Multiple sequence alignment - TraesCS7A01G250500

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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 TraesCS7A01G250500 chr7A 100.000 5064 0 0 1 5064 232743847 232748910 0.000000e+00 9352.0
1 TraesCS7A01G250500 chr7A 96.903 226 6 1 1 225 669666399 669666624 1.330000e-100 377.0
2 TraesCS7A01G250500 chr7A 97.285 221 6 0 1 221 566529918 566530138 4.790000e-100 375.0
3 TraesCS7A01G250500 chr7D 95.506 1691 67 4 2402 4087 220511100 220512786 0.000000e+00 2693.0
4 TraesCS7A01G250500 chr7D 92.978 1182 64 10 216 1382 220508799 220509976 0.000000e+00 1705.0
5 TraesCS7A01G250500 chr7D 94.862 798 27 6 1606 2400 220510056 220510842 0.000000e+00 1234.0
6 TraesCS7A01G250500 chr7D 88.786 651 36 18 4445 5063 220513122 220513767 0.000000e+00 763.0
7 TraesCS7A01G250500 chr7D 85.205 365 20 13 4106 4463 220512775 220513112 1.350000e-90 344.0
8 TraesCS7A01G250500 chr7B 94.027 1691 83 8 1859 3545 178416974 178415298 0.000000e+00 2547.0
9 TraesCS7A01G250500 chr7B 90.242 1281 73 19 216 1452 178418578 178417306 0.000000e+00 1626.0
10 TraesCS7A01G250500 chr7B 96.604 265 8 1 1606 1869 178417263 178416999 6.020000e-119 438.0
11 TraesCS7A01G250500 chr7B 88.304 342 30 4 3745 4085 178415225 178414893 7.900000e-108 401.0
12 TraesCS7A01G250500 chr7B 95.480 177 8 0 4746 4922 178407796 178407620 2.980000e-72 283.0
13 TraesCS7A01G250500 chr7B 93.793 145 6 2 4922 5063 178407566 178407422 1.100000e-51 215.0
14 TraesCS7A01G250500 chr6A 98.636 220 3 0 1 220 586802465 586802246 1.710000e-104 390.0
15 TraesCS7A01G250500 chr6A 97.738 221 5 0 1 221 421525063 421524843 1.030000e-101 381.0
16 TraesCS7A01G250500 chr6A 97.297 222 6 0 1 222 13387492 13387271 1.330000e-100 377.0
17 TraesCS7A01G250500 chr6A 79.024 205 38 3 4450 4651 115321771 115321973 8.840000e-28 135.0
18 TraesCS7A01G250500 chr5A 97.717 219 5 0 1 219 618310062 618310280 1.330000e-100 377.0
19 TraesCS7A01G250500 chr5A 75.918 245 45 8 4436 4680 660884791 660884561 4.140000e-21 113.0
20 TraesCS7A01G250500 chr4A 97.717 219 5 0 1 219 212811795 212812013 1.330000e-100 377.0
21 TraesCS7A01G250500 chr2A 97.717 219 4 1 1 219 11647281 11647498 4.790000e-100 375.0
22 TraesCS7A01G250500 chr2A 91.765 85 7 0 1524 1608 102688124 102688040 8.910000e-23 119.0
23 TraesCS7A01G250500 chr3A 96.861 223 7 0 1 223 652219352 652219574 1.720000e-99 374.0
24 TraesCS7A01G250500 chr2B 96.471 85 1 2 1523 1607 799282668 799282586 6.840000e-29 139.0
25 TraesCS7A01G250500 chr5D 92.391 92 7 0 1520 1611 50780523 50780432 1.140000e-26 132.0
26 TraesCS7A01G250500 chr5D 91.011 89 7 1 1523 1610 47332334 47332246 8.910000e-23 119.0
27 TraesCS7A01G250500 chr5B 92.135 89 6 1 1523 1610 50469213 50469125 1.910000e-24 124.0
28 TraesCS7A01G250500 chr5B 92.045 88 7 0 1523 1610 565770563 565770476 1.910000e-24 124.0
29 TraesCS7A01G250500 chr5B 88.571 105 9 3 1522 1625 565770478 565770580 1.910000e-24 124.0
30 TraesCS7A01G250500 chr5B 78.889 180 28 8 4513 4688 617257464 617257637 4.140000e-21 113.0
31 TraesCS7A01G250500 chr1D 91.954 87 7 0 1521 1607 60287422 60287336 6.890000e-24 122.0
32 TraesCS7A01G250500 chr3B 77.295 207 39 7 4484 4687 719827305 719827104 1.150000e-21 115.0
33 TraesCS7A01G250500 chr4D 87.368 95 11 1 1513 1607 179862443 179862536 1.930000e-19 108.0
34 TraesCS7A01G250500 chr6D 75.248 202 37 7 4483 4672 333593571 333593771 3.250000e-12 84.2


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 TraesCS7A01G250500 chr7A 232743847 232748910 5063 False 9352.0 9352 100.00000 1 5064 1 chr7A.!!$F1 5063
1 TraesCS7A01G250500 chr7D 220508799 220513767 4968 False 1347.8 2693 91.46740 216 5063 5 chr7D.!!$F1 4847
2 TraesCS7A01G250500 chr7B 178414893 178418578 3685 True 1253.0 2547 92.29425 216 4085 4 chr7B.!!$R2 3869

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
249 250 0.315251 CTCTGAGGACGACTGTTGCA 59.685 55.0 0.00 0.0 0.0 4.08 F
1114 1163 0.655733 GACGGCGAATAACATGTGGG 59.344 55.0 16.62 0.0 0.0 4.61 F
1126 1175 0.817013 CATGTGGGTATTGTGGTGCC 59.183 55.0 0.00 0.0 0.0 5.01 F
2881 3231 0.820891 CCAGGTGCATCATAGTGGCC 60.821 60.0 0.00 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1249 1304 0.455410 TTAGCCATGAAATGCGCCAC 59.545 50.0 4.18 0.00 44.97 5.01 R
2991 3341 0.107066 TACCGGTCGGATCAGCAGTA 60.107 55.0 12.40 0.00 38.96 2.74 R
3058 3408 0.852136 CACGAAAAGCCCTTTTTGCG 59.148 50.0 16.79 13.74 44.05 4.85 R
4633 5026 0.461339 CTGGGAAGCATGGCAATTGC 60.461 55.0 22.47 22.47 40.45 3.56 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
24 25 7.812309 AAAGTCAAGCTTTGTAAACTTTGAC 57.188 32.000 14.76 14.88 45.00 3.18
25 26 6.759497 AGTCAAGCTTTGTAAACTTTGACT 57.241 33.333 17.37 17.37 32.23 3.41
26 27 7.859325 AGTCAAGCTTTGTAAACTTTGACTA 57.141 32.000 19.57 0.00 33.77 2.59
27 28 8.276252 AGTCAAGCTTTGTAAACTTTGACTAA 57.724 30.769 19.57 0.00 33.77 2.24
28 29 8.398665 AGTCAAGCTTTGTAAACTTTGACTAAG 58.601 33.333 19.57 3.76 39.87 2.18
164 165 9.823647 TTTCTATAAATTTGGTCAAACTTTGCA 57.176 25.926 0.00 0.00 32.51 4.08
165 166 9.823647 TTCTATAAATTTGGTCAAACTTTGCAA 57.176 25.926 0.00 0.00 32.51 4.08
166 167 9.823647 TCTATAAATTTGGTCAAACTTTGCAAA 57.176 25.926 12.14 12.14 32.51 3.68
178 179 3.769536 ACTTTGCAAAGTTTGACTTCGG 58.230 40.909 33.85 11.40 46.52 4.30
179 180 3.192633 ACTTTGCAAAGTTTGACTTCGGT 59.807 39.130 33.85 12.02 46.52 4.69
180 181 3.414549 TTGCAAAGTTTGACTTCGGTC 57.585 42.857 19.82 0.00 37.47 4.79
193 194 5.405331 GACTTCGGTCAAACCTAATATGC 57.595 43.478 0.00 0.00 43.91 3.14
194 195 4.839121 ACTTCGGTCAAACCTAATATGCA 58.161 39.130 0.00 0.00 35.66 3.96
195 196 4.876107 ACTTCGGTCAAACCTAATATGCAG 59.124 41.667 0.00 0.00 35.66 4.41
196 197 4.746535 TCGGTCAAACCTAATATGCAGA 57.253 40.909 0.00 0.00 35.66 4.26
197 198 4.439057 TCGGTCAAACCTAATATGCAGAC 58.561 43.478 0.00 0.00 35.66 3.51
198 199 4.161565 TCGGTCAAACCTAATATGCAGACT 59.838 41.667 0.00 0.00 35.66 3.24
199 200 4.271049 CGGTCAAACCTAATATGCAGACTG 59.729 45.833 0.00 0.00 35.66 3.51
200 201 5.428253 GGTCAAACCTAATATGCAGACTGA 58.572 41.667 6.65 0.00 34.73 3.41
201 202 5.880332 GGTCAAACCTAATATGCAGACTGAA 59.120 40.000 6.65 0.00 34.73 3.02
202 203 6.543831 GGTCAAACCTAATATGCAGACTGAAT 59.456 38.462 6.65 3.39 34.73 2.57
203 204 7.715249 GGTCAAACCTAATATGCAGACTGAATA 59.285 37.037 6.65 6.06 34.73 1.75
204 205 9.109393 GTCAAACCTAATATGCAGACTGAATAA 57.891 33.333 7.25 0.00 0.00 1.40
205 206 9.679661 TCAAACCTAATATGCAGACTGAATAAA 57.320 29.630 7.25 0.00 0.00 1.40
209 210 8.612619 ACCTAATATGCAGACTGAATAAAAACG 58.387 33.333 7.25 0.00 0.00 3.60
210 211 8.070171 CCTAATATGCAGACTGAATAAAAACGG 58.930 37.037 7.25 1.34 0.00 4.44
211 212 7.624360 AATATGCAGACTGAATAAAAACGGA 57.376 32.000 7.25 0.00 0.00 4.69
212 213 5.551760 ATGCAGACTGAATAAAAACGGAG 57.448 39.130 6.65 0.00 0.00 4.63
213 214 3.751175 TGCAGACTGAATAAAAACGGAGG 59.249 43.478 6.65 0.00 0.00 4.30
214 215 3.127030 GCAGACTGAATAAAAACGGAGGG 59.873 47.826 6.65 0.00 0.00 4.30
249 250 0.315251 CTCTGAGGACGACTGTTGCA 59.685 55.000 0.00 0.00 0.00 4.08
251 252 2.164422 CTCTGAGGACGACTGTTGCATA 59.836 50.000 0.00 0.00 0.00 3.14
258 259 3.930229 GGACGACTGTTGCATATGTGTAA 59.070 43.478 4.29 0.00 0.00 2.41
299 303 2.572104 AGCCCGTAACCTTCTCTCATTT 59.428 45.455 0.00 0.00 0.00 2.32
425 437 4.396790 CGTGGCCCTTTGCTTTTATAAGTA 59.603 41.667 0.00 0.00 40.92 2.24
426 438 5.106078 CGTGGCCCTTTGCTTTTATAAGTAA 60.106 40.000 0.00 0.00 40.92 2.24
481 493 2.453983 GCAAAAACCTGCCATTGCTA 57.546 45.000 2.33 0.00 43.58 3.49
619 633 4.222588 TGGCATTTTCTCTATTTTGGGGTG 59.777 41.667 0.00 0.00 0.00 4.61
646 663 5.295431 TGTGATGTTAATTTTCAGAGGCG 57.705 39.130 0.00 0.00 0.00 5.52
698 719 1.491754 ACAGACATATGGGAGCATGCA 59.508 47.619 21.98 0.00 0.00 3.96
731 752 5.652744 AGATATCACGGCGAACATAAAAC 57.347 39.130 16.62 3.43 0.00 2.43
763 784 9.132521 CAACACCTCAAAATCTATTGTGAATTC 57.867 33.333 0.00 0.00 33.86 2.17
790 811 5.071788 AGAGATAACAAGTGTGGGAGTTCAA 59.928 40.000 0.00 0.00 0.00 2.69
859 887 1.393603 GGCTTATCCAAGTGCCTTCC 58.606 55.000 0.00 0.00 41.92 3.46
897 928 2.304761 GGAACCACACAGACCTGGATAA 59.695 50.000 0.00 0.00 34.19 1.75
970 1001 1.890174 GGCACCAGCAACCATTACC 59.110 57.895 0.00 0.00 44.61 2.85
987 1018 1.112315 ACCGGCATTCAAACAAGGCA 61.112 50.000 0.00 0.00 0.00 4.75
997 1028 1.682854 CAAACAAGGCAAGCAGGAAGA 59.317 47.619 0.00 0.00 0.00 2.87
998 1029 2.071778 AACAAGGCAAGCAGGAAGAA 57.928 45.000 0.00 0.00 0.00 2.52
1060 1091 1.736612 CTTCTTCTTCTCCAGCTGCC 58.263 55.000 8.66 0.00 0.00 4.85
1114 1163 0.655733 GACGGCGAATAACATGTGGG 59.344 55.000 16.62 0.00 0.00 4.61
1126 1175 0.817013 CATGTGGGTATTGTGGTGCC 59.183 55.000 0.00 0.00 0.00 5.01
1146 1195 3.006967 GCCACAGGAGTAGAAGAAGAACA 59.993 47.826 0.00 0.00 0.00 3.18
1151 1200 4.159506 CAGGAGTAGAAGAAGAACAGGGAG 59.840 50.000 0.00 0.00 0.00 4.30
1227 1282 1.250328 CAGAGCCCATTGAACAGCAA 58.750 50.000 0.00 0.00 41.53 3.91
1231 1286 4.082081 CAGAGCCCATTGAACAGCAAAATA 60.082 41.667 0.00 0.00 40.48 1.40
1238 1293 7.546358 CCCATTGAACAGCAAAATATAGACAA 58.454 34.615 0.00 0.00 40.48 3.18
1301 1356 7.491372 GCAGTAAATAGTAGCACTGTAATGTCA 59.509 37.037 9.20 0.00 40.40 3.58
1352 1407 2.109128 TGCCTTGGGGAATCTGTACAAA 59.891 45.455 0.00 0.00 33.58 2.83
1361 1416 5.337009 GGGGAATCTGTACAAAGAGAACGTA 60.337 44.000 0.00 0.00 0.00 3.57
1384 1439 7.094334 CGTAGCTGATAATGAGTATACTTCCCA 60.094 40.741 6.88 0.81 0.00 4.37
1459 1514 4.500375 GCTGAACATTTTTCACTTGCCTCT 60.500 41.667 0.00 0.00 0.00 3.69
1460 1515 5.278463 GCTGAACATTTTTCACTTGCCTCTA 60.278 40.000 0.00 0.00 0.00 2.43
1461 1516 6.571150 GCTGAACATTTTTCACTTGCCTCTAT 60.571 38.462 0.00 0.00 0.00 1.98
1462 1517 7.288810 TGAACATTTTTCACTTGCCTCTATT 57.711 32.000 0.00 0.00 0.00 1.73
1463 1518 7.725251 TGAACATTTTTCACTTGCCTCTATTT 58.275 30.769 0.00 0.00 0.00 1.40
1464 1519 8.203485 TGAACATTTTTCACTTGCCTCTATTTT 58.797 29.630 0.00 0.00 0.00 1.82
1465 1520 8.593492 AACATTTTTCACTTGCCTCTATTTTC 57.407 30.769 0.00 0.00 0.00 2.29
1466 1521 7.154656 ACATTTTTCACTTGCCTCTATTTTCC 58.845 34.615 0.00 0.00 0.00 3.13
1467 1522 6.976934 TTTTTCACTTGCCTCTATTTTCCT 57.023 33.333 0.00 0.00 0.00 3.36
1468 1523 6.575162 TTTTCACTTGCCTCTATTTTCCTC 57.425 37.500 0.00 0.00 0.00 3.71
1469 1524 5.505181 TTCACTTGCCTCTATTTTCCTCT 57.495 39.130 0.00 0.00 0.00 3.69
1470 1525 6.620877 TTCACTTGCCTCTATTTTCCTCTA 57.379 37.500 0.00 0.00 0.00 2.43
1515 1570 1.811965 TGCGATCCAACCATTTGACAG 59.188 47.619 0.00 0.00 34.24 3.51
1524 1579 6.744112 TCCAACCATTTGACAGAACAAATAC 58.256 36.000 0.00 0.00 45.00 1.89
1525 1580 6.549364 TCCAACCATTTGACAGAACAAATACT 59.451 34.615 0.00 0.00 45.00 2.12
1527 1582 6.575162 ACCATTTGACAGAACAAATACTCC 57.425 37.500 0.00 0.00 45.00 3.85
1528 1583 5.476945 ACCATTTGACAGAACAAATACTCCC 59.523 40.000 0.00 0.00 45.00 4.30
1529 1584 5.711976 CCATTTGACAGAACAAATACTCCCT 59.288 40.000 0.00 0.00 45.00 4.20
1530 1585 6.127897 CCATTTGACAGAACAAATACTCCCTC 60.128 42.308 0.00 0.00 45.00 4.30
1531 1586 5.825593 TTGACAGAACAAATACTCCCTCT 57.174 39.130 0.00 0.00 0.00 3.69
1533 1588 4.593206 TGACAGAACAAATACTCCCTCTGT 59.407 41.667 2.34 2.34 44.59 3.41
1534 1589 5.778241 TGACAGAACAAATACTCCCTCTGTA 59.222 40.000 2.71 0.00 42.59 2.74
1535 1590 6.269077 TGACAGAACAAATACTCCCTCTGTAA 59.731 38.462 2.71 0.00 42.59 2.41
1536 1591 6.465084 ACAGAACAAATACTCCCTCTGTAAC 58.535 40.000 0.84 0.00 41.19 2.50
1537 1592 6.270231 ACAGAACAAATACTCCCTCTGTAACT 59.730 38.462 0.84 0.00 41.19 2.24
1538 1593 7.162082 CAGAACAAATACTCCCTCTGTAACTT 58.838 38.462 0.00 0.00 0.00 2.66
1539 1594 8.311836 CAGAACAAATACTCCCTCTGTAACTTA 58.688 37.037 0.00 0.00 0.00 2.24
1540 1595 8.877195 AGAACAAATACTCCCTCTGTAACTTAA 58.123 33.333 0.00 0.00 0.00 1.85
1541 1596 9.668497 GAACAAATACTCCCTCTGTAACTTAAT 57.332 33.333 0.00 0.00 0.00 1.40
1549 1604 9.710818 ACTCCCTCTGTAACTTAATATAAGACA 57.289 33.333 4.24 0.00 0.00 3.41
1601 1656 8.862550 AAACGTCTTATATTAAGTTACGGAGG 57.137 34.615 11.01 0.00 33.44 4.30
1602 1657 6.974965 ACGTCTTATATTAAGTTACGGAGGG 58.025 40.000 11.01 0.00 33.44 4.30
1603 1658 6.772716 ACGTCTTATATTAAGTTACGGAGGGA 59.227 38.462 11.01 0.00 33.44 4.20
1604 1659 7.040823 ACGTCTTATATTAAGTTACGGAGGGAG 60.041 40.741 11.01 0.00 33.44 4.30
1605 1660 7.040823 CGTCTTATATTAAGTTACGGAGGGAGT 60.041 40.741 0.00 0.00 0.00 3.85
1606 1661 9.289782 GTCTTATATTAAGTTACGGAGGGAGTA 57.710 37.037 0.00 0.00 0.00 2.59
1612 1667 7.693969 TTAAGTTACGGAGGGAGTATATAGC 57.306 40.000 0.00 0.00 0.00 2.97
1613 1668 5.252586 AGTTACGGAGGGAGTATATAGCA 57.747 43.478 0.00 0.00 0.00 3.49
1614 1669 5.638133 AGTTACGGAGGGAGTATATAGCAA 58.362 41.667 0.00 0.00 0.00 3.91
1615 1670 5.711036 AGTTACGGAGGGAGTATATAGCAAG 59.289 44.000 0.00 0.00 0.00 4.01
1618 1673 3.444388 CGGAGGGAGTATATAGCAAGACC 59.556 52.174 0.00 0.00 0.00 3.85
1676 1731 6.146347 TGGCCAATTAAATTTTCTTTGCGTAC 59.854 34.615 0.61 0.00 0.00 3.67
1678 1733 7.148490 GGCCAATTAAATTTTCTTTGCGTACAT 60.148 33.333 0.00 0.00 0.00 2.29
1717 1772 6.040391 TGCAAATACCCAATGTTATAGAAGGC 59.960 38.462 0.00 0.00 0.00 4.35
1938 2029 9.388346 GAACTGTACAATCATAGACTAGAATCG 57.612 37.037 0.00 0.00 0.00 3.34
1940 2031 8.779303 ACTGTACAATCATAGACTAGAATCGAG 58.221 37.037 0.00 0.00 0.00 4.04
2092 2184 7.307493 TCTTGATCTTTAAACATCATCACCG 57.693 36.000 6.94 0.00 0.00 4.94
2136 2228 8.618240 TCCCTAATTAGGATTGACTTTGTAGA 57.382 34.615 29.75 12.43 46.63 2.59
2247 2339 2.165030 CCATGATGCAGGGACTTTTGAC 59.835 50.000 0.00 0.00 37.52 3.18
2329 2421 5.351948 AGGTTTGCATGTGTTTAAAAGGT 57.648 34.783 0.00 0.00 0.00 3.50
2881 3231 0.820891 CCAGGTGCATCATAGTGGCC 60.821 60.000 0.00 0.00 0.00 5.36
2902 3252 5.639082 GGCCTGTCATTTTACAAATTCCTTG 59.361 40.000 0.00 0.00 41.19 3.61
2936 3286 5.163612 CCAAACTTTTAGCTATTCCAGAGGC 60.164 44.000 0.00 0.00 0.00 4.70
2987 3337 7.320399 TCTTCTGAACTAACGCATTTCTCATA 58.680 34.615 0.00 0.00 0.00 2.15
2991 3341 8.414003 TCTGAACTAACGCATTTCTCATATAGT 58.586 33.333 0.00 0.00 0.00 2.12
3003 3353 6.502136 TTCTCATATAGTACTGCTGATCCG 57.498 41.667 5.39 0.00 0.00 4.18
3058 3408 4.630111 TGTGGCCTTGAAAACATCATTTC 58.370 39.130 3.32 0.00 38.03 2.17
3083 3433 2.640316 AAGGGCTTTTCGTGAGTCTT 57.360 45.000 0.00 0.00 0.00 3.01
3117 3467 4.710324 ACAACCTCTGTGAATTTCCGTTA 58.290 39.130 0.00 0.00 36.69 3.18
3127 3477 9.226606 TCTGTGAATTTCCGTTATCTATTTTGT 57.773 29.630 0.00 0.00 0.00 2.83
3153 3503 3.695830 ACCGAATGAAACTTAGCTCCA 57.304 42.857 0.00 0.00 0.00 3.86
3339 3689 6.237569 GCTTTTGATAACGCCTATTTCAAAGC 60.238 38.462 0.00 0.00 37.53 3.51
3371 3721 2.390599 CCACGGCCGACTTCATGTG 61.391 63.158 35.90 17.04 0.00 3.21
3375 3725 1.354337 CGGCCGACTTCATGTGAGTG 61.354 60.000 24.07 0.00 0.00 3.51
3380 3730 2.094894 CCGACTTCATGTGAGTGATTGC 59.905 50.000 8.80 0.00 0.00 3.56
3388 3738 6.769608 TCATGTGAGTGATTGCGATATTAC 57.230 37.500 0.00 0.00 0.00 1.89
3391 3741 5.610398 TGTGAGTGATTGCGATATTACCAT 58.390 37.500 0.00 0.00 0.00 3.55
3534 3886 9.751542 AAGGTATTCTATTGAAATAGACAGTCG 57.248 33.333 11.44 0.00 45.12 4.18
3540 3892 7.103641 TCTATTGAAATAGACAGTCGGCTTTT 58.896 34.615 8.39 0.00 41.71 2.27
3545 3897 6.932400 TGAAATAGACAGTCGGCTTTTCTTAA 59.068 34.615 11.27 0.00 0.00 1.85
3558 3910 7.771361 TCGGCTTTTCTTAACAATACATATCCA 59.229 33.333 0.00 0.00 0.00 3.41
3587 3942 6.180472 AGGGTTCATTCGACAAAGTTATGAT 58.820 36.000 0.00 0.00 0.00 2.45
3621 3976 4.174009 CAGATGATTTGGCTTGCTTCAAG 58.826 43.478 2.40 2.40 43.57 3.02
3623 3978 4.282703 AGATGATTTGGCTTGCTTCAAGTT 59.717 37.500 8.18 0.00 42.77 2.66
3635 3990 3.941483 TGCTTCAAGTTAGCCAGATAAGC 59.059 43.478 0.00 0.00 37.85 3.09
3650 4005 5.998553 CAGATAAGCTGGCTTACATGAATG 58.001 41.667 15.91 6.56 40.76 2.67
3679 4034 4.264895 ACTCAGAATAGTTCTAGGGGTGGT 60.265 45.833 0.00 0.00 38.11 4.16
3706 4061 7.543868 CCTAGCTTATAACATGCTGTAGATCAC 59.456 40.741 7.72 0.00 38.10 3.06
3805 4160 5.957798 ACAAGCACCAATGAATGAACATAG 58.042 37.500 0.00 0.00 0.00 2.23
3894 4250 1.680338 ACGCCAAATGGATCTTAGCC 58.320 50.000 2.98 0.00 37.39 3.93
3923 4279 4.034048 CCTTGCATATTTACGTCAGGTGAC 59.966 45.833 0.00 0.00 41.47 3.67
3942 4300 1.153489 CGGCCCACTGACATCAGAG 60.153 63.158 15.76 7.58 46.59 3.35
3943 4301 1.607801 CGGCCCACTGACATCAGAGA 61.608 60.000 15.76 0.00 46.59 3.10
3967 4325 2.584835 AAACTGCTTGCAGGTGGATA 57.415 45.000 23.98 0.00 0.00 2.59
4140 4498 1.916181 CAATAAGGAGGTGTCACCCCT 59.084 52.381 18.80 19.86 39.75 4.79
4141 4499 1.584724 ATAAGGAGGTGTCACCCCTG 58.415 55.000 24.66 0.00 39.75 4.45
4172 4531 4.577693 GCCTCTGAATCTATTGATGCACAA 59.422 41.667 0.00 0.00 42.95 3.33
4174 4533 6.726230 CCTCTGAATCTATTGATGCACAAAG 58.274 40.000 5.94 5.75 42.03 2.77
4198 4557 6.016276 AGCAAGTGTAAGATTCGTGGAAATTT 60.016 34.615 0.00 0.00 0.00 1.82
4200 4559 7.358352 GCAAGTGTAAGATTCGTGGAAATTTTG 60.358 37.037 0.00 0.00 0.00 2.44
4202 4561 7.360361 AGTGTAAGATTCGTGGAAATTTTGTC 58.640 34.615 0.00 0.00 0.00 3.18
4217 4576 4.365514 TTTTGTCTGCTCATTCCCTGTA 57.634 40.909 0.00 0.00 0.00 2.74
4219 4578 5.692115 TTTGTCTGCTCATTCCCTGTATA 57.308 39.130 0.00 0.00 0.00 1.47
4220 4579 5.894298 TTGTCTGCTCATTCCCTGTATAT 57.106 39.130 0.00 0.00 0.00 0.86
4221 4580 5.894298 TGTCTGCTCATTCCCTGTATATT 57.106 39.130 0.00 0.00 0.00 1.28
4222 4581 5.614308 TGTCTGCTCATTCCCTGTATATTG 58.386 41.667 0.00 0.00 0.00 1.90
4223 4582 4.453819 GTCTGCTCATTCCCTGTATATTGC 59.546 45.833 0.00 0.00 0.00 3.56
4224 4583 4.349048 TCTGCTCATTCCCTGTATATTGCT 59.651 41.667 0.00 0.00 0.00 3.91
4225 4584 5.052693 TGCTCATTCCCTGTATATTGCTT 57.947 39.130 0.00 0.00 0.00 3.91
4226 4585 5.448654 TGCTCATTCCCTGTATATTGCTTT 58.551 37.500 0.00 0.00 0.00 3.51
4227 4586 5.300034 TGCTCATTCCCTGTATATTGCTTTG 59.700 40.000 0.00 0.00 0.00 2.77
4228 4587 5.278660 GCTCATTCCCTGTATATTGCTTTGG 60.279 44.000 0.00 0.00 0.00 3.28
4229 4588 4.584325 TCATTCCCTGTATATTGCTTTGGC 59.416 41.667 0.00 0.00 39.26 4.52
4230 4589 3.951563 TCCCTGTATATTGCTTTGGCT 57.048 42.857 0.00 0.00 39.59 4.75
4231 4590 3.820557 TCCCTGTATATTGCTTTGGCTC 58.179 45.455 0.00 0.00 39.59 4.70
4256 4615 6.503524 GTTTGGAGCTCAGAAAATTTGTACA 58.496 36.000 17.19 0.00 0.00 2.90
4262 4621 8.084684 GGAGCTCAGAAAATTTGTACAGAAAAT 58.915 33.333 17.19 0.00 0.00 1.82
4281 4640 8.621286 CAGAAAATAAACTACAGTTTGTCTGGT 58.379 33.333 15.87 0.00 46.56 4.00
4307 4666 0.747283 ACGGATCGACCTAGCGTTCT 60.747 55.000 0.00 0.00 36.31 3.01
4327 4686 4.695014 TGCTGGGGCAGAAAACAA 57.305 50.000 0.00 0.00 44.28 2.83
4328 4687 2.907703 TGCTGGGGCAGAAAACAAA 58.092 47.368 0.00 0.00 44.28 2.83
4329 4688 0.463620 TGCTGGGGCAGAAAACAAAC 59.536 50.000 0.00 0.00 44.28 2.93
4330 4689 0.752658 GCTGGGGCAGAAAACAAACT 59.247 50.000 0.00 0.00 38.54 2.66
4331 4690 1.960689 GCTGGGGCAGAAAACAAACTA 59.039 47.619 0.00 0.00 38.54 2.24
4332 4691 2.288213 GCTGGGGCAGAAAACAAACTAC 60.288 50.000 0.00 0.00 38.54 2.73
4333 4692 2.955660 CTGGGGCAGAAAACAAACTACA 59.044 45.455 0.00 0.00 32.44 2.74
4334 4693 2.955660 TGGGGCAGAAAACAAACTACAG 59.044 45.455 0.00 0.00 0.00 2.74
4335 4694 2.956333 GGGGCAGAAAACAAACTACAGT 59.044 45.455 0.00 0.00 0.00 3.55
4336 4695 3.383505 GGGGCAGAAAACAAACTACAGTT 59.616 43.478 0.00 0.00 40.50 3.16
4337 4696 8.298349 CTGGGGCAGAAAACAAACTACAGTTT 62.298 42.308 1.47 1.47 40.14 2.66
4396 4755 3.576078 TTCCAGACTGAACAATGTGGT 57.424 42.857 3.32 0.00 0.00 4.16
4397 4756 4.698201 TTCCAGACTGAACAATGTGGTA 57.302 40.909 3.32 0.00 0.00 3.25
4399 4758 4.641396 TCCAGACTGAACAATGTGGTAAG 58.359 43.478 3.32 0.00 0.00 2.34
4418 4783 1.112950 GGGGTACGAGAGGAAGGAAG 58.887 60.000 0.00 0.00 0.00 3.46
4432 4797 3.304458 GGAAGGAAGTGGTTAAAGTTGCG 60.304 47.826 0.00 0.00 0.00 4.85
4446 4839 7.642586 GGTTAAAGTTGCGGTAATGCTATTAAG 59.357 37.037 0.00 0.00 35.36 1.85
4456 4849 7.448228 CGGTAATGCTATTAAGATGATGTTCG 58.552 38.462 0.00 0.00 0.00 3.95
4482 4875 3.006752 GGCAGGGATGACAAATCAAACAA 59.993 43.478 0.00 0.00 38.69 2.83
4508 4901 7.979115 TTTTTATGGCAGTTTATATTGTCGC 57.021 32.000 0.00 0.00 0.00 5.19
4510 4903 1.937223 TGGCAGTTTATATTGTCGCGG 59.063 47.619 6.13 0.00 0.00 6.46
4520 4913 0.322997 ATTGTCGCGGGGATGGAAAA 60.323 50.000 6.13 0.00 0.00 2.29
4523 4916 0.815095 GTCGCGGGGATGGAAAATTT 59.185 50.000 6.13 0.00 0.00 1.82
4524 4917 2.018515 GTCGCGGGGATGGAAAATTTA 58.981 47.619 6.13 0.00 0.00 1.40
4525 4918 2.032924 GTCGCGGGGATGGAAAATTTAG 59.967 50.000 6.13 0.00 0.00 1.85
4527 4920 2.425668 CGCGGGGATGGAAAATTTAGTT 59.574 45.455 0.00 0.00 0.00 2.24
4528 4921 3.119280 CGCGGGGATGGAAAATTTAGTTT 60.119 43.478 0.00 0.00 0.00 2.66
4567 4960 8.868522 ATCCTGACAAATAACTGAATTGAAGA 57.131 30.769 0.00 0.00 0.00 2.87
4568 4961 8.690203 TCCTGACAAATAACTGAATTGAAGAA 57.310 30.769 0.00 0.00 0.00 2.52
4589 4982 4.978083 AGATTTGCCATGCTTGTCTAAG 57.022 40.909 0.00 0.00 36.97 2.18
4603 4996 6.406093 CTTGTCTAAGCTTGTCATTCTCAG 57.594 41.667 9.86 0.00 0.00 3.35
4605 4998 3.620821 GTCTAAGCTTGTCATTCTCAGCC 59.379 47.826 9.86 0.00 0.00 4.85
4634 5027 3.802722 TTGCAATGCAAATTTTACCGC 57.197 38.095 19.21 0.00 45.96 5.68
4661 5054 3.257933 GCTTCCCAGCTGACGTTG 58.742 61.111 17.39 0.00 43.51 4.10
4663 5056 1.371183 CTTCCCAGCTGACGTTGGA 59.629 57.895 17.39 10.14 43.57 3.53
4729 5122 1.994779 CGGAATTGCAGTGCCAAAATC 59.005 47.619 13.72 3.68 0.00 2.17
4745 5138 5.682212 GCCAAAATCCCGCTCAAATTTATCT 60.682 40.000 0.00 0.00 0.00 1.98
4778 5175 2.202797 CTGACGGGCGGACATGAG 60.203 66.667 0.00 0.00 0.00 2.90
4865 5267 1.471964 GAGTGATTAGCGCAGAGACG 58.528 55.000 11.47 0.00 0.00 4.18
4918 5320 4.711949 AGTGGCTGGCTCCGCTTG 62.712 66.667 2.00 0.00 44.01 4.01
4942 5369 0.252421 TGAGCCCTCTGTCACTCCAT 60.252 55.000 0.00 0.00 0.00 3.41
4949 5376 2.174360 CTCTGTCACTCCATGAGTCCA 58.826 52.381 0.00 0.00 41.37 4.02
4952 5379 2.235650 CTGTCACTCCATGAGTCCATGT 59.764 50.000 0.00 0.00 46.68 3.21
4953 5380 2.234661 TGTCACTCCATGAGTCCATGTC 59.765 50.000 0.00 0.00 46.68 3.06
4954 5381 1.833630 TCACTCCATGAGTCCATGTCC 59.166 52.381 0.00 0.00 46.68 4.02
4955 5382 1.556451 CACTCCATGAGTCCATGTCCA 59.444 52.381 0.00 0.00 46.68 4.02
4956 5383 2.172082 CACTCCATGAGTCCATGTCCAT 59.828 50.000 0.00 0.00 46.68 3.41
4957 5384 2.172082 ACTCCATGAGTCCATGTCCATG 59.828 50.000 0.00 0.14 46.68 3.66
4958 5385 2.436911 CTCCATGAGTCCATGTCCATGA 59.563 50.000 8.82 0.00 46.68 3.07
4976 5403 2.240612 GAACAGGTAAAGCCGCTGCG 62.241 60.000 16.34 16.34 44.33 5.18
4984 5411 2.167398 AAAGCCGCTGCGTCCTAGAA 62.167 55.000 21.59 0.00 44.33 2.10
5045 5472 2.364317 CCTCCTTCCTCCTCGCCA 60.364 66.667 0.00 0.00 0.00 5.69
5063 5490 0.250727 CAGACACCAACCATTCCCGT 60.251 55.000 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.158099 AGTCAAAGTTTACAAAGCTTGACTT 57.842 32.000 17.55 3.36 42.47 3.01
2 3 6.759497 AGTCAAAGTTTACAAAGCTTGACT 57.241 33.333 17.55 17.55 41.47 3.41
3 4 8.182227 ACTTAGTCAAAGTTTACAAAGCTTGAC 58.818 33.333 0.00 14.97 46.61 3.18
4 5 8.276252 ACTTAGTCAAAGTTTACAAAGCTTGA 57.724 30.769 0.00 0.00 46.61 3.02
138 139 9.823647 TGCAAAGTTTGACCAAATTTATAGAAA 57.176 25.926 19.82 0.00 31.37 2.52
139 140 9.823647 TTGCAAAGTTTGACCAAATTTATAGAA 57.176 25.926 19.82 0.00 31.37 2.10
140 141 9.823647 TTTGCAAAGTTTGACCAAATTTATAGA 57.176 25.926 19.82 0.00 31.37 1.98
142 143 9.606631 ACTTTGCAAAGTTTGACCAAATTTATA 57.393 25.926 33.85 0.00 46.52 0.98
143 144 8.504812 ACTTTGCAAAGTTTGACCAAATTTAT 57.495 26.923 33.85 10.04 46.52 1.40
144 145 7.913674 ACTTTGCAAAGTTTGACCAAATTTA 57.086 28.000 33.85 0.00 46.52 1.40
145 146 6.816134 ACTTTGCAAAGTTTGACCAAATTT 57.184 29.167 33.85 11.08 46.52 1.82
156 157 6.128842 GACCGAAGTCAAACTTTGCAAAGTT 61.129 40.000 39.24 39.24 45.31 2.66
157 158 4.674362 GACCGAAGTCAAACTTTGCAAAGT 60.674 41.667 33.85 33.85 45.47 2.66
158 159 3.769536 ACCGAAGTCAAACTTTGCAAAG 58.230 40.909 32.53 32.53 38.80 2.77
159 160 3.765026 GACCGAAGTCAAACTTTGCAAA 58.235 40.909 12.14 12.14 38.80 3.68
160 161 3.414549 GACCGAAGTCAAACTTTGCAA 57.585 42.857 0.00 0.00 38.80 4.08
171 172 4.873827 TGCATATTAGGTTTGACCGAAGTC 59.126 41.667 0.00 0.00 44.90 3.01
172 173 4.839121 TGCATATTAGGTTTGACCGAAGT 58.161 39.130 0.00 0.00 44.90 3.01
173 174 5.006746 GTCTGCATATTAGGTTTGACCGAAG 59.993 44.000 0.00 0.00 44.90 3.79
174 175 4.873827 GTCTGCATATTAGGTTTGACCGAA 59.126 41.667 0.00 0.00 44.90 4.30
175 176 4.161565 AGTCTGCATATTAGGTTTGACCGA 59.838 41.667 0.00 0.00 44.90 4.69
176 177 4.271049 CAGTCTGCATATTAGGTTTGACCG 59.729 45.833 0.00 0.00 44.90 4.79
177 178 5.428253 TCAGTCTGCATATTAGGTTTGACC 58.572 41.667 0.00 0.00 38.99 4.02
178 179 6.985188 TTCAGTCTGCATATTAGGTTTGAC 57.015 37.500 0.00 0.00 0.00 3.18
179 180 9.679661 TTTATTCAGTCTGCATATTAGGTTTGA 57.320 29.630 0.00 0.00 0.00 2.69
183 184 8.612619 CGTTTTTATTCAGTCTGCATATTAGGT 58.387 33.333 0.00 0.00 0.00 3.08
184 185 8.070171 CCGTTTTTATTCAGTCTGCATATTAGG 58.930 37.037 0.00 0.00 0.00 2.69
185 186 8.826710 TCCGTTTTTATTCAGTCTGCATATTAG 58.173 33.333 0.00 0.00 0.00 1.73
186 187 8.725405 TCCGTTTTTATTCAGTCTGCATATTA 57.275 30.769 0.00 0.00 0.00 0.98
187 188 7.201732 CCTCCGTTTTTATTCAGTCTGCATATT 60.202 37.037 0.00 0.00 0.00 1.28
188 189 6.260936 CCTCCGTTTTTATTCAGTCTGCATAT 59.739 38.462 0.00 0.00 0.00 1.78
189 190 5.584649 CCTCCGTTTTTATTCAGTCTGCATA 59.415 40.000 0.00 0.00 0.00 3.14
190 191 4.396166 CCTCCGTTTTTATTCAGTCTGCAT 59.604 41.667 0.00 0.00 0.00 3.96
191 192 3.751175 CCTCCGTTTTTATTCAGTCTGCA 59.249 43.478 0.00 0.00 0.00 4.41
192 193 3.127030 CCCTCCGTTTTTATTCAGTCTGC 59.873 47.826 0.00 0.00 0.00 4.26
193 194 4.575885 TCCCTCCGTTTTTATTCAGTCTG 58.424 43.478 0.00 0.00 0.00 3.51
194 195 4.286291 ACTCCCTCCGTTTTTATTCAGTCT 59.714 41.667 0.00 0.00 0.00 3.24
195 196 4.576879 ACTCCCTCCGTTTTTATTCAGTC 58.423 43.478 0.00 0.00 0.00 3.51
196 197 4.635699 ACTCCCTCCGTTTTTATTCAGT 57.364 40.909 0.00 0.00 0.00 3.41
197 198 7.625828 AAATACTCCCTCCGTTTTTATTCAG 57.374 36.000 0.00 0.00 0.00 3.02
198 199 9.689501 AATAAATACTCCCTCCGTTTTTATTCA 57.310 29.630 0.00 0.00 35.52 2.57
203 204 9.828039 CTACTAATAAATACTCCCTCCGTTTTT 57.172 33.333 0.00 0.00 0.00 1.94
204 205 7.930325 GCTACTAATAAATACTCCCTCCGTTTT 59.070 37.037 0.00 0.00 0.00 2.43
205 206 7.289549 AGCTACTAATAAATACTCCCTCCGTTT 59.710 37.037 0.00 0.00 0.00 3.60
206 207 6.781507 AGCTACTAATAAATACTCCCTCCGTT 59.218 38.462 0.00 0.00 0.00 4.44
207 208 6.313324 AGCTACTAATAAATACTCCCTCCGT 58.687 40.000 0.00 0.00 0.00 4.69
208 209 6.660094 AGAGCTACTAATAAATACTCCCTCCG 59.340 42.308 0.00 0.00 0.00 4.63
209 210 7.670559 TCAGAGCTACTAATAAATACTCCCTCC 59.329 40.741 0.00 0.00 0.00 4.30
210 211 8.638629 TCAGAGCTACTAATAAATACTCCCTC 57.361 38.462 0.00 0.00 0.00 4.30
211 212 7.672239 CCTCAGAGCTACTAATAAATACTCCCT 59.328 40.741 0.00 0.00 0.00 4.20
212 213 7.670559 TCCTCAGAGCTACTAATAAATACTCCC 59.329 40.741 0.00 0.00 0.00 4.30
213 214 8.517056 GTCCTCAGAGCTACTAATAAATACTCC 58.483 40.741 0.00 0.00 0.00 3.85
214 215 8.231837 CGTCCTCAGAGCTACTAATAAATACTC 58.768 40.741 0.00 0.00 0.00 2.59
258 259 7.159372 CGGGCTTACATAAATAGGTTACAGAT 58.841 38.462 0.00 0.00 0.00 2.90
309 313 7.366847 AGTTCTCTGCTGTAATATACATGGT 57.633 36.000 0.00 0.00 38.15 3.55
405 415 6.931838 AGTTTACTTATAAAAGCAAAGGGCC 58.068 36.000 0.00 0.00 46.50 5.80
425 437 3.142174 GACAGGAGCAAAGCAGTAGTTT 58.858 45.455 0.00 0.00 0.00 2.66
426 438 2.104792 TGACAGGAGCAAAGCAGTAGTT 59.895 45.455 0.00 0.00 0.00 2.24
481 493 5.533903 AGCAGTCATTTTCACAGAACAAGAT 59.466 36.000 0.00 0.00 0.00 2.40
619 633 8.650714 GCCTCTGAAAATTAACATCACAAAATC 58.349 33.333 0.00 0.00 0.00 2.17
646 663 7.759433 CCATAACAAAGTATGGTCAATGTTTCC 59.241 37.037 3.50 0.00 43.84 3.13
712 733 3.995048 TGTGTTTTATGTTCGCCGTGATA 59.005 39.130 0.00 0.00 0.00 2.15
731 752 6.808008 ATAGATTTTGAGGTGTTGACTGTG 57.192 37.500 0.00 0.00 0.00 3.66
763 784 4.248859 CTCCCACACTTGTTATCTCTGTG 58.751 47.826 0.00 0.00 33.45 3.66
768 789 4.974645 TGAACTCCCACACTTGTTATCT 57.025 40.909 0.00 0.00 0.00 1.98
790 811 5.989477 TGTAGTGCTGTAAGAATATGCCTT 58.011 37.500 0.00 0.00 34.07 4.35
859 887 4.087892 CCAGCAGACGGTCCCCAG 62.088 72.222 4.14 0.00 0.00 4.45
871 900 1.148273 GTCTGTGTGGTTCCCAGCA 59.852 57.895 0.00 0.00 32.34 4.41
897 928 2.023888 AGTCAGCCTATCTACACCTGGT 60.024 50.000 0.00 0.00 0.00 4.00
904 935 4.215399 CAGCTCACTAGTCAGCCTATCTAC 59.785 50.000 15.87 0.00 36.17 2.59
905 936 4.141367 ACAGCTCACTAGTCAGCCTATCTA 60.141 45.833 15.87 0.00 36.17 1.98
970 1001 1.421382 CTTGCCTTGTTTGAATGCCG 58.579 50.000 0.00 0.00 0.00 5.69
987 1018 1.914798 AGCTCCATCTTCTTCCTGCTT 59.085 47.619 0.00 0.00 0.00 3.91
997 1028 2.356535 GGATGTTGGTGAGCTCCATCTT 60.357 50.000 21.65 9.23 37.33 2.40
998 1029 1.211457 GGATGTTGGTGAGCTCCATCT 59.789 52.381 21.65 1.71 37.33 2.90
1060 1091 0.732571 AGGCGATGCAAACATTACCG 59.267 50.000 0.00 0.00 36.35 4.02
1126 1175 4.322349 CCCTGTTCTTCTTCTACTCCTGTG 60.322 50.000 0.00 0.00 0.00 3.66
1146 1195 1.207791 CTGTTATCACAGCCCTCCCT 58.792 55.000 0.00 0.00 44.16 4.20
1249 1304 0.455410 TTAGCCATGAAATGCGCCAC 59.545 50.000 4.18 0.00 44.97 5.01
1301 1356 1.129251 CAGCAATGCGTCGATGTTCTT 59.871 47.619 6.48 0.00 0.00 2.52
1334 1389 5.165961 TCTCTTTGTACAGATTCCCCAAG 57.834 43.478 0.00 0.00 0.00 3.61
1352 1407 7.753309 ATACTCATTATCAGCTACGTTCTCT 57.247 36.000 0.00 0.00 0.00 3.10
1361 1416 6.014156 GGTGGGAAGTATACTCATTATCAGCT 60.014 42.308 5.70 0.00 0.00 4.24
1384 1439 5.337788 AGTCTCAATCCTCAAACTCTAGGT 58.662 41.667 0.00 0.00 34.30 3.08
1462 1517 9.436957 GTTTATTGTGTGAGAGAATAGAGGAAA 57.563 33.333 0.00 0.00 0.00 3.13
1463 1518 8.816894 AGTTTATTGTGTGAGAGAATAGAGGAA 58.183 33.333 0.00 0.00 0.00 3.36
1464 1519 8.367660 AGTTTATTGTGTGAGAGAATAGAGGA 57.632 34.615 0.00 0.00 0.00 3.71
1465 1520 8.877779 CAAGTTTATTGTGTGAGAGAATAGAGG 58.122 37.037 0.00 0.00 0.00 3.69
1466 1521 9.429359 ACAAGTTTATTGTGTGAGAGAATAGAG 57.571 33.333 0.00 0.00 0.00 2.43
1515 1570 9.668497 ATTAAGTTACAGAGGGAGTATTTGTTC 57.332 33.333 0.00 0.00 0.00 3.18
1551 1606 3.628032 TGGCACTATCGTTGTGTCAAAAA 59.372 39.130 9.23 0.00 45.40 1.94
1552 1607 3.206964 TGGCACTATCGTTGTGTCAAAA 58.793 40.909 9.23 0.00 45.40 2.44
1553 1608 2.839975 TGGCACTATCGTTGTGTCAAA 58.160 42.857 9.23 0.00 45.40 2.69
1554 1609 2.535012 TGGCACTATCGTTGTGTCAA 57.465 45.000 9.23 0.00 45.40 3.18
1555 1610 2.535012 TTGGCACTATCGTTGTGTCA 57.465 45.000 7.99 7.99 46.48 3.58
1556 1611 3.889196 TTTTGGCACTATCGTTGTGTC 57.111 42.857 0.00 0.00 40.12 3.67
1575 1630 9.305925 CCTCCGTAACTTAATATAAGACGTTTT 57.694 33.333 4.24 0.00 0.00 2.43
1576 1631 7.922811 CCCTCCGTAACTTAATATAAGACGTTT 59.077 37.037 4.24 0.00 0.00 3.60
1577 1632 7.285401 TCCCTCCGTAACTTAATATAAGACGTT 59.715 37.037 4.24 0.00 0.00 3.99
1578 1633 6.772716 TCCCTCCGTAACTTAATATAAGACGT 59.227 38.462 4.24 0.00 0.00 4.34
1579 1634 7.040823 ACTCCCTCCGTAACTTAATATAAGACG 60.041 40.741 4.24 4.71 0.00 4.18
1580 1635 8.175925 ACTCCCTCCGTAACTTAATATAAGAC 57.824 38.462 4.24 0.00 0.00 3.01
1586 1641 9.401058 GCTATATACTCCCTCCGTAACTTAATA 57.599 37.037 0.00 0.00 0.00 0.98
1587 1642 7.892241 TGCTATATACTCCCTCCGTAACTTAAT 59.108 37.037 0.00 0.00 0.00 1.40
1588 1643 7.233632 TGCTATATACTCCCTCCGTAACTTAA 58.766 38.462 0.00 0.00 0.00 1.85
1589 1644 6.782986 TGCTATATACTCCCTCCGTAACTTA 58.217 40.000 0.00 0.00 0.00 2.24
1590 1645 5.638133 TGCTATATACTCCCTCCGTAACTT 58.362 41.667 0.00 0.00 0.00 2.66
1591 1646 5.252586 TGCTATATACTCCCTCCGTAACT 57.747 43.478 0.00 0.00 0.00 2.24
1592 1647 5.709164 TCTTGCTATATACTCCCTCCGTAAC 59.291 44.000 0.00 0.00 0.00 2.50
1593 1648 5.709164 GTCTTGCTATATACTCCCTCCGTAA 59.291 44.000 0.00 0.00 0.00 3.18
1594 1649 5.251764 GTCTTGCTATATACTCCCTCCGTA 58.748 45.833 0.00 0.00 0.00 4.02
1595 1650 4.080687 GTCTTGCTATATACTCCCTCCGT 58.919 47.826 0.00 0.00 0.00 4.69
1596 1651 3.444388 GGTCTTGCTATATACTCCCTCCG 59.556 52.174 0.00 0.00 0.00 4.63
1597 1652 4.417437 TGGTCTTGCTATATACTCCCTCC 58.583 47.826 0.00 0.00 0.00 4.30
1598 1653 5.775701 TCTTGGTCTTGCTATATACTCCCTC 59.224 44.000 0.00 0.00 0.00 4.30
1599 1654 5.716979 TCTTGGTCTTGCTATATACTCCCT 58.283 41.667 0.00 0.00 0.00 4.20
1600 1655 6.420913 TTCTTGGTCTTGCTATATACTCCC 57.579 41.667 0.00 0.00 0.00 4.30
1601 1656 8.910351 AAATTCTTGGTCTTGCTATATACTCC 57.090 34.615 0.00 0.00 0.00 3.85
1606 1661 8.907885 GGAAGAAAATTCTTGGTCTTGCTATAT 58.092 33.333 12.85 0.00 46.84 0.86
1607 1662 7.888021 TGGAAGAAAATTCTTGGTCTTGCTATA 59.112 33.333 12.85 0.00 46.84 1.31
1608 1663 6.721208 TGGAAGAAAATTCTTGGTCTTGCTAT 59.279 34.615 12.85 0.00 46.84 2.97
1609 1664 6.068010 TGGAAGAAAATTCTTGGTCTTGCTA 58.932 36.000 12.85 0.00 46.84 3.49
1610 1665 4.895297 TGGAAGAAAATTCTTGGTCTTGCT 59.105 37.500 12.85 0.00 46.84 3.91
1611 1666 5.200368 TGGAAGAAAATTCTTGGTCTTGC 57.800 39.130 12.85 2.18 46.84 4.01
1612 1667 6.264067 AGACTGGAAGAAAATTCTTGGTCTTG 59.736 38.462 12.85 1.30 46.84 3.02
1613 1668 6.264067 CAGACTGGAAGAAAATTCTTGGTCTT 59.736 38.462 20.62 5.68 46.84 3.01
1614 1669 5.767168 CAGACTGGAAGAAAATTCTTGGTCT 59.233 40.000 12.85 16.83 46.84 3.85
1615 1670 5.563671 GCAGACTGGAAGAAAATTCTTGGTC 60.564 44.000 12.85 15.31 46.84 4.02
1618 1673 5.702349 AGCAGACTGGAAGAAAATTCTTG 57.298 39.130 12.85 2.27 46.84 3.02
1676 1731 1.751927 GCAGGACCTGAGGCCAATG 60.752 63.158 26.25 5.97 32.44 2.82
1678 1733 2.005606 TTTGCAGGACCTGAGGCCAA 62.006 55.000 26.25 15.92 32.44 4.52
1717 1772 1.068748 AGCAACAGCAGCAAAATCTCG 60.069 47.619 0.00 0.00 0.00 4.04
1788 1843 9.376075 CATAGGAATGTAATAGTGGCTGAATAG 57.624 37.037 0.00 0.00 0.00 1.73
1881 1972 6.839124 TGACCATAAAGAAAATGCTCACAT 57.161 33.333 0.00 0.00 38.49 3.21
1938 2029 5.717178 TGCCTATGATCCACTTCCTATACTC 59.283 44.000 0.00 0.00 0.00 2.59
1940 2031 6.360370 TTGCCTATGATCCACTTCCTATAC 57.640 41.667 0.00 0.00 0.00 1.47
1945 2036 4.090761 TGATTGCCTATGATCCACTTCC 57.909 45.455 0.00 0.00 0.00 3.46
2092 2184 5.495640 AGGGAACTTCTTTGAGATCATCAC 58.504 41.667 0.00 0.00 37.44 3.06
2136 2228 5.820404 TTGATCCATCATATGAGTCAGCT 57.180 39.130 11.78 0.00 36.56 4.24
2881 3231 6.128742 GCTGCAAGGAATTTGTAAAATGACAG 60.129 38.462 0.00 0.00 39.08 3.51
2902 3252 5.230182 AGCTAAAAGTTTGGTTAATGCTGC 58.770 37.500 0.00 0.00 0.00 5.25
2936 3286 6.422776 AATGACAAGCACTAAATAGGAACG 57.577 37.500 0.00 0.00 0.00 3.95
2987 3337 1.880675 CGGTCGGATCAGCAGTACTAT 59.119 52.381 0.00 0.00 0.00 2.12
2991 3341 0.107066 TACCGGTCGGATCAGCAGTA 60.107 55.000 12.40 0.00 38.96 2.74
3003 3353 3.672767 TCTTCAGGAAGTTTACCGGTC 57.327 47.619 12.40 0.00 39.38 4.79
3058 3408 0.852136 CACGAAAAGCCCTTTTTGCG 59.148 50.000 16.79 13.74 44.05 4.85
3083 3433 3.509575 ACAGAGGTTGTTGAACAAAAGCA 59.490 39.130 12.89 0.00 40.15 3.91
3127 3477 8.644216 TGGAGCTAAGTTTCATTCGGTAATATA 58.356 33.333 0.00 0.00 0.00 0.86
3128 3478 7.506114 TGGAGCTAAGTTTCATTCGGTAATAT 58.494 34.615 0.00 0.00 0.00 1.28
3136 3486 3.127721 GCCACTGGAGCTAAGTTTCATTC 59.872 47.826 0.00 0.00 0.00 2.67
3339 3689 0.671781 CCGTGGCTTCTCAAGGAGTG 60.672 60.000 0.00 0.00 38.32 3.51
3371 3721 6.974932 ATGATGGTAATATCGCAATCACTC 57.025 37.500 0.30 0.00 0.00 3.51
3375 3725 5.882557 AGGGAATGATGGTAATATCGCAATC 59.117 40.000 0.00 0.00 0.00 2.67
3388 3738 5.339423 AGGGGTATTAAAGGGAATGATGG 57.661 43.478 0.00 0.00 0.00 3.51
3391 3741 9.207868 CAAATTAAGGGGTATTAAAGGGAATGA 57.792 33.333 0.00 0.00 0.00 2.57
3524 3876 5.790593 TGTTAAGAAAAGCCGACTGTCTAT 58.209 37.500 6.21 0.00 0.00 1.98
3525 3877 5.204409 TGTTAAGAAAAGCCGACTGTCTA 57.796 39.130 6.21 0.00 0.00 2.59
3558 3910 9.847224 ATAACTTTGTCGAATGAACCCTAATAT 57.153 29.630 0.00 0.00 0.00 1.28
3560 3912 7.827236 TCATAACTTTGTCGAATGAACCCTAAT 59.173 33.333 0.00 0.00 0.00 1.73
3573 3925 7.095857 GGCTCTAAGATGATCATAACTTTGTCG 60.096 40.741 8.54 7.07 0.00 4.35
3615 3970 5.731599 CAGCTTATCTGGCTAACTTGAAG 57.268 43.478 0.00 0.00 39.15 3.02
3627 3982 5.048921 CCATTCATGTAAGCCAGCTTATCTG 60.049 44.000 14.75 14.13 40.18 2.90
3635 3990 6.150976 TGAGTTTTACCATTCATGTAAGCCAG 59.849 38.462 0.00 0.00 0.00 4.85
3643 3998 9.994432 GAACTATTCTGAGTTTTACCATTCATG 57.006 33.333 0.00 0.00 39.79 3.07
3650 4005 7.092979 ACCCCTAGAACTATTCTGAGTTTTACC 60.093 40.741 1.26 0.00 39.79 2.85
3706 4061 6.583806 GCAAATGGTGTTTAGAAGATTGTGAG 59.416 38.462 0.00 0.00 0.00 3.51
3798 4153 4.507710 TCAGTCAGATGGCAACTATGTTC 58.492 43.478 0.00 0.00 37.61 3.18
3805 4160 4.293415 CAAAAGTTCAGTCAGATGGCAAC 58.707 43.478 0.00 0.00 0.00 4.17
3869 4225 4.497291 AAGATCCATTTGGCGTAGGTTA 57.503 40.909 0.00 0.00 34.44 2.85
3894 4250 6.692681 CCTGACGTAAATATGCAAGGAAAATG 59.307 38.462 0.00 0.00 0.00 2.32
3923 4279 2.124983 CTGATGTCAGTGGGCCGG 60.125 66.667 0.00 0.00 39.09 6.13
3942 4300 2.031682 CACCTGCAAGCAGTTTAGTGTC 60.032 50.000 19.60 0.00 42.15 3.67
3943 4301 1.949525 CACCTGCAAGCAGTTTAGTGT 59.050 47.619 19.60 7.34 42.15 3.55
3967 4325 2.296471 CTGGTCCTCCGCGTAGATATTT 59.704 50.000 4.92 0.00 36.30 1.40
4113 4471 5.300792 GGTGACACCTCCTTATTGACAAAAA 59.699 40.000 17.84 0.00 34.73 1.94
4114 4472 4.825085 GGTGACACCTCCTTATTGACAAAA 59.175 41.667 17.84 0.00 34.73 2.44
4115 4473 4.394729 GGTGACACCTCCTTATTGACAAA 58.605 43.478 17.84 0.00 34.73 2.83
4116 4474 3.244770 GGGTGACACCTCCTTATTGACAA 60.245 47.826 23.72 0.00 38.64 3.18
4117 4475 2.304761 GGGTGACACCTCCTTATTGACA 59.695 50.000 23.72 0.00 38.64 3.58
4172 4531 4.002906 TCCACGAATCTTACACTTGCTT 57.997 40.909 0.00 0.00 0.00 3.91
4174 4533 4.742438 TTTCCACGAATCTTACACTTGC 57.258 40.909 0.00 0.00 0.00 4.01
4198 4557 5.894298 ATATACAGGGAATGAGCAGACAA 57.106 39.130 0.00 0.00 0.00 3.18
4200 4559 4.453819 GCAATATACAGGGAATGAGCAGAC 59.546 45.833 0.00 0.00 0.00 3.51
4202 4561 4.649692 AGCAATATACAGGGAATGAGCAG 58.350 43.478 0.00 0.00 0.00 4.24
4217 4576 3.088532 TCCAAACGAGCCAAAGCAATAT 58.911 40.909 0.00 0.00 43.56 1.28
4219 4578 1.270550 CTCCAAACGAGCCAAAGCAAT 59.729 47.619 0.00 0.00 43.56 3.56
4220 4579 0.667993 CTCCAAACGAGCCAAAGCAA 59.332 50.000 0.00 0.00 43.56 3.91
4221 4580 2.330254 CTCCAAACGAGCCAAAGCA 58.670 52.632 0.00 0.00 43.56 3.91
4229 4588 4.756084 AATTTTCTGAGCTCCAAACGAG 57.244 40.909 12.15 0.13 42.04 4.18
4230 4589 4.338118 ACAAATTTTCTGAGCTCCAAACGA 59.662 37.500 12.15 0.00 0.00 3.85
4231 4590 4.610945 ACAAATTTTCTGAGCTCCAAACG 58.389 39.130 12.15 3.54 0.00 3.60
4256 4615 8.747538 ACCAGACAAACTGTAGTTTATTTTCT 57.252 30.769 9.47 6.89 45.54 2.52
4262 4621 6.017440 GCATGAACCAGACAAACTGTAGTTTA 60.017 38.462 9.47 0.00 45.54 2.01
4270 4629 1.603802 CGTGCATGAACCAGACAAACT 59.396 47.619 0.00 0.00 0.00 2.66
4281 4640 1.067060 CTAGGTCGATCCGTGCATGAA 59.933 52.381 7.72 0.00 41.99 2.57
4327 4686 3.613030 ACGGACCAAACAAACTGTAGTT 58.387 40.909 0.00 0.00 40.50 2.24
4328 4687 3.271055 ACGGACCAAACAAACTGTAGT 57.729 42.857 0.00 0.00 0.00 2.73
4329 4688 4.625972 AAACGGACCAAACAAACTGTAG 57.374 40.909 0.00 0.00 0.00 2.74
4330 4689 4.217983 ACAAAACGGACCAAACAAACTGTA 59.782 37.500 0.00 0.00 0.00 2.74
4331 4690 3.006003 ACAAAACGGACCAAACAAACTGT 59.994 39.130 0.00 0.00 0.00 3.55
4332 4691 3.580731 ACAAAACGGACCAAACAAACTG 58.419 40.909 0.00 0.00 0.00 3.16
4333 4692 3.945981 ACAAAACGGACCAAACAAACT 57.054 38.095 0.00 0.00 0.00 2.66
4334 4693 3.988517 TCAACAAAACGGACCAAACAAAC 59.011 39.130 0.00 0.00 0.00 2.93
4335 4694 3.988517 GTCAACAAAACGGACCAAACAAA 59.011 39.130 0.00 0.00 0.00 2.83
4336 4695 3.005472 TGTCAACAAAACGGACCAAACAA 59.995 39.130 0.00 0.00 0.00 2.83
4337 4696 2.557056 TGTCAACAAAACGGACCAAACA 59.443 40.909 0.00 0.00 0.00 2.83
4338 4697 3.219052 TGTCAACAAAACGGACCAAAC 57.781 42.857 0.00 0.00 0.00 2.93
4339 4698 3.444034 TCATGTCAACAAAACGGACCAAA 59.556 39.130 0.00 0.00 0.00 3.28
4396 4755 1.925255 TCCTTCCTCTCGTACCCCTTA 59.075 52.381 0.00 0.00 0.00 2.69
4397 4756 0.708802 TCCTTCCTCTCGTACCCCTT 59.291 55.000 0.00 0.00 0.00 3.95
4399 4758 1.112950 CTTCCTTCCTCTCGTACCCC 58.887 60.000 0.00 0.00 0.00 4.95
4418 4783 3.057806 AGCATTACCGCAACTTTAACCAC 60.058 43.478 0.00 0.00 0.00 4.16
4432 4797 8.311650 ACGAACATCATCTTAATAGCATTACC 57.688 34.615 0.00 0.00 0.00 2.85
4446 4839 1.133025 CCCTGCCAAACGAACATCATC 59.867 52.381 0.00 0.00 0.00 2.92
4456 4849 2.562298 TGATTTGTCATCCCTGCCAAAC 59.438 45.455 0.00 0.00 0.00 2.93
4459 4852 2.562298 GTTTGATTTGTCATCCCTGCCA 59.438 45.455 0.00 0.00 0.00 4.92
4495 4888 2.482721 CCATCCCCGCGACAATATAAAC 59.517 50.000 8.23 0.00 0.00 2.01
4508 4901 4.180817 GCAAACTAAATTTTCCATCCCCG 58.819 43.478 0.00 0.00 0.00 5.73
4510 4903 5.122239 GCTTGCAAACTAAATTTTCCATCCC 59.878 40.000 0.00 0.00 0.00 3.85
4520 4913 1.339610 TGCCGTGCTTGCAAACTAAAT 59.660 42.857 0.00 0.00 35.40 1.40
4523 4916 2.409399 TTGCCGTGCTTGCAAACTA 58.591 47.368 0.00 0.00 45.11 2.24
4524 4917 3.205395 TTGCCGTGCTTGCAAACT 58.795 50.000 0.00 0.00 45.11 2.66
4527 4920 1.006337 GGATTTGCCGTGCTTGCAA 60.006 52.632 0.00 0.00 46.30 4.08
4528 4921 1.902918 AGGATTTGCCGTGCTTGCA 60.903 52.632 0.00 0.00 43.43 4.08
4567 4960 5.320549 CTTAGACAAGCATGGCAAATCTT 57.679 39.130 0.00 0.00 36.86 2.40
4568 4961 4.978083 CTTAGACAAGCATGGCAAATCT 57.022 40.909 0.00 0.00 36.86 2.40
4589 4982 1.881973 TGTTGGCTGAGAATGACAAGC 59.118 47.619 0.00 0.00 0.00 4.01
4603 4996 4.681835 TTGCATTGCAATTTATGTTGGC 57.318 36.364 19.77 8.15 43.99 4.52
4625 5018 2.093553 AGCATGGCAATTGCGGTAAAAT 60.094 40.909 23.48 7.74 44.82 1.82
4627 5020 0.894141 AGCATGGCAATTGCGGTAAA 59.106 45.000 23.48 7.50 44.82 2.01
4630 5023 1.216178 GAAGCATGGCAATTGCGGT 59.784 52.632 23.48 12.96 44.82 5.68
4631 5024 1.519898 GGAAGCATGGCAATTGCGG 60.520 57.895 23.48 16.14 44.82 5.69
4632 5025 1.519898 GGGAAGCATGGCAATTGCG 60.520 57.895 23.48 11.57 44.82 4.85
4633 5026 0.461339 CTGGGAAGCATGGCAATTGC 60.461 55.000 22.47 22.47 40.45 3.56
4634 5027 0.461339 GCTGGGAAGCATGGCAATTG 60.461 55.000 0.00 0.00 34.41 2.32
4661 5054 1.125633 TAGGACCGGCTTAACCATCC 58.874 55.000 0.00 0.00 41.81 3.51
4663 5056 2.574824 ACTTTAGGACCGGCTTAACCAT 59.425 45.455 0.00 0.00 39.03 3.55
4708 5101 0.749649 TTTTGGCACTGCAATTCCGT 59.250 45.000 2.82 0.00 0.00 4.69
4729 5122 4.981806 TTTCCAGATAAATTTGAGCGGG 57.018 40.909 0.00 0.74 0.00 6.13
4778 5175 1.445582 CTGTCACCTTCGTACCGGC 60.446 63.158 0.00 0.00 0.00 6.13
4790 5187 1.077123 CTCACATGCTCTGCTGTCAC 58.923 55.000 0.00 0.00 0.00 3.67
4942 5369 2.026915 CCTGTTCATGGACATGGACTCA 60.027 50.000 20.94 4.88 45.46 3.41
4949 5376 3.356290 GGCTTTACCTGTTCATGGACAT 58.644 45.455 7.44 0.00 34.51 3.06
4951 5378 1.737793 CGGCTTTACCTGTTCATGGAC 59.262 52.381 0.00 0.00 35.61 4.02
4952 5379 1.948611 GCGGCTTTACCTGTTCATGGA 60.949 52.381 0.00 0.00 35.61 3.41
4953 5380 0.451783 GCGGCTTTACCTGTTCATGG 59.548 55.000 0.00 0.00 35.61 3.66
4954 5381 1.131126 CAGCGGCTTTACCTGTTCATG 59.869 52.381 0.00 0.00 35.61 3.07
4955 5382 1.453155 CAGCGGCTTTACCTGTTCAT 58.547 50.000 0.00 0.00 35.61 2.57
4956 5383 1.234615 GCAGCGGCTTTACCTGTTCA 61.235 55.000 0.00 0.00 36.96 3.18
4957 5384 1.502190 GCAGCGGCTTTACCTGTTC 59.498 57.895 0.00 0.00 36.96 3.18
4958 5385 2.325082 CGCAGCGGCTTTACCTGTT 61.325 57.895 7.00 0.00 38.10 3.16
4976 5403 1.693627 TCGCCTGGATCTTCTAGGAC 58.306 55.000 10.74 2.17 46.88 3.85
5021 5448 2.273776 GAGGAAGGAGGGCTTGGC 59.726 66.667 0.00 0.00 0.00 4.52
5029 5456 1.380515 TCTGGCGAGGAGGAAGGAG 60.381 63.158 0.00 0.00 0.00 3.69
5045 5472 2.151369 ACGGGAATGGTTGGTGTCT 58.849 52.632 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.