Multiple sequence alignment - TraesCS5B01G090500

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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 TraesCS5B01G090500 chr5B 100.000 4354 0 0 1 4354 116846078 116841725 0.000000e+00 8041
1 TraesCS5B01G090500 chr5B 93.451 397 24 2 321 715 539019315 539018919 4.850000e-164 588
2 TraesCS5B01G090500 chr5B 90.576 191 11 5 2790 2973 116843103 116842913 3.360000e-61 246
3 TraesCS5B01G090500 chr5B 90.576 191 11 5 2976 3166 116843289 116843106 3.360000e-61 246
4 TraesCS5B01G090500 chr5D 91.113 1913 134 16 887 2773 107568769 107566867 0.000000e+00 2558
5 TraesCS5B01G090500 chr5D 93.811 921 41 13 2790 3706 107566622 107565714 0.000000e+00 1371
6 TraesCS5B01G090500 chr5D 90.075 665 35 11 3691 4345 107565694 107565051 0.000000e+00 833
7 TraesCS5B01G090500 chr5D 90.201 398 26 9 2775 3166 107566829 107566439 1.400000e-139 507
8 TraesCS5B01G090500 chr5D 95.000 180 8 1 713 892 107568975 107568797 9.220000e-72 281
9 TraesCS5B01G090500 chr5D 92.784 194 7 3 2976 3166 107566814 107566625 1.540000e-69 274
10 TraesCS5B01G090500 chr5D 91.099 191 12 4 2790 2975 107566436 107566246 2.010000e-63 254
11 TraesCS5B01G090500 chr5D 95.294 85 3 1 3 87 107569044 107568961 2.730000e-27 134
12 TraesCS5B01G090500 chr5A 91.147 1909 126 19 887 2773 110374524 110372637 0.000000e+00 2549
13 TraesCS5B01G090500 chr5A 93.177 894 42 14 2775 3660 110372599 110371717 0.000000e+00 1295
14 TraesCS5B01G090500 chr5A 89.193 657 38 10 3702 4344 110371722 110371085 0.000000e+00 789
15 TraesCS5B01G090500 chr5A 92.147 191 10 4 2790 2975 110372395 110372205 9.280000e-67 265
16 TraesCS5B01G090500 chr5A 93.855 179 6 2 714 892 110374725 110374552 9.280000e-67 265
17 TraesCS5B01G090500 chr5A 90.674 193 12 4 2975 3166 110372585 110372398 7.230000e-63 252
18 TraesCS5B01G090500 chr5A 93.103 87 2 3 1 87 110374793 110374711 1.640000e-24 124
19 TraesCS5B01G090500 chr4D 93.532 402 24 2 313 713 88469812 88470212 8.060000e-167 597
20 TraesCS5B01G090500 chr4D 90.686 204 19 0 113 316 88469579 88469782 5.550000e-69 272
21 TraesCS5B01G090500 chr7D 93.216 398 25 2 320 715 371787320 371787717 6.270000e-163 584
22 TraesCS5B01G090500 chr7D 92.658 395 26 3 318 710 94928512 94928119 2.270000e-157 566
23 TraesCS5B01G090500 chr7D 91.707 205 16 1 113 316 94928750 94928546 2.560000e-72 283
24 TraesCS5B01G090500 chr7D 92.079 202 15 1 115 316 371787084 371787284 2.560000e-72 283
25 TraesCS5B01G090500 chr2A 92.172 396 29 2 320 713 693244687 693245082 3.800000e-155 558
26 TraesCS5B01G090500 chr2A 88.725 204 23 0 113 316 693244448 693244651 2.600000e-62 250
27 TraesCS5B01G090500 chr2B 89.698 398 27 6 320 715 777842660 777842275 3.020000e-136 496
28 TraesCS5B01G090500 chr2B 90.686 204 19 0 113 316 777842899 777842696 5.550000e-69 272
29 TraesCS5B01G090500 chr4B 90.948 232 17 3 486 715 632397077 632396848 4.230000e-80 309


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 TraesCS5B01G090500 chr5B 116841725 116846078 4353 True 2844.333333 8041 93.717333 1 4354 3 chr5B.!!$R2 4353
1 TraesCS5B01G090500 chr5D 107565051 107569044 3993 True 776.500000 2558 92.422125 3 4345 8 chr5D.!!$R1 4342
2 TraesCS5B01G090500 chr5A 110371085 110374793 3708 True 791.285714 2549 91.899429 1 4344 7 chr5A.!!$R1 4343
3 TraesCS5B01G090500 chr4D 88469579 88470212 633 False 434.500000 597 92.109000 113 713 2 chr4D.!!$F1 600
4 TraesCS5B01G090500 chr7D 371787084 371787717 633 False 433.500000 584 92.647500 115 715 2 chr7D.!!$F1 600
5 TraesCS5B01G090500 chr7D 94928119 94928750 631 True 424.500000 566 92.182500 113 710 2 chr7D.!!$R1 597
6 TraesCS5B01G090500 chr2A 693244448 693245082 634 False 404.000000 558 90.448500 113 713 2 chr2A.!!$F1 600
7 TraesCS5B01G090500 chr2B 777842275 777842899 624 True 384.000000 496 90.192000 113 715 2 chr2B.!!$R1 602

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
240 241 0.112412 AGGGTCAATTTCTTGCCGGT 59.888 50.0 1.9 0.0 32.54 5.28 F
1228 1309 0.032403 GCCCCGTTGTTGGTTTTACC 59.968 55.0 0.0 0.0 39.22 2.85 F
1485 1590 0.547954 ACTCCCTCCCTCTGGAAACC 60.548 60.0 0.0 0.0 41.17 3.27 F
1488 1593 0.846870 CCCTCCCTCTGGAAACCCTT 60.847 60.0 0.0 0.0 41.17 3.95 F
3168 3521 0.167470 CATGAACTGTTGAGCCTGCG 59.833 55.0 0.0 0.0 0.00 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1331 1416 0.108138 AGCAGCAACCTCCATCGTAC 60.108 55.000 0.00 0.00 0.00 3.67 R
2925 3276 0.108585 ATGACTGCAACGGTGACCTT 59.891 50.000 3.55 0.00 0.00 3.50 R
3110 3463 0.877071 GCAACAGTGACCATGGAGTG 59.123 55.000 21.47 12.76 0.00 3.51 R
3245 3599 1.139058 ACGATCCTGTGGCAATAGGTC 59.861 52.381 16.09 12.38 36.14 3.85 R
4110 4505 0.178068 ACCGTCGGATTTCTGGATGG 59.822 55.000 20.51 8.11 41.59 3.51 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
78 79 5.835113 ACAAACTACACTCACAAGCAATT 57.165 34.783 0.00 0.00 0.00 2.32
79 80 6.207691 ACAAACTACACTCACAAGCAATTT 57.792 33.333 0.00 0.00 0.00 1.82
80 81 6.630071 ACAAACTACACTCACAAGCAATTTT 58.370 32.000 0.00 0.00 0.00 1.82
81 82 6.751888 ACAAACTACACTCACAAGCAATTTTC 59.248 34.615 0.00 0.00 0.00 2.29
82 83 5.438761 ACTACACTCACAAGCAATTTTCC 57.561 39.130 0.00 0.00 0.00 3.13
83 84 4.887071 ACTACACTCACAAGCAATTTTCCA 59.113 37.500 0.00 0.00 0.00 3.53
84 85 4.311816 ACACTCACAAGCAATTTTCCAG 57.688 40.909 0.00 0.00 0.00 3.86
85 86 3.953612 ACACTCACAAGCAATTTTCCAGA 59.046 39.130 0.00 0.00 0.00 3.86
86 87 4.586001 ACACTCACAAGCAATTTTCCAGAT 59.414 37.500 0.00 0.00 0.00 2.90
87 88 4.921515 CACTCACAAGCAATTTTCCAGATG 59.078 41.667 0.00 0.00 0.00 2.90
88 89 4.586001 ACTCACAAGCAATTTTCCAGATGT 59.414 37.500 0.00 0.00 0.00 3.06
89 90 5.069516 ACTCACAAGCAATTTTCCAGATGTT 59.930 36.000 0.00 0.00 0.00 2.71
90 91 5.291178 TCACAAGCAATTTTCCAGATGTTG 58.709 37.500 0.00 0.00 0.00 3.33
100 101 2.483014 CCAGATGTTGGTCGGGTTAA 57.517 50.000 0.00 0.00 42.41 2.01
101 102 2.785562 CCAGATGTTGGTCGGGTTAAA 58.214 47.619 0.00 0.00 42.41 1.52
102 103 3.352648 CCAGATGTTGGTCGGGTTAAAT 58.647 45.455 0.00 0.00 42.41 1.40
103 104 4.519213 CCAGATGTTGGTCGGGTTAAATA 58.481 43.478 0.00 0.00 42.41 1.40
104 105 4.334481 CCAGATGTTGGTCGGGTTAAATAC 59.666 45.833 0.00 0.00 42.41 1.89
105 106 4.938832 CAGATGTTGGTCGGGTTAAATACA 59.061 41.667 0.00 0.00 0.00 2.29
106 107 5.588648 CAGATGTTGGTCGGGTTAAATACAT 59.411 40.000 0.00 0.00 0.00 2.29
107 108 5.588648 AGATGTTGGTCGGGTTAAATACATG 59.411 40.000 0.00 0.00 0.00 3.21
108 109 3.440872 TGTTGGTCGGGTTAAATACATGC 59.559 43.478 0.00 0.00 0.00 4.06
109 110 3.351794 TGGTCGGGTTAAATACATGCA 57.648 42.857 0.00 0.00 0.00 3.96
110 111 3.011119 TGGTCGGGTTAAATACATGCAC 58.989 45.455 0.00 0.00 0.00 4.57
111 112 3.275999 GGTCGGGTTAAATACATGCACT 58.724 45.455 0.00 0.00 0.00 4.40
132 133 5.640783 CACTCACATGCTACTCATTCTTTCA 59.359 40.000 0.00 0.00 31.79 2.69
155 156 1.134848 ACCAGCTTCATCTTCGAGCTC 60.135 52.381 2.73 2.73 44.44 4.09
184 185 3.409026 TCAAAGTTCAGAGAGAAGGGC 57.591 47.619 0.00 0.00 36.78 5.19
213 214 2.080286 AGTACGACATGCAACCTCAC 57.920 50.000 0.00 0.00 0.00 3.51
238 239 0.447801 CGAGGGTCAATTTCTTGCCG 59.552 55.000 0.00 0.00 32.54 5.69
240 241 0.112412 AGGGTCAATTTCTTGCCGGT 59.888 50.000 1.90 0.00 32.54 5.28
253 254 4.386951 CCGGTGATGGACGGCACA 62.387 66.667 0.00 0.00 43.96 4.57
316 318 0.616111 AGGAATGGAGAGCGAGGTGT 60.616 55.000 0.00 0.00 0.00 4.16
367 401 5.523916 GTCGAAGGTATAACTGATGCAACAT 59.476 40.000 0.00 0.00 0.00 2.71
383 417 3.507622 GCAACATTCTTAGAAGCCTTGGT 59.492 43.478 0.03 0.00 0.00 3.67
635 670 3.884895 AGATATTGGTCGCCATGTTTGA 58.115 40.909 0.00 0.00 31.53 2.69
666 703 3.838317 TCCTCATGACCCCTAATTATCCG 59.162 47.826 0.00 0.00 0.00 4.18
682 719 6.990341 ATTATCCGTGTAAACCTTGTTACC 57.010 37.500 0.00 0.00 33.76 2.85
827 864 0.461961 CCGAGGAGGTCACAAGGATC 59.538 60.000 0.00 0.00 34.51 3.36
850 887 1.851021 TTTCTCGCCGCACAACCATG 61.851 55.000 0.00 0.00 0.00 3.66
851 888 4.465512 CTCGCCGCACAACCATGC 62.466 66.667 0.00 0.00 42.48 4.06
936 1010 2.899339 GATCGGGGAAGCAGCAGC 60.899 66.667 0.00 0.00 42.56 5.25
986 1062 2.202864 GGAGAAGCAGCTCGCCTC 60.203 66.667 0.00 3.11 44.04 4.70
1008 1089 0.904865 CTAGCCTCGCCATGGGGATA 60.905 60.000 29.72 18.72 36.50 2.59
1024 1105 0.454620 GATAGGCTACGTCATCGGCG 60.455 60.000 0.00 0.00 41.85 6.46
1190 1271 2.833582 TCAGATCCTCGGCCGACC 60.834 66.667 27.28 13.65 0.00 4.79
1216 1297 3.311110 TTCTCGAGCTGCCCCGTT 61.311 61.111 7.81 0.00 0.00 4.44
1224 1305 2.791868 GCTGCCCCGTTGTTGGTTT 61.792 57.895 0.00 0.00 0.00 3.27
1228 1309 0.032403 GCCCCGTTGTTGGTTTTACC 59.968 55.000 0.00 0.00 39.22 2.85
1282 1367 1.448540 CCTGTGTGCTGATCCCGTC 60.449 63.158 0.00 0.00 0.00 4.79
1331 1416 4.809958 AGAATCATGACAGAGCTCGAATTG 59.190 41.667 8.37 3.41 0.00 2.32
1362 1447 4.643387 GCTGCTGGGGTTGGTCGT 62.643 66.667 0.00 0.00 0.00 4.34
1386 1471 3.012518 GGTTCCAGGATCTGATTGTGTG 58.987 50.000 0.00 0.00 32.44 3.82
1388 1473 3.339253 TCCAGGATCTGATTGTGTGTG 57.661 47.619 0.00 0.00 32.44 3.82
1483 1588 1.201429 GCACTCCCTCCCTCTGGAAA 61.201 60.000 0.00 0.00 41.17 3.13
1484 1589 0.615850 CACTCCCTCCCTCTGGAAAC 59.384 60.000 0.00 0.00 41.17 2.78
1485 1590 0.547954 ACTCCCTCCCTCTGGAAACC 60.548 60.000 0.00 0.00 41.17 3.27
1486 1591 1.229853 TCCCTCCCTCTGGAAACCC 60.230 63.158 0.00 0.00 41.17 4.11
1487 1592 1.229984 CCCTCCCTCTGGAAACCCT 60.230 63.158 0.00 0.00 41.17 4.34
1488 1593 0.846870 CCCTCCCTCTGGAAACCCTT 60.847 60.000 0.00 0.00 41.17 3.95
1489 1594 1.076438 CCTCCCTCTGGAAACCCTTT 58.924 55.000 0.00 0.00 41.17 3.11
1490 1595 2.275466 CCTCCCTCTGGAAACCCTTTA 58.725 52.381 0.00 0.00 41.17 1.85
1491 1596 2.853077 CCTCCCTCTGGAAACCCTTTAT 59.147 50.000 0.00 0.00 41.17 1.40
1492 1597 3.117851 CCTCCCTCTGGAAACCCTTTATC 60.118 52.174 0.00 0.00 41.17 1.75
1494 1599 4.183916 TCCCTCTGGAAACCCTTTATCTT 58.816 43.478 0.00 0.00 37.86 2.40
1495 1600 4.018415 TCCCTCTGGAAACCCTTTATCTTG 60.018 45.833 0.00 0.00 37.86 3.02
1496 1601 3.696548 CCTCTGGAAACCCTTTATCTTGC 59.303 47.826 0.00 0.00 0.00 4.01
1497 1602 3.696548 CTCTGGAAACCCTTTATCTTGCC 59.303 47.826 0.00 0.00 0.00 4.52
1498 1603 3.075283 TCTGGAAACCCTTTATCTTGCCA 59.925 43.478 0.00 0.00 0.00 4.92
1499 1604 4.026052 CTGGAAACCCTTTATCTTGCCAT 58.974 43.478 0.00 0.00 0.00 4.40
1500 1605 3.768757 TGGAAACCCTTTATCTTGCCATG 59.231 43.478 0.00 0.00 0.00 3.66
1501 1606 3.769300 GGAAACCCTTTATCTTGCCATGT 59.231 43.478 0.00 0.00 0.00 3.21
1502 1607 4.953579 GGAAACCCTTTATCTTGCCATGTA 59.046 41.667 0.00 0.00 0.00 2.29
1503 1608 5.420739 GGAAACCCTTTATCTTGCCATGTAA 59.579 40.000 0.00 0.00 0.00 2.41
1504 1609 5.914898 AACCCTTTATCTTGCCATGTAAC 57.085 39.130 0.00 0.00 0.00 2.50
1505 1610 4.929479 ACCCTTTATCTTGCCATGTAACA 58.071 39.130 0.00 0.00 0.00 2.41
1506 1611 4.705023 ACCCTTTATCTTGCCATGTAACAC 59.295 41.667 0.00 0.00 0.00 3.32
1507 1612 4.704540 CCCTTTATCTTGCCATGTAACACA 59.295 41.667 0.00 0.00 0.00 3.72
1508 1613 5.360714 CCCTTTATCTTGCCATGTAACACAT 59.639 40.000 0.00 0.00 39.91 3.21
1509 1614 6.545666 CCCTTTATCTTGCCATGTAACACATA 59.454 38.462 0.00 0.00 36.53 2.29
1510 1615 7.231317 CCCTTTATCTTGCCATGTAACACATAT 59.769 37.037 0.00 0.00 36.53 1.78
1511 1616 8.077991 CCTTTATCTTGCCATGTAACACATATG 58.922 37.037 0.00 0.00 36.53 1.78
1544 1650 6.468637 GCGTAGTCTTGCTTTCTAAGTACTAC 59.531 42.308 0.00 0.00 36.60 2.73
1545 1651 7.524912 CGTAGTCTTGCTTTCTAAGTACTACA 58.475 38.462 0.00 0.00 37.87 2.74
1552 1658 9.469807 CTTGCTTTCTAAGTACTACATATCTGG 57.530 37.037 0.00 0.00 0.00 3.86
1553 1659 7.952671 TGCTTTCTAAGTACTACATATCTGGG 58.047 38.462 0.00 0.00 0.00 4.45
1563 1669 2.057922 ACATATCTGGGTAGCTTGGGG 58.942 52.381 0.00 0.00 0.00 4.96
1587 1693 2.597040 CGTAGTTTTGCGCAACGTGTTA 60.597 45.455 24.99 3.61 0.00 2.41
1588 1694 2.546195 AGTTTTGCGCAACGTGTTAA 57.454 40.000 24.99 10.71 0.00 2.01
1597 1703 2.470140 CGCAACGTGTTAAGCTCGTAAG 60.470 50.000 0.00 0.00 45.05 2.34
1607 1713 7.031975 GTGTTAAGCTCGTAAGTATGTAGGTT 58.968 38.462 0.00 0.00 39.48 3.50
1636 1742 8.999431 ACCATGATTTGTACAGTAGTAACAAAG 58.001 33.333 13.06 5.23 36.09 2.77
1648 1754 8.873144 ACAGTAGTAACAAAGTACCCAATAGAA 58.127 33.333 0.00 0.00 34.94 2.10
1669 1778 0.963962 ATTTCTGTGGTGGCTGCTTG 59.036 50.000 0.00 0.00 0.00 4.01
1677 1786 2.295909 GTGGTGGCTGCTTGTGATTTAA 59.704 45.455 0.00 0.00 0.00 1.52
1679 1788 3.056678 TGGTGGCTGCTTGTGATTTAATG 60.057 43.478 0.00 0.00 0.00 1.90
1688 1797 9.226345 GCTGCTTGTGATTTAATGTAATTCTAC 57.774 33.333 0.00 0.00 37.87 2.59
1700 1809 5.783100 TGTAATTCTACGTAAAAAGGCCG 57.217 39.130 0.00 0.00 0.00 6.13
1706 1815 6.799926 TTCTACGTAAAAAGGCCGTTTATT 57.200 33.333 17.33 5.36 0.00 1.40
1707 1816 7.897575 TTCTACGTAAAAAGGCCGTTTATTA 57.102 32.000 17.33 4.34 0.00 0.98
1734 1843 6.490040 AGCACTAATAATTCGGGCATGTTATT 59.510 34.615 0.00 0.00 33.00 1.40
1747 1856 6.625740 CGGGCATGTTATTCTCAGAAAATTGT 60.626 38.462 0.00 0.00 0.00 2.71
1752 1861 9.695526 CATGTTATTCTCAGAAAATTGTGGAAA 57.304 29.630 0.00 0.00 0.00 3.13
1765 1874 8.706322 AAAATTGTGGAAACTTATACCTCAGT 57.294 30.769 0.00 0.00 0.00 3.41
1802 1911 2.360801 ACGTTGCATAACCTGTGCTTTT 59.639 40.909 0.00 0.00 42.92 2.27
1819 1928 2.886862 TTTTGTTGTGCAGGTGATGG 57.113 45.000 0.00 0.00 0.00 3.51
1839 1948 4.798344 CAGCTGCTCCTGGGGCTG 62.798 72.222 21.13 20.54 44.45 4.85
1878 1987 2.092429 AGGTGTCTCTGTTCCAGCAAAA 60.092 45.455 0.00 0.00 0.00 2.44
1975 2085 6.729690 ATCTTGAGTTTTTGTTTGGGATCA 57.270 33.333 0.00 0.00 0.00 2.92
2046 2156 7.102847 ACTCAGCTGTAGTTTCCTTCTATAC 57.897 40.000 14.67 0.00 0.00 1.47
2051 2161 6.377712 AGCTGTAGTTTCCTTCTATACTTCGT 59.622 38.462 0.00 0.00 0.00 3.85
2053 2163 7.458409 TGTAGTTTCCTTCTATACTTCGTGT 57.542 36.000 0.00 0.00 0.00 4.49
2109 2219 2.666272 TTACAGGAAATGTGGCCACA 57.334 45.000 39.23 39.23 43.80 4.17
2175 2285 8.635765 AATGTCATGGAGTTAACTGTTATGTT 57.364 30.769 14.14 3.13 0.00 2.71
2241 2353 4.590647 TCCCCAATAACATGCTTTTGTCAA 59.409 37.500 0.00 0.00 0.00 3.18
2248 2360 1.710249 CATGCTTTTGTCAAACGAGCG 59.290 47.619 14.36 1.70 36.17 5.03
2314 2426 3.426191 CACAATTACATGCACACAACAGC 59.574 43.478 0.00 0.00 0.00 4.40
2400 2519 1.382522 AACCGCACATATTCAGGCAG 58.617 50.000 0.00 0.00 0.00 4.85
2439 2558 2.905736 TCACAAGTCAGACATGGGATCA 59.094 45.455 6.64 0.00 22.37 2.92
2467 2586 5.781210 TGCATAGACTCTTGATTCTCGAT 57.219 39.130 0.00 0.00 0.00 3.59
2488 2607 7.269316 TCGATTGTGTAAGCACCTATGAATTA 58.731 34.615 0.00 0.00 44.65 1.40
2501 2620 5.163405 ACCTATGAATTAGATGCAGTGACGT 60.163 40.000 0.00 0.00 0.00 4.34
2530 2649 2.165998 AGCTTGAATTGAAGAGGGCAC 58.834 47.619 9.00 0.00 0.00 5.01
2562 2681 2.930682 GAGCTATGTCGGACCTTTGAAC 59.069 50.000 5.55 0.00 0.00 3.18
2732 2854 7.201427 CGCCTGAAATGTTTATGGTGTTATTTG 60.201 37.037 0.00 0.00 0.00 2.32
2773 2895 7.416326 GCCAAATAATCCCTGATAGTTCGTTTT 60.416 37.037 0.00 0.00 0.00 2.43
2788 3138 4.657436 TCGTTTTATGGGCTTTTGTTGT 57.343 36.364 0.00 0.00 0.00 3.32
2794 3144 6.656632 TTTATGGGCTTTTGTTGTCACATA 57.343 33.333 0.00 0.00 31.06 2.29
2811 3161 5.233476 GTCACATATTGCTGAATTTGCCATG 59.767 40.000 2.64 0.00 0.00 3.66
2819 3169 2.696707 CTGAATTTGCCATGGTATGCCT 59.303 45.455 14.67 0.00 35.27 4.75
2839 3190 2.840651 CTGAAGTCACCTTACCTCCCAT 59.159 50.000 0.00 0.00 0.00 4.00
2840 3191 4.030913 CTGAAGTCACCTTACCTCCCATA 58.969 47.826 0.00 0.00 0.00 2.74
2859 3210 5.832595 CCCATATATGTGGATGGTTTGTCAA 59.167 40.000 19.41 0.00 42.02 3.18
2870 3221 9.271828 GTGGATGGTTTGTCAAGAAATAAAAAT 57.728 29.630 0.00 0.00 0.00 1.82
2925 3276 9.733556 TTCCTATTTAATGCTTTGTGAAGACTA 57.266 29.630 0.00 0.00 34.71 2.59
2940 3293 1.000955 AGACTAAGGTCACCGTTGCAG 59.999 52.381 0.00 0.00 44.36 4.41
3056 3409 6.868339 GTGGATGGTTTGTCAGGAAATAAAAG 59.132 38.462 0.00 0.00 0.00 2.27
3109 3462 8.028938 GCTTTCCTATTTAATGCTTTGTGAAGA 58.971 33.333 0.00 0.00 34.71 2.87
3110 3463 9.346725 CTTTCCTATTTAATGCTTTGTGAAGAC 57.653 33.333 0.00 0.00 34.71 3.01
3145 3498 8.116753 GTCACTGTTGCACTCATATTATGTTAC 58.883 37.037 3.67 0.00 0.00 2.50
3166 3519 2.422479 CCATCATGAACTGTTGAGCCTG 59.578 50.000 0.00 0.00 0.00 4.85
3168 3521 0.167470 CATGAACTGTTGAGCCTGCG 59.833 55.000 0.00 0.00 0.00 5.18
3194 3547 6.161381 AGCAGCTTTCCTTATGTTTTGAATG 58.839 36.000 0.00 0.00 0.00 2.67
3232 3586 3.536570 GAACTCTGCTACCCATTTCCTC 58.463 50.000 0.00 0.00 0.00 3.71
3233 3587 1.840635 ACTCTGCTACCCATTTCCTCC 59.159 52.381 0.00 0.00 0.00 4.30
3234 3588 2.122768 CTCTGCTACCCATTTCCTCCT 58.877 52.381 0.00 0.00 0.00 3.69
3245 3599 4.502259 CCCATTTCCTCCTGTCTCTAATCG 60.502 50.000 0.00 0.00 0.00 3.34
3354 3708 6.257411 CGCAGACTTGAAGTTGAAGATATGAT 59.743 38.462 9.20 0.00 0.00 2.45
3376 3730 8.010733 TGATCAAATTCTGTTCCTTTCTTGTT 57.989 30.769 0.00 0.00 0.00 2.83
3433 3787 5.003804 AGTTATTCTTGTGTCACCCATGTC 58.996 41.667 0.00 0.00 0.00 3.06
3449 3803 3.267031 CCATGTCTTAAGAGGGGGAAAGT 59.733 47.826 5.12 0.00 0.00 2.66
3686 4042 3.259123 AGCTTGTTGCCCTAAAATCCTTG 59.741 43.478 0.00 0.00 44.23 3.61
3725 4115 4.428209 CTCATAGAATGCGTTCTGTCTGT 58.572 43.478 27.81 6.28 44.27 3.41
3735 4125 3.248602 GCGTTCTGTCTGTGACTGAAAAT 59.751 43.478 17.22 0.00 46.35 1.82
3736 4126 4.260784 GCGTTCTGTCTGTGACTGAAAATT 60.261 41.667 17.22 0.00 46.35 1.82
3737 4127 5.200454 CGTTCTGTCTGTGACTGAAAATTG 58.800 41.667 17.22 7.94 46.35 2.32
3739 4129 6.019075 CGTTCTGTCTGTGACTGAAAATTGTA 60.019 38.462 17.22 0.00 46.35 2.41
3741 4131 8.345565 GTTCTGTCTGTGACTGAAAATTGTATT 58.654 33.333 17.22 0.00 46.35 1.89
3742 4132 8.450578 TCTGTCTGTGACTGAAAATTGTATTT 57.549 30.769 5.11 0.00 37.52 1.40
3863 4258 3.996921 TTTTGGTGGCATGGCATAATT 57.003 38.095 26.07 0.00 0.00 1.40
3865 4260 1.121378 TGGTGGCATGGCATAATTGG 58.879 50.000 26.07 0.00 0.00 3.16
3882 4277 2.328099 GGCACTTCCCTCACTTGCG 61.328 63.158 0.00 0.00 33.84 4.85
3885 4280 1.813513 CACTTCCCTCACTTGCGATT 58.186 50.000 0.00 0.00 0.00 3.34
3886 4281 1.466167 CACTTCCCTCACTTGCGATTG 59.534 52.381 0.00 0.00 0.00 2.67
3888 4283 2.224523 ACTTCCCTCACTTGCGATTGAA 60.225 45.455 0.00 0.00 0.00 2.69
3889 4284 2.787473 TCCCTCACTTGCGATTGAAT 57.213 45.000 0.00 0.00 0.00 2.57
3890 4285 2.358957 TCCCTCACTTGCGATTGAATG 58.641 47.619 0.00 0.00 0.00 2.67
3891 4286 1.202222 CCCTCACTTGCGATTGAATGC 60.202 52.381 0.00 0.00 0.00 3.56
3892 4287 1.469703 CCTCACTTGCGATTGAATGCA 59.530 47.619 0.00 0.00 39.81 3.96
3893 4288 2.098607 CCTCACTTGCGATTGAATGCAT 59.901 45.455 0.00 0.00 41.42 3.96
3912 4307 6.271488 TGCATTTTCTTTACCAATCTGGAG 57.729 37.500 0.00 0.00 40.96 3.86
3933 4328 4.677584 AGTAAATCACGTGCAAGCAAAAA 58.322 34.783 11.67 0.00 0.00 1.94
3993 4388 6.545666 TGTGGTTCCAATGACATATGGATTAC 59.454 38.462 15.62 12.69 44.83 1.89
3994 4389 5.762711 TGGTTCCAATGACATATGGATTACG 59.237 40.000 15.62 0.02 44.83 3.18
4110 4505 0.931005 GACGATCAAATCAGACCGCC 59.069 55.000 0.00 0.00 0.00 6.13
4143 4538 1.806623 CGACGGTCATGAATCCTTCCC 60.807 57.143 9.10 0.00 0.00 3.97
4218 4621 0.316204 CCTTCACAGCCAAGCAAAGG 59.684 55.000 0.00 0.00 0.00 3.11
4232 4636 1.955778 GCAAAGGGCCAAAAGCAAAAT 59.044 42.857 6.18 0.00 46.50 1.82
4260 4664 2.813474 TTGGCAGATTCCGCGTCG 60.813 61.111 4.92 0.00 0.00 5.12
4261 4665 3.289704 TTGGCAGATTCCGCGTCGA 62.290 57.895 4.92 0.00 0.00 4.20
4262 4666 2.279517 GGCAGATTCCGCGTCGAT 60.280 61.111 4.92 0.00 0.00 3.59
4263 4667 2.303676 GGCAGATTCCGCGTCGATC 61.304 63.158 4.92 5.42 0.00 3.69
4264 4668 1.588932 GCAGATTCCGCGTCGATCA 60.589 57.895 4.92 0.00 0.00 2.92
4265 4669 1.812214 GCAGATTCCGCGTCGATCAC 61.812 60.000 4.92 0.00 0.00 3.06
4334 4738 2.063378 CCTCCACCCCAGCTCTCTC 61.063 68.421 0.00 0.00 0.00 3.20
4336 4740 0.260230 CTCCACCCCAGCTCTCTCTA 59.740 60.000 0.00 0.00 0.00 2.43
4345 4749 3.329386 CCAGCTCTCTCTATCTCTCTCG 58.671 54.545 0.00 0.00 0.00 4.04
4346 4750 2.738846 CAGCTCTCTCTATCTCTCTCGC 59.261 54.545 0.00 0.00 0.00 5.03
4347 4751 1.726791 GCTCTCTCTATCTCTCTCGCG 59.273 57.143 0.00 0.00 0.00 5.87
4348 4752 2.866460 GCTCTCTCTATCTCTCTCGCGT 60.866 54.545 5.77 0.00 0.00 6.01
4349 4753 3.390135 CTCTCTCTATCTCTCTCGCGTT 58.610 50.000 5.77 0.00 0.00 4.84
4350 4754 3.386486 TCTCTCTATCTCTCTCGCGTTC 58.614 50.000 5.77 0.00 0.00 3.95
4351 4755 2.128821 TCTCTATCTCTCTCGCGTTCG 58.871 52.381 5.77 0.00 0.00 3.95
4352 4756 2.128821 CTCTATCTCTCTCGCGTTCGA 58.871 52.381 5.77 0.28 43.28 3.71
4353 4757 1.859703 TCTATCTCTCTCGCGTTCGAC 59.140 52.381 5.77 0.00 40.21 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 4.938832 TGTATTTAACCCGACCAACATCTG 59.061 41.667 0.00 0.00 0.00 2.90
83 84 5.168647 TGTATTTAACCCGACCAACATCT 57.831 39.130 0.00 0.00 0.00 2.90
84 85 5.732247 GCATGTATTTAACCCGACCAACATC 60.732 44.000 0.00 0.00 0.00 3.06
85 86 4.097286 GCATGTATTTAACCCGACCAACAT 59.903 41.667 0.00 0.00 0.00 2.71
86 87 3.440872 GCATGTATTTAACCCGACCAACA 59.559 43.478 0.00 0.00 0.00 3.33
87 88 3.440872 TGCATGTATTTAACCCGACCAAC 59.559 43.478 0.00 0.00 0.00 3.77
88 89 3.440872 GTGCATGTATTTAACCCGACCAA 59.559 43.478 0.00 0.00 0.00 3.67
89 90 3.011119 GTGCATGTATTTAACCCGACCA 58.989 45.455 0.00 0.00 0.00 4.02
90 91 3.275999 AGTGCATGTATTTAACCCGACC 58.724 45.455 0.00 0.00 0.00 4.79
91 92 3.936453 TGAGTGCATGTATTTAACCCGAC 59.064 43.478 0.00 0.00 0.00 4.79
92 93 3.936453 GTGAGTGCATGTATTTAACCCGA 59.064 43.478 0.00 0.00 0.00 5.14
93 94 3.687212 TGTGAGTGCATGTATTTAACCCG 59.313 43.478 0.00 0.00 0.00 5.28
94 95 5.581605 CATGTGAGTGCATGTATTTAACCC 58.418 41.667 0.00 0.00 40.81 4.11
95 96 5.036737 GCATGTGAGTGCATGTATTTAACC 58.963 41.667 7.71 0.00 45.75 2.85
107 108 3.529533 AGAATGAGTAGCATGTGAGTGC 58.470 45.455 0.00 0.00 45.38 4.40
108 109 5.640783 TGAAAGAATGAGTAGCATGTGAGTG 59.359 40.000 0.00 0.00 37.28 3.51
109 110 5.798132 TGAAAGAATGAGTAGCATGTGAGT 58.202 37.500 0.00 0.00 37.28 3.41
110 111 6.537660 TCATGAAAGAATGAGTAGCATGTGAG 59.462 38.462 0.00 0.00 37.28 3.51
111 112 6.314648 GTCATGAAAGAATGAGTAGCATGTGA 59.685 38.462 0.00 0.00 37.24 3.58
132 133 2.741228 GCTCGAAGATGAAGCTGGTCAT 60.741 50.000 0.36 0.36 41.01 3.06
155 156 9.752274 CTTCTCTCTGAACTTTGAATATTTTCG 57.248 33.333 0.00 0.00 34.39 3.46
184 185 2.799917 GCATGTCGTACTAAGGGAGCAG 60.800 54.545 0.00 0.00 0.00 4.24
224 225 2.415893 CCATCACCGGCAAGAAATTGAC 60.416 50.000 0.00 0.00 0.00 3.18
228 229 1.463674 GTCCATCACCGGCAAGAAAT 58.536 50.000 0.00 0.00 0.00 2.17
238 239 2.436646 CCTGTGCCGTCCATCACC 60.437 66.667 0.00 0.00 32.51 4.02
240 241 2.927856 ACCCTGTGCCGTCCATCA 60.928 61.111 0.00 0.00 0.00 3.07
253 254 1.420532 TTTAACCCGACCAGCACCCT 61.421 55.000 0.00 0.00 0.00 4.34
367 401 4.464951 TCGACATACCAAGGCTTCTAAGAA 59.535 41.667 0.00 0.00 0.00 2.52
402 436 1.207811 TCCATGAGATCAAGCGCAAGA 59.792 47.619 11.47 7.32 43.02 3.02
570 605 3.228188 ACTGTGAGCTTCCCAATTGAA 57.772 42.857 7.12 0.00 0.00 2.69
635 670 0.399233 GGTCATGAGGAGCCCCTAGT 60.399 60.000 0.00 0.00 44.53 2.57
682 719 7.092716 AGCAGTAAACCAAGCTTTATTGAATG 58.907 34.615 0.00 0.00 32.52 2.67
715 752 3.319122 AGGATTTGCTATCCGGAAATTGC 59.681 43.478 9.01 11.26 42.74 3.56
716 753 6.263168 AGTTAGGATTTGCTATCCGGAAATTG 59.737 38.462 9.01 0.00 42.74 2.32
717 754 6.365520 AGTTAGGATTTGCTATCCGGAAATT 58.634 36.000 9.01 0.00 42.74 1.82
718 755 5.941788 AGTTAGGATTTGCTATCCGGAAAT 58.058 37.500 9.01 2.39 44.96 2.17
719 756 5.367945 AGTTAGGATTTGCTATCCGGAAA 57.632 39.130 9.01 0.00 42.87 3.13
765 802 2.540931 TGTCGGTCGCTGTAACTTTTTC 59.459 45.455 0.00 0.00 0.00 2.29
827 864 2.250939 TTGTGCGGCGAGAAACCAG 61.251 57.895 12.98 0.00 0.00 4.00
986 1062 4.976925 CCATGGCGAGGCTAGGCG 62.977 72.222 15.88 3.16 36.92 5.52
991 1067 2.122413 TATCCCCATGGCGAGGCT 60.122 61.111 6.09 0.00 0.00 4.58
1008 1089 3.122250 GACGCCGATGACGTAGCCT 62.122 63.158 0.00 0.00 45.24 4.58
1216 1297 1.420891 ACCCTAGCGGTAAAACCAACA 59.579 47.619 0.00 0.00 45.97 3.33
1228 1309 3.188873 CGACCTAGATCTAAACCCTAGCG 59.811 52.174 3.57 0.00 31.08 4.26
1282 1367 2.170187 AGCTCAGCTGTCCCAAATCTAG 59.830 50.000 14.67 0.17 37.57 2.43
1331 1416 0.108138 AGCAGCAACCTCCATCGTAC 60.108 55.000 0.00 0.00 0.00 3.67
1362 1447 4.536090 ACACAATCAGATCCTGGAACCTAA 59.464 41.667 0.00 0.00 31.51 2.69
1386 1471 0.455410 TCTGCAGCAACAACAACCAC 59.545 50.000 9.47 0.00 0.00 4.16
1388 1473 1.664016 CGATCTGCAGCAACAACAACC 60.664 52.381 9.47 0.00 0.00 3.77
1452 1540 0.178068 GGGAGTGCACGTACATCCAT 59.822 55.000 20.15 0.00 0.00 3.41
1483 1588 4.705023 GTGTTACATGGCAAGATAAAGGGT 59.295 41.667 0.00 0.00 0.00 4.34
1484 1589 4.704540 TGTGTTACATGGCAAGATAAAGGG 59.295 41.667 0.00 0.00 0.00 3.95
1485 1590 5.895636 TGTGTTACATGGCAAGATAAAGG 57.104 39.130 0.00 0.00 0.00 3.11
1486 1591 8.623903 ACATATGTGTTACATGGCAAGATAAAG 58.376 33.333 7.78 0.00 39.53 1.85
1487 1592 8.518430 ACATATGTGTTACATGGCAAGATAAA 57.482 30.769 7.78 0.00 39.53 1.40
1488 1593 8.518430 AACATATGTGTTACATGGCAAGATAA 57.482 30.769 9.63 0.00 46.37 1.75
1503 1608 2.099141 ACGCAGCAGAACATATGTGT 57.901 45.000 9.63 0.00 41.28 3.72
1504 1609 3.190079 ACTACGCAGCAGAACATATGTG 58.810 45.455 9.63 0.00 0.00 3.21
1505 1610 3.131223 AGACTACGCAGCAGAACATATGT 59.869 43.478 1.41 1.41 0.00 2.29
1506 1611 3.711086 AGACTACGCAGCAGAACATATG 58.289 45.455 0.00 0.00 0.00 1.78
1507 1612 4.115516 CAAGACTACGCAGCAGAACATAT 58.884 43.478 0.00 0.00 0.00 1.78
1508 1613 3.511699 CAAGACTACGCAGCAGAACATA 58.488 45.455 0.00 0.00 0.00 2.29
1509 1614 2.341257 CAAGACTACGCAGCAGAACAT 58.659 47.619 0.00 0.00 0.00 2.71
1510 1615 1.783284 CAAGACTACGCAGCAGAACA 58.217 50.000 0.00 0.00 0.00 3.18
1511 1616 0.440371 GCAAGACTACGCAGCAGAAC 59.560 55.000 0.00 0.00 0.00 3.01
1544 1650 1.352352 CCCCCAAGCTACCCAGATATG 59.648 57.143 0.00 0.00 0.00 1.78
1545 1651 1.747444 CCCCCAAGCTACCCAGATAT 58.253 55.000 0.00 0.00 0.00 1.63
1574 1680 1.567537 GAGCTTAACACGTTGCGCA 59.432 52.632 5.66 5.66 0.00 6.09
1581 1687 5.680229 CCTACATACTTACGAGCTTAACACG 59.320 44.000 0.00 0.00 38.43 4.49
1582 1688 6.558909 ACCTACATACTTACGAGCTTAACAC 58.441 40.000 0.00 0.00 0.00 3.32
1587 1693 7.038048 GGTTAAACCTACATACTTACGAGCTT 58.962 38.462 0.00 0.00 34.73 3.74
1588 1694 6.153340 TGGTTAAACCTACATACTTACGAGCT 59.847 38.462 0.00 0.00 39.58 4.09
1607 1713 9.999660 TGTTACTACTGTACAAATCATGGTTAA 57.000 29.630 0.00 0.00 0.00 2.01
1636 1742 7.312899 CACCACAGAAATTTTCTATTGGGTAC 58.687 38.462 27.18 0.00 42.43 3.34
1638 1744 5.245977 CCACCACAGAAATTTTCTATTGGGT 59.754 40.000 27.18 20.61 42.43 4.51
1648 1754 1.708341 AGCAGCCACCACAGAAATTT 58.292 45.000 0.00 0.00 0.00 1.82
1677 1786 5.876460 ACGGCCTTTTTACGTAGAATTACAT 59.124 36.000 0.00 0.00 39.30 2.29
1679 1788 5.784750 ACGGCCTTTTTACGTAGAATTAC 57.215 39.130 0.00 0.00 39.30 1.89
1688 1797 6.630045 GTGCTATAATAAACGGCCTTTTTACG 59.370 38.462 13.02 0.00 0.00 3.18
1700 1809 9.983804 GCCCGAATTATTAGTGCTATAATAAAC 57.016 33.333 14.05 11.32 39.69 2.01
1706 1815 6.707290 ACATGCCCGAATTATTAGTGCTATA 58.293 36.000 0.00 0.00 0.00 1.31
1707 1816 5.560724 ACATGCCCGAATTATTAGTGCTAT 58.439 37.500 0.00 0.00 0.00 2.97
1734 1843 9.010029 GGTATAAGTTTCCACAATTTTCTGAGA 57.990 33.333 0.00 0.00 0.00 3.27
1752 1861 4.532521 ACAGCCTGAAACTGAGGTATAAGT 59.467 41.667 0.00 0.00 38.55 2.24
1765 1874 3.732471 GCAACGTAAACAACAGCCTGAAA 60.732 43.478 0.00 0.00 0.00 2.69
1768 1877 1.064803 TGCAACGTAAACAACAGCCTG 59.935 47.619 0.00 0.00 0.00 4.85
1771 1880 3.666797 GGTTATGCAACGTAAACAACAGC 59.333 43.478 0.00 0.00 35.34 4.40
1802 1911 1.031235 CACCATCACCTGCACAACAA 58.969 50.000 0.00 0.00 0.00 2.83
1839 1948 1.741327 CTGCCCACATGCATAAGGCC 61.741 60.000 23.67 10.10 43.18 5.19
1965 2075 4.680110 CGACTATACGTCATGATCCCAAAC 59.320 45.833 0.00 0.00 42.98 2.93
1967 2077 3.887110 ACGACTATACGTCATGATCCCAA 59.113 43.478 0.00 0.00 43.02 4.12
1975 2085 7.605309 TGTATCCAATCTACGACTATACGTCAT 59.395 37.037 0.00 0.00 45.32 3.06
2046 2156 8.334016 TGTTTCATAATTTGTCAAACACGAAG 57.666 30.769 0.00 0.00 33.17 3.79
2051 2161 8.474025 AGTTCCTGTTTCATAATTTGTCAAACA 58.526 29.630 0.00 0.00 35.99 2.83
2067 2177 6.894339 AATCCATTTCGTAAGTTCCTGTTT 57.106 33.333 0.00 0.00 39.48 2.83
2109 2219 5.887598 TCATCATGCAAAGCTGTAAAGGTAT 59.112 36.000 0.00 0.00 0.00 2.73
2248 2360 6.375377 CATCTCTCTTTCAGCCGTACTATAC 58.625 44.000 0.00 0.00 0.00 1.47
2302 2414 1.036481 ATGGTGTGCTGTTGTGTGCA 61.036 50.000 0.00 0.00 36.79 4.57
2439 2558 7.975058 CGAGAATCAAGAGTCTATGCATCATAT 59.025 37.037 0.19 0.00 35.71 1.78
2501 2620 6.205464 CCTCTTCAATTCAAGCTAACAAGTGA 59.795 38.462 0.00 0.00 0.00 3.41
2530 2649 3.358775 CGACATAGCTCAGAAACGAGAG 58.641 50.000 0.00 0.00 34.79 3.20
2562 2681 2.858344 CCAAGCGAATGTAAGGTACTCG 59.142 50.000 0.00 0.00 38.49 4.18
2697 2819 7.759433 CCATAAACATTTCAGGCGTAGAAAAAT 59.241 33.333 6.84 0.00 38.36 1.82
2704 2826 4.328536 ACACCATAAACATTTCAGGCGTA 58.671 39.130 0.00 0.00 0.00 4.42
2743 2865 1.679139 TCAGGGATTATTTGGCGCTG 58.321 50.000 7.64 0.00 42.04 5.18
2748 2870 7.568199 AAACGAACTATCAGGGATTATTTGG 57.432 36.000 0.00 0.00 0.00 3.28
2773 2895 6.629128 CAATATGTGACAACAAAAGCCCATA 58.371 36.000 0.00 0.00 40.46 2.74
2788 3138 5.353111 CATGGCAAATTCAGCAATATGTGA 58.647 37.500 0.00 0.00 0.00 3.58
2794 3144 4.699637 CATACCATGGCAAATTCAGCAAT 58.300 39.130 13.04 0.00 0.00 3.56
2839 3190 8.821686 ATTTCTTGACAAACCATCCACATATA 57.178 30.769 0.00 0.00 0.00 0.86
2840 3191 7.722949 ATTTCTTGACAAACCATCCACATAT 57.277 32.000 0.00 0.00 0.00 1.78
2876 3227 7.823799 GGAAAGCCATATCAGGAAAATTCAAAA 59.176 33.333 0.00 0.00 0.00 2.44
2925 3276 0.108585 ATGACTGCAACGGTGACCTT 59.891 50.000 3.55 0.00 0.00 3.50
3109 3462 1.815408 GCAACAGTGACCATGGAGTGT 60.815 52.381 21.47 13.48 0.00 3.55
3110 3463 0.877071 GCAACAGTGACCATGGAGTG 59.123 55.000 21.47 12.76 0.00 3.51
3145 3498 2.422479 CAGGCTCAACAGTTCATGATGG 59.578 50.000 0.00 0.00 32.75 3.51
3166 3519 2.280628 ACATAAGGAAAGCTGCTACGC 58.719 47.619 0.90 0.00 0.00 4.42
3168 3521 6.254281 TCAAAACATAAGGAAAGCTGCTAC 57.746 37.500 0.90 0.00 0.00 3.58
3194 3547 1.553690 TTCCTCCCTAGGCAGTGTGC 61.554 60.000 2.05 0.00 43.31 4.57
3215 3568 1.839994 CAGGAGGAAATGGGTAGCAGA 59.160 52.381 0.00 0.00 0.00 4.26
3232 3586 4.551388 GCAATAGGTCGATTAGAGACAGG 58.449 47.826 0.00 0.00 40.20 4.00
3233 3587 4.038042 TGGCAATAGGTCGATTAGAGACAG 59.962 45.833 0.00 0.00 40.20 3.51
3234 3588 3.958147 TGGCAATAGGTCGATTAGAGACA 59.042 43.478 0.00 0.00 40.20 3.41
3245 3599 1.139058 ACGATCCTGTGGCAATAGGTC 59.861 52.381 16.09 12.38 36.14 3.85
3354 3708 8.912988 ACATAACAAGAAAGGAACAGAATTTGA 58.087 29.630 0.00 0.00 0.00 2.69
3376 3730 4.043561 TCCTCTTGGGCAAAAGGTTACATA 59.956 41.667 0.00 0.00 34.39 2.29
3537 3893 1.834263 ACTTGCACTAGATCAGGTCCC 59.166 52.381 0.00 0.00 0.00 4.46
3622 3978 4.922692 TGATAAATTTTGCAAACGCTCCAG 59.077 37.500 12.39 0.00 0.00 3.86
3660 4016 4.380550 GGATTTTAGGGCAACAAGCTACAC 60.381 45.833 0.00 0.00 44.79 2.90
3686 4042 8.876275 TTCTATGAGCAATGAAATATTTTGGC 57.124 30.769 1.43 4.50 0.00 4.52
3714 4104 5.200454 CAATTTTCAGTCACAGACAGAACG 58.800 41.667 4.75 0.00 37.69 3.95
3748 4138 1.066071 TCACAAACAGAACGGTGACCA 60.066 47.619 1.11 0.00 35.51 4.02
3755 4145 5.799936 ACAATTTTCAGTCACAAACAGAACG 59.200 36.000 0.00 0.00 33.60 3.95
3823 4217 1.290203 ATAGAAAGCACGACATGGCG 58.710 50.000 21.98 21.98 34.54 5.69
3831 4225 2.986479 GCCACCAAAAATAGAAAGCACG 59.014 45.455 0.00 0.00 0.00 5.34
3834 4228 3.934579 CCATGCCACCAAAAATAGAAAGC 59.065 43.478 0.00 0.00 0.00 3.51
3863 4258 1.228245 GCAAGTGAGGGAAGTGCCA 60.228 57.895 0.00 0.00 38.95 4.92
3865 4260 0.674895 ATCGCAAGTGAGGGAAGTGC 60.675 55.000 0.00 0.00 39.48 4.40
3882 4277 9.374838 AGATTGGTAAAGAAAATGCATTCAATC 57.625 29.630 24.54 24.54 37.85 2.67
3885 4280 7.039152 TCCAGATTGGTAAAGAAAATGCATTCA 60.039 33.333 13.38 0.44 39.03 2.57
3886 4281 7.322664 TCCAGATTGGTAAAGAAAATGCATTC 58.677 34.615 13.38 1.61 39.03 2.67
3888 4283 6.438425 ACTCCAGATTGGTAAAGAAAATGCAT 59.562 34.615 0.00 0.00 39.03 3.96
3889 4284 5.774690 ACTCCAGATTGGTAAAGAAAATGCA 59.225 36.000 0.00 0.00 39.03 3.96
3890 4285 6.272822 ACTCCAGATTGGTAAAGAAAATGC 57.727 37.500 0.00 0.00 39.03 3.56
3893 4288 9.581289 TGATTTACTCCAGATTGGTAAAGAAAA 57.419 29.630 0.00 0.00 38.33 2.29
3912 4307 4.502645 AGTTTTTGCTTGCACGTGATTTAC 59.497 37.500 22.23 0.69 0.00 2.01
3933 4328 4.452455 CGAAATGACAAGTCTAGCCAAAGT 59.548 41.667 1.53 0.00 0.00 2.66
3993 4388 5.180492 ACATGGTAATGACAAAACTGGTACG 59.820 40.000 0.00 0.00 37.24 3.67
3994 4389 6.569179 ACATGGTAATGACAAAACTGGTAC 57.431 37.500 0.00 0.00 37.24 3.34
4105 4500 1.227383 GGATTTCTGGATGGGCGGT 59.773 57.895 0.00 0.00 0.00 5.68
4110 4505 0.178068 ACCGTCGGATTTCTGGATGG 59.822 55.000 20.51 8.11 41.59 3.51
4232 4636 1.830587 ATCTGCCAACGTGGAGAGCA 61.831 55.000 8.04 0.59 40.96 4.26
4260 4664 1.226717 GGGACAGCGAGACGTGATC 60.227 63.158 0.00 0.00 0.00 2.92
4261 4665 2.885861 GGGACAGCGAGACGTGAT 59.114 61.111 0.00 0.00 0.00 3.06
4262 4666 3.733960 CGGGACAGCGAGACGTGA 61.734 66.667 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.