Multiple sequence alignment - TraesCS4A01G105200

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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 TraesCS4A01G105200 chr4A 100.000 4152 0 0 1 4152 119079644 119083795 0.000000e+00 7668.0
1 TraesCS4A01G105200 chr4A 80.970 268 13 19 1056 1305 538908722 538908475 1.190000e-40 178.0
2 TraesCS4A01G105200 chr4D 94.249 1617 74 7 1645 3244 346453613 346451999 0.000000e+00 2453.0
3 TraesCS4A01G105200 chr4D 87.879 1353 56 37 1 1340 346455210 346453953 0.000000e+00 1491.0
4 TraesCS4A01G105200 chr4D 92.697 671 28 4 3500 4152 346451837 346451170 0.000000e+00 948.0
5 TraesCS4A01G105200 chr4D 97.959 147 3 0 3406 3552 346452000 346451854 5.330000e-64 255.0
6 TraesCS4A01G105200 chr4D 85.321 109 12 3 1544 1648 346453808 346453700 4.390000e-20 110.0
7 TraesCS4A01G105200 chr4B 93.121 1541 94 9 1645 3179 427498287 427496753 0.000000e+00 2248.0
8 TraesCS4A01G105200 chr4B 92.653 735 31 6 3437 4152 427496657 427495927 0.000000e+00 1037.0
9 TraesCS4A01G105200 chr4B 85.714 945 55 36 122 1053 427499863 427498986 0.000000e+00 924.0
10 TraesCS4A01G105200 chr4B 82.641 409 42 20 1110 1510 427498959 427498572 6.650000e-88 335.0
11 TraesCS4A01G105200 chr4B 80.669 269 18 9 1053 1305 385957453 385957703 1.190000e-40 178.0
12 TraesCS4A01G105200 chr4B 92.857 70 5 0 1544 1613 427498569 427498500 7.340000e-18 102.0
13 TraesCS4A01G105200 chr4B 91.489 47 2 2 3197 3243 651808271 651808227 3.470000e-06 63.9
14 TraesCS4A01G105200 chr7B 96.491 171 5 1 3237 3407 500023013 500023182 8.790000e-72 281.0
15 TraesCS4A01G105200 chr7B 96.951 164 5 0 3241 3404 745673968 745674131 4.090000e-70 276.0
16 TraesCS4A01G105200 chr7B 95.882 170 6 1 3239 3407 534818745 534818576 1.470000e-69 274.0
17 TraesCS4A01G105200 chr7B 91.371 197 12 4 3218 3410 538750048 538750243 8.850000e-67 265.0
18 TraesCS4A01G105200 chr2A 95.906 171 7 0 3240 3410 199082319 199082149 1.140000e-70 278.0
19 TraesCS4A01G105200 chr2A 93.956 182 10 1 3233 3414 12428614 12428434 1.470000e-69 274.0
20 TraesCS4A01G105200 chr2A 90.000 160 14 2 1208 1366 737426201 737426043 5.440000e-49 206.0
21 TraesCS4A01G105200 chr3B 94.350 177 8 2 3233 3407 527758645 527758469 1.900000e-68 270.0
22 TraesCS4A01G105200 chr6B 93.370 181 11 1 3238 3417 670288346 670288526 2.460000e-67 267.0
23 TraesCS4A01G105200 chr6B 93.939 165 10 0 3243 3407 716638195 716638359 2.480000e-62 250.0
24 TraesCS4A01G105200 chr6B 93.750 48 3 0 3406 3453 213239648 213239695 5.760000e-09 73.1
25 TraesCS4A01G105200 chr5A 93.082 159 10 1 1208 1366 692541494 692541651 8.980000e-57 231.0
26 TraesCS4A01G105200 chr5A 91.824 159 12 1 1208 1366 692548063 692548220 1.940000e-53 220.0
27 TraesCS4A01G105200 chr2B 80.645 279 18 19 1045 1305 17220001 17219741 2.550000e-42 183.0
28 TraesCS4A01G105200 chr2B 80.669 269 18 17 1053 1305 127202852 127203102 1.190000e-40 178.0
29 TraesCS4A01G105200 chr2B 80.784 255 18 14 1067 1305 414953186 414953425 1.980000e-38 171.0
30 TraesCS4A01G105200 chr2B 90.000 50 4 1 3197 3246 38218225 38218273 3.470000e-06 63.9
31 TraesCS4A01G105200 chr1B 77.344 256 42 11 1056 1305 686995465 686995220 2.010000e-28 137.0
32 TraesCS4A01G105200 chr2D 96.875 32 0 1 860 891 31954648 31954618 8.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G105200 chr4A 119079644 119083795 4151 False 7668.0 7668 100.0000 1 4152 1 chr4A.!!$F1 4151
1 TraesCS4A01G105200 chr4D 346451170 346455210 4040 True 1051.4 2453 91.6210 1 4152 5 chr4D.!!$R1 4151
2 TraesCS4A01G105200 chr4B 427495927 427499863 3936 True 929.2 2248 89.3972 122 4152 5 chr4B.!!$R2 4030

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
253 254 0.179004 TCAAGGGAAGAAGCGCCAAA 60.179 50.0 2.29 0.00 0.00 3.28 F
1519 1573 0.039165 TCGATTGATCGGCTCGATGG 60.039 55.0 13.68 0.00 47.00 3.51 F
1770 2005 0.107945 GCCAGGAAGCCAGTACTGAG 60.108 60.0 24.68 14.75 32.86 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1637 1782 0.586802 GACAGCAACTTCCGTTCCAC 59.413 55.000 0.00 0.0 0.00 4.02 R
3007 3257 1.215382 CGATGCGAGTCCTGAACCA 59.785 57.895 0.00 0.0 0.00 3.67 R
3715 4086 1.406887 GCCGGCTGACTCCAGATAAAA 60.407 52.381 22.15 0.0 43.02 1.52 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
44 45 1.879380 CACACTTTCTTGGCGGAATCA 59.121 47.619 0.00 0.00 0.00 2.57
75 76 1.725931 CGCGAAGAAATGGACTTGCAC 60.726 52.381 0.00 0.00 0.00 4.57
119 120 2.313374 GACTCGAACGATTGCGCG 59.687 61.111 0.00 0.00 42.48 6.86
121 122 1.129879 GACTCGAACGATTGCGCGTA 61.130 55.000 8.43 0.00 44.86 4.42
122 123 1.132199 ACTCGAACGATTGCGCGTAG 61.132 55.000 8.43 0.00 44.86 3.51
123 124 0.860203 CTCGAACGATTGCGCGTAGA 60.860 55.000 8.43 0.00 44.86 2.59
124 125 0.454789 TCGAACGATTGCGCGTAGAA 60.455 50.000 8.43 0.00 44.86 2.10
125 126 0.570734 CGAACGATTGCGCGTAGAAT 59.429 50.000 8.43 3.74 44.86 2.40
126 127 1.776897 CGAACGATTGCGCGTAGAATA 59.223 47.619 8.43 0.00 44.86 1.75
142 143 5.006358 CGTAGAATACCCAAAAATCACGAGG 59.994 44.000 0.00 0.00 38.71 4.63
158 159 2.414594 GGAAGCATTGCGGCATCC 59.585 61.111 2.28 3.30 43.47 3.51
165 166 1.574134 CATTGCGGCATCCCAAATTC 58.426 50.000 2.28 0.00 0.00 2.17
212 213 1.174712 ATGGCATGGCACTATTCCGC 61.175 55.000 25.84 0.00 0.00 5.54
230 231 1.660052 CGCACACATTTCACGAACCAG 60.660 52.381 0.00 0.00 0.00 4.00
239 240 2.455674 TCACGAACCAGACATCAAGG 57.544 50.000 0.00 0.00 0.00 3.61
253 254 0.179004 TCAAGGGAAGAAGCGCCAAA 60.179 50.000 2.29 0.00 0.00 3.28
340 341 0.875908 ATCCGATCAACCGCACGATG 60.876 55.000 0.00 0.00 0.00 3.84
439 440 0.528684 GGCGTCATCGGAGAAGAAGG 60.529 60.000 0.00 0.00 43.58 3.46
442 443 1.066303 CGTCATCGGAGAAGAAGGAGG 59.934 57.143 0.00 0.00 43.58 4.30
513 514 2.509336 GCGCACGTACCAGCTGAT 60.509 61.111 17.39 0.00 0.00 2.90
663 670 2.390599 CGTCGGAATGCAGTGGTGG 61.391 63.158 0.00 0.00 0.00 4.61
678 685 2.540910 TGGAGGGAGGGAGGGAGT 60.541 66.667 0.00 0.00 0.00 3.85
688 695 1.003573 GGAGGGAGTGAGGGATGGT 59.996 63.158 0.00 0.00 0.00 3.55
689 696 1.341156 GGAGGGAGTGAGGGATGGTG 61.341 65.000 0.00 0.00 0.00 4.17
690 697 1.307343 AGGGAGTGAGGGATGGTGG 60.307 63.158 0.00 0.00 0.00 4.61
701 708 0.681243 GGATGGTGGAAGGGAAGTGC 60.681 60.000 0.00 0.00 0.00 4.40
702 709 1.002134 ATGGTGGAAGGGAAGTGCG 60.002 57.895 0.00 0.00 0.00 5.34
703 710 3.056328 GGTGGAAGGGAAGTGCGC 61.056 66.667 0.00 0.00 0.00 6.09
704 711 2.281484 GTGGAAGGGAAGTGCGCA 60.281 61.111 5.66 5.66 0.00 6.09
831 843 1.681327 CGAGGAAGGACGGAAGGGA 60.681 63.158 0.00 0.00 0.00 4.20
833 845 0.466124 GAGGAAGGACGGAAGGGATG 59.534 60.000 0.00 0.00 0.00 3.51
834 846 1.153147 GGAAGGACGGAAGGGATGC 60.153 63.158 0.00 0.00 0.00 3.91
1004 1017 1.275573 AGTACGCCTTCCTTTGGACTC 59.724 52.381 0.00 0.00 0.00 3.36
1006 1019 0.765510 ACGCCTTCCTTTGGACTCTT 59.234 50.000 0.00 0.00 0.00 2.85
1007 1020 1.270893 ACGCCTTCCTTTGGACTCTTC 60.271 52.381 0.00 0.00 0.00 2.87
1008 1021 1.002544 CGCCTTCCTTTGGACTCTTCT 59.997 52.381 0.00 0.00 0.00 2.85
1009 1022 2.551071 CGCCTTCCTTTGGACTCTTCTT 60.551 50.000 0.00 0.00 0.00 2.52
1010 1023 3.491342 GCCTTCCTTTGGACTCTTCTTT 58.509 45.455 0.00 0.00 0.00 2.52
1053 1067 2.435059 GCTCAGGCACGTCCTTCC 60.435 66.667 4.08 0.00 44.75 3.46
1054 1068 2.948720 GCTCAGGCACGTCCTTCCT 61.949 63.158 4.08 0.00 44.75 3.36
1055 1069 1.674057 CTCAGGCACGTCCTTCCTT 59.326 57.895 4.08 0.00 44.75 3.36
1056 1070 0.671781 CTCAGGCACGTCCTTCCTTG 60.672 60.000 4.08 0.00 44.75 3.61
1057 1071 2.032681 AGGCACGTCCTTCCTTGC 59.967 61.111 1.23 0.00 44.75 4.01
1060 1079 3.423154 CACGTCCTTCCTTGCGCC 61.423 66.667 4.18 0.00 0.00 6.53
1085 1104 4.988598 CCGCCGCAGTCTGTTGGT 62.989 66.667 12.92 0.00 0.00 3.67
1086 1105 3.414700 CGCCGCAGTCTGTTGGTC 61.415 66.667 12.92 6.45 0.00 4.02
1087 1106 3.414700 GCCGCAGTCTGTTGGTCG 61.415 66.667 12.92 3.20 0.00 4.79
1088 1107 3.414700 CCGCAGTCTGTTGGTCGC 61.415 66.667 0.93 0.00 0.00 5.19
1089 1108 3.767230 CGCAGTCTGTTGGTCGCG 61.767 66.667 0.00 0.00 36.47 5.87
1090 1109 3.414700 GCAGTCTGTTGGTCGCGG 61.415 66.667 6.13 0.00 0.00 6.46
1091 1110 2.029073 CAGTCTGTTGGTCGCGGT 59.971 61.111 6.13 0.00 0.00 5.68
1092 1111 1.594293 CAGTCTGTTGGTCGCGGTT 60.594 57.895 6.13 0.00 0.00 4.44
1093 1112 1.145377 AGTCTGTTGGTCGCGGTTT 59.855 52.632 6.13 0.00 0.00 3.27
1094 1113 0.878961 AGTCTGTTGGTCGCGGTTTC 60.879 55.000 6.13 0.00 0.00 2.78
1095 1114 1.595929 TCTGTTGGTCGCGGTTTCC 60.596 57.895 6.13 4.91 0.00 3.13
1134 1153 3.925090 GATGGGGGAGTACGGCGG 61.925 72.222 13.24 0.00 0.00 6.13
1336 1361 2.709475 CGCAAGATGGTAAGCGCC 59.291 61.111 2.29 0.00 43.80 6.53
1337 1362 2.823829 CGCAAGATGGTAAGCGCCC 61.824 63.158 2.29 0.00 43.80 6.13
1338 1363 2.481471 GCAAGATGGTAAGCGCCCC 61.481 63.158 2.29 1.87 0.00 5.80
1339 1364 2.180204 CAAGATGGTAAGCGCCCCG 61.180 63.158 2.29 0.00 0.00 5.73
1340 1365 3.400599 AAGATGGTAAGCGCCCCGG 62.401 63.158 2.29 0.00 0.00 5.73
1357 1382 4.179579 GCCGCTCACCCGCATTTC 62.180 66.667 0.00 0.00 0.00 2.17
1358 1383 3.508840 CCGCTCACCCGCATTTCC 61.509 66.667 0.00 0.00 0.00 3.13
1359 1384 3.508840 CGCTCACCCGCATTTCCC 61.509 66.667 0.00 0.00 0.00 3.97
1360 1385 3.140814 GCTCACCCGCATTTCCCC 61.141 66.667 0.00 0.00 0.00 4.81
1361 1386 2.824041 CTCACCCGCATTTCCCCG 60.824 66.667 0.00 0.00 0.00 5.73
1362 1387 3.323286 TCACCCGCATTTCCCCGA 61.323 61.111 0.00 0.00 0.00 5.14
1363 1388 2.824041 CACCCGCATTTCCCCGAG 60.824 66.667 0.00 0.00 0.00 4.63
1364 1389 4.796495 ACCCGCATTTCCCCGAGC 62.796 66.667 0.00 0.00 0.00 5.03
1365 1390 4.794648 CCCGCATTTCCCCGAGCA 62.795 66.667 0.00 0.00 0.00 4.26
1366 1391 3.508840 CCGCATTTCCCCGAGCAC 61.509 66.667 0.00 0.00 0.00 4.40
1367 1392 2.436646 CGCATTTCCCCGAGCACT 60.437 61.111 0.00 0.00 0.00 4.40
1385 1410 1.298859 CTTCCCGTGCTTGCTACCAC 61.299 60.000 0.00 0.00 0.00 4.16
1435 1484 4.629634 TGTCTCACACACACTTGTTACTTG 59.370 41.667 0.00 0.00 31.66 3.16
1451 1504 1.001406 ACTTGGTGAGTACTGCAGAGC 59.999 52.381 23.35 12.38 36.65 4.09
1485 1539 9.719355 TGTCTTAGTTGAGAAATTATGTAAGCA 57.281 29.630 0.00 0.00 0.00 3.91
1489 1543 6.489675 AGTTGAGAAATTATGTAAGCATGCG 58.510 36.000 13.01 0.00 36.58 4.73
1506 1560 1.062440 TGCGCTTACTTGCATCGATTG 59.938 47.619 9.73 0.00 35.90 2.67
1507 1561 1.327460 GCGCTTACTTGCATCGATTGA 59.673 47.619 0.00 0.00 0.00 2.57
1508 1562 2.032549 GCGCTTACTTGCATCGATTGAT 60.033 45.455 0.00 0.00 34.28 2.57
1509 1563 3.792294 CGCTTACTTGCATCGATTGATC 58.208 45.455 0.00 0.00 30.49 2.92
1518 1572 1.988063 ATCGATTGATCGGCTCGATG 58.012 50.000 19.70 1.38 47.00 3.84
1519 1573 0.039165 TCGATTGATCGGCTCGATGG 60.039 55.000 13.68 0.00 47.00 3.51
1520 1574 1.010935 CGATTGATCGGCTCGATGGG 61.011 60.000 13.68 0.00 47.00 4.00
1521 1575 0.671781 GATTGATCGGCTCGATGGGG 60.672 60.000 13.68 0.00 47.00 4.96
1522 1576 2.738213 ATTGATCGGCTCGATGGGGC 62.738 60.000 13.68 0.00 47.00 5.80
1523 1577 4.688966 GATCGGCTCGATGGGGCC 62.689 72.222 8.90 8.90 47.00 5.80
1527 1581 2.362375 GGCTCGATGGGGCCAAAA 60.362 61.111 14.68 0.00 46.84 2.44
1528 1582 1.758122 GGCTCGATGGGGCCAAAAT 60.758 57.895 14.68 0.00 46.84 1.82
1529 1583 1.735973 GCTCGATGGGGCCAAAATC 59.264 57.895 4.39 4.37 0.00 2.17
1530 1584 1.037030 GCTCGATGGGGCCAAAATCA 61.037 55.000 4.39 0.00 0.00 2.57
1531 1585 1.473258 CTCGATGGGGCCAAAATCAA 58.527 50.000 4.39 0.00 0.00 2.57
1532 1586 1.824230 CTCGATGGGGCCAAAATCAAA 59.176 47.619 4.39 0.00 0.00 2.69
1533 1587 1.824230 TCGATGGGGCCAAAATCAAAG 59.176 47.619 4.39 0.00 0.00 2.77
1534 1588 1.550072 CGATGGGGCCAAAATCAAAGT 59.450 47.619 4.39 0.00 0.00 2.66
1538 1592 3.515562 TGGGGCCAAAATCAAAGTGTAT 58.484 40.909 4.39 0.00 0.00 2.29
1540 1594 4.252878 GGGGCCAAAATCAAAGTGTATTG 58.747 43.478 4.39 0.00 0.00 1.90
1542 1596 5.170748 GGGCCAAAATCAAAGTGTATTGAG 58.829 41.667 4.39 0.00 42.21 3.02
1561 1615 7.902920 ATTGAGCTGTAAATAAATGGGTGAT 57.097 32.000 0.00 0.00 0.00 3.06
1564 1618 6.486657 TGAGCTGTAAATAAATGGGTGATAGC 59.513 38.462 0.00 0.00 0.00 2.97
1609 1663 6.094325 GGTGATCTGGGTATAGAATCTACTCG 59.906 46.154 0.00 0.00 0.00 4.18
1613 1667 7.550597 TCTGGGTATAGAATCTACTCGTAGA 57.449 40.000 9.04 9.04 45.24 2.59
1641 1786 6.874278 TTCCTTCTCTAATCTGAATGTGGA 57.126 37.500 0.00 0.00 0.00 4.02
1664 1899 2.734606 CGGAAGTTGCTGTCGTAAATCA 59.265 45.455 0.00 0.00 0.00 2.57
1694 1929 2.277969 GCCGAGCATCATCCATCATAG 58.722 52.381 0.00 0.00 33.17 2.23
1743 1978 7.840342 AAAGCTTGATGTCAGAACTGTATAG 57.160 36.000 0.00 0.00 0.00 1.31
1770 2005 0.107945 GCCAGGAAGCCAGTACTGAG 60.108 60.000 24.68 14.75 32.86 3.35
1808 2043 2.245942 CTCGATGTCTGTGACACTTCG 58.754 52.381 13.98 13.98 45.65 3.79
1918 2153 2.320805 CTGACCATTCAGCAAACGTG 57.679 50.000 0.00 0.00 42.99 4.49
1951 2186 5.353394 TTTCTACCAGTATTGTGGCCTAG 57.647 43.478 3.32 0.00 41.90 3.02
1970 2205 4.457949 CCTAGTTTAAATGTTGGACGGCTT 59.542 41.667 0.00 0.00 0.00 4.35
1975 2210 5.554822 TTAAATGTTGGACGGCTTATGAC 57.445 39.130 0.00 0.00 0.00 3.06
1979 2214 1.659098 GTTGGACGGCTTATGACTTCG 59.341 52.381 0.00 0.00 0.00 3.79
2121 2364 3.848019 GCTGCATCATTGTTAACAAGTCG 59.152 43.478 24.22 15.62 39.47 4.18
2155 2398 4.134563 GCTTCTTTACTCAGGTGGAACAA 58.865 43.478 0.00 0.00 44.16 2.83
2248 2491 0.960364 TGGAGAAAATGCAGGTCGGC 60.960 55.000 0.00 0.00 0.00 5.54
2398 2641 3.993081 CACTGCCAGTACTCTTTCTTCAG 59.007 47.826 0.00 0.00 0.00 3.02
2506 2749 0.987294 AGGATGGTGTGGGACTTCTG 59.013 55.000 0.00 0.00 0.00 3.02
2619 2867 4.507710 TGATCACCACTCTGCATACTTTC 58.492 43.478 0.00 0.00 0.00 2.62
2678 2926 3.734463 TGTGAATTTACTCCAGCGAACA 58.266 40.909 1.75 0.00 0.00 3.18
2903 3152 6.322712 ACATTAGAACTTTGGCCACAGTAAAA 59.677 34.615 24.48 17.79 0.00 1.52
2997 3247 9.768215 TTTAAGGAATATCATGGAAAGGAAAGT 57.232 29.630 0.00 0.00 0.00 2.66
3007 3257 4.479158 TGGAAAGGAAAGTAACATTGCCT 58.521 39.130 0.00 0.00 29.24 4.75
3024 3274 3.056628 CTGGTTCAGGACTCGCATC 57.943 57.895 0.00 0.00 0.00 3.91
3042 3293 3.829948 CATCGTTGCATCTCTTTTTGCT 58.170 40.909 0.00 0.00 39.60 3.91
3086 3338 4.384098 GCCTTTATTCATTGGAAAAGGGGG 60.384 45.833 18.60 0.00 39.69 5.40
3159 3412 2.738314 GGAACTGCAATGCCAAAACATC 59.262 45.455 1.53 0.00 0.00 3.06
3170 3423 3.181434 TGCCAAAACATCAGTACTCCCTT 60.181 43.478 0.00 0.00 0.00 3.95
3179 3463 6.838382 ACATCAGTACTCCCTTTGTAAAGTT 58.162 36.000 0.00 0.00 34.20 2.66
3196 3480 8.603242 TGTAAAGTTGTGATCTAAAAGGTCTC 57.397 34.615 0.00 0.00 0.00 3.36
3210 3494 6.502074 AAAAGGTCTCATATTACTCCCTCC 57.498 41.667 0.00 0.00 0.00 4.30
3250 3537 9.706691 TGATCGTTTAAATCATTATACTCCCTC 57.293 33.333 0.00 0.00 0.00 4.30
3251 3538 9.152595 GATCGTTTAAATCATTATACTCCCTCC 57.847 37.037 0.00 0.00 0.00 4.30
3252 3539 7.149973 TCGTTTAAATCATTATACTCCCTCCG 58.850 38.462 0.00 0.00 0.00 4.63
3253 3540 6.927381 CGTTTAAATCATTATACTCCCTCCGT 59.073 38.462 0.00 0.00 0.00 4.69
3254 3541 7.440255 CGTTTAAATCATTATACTCCCTCCGTT 59.560 37.037 0.00 0.00 0.00 4.44
3255 3542 9.117183 GTTTAAATCATTATACTCCCTCCGTTT 57.883 33.333 0.00 0.00 0.00 3.60
3256 3543 9.689501 TTTAAATCATTATACTCCCTCCGTTTT 57.310 29.630 0.00 0.00 0.00 2.43
3257 3544 7.803279 AAATCATTATACTCCCTCCGTTTTC 57.197 36.000 0.00 0.00 0.00 2.29
3258 3545 5.943349 TCATTATACTCCCTCCGTTTTCA 57.057 39.130 0.00 0.00 0.00 2.69
3259 3546 6.302535 TCATTATACTCCCTCCGTTTTCAA 57.697 37.500 0.00 0.00 0.00 2.69
3260 3547 6.713276 TCATTATACTCCCTCCGTTTTCAAA 58.287 36.000 0.00 0.00 0.00 2.69
3261 3548 7.343357 TCATTATACTCCCTCCGTTTTCAAAT 58.657 34.615 0.00 0.00 0.00 2.32
3262 3549 8.487848 TCATTATACTCCCTCCGTTTTCAAATA 58.512 33.333 0.00 0.00 0.00 1.40
3263 3550 9.116067 CATTATACTCCCTCCGTTTTCAAATAA 57.884 33.333 0.00 0.00 0.00 1.40
3264 3551 9.862149 ATTATACTCCCTCCGTTTTCAAATAAT 57.138 29.630 0.00 0.00 0.00 1.28
3265 3552 9.689501 TTATACTCCCTCCGTTTTCAAATAATT 57.310 29.630 0.00 0.00 0.00 1.40
3266 3553 6.267496 ACTCCCTCCGTTTTCAAATAATTG 57.733 37.500 0.00 0.00 37.92 2.32
3267 3554 5.773176 ACTCCCTCCGTTTTCAAATAATTGT 59.227 36.000 0.00 0.00 37.79 2.71
3268 3555 6.072119 ACTCCCTCCGTTTTCAAATAATTGTC 60.072 38.462 0.00 0.00 37.79 3.18
3269 3556 6.007703 TCCCTCCGTTTTCAAATAATTGTCT 58.992 36.000 0.00 0.00 37.79 3.41
3270 3557 6.492087 TCCCTCCGTTTTCAAATAATTGTCTT 59.508 34.615 0.00 0.00 37.79 3.01
3271 3558 7.014808 TCCCTCCGTTTTCAAATAATTGTCTTT 59.985 33.333 0.00 0.00 37.79 2.52
3272 3559 7.328493 CCCTCCGTTTTCAAATAATTGTCTTTC 59.672 37.037 0.00 0.00 37.79 2.62
3273 3560 8.082242 CCTCCGTTTTCAAATAATTGTCTTTCT 58.918 33.333 0.00 0.00 37.79 2.52
3288 3575 7.452880 TTGTCTTTCTAACCATCTCAAATGG 57.547 36.000 2.52 2.52 44.54 3.16
3289 3576 6.778821 TGTCTTTCTAACCATCTCAAATGGA 58.221 36.000 10.91 0.00 41.64 3.41
3290 3577 6.655003 TGTCTTTCTAACCATCTCAAATGGAC 59.345 38.462 10.91 0.00 41.64 4.02
3291 3578 6.881602 GTCTTTCTAACCATCTCAAATGGACT 59.118 38.462 10.91 0.81 41.64 3.85
3292 3579 8.041323 GTCTTTCTAACCATCTCAAATGGACTA 58.959 37.037 10.91 1.85 41.64 2.59
3293 3580 8.041323 TCTTTCTAACCATCTCAAATGGACTAC 58.959 37.037 10.91 0.00 41.64 2.73
3294 3581 6.867519 TCTAACCATCTCAAATGGACTACA 57.132 37.500 10.91 0.00 41.64 2.74
3295 3582 7.252612 TCTAACCATCTCAAATGGACTACAA 57.747 36.000 10.91 0.00 41.64 2.41
3296 3583 7.103641 TCTAACCATCTCAAATGGACTACAAC 58.896 38.462 10.91 0.00 41.64 3.32
3297 3584 5.241403 ACCATCTCAAATGGACTACAACA 57.759 39.130 10.91 0.00 41.64 3.33
3298 3585 5.819991 ACCATCTCAAATGGACTACAACAT 58.180 37.500 10.91 0.00 41.64 2.71
3299 3586 6.957631 ACCATCTCAAATGGACTACAACATA 58.042 36.000 10.91 0.00 41.64 2.29
3300 3587 6.823689 ACCATCTCAAATGGACTACAACATAC 59.176 38.462 10.91 0.00 41.64 2.39
3301 3588 6.018751 CCATCTCAAATGGACTACAACATACG 60.019 42.308 0.00 0.00 41.64 3.06
3302 3589 6.275494 TCTCAAATGGACTACAACATACGA 57.725 37.500 0.00 0.00 0.00 3.43
3303 3590 6.693466 TCTCAAATGGACTACAACATACGAA 58.307 36.000 0.00 0.00 0.00 3.85
3304 3591 7.327975 TCTCAAATGGACTACAACATACGAAT 58.672 34.615 0.00 0.00 0.00 3.34
3305 3592 7.277760 TCTCAAATGGACTACAACATACGAATG 59.722 37.037 0.00 0.00 39.17 2.67
3307 3594 8.035984 TCAAATGGACTACAACATACGAATGTA 58.964 33.333 0.00 0.00 45.79 2.29
3308 3595 8.826710 CAAATGGACTACAACATACGAATGTAT 58.173 33.333 0.00 0.00 45.79 2.29
3336 3623 8.764524 AGACATGTTTTAGAGTGTAGATTCAC 57.235 34.615 0.00 0.00 38.46 3.18
3347 3634 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
3348 3635 6.471146 AGTGTAGATTCACTCATTTTGCTCT 58.529 36.000 0.00 0.00 44.07 4.09
3349 3636 6.370994 AGTGTAGATTCACTCATTTTGCTCTG 59.629 38.462 0.00 0.00 44.07 3.35
3350 3637 6.148480 GTGTAGATTCACTCATTTTGCTCTGT 59.852 38.462 0.00 0.00 35.68 3.41
3351 3638 7.331934 GTGTAGATTCACTCATTTTGCTCTGTA 59.668 37.037 0.00 0.00 35.68 2.74
3352 3639 8.043113 TGTAGATTCACTCATTTTGCTCTGTAT 58.957 33.333 0.00 0.00 0.00 2.29
3353 3640 7.317842 AGATTCACTCATTTTGCTCTGTATG 57.682 36.000 0.00 0.00 0.00 2.39
3354 3641 6.883217 AGATTCACTCATTTTGCTCTGTATGT 59.117 34.615 0.00 0.00 0.00 2.29
3355 3642 8.043113 AGATTCACTCATTTTGCTCTGTATGTA 58.957 33.333 0.00 0.00 0.00 2.29
3356 3643 7.601073 TTCACTCATTTTGCTCTGTATGTAG 57.399 36.000 0.00 0.00 0.00 2.74
3357 3644 6.701340 TCACTCATTTTGCTCTGTATGTAGT 58.299 36.000 0.00 0.00 0.00 2.73
3358 3645 6.813649 TCACTCATTTTGCTCTGTATGTAGTC 59.186 38.462 0.00 0.00 0.00 2.59
3359 3646 6.591448 CACTCATTTTGCTCTGTATGTAGTCA 59.409 38.462 0.00 0.00 0.00 3.41
3360 3647 6.591834 ACTCATTTTGCTCTGTATGTAGTCAC 59.408 38.462 0.00 0.00 0.00 3.67
3361 3648 6.701340 TCATTTTGCTCTGTATGTAGTCACT 58.299 36.000 0.00 0.00 0.00 3.41
3362 3649 7.161404 TCATTTTGCTCTGTATGTAGTCACTT 58.839 34.615 0.00 0.00 0.00 3.16
3363 3650 6.785488 TTTTGCTCTGTATGTAGTCACTTG 57.215 37.500 0.00 0.00 0.00 3.16
3364 3651 5.468540 TTGCTCTGTATGTAGTCACTTGT 57.531 39.130 0.00 0.00 0.00 3.16
3365 3652 5.468540 TGCTCTGTATGTAGTCACTTGTT 57.531 39.130 0.00 0.00 0.00 2.83
3366 3653 5.230182 TGCTCTGTATGTAGTCACTTGTTG 58.770 41.667 0.00 0.00 0.00 3.33
3367 3654 5.010617 TGCTCTGTATGTAGTCACTTGTTGA 59.989 40.000 0.00 0.00 0.00 3.18
3368 3655 5.926542 GCTCTGTATGTAGTCACTTGTTGAA 59.073 40.000 0.00 0.00 35.39 2.69
3369 3656 6.423905 GCTCTGTATGTAGTCACTTGTTGAAA 59.576 38.462 0.00 0.00 35.39 2.69
3370 3657 7.118390 GCTCTGTATGTAGTCACTTGTTGAAAT 59.882 37.037 0.00 0.00 35.39 2.17
3371 3658 8.534333 TCTGTATGTAGTCACTTGTTGAAATC 57.466 34.615 0.00 0.00 35.39 2.17
3372 3659 8.367911 TCTGTATGTAGTCACTTGTTGAAATCT 58.632 33.333 0.00 0.00 35.39 2.40
3373 3660 8.534333 TGTATGTAGTCACTTGTTGAAATCTC 57.466 34.615 0.00 0.00 35.39 2.75
3374 3661 8.367911 TGTATGTAGTCACTTGTTGAAATCTCT 58.632 33.333 0.00 0.00 35.39 3.10
3375 3662 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
3376 3663 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
3377 3664 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
3378 3665 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
3379 3666 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
3380 3667 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
3381 3668 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
3382 3669 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
3383 3670 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
3384 3671 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
3385 3672 9.566432 ACTTGTTGAAATCTCTAGAAAGACAAT 57.434 29.630 0.00 0.00 0.00 2.71
3398 3685 9.595823 TCTAGAAAGACAATTATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
3399 3686 9.595823 CTAGAAAGACAATTATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
3400 3687 8.494016 AGAAAGACAATTATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
3401 3688 7.553044 AGAAAGACAATTATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
3402 3689 5.681639 AGACAATTATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
3403 3690 5.427481 AGACAATTATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
3404 3691 5.681639 ACAATTATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
3415 3702 4.344390 GGAACGGAGGGAGTATTAGTGATT 59.656 45.833 0.00 0.00 0.00 2.57
3458 3745 2.829120 ACAGAGGGAGTAGAAGTGAAGC 59.171 50.000 0.00 0.00 0.00 3.86
3673 4039 1.392589 GAGGGGTAACATGCATGGTG 58.607 55.000 27.55 5.78 39.74 4.17
3688 4059 0.523072 TGGTGCTTACTACGACGGAC 59.477 55.000 0.00 0.00 0.00 4.79
3713 4084 8.540388 ACGGCCACATAGATTAGATATTACAAT 58.460 33.333 2.24 0.00 0.00 2.71
3855 4234 0.891373 AGGGTCGTGTCATCTGTCTG 59.109 55.000 0.00 0.00 0.00 3.51
3972 4351 1.545582 GCACCTGAAAATAGCCAAGCA 59.454 47.619 0.00 0.00 0.00 3.91
3975 4354 3.698040 CACCTGAAAATAGCCAAGCAGAT 59.302 43.478 0.00 0.00 0.00 2.90
3991 4370 2.905075 CAGATGAGGCCGTCAATACAA 58.095 47.619 8.66 0.00 39.19 2.41
4007 4386 5.180492 TCAATACAAACCATCAGAAACGTCC 59.820 40.000 0.00 0.00 0.00 4.79
4013 4392 1.811965 CCATCAGAAACGTCCAATGCA 59.188 47.619 0.00 0.00 0.00 3.96
4077 4456 0.959553 TCCTACGCCTATGCTGCTAC 59.040 55.000 0.00 0.00 34.43 3.58
4090 4469 1.004927 GCTGCTACGCTATTCCGTTTG 60.005 52.381 0.00 0.00 42.20 2.93
4091 4470 1.003851 TGCTACGCTATTCCGTTTGC 58.996 50.000 0.00 0.00 42.20 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 7.280205 AGTCCATTTCTTCGCGATTAAGTAATT 59.720 33.333 10.88 0.00 0.00 1.40
75 76 5.067674 TGCATTCTTGGGAATTAGGATTTCG 59.932 40.000 0.00 0.00 39.87 3.46
119 120 6.110707 TCCTCGTGATTTTTGGGTATTCTAC 58.889 40.000 0.00 0.00 0.00 2.59
120 121 6.302535 TCCTCGTGATTTTTGGGTATTCTA 57.697 37.500 0.00 0.00 0.00 2.10
121 122 5.174037 TCCTCGTGATTTTTGGGTATTCT 57.826 39.130 0.00 0.00 0.00 2.40
122 123 5.676331 GCTTCCTCGTGATTTTTGGGTATTC 60.676 44.000 0.00 0.00 0.00 1.75
123 124 4.157840 GCTTCCTCGTGATTTTTGGGTATT 59.842 41.667 0.00 0.00 0.00 1.89
124 125 3.694566 GCTTCCTCGTGATTTTTGGGTAT 59.305 43.478 0.00 0.00 0.00 2.73
125 126 3.078837 GCTTCCTCGTGATTTTTGGGTA 58.921 45.455 0.00 0.00 0.00 3.69
126 127 1.886542 GCTTCCTCGTGATTTTTGGGT 59.113 47.619 0.00 0.00 0.00 4.51
142 143 1.947597 TTGGGATGCCGCAATGCTTC 61.948 55.000 2.94 0.00 39.81 3.86
158 159 4.962384 CCGTCTTCGTTCCCAGAATTTGG 61.962 52.174 1.03 1.03 40.01 3.28
165 166 2.434359 GCCCGTCTTCGTTCCCAG 60.434 66.667 0.00 0.00 35.01 4.45
196 197 1.356624 GTGCGGAATAGTGCCATGC 59.643 57.895 0.00 0.00 0.00 4.06
212 213 2.611751 TGTCTGGTTCGTGAAATGTGTG 59.388 45.455 0.00 0.00 0.00 3.82
230 231 0.729690 GCGCTTCTTCCCTTGATGTC 59.270 55.000 0.00 0.00 0.00 3.06
239 240 1.335964 GGTTTCTTTGGCGCTTCTTCC 60.336 52.381 7.64 0.00 0.00 3.46
253 254 1.299976 GGCTGATCCCGTGGTTTCT 59.700 57.895 0.00 0.00 0.00 2.52
317 318 1.369625 GTGCGGTTGATCGGATTCTT 58.630 50.000 0.00 0.00 32.32 2.52
391 392 1.597027 CGGTTCTTGGCCGTGTCTT 60.597 57.895 0.00 0.00 43.84 3.01
392 393 2.030562 CGGTTCTTGGCCGTGTCT 59.969 61.111 0.00 0.00 43.84 3.41
427 428 1.000496 TCCTCCTCCTTCTTCTCCGA 59.000 55.000 0.00 0.00 0.00 4.55
428 429 1.064314 TCTCCTCCTCCTTCTTCTCCG 60.064 57.143 0.00 0.00 0.00 4.63
439 440 1.202592 GCGGGAATTCTTCTCCTCCTC 60.203 57.143 5.23 0.00 33.11 3.71
442 443 1.657822 GTGCGGGAATTCTTCTCCTC 58.342 55.000 5.23 0.00 33.11 3.71
642 643 1.811266 CCACTGCATTCCGACGAGG 60.811 63.158 0.00 0.00 42.97 4.63
643 644 1.079819 ACCACTGCATTCCGACGAG 60.080 57.895 0.00 0.00 0.00 4.18
644 645 1.374125 CACCACTGCATTCCGACGA 60.374 57.895 0.00 0.00 0.00 4.20
647 648 1.296392 CTCCACCACTGCATTCCGA 59.704 57.895 0.00 0.00 0.00 4.55
663 670 1.075600 CTCACTCCCTCCCTCCCTC 60.076 68.421 0.00 0.00 0.00 4.30
678 685 0.178846 TTCCCTTCCACCATCCCTCA 60.179 55.000 0.00 0.00 0.00 3.86
688 695 2.032528 CTGCGCACTTCCCTTCCA 59.967 61.111 5.66 0.00 0.00 3.53
689 696 3.435186 GCTGCGCACTTCCCTTCC 61.435 66.667 5.66 0.00 0.00 3.46
690 697 3.793144 CGCTGCGCACTTCCCTTC 61.793 66.667 5.66 0.00 0.00 3.46
701 708 4.093952 CTCAAACCCTGCGCTGCG 62.094 66.667 19.17 19.17 0.00 5.18
702 709 2.669569 TCTCAAACCCTGCGCTGC 60.670 61.111 9.73 0.00 0.00 5.25
703 710 2.684843 GCTCTCAAACCCTGCGCTG 61.685 63.158 9.73 8.47 0.00 5.18
704 711 2.359230 GCTCTCAAACCCTGCGCT 60.359 61.111 9.73 0.00 0.00 5.92
717 724 2.943978 CGTTCCAACCTCCGGCTCT 61.944 63.158 0.00 0.00 0.00 4.09
831 843 4.377708 TGAGGACAGTGCGCGCAT 62.378 61.111 38.62 22.76 0.00 4.73
834 846 4.363990 ACCTGAGGACAGTGCGCG 62.364 66.667 4.99 0.00 42.05 6.86
835 847 2.740055 CACCTGAGGACAGTGCGC 60.740 66.667 4.99 0.00 42.05 6.09
836 848 2.740055 GCACCTGAGGACAGTGCG 60.740 66.667 4.99 0.00 42.05 5.34
837 849 2.359230 GGCACCTGAGGACAGTGC 60.359 66.667 4.99 4.03 43.40 4.40
1010 1023 5.745227 ACTCACAGAGACCAAAGAGAAAAA 58.255 37.500 0.31 0.00 33.32 1.94
1015 1028 3.312828 CGAACTCACAGAGACCAAAGAG 58.687 50.000 0.31 0.00 33.32 2.85
1032 1046 3.112709 GGACGTGCCTGAGCGAAC 61.113 66.667 0.00 0.00 44.31 3.95
1077 1096 1.595929 GGAAACCGCGACCAACAGA 60.596 57.895 8.23 0.00 0.00 3.41
1078 1097 2.943653 GGAAACCGCGACCAACAG 59.056 61.111 8.23 0.00 0.00 3.16
1080 1099 3.719144 CCGGAAACCGCGACCAAC 61.719 66.667 8.23 0.00 46.86 3.77
1081 1100 4.992511 CCCGGAAACCGCGACCAA 62.993 66.667 8.23 0.00 46.86 3.67
1103 1122 4.598894 CATCTCCGCCTCGCCCAG 62.599 72.222 0.00 0.00 0.00 4.45
1340 1365 4.179579 GAAATGCGGGTGAGCGGC 62.180 66.667 7.26 7.26 40.67 6.53
1341 1366 3.508840 GGAAATGCGGGTGAGCGG 61.509 66.667 0.00 0.00 40.67 5.52
1342 1367 3.508840 GGGAAATGCGGGTGAGCG 61.509 66.667 0.00 0.00 40.67 5.03
1343 1368 3.140814 GGGGAAATGCGGGTGAGC 61.141 66.667 0.00 0.00 37.71 4.26
1344 1369 2.824041 CGGGGAAATGCGGGTGAG 60.824 66.667 0.00 0.00 0.00 3.51
1345 1370 3.323286 TCGGGGAAATGCGGGTGA 61.323 61.111 0.00 0.00 0.00 4.02
1346 1371 2.824041 CTCGGGGAAATGCGGGTG 60.824 66.667 0.00 0.00 0.00 4.61
1347 1372 4.796495 GCTCGGGGAAATGCGGGT 62.796 66.667 0.00 0.00 0.00 5.28
1348 1373 4.794648 TGCTCGGGGAAATGCGGG 62.795 66.667 0.00 0.00 0.00 6.13
1349 1374 3.508840 GTGCTCGGGGAAATGCGG 61.509 66.667 0.00 0.00 0.00 5.69
1350 1375 1.982073 GAAGTGCTCGGGGAAATGCG 61.982 60.000 0.00 0.00 0.00 4.73
1351 1376 1.657751 GGAAGTGCTCGGGGAAATGC 61.658 60.000 0.00 0.00 0.00 3.56
1352 1377 1.032114 GGGAAGTGCTCGGGGAAATG 61.032 60.000 0.00 0.00 0.00 2.32
1353 1378 1.303282 GGGAAGTGCTCGGGGAAAT 59.697 57.895 0.00 0.00 0.00 2.17
1354 1379 2.754375 GGGAAGTGCTCGGGGAAA 59.246 61.111 0.00 0.00 0.00 3.13
1355 1380 3.702048 CGGGAAGTGCTCGGGGAA 61.702 66.667 0.00 0.00 36.65 3.97
1365 1390 1.003718 GGTAGCAAGCACGGGAAGT 60.004 57.895 0.00 0.00 0.00 3.01
1366 1391 1.003839 TGGTAGCAAGCACGGGAAG 60.004 57.895 0.00 0.00 0.00 3.46
1367 1392 1.302192 GTGGTAGCAAGCACGGGAA 60.302 57.895 0.00 0.00 43.60 3.97
1385 1410 3.432608 CCGTGGTTAGGTTATGGTAAGGG 60.433 52.174 0.00 0.00 0.00 3.95
1435 1484 0.605589 ACAGCTCTGCAGTACTCACC 59.394 55.000 14.67 0.00 0.00 4.02
1506 1560 4.688966 GGCCCCATCGAGCCGATC 62.689 72.222 7.06 0.00 45.19 3.69
1511 1565 1.037030 TGATTTTGGCCCCATCGAGC 61.037 55.000 0.00 0.00 0.00 5.03
1512 1566 1.473258 TTGATTTTGGCCCCATCGAG 58.527 50.000 0.00 0.00 0.00 4.04
1513 1567 1.824230 CTTTGATTTTGGCCCCATCGA 59.176 47.619 0.00 0.00 0.00 3.59
1514 1568 1.550072 ACTTTGATTTTGGCCCCATCG 59.450 47.619 0.00 0.00 0.00 3.84
1515 1569 2.302733 ACACTTTGATTTTGGCCCCATC 59.697 45.455 0.00 0.00 0.00 3.51
1516 1570 2.337849 ACACTTTGATTTTGGCCCCAT 58.662 42.857 0.00 0.00 0.00 4.00
1517 1571 1.799933 ACACTTTGATTTTGGCCCCA 58.200 45.000 0.00 0.00 0.00 4.96
1518 1572 4.020662 TCAATACACTTTGATTTTGGCCCC 60.021 41.667 0.00 0.00 30.82 5.80
1519 1573 5.146010 TCAATACACTTTGATTTTGGCCC 57.854 39.130 0.00 0.00 30.82 5.80
1520 1574 4.627035 GCTCAATACACTTTGATTTTGGCC 59.373 41.667 0.00 0.00 35.20 5.36
1521 1575 5.346822 CAGCTCAATACACTTTGATTTTGGC 59.653 40.000 0.00 0.00 35.20 4.52
1522 1576 6.449698 ACAGCTCAATACACTTTGATTTTGG 58.550 36.000 0.00 0.00 35.20 3.28
1523 1577 9.462174 TTTACAGCTCAATACACTTTGATTTTG 57.538 29.630 0.00 0.00 35.20 2.44
1531 1585 8.686334 CCCATTTATTTACAGCTCAATACACTT 58.314 33.333 0.00 0.00 0.00 3.16
1532 1586 7.834181 ACCCATTTATTTACAGCTCAATACACT 59.166 33.333 0.00 0.00 0.00 3.55
1533 1587 7.915397 CACCCATTTATTTACAGCTCAATACAC 59.085 37.037 0.00 0.00 0.00 2.90
1534 1588 7.831690 TCACCCATTTATTTACAGCTCAATACA 59.168 33.333 0.00 0.00 0.00 2.29
1538 1592 7.013274 GCTATCACCCATTTATTTACAGCTCAA 59.987 37.037 0.00 0.00 0.00 3.02
1540 1594 6.072452 GGCTATCACCCATTTATTTACAGCTC 60.072 42.308 0.00 0.00 0.00 4.09
1542 1596 6.013842 GGCTATCACCCATTTATTTACAGC 57.986 41.667 0.00 0.00 0.00 4.40
1561 1615 5.185635 CCTTGTCAAATTTTCTGATGGGCTA 59.814 40.000 0.00 0.00 0.00 3.93
1564 1618 5.010922 TCACCTTGTCAAATTTTCTGATGGG 59.989 40.000 0.00 0.00 0.00 4.00
1615 1669 8.331740 TCCACATTCAGATTAGAGAAGGAATTT 58.668 33.333 0.00 0.00 30.75 1.82
1616 1670 7.865820 TCCACATTCAGATTAGAGAAGGAATT 58.134 34.615 0.00 0.00 30.75 2.17
1618 1672 6.874278 TCCACATTCAGATTAGAGAAGGAA 57.126 37.500 0.00 0.00 30.75 3.36
1619 1673 6.628175 CGTTCCACATTCAGATTAGAGAAGGA 60.628 42.308 0.00 0.00 30.75 3.36
1620 1674 5.521735 CGTTCCACATTCAGATTAGAGAAGG 59.478 44.000 0.00 0.00 0.00 3.46
1621 1675 5.521735 CCGTTCCACATTCAGATTAGAGAAG 59.478 44.000 0.00 0.00 0.00 2.85
1622 1676 5.186992 TCCGTTCCACATTCAGATTAGAGAA 59.813 40.000 0.00 0.00 0.00 2.87
1623 1677 4.709886 TCCGTTCCACATTCAGATTAGAGA 59.290 41.667 0.00 0.00 0.00 3.10
1637 1782 0.586802 GACAGCAACTTCCGTTCCAC 59.413 55.000 0.00 0.00 0.00 4.02
1641 1786 2.228138 TTACGACAGCAACTTCCGTT 57.772 45.000 0.00 0.00 35.05 4.44
1650 1885 2.734606 CGGAGTTTGATTTACGACAGCA 59.265 45.455 0.00 0.00 0.00 4.41
1721 1956 6.537453 ACTATACAGTTCTGACATCAAGCT 57.463 37.500 6.83 0.00 0.00 3.74
1726 1961 7.622256 GCAACACAACTATACAGTTCTGACATC 60.622 40.741 6.83 0.00 43.30 3.06
1743 1978 1.363807 GGCTTCCTGGCAACACAAC 59.636 57.895 0.00 0.00 46.17 3.32
1791 2026 2.440539 ACCGAAGTGTCACAGACATC 57.559 50.000 5.62 0.00 44.63 3.06
1808 2043 4.142381 GGATGAGCTGGTTGTTGAAATACC 60.142 45.833 0.00 0.00 0.00 2.73
1926 2161 4.227300 AGGCCACAATACTGGTAGAAATCA 59.773 41.667 5.01 0.00 33.30 2.57
1951 2186 5.798434 GTCATAAGCCGTCCAACATTTAAAC 59.202 40.000 0.00 0.00 0.00 2.01
1975 2210 5.288543 CTGGAAAATTTCAGGAGACGAAG 57.711 43.478 8.09 0.00 0.00 3.79
2121 2364 4.741342 AGTAAAGAAGCATGCAAATCAGC 58.259 39.130 21.98 5.08 0.00 4.26
2155 2398 2.943265 AGCAATGGCACCTCCCCT 60.943 61.111 0.00 0.00 44.61 4.79
2248 2491 7.653311 TGAAACATCATCTATCATAACCGTGAG 59.347 37.037 0.00 0.00 0.00 3.51
2426 2669 2.669364 GCAATTCTGCCAAGACACAAG 58.331 47.619 0.00 0.00 43.26 3.16
2448 2691 4.701651 CCTCATGAATAAGAACCACAAGCA 59.298 41.667 0.00 0.00 0.00 3.91
2671 2919 4.323417 TCACAATAAGACCAATGTTCGCT 58.677 39.130 0.00 0.00 0.00 4.93
2678 2926 5.657745 TGCCATCATTCACAATAAGACCAAT 59.342 36.000 0.00 0.00 0.00 3.16
3007 3257 1.215382 CGATGCGAGTCCTGAACCA 59.785 57.895 0.00 0.00 0.00 3.67
3024 3274 5.393902 AAAAAGCAAAAAGAGATGCAACG 57.606 34.783 0.00 0.00 44.95 4.10
3086 3338 4.274950 ACAGGCTTACAATGTTGTGTACAC 59.725 41.667 19.36 19.36 42.31 2.90
3159 3412 6.053005 TCACAACTTTACAAAGGGAGTACTG 58.947 40.000 0.00 0.00 40.31 2.74
3170 3423 8.974060 AGACCTTTTAGATCACAACTTTACAA 57.026 30.769 0.00 0.00 0.00 2.41
3234 3521 6.895782 TGAAAACGGAGGGAGTATAATGATT 58.104 36.000 0.00 0.00 0.00 2.57
3243 3530 5.773176 ACAATTATTTGAAAACGGAGGGAGT 59.227 36.000 4.42 0.00 36.64 3.85
3244 3531 6.151144 AGACAATTATTTGAAAACGGAGGGAG 59.849 38.462 4.42 0.00 36.64 4.30
3245 3532 6.007703 AGACAATTATTTGAAAACGGAGGGA 58.992 36.000 4.42 0.00 36.64 4.20
3246 3533 6.267496 AGACAATTATTTGAAAACGGAGGG 57.733 37.500 4.42 0.00 36.64 4.30
3247 3534 8.082242 AGAAAGACAATTATTTGAAAACGGAGG 58.918 33.333 4.42 0.00 36.64 4.30
3262 3549 8.526147 CCATTTGAGATGGTTAGAAAGACAATT 58.474 33.333 0.00 0.00 34.56 2.32
3263 3550 7.890127 TCCATTTGAGATGGTTAGAAAGACAAT 59.110 33.333 1.63 0.00 40.06 2.71
3264 3551 7.174946 GTCCATTTGAGATGGTTAGAAAGACAA 59.825 37.037 1.63 0.00 40.06 3.18
3265 3552 6.655003 GTCCATTTGAGATGGTTAGAAAGACA 59.345 38.462 1.63 0.00 40.06 3.41
3266 3553 6.881602 AGTCCATTTGAGATGGTTAGAAAGAC 59.118 38.462 1.63 0.00 40.06 3.01
3267 3554 7.020827 AGTCCATTTGAGATGGTTAGAAAGA 57.979 36.000 1.63 0.00 40.06 2.52
3268 3555 7.824289 TGTAGTCCATTTGAGATGGTTAGAAAG 59.176 37.037 1.63 0.00 40.06 2.62
3269 3556 7.685481 TGTAGTCCATTTGAGATGGTTAGAAA 58.315 34.615 1.63 0.00 40.06 2.52
3270 3557 7.252612 TGTAGTCCATTTGAGATGGTTAGAA 57.747 36.000 1.63 0.00 40.06 2.10
3271 3558 6.867519 TGTAGTCCATTTGAGATGGTTAGA 57.132 37.500 1.63 0.00 40.06 2.10
3272 3559 6.878923 TGTTGTAGTCCATTTGAGATGGTTAG 59.121 38.462 1.63 0.00 40.06 2.34
3273 3560 6.774673 TGTTGTAGTCCATTTGAGATGGTTA 58.225 36.000 1.63 0.00 40.06 2.85
3274 3561 5.630121 TGTTGTAGTCCATTTGAGATGGTT 58.370 37.500 1.63 0.00 40.06 3.67
3275 3562 5.241403 TGTTGTAGTCCATTTGAGATGGT 57.759 39.130 1.63 0.00 40.06 3.55
3276 3563 6.018751 CGTATGTTGTAGTCCATTTGAGATGG 60.019 42.308 0.00 0.00 40.48 3.51
3277 3564 6.756542 TCGTATGTTGTAGTCCATTTGAGATG 59.243 38.462 0.00 0.00 0.00 2.90
3278 3565 6.873997 TCGTATGTTGTAGTCCATTTGAGAT 58.126 36.000 0.00 0.00 0.00 2.75
3279 3566 6.275494 TCGTATGTTGTAGTCCATTTGAGA 57.725 37.500 0.00 0.00 0.00 3.27
3280 3567 6.961359 TTCGTATGTTGTAGTCCATTTGAG 57.039 37.500 0.00 0.00 0.00 3.02
3281 3568 6.876789 ACATTCGTATGTTGTAGTCCATTTGA 59.123 34.615 1.31 0.00 42.29 2.69
3282 3569 7.072177 ACATTCGTATGTTGTAGTCCATTTG 57.928 36.000 1.31 0.00 42.29 2.32
3283 3570 8.958119 ATACATTCGTATGTTGTAGTCCATTT 57.042 30.769 13.12 0.00 42.29 2.32
3310 3597 9.856488 GTGAATCTACACTCTAAAACATGTCTA 57.144 33.333 0.00 0.00 37.73 2.59
3311 3598 8.589338 AGTGAATCTACACTCTAAAACATGTCT 58.411 33.333 0.00 0.00 46.36 3.41
3312 3599 8.764524 AGTGAATCTACACTCTAAAACATGTC 57.235 34.615 0.00 0.00 46.36 3.06
3325 3612 6.148480 ACAGAGCAAAATGAGTGAATCTACAC 59.852 38.462 0.00 0.00 40.60 2.90
3326 3613 6.233434 ACAGAGCAAAATGAGTGAATCTACA 58.767 36.000 0.00 0.00 0.00 2.74
3327 3614 6.734104 ACAGAGCAAAATGAGTGAATCTAC 57.266 37.500 0.00 0.00 0.00 2.59
3328 3615 8.043113 ACATACAGAGCAAAATGAGTGAATCTA 58.957 33.333 0.00 0.00 0.00 1.98
3329 3616 6.883217 ACATACAGAGCAAAATGAGTGAATCT 59.117 34.615 0.00 0.00 0.00 2.40
3330 3617 7.081526 ACATACAGAGCAAAATGAGTGAATC 57.918 36.000 0.00 0.00 0.00 2.52
3331 3618 7.826252 ACTACATACAGAGCAAAATGAGTGAAT 59.174 33.333 0.00 0.00 0.00 2.57
3332 3619 7.161404 ACTACATACAGAGCAAAATGAGTGAA 58.839 34.615 0.00 0.00 0.00 3.18
3333 3620 6.701340 ACTACATACAGAGCAAAATGAGTGA 58.299 36.000 0.00 0.00 0.00 3.41
3334 3621 6.591448 TGACTACATACAGAGCAAAATGAGTG 59.409 38.462 0.00 0.00 0.00 3.51
3335 3622 6.591834 GTGACTACATACAGAGCAAAATGAGT 59.408 38.462 0.00 0.00 0.00 3.41
3336 3623 6.815641 AGTGACTACATACAGAGCAAAATGAG 59.184 38.462 0.00 0.00 0.00 2.90
3337 3624 6.701340 AGTGACTACATACAGAGCAAAATGA 58.299 36.000 0.00 0.00 0.00 2.57
3338 3625 6.974932 AGTGACTACATACAGAGCAAAATG 57.025 37.500 0.00 0.00 0.00 2.32
3339 3626 6.936900 ACAAGTGACTACATACAGAGCAAAAT 59.063 34.615 0.00 0.00 0.00 1.82
3340 3627 6.288294 ACAAGTGACTACATACAGAGCAAAA 58.712 36.000 0.00 0.00 0.00 2.44
3341 3628 5.853936 ACAAGTGACTACATACAGAGCAAA 58.146 37.500 0.00 0.00 0.00 3.68
3342 3629 5.468540 ACAAGTGACTACATACAGAGCAA 57.531 39.130 0.00 0.00 0.00 3.91
3343 3630 5.010617 TCAACAAGTGACTACATACAGAGCA 59.989 40.000 0.00 0.00 0.00 4.26
3344 3631 5.470368 TCAACAAGTGACTACATACAGAGC 58.530 41.667 0.00 0.00 0.00 4.09
3345 3632 7.946655 TTTCAACAAGTGACTACATACAGAG 57.053 36.000 0.00 0.00 35.39 3.35
3346 3633 8.367911 AGATTTCAACAAGTGACTACATACAGA 58.632 33.333 0.00 0.00 35.39 3.41
3347 3634 8.539770 AGATTTCAACAAGTGACTACATACAG 57.460 34.615 0.00 0.00 35.39 2.74
3348 3635 8.367911 AGAGATTTCAACAAGTGACTACATACA 58.632 33.333 0.00 0.00 35.39 2.29
3349 3636 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
3351 3638 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
3352 3639 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
3353 3640 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
3354 3641 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
3355 3642 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
3356 3643 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
3357 3644 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
3358 3645 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
3359 3646 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
3372 3659 9.595823 CCGTTCCTAAATAATTGTCTTTCTAGA 57.404 33.333 0.00 0.00 0.00 2.43
3373 3660 9.595823 TCCGTTCCTAAATAATTGTCTTTCTAG 57.404 33.333 0.00 0.00 0.00 2.43
3374 3661 9.595823 CTCCGTTCCTAAATAATTGTCTTTCTA 57.404 33.333 0.00 0.00 0.00 2.10
3375 3662 7.553044 CCTCCGTTCCTAAATAATTGTCTTTCT 59.447 37.037 0.00 0.00 0.00 2.52
3376 3663 7.201705 CCCTCCGTTCCTAAATAATTGTCTTTC 60.202 40.741 0.00 0.00 0.00 2.62
3377 3664 6.602009 CCCTCCGTTCCTAAATAATTGTCTTT 59.398 38.462 0.00 0.00 0.00 2.52
3378 3665 6.069847 TCCCTCCGTTCCTAAATAATTGTCTT 60.070 38.462 0.00 0.00 0.00 3.01
3379 3666 5.427481 TCCCTCCGTTCCTAAATAATTGTCT 59.573 40.000 0.00 0.00 0.00 3.41
3380 3667 5.677567 TCCCTCCGTTCCTAAATAATTGTC 58.322 41.667 0.00 0.00 0.00 3.18
3381 3668 5.191124 ACTCCCTCCGTTCCTAAATAATTGT 59.809 40.000 0.00 0.00 0.00 2.71
3382 3669 5.681639 ACTCCCTCCGTTCCTAAATAATTG 58.318 41.667 0.00 0.00 0.00 2.32
3383 3670 5.970501 ACTCCCTCCGTTCCTAAATAATT 57.029 39.130 0.00 0.00 0.00 1.40
3384 3671 7.628501 AATACTCCCTCCGTTCCTAAATAAT 57.371 36.000 0.00 0.00 0.00 1.28
3385 3672 7.786464 ACTAATACTCCCTCCGTTCCTAAATAA 59.214 37.037 0.00 0.00 0.00 1.40
3386 3673 7.232127 CACTAATACTCCCTCCGTTCCTAAATA 59.768 40.741 0.00 0.00 0.00 1.40
3387 3674 6.041751 CACTAATACTCCCTCCGTTCCTAAAT 59.958 42.308 0.00 0.00 0.00 1.40
3388 3675 5.361857 CACTAATACTCCCTCCGTTCCTAAA 59.638 44.000 0.00 0.00 0.00 1.85
3389 3676 4.891756 CACTAATACTCCCTCCGTTCCTAA 59.108 45.833 0.00 0.00 0.00 2.69
3390 3677 4.166725 TCACTAATACTCCCTCCGTTCCTA 59.833 45.833 0.00 0.00 0.00 2.94
3391 3678 3.053095 TCACTAATACTCCCTCCGTTCCT 60.053 47.826 0.00 0.00 0.00 3.36
3392 3679 3.294214 TCACTAATACTCCCTCCGTTCC 58.706 50.000 0.00 0.00 0.00 3.62
3393 3680 5.532664 AATCACTAATACTCCCTCCGTTC 57.467 43.478 0.00 0.00 0.00 3.95
3394 3681 5.952347 AAATCACTAATACTCCCTCCGTT 57.048 39.130 0.00 0.00 0.00 4.44
3395 3682 7.093201 TGTTTAAATCACTAATACTCCCTCCGT 60.093 37.037 0.00 0.00 0.00 4.69
3396 3683 7.270047 TGTTTAAATCACTAATACTCCCTCCG 58.730 38.462 0.00 0.00 0.00 4.63
3397 3684 9.110502 CTTGTTTAAATCACTAATACTCCCTCC 57.889 37.037 0.00 0.00 0.00 4.30
3398 3685 8.613482 GCTTGTTTAAATCACTAATACTCCCTC 58.387 37.037 0.00 0.00 0.00 4.30
3399 3686 8.329502 AGCTTGTTTAAATCACTAATACTCCCT 58.670 33.333 0.00 0.00 0.00 4.20
3400 3687 8.507524 AGCTTGTTTAAATCACTAATACTCCC 57.492 34.615 0.00 0.00 0.00 4.30
3458 3745 4.733405 GTGTTCTAAAGTCAAAAGGTTGCG 59.267 41.667 0.00 0.00 34.50 4.85
3673 4039 1.584742 GCCGTCCGTCGTAGTAAGC 60.585 63.158 0.00 0.00 37.94 3.09
3688 4059 8.948631 ATTGTAATATCTAATCTATGTGGCCG 57.051 34.615 0.00 0.00 0.00 6.13
3715 4086 1.406887 GCCGGCTGACTCCAGATAAAA 60.407 52.381 22.15 0.00 43.02 1.52
3718 4089 2.134287 GGCCGGCTGACTCCAGATA 61.134 63.158 28.56 0.00 43.02 1.98
3729 4100 1.645402 ATTATTGTCCCTGGCCGGCT 61.645 55.000 28.56 5.16 0.00 5.52
3821 4192 0.252103 ACCCTCCCTTCTGTAGCGAA 60.252 55.000 0.00 0.00 0.00 4.70
3822 4193 0.683504 GACCCTCCCTTCTGTAGCGA 60.684 60.000 0.00 0.00 0.00 4.93
3869 4248 4.241681 GACAGTCTGGACAAGAAGATGAC 58.758 47.826 4.53 0.00 36.40 3.06
3929 4308 3.244596 GGTACCAAAGCAGGAAGAGACTT 60.245 47.826 7.15 0.00 0.00 3.01
3972 4351 3.270877 GTTTGTATTGACGGCCTCATCT 58.729 45.455 0.00 0.00 0.00 2.90
3975 4354 1.072489 TGGTTTGTATTGACGGCCTCA 59.928 47.619 0.00 0.26 0.00 3.86
3991 4370 2.228822 GCATTGGACGTTTCTGATGGTT 59.771 45.455 0.00 0.00 0.00 3.67
4013 4392 3.812053 GGAGTGCGATTTTATCTGCTGAT 59.188 43.478 11.14 11.14 36.74 2.90
4077 4456 1.062525 GCCAGCAAACGGAATAGCG 59.937 57.895 0.00 0.00 0.00 4.26
4127 4506 3.088532 AGAGCGAGAGAGAAACATGAGT 58.911 45.455 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.