Multiple sequence alignment - TraesCS7D01G133600

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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 TraesCS7D01G133600 chr7D 100.000 7738 0 0 1 7738 84795679 84803416 0.000000e+00 14290.0
1 TraesCS7D01G133600 chr7D 92.744 317 14 3 1298 1605 126646030 126646346 4.260000e-122 449.0
2 TraesCS7D01G133600 chr7D 88.889 351 25 11 412 752 75930981 75930635 3.340000e-113 420.0
3 TraesCS7D01G133600 chr7D 83.871 403 35 15 7358 7737 85206667 85207062 2.660000e-94 357.0
4 TraesCS7D01G133600 chr7D 85.866 283 32 8 471 748 60440560 60440281 2.110000e-75 294.0
5 TraesCS7D01G133600 chr7D 94.245 139 7 1 1157 1294 126645011 126645149 2.190000e-50 211.0
6 TraesCS7D01G133600 chr7A 94.257 4179 143 28 1709 5827 85959124 85963265 0.000000e+00 6298.0
7 TraesCS7D01G133600 chr7A 89.022 1339 125 14 5844 7167 85963249 85964580 0.000000e+00 1639.0
8 TraesCS7D01G133600 chr7A 89.592 932 64 20 384 1296 85957746 85958663 0.000000e+00 1153.0
9 TraesCS7D01G133600 chr7A 87.766 564 35 10 7178 7738 85964623 85965155 5.100000e-176 628.0
10 TraesCS7D01G133600 chr7A 93.575 358 19 4 1349 1704 85958663 85959018 1.480000e-146 531.0
11 TraesCS7D01G133600 chr7A 90.286 350 26 8 404 748 80067777 80067431 1.180000e-122 451.0
12 TraesCS7D01G133600 chr7A 82.630 403 41 16 7358 7737 86227606 86228002 5.790000e-86 329.0
13 TraesCS7D01G133600 chr7A 87.072 263 31 3 493 753 64729357 64729096 2.110000e-75 294.0
14 TraesCS7D01G133600 chr7A 92.617 149 5 3 289 431 85957605 85957753 7.870000e-50 209.0
15 TraesCS7D01G133600 chr7A 86.719 128 8 2 76 194 85957193 85957320 4.870000e-27 134.0
16 TraesCS7D01G133600 chr7B 96.133 2198 85 0 3630 5827 34493706 34495903 0.000000e+00 3589.0
17 TraesCS7D01G133600 chr7B 95.932 1893 60 9 1711 3594 34491822 34493706 0.000000e+00 3053.0
18 TraesCS7D01G133600 chr7B 91.745 1914 119 17 5844 7738 34495887 34497780 0.000000e+00 2623.0
19 TraesCS7D01G133600 chr7B 86.301 1241 95 44 67 1273 34490070 34491269 0.000000e+00 1280.0
20 TraesCS7D01G133600 chr7B 92.593 702 42 6 7039 7738 34516121 34516814 0.000000e+00 1000.0
21 TraesCS7D01G133600 chr7B 86.775 431 34 6 508 933 34424310 34424722 7.080000e-125 459.0
22 TraesCS7D01G133600 chr7B 91.343 335 18 8 423 749 22062698 22062367 1.530000e-121 448.0
23 TraesCS7D01G133600 chr7B 89.124 331 16 8 1 331 34420191 34420501 2.020000e-105 394.0
24 TraesCS7D01G133600 chr7B 87.143 280 32 4 472 748 2943736 2943458 1.620000e-81 315.0
25 TraesCS7D01G133600 chr7B 82.011 378 35 12 7384 7737 34821679 34822047 2.730000e-74 291.0
26 TraesCS7D01G133600 chr7B 83.117 231 11 17 7098 7328 34514865 34515067 1.330000e-42 185.0
27 TraesCS7D01G133600 chr7B 85.000 140 16 3 1574 1708 34491582 34491721 3.770000e-28 137.0
28 TraesCS7D01G133600 chr5D 93.542 960 39 12 1711 2659 395262260 395263207 0.000000e+00 1408.0
29 TraesCS7D01G133600 chr5D 91.312 564 37 7 1157 1709 395261600 395262162 0.000000e+00 760.0
30 TraesCS7D01G133600 chr5B 92.896 732 35 8 1936 2659 475688796 475689518 0.000000e+00 1048.0
31 TraesCS7D01G133600 chr5B 90.179 560 44 9 1160 1709 475687952 475688510 0.000000e+00 719.0
32 TraesCS7D01G133600 chr5B 93.750 192 9 2 1711 1902 475688607 475688795 1.270000e-72 285.0
33 TraesCS7D01G133600 chr2D 97.143 35 1 0 5724 5758 126995838 126995872 8.380000e-05 60.2
34 TraesCS7D01G133600 chr2A 97.143 35 1 0 5724 5758 133698269 133698303 8.380000e-05 60.2
35 TraesCS7D01G133600 chr2A 97.143 35 1 0 5724 5758 764234517 764234551 8.380000e-05 60.2
36 TraesCS7D01G133600 chr2A 89.130 46 4 1 7123 7168 704759915 704759871 1.000000e-03 56.5


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 TraesCS7D01G133600 chr7D 84795679 84803416 7737 False 14290.000000 14290 100.000000 1 7738 1 chr7D.!!$F1 7737
1 TraesCS7D01G133600 chr7D 126645011 126646346 1335 False 330.000000 449 93.494500 1157 1605 2 chr7D.!!$F3 448
2 TraesCS7D01G133600 chr7A 85957193 85965155 7962 False 1513.142857 6298 90.506857 76 7738 7 chr7A.!!$F2 7662
3 TraesCS7D01G133600 chr7B 34490070 34497780 7710 False 2136.400000 3589 91.022200 67 7738 5 chr7B.!!$F3 7671
4 TraesCS7D01G133600 chr7B 34514865 34516814 1949 False 592.500000 1000 87.855000 7039 7738 2 chr7B.!!$F4 699
5 TraesCS7D01G133600 chr7B 34420191 34424722 4531 False 426.500000 459 87.949500 1 933 2 chr7B.!!$F2 932
6 TraesCS7D01G133600 chr5D 395261600 395263207 1607 False 1084.000000 1408 92.427000 1157 2659 2 chr5D.!!$F1 1502
7 TraesCS7D01G133600 chr5B 475687952 475689518 1566 False 684.000000 1048 92.275000 1160 2659 3 chr5B.!!$F1 1499

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
49 50 0.034756 TAACCCATCCCATCGATGCG 59.965 55.000 20.25 12.01 46.17 4.73 F
504 868 0.036765 GTGGTGCGATTAGTCCCACA 60.037 55.000 5.52 0.00 43.96 4.17 F
898 4793 0.179108 CGCTTCCCCCTCTAAACGAG 60.179 60.000 0.00 0.00 39.57 4.18 F
987 4895 1.110518 TGCCCCAAAACGTTCTTCCC 61.111 55.000 0.00 0.00 0.00 3.97 F
2358 7342 1.751927 CCAGCCCTGCAAGACATCC 60.752 63.158 0.00 0.00 34.07 3.51 F
2699 7692 2.684881 CCGCACCAGCTAGAAAATCATT 59.315 45.455 0.00 0.00 39.10 2.57 F
2741 7734 4.678509 TTTAGTATGAGCACTTTTGGCG 57.321 40.909 0.00 0.00 36.08 5.69 F
3171 8164 5.070001 ACTTAATTGCCACTAAGCACTTGA 58.930 37.500 0.05 0.00 43.97 3.02 F
4342 9396 1.202568 TCTCACCCGATGATGATGTGC 60.203 52.381 0.00 0.00 36.48 4.57 F
6011 11099 1.003580 TGTGCCATCTTCCCAGTCTTC 59.996 52.381 0.00 0.00 0.00 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1242 5169 0.039764 AGATGGTGGAGACGAGGACA 59.960 55.0 0.00 0.0 0.00 4.02 R
1888 6868 0.320771 ACGAGCACACACATTCTCCC 60.321 55.0 0.00 0.0 0.00 4.30 R
2358 7342 2.806244 CCTGTCTGGAAAAGGTTACACG 59.194 50.0 0.00 0.0 38.35 4.49 R
2718 7711 5.457140 CGCCAAAAGTGCTCATACTAAAAA 58.543 37.5 0.00 0.0 0.00 1.94 R
3616 8670 0.101759 CTGCACAGCAAGCACAAAGT 59.898 50.0 0.00 0.0 38.41 2.66 R
3622 8676 0.108396 TACTTCCTGCACAGCAAGCA 59.892 50.0 1.16 0.0 38.41 3.91 R
3625 8679 0.397941 AGCTACTTCCTGCACAGCAA 59.602 50.0 0.00 0.0 38.41 3.91 R
4949 10003 1.315690 CAATTGCTCGGCATCTCCAT 58.684 50.0 0.00 0.0 38.76 3.41 R
6110 11209 0.394565 AGGTGAGCCACTCAGTGAAC 59.605 55.0 6.30 0.0 41.46 3.18 R
6885 11984 0.102120 CTCACCCTGCTGACGATCTC 59.898 60.0 0.00 0.0 0.00 2.75 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
49 50 0.034756 TAACCCATCCCATCGATGCG 59.965 55.000 20.25 12.01 46.17 4.73
68 69 3.034406 CGCCACTCGCTAATAAACAAC 57.966 47.619 0.00 0.00 34.21 3.32
71 72 4.026804 CGCCACTCGCTAATAAACAACTAG 60.027 45.833 0.00 0.00 34.21 2.57
216 225 0.541863 GTCCCCGACCAGAATGATGT 59.458 55.000 0.00 0.00 39.69 3.06
243 252 1.089112 CATGCCACTTGCGATTCTCA 58.911 50.000 0.00 0.00 45.60 3.27
244 253 1.469703 CATGCCACTTGCGATTCTCAA 59.530 47.619 0.00 0.00 45.60 3.02
245 254 1.825090 TGCCACTTGCGATTCTCAAT 58.175 45.000 0.00 0.00 45.60 2.57
246 255 1.739466 TGCCACTTGCGATTCTCAATC 59.261 47.619 0.00 0.00 45.60 2.67
248 257 2.031437 GCCACTTGCGATTCTCAATCTC 59.969 50.000 0.00 0.00 35.73 2.75
250 259 3.875727 CCACTTGCGATTCTCAATCTCAT 59.124 43.478 0.00 0.00 33.12 2.90
251 260 4.025061 CCACTTGCGATTCTCAATCTCATC 60.025 45.833 0.00 0.00 33.12 2.92
252 261 4.809958 CACTTGCGATTCTCAATCTCATCT 59.190 41.667 0.00 0.00 33.12 2.90
255 264 7.010830 CACTTGCGATTCTCAATCTCATCTAAA 59.989 37.037 0.00 0.00 33.12 1.85
256 265 7.550551 ACTTGCGATTCTCAATCTCATCTAAAA 59.449 33.333 0.00 0.00 33.12 1.52
392 598 2.106332 CCGTATCAGGCCCACGAC 59.894 66.667 15.87 2.40 37.89 4.34
480 844 1.588139 CGTATCCGTCGGTTGGCTC 60.588 63.158 11.88 0.00 0.00 4.70
504 868 0.036765 GTGGTGCGATTAGTCCCACA 60.037 55.000 5.52 0.00 43.96 4.17
552 4443 0.767060 AGCGGGGTATAAGAAGGGGG 60.767 60.000 0.00 0.00 0.00 5.40
692 4583 4.225942 TCATGGGCTACTGAGAATTTCTGT 59.774 41.667 3.03 0.00 40.57 3.41
775 4670 2.760092 GGCCTGATTGAACTTTGCCATA 59.240 45.455 0.00 0.00 37.36 2.74
794 4689 7.036829 TGCCATACACATGATTCTGAAATTTG 58.963 34.615 0.00 0.00 33.67 2.32
812 4707 7.661437 TGAAATTTGGATATACCTCGAGGATTG 59.339 37.037 37.69 11.84 39.86 2.67
817 4712 5.839063 TGGATATACCTCGAGGATTGTTCTT 59.161 40.000 37.69 15.17 39.86 2.52
823 4718 4.689345 ACCTCGAGGATTGTTCTTTTTACG 59.311 41.667 37.69 5.14 38.94 3.18
824 4719 4.689345 CCTCGAGGATTGTTCTTTTTACGT 59.311 41.667 28.21 0.00 37.39 3.57
825 4720 5.865552 CCTCGAGGATTGTTCTTTTTACGTA 59.134 40.000 28.21 0.00 37.39 3.57
827 4722 7.064253 CCTCGAGGATTGTTCTTTTTACGTATT 59.936 37.037 28.21 0.00 37.39 1.89
888 4783 0.960861 CTCAGAAAACCGCTTCCCCC 60.961 60.000 0.00 0.00 0.00 5.40
898 4793 0.179108 CGCTTCCCCCTCTAAACGAG 60.179 60.000 0.00 0.00 39.57 4.18
908 4803 2.338500 CTCTAAACGAGAAGCCGCTTT 58.662 47.619 7.16 0.00 42.62 3.51
969 4868 1.442184 CCGACGACTCGACCAACTG 60.442 63.158 5.20 0.00 43.06 3.16
970 4869 2.081212 CGACGACTCGACCAACTGC 61.081 63.158 5.20 0.00 43.06 4.40
984 4892 1.136110 CAACTGCCCCAAAACGTTCTT 59.864 47.619 0.00 0.00 0.00 2.52
987 4895 1.110518 TGCCCCAAAACGTTCTTCCC 61.111 55.000 0.00 0.00 0.00 3.97
990 4898 2.036387 CCCCAAAACGTTCTTCCCTTT 58.964 47.619 0.00 0.00 0.00 3.11
991 4899 2.035449 CCCCAAAACGTTCTTCCCTTTC 59.965 50.000 0.00 0.00 0.00 2.62
992 4900 2.287368 CCCAAAACGTTCTTCCCTTTCG 60.287 50.000 0.00 0.00 0.00 3.46
993 4901 2.381589 CAAAACGTTCTTCCCTTTCGC 58.618 47.619 0.00 0.00 0.00 4.70
1003 4930 3.204827 CCTTTCGCGCCTCCATGG 61.205 66.667 4.97 4.97 39.35 3.66
1242 5169 2.678934 TTCGCGCTCTACCACCCT 60.679 61.111 5.56 0.00 0.00 4.34
1381 6204 4.193826 TGTTCTACTGACAATCTGGCTC 57.806 45.455 0.00 0.00 0.00 4.70
1612 6485 5.945784 ACATGCTAAAGTTGGAGCTGATAAA 59.054 36.000 10.48 0.00 39.54 1.40
1704 6580 8.656849 ACTATACGTTGCTATCTCTTGTTTTTG 58.343 33.333 0.00 0.00 0.00 2.44
1705 6581 7.667043 ATACGTTGCTATCTCTTGTTTTTGA 57.333 32.000 0.00 0.00 0.00 2.69
1707 6583 6.970484 ACGTTGCTATCTCTTGTTTTTGATT 58.030 32.000 0.00 0.00 0.00 2.57
1728 6708 7.715657 TGATTATCATCAAATTACCTGTTGGC 58.284 34.615 0.00 0.00 36.41 4.52
1854 6834 4.507756 GGTTTGTTCTGCTCACCATTTTTC 59.492 41.667 0.00 0.00 0.00 2.29
1888 6868 7.488150 GGTTCTTCTTTTGTTCAGTTTTACTGG 59.512 37.037 6.96 0.00 45.94 4.00
2111 7095 2.175715 AGGCTGTTCAGGTTTTCTTCCT 59.824 45.455 1.97 0.00 35.45 3.36
2129 7113 6.385033 TCTTCCTACTTAAACTGCGTTCTAC 58.615 40.000 0.00 0.00 0.00 2.59
2200 7184 3.942829 TGCCTATCTCTGGTTTGTTGAG 58.057 45.455 0.00 0.00 0.00 3.02
2358 7342 1.751927 CCAGCCCTGCAAGACATCC 60.752 63.158 0.00 0.00 34.07 3.51
2382 7366 2.755952 AACCTTTTCCAGACAGGCTT 57.244 45.000 0.00 0.00 37.29 4.35
2414 7398 7.948278 AAGACTGCCGTATTAAGATACATTC 57.052 36.000 0.00 0.00 38.42 2.67
2607 7600 7.210174 TCTTATATTTCACGTCTTCATCAGGG 58.790 38.462 0.00 0.00 0.00 4.45
2699 7692 2.684881 CCGCACCAGCTAGAAAATCATT 59.315 45.455 0.00 0.00 39.10 2.57
2711 7704 4.911390 AGAAAATCATTCAAGTCGGAGGT 58.089 39.130 0.00 0.00 0.00 3.85
2715 7708 7.447238 AGAAAATCATTCAAGTCGGAGGTTTTA 59.553 33.333 0.00 0.00 0.00 1.52
2716 7709 6.496338 AATCATTCAAGTCGGAGGTTTTAC 57.504 37.500 0.00 0.00 0.00 2.01
2741 7734 4.678509 TTTAGTATGAGCACTTTTGGCG 57.321 40.909 0.00 0.00 36.08 5.69
3025 8018 6.742756 TCCTCAATCTCCTCTTTCTAAGGTA 58.257 40.000 0.00 0.00 35.29 3.08
3058 8051 7.992754 AATGACTCCTATAATGATTTGGAGC 57.007 36.000 16.15 11.68 45.86 4.70
3088 8081 8.220755 TGTTTCTAACTGCTGACATTAGTTTT 57.779 30.769 9.05 0.00 36.22 2.43
3112 8105 5.538813 TCTCATTGCGAACTATAGTACCCAT 59.461 40.000 5.65 0.00 0.00 4.00
3171 8164 5.070001 ACTTAATTGCCACTAAGCACTTGA 58.930 37.500 0.05 0.00 43.97 3.02
3192 8185 8.952278 ACTTGACTGTTAACTGTTGAAAATGTA 58.048 29.630 17.86 0.00 0.00 2.29
3212 8205 7.818997 ATGTATTGGATCGAGTCTGTTACTA 57.181 36.000 0.00 0.00 39.07 1.82
3269 8262 6.421377 ACAAAAGTCAACATTTGCTTTTCC 57.579 33.333 9.95 0.00 41.00 3.13
3378 8371 8.724310 ACAGATTAACCTAGGCCAGTTTATATT 58.276 33.333 9.30 0.00 0.00 1.28
3404 8397 5.447818 GGCACAGTACAATAATGCTTCTCAC 60.448 44.000 0.00 0.00 36.52 3.51
3602 8656 9.403583 TCAAATCCTTTATGTATTAACAGTCCC 57.596 33.333 0.00 0.00 39.49 4.46
3603 8657 9.408648 CAAATCCTTTATGTATTAACAGTCCCT 57.591 33.333 0.00 0.00 39.49 4.20
3604 8658 9.628500 AAATCCTTTATGTATTAACAGTCCCTC 57.372 33.333 0.00 0.00 39.49 4.30
3605 8659 7.743116 TCCTTTATGTATTAACAGTCCCTCA 57.257 36.000 0.00 0.00 39.49 3.86
3606 8660 8.331931 TCCTTTATGTATTAACAGTCCCTCAT 57.668 34.615 0.00 0.00 39.49 2.90
3607 8661 8.778059 TCCTTTATGTATTAACAGTCCCTCATT 58.222 33.333 0.00 0.00 39.49 2.57
3608 8662 9.408648 CCTTTATGTATTAACAGTCCCTCATTT 57.591 33.333 0.00 0.00 39.49 2.32
3610 8664 9.967451 TTTATGTATTAACAGTCCCTCATTTGA 57.033 29.630 0.00 0.00 39.49 2.69
3611 8665 9.613428 TTATGTATTAACAGTCCCTCATTTGAG 57.387 33.333 0.39 0.39 39.49 3.02
3612 8666 7.016153 TGTATTAACAGTCCCTCATTTGAGT 57.984 36.000 6.81 0.00 40.48 3.41
3613 8667 7.458397 TGTATTAACAGTCCCTCATTTGAGTT 58.542 34.615 6.81 0.00 40.48 3.01
3614 8668 7.942341 TGTATTAACAGTCCCTCATTTGAGTTT 59.058 33.333 6.81 0.00 40.48 2.66
3615 8669 7.839680 ATTAACAGTCCCTCATTTGAGTTTT 57.160 32.000 6.81 0.00 40.48 2.43
3616 8670 8.934023 ATTAACAGTCCCTCATTTGAGTTTTA 57.066 30.769 6.81 0.00 40.48 1.52
3617 8671 6.635030 AACAGTCCCTCATTTGAGTTTTAC 57.365 37.500 6.81 0.29 40.48 2.01
3618 8672 5.941788 ACAGTCCCTCATTTGAGTTTTACT 58.058 37.500 6.81 2.30 40.48 2.24
3619 8673 6.365520 ACAGTCCCTCATTTGAGTTTTACTT 58.634 36.000 6.81 0.00 40.48 2.24
3620 8674 6.833933 ACAGTCCCTCATTTGAGTTTTACTTT 59.166 34.615 6.81 0.00 40.48 2.66
3621 8675 7.141363 CAGTCCCTCATTTGAGTTTTACTTTG 58.859 38.462 6.81 0.00 40.48 2.77
3622 8676 6.833933 AGTCCCTCATTTGAGTTTTACTTTGT 59.166 34.615 6.81 0.00 40.48 2.83
3623 8677 6.918022 GTCCCTCATTTGAGTTTTACTTTGTG 59.082 38.462 6.81 0.00 40.48 3.33
3624 8678 5.691754 CCCTCATTTGAGTTTTACTTTGTGC 59.308 40.000 6.81 0.00 40.48 4.57
3625 8679 6.461509 CCCTCATTTGAGTTTTACTTTGTGCT 60.462 38.462 6.81 0.00 40.48 4.40
3626 8680 6.980397 CCTCATTTGAGTTTTACTTTGTGCTT 59.020 34.615 6.81 0.00 40.48 3.91
3627 8681 7.043192 CCTCATTTGAGTTTTACTTTGTGCTTG 60.043 37.037 6.81 0.00 40.48 4.01
3628 8682 6.255453 TCATTTGAGTTTTACTTTGTGCTTGC 59.745 34.615 0.00 0.00 0.00 4.01
3629 8683 4.981806 TGAGTTTTACTTTGTGCTTGCT 57.018 36.364 0.00 0.00 0.00 3.91
3853 8907 4.458989 TCAAGTTCAGATAACCACAATGGC 59.541 41.667 0.00 0.00 42.67 4.40
4310 9364 9.548208 GTTTCATGACTTTATTTCAGTAAGAGC 57.452 33.333 0.00 0.00 0.00 4.09
4336 9390 3.058432 GCATTTGATCTCACCCGATGATG 60.058 47.826 0.00 0.00 36.48 3.07
4342 9396 1.202568 TCTCACCCGATGATGATGTGC 60.203 52.381 0.00 0.00 36.48 4.57
4381 9435 4.520492 AGAACTTGCTATCCCAAACTTGTG 59.480 41.667 0.00 0.00 0.00 3.33
4509 9563 6.036517 CAGAACTACTTCATAACATGACTGCC 59.963 42.308 0.00 0.00 39.39 4.85
4525 9579 3.794270 CCGACATGGCCGTAACTG 58.206 61.111 0.00 0.00 0.00 3.16
4564 9618 5.066505 ACACAAACTTTCAGGTTGCTTCTAG 59.933 40.000 1.29 0.00 46.53 2.43
4574 9628 2.567615 GGTTGCTTCTAGAGGGAGTTCA 59.432 50.000 3.79 0.00 0.00 3.18
4664 9718 7.739498 TTGTAAAGAAGGTGTTTCTGGATAC 57.261 36.000 0.00 0.00 45.41 2.24
4716 9770 4.573201 GCAGTGTTGGTACAGTTTTGTCTA 59.427 41.667 0.00 0.00 42.39 2.59
4717 9771 5.065474 GCAGTGTTGGTACAGTTTTGTCTAA 59.935 40.000 0.00 0.00 42.39 2.10
4786 9840 3.766151 TCTGGAAAGTACGAGTTATGCG 58.234 45.455 0.00 0.00 0.00 4.73
4799 9853 3.360533 AGTTATGCGTAGACATCGAACG 58.639 45.455 2.30 2.30 39.55 3.95
4800 9854 2.394545 TATGCGTAGACATCGAACGG 57.605 50.000 8.50 0.00 37.12 4.44
4822 9876 6.998074 ACGGATAAAGGAGATTGAATATGCAA 59.002 34.615 0.00 0.00 0.00 4.08
4851 9905 4.133078 GTCCAAAGCTATCTCATCCAAGG 58.867 47.826 0.00 0.00 0.00 3.61
4870 9924 1.340017 GGATCAGGCCACTTGCTTACA 60.340 52.381 5.01 0.00 40.92 2.41
4949 10003 5.924356 TCAGTTTACTGGAGAATTGTCACA 58.076 37.500 9.82 0.00 43.91 3.58
5016 10070 3.144506 ACTGGAGAACTTTCATGCTGTG 58.855 45.455 0.00 0.00 0.00 3.66
5020 10074 3.057946 GGAGAACTTTCATGCTGTGGTTC 60.058 47.826 0.00 0.00 34.95 3.62
5058 10112 3.192422 AGATCATGCGTCCAGTAGATAGC 59.808 47.826 0.00 0.00 0.00 2.97
5138 10192 5.356470 AGCAAATGATCTCTTACTTGAAGGC 59.644 40.000 0.00 0.00 35.67 4.35
5245 10299 4.751060 TGCTCATTGGAATGCTGAAAATC 58.249 39.130 0.00 0.00 36.36 2.17
5249 10303 5.782047 TCATTGGAATGCTGAAAATCGTTT 58.218 33.333 0.00 0.00 36.36 3.60
5285 10339 1.808945 CATGACACAAGACTTGGAGGC 59.191 52.381 19.16 13.42 34.12 4.70
5348 10402 3.327757 TCCAGTTATTGTTCAGAGCCTGT 59.672 43.478 2.68 0.00 32.61 4.00
5484 10538 8.554490 ACATTACTATCCTATCTGTTCTTGGT 57.446 34.615 0.00 0.00 0.00 3.67
5562 10616 6.982852 AGAGAGAGAAGTAACGACAAATGAA 58.017 36.000 0.00 0.00 0.00 2.57
5626 10680 1.238439 GAAGCTTGCTAACAGGTGCA 58.762 50.000 2.10 0.00 37.42 4.57
5640 10694 3.638160 ACAGGTGCATTGAATCACACTTT 59.362 39.130 8.02 0.00 35.04 2.66
5706 10784 5.365025 TGCCAAGCTCAGTAATCTCTAATCT 59.635 40.000 0.00 0.00 0.00 2.40
5796 10876 2.290641 CACCAAGTCACAAGCAGGTAAC 59.709 50.000 0.00 0.00 0.00 2.50
5818 10898 7.701539 AACTAACCAGATTCACAATATTGCA 57.298 32.000 15.48 0.00 0.00 4.08
5819 10899 7.325660 ACTAACCAGATTCACAATATTGCAG 57.674 36.000 15.48 8.59 0.00 4.41
5820 10900 7.112122 ACTAACCAGATTCACAATATTGCAGA 58.888 34.615 15.48 10.78 0.00 4.26
5821 10901 7.776969 ACTAACCAGATTCACAATATTGCAGAT 59.223 33.333 15.48 6.56 0.00 2.90
5822 10902 7.414222 AACCAGATTCACAATATTGCAGATT 57.586 32.000 15.48 9.81 0.00 2.40
5823 10903 8.523915 AACCAGATTCACAATATTGCAGATTA 57.476 30.769 15.48 1.04 0.00 1.75
5824 10904 8.523915 ACCAGATTCACAATATTGCAGATTAA 57.476 30.769 15.48 0.38 0.00 1.40
5825 10905 9.139734 ACCAGATTCACAATATTGCAGATTAAT 57.860 29.630 15.48 4.93 0.00 1.40
5826 10906 9.976511 CCAGATTCACAATATTGCAGATTAATT 57.023 29.630 15.48 0.00 0.00 1.40
5912 11000 4.833478 ACATCTCTGCCTTCTGTTATGT 57.167 40.909 0.00 0.00 0.00 2.29
6001 11089 3.565307 TCTTTGAGGTTTGTGCCATCTT 58.435 40.909 0.00 0.00 0.00 2.40
6010 11098 1.067295 TGTGCCATCTTCCCAGTCTT 58.933 50.000 0.00 0.00 0.00 3.01
6011 11099 1.003580 TGTGCCATCTTCCCAGTCTTC 59.996 52.381 0.00 0.00 0.00 2.87
6022 11110 1.272092 CCCAGTCTTCAAGGGCATCAA 60.272 52.381 0.00 0.00 35.44 2.57
6029 11117 4.012374 TCTTCAAGGGCATCAACTTCATC 58.988 43.478 0.00 0.00 0.00 2.92
6031 11119 3.614092 TCAAGGGCATCAACTTCATCTC 58.386 45.455 0.00 0.00 0.00 2.75
6035 11123 2.941720 GGGCATCAACTTCATCTCTGTC 59.058 50.000 0.00 0.00 0.00 3.51
6038 11126 4.094590 GGCATCAACTTCATCTCTGTCAAG 59.905 45.833 0.00 0.00 0.00 3.02
6040 11128 4.341366 TCAACTTCATCTCTGTCAAGCA 57.659 40.909 0.00 0.00 0.00 3.91
6041 11129 4.903054 TCAACTTCATCTCTGTCAAGCAT 58.097 39.130 0.00 0.00 0.00 3.79
6098 11197 1.065199 ACCACATCATCCGTGCAGATT 60.065 47.619 0.00 0.00 32.85 2.40
6110 11209 2.810274 CGTGCAGATTATTGGGGATCAG 59.190 50.000 0.00 0.00 0.00 2.90
6113 11212 4.276926 GTGCAGATTATTGGGGATCAGTTC 59.723 45.833 0.00 0.00 0.00 3.01
6142 11241 3.455910 TGGCTCACCTTATCTAGCACATT 59.544 43.478 0.00 0.00 36.68 2.71
6147 11246 6.684111 GCTCACCTTATCTAGCACATTGTACT 60.684 42.308 0.00 0.00 35.05 2.73
6176 11275 4.021102 ACGTCAAGGAGAAACCATTGAT 57.979 40.909 0.00 0.00 42.04 2.57
6202 11301 3.117491 TGAGAAACTCTGGCTCAACAG 57.883 47.619 0.00 0.00 35.87 3.16
6210 11309 1.835483 CTGGCTCAACAGTGTCACGC 61.835 60.000 0.00 0.00 33.81 5.34
6211 11310 1.887242 GGCTCAACAGTGTCACGCA 60.887 57.895 0.00 0.00 0.00 5.24
6219 11318 3.036084 GTGTCACGCACCTGACGG 61.036 66.667 0.19 0.00 43.14 4.79
6293 11392 1.157870 AAGCGGCGATTAATCACCCG 61.158 55.000 27.51 27.51 41.45 5.28
6297 11396 2.389386 GCGATTAATCACCCGCACA 58.611 52.632 15.57 0.00 46.04 4.57
6320 11419 0.675083 CCATTTCAGCTGCAACCACA 59.325 50.000 9.47 0.00 0.00 4.17
6328 11427 2.343506 CTGCAACCACAGCAATCCA 58.656 52.632 0.00 0.00 42.17 3.41
6392 11491 0.234884 GTCGTTCAGTTTCCAAGGCG 59.765 55.000 0.00 0.00 0.00 5.52
6403 11502 1.377725 CCAAGGCGGATGAGCTGTT 60.378 57.895 0.00 0.00 36.56 3.16
6414 11513 2.751166 TGAGCTGTTTCTAGACAGGC 57.249 50.000 12.20 5.07 45.59 4.85
6545 11644 1.299926 GTCAAGCACGACTGACCGT 60.300 57.895 0.00 0.00 44.43 4.83
6546 11645 0.039798 GTCAAGCACGACTGACCGTA 60.040 55.000 0.00 0.00 41.29 4.02
6566 11665 4.634004 CGTAGGCAAAGTAATGGTGAATCA 59.366 41.667 0.00 0.00 0.00 2.57
6608 11707 1.416030 GGGAGGAAGAGGCTGAAGATC 59.584 57.143 0.00 0.00 0.00 2.75
6617 11716 4.491675 AGAGGCTGAAGATCATGAGGTAT 58.508 43.478 0.09 0.00 0.00 2.73
6748 11847 6.431722 AGAGGAAGAGATAGTAGCTTCAACT 58.568 40.000 0.00 0.00 39.72 3.16
6794 11893 9.541143 CATGGTTGTGTACTTGTATATGTATCA 57.459 33.333 0.00 0.00 0.00 2.15
6796 11895 9.373603 TGGTTGTGTACTTGTATATGTATCAAC 57.626 33.333 17.23 17.23 35.89 3.18
6852 11951 7.095102 GGAAAATAGTGTACGCCTAACAAGAAA 60.095 37.037 1.98 0.00 0.00 2.52
6880 11979 3.814842 CCAAGACATCACTGTGCTTTACA 59.185 43.478 2.12 0.00 35.14 2.41
6892 11991 3.326747 GTGCTTTACACCAAGAGATCGT 58.673 45.455 0.00 0.00 44.02 3.73
6918 12017 3.838271 TGAGGAGCGATGCCGTCC 61.838 66.667 0.00 0.00 38.24 4.79
6922 12021 4.241555 GAGCGATGCCGTCCCCAT 62.242 66.667 0.00 0.00 38.24 4.00
6926 12025 2.111878 GATGCCGTCCCCATCCTG 59.888 66.667 0.00 0.00 34.43 3.86
6927 12026 4.195334 ATGCCGTCCCCATCCTGC 62.195 66.667 0.00 0.00 0.00 4.85
6930 12029 4.838152 CCGTCCCCATCCTGCACG 62.838 72.222 0.00 0.00 0.00 5.34
7169 12277 4.776349 TCAAACTGTCCAACACACTGTAT 58.224 39.130 0.00 0.00 0.00 2.29
7236 12375 8.150945 AGTTTCTCTTGACTTATGAGCAGTTAA 58.849 33.333 0.00 0.00 32.20 2.01
7305 12444 7.796054 AGCTAGGAGTTATCTAAGCATTTCAA 58.204 34.615 0.00 0.00 36.33 2.69
7367 12506 4.902443 TCAGAACCGATACTCATCAGAC 57.098 45.455 0.00 0.00 0.00 3.51
7370 12509 3.312973 AGAACCGATACTCATCAGACGTC 59.687 47.826 7.70 7.70 0.00 4.34
7479 12620 4.018506 CCAGGGGCCATACATCATATAACA 60.019 45.833 4.39 0.00 0.00 2.41
7507 12648 4.873827 TGAAAAGTTCAACAAGTACGAGCT 59.126 37.500 0.00 0.00 36.59 4.09
7542 12683 7.228706 AGCATTTGGAAATAATAGTAGGAACGG 59.771 37.037 0.00 0.00 0.00 4.44
7577 12721 1.455217 GCTGGCTGGCATCTGGAAT 60.455 57.895 3.74 0.00 0.00 3.01
7579 12723 1.481871 CTGGCTGGCATCTGGAATTT 58.518 50.000 3.74 0.00 0.00 1.82
7603 12749 0.445436 GCTGGAGTTGAATGTGCGAG 59.555 55.000 0.00 0.00 0.00 5.03
7604 12750 0.445436 CTGGAGTTGAATGTGCGAGC 59.555 55.000 0.00 0.00 0.00 5.03
7632 12781 1.642762 AGTTTGATGGGCTTCCTGGAT 59.357 47.619 0.00 0.00 0.00 3.41
7637 12786 0.549950 ATGGGCTTCCTGGATCACTG 59.450 55.000 0.00 0.00 0.00 3.66
7704 12853 0.540365 ACTGGCCACATCCTGTTTGG 60.540 55.000 0.00 0.00 35.13 3.28
7719 12868 4.036852 CCTGTTTGGTCTCCTCTTTTTCAC 59.963 45.833 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 4.868734 ACTAGTTGTTTATTAGCGAGTGGC 59.131 41.667 0.00 0.00 44.05 5.01
67 68 5.379706 ACTTGGTACGGGATACTACTAGT 57.620 43.478 0.00 0.00 33.87 2.57
68 69 5.506982 GCAACTTGGTACGGGATACTACTAG 60.507 48.000 0.00 0.00 33.87 2.57
71 72 3.131755 AGCAACTTGGTACGGGATACTAC 59.868 47.826 0.00 0.00 33.87 2.73
197 206 0.541863 ACATCATTCTGGTCGGGGAC 59.458 55.000 0.00 0.00 0.00 4.46
198 207 0.541392 CACATCATTCTGGTCGGGGA 59.459 55.000 0.00 0.00 0.00 4.81
255 264 8.572185 AGGCCGTGCATTTTTATTTTTATTTTT 58.428 25.926 0.00 0.00 0.00 1.94
256 265 8.105097 AGGCCGTGCATTTTTATTTTTATTTT 57.895 26.923 0.00 0.00 0.00 1.82
266 275 1.524848 TCGAAGGCCGTGCATTTTTA 58.475 45.000 0.00 0.00 39.75 1.52
302 502 2.037251 CCAACTGGAGAGGAGAACGAAA 59.963 50.000 0.00 0.00 37.39 3.46
439 802 4.680237 CACGGACGGGCAAGCAGA 62.680 66.667 0.00 0.00 0.00 4.26
536 4427 0.477204 GCACCCCCTTCTTATACCCC 59.523 60.000 0.00 0.00 0.00 4.95
677 4568 5.104900 GGAGCCCTTACAGAAATTCTCAGTA 60.105 44.000 0.00 0.00 0.00 2.74
735 4626 7.967908 TCAGGCCAAAGGTAAATTTTGAATTA 58.032 30.769 5.01 0.00 37.65 1.40
794 4689 5.986501 AGAACAATCCTCGAGGTATATCC 57.013 43.478 30.17 16.36 36.34 2.59
801 4696 4.689345 ACGTAAAAAGAACAATCCTCGAGG 59.311 41.667 26.32 26.32 0.00 4.63
898 4793 2.360475 AGCAGGGAAAGCGGCTTC 60.360 61.111 16.70 9.39 37.01 3.86
908 4803 2.046009 TTACGCCAACACAGCAGGGA 62.046 55.000 0.00 0.00 0.00 4.20
969 4868 0.826256 AGGGAAGAACGTTTTGGGGC 60.826 55.000 0.46 0.00 0.00 5.80
970 4869 1.699730 AAGGGAAGAACGTTTTGGGG 58.300 50.000 0.46 0.00 0.00 4.96
1072 4999 3.324930 CTGCAGGTGGAGGAGGCA 61.325 66.667 5.57 0.00 0.00 4.75
1242 5169 0.039764 AGATGGTGGAGACGAGGACA 59.960 55.000 0.00 0.00 0.00 4.02
1322 6137 3.754965 TCCACCAAGATTTCTTCACTGG 58.245 45.455 0.00 0.00 36.26 4.00
1323 6138 5.242393 ACATTCCACCAAGATTTCTTCACTG 59.758 40.000 0.00 0.00 33.11 3.66
1326 6141 4.523943 CCACATTCCACCAAGATTTCTTCA 59.476 41.667 0.00 0.00 33.11 3.02
1366 6189 1.277557 GACAGGAGCCAGATTGTCAGT 59.722 52.381 2.75 0.00 39.67 3.41
1444 6314 9.872684 ATGGATCTGAGACAATGGTTTATTAAT 57.127 29.630 0.00 0.00 0.00 1.40
1557 6428 6.294675 CAGAGTACCTGCCATGAAATGAAAAA 60.295 38.462 0.00 0.00 40.80 1.94
1683 6559 6.560253 ATCAAAAACAAGAGATAGCAACGT 57.440 33.333 0.00 0.00 0.00 3.99
1704 6580 7.945134 AGCCAACAGGTAATTTGATGATAATC 58.055 34.615 0.00 0.00 0.00 1.75
1705 6581 7.902920 AGCCAACAGGTAATTTGATGATAAT 57.097 32.000 0.00 0.00 0.00 1.28
1707 6583 6.889177 TCAAGCCAACAGGTAATTTGATGATA 59.111 34.615 0.00 0.00 0.00 2.15
1854 6834 6.090129 TGAACAAAAGAAGAACCTGAAAACG 58.910 36.000 0.00 0.00 0.00 3.60
1888 6868 0.320771 ACGAGCACACACATTCTCCC 60.321 55.000 0.00 0.00 0.00 4.30
2129 7113 5.010012 ACCAAACAAAAGAGAGGTAATGCAG 59.990 40.000 0.00 0.00 0.00 4.41
2358 7342 2.806244 CCTGTCTGGAAAAGGTTACACG 59.194 50.000 0.00 0.00 38.35 4.49
2382 7366 7.829725 TCTTAATACGGCAGTCTTAACACTTA 58.170 34.615 0.00 0.00 29.60 2.24
2511 7495 9.298373 TACTGAAGAGTGTTGCCATTGCAATTT 62.298 37.037 9.83 0.00 45.18 1.82
2607 7600 9.912634 TCATCTATGAACAATTTGTTTTTCCTC 57.087 29.630 15.54 3.34 41.28 3.71
2715 7708 6.516693 GCCAAAAGTGCTCATACTAAAAAGGT 60.517 38.462 0.00 0.00 0.00 3.50
2716 7709 5.863935 GCCAAAAGTGCTCATACTAAAAAGG 59.136 40.000 0.00 0.00 0.00 3.11
2718 7711 5.457140 CGCCAAAAGTGCTCATACTAAAAA 58.543 37.500 0.00 0.00 0.00 1.94
3058 8051 7.840342 AATGTCAGCAGTTAGAAACATCTAG 57.160 36.000 0.00 0.00 0.00 2.43
3088 8081 4.891168 TGGGTACTATAGTTCGCAATGAGA 59.109 41.667 21.68 3.23 35.89 3.27
3112 8105 9.577110 CCGACTTACAGTTATAAAGACACAATA 57.423 33.333 0.00 0.00 0.00 1.90
3137 8130 4.335594 GTGGCAATTAAGTCTGTGATACCC 59.664 45.833 0.00 0.00 0.00 3.69
3171 8164 8.908903 TCCAATACATTTTCAACAGTTAACAGT 58.091 29.630 8.61 2.62 0.00 3.55
3192 8185 8.692710 TGTATTTAGTAACAGACTCGATCCAAT 58.307 33.333 0.00 0.00 39.81 3.16
3269 8262 0.447801 GGCCATTTCAGTGCTACACG 59.552 55.000 0.00 0.00 39.64 4.49
3378 8371 5.009631 AGAAGCATTATTGTACTGTGCCAA 58.990 37.500 0.00 0.00 36.50 4.52
3594 8648 6.365520 AGTAAAACTCAAATGAGGGACTGTT 58.634 36.000 14.50 0.00 46.13 3.16
3595 8649 5.941788 AGTAAAACTCAAATGAGGGACTGT 58.058 37.500 14.50 0.00 46.13 3.55
3596 8650 6.884280 AAGTAAAACTCAAATGAGGGACTG 57.116 37.500 14.50 0.00 46.13 3.51
3597 8651 6.833933 ACAAAGTAAAACTCAAATGAGGGACT 59.166 34.615 14.50 8.59 46.13 3.85
3598 8652 6.918022 CACAAAGTAAAACTCAAATGAGGGAC 59.082 38.462 14.50 6.73 46.13 4.46
3599 8653 6.460953 GCACAAAGTAAAACTCAAATGAGGGA 60.461 38.462 14.50 0.00 46.13 4.20
3600 8654 5.691754 GCACAAAGTAAAACTCAAATGAGGG 59.308 40.000 14.50 0.00 46.13 4.30
3601 8655 6.507023 AGCACAAAGTAAAACTCAAATGAGG 58.493 36.000 14.50 0.00 46.13 3.86
3603 8657 6.255453 GCAAGCACAAAGTAAAACTCAAATGA 59.745 34.615 0.00 0.00 0.00 2.57
3604 8658 6.256321 AGCAAGCACAAAGTAAAACTCAAATG 59.744 34.615 0.00 0.00 0.00 2.32
3605 8659 6.256321 CAGCAAGCACAAAGTAAAACTCAAAT 59.744 34.615 0.00 0.00 0.00 2.32
3606 8660 5.576384 CAGCAAGCACAAAGTAAAACTCAAA 59.424 36.000 0.00 0.00 0.00 2.69
3607 8661 5.101628 CAGCAAGCACAAAGTAAAACTCAA 58.898 37.500 0.00 0.00 0.00 3.02
3608 8662 4.157656 ACAGCAAGCACAAAGTAAAACTCA 59.842 37.500 0.00 0.00 0.00 3.41
3609 8663 4.500477 CACAGCAAGCACAAAGTAAAACTC 59.500 41.667 0.00 0.00 0.00 3.01
3610 8664 4.423732 CACAGCAAGCACAAAGTAAAACT 58.576 39.130 0.00 0.00 0.00 2.66
3611 8665 3.000222 GCACAGCAAGCACAAAGTAAAAC 60.000 43.478 0.00 0.00 0.00 2.43
3612 8666 3.186119 GCACAGCAAGCACAAAGTAAAA 58.814 40.909 0.00 0.00 0.00 1.52
3613 8667 2.165234 TGCACAGCAAGCACAAAGTAAA 59.835 40.909 0.00 0.00 37.02 2.01
3614 8668 1.747924 TGCACAGCAAGCACAAAGTAA 59.252 42.857 0.00 0.00 37.02 2.24
3615 8669 1.334556 CTGCACAGCAAGCACAAAGTA 59.665 47.619 0.00 0.00 38.41 2.24
3616 8670 0.101759 CTGCACAGCAAGCACAAAGT 59.898 50.000 0.00 0.00 38.41 2.66
3617 8671 0.596600 CCTGCACAGCAAGCACAAAG 60.597 55.000 0.00 0.00 38.41 2.77
3618 8672 1.036481 TCCTGCACAGCAAGCACAAA 61.036 50.000 0.00 0.00 38.41 2.83
3619 8673 1.036481 TTCCTGCACAGCAAGCACAA 61.036 50.000 0.00 0.00 38.41 3.33
3620 8674 1.449726 CTTCCTGCACAGCAAGCACA 61.450 55.000 0.00 0.00 38.41 4.57
3621 8675 1.285023 CTTCCTGCACAGCAAGCAC 59.715 57.895 0.00 0.00 38.41 4.40
3622 8676 0.108396 TACTTCCTGCACAGCAAGCA 59.892 50.000 1.16 0.00 38.41 3.91
3623 8677 0.801251 CTACTTCCTGCACAGCAAGC 59.199 55.000 1.16 0.00 38.41 4.01
3624 8678 0.801251 GCTACTTCCTGCACAGCAAG 59.199 55.000 0.00 0.00 38.41 4.01
3625 8679 0.397941 AGCTACTTCCTGCACAGCAA 59.602 50.000 0.00 0.00 38.41 3.91
3626 8680 0.397941 AAGCTACTTCCTGCACAGCA 59.602 50.000 0.00 0.00 36.92 4.41
3627 8681 1.198637 CAAAGCTACTTCCTGCACAGC 59.801 52.381 0.00 0.00 0.00 4.40
3628 8682 1.808945 CCAAAGCTACTTCCTGCACAG 59.191 52.381 0.00 0.00 0.00 3.66
3629 8683 1.419762 TCCAAAGCTACTTCCTGCACA 59.580 47.619 0.00 0.00 0.00 4.57
3944 8998 3.645212 TGCATCCACCAAATTTTTCCAGA 59.355 39.130 0.00 0.00 0.00 3.86
3983 9037 7.647827 TGTCCCCTGATCCATATTTTCTAAAA 58.352 34.615 0.00 0.00 0.00 1.52
4240 9294 5.769662 ACAGTGGCTTGTTCTGATTATCAAA 59.230 36.000 0.00 0.00 33.93 2.69
4310 9364 2.103094 TCGGGTGAGATCAAATGCCTAG 59.897 50.000 0.00 0.00 0.00 3.02
4381 9435 1.589716 AACAAGGCCTTGAGATGCGC 61.590 55.000 44.50 0.00 42.93 6.09
4509 9563 1.999048 TAACAGTTACGGCCATGTCG 58.001 50.000 2.24 4.47 36.42 4.35
4564 9618 3.477210 ACACTGAACTTGAACTCCCTC 57.523 47.619 0.00 0.00 0.00 4.30
4574 9628 6.151144 AGCAAACTTTGAGTTACACTGAACTT 59.849 34.615 5.65 0.00 39.79 2.66
4664 9718 4.753107 TGTTACTCTTTTGCTTTCCTACCG 59.247 41.667 0.00 0.00 0.00 4.02
4716 9770 6.761714 CCTCTACAGTACACTTCACAAACTTT 59.238 38.462 0.00 0.00 0.00 2.66
4717 9771 6.097839 TCCTCTACAGTACACTTCACAAACTT 59.902 38.462 0.00 0.00 0.00 2.66
4786 9840 5.008415 TCTCCTTTATCCGTTCGATGTCTAC 59.992 44.000 0.00 0.00 31.92 2.59
4822 9876 4.592942 TGAGATAGCTTTGGACTGCATTT 58.407 39.130 0.00 0.00 0.00 2.32
4833 9887 5.221884 CCTGATCCTTGGATGAGATAGCTTT 60.222 44.000 15.95 0.00 0.00 3.51
4851 9905 2.113860 TGTAAGCAAGTGGCCTGATC 57.886 50.000 3.32 0.00 46.50 2.92
4949 10003 1.315690 CAATTGCTCGGCATCTCCAT 58.684 50.000 0.00 0.00 38.76 3.41
5058 10112 4.401202 ACCAACCATTTTATTCTTAGCCGG 59.599 41.667 0.00 0.00 0.00 6.13
5138 10192 2.558286 CCACTTGCACCACAGCCAG 61.558 63.158 0.00 0.00 33.80 4.85
5209 10263 4.529769 CCAATGAGCAGATATACTCCCAGA 59.470 45.833 0.00 0.00 31.65 3.86
5245 10299 3.652274 TGTTAAGGTAACCCTCGAAACG 58.348 45.455 0.00 0.00 41.56 3.60
5249 10303 3.833650 TGTCATGTTAAGGTAACCCTCGA 59.166 43.478 0.00 0.00 41.56 4.04
5285 10339 2.403252 AACCTCAATAACCAGCTCCG 57.597 50.000 0.00 0.00 0.00 4.63
5348 10402 5.876357 AGTGCTCTAGGAAAACCATGTAAA 58.124 37.500 0.00 0.00 0.00 2.01
5388 10442 8.181904 AGGACATGTTTTCATCAACTATGTTT 57.818 30.769 0.00 0.00 38.64 2.83
5389 10443 7.448161 TGAGGACATGTTTTCATCAACTATGTT 59.552 33.333 0.00 0.00 38.64 2.71
5582 10636 4.105858 AGCTACCCAAGAAAAGGTTAGGTT 59.894 41.667 0.00 0.00 37.59 3.50
5626 10680 9.683069 GTGTTTCATCTAAAAGTGTGATTCAAT 57.317 29.630 0.00 0.00 0.00 2.57
5664 10719 4.411927 TGGCATCTTTTTAAGGTAGGCAA 58.588 39.130 0.00 0.00 31.03 4.52
5796 10876 7.558161 TCTGCAATATTGTGAATCTGGTTAG 57.442 36.000 16.61 0.44 0.00 2.34
5847 10927 7.094508 TGCCGCTATTGAAATTAATCTTCAA 57.905 32.000 19.12 19.12 44.55 2.69
5848 10928 6.691754 TGCCGCTATTGAAATTAATCTTCA 57.308 33.333 8.21 8.21 0.00 3.02
5849 10929 6.142958 GCTTGCCGCTATTGAAATTAATCTTC 59.857 38.462 0.00 0.00 35.14 2.87
5850 10930 5.979517 GCTTGCCGCTATTGAAATTAATCTT 59.020 36.000 0.00 0.00 35.14 2.40
5868 10948 3.828875 ATAGACTAAGTCCAGCTTGCC 57.171 47.619 0.00 0.00 38.05 4.52
5943 11031 2.102420 TCGTCGATGTAAGATGCCCAAT 59.898 45.455 4.21 0.00 0.00 3.16
5948 11036 3.061797 CGTCTTTCGTCGATGTAAGATGC 60.062 47.826 24.38 14.94 34.52 3.91
5970 11058 6.511929 GCACAAACCTCAAAGAGTAGAAGAAC 60.512 42.308 0.00 0.00 0.00 3.01
6001 11089 0.620556 GATGCCCTTGAAGACTGGGA 59.379 55.000 0.91 0.00 43.47 4.37
6010 11098 3.265221 AGAGATGAAGTTGATGCCCTTGA 59.735 43.478 0.00 0.00 0.00 3.02
6011 11099 3.377485 CAGAGATGAAGTTGATGCCCTTG 59.623 47.826 0.00 0.00 0.00 3.61
6022 11110 9.087871 AGTATATATGCTTGACAGAGATGAAGT 57.912 33.333 0.00 0.00 0.00 3.01
6029 11117 8.546244 CACACAAAGTATATATGCTTGACAGAG 58.454 37.037 15.71 8.41 32.96 3.35
6031 11119 8.424274 TCACACAAAGTATATATGCTTGACAG 57.576 34.615 15.71 9.46 32.96 3.51
6035 11123 8.961092 GCATTTCACACAAAGTATATATGCTTG 58.039 33.333 15.71 12.17 32.96 4.01
6079 11178 1.671979 AATCTGCACGGATGATGTGG 58.328 50.000 0.00 0.00 37.80 4.17
6110 11209 0.394565 AGGTGAGCCACTCAGTGAAC 59.605 55.000 6.30 0.00 41.46 3.18
6113 11212 2.499289 AGATAAGGTGAGCCACTCAGTG 59.501 50.000 0.00 0.00 41.46 3.66
6119 11218 2.168521 TGTGCTAGATAAGGTGAGCCAC 59.831 50.000 0.00 0.00 37.19 5.01
6142 11241 5.358725 TCTCCTTGACGTATTATGCAGTACA 59.641 40.000 0.00 0.00 0.00 2.90
6147 11246 4.873827 GGTTTCTCCTTGACGTATTATGCA 59.126 41.667 0.00 0.00 0.00 3.96
6176 11275 1.696336 AGCCAGAGTTTCTCAAGCTGA 59.304 47.619 10.96 0.00 38.84 4.26
6202 11301 3.036084 CCGTCAGGTGCGTGACAC 61.036 66.667 20.25 0.00 46.19 3.67
6219 11318 2.125512 ACTGATGAGCCGGTTCGC 60.126 61.111 14.03 8.79 0.00 4.70
6223 11322 1.593787 CAGTCACTGATGAGCCGGT 59.406 57.895 0.00 0.00 34.75 5.28
6293 11392 1.980772 AGCTGAAATGGGGCTGTGC 60.981 57.895 0.00 0.00 34.82 4.57
6297 11396 1.228956 TTGCAGCTGAAATGGGGCT 60.229 52.632 20.43 0.00 36.70 5.19
6328 11427 1.470996 GCTGGATCCTGGCGATCTCT 61.471 60.000 19.23 0.00 45.90 3.10
6392 11491 3.791245 CCTGTCTAGAAACAGCTCATCC 58.209 50.000 6.14 0.00 44.34 3.51
6403 11502 1.573108 CTTCCCTGGCCTGTCTAGAA 58.427 55.000 3.32 3.11 0.00 2.10
6414 11513 1.141858 GCAGTTAGGATCCTTCCCTGG 59.858 57.143 22.03 6.53 43.76 4.45
6441 11540 1.517832 CGAAGACCCTCTCGGCATT 59.482 57.895 0.00 0.00 33.26 3.56
6443 11542 3.760035 GCGAAGACCCTCTCGGCA 61.760 66.667 0.00 0.00 33.26 5.69
6545 11644 5.815581 AGTGATTCACCATTACTTTGCCTA 58.184 37.500 13.14 0.00 34.49 3.93
6546 11645 4.666512 AGTGATTCACCATTACTTTGCCT 58.333 39.130 13.14 0.00 34.49 4.75
6548 11647 5.392380 CCTGAGTGATTCACCATTACTTTGC 60.392 44.000 13.14 0.00 31.84 3.68
6551 11650 4.289672 ACCCTGAGTGATTCACCATTACTT 59.710 41.667 13.14 0.00 31.84 2.24
6566 11665 2.681778 CCAGCGGAGACCCTGAGT 60.682 66.667 0.00 0.00 0.00 3.41
6608 11707 1.942657 CCGTTGCCTGAATACCTCATG 59.057 52.381 0.00 0.00 32.14 3.07
6617 11716 2.150719 TCCCTTCCCGTTGCCTGAA 61.151 57.895 0.00 0.00 0.00 3.02
6748 11847 2.985311 TGGCATACATACATGGGGATGA 59.015 45.455 9.83 0.00 0.00 2.92
6794 11893 2.231820 GCGTAGGCTTCACGTTGTT 58.768 52.632 11.11 0.00 41.41 2.83
6872 11971 3.006430 TGACGATCTCTTGGTGTAAAGCA 59.994 43.478 0.00 0.00 0.00 3.91
6880 11979 0.534412 CCTGCTGACGATCTCTTGGT 59.466 55.000 0.00 0.00 0.00 3.67
6884 11983 0.323816 TCACCCTGCTGACGATCTCT 60.324 55.000 0.00 0.00 0.00 3.10
6885 11984 0.102120 CTCACCCTGCTGACGATCTC 59.898 60.000 0.00 0.00 0.00 2.75
6887 11986 1.142748 CCTCACCCTGCTGACGATC 59.857 63.158 0.00 0.00 0.00 3.69
6888 11987 1.305297 TCCTCACCCTGCTGACGAT 60.305 57.895 0.00 0.00 0.00 3.73
6889 11988 1.979155 CTCCTCACCCTGCTGACGA 60.979 63.158 0.00 0.00 0.00 4.20
6890 11989 2.575993 CTCCTCACCCTGCTGACG 59.424 66.667 0.00 0.00 0.00 4.35
6892 11991 3.385384 CGCTCCTCACCCTGCTGA 61.385 66.667 0.00 0.00 0.00 4.26
6945 12044 1.227089 CTGACGAATGGAGAGCGGG 60.227 63.158 0.00 0.00 0.00 6.13
7073 12181 4.848299 GCTATGAGAAAAACAAACTCAGCG 59.152 41.667 0.00 0.00 42.55 5.18
7367 12506 1.273688 TCATTGTCGTATTGCGGACG 58.726 50.000 0.00 0.00 41.72 4.79
7370 12509 3.463533 TGTTTCATTGTCGTATTGCGG 57.536 42.857 0.00 0.00 41.72 5.69
7416 12556 6.071616 TGTTTTTGTACCTGGATTATGCTTCC 60.072 38.462 0.00 0.00 0.00 3.46
7424 12564 8.357402 GTCAAGTTATGTTTTTGTACCTGGATT 58.643 33.333 0.00 0.00 0.00 3.01
7479 12620 6.592607 TCGTACTTGTTGAACTTTTCAGTCTT 59.407 34.615 0.00 0.00 41.38 3.01
7542 12683 4.642437 AGCCAGCTTAAATTCCTAGCTTTC 59.358 41.667 0.00 2.95 42.30 2.62
7577 12721 3.318839 CACATTCAACTCCAGCTTCCAAA 59.681 43.478 0.00 0.00 0.00 3.28
7579 12723 2.507484 CACATTCAACTCCAGCTTCCA 58.493 47.619 0.00 0.00 0.00 3.53
7603 12749 1.009829 CCCATCAAACTAGAGTGCGC 58.990 55.000 0.00 0.00 0.00 6.09
7604 12750 1.009829 GCCCATCAAACTAGAGTGCG 58.990 55.000 0.00 0.00 0.00 5.34
7637 12786 1.616374 GATTCTCCGAGTGGATCCTCC 59.384 57.143 14.23 3.45 45.33 4.30
7704 12853 2.810852 CAGCTGGTGAAAAAGAGGAGAC 59.189 50.000 5.57 0.00 0.00 3.36
7719 12868 2.428834 TTGGAAGGTTTGCAGCTGG 58.571 52.632 17.12 0.00 30.85 4.85


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

AutoCloner maintained by Alex Coulton.