.00 4.85
4194 7361 7.568349 ACTTCTGACTCATATAAAATGCTGGA 58.432 34.615 0.00 0.00 0.00 3.86
4195 7362 8.049117 ACTTCTGACTCATATAAAATGCTGGAA 58.951 33.333 0.00 0.00 0.00 3.53
4196 7363 7.792374 TCTGACTCATATAAAATGCTGGAAC 57.208 36.000 0.00 0.00 0.00 3.62
4197 7364 7.337938 TCTGACTCATATAAAATGCTGGAACA 58.662 34.615 0.00 0.00 0.00 3.18
4198 7365 7.828717 TCTGACTCATATAAAATGCTGGAACAA 59.171 33.333 0.00 0.00 38.70 2.83
4199 7366 8.347004 TGACTCATATAAAATGCTGGAACAAA 57.653 30.769 0.00 0.00 38.70 2.83
4200 7367 8.461222 TGACTCATATAAAATGCTGGAACAAAG 58.539 33.333 0.00 0.00 38.70 2.77
4201 7368 8.353423 ACTCATATAAAATGCTGGAACAAAGT 57.647 30.769 0.00 0.00 38.70 2.66
4202 7369 8.806146 ACTCATATAAAATGCTGGAACAAAGTT 58.194 29.630 0.00 0.00 38.70 2.66
4206 7373 7.832503 ATAAAATGCTGGAACAAAGTTATGC 57.167 32.000 0.00 0.00 38.70 3.14
4207 7374 5.473066 AAATGCTGGAACAAAGTTATGCT 57.527 34.783 0.00 0.00 38.70 3.79
4208 7375 4.708726 ATGCTGGAACAAAGTTATGCTC 57.291 40.909 0.00 0.00 38.70 4.26
4209 7376 3.485394 TGCTGGAACAAAGTTATGCTCA 58.515 40.909 0.00 0.00 38.70 4.26
4210 7377 3.888323 TGCTGGAACAAAGTTATGCTCAA 59.112 39.130 0.00 0.00 38.70 3.02
4211 7378 4.340666 TGCTGGAACAAAGTTATGCTCAAA 59.659 37.500 0.00 0.00 38.70 2.69
4212 7379 5.163468 TGCTGGAACAAAGTTATGCTCAAAA 60.163 36.000 0.00 0.00 38.70 2.44
4213 7380 5.403466 GCTGGAACAAAGTTATGCTCAAAAG 59.597 40.000 0.00 0.00 38.70 2.27
4214 7381 6.707440 TGGAACAAAGTTATGCTCAAAAGA 57.293 33.333 0.00 0.00 31.92 2.52
4215 7382 6.738114 TGGAACAAAGTTATGCTCAAAAGAG 58.262 36.000 0.00 0.00 31.92 2.85
4216 7383 6.545666 TGGAACAAAGTTATGCTCAAAAGAGA 59.454 34.615 0.00 0.00 31.92 3.10
4217 7384 7.231317 TGGAACAAAGTTATGCTCAAAAGAGAT 59.769 33.333 0.00 0.00 31.92 2.75
4218 7385 7.540055 GGAACAAAGTTATGCTCAAAAGAGATG 59.460 37.037 0.00 0.00 0.00 2.90
4219 7386 6.385033 ACAAAGTTATGCTCAAAAGAGATGC 58.615 36.000 0.00 0.00 0.00 3.91
4220 7387 6.016024 ACAAAGTTATGCTCAAAAGAGATGCA 60.016 34.615 0.00 0.00 38.05 3.96
4221 7388 6.579666 AAGTTATGCTCAAAAGAGATGCAA 57.420 33.333 0.00 0.00 37.20 4.08
4222 7389 6.770746 AGTTATGCTCAAAAGAGATGCAAT 57.229 33.333 0.00 0.00 37.20 3.56
4223 7390 7.166691 AGTTATGCTCAAAAGAGATGCAATT 57.833 32.000 0.00 0.00 37.20 2.32
4224 7391 7.609056 AGTTATGCTCAAAAGAGATGCAATTT 58.391 30.769 0.00 0.00 37.20 1.82
4225 7392 7.544566 AGTTATGCTCAAAAGAGATGCAATTTG 59.455 33.333 0.00 0.00 37.20 2.32
4226 7393 3.991773 TGCTCAAAAGAGATGCAATTTGC 59.008 39.130 14.49 14.49 45.29 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 6.251801 CCCGCCACTAATTATTTAAAAACACG 59.748 38.462 0.00 0.00 0.00 4.49
187 191 9.294030 CGAGCTTAGAATTAGAAATGCATTTTT 57.706 29.630 24.81 21.28 0.00 1.94
195 199 9.699703 GGAGTATTCGAGCTTAGAATTAGAAAT 57.300 33.333 19.06 5.31 38.96 2.17
293 304 7.447374 AATGTGATTTCATCGGAAAACTACA 57.553 32.000 0.00 0.00 45.52 2.74
294 305 6.682863 CGAATGTGATTTCATCGGAAAACTAC 59.317 38.462 0.00 0.00 45.52 2.73
398 429 5.412594 ACATTTCTAATGCTCTGAGCGAAAA 59.587 36.000 24.14 18.71 46.26 2.29
500 533 9.326413 TCAAAAACAAACAAACAAAAGGAGTAA 57.674 25.926 0.00 0.00 0.00 2.24
505 538 5.563374 CGCTCAAAAACAAACAAACAAAAGG 59.437 36.000 0.00 0.00 0.00 3.11
524 559 6.913673 GTGAATACTAAAACAAAAACCGCTCA 59.086 34.615 0.00 0.00 0.00 4.26
550 590 0.951558 GTGGAGTTCAAATGCACCGT 59.048 50.000 0.00 0.00 33.34 4.83
563 603 0.252284 AGGAGAATGGGACGTGGAGT 60.252 55.000 0.00 0.00 0.00 3.85
582 636 1.301623 CCATGTTCGGGTTAGGCCA 59.698 57.895 5.01 0.00 39.65 5.36
622 676 3.605634 CCATTTGTTCGATCCTGGTGTA 58.394 45.455 0.00 0.00 0.00 2.90
626 680 1.402968 CTGCCATTTGTTCGATCCTGG 59.597 52.381 0.00 0.00 0.00 4.45
749 808 3.502211 TGCTTCGATTCTTTTTCTGGGAC 59.498 43.478 0.00 0.00 0.00 4.46
755 814 5.990408 TCTCAGTTGCTTCGATTCTTTTTC 58.010 37.500 0.00 0.00 0.00 2.29
793 852 1.454572 TTCCGTGTTGCTGCAATGCT 61.455 50.000 19.11 0.00 0.00 3.79
808 867 1.532868 CAAGTTGAGTCCTTGCTTCCG 59.467 52.381 0.00 0.00 33.55 4.30
938 997 4.763793 CCTCTCAACACATTTCTGTTCCAT 59.236 41.667 0.00 0.00 31.73 3.41
939 998 4.136796 CCTCTCAACACATTTCTGTTCCA 58.863 43.478 0.00 0.00 31.73 3.53
940 999 3.503748 CCCTCTCAACACATTTCTGTTCC 59.496 47.826 0.00 0.00 31.73 3.62
941 1000 4.389374 TCCCTCTCAACACATTTCTGTTC 58.611 43.478 0.00 0.00 31.73 3.18
942 1001 4.437682 TCCCTCTCAACACATTTCTGTT 57.562 40.909 0.00 0.00 34.56 3.16
943 1002 4.437682 TTCCCTCTCAACACATTTCTGT 57.562 40.909 0.00 0.00 35.44 3.41
944 1003 5.972107 ATTTCCCTCTCAACACATTTCTG 57.028 39.130 0.00 0.00 0.00 3.02
956 1021 5.353111 CGAGTCCTTTCTTATTTCCCTCTC 58.647 45.833 0.00 0.00 0.00 3.20
1014 1083 2.876645 GCCTCGTCGCTCTGAACG 60.877 66.667 0.00 0.00 0.00 3.95
1324 4086 0.389948 CGAAGGGTCAGACGGAAAGG 60.390 60.000 0.00 0.00 0.00 3.11
1377 4139 4.988598 ACCGGTTCTGCGCACAGG 62.989 66.667 5.66 10.36 44.59 4.00
1557 4354 2.635443 CCCGTGACAATGTTGGGCC 61.635 63.158 0.00 0.00 32.09 5.80
1615 4412 6.095300 CCATTTGTGATGAAGCAGGTAATGTA 59.905 38.462 0.00 0.00 0.00 2.29
1616 4413 5.105635 CCATTTGTGATGAAGCAGGTAATGT 60.106 40.000 0.00 0.00 0.00 2.71
1621 4418 3.159213 TCCATTTGTGATGAAGCAGGT 57.841 42.857 0.00 0.00 0.00 4.00
1636 4439 6.207417 CAGACACAGGTTATTTCTGTTCCATT 59.793 38.462 0.00 0.00 42.87 3.16
1642 4445 4.040952 AGAGCAGACACAGGTTATTTCTGT 59.959 41.667 0.00 0.00 45.29 3.41
1648 4451 1.404717 CGCAGAGCAGACACAGGTTAT 60.405 52.381 0.00 0.00 0.00 1.89
1908 4770 2.224523 ACGGATTTGAAGAACTGCTGGA 60.225 45.455 0.00 0.00 0.00 3.86
1983 4870 2.360852 CCACCTGCCAGCCAGAAG 60.361 66.667 0.00 0.00 44.64 2.85
1984 4871 3.970410 CCCACCTGCCAGCCAGAA 61.970 66.667 0.00 0.00 44.64 3.02
1985 4872 4.980592 TCCCACCTGCCAGCCAGA 62.981 66.667 0.00 0.00 44.64 3.86
1986 4873 4.729918 GTCCCACCTGCCAGCCAG 62.730 72.222 0.00 0.00 41.41 4.85
2090 4977 2.745821 GCTGACATTGATGCTCTTCACA 59.254 45.455 0.00 0.00 0.00 3.58
2105 4992 1.301401 GTACTTGTGCCCGCTGACA 60.301 57.895 0.00 0.00 0.00 3.58
2264 5151 5.104527 TCTGTTGATCGGTTAATTCTGGGAT 60.105 40.000 0.00 0.00 0.00 3.85
2308 5232 5.815222 TCAAGAACTTGAAGTCGAATGACAA 59.185 36.000 13.78 5.83 45.56 3.18
2368 5292 4.513318 TGGTAATATTGCGCGATGATTTGA 59.487 37.500 20.71 0.00 0.00 2.69
2392 5316 2.666994 CTCGAAACCTAGCCGAAGAAAC 59.333 50.000 0.00 0.00 31.59 2.78
2453 5377 8.737168 TGCTATTCTGTGCTCTGTAAATAAAT 57.263 30.769 0.00 0.00 0.00 1.40
2455 5379 7.331026 ACTGCTATTCTGTGCTCTGTAAATAA 58.669 34.615 0.00 0.00 0.00 1.40
2898 5832 2.752238 CTGACGGACGCCTCCTCT 60.752 66.667 0.07 0.00 33.79 3.69
2997 5931 0.179037 GGCATAGCAGTCATCTGGCA 60.179 55.000 0.00 0.00 41.57 4.92
3013 5947 1.745115 GTAGCACAATCGGCAGGCA 60.745 57.895 0.00 0.00 0.00 4.75
3036 5970 3.118000 GGGGTGGAGGGAGTAGTAATTTG 60.118 52.174 0.00 0.00 0.00 2.32
3055 5989 2.930826 ATTTACTCTATGCCGTGGGG 57.069 50.000 0.00 0.00 0.00 4.96
3175 6109 6.816616 TTTTTAACAAAGAGGATTTGGGGT 57.183 33.333 5.43 0.00 33.92 4.95
3450 6399 1.740285 GCGTGGATCCGGTCACTAT 59.260 57.895 7.39 0.00 0.00 2.12
3776 6884 1.923395 ATGTCCCCTTCCCTCGCAA 60.923 57.895 0.00 0.00 0.00 4.85
3802 6937 6.013379 TCTCTGTCTTATCTTCAACCAGACT 58.987 40.000 0.00 0.00 35.80 3.24
4095 7262 4.158394 ACTTGCAAAATGATCTTATGCCGT 59.842 37.500 0.00 9.45 36.20 5.68
4096 7263 4.675510 ACTTGCAAAATGATCTTATGCCG 58.324 39.130 0.00 9.02 36.20 5.69
4097 7264 5.870978 ACAACTTGCAAAATGATCTTATGCC 59.129 36.000 15.79 1.83 36.20 4.40
4098 7265 6.956299 ACAACTTGCAAAATGATCTTATGC 57.044 33.333 15.79 10.60 37.52 3.14
4101 7268 8.977505 GCTAAAACAACTTGCAAAATGATCTTA 58.022 29.630 15.79 9.52 0.00 2.10
4103 7270 7.212274 AGCTAAAACAACTTGCAAAATGATCT 58.788 30.769 15.79 4.38 0.00 2.75
4104 7271 7.412137 AGCTAAAACAACTTGCAAAATGATC 57.588 32.000 15.79 0.00 0.00 2.92
4106 7273 7.002816 CAAGCTAAAACAACTTGCAAAATGA 57.997 32.000 15.79 0.00 34.90 2.57
4114 7281 5.164002 ACGTTTTGCAAGCTAAAACAACTTG 60.164 36.000 18.63 8.16 44.28 3.16
4115 7282 4.926832 ACGTTTTGCAAGCTAAAACAACTT 59.073 33.333 18.63 0.00 44.28 2.66
4116 7283 4.490743 ACGTTTTGCAAGCTAAAACAACT 58.509 34.783 18.63 3.11 44.28 3.16
4117 7284 4.833469 ACGTTTTGCAAGCTAAAACAAC 57.167 36.364 18.63 4.50 44.28 3.32
4118 7285 5.847670 AAACGTTTTGCAAGCTAAAACAA 57.152 30.435 18.63 5.59 44.28 2.83
4119 7286 5.405571 TGAAAACGTTTTGCAAGCTAAAACA 59.594 32.000 29.67 13.91 44.28 2.83
4120 7287 5.848786 TGAAAACGTTTTGCAAGCTAAAAC 58.151 33.333 29.67 11.58 41.97 2.43
4121 7288 6.654793 ATGAAAACGTTTTGCAAGCTAAAA 57.345 29.167 29.67 0.90 0.00 1.52
4122 7289 7.938563 ATATGAAAACGTTTTGCAAGCTAAA 57.061 28.000 29.67 10.70 0.00 1.85
4123 7290 7.938563 AATATGAAAACGTTTTGCAAGCTAA 57.061 28.000 29.67 8.43 0.00 3.09
4124 7291 9.071221 CATAATATGAAAACGTTTTGCAAGCTA 57.929 29.630 29.67 15.64 0.00 3.32
4125 7292 7.063308 CCATAATATGAAAACGTTTTGCAAGCT 59.937 33.333 29.67 14.28 0.00 3.74
4126 7293 7.062839 TCCATAATATGAAAACGTTTTGCAAGC 59.937 33.333 29.67 15.47 0.00 4.01
4127 7294 8.459521 TCCATAATATGAAAACGTTTTGCAAG 57.540 30.769 29.67 11.13 0.00 4.01
4128 7295 7.062839 GCTCCATAATATGAAAACGTTTTGCAA 59.937 33.333 29.67 15.47 0.00 4.08
4129 7296 6.529829 GCTCCATAATATGAAAACGTTTTGCA 59.470 34.615 29.67 24.11 0.00 4.08
4130 7297 6.529829 TGCTCCATAATATGAAAACGTTTTGC 59.470 34.615 29.67 20.51 0.00 3.68
4131 7298 7.967854 TCTGCTCCATAATATGAAAACGTTTTG 59.032 33.333 29.67 13.71 0.00 2.44
4132 7299 8.050778 TCTGCTCCATAATATGAAAACGTTTT 57.949 30.769 25.46 25.46 0.00 2.43
4133 7300 7.201732 CCTCTGCTCCATAATATGAAAACGTTT 60.202 37.037 7.96 7.96 0.00 3.60
4134 7301 6.260936 CCTCTGCTCCATAATATGAAAACGTT 59.739 38.462 1.10 0.00 0.00 3.99
4135 7302 5.760253 CCTCTGCTCCATAATATGAAAACGT 59.240 40.000 1.10 0.00 0.00 3.99
4136 7303 5.991606 TCCTCTGCTCCATAATATGAAAACG 59.008 40.000 1.10 0.00 0.00 3.60
4137 7304 7.500559 ACTTCCTCTGCTCCATAATATGAAAAC 59.499 37.037 1.10 0.00 0.00 2.43
4138 7305 7.577303 ACTTCCTCTGCTCCATAATATGAAAA 58.423 34.615 1.10 0.00 0.00 2.29
4139 7306 7.141758 ACTTCCTCTGCTCCATAATATGAAA 57.858 36.000 1.10 0.00 0.00 2.69
4140 7307 6.753913 ACTTCCTCTGCTCCATAATATGAA 57.246 37.500 1.10 0.00 0.00 2.57
4141 7308 6.071896 CGTACTTCCTCTGCTCCATAATATGA 60.072 42.308 1.10 0.00 0.00 2.15
4142 7309 6.096036 CGTACTTCCTCTGCTCCATAATATG 58.904 44.000 0.00 0.00 0.00 1.78
4143 7310 5.186021 CCGTACTTCCTCTGCTCCATAATAT 59.814 44.000 0.00 0.00 0.00 1.28
4144 7311 4.523173 CCGTACTTCCTCTGCTCCATAATA 59.477 45.833 0.00 0.00 0.00 0.98
4145 7312 3.322254 CCGTACTTCCTCTGCTCCATAAT 59.678 47.826 0.00 0.00 0.00 1.28
4146 7313 2.693591 CCGTACTTCCTCTGCTCCATAA 59.306 50.000 0.00 0.00 0.00 1.90
4147 7314 2.092049 TCCGTACTTCCTCTGCTCCATA 60.092 50.000 0.00 0.00 0.00 2.74
4148 7315 1.115467 CCGTACTTCCTCTGCTCCAT 58.885 55.000 0.00 0.00 0.00 3.41
4149 7316 0.039180 TCCGTACTTCCTCTGCTCCA 59.961 55.000 0.00 0.00 0.00 3.86
4150 7317 1.135053 GTTCCGTACTTCCTCTGCTCC 60.135 57.143 0.00 0.00 0.00 4.70
4151 7318 1.819903 AGTTCCGTACTTCCTCTGCTC 59.180 52.381 0.00 0.00 31.29 4.26
4152 7319 1.926108 AGTTCCGTACTTCCTCTGCT 58.074 50.000 0.00 0.00 31.29 4.24
4153 7320 2.745515 AAGTTCCGTACTTCCTCTGC 57.254 50.000 0.00 0.00 43.67 4.26
4161 7328 7.876936 TTATATGAGTCAGAAGTTCCGTACT 57.123 36.000 0.00 0.68 39.32 2.73
4162 7329 8.922058 TTTTATATGAGTCAGAAGTTCCGTAC 57.078 34.615 0.00 0.00 0.00 3.67
4163 7330 9.529325 CATTTTATATGAGTCAGAAGTTCCGTA 57.471 33.333 0.00 0.00 0.00 4.02
4164 7331 7.011482 GCATTTTATATGAGTCAGAAGTTCCGT 59.989 37.037 0.00 0.00 0.00 4.69
4165 7332 7.225538 AGCATTTTATATGAGTCAGAAGTTCCG 59.774 37.037 0.00 0.00 0.00 4.30
4166 7333 8.341173 CAGCATTTTATATGAGTCAGAAGTTCC 58.659 37.037 0.00 0.00 0.00 3.62
4167 7334 8.341173 CCAGCATTTTATATGAGTCAGAAGTTC 58.659 37.037 0.00 0.00 0.00 3.01
4168 7335 8.049117 TCCAGCATTTTATATGAGTCAGAAGTT 58.951 33.333 0.00 0.00 0.00 2.66
4169 7336 7.568349 TCCAGCATTTTATATGAGTCAGAAGT 58.432 34.615 0.00 0.00 0.00 3.01
4170 7337 8.341173 GTTCCAGCATTTTATATGAGTCAGAAG 58.659 37.037 0.00 0.00 0.00 2.85
4171 7338 7.828717 TGTTCCAGCATTTTATATGAGTCAGAA 59.171 33.333 0.00 0.00 0.00 3.02
4172 7339 7.337938 TGTTCCAGCATTTTATATGAGTCAGA 58.662 34.615 0.00 0.00 0.00 3.27
4173 7340 7.558161 TGTTCCAGCATTTTATATGAGTCAG 57.442 36.000 0.00 0.00 0.00 3.51
4174 7341 7.936496 TTGTTCCAGCATTTTATATGAGTCA 57.064 32.000 0.00 0.00 0.00 3.41
4175 7342 8.462016 ACTTTGTTCCAGCATTTTATATGAGTC 58.538 33.333 0.00 0.00 0.00 3.36
4176 7343 8.353423 ACTTTGTTCCAGCATTTTATATGAGT 57.647 30.769 0.00 0.00 0.00 3.41
4180 7347 9.533253 GCATAACTTTGTTCCAGCATTTTATAT 57.467 29.630 0.00 0.00 0.00 0.86
4181 7348 8.748412 AGCATAACTTTGTTCCAGCATTTTATA 58.252 29.630 0.00 0.00 0.00 0.98
4182 7349 7.614494 AGCATAACTTTGTTCCAGCATTTTAT 58.386 30.769 0.00 0.00 0.00 1.40
4183 7350 6.991938 AGCATAACTTTGTTCCAGCATTTTA 58.008 32.000 0.00 0.00 0.00 1.52
4184 7351 5.857268 AGCATAACTTTGTTCCAGCATTTT 58.143 33.333 0.00 0.00 0.00 1.82
4185 7352 5.010922 TGAGCATAACTTTGTTCCAGCATTT 59.989 36.000 0.00 0.00 0.00 2.32
4186 7353 4.523943 TGAGCATAACTTTGTTCCAGCATT 59.476 37.500 0.00 0.00 0.00 3.56
4187 7354 4.081406 TGAGCATAACTTTGTTCCAGCAT 58.919 39.130 0.00 0.00 0.00 3.79
4188 7355 3.485394 TGAGCATAACTTTGTTCCAGCA 58.515 40.909 0.00 0.00 0.00 4.41
4189 7356 4.503741 TTGAGCATAACTTTGTTCCAGC 57.496 40.909 0.00 0.00 0.00 4.85
4190 7357 6.738114 TCTTTTGAGCATAACTTTGTTCCAG 58.262 36.000 0.00 0.00 0.00 3.86
4191 7358 6.545666 TCTCTTTTGAGCATAACTTTGTTCCA 59.454 34.615 0.00 0.00 45.83 3.53
4192 7359 6.970484 TCTCTTTTGAGCATAACTTTGTTCC 58.030 36.000 0.00 0.00 45.83 3.62
4193 7360 7.061557 GCATCTCTTTTGAGCATAACTTTGTTC 59.938 37.037 0.00 0.00 45.83 3.18
4194 7361 6.865205 GCATCTCTTTTGAGCATAACTTTGTT 59.135 34.615 0.00 0.00 45.83 2.83
4195 7362 6.016024 TGCATCTCTTTTGAGCATAACTTTGT 60.016 34.615 0.00 0.00 45.83 2.83
4196 7363 6.384224 TGCATCTCTTTTGAGCATAACTTTG 58.616 36.000 0.00 0.00 45.83 2.77
4197 7364 6.579666 TGCATCTCTTTTGAGCATAACTTT 57.420 33.333 0.00 0.00 45.83 2.66
4198 7365 6.579666 TTGCATCTCTTTTGAGCATAACTT 57.420 33.333 0.00 0.00 45.83 2.66
4199 7366 6.770746 ATTGCATCTCTTTTGAGCATAACT 57.229 33.333 0.00 0.00 45.83 2.24
4200 7367 7.672738 CAAATTGCATCTCTTTTGAGCATAAC 58.327 34.615 0.00 0.00 45.83 1.89
4201 7368 6.311935 GCAAATTGCATCTCTTTTGAGCATAA 59.688 34.615 13.73 0.00 43.78 1.90
4202 7369 5.808540 GCAAATTGCATCTCTTTTGAGCATA 59.191 36.000 13.73 0.00 43.78 3.14
4203 7370 4.630069 GCAAATTGCATCTCTTTTGAGCAT 59.370 37.500 13.73 0.00 43.78 3.79
4204 7371 3.991773 GCAAATTGCATCTCTTTTGAGCA 59.008 39.130 13.73 0.00 43.78 4.26
4205 7372 4.579270 GCAAATTGCATCTCTTTTGAGC 57.421 40.909 13.73 0.00 43.78 4.26


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

AutoCloner maintained by Alex Coulton.