Multiple sequence alignment - TraesCS4A01G063800

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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 TraesCS4A01G063800 chr4A 100.000 4726 0 0 1 4726 60667202 60671927 0.000000e+00 8728.0
1 TraesCS4A01G063800 chr4A 90.091 1211 78 24 1572 2765 602453805 602454990 0.000000e+00 1533.0
2 TraesCS4A01G063800 chr4A 86.076 158 20 2 3417 3573 579430514 579430670 8.130000e-38 169.0
3 TraesCS4A01G063800 chr4B 87.020 1926 121 67 2853 4713 499900624 499902485 0.000000e+00 2052.0
4 TraesCS4A01G063800 chr4B 86.962 1557 115 38 867 2381 499898638 499900148 0.000000e+00 1670.0
5 TraesCS4A01G063800 chr4B 90.159 315 26 4 407 719 499898186 499898497 5.690000e-109 405.0
6 TraesCS4A01G063800 chr4B 95.928 221 6 2 2577 2796 499900286 499900504 5.820000e-94 355.0
7 TraesCS4A01G063800 chr4D 85.862 1839 122 75 2832 4625 403147624 403149369 0.000000e+00 1829.0
8 TraesCS4A01G063800 chr4D 81.671 1233 96 46 8 1139 403144695 403145898 0.000000e+00 905.0
9 TraesCS4A01G063800 chr4D 88.375 757 53 19 1124 1869 403145943 403146675 0.000000e+00 878.0
10 TraesCS4A01G063800 chr4D 93.060 317 12 5 2486 2802 403147324 403147630 5.580000e-124 455.0
11 TraesCS4A01G063800 chr4D 91.549 142 12 0 3579 3720 22947019 22946878 3.730000e-46 196.0
12 TraesCS4A01G063800 chr4D 86.076 158 20 2 3417 3573 22947268 22947112 8.130000e-38 169.0
13 TraesCS4A01G063800 chr4D 82.906 117 15 5 302 416 201715063 201715176 3.010000e-17 100.0
14 TraesCS4A01G063800 chr4D 100.000 37 0 0 380 416 327727450 327727414 8.490000e-08 69.4
15 TraesCS4A01G063800 chr2D 90.653 1241 75 26 1572 2796 638528437 638529652 0.000000e+00 1611.0
16 TraesCS4A01G063800 chr2D 86.486 74 10 0 341 414 310296004 310295931 1.090000e-11 82.4
17 TraesCS4A01G063800 chrUn 89.992 1239 85 22 1574 2799 16239673 16238461 0.000000e+00 1565.0
18 TraesCS4A01G063800 chrUn 79.104 134 23 4 283 414 96131936 96131806 2.340000e-13 87.9
19 TraesCS4A01G063800 chr6B 89.389 1244 90 25 1573 2799 517992568 517991350 0.000000e+00 1528.0
20 TraesCS4A01G063800 chr6B 81.548 168 23 5 3417 3580 577184685 577184522 1.070000e-26 132.0
21 TraesCS4A01G063800 chr6B 88.889 99 11 0 1464 1562 577186467 577186369 6.420000e-24 122.0
22 TraesCS4A01G063800 chr3B 89.444 1241 82 24 1572 2796 412291971 412293178 0.000000e+00 1520.0
23 TraesCS4A01G063800 chr2A 89.194 1240 84 26 1574 2796 657882923 657884129 0.000000e+00 1502.0
24 TraesCS4A01G063800 chr7B 89.130 1242 83 27 1572 2796 16885282 16886488 0.000000e+00 1498.0
25 TraesCS4A01G063800 chr5A 89.068 1244 85 27 1572 2799 525542515 525541307 0.000000e+00 1496.0
26 TraesCS4A01G063800 chr5A 90.710 549 38 9 2631 3176 557715294 557715832 0.000000e+00 719.0
27 TraesCS4A01G063800 chr5A 86.538 52 6 1 403 454 503687517 503687567 6.610000e-04 56.5
28 TraesCS4A01G063800 chr7D 91.389 871 55 11 1610 2470 592376935 592377795 0.000000e+00 1175.0
29 TraesCS4A01G063800 chr6D 90.976 543 38 7 2631 3171 168004421 168004954 0.000000e+00 721.0
30 TraesCS4A01G063800 chr6D 90.965 487 35 5 2692 3176 167990825 167991304 0.000000e+00 647.0
31 TraesCS4A01G063800 chr6D 89.899 99 10 0 1464 1562 386293250 386293152 1.380000e-25 128.0
32 TraesCS4A01G063800 chr6D 80.952 168 24 5 3417 3580 386291562 386291399 4.960000e-25 126.0
33 TraesCS4A01G063800 chr7A 90.528 549 37 10 2631 3176 60646729 60647265 0.000000e+00 712.0
34 TraesCS4A01G063800 chr7A 81.579 114 16 4 303 414 49052814 49052704 6.510000e-14 89.8
35 TraesCS4A01G063800 chr1A 89.194 546 46 9 2634 3176 232732425 232731890 0.000000e+00 669.0
36 TraesCS4A01G063800 chr1A 79.545 88 10 6 302 387 277634886 277634967 6.610000e-04 56.5
37 TraesCS4A01G063800 chr6A 94.048 84 5 0 3497 3580 531395082 531394999 1.380000e-25 128.0
38 TraesCS4A01G063800 chr6A 89.899 99 10 0 1464 1562 531397007 531396909 1.380000e-25 128.0
39 TraesCS4A01G063800 chr1D 78.571 210 34 4 260 459 487280101 487280309 1.380000e-25 128.0
40 TraesCS4A01G063800 chr3A 85.965 114 11 5 304 415 34043449 34043339 2.990000e-22 117.0
41 TraesCS4A01G063800 chr3D 92.308 52 4 0 363 414 8264628 8264679 1.820000e-09 75.0


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 TraesCS4A01G063800 chr4A 60667202 60671927 4725 False 8728.00 8728 100.00000 1 4726 1 chr4A.!!$F1 4725
1 TraesCS4A01G063800 chr4A 602453805 602454990 1185 False 1533.00 1533 90.09100 1572 2765 1 chr4A.!!$F3 1193
2 TraesCS4A01G063800 chr4B 499898186 499902485 4299 False 1120.50 2052 90.01725 407 4713 4 chr4B.!!$F1 4306
3 TraesCS4A01G063800 chr4D 403144695 403149369 4674 False 1016.75 1829 87.24200 8 4625 4 chr4D.!!$F2 4617
4 TraesCS4A01G063800 chr2D 638528437 638529652 1215 False 1611.00 1611 90.65300 1572 2796 1 chr2D.!!$F1 1224
5 TraesCS4A01G063800 chrUn 16238461 16239673 1212 True 1565.00 1565 89.99200 1574 2799 1 chrUn.!!$R1 1225
6 TraesCS4A01G063800 chr6B 517991350 517992568 1218 True 1528.00 1528 89.38900 1573 2799 1 chr6B.!!$R1 1226
7 TraesCS4A01G063800 chr3B 412291971 412293178 1207 False 1520.00 1520 89.44400 1572 2796 1 chr3B.!!$F1 1224
8 TraesCS4A01G063800 chr2A 657882923 657884129 1206 False 1502.00 1502 89.19400 1574 2796 1 chr2A.!!$F1 1222
9 TraesCS4A01G063800 chr7B 16885282 16886488 1206 False 1498.00 1498 89.13000 1572 2796 1 chr7B.!!$F1 1224
10 TraesCS4A01G063800 chr5A 525541307 525542515 1208 True 1496.00 1496 89.06800 1572 2799 1 chr5A.!!$R1 1227
11 TraesCS4A01G063800 chr5A 557715294 557715832 538 False 719.00 719 90.71000 2631 3176 1 chr5A.!!$F2 545
12 TraesCS4A01G063800 chr7D 592376935 592377795 860 False 1175.00 1175 91.38900 1610 2470 1 chr7D.!!$F1 860
13 TraesCS4A01G063800 chr6D 168004421 168004954 533 False 721.00 721 90.97600 2631 3171 1 chr6D.!!$F2 540
14 TraesCS4A01G063800 chr7A 60646729 60647265 536 False 712.00 712 90.52800 2631 3176 1 chr7A.!!$F1 545
15 TraesCS4A01G063800 chr1A 232731890 232732425 535 True 669.00 669 89.19400 2634 3176 1 chr1A.!!$R1 542

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
243 274 0.250467 CTACAAGCAGCCACCACACT 60.250 55.0 0.0 0.0 0.0 3.55 F
247 278 0.820891 AAGCAGCCACCACACTTGAG 60.821 55.0 0.0 0.0 0.0 3.02 F
1375 1548 0.829990 TGCACACACCTCTCAACTCA 59.170 50.0 0.0 0.0 0.0 3.41 F
1744 1919 1.168714 CCTTGTAAGTCCTTGCTGCC 58.831 55.0 0.0 0.0 0.0 4.85 F
3257 3663 0.394565 CCCCTGCTGATACCTACTGC 59.605 60.0 0.0 0.0 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2030 2249 0.610232 ATGAGCCAAGCAGGTCAACC 60.610 55.0 7.28 0.0 40.61 3.77 R
2147 2378 0.813821 GCCTCTGATTTGGCTGGAAC 59.186 55.0 0.00 0.0 45.26 3.62 R
2319 2560 0.035881 TCTCCTCAGCTGCAACCTTG 59.964 55.0 9.47 0.0 0.00 3.61 R
3271 3681 0.179134 GTCAGTTGCGATACGAGGCT 60.179 55.0 0.00 0.0 0.00 4.58 R
4103 4573 0.169230 CAGAGAGACGGACAAGGACG 59.831 60.0 0.00 0.0 0.00 4.79 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
30 31 0.391661 CATCGAACCACCACCTCCAG 60.392 60.000 0.00 0.00 0.00 3.86
69 70 3.345808 GCTGCCGAACGAAGTGCA 61.346 61.111 0.00 0.00 45.00 4.57
71 72 1.082756 CTGCCGAACGAAGTGCAAC 60.083 57.895 0.00 0.00 45.00 4.17
74 75 1.278637 CCGAACGAAGTGCAACCAC 59.721 57.895 0.00 0.00 45.00 4.16
75 76 1.433053 CCGAACGAAGTGCAACCACA 61.433 55.000 0.00 0.00 45.00 4.17
85 86 5.615544 CGAAGTGCAACCACAAATAGAGAAG 60.616 44.000 0.00 0.00 44.53 2.85
92 93 4.430441 ACCACAAATAGAGAAGAGGAGGT 58.570 43.478 0.00 0.00 0.00 3.85
108 123 4.699522 GTCGAGCCACCACCACCC 62.700 72.222 0.00 0.00 0.00 4.61
130 145 2.890474 CACCATCGCCACGGTAGC 60.890 66.667 0.00 0.00 32.98 3.58
177 208 1.472878 GAAGGAAAAGATTGACCGCCC 59.527 52.381 0.00 0.00 0.00 6.13
181 212 2.764637 AAAAGATTGACCGCCCGCCT 62.765 55.000 0.00 0.00 0.00 5.52
196 227 2.441532 CCTCCGCCGTCCTAGGAA 60.442 66.667 14.65 0.00 33.10 3.36
197 228 2.491022 CCTCCGCCGTCCTAGGAAG 61.491 68.421 14.65 16.02 33.10 3.46
198 229 3.140225 CTCCGCCGTCCTAGGAAGC 62.140 68.421 14.65 18.28 33.10 3.86
203 234 1.987855 CCGTCCTAGGAAGCCACCA 60.988 63.158 14.65 0.00 0.00 4.17
228 259 4.508128 GCCGCCGCTACAGCTACA 62.508 66.667 0.00 0.00 39.32 2.74
243 274 0.250467 CTACAAGCAGCCACCACACT 60.250 55.000 0.00 0.00 0.00 3.55
246 277 1.102809 CAAGCAGCCACCACACTTGA 61.103 55.000 0.00 0.00 40.06 3.02
247 278 0.820891 AAGCAGCCACCACACTTGAG 60.821 55.000 0.00 0.00 0.00 3.02
248 279 1.526917 GCAGCCACCACACTTGAGT 60.527 57.895 0.00 0.00 0.00 3.41
277 308 4.760047 GTGACGCCTGGCATCCGT 62.760 66.667 20.29 8.16 37.99 4.69
330 361 3.075005 GCCCCACCACGCTAGAGA 61.075 66.667 0.00 0.00 0.00 3.10
343 374 1.406180 GCTAGAGAACGAAGAGTCCCC 59.594 57.143 0.00 0.00 0.00 4.81
347 378 2.920912 AACGAAGAGTCCCCGCCA 60.921 61.111 0.00 0.00 0.00 5.69
482 515 2.351276 GGGGCGAGCTTTTCTCCA 59.649 61.111 0.00 0.00 38.62 3.86
525 558 1.855295 TACCACGGCTGATCCTAACA 58.145 50.000 0.00 0.00 0.00 2.41
555 588 6.190954 ACTTGTAACCAGATAATTTTCGCC 57.809 37.500 0.00 0.00 0.00 5.54
565 600 6.254157 CCAGATAATTTTCGCCATGTTTCTTG 59.746 38.462 0.00 0.00 0.00 3.02
588 623 3.125316 CACGGCCTCAAAACTTAAGCTAG 59.875 47.826 0.00 0.00 0.00 3.42
594 629 4.082733 CCTCAAAACTTAAGCTAGTTGCCC 60.083 45.833 1.29 0.00 44.23 5.36
603 638 3.508845 AGCTAGTTGCCCTCTCAAAAA 57.491 42.857 0.00 0.00 44.23 1.94
635 671 3.909662 GCCATGTGCTCGGTCAAT 58.090 55.556 0.00 0.00 36.87 2.57
643 679 2.550606 TGTGCTCGGTCAATTTACAACC 59.449 45.455 0.00 0.00 0.00 3.77
868 924 7.411274 TGAAACAGAAAAACGAATCAATACGT 58.589 30.769 0.00 0.00 44.57 3.57
869 925 8.549548 TGAAACAGAAAAACGAATCAATACGTA 58.450 29.630 0.00 0.00 41.87 3.57
870 926 8.928844 AAACAGAAAAACGAATCAATACGTAG 57.071 30.769 0.08 0.00 41.87 3.51
871 927 6.531439 ACAGAAAAACGAATCAATACGTAGC 58.469 36.000 0.08 0.00 41.87 3.58
872 928 5.957796 CAGAAAAACGAATCAATACGTAGCC 59.042 40.000 0.08 0.00 41.87 3.93
873 929 4.870221 AAAACGAATCAATACGTAGCCC 57.130 40.909 0.08 0.00 41.87 5.19
874 930 3.530265 AACGAATCAATACGTAGCCCA 57.470 42.857 0.08 0.00 41.87 5.36
958 1042 2.102084 GAGCTGCACACCTCATCTCATA 59.898 50.000 1.02 0.00 29.77 2.15
1095 1202 0.831307 CAGTTACCTACCAGCCTCCC 59.169 60.000 0.00 0.00 0.00 4.30
1101 1213 2.365635 TACCAGCCTCCCCTGCTC 60.366 66.667 0.00 0.00 36.81 4.26
1122 1234 3.172339 CCCCATCTCCTCCTGATCTTAG 58.828 54.545 0.00 0.00 0.00 2.18
1139 1251 4.027437 TCTTAGGAGGAGGAAGAAGAAGC 58.973 47.826 0.00 0.00 0.00 3.86
1166 1337 4.115516 TCTGCAAGATCGTCTTCTTATGC 58.884 43.478 0.00 0.00 38.67 3.14
1172 1343 6.292061 GCAAGATCGTCTTCTTATGCTACTTG 60.292 42.308 0.00 0.00 33.78 3.16
1190 1361 2.183409 GCATTCTGCACCCATCGTT 58.817 52.632 0.00 0.00 44.26 3.85
1192 1363 1.067635 GCATTCTGCACCCATCGTTTT 60.068 47.619 0.00 0.00 44.26 2.43
1223 1394 4.065088 TGCTACAGCTCGAATTTTTCTGT 58.935 39.130 2.44 0.00 42.66 3.41
1262 1434 3.925688 TCTGACGAATTTTATCTGCGC 57.074 42.857 0.00 0.00 0.00 6.09
1312 1485 2.358898 GCTCTGTTTGTTTTGCTCAGGA 59.641 45.455 0.00 0.00 0.00 3.86
1375 1548 0.829990 TGCACACACCTCTCAACTCA 59.170 50.000 0.00 0.00 0.00 3.41
1377 1550 1.871080 CACACACCTCTCAACTCACC 58.129 55.000 0.00 0.00 0.00 4.02
1404 1577 2.928757 CTCTCGTTCTTGGCTGATGAAG 59.071 50.000 0.00 0.00 0.00 3.02
1431 1604 5.793952 CGCTGAATCTCACTGAAATTTTCTG 59.206 40.000 12.80 12.80 35.09 3.02
1436 1610 8.906867 TGAATCTCACTGAAATTTTCTGTTTCT 58.093 29.630 16.29 3.48 39.43 2.52
1475 1649 3.124921 GTGAACGGCCCCATCACG 61.125 66.667 12.75 0.00 34.72 4.35
1603 1777 7.280205 TCTCGCCTTCTCTAATGGTTTTATTTC 59.720 37.037 0.00 0.00 0.00 2.17
1742 1917 2.039084 ACCTCCTTGTAAGTCCTTGCTG 59.961 50.000 0.00 0.00 0.00 4.41
1744 1919 1.168714 CCTTGTAAGTCCTTGCTGCC 58.831 55.000 0.00 0.00 0.00 4.85
1752 1930 2.728007 AGTCCTTGCTGCCTTTTATCC 58.272 47.619 0.00 0.00 0.00 2.59
1759 1937 2.308570 TGCTGCCTTTTATCCTCCTTGA 59.691 45.455 0.00 0.00 0.00 3.02
1871 2055 4.016444 GGAAACATAGTTTCTGGGCATCA 58.984 43.478 18.65 0.00 0.00 3.07
2016 2235 1.807742 GCGCCCTGTTGTATAAACACA 59.192 47.619 0.00 0.00 34.61 3.72
2025 2244 9.405587 CCCTGTTGTATAAACACACTAAAATTG 57.594 33.333 0.00 0.00 34.61 2.32
2030 2249 9.457110 TTGTATAAACACACTAAAATTGCACTG 57.543 29.630 0.00 0.00 34.61 3.66
2039 2258 3.457610 AAAATTGCACTGGTTGACCTG 57.542 42.857 5.61 5.61 40.37 4.00
2114 2343 3.489229 GCCTTTCAGACAACTGTTTGACC 60.489 47.826 2.76 0.00 43.81 4.02
2133 2362 6.509418 TGACCAGCACAAATCTTAAATACC 57.491 37.500 0.00 0.00 0.00 2.73
2155 2393 3.906014 GAACTGAGAAAAGTTCCAGCC 57.094 47.619 5.91 0.00 46.88 4.85
2198 2436 1.195900 TGTATTTGGCGCAAAGTCGTC 59.804 47.619 10.83 0.00 36.76 4.20
2319 2560 1.839424 CCAAGATCTTCAACACCCCC 58.161 55.000 4.57 0.00 0.00 5.40
2363 2604 2.350197 GGTACGAATACCTCCGTCGATG 60.350 54.545 0.00 0.00 46.68 3.84
2399 2691 4.023792 TGTTGCTGCAGTGTTTCATCTAAG 60.024 41.667 16.64 0.00 0.00 2.18
2416 2711 1.433534 AAGAGTTGTAGCGCTCTTGC 58.566 50.000 16.34 3.14 46.58 4.01
2445 2741 6.462073 AAATACATACACACGTGAGAACAC 57.538 37.500 25.01 0.00 42.88 3.32
2457 2753 6.200286 ACACGTGAGAACACAATAAGTTGTAG 59.800 38.462 25.01 0.00 46.49 2.74
2458 2754 6.200286 CACGTGAGAACACAATAAGTTGTAGT 59.800 38.462 10.90 0.00 46.49 2.73
2459 2755 7.380333 CACGTGAGAACACAATAAGTTGTAGTA 59.620 37.037 10.90 0.00 46.49 1.82
2482 2778 9.650714 AGTACAATATAGATAAGTACCACACCA 57.349 33.333 0.00 0.00 36.58 4.17
2555 2855 9.342308 TCATGTTCCTGGAATTACAGATTTATC 57.658 33.333 19.85 4.20 40.97 1.75
2558 2858 9.832445 TGTTCCTGGAATTACAGATTTATCTAC 57.168 33.333 19.85 5.60 40.97 2.59
2619 2921 3.320610 TGGAGGACCACAAAATTTGGA 57.679 42.857 10.71 0.00 41.77 3.53
2640 2942 5.016831 GGAGGTTTCCACATTTGTATCCTT 58.983 41.667 0.00 0.00 43.45 3.36
2641 2943 6.184789 GGAGGTTTCCACATTTGTATCCTTA 58.815 40.000 0.00 0.00 43.45 2.69
2802 3124 7.274447 TCAGGCAAGAAAATTCTCAACAAATT 58.726 30.769 0.00 0.00 36.28 1.82
2908 3287 8.461222 GGTTTTCAGATGATATTGATTGTGTGA 58.539 33.333 0.00 0.00 0.00 3.58
3079 3475 4.884164 ACTTGGTTCCTCTCTTGTCAAAAG 59.116 41.667 0.00 0.00 0.00 2.27
3087 3483 3.397482 TCTCTTGTCAAAAGAGCTCTGC 58.603 45.455 19.06 6.30 42.58 4.26
3088 3484 3.070734 TCTCTTGTCAAAAGAGCTCTGCT 59.929 43.478 19.06 4.70 42.58 4.24
3089 3485 4.281941 TCTCTTGTCAAAAGAGCTCTGCTA 59.718 41.667 19.06 0.18 42.58 3.49
3090 3486 5.046735 TCTCTTGTCAAAAGAGCTCTGCTAT 60.047 40.000 19.06 0.00 42.58 2.97
3097 3493 2.978156 AGAGCTCTGCTATCTAGGCT 57.022 50.000 17.42 0.00 39.88 4.58
3106 3503 1.811941 GCTATCTAGGCTTGGGTGTGC 60.812 57.143 0.00 0.00 0.00 4.57
3251 3657 2.823758 GCCCTCCCCTGCTGATACC 61.824 68.421 0.00 0.00 0.00 2.73
3256 3662 1.967066 CTCCCCTGCTGATACCTACTG 59.033 57.143 0.00 0.00 0.00 2.74
3257 3663 0.394565 CCCCTGCTGATACCTACTGC 59.605 60.000 0.00 0.00 0.00 4.40
3258 3664 1.123077 CCCTGCTGATACCTACTGCA 58.877 55.000 0.00 0.00 39.20 4.41
3259 3665 1.486310 CCCTGCTGATACCTACTGCAA 59.514 52.381 0.00 0.00 40.46 4.08
3269 3679 8.446273 GCTGATACCTACTGCAATGTATTATTG 58.554 37.037 0.00 0.00 33.57 1.90
3271 3681 8.655901 TGATACCTACTGCAATGTATTATTGGA 58.344 33.333 0.00 0.00 0.00 3.53
3279 3689 4.994852 GCAATGTATTATTGGAGCCTCGTA 59.005 41.667 0.00 0.00 0.00 3.43
3303 3713 2.485814 GCAACTGACTGAATCTGGTTCC 59.514 50.000 0.00 0.00 35.91 3.62
3308 3728 5.006386 ACTGACTGAATCTGGTTCCAATTC 58.994 41.667 0.00 14.07 35.91 2.17
3312 3732 4.878397 ACTGAATCTGGTTCCAATTCGATC 59.122 41.667 0.00 0.00 35.91 3.69
3680 4105 2.438434 GCCTCCAACATGGACCCG 60.438 66.667 0.00 0.00 42.67 5.28
3721 4146 2.360980 CGAGACCACCCTCCTCCT 59.639 66.667 0.00 0.00 0.00 3.69
3722 4147 1.755008 CGAGACCACCCTCCTCCTC 60.755 68.421 0.00 0.00 0.00 3.71
3723 4148 1.700985 GAGACCACCCTCCTCCTCT 59.299 63.158 0.00 0.00 0.00 3.69
3724 4149 0.686112 GAGACCACCCTCCTCCTCTG 60.686 65.000 0.00 0.00 0.00 3.35
3725 4150 1.149782 AGACCACCCTCCTCCTCTGA 61.150 60.000 0.00 0.00 0.00 3.27
3726 4151 0.686112 GACCACCCTCCTCCTCTGAG 60.686 65.000 0.00 0.00 38.42 3.35
3727 4152 2.063378 CCACCCTCCTCCTCTGAGC 61.063 68.421 0.00 0.00 37.29 4.26
3758 4183 4.740922 CAGCCAATGCCTACCACA 57.259 55.556 0.00 0.00 38.69 4.17
3759 4184 2.183409 CAGCCAATGCCTACCACAC 58.817 57.895 0.00 0.00 38.69 3.82
3761 4186 2.406616 GCCAATGCCTACCACACCG 61.407 63.158 0.00 0.00 0.00 4.94
3762 4187 2.406616 CCAATGCCTACCACACCGC 61.407 63.158 0.00 0.00 0.00 5.68
3764 4189 3.969250 AATGCCTACCACACCGCCG 62.969 63.158 0.00 0.00 0.00 6.46
3786 4215 0.099082 CGACACTTAGCCTCTCGACC 59.901 60.000 0.00 0.00 0.00 4.79
3787 4216 1.465794 GACACTTAGCCTCTCGACCT 58.534 55.000 0.00 0.00 0.00 3.85
3805 4234 2.356818 CTTCTCGATCGAGGGTGGCC 62.357 65.000 37.28 0.00 42.20 5.36
3813 4242 0.394216 TCGAGGGTGGCCATTGATTG 60.394 55.000 9.72 0.00 0.00 2.67
3826 4255 5.355910 GGCCATTGATTGATTTCTGCAAAAT 59.644 36.000 0.00 6.57 0.00 1.82
3835 4264 5.347342 TGATTTCTGCAAAATGTTTCGTGT 58.653 33.333 10.33 0.00 0.00 4.49
3841 4270 3.304559 TGCAAAATGTTTCGTGTTTTCCG 59.695 39.130 0.00 0.00 0.00 4.30
3861 4290 3.555518 CGTTTCTTTTGCAAGGTCTAGC 58.444 45.455 0.00 0.00 0.00 3.42
3914 4352 6.316890 ACTCGTTCAGATAAGAGTAAGAGTCC 59.683 42.308 0.00 0.00 41.57 3.85
3922 4360 6.601613 AGATAAGAGTAAGAGTCCTCAGTGTG 59.398 42.308 0.00 0.00 0.00 3.82
3945 4386 7.147976 GTGCTCTGAAAATAATGTTGTTTCCT 58.852 34.615 0.00 0.00 31.57 3.36
3952 4393 8.093927 TGAAAATAATGTTGTTTCCTCATTCCC 58.906 33.333 0.00 0.00 34.35 3.97
3973 4414 6.442961 TCCCATAAATGAAATCATGGAACCT 58.557 36.000 0.00 0.00 40.37 3.50
3974 4415 6.902416 TCCCATAAATGAAATCATGGAACCTT 59.098 34.615 0.00 0.00 40.37 3.50
3975 4416 6.987992 CCCATAAATGAAATCATGGAACCTTG 59.012 38.462 0.00 0.00 40.37 3.61
3976 4417 7.364939 CCCATAAATGAAATCATGGAACCTTGT 60.365 37.037 0.00 0.00 40.37 3.16
3977 4418 7.493320 CCATAAATGAAATCATGGAACCTTGTG 59.507 37.037 0.00 0.00 40.37 3.33
3978 4419 6.669125 AAATGAAATCATGGAACCTTGTGA 57.331 33.333 0.00 2.71 36.56 3.58
3987 4428 3.420893 TGGAACCTTGTGATGTGATTCC 58.579 45.455 0.00 0.00 35.68 3.01
4054 4504 1.371558 GCTCTTTCCACGTCACCCT 59.628 57.895 0.00 0.00 0.00 4.34
4055 4505 0.250338 GCTCTTTCCACGTCACCCTT 60.250 55.000 0.00 0.00 0.00 3.95
4056 4506 1.001633 GCTCTTTCCACGTCACCCTTA 59.998 52.381 0.00 0.00 0.00 2.69
4057 4507 2.931320 GCTCTTTCCACGTCACCCTTAG 60.931 54.545 0.00 0.00 0.00 2.18
4058 4508 1.001633 TCTTTCCACGTCACCCTTAGC 59.998 52.381 0.00 0.00 0.00 3.09
4059 4509 0.035739 TTTCCACGTCACCCTTAGCC 59.964 55.000 0.00 0.00 0.00 3.93
4060 4510 0.834687 TTCCACGTCACCCTTAGCCT 60.835 55.000 0.00 0.00 0.00 4.58
4061 4511 0.040058 TCCACGTCACCCTTAGCCTA 59.960 55.000 0.00 0.00 0.00 3.93
4083 4533 1.260297 GCCCAACAAAATTGACGTTGC 59.740 47.619 0.00 0.00 38.92 4.17
4084 4534 2.544685 CCCAACAAAATTGACGTTGCA 58.455 42.857 0.00 0.00 38.92 4.08
4085 4535 2.932614 CCCAACAAAATTGACGTTGCAA 59.067 40.909 0.00 0.00 38.92 4.08
4086 4536 3.242252 CCCAACAAAATTGACGTTGCAAC 60.242 43.478 19.89 19.89 38.92 4.17
4087 4537 3.242252 CCAACAAAATTGACGTTGCAACC 60.242 43.478 23.42 11.20 38.92 3.77
4088 4538 3.238108 ACAAAATTGACGTTGCAACCA 57.762 38.095 23.42 13.75 0.00 3.67
4089 4539 3.589988 ACAAAATTGACGTTGCAACCAA 58.410 36.364 23.42 21.06 0.00 3.67
4090 4540 3.997021 ACAAAATTGACGTTGCAACCAAA 59.003 34.783 23.42 15.01 31.68 3.28
4091 4541 4.143009 ACAAAATTGACGTTGCAACCAAAC 60.143 37.500 23.42 12.36 31.68 2.93
4092 4542 2.217429 ATTGACGTTGCAACCAAACC 57.783 45.000 23.42 8.82 31.68 3.27
4093 4543 0.179161 TTGACGTTGCAACCAAACCG 60.179 50.000 23.42 13.23 31.68 4.44
4124 4594 1.153939 CCTTGTCCGTCTCTCTGCG 60.154 63.158 0.00 0.00 0.00 5.18
4137 4607 0.386478 CTCTGCGTTTTGAGGCAAGC 60.386 55.000 0.00 0.00 38.94 4.01
4193 4676 1.300080 CAACTTGTTGCGGCCCAAG 60.300 57.895 21.05 21.05 42.91 3.61
4216 4702 5.186797 AGGCATCTTATCTTATCTTCCCTCG 59.813 44.000 0.00 0.00 0.00 4.63
4281 4770 3.959535 TGATGTTGGGCCATTCTTTTC 57.040 42.857 7.26 0.00 0.00 2.29
4282 4771 3.509442 TGATGTTGGGCCATTCTTTTCT 58.491 40.909 7.26 0.00 0.00 2.52
4283 4772 3.511146 TGATGTTGGGCCATTCTTTTCTC 59.489 43.478 7.26 0.00 0.00 2.87
4284 4773 1.885887 TGTTGGGCCATTCTTTTCTCG 59.114 47.619 7.26 0.00 0.00 4.04
4285 4774 0.887933 TTGGGCCATTCTTTTCTCGC 59.112 50.000 7.26 0.00 0.00 5.03
4286 4775 0.251121 TGGGCCATTCTTTTCTCGCA 60.251 50.000 0.00 0.00 0.00 5.10
4287 4776 0.171231 GGGCCATTCTTTTCTCGCAC 59.829 55.000 4.39 0.00 0.00 5.34
4288 4777 0.881118 GGCCATTCTTTTCTCGCACA 59.119 50.000 0.00 0.00 0.00 4.57
4289 4778 1.401539 GGCCATTCTTTTCTCGCACAC 60.402 52.381 0.00 0.00 0.00 3.82
4290 4779 1.401539 GCCATTCTTTTCTCGCACACC 60.402 52.381 0.00 0.00 0.00 4.16
4291 4780 2.154462 CCATTCTTTTCTCGCACACCT 58.846 47.619 0.00 0.00 0.00 4.00
4292 4781 2.554032 CCATTCTTTTCTCGCACACCTT 59.446 45.455 0.00 0.00 0.00 3.50
4293 4782 3.004734 CCATTCTTTTCTCGCACACCTTT 59.995 43.478 0.00 0.00 0.00 3.11
4294 4783 3.963383 TTCTTTTCTCGCACACCTTTC 57.037 42.857 0.00 0.00 0.00 2.62
4295 4784 3.194005 TCTTTTCTCGCACACCTTTCT 57.806 42.857 0.00 0.00 0.00 2.52
4296 4785 3.131396 TCTTTTCTCGCACACCTTTCTC 58.869 45.455 0.00 0.00 0.00 2.87
4297 4786 2.910688 TTTCTCGCACACCTTTCTCT 57.089 45.000 0.00 0.00 0.00 3.10
4298 4787 2.910688 TTCTCGCACACCTTTCTCTT 57.089 45.000 0.00 0.00 0.00 2.85
4356 4863 2.731451 GGCGAAAAGTTGGAATTTCAGC 59.269 45.455 0.00 0.00 35.72 4.26
4417 4925 0.532573 ATCTGCGGGTAGTGACACTG 59.467 55.000 18.58 2.27 0.00 3.66
4420 4928 1.374252 GCGGGTAGTGACACTGTGG 60.374 63.158 18.58 5.96 0.00 4.17
4439 4947 0.598680 GTCGATGCTTCTCCATCCGG 60.599 60.000 0.00 0.00 38.68 5.14
4459 4967 1.063642 GGAATGGGAGAAAAGGGAGGG 60.064 57.143 0.00 0.00 0.00 4.30
4460 4968 1.010795 AATGGGAGAAAAGGGAGGGG 58.989 55.000 0.00 0.00 0.00 4.79
4461 4969 0.123266 ATGGGAGAAAAGGGAGGGGA 59.877 55.000 0.00 0.00 0.00 4.81
4462 4970 0.550147 TGGGAGAAAAGGGAGGGGAG 60.550 60.000 0.00 0.00 0.00 4.30
4463 4971 0.253207 GGGAGAAAAGGGAGGGGAGA 60.253 60.000 0.00 0.00 0.00 3.71
4464 4972 1.670059 GGAGAAAAGGGAGGGGAGAA 58.330 55.000 0.00 0.00 0.00 2.87
4465 4973 1.993301 GGAGAAAAGGGAGGGGAGAAA 59.007 52.381 0.00 0.00 0.00 2.52
4466 4974 2.025793 GGAGAAAAGGGAGGGGAGAAAG 60.026 54.545 0.00 0.00 0.00 2.62
4467 4975 1.356059 AGAAAAGGGAGGGGAGAAAGC 59.644 52.381 0.00 0.00 0.00 3.51
4548 5056 0.819582 GGTCCTGCACCATTGGATTG 59.180 55.000 10.37 0.00 45.98 2.67
4639 5147 2.284190 GAACCATACTCAGCCTGCTTC 58.716 52.381 0.00 0.00 0.00 3.86
4640 5148 1.279496 ACCATACTCAGCCTGCTTCA 58.721 50.000 0.00 0.00 0.00 3.02
4642 5150 2.012673 CCATACTCAGCCTGCTTCAAC 58.987 52.381 0.00 0.00 0.00 3.18
4643 5151 2.616256 CCATACTCAGCCTGCTTCAACA 60.616 50.000 0.00 0.00 0.00 3.33
4655 5167 4.260990 CCTGCTTCAACATACAAAACGTCA 60.261 41.667 0.00 0.00 0.00 4.35
4674 5186 4.111916 GTCAACACCAAAATTGTGTCTGG 58.888 43.478 0.97 0.00 34.95 3.86
4679 5193 4.648762 ACACCAAAATTGTGTCTGGATCAA 59.351 37.500 0.00 0.00 32.97 2.57
4713 5227 2.236766 GGCATAGGCAGCAGATCAAAT 58.763 47.619 0.15 0.00 43.71 2.32
4714 5228 2.626743 GGCATAGGCAGCAGATCAAATT 59.373 45.455 0.15 0.00 43.71 1.82
4715 5229 3.822735 GGCATAGGCAGCAGATCAAATTA 59.177 43.478 0.15 0.00 43.71 1.40
4716 5230 4.279169 GGCATAGGCAGCAGATCAAATTAA 59.721 41.667 0.15 0.00 43.71 1.40
4717 5231 5.218139 GCATAGGCAGCAGATCAAATTAAC 58.782 41.667 0.00 0.00 40.72 2.01
4718 5232 5.221106 GCATAGGCAGCAGATCAAATTAACA 60.221 40.000 0.00 0.00 40.72 2.41
4719 5233 4.978083 AGGCAGCAGATCAAATTAACAG 57.022 40.909 0.00 0.00 0.00 3.16
4720 5234 4.338879 AGGCAGCAGATCAAATTAACAGT 58.661 39.130 0.00 0.00 0.00 3.55
4721 5235 4.157289 AGGCAGCAGATCAAATTAACAGTG 59.843 41.667 0.00 0.00 0.00 3.66
4722 5236 4.156556 GGCAGCAGATCAAATTAACAGTGA 59.843 41.667 0.00 0.00 0.00 3.41
4723 5237 5.335897 GGCAGCAGATCAAATTAACAGTGAA 60.336 40.000 0.00 0.00 0.00 3.18
4724 5238 6.151691 GCAGCAGATCAAATTAACAGTGAAA 58.848 36.000 0.00 0.00 0.00 2.69
4725 5239 6.088616 GCAGCAGATCAAATTAACAGTGAAAC 59.911 38.462 0.00 0.00 0.00 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.135972 GTGGTTCGATGTGTGTGATGC 60.136 52.381 0.00 0.00 0.00 3.91
4 5 0.466124 TGGTGGTTCGATGTGTGTGA 59.534 50.000 0.00 0.00 0.00 3.58
5 6 0.586319 GTGGTGGTTCGATGTGTGTG 59.414 55.000 0.00 0.00 0.00 3.82
6 7 0.534203 GGTGGTGGTTCGATGTGTGT 60.534 55.000 0.00 0.00 0.00 3.72
7 8 0.250295 AGGTGGTGGTTCGATGTGTG 60.250 55.000 0.00 0.00 0.00 3.82
8 9 0.034896 GAGGTGGTGGTTCGATGTGT 59.965 55.000 0.00 0.00 0.00 3.72
9 10 0.673644 GGAGGTGGTGGTTCGATGTG 60.674 60.000 0.00 0.00 0.00 3.21
10 11 1.125093 TGGAGGTGGTGGTTCGATGT 61.125 55.000 0.00 0.00 0.00 3.06
11 12 0.391661 CTGGAGGTGGTGGTTCGATG 60.392 60.000 0.00 0.00 0.00 3.84
12 13 1.983224 CTGGAGGTGGTGGTTCGAT 59.017 57.895 0.00 0.00 0.00 3.59
13 14 2.879233 GCTGGAGGTGGTGGTTCGA 61.879 63.158 0.00 0.00 0.00 3.71
14 15 2.358737 GCTGGAGGTGGTGGTTCG 60.359 66.667 0.00 0.00 0.00 3.95
15 16 2.034221 GGCTGGAGGTGGTGGTTC 59.966 66.667 0.00 0.00 0.00 3.62
51 52 3.044305 GCACTTCGTTCGGCAGCT 61.044 61.111 0.00 0.00 0.00 4.24
62 63 5.470098 TCTTCTCTATTTGTGGTTGCACTTC 59.530 40.000 0.00 0.00 0.00 3.01
69 70 4.846940 ACCTCCTCTTCTCTATTTGTGGTT 59.153 41.667 0.00 0.00 0.00 3.67
71 72 4.440802 CGACCTCCTCTTCTCTATTTGTGG 60.441 50.000 0.00 0.00 0.00 4.17
74 75 4.499019 GCTCGACCTCCTCTTCTCTATTTG 60.499 50.000 0.00 0.00 0.00 2.32
75 76 3.634910 GCTCGACCTCCTCTTCTCTATTT 59.365 47.826 0.00 0.00 0.00 1.40
111 126 4.460683 TACCGTGGCGATGGTGGC 62.461 66.667 21.74 0.00 41.96 5.01
147 162 1.897398 CTTTTCCTTCGGGCGACACG 61.897 60.000 0.00 0.00 34.44 4.49
156 187 1.130561 GGCGGTCAATCTTTTCCTTCG 59.869 52.381 0.00 0.00 0.00 3.79
158 189 1.545841 GGGCGGTCAATCTTTTCCTT 58.454 50.000 0.00 0.00 0.00 3.36
162 193 2.340328 GGCGGGCGGTCAATCTTTT 61.340 57.895 0.00 0.00 0.00 2.27
181 212 3.145551 GCTTCCTAGGACGGCGGA 61.146 66.667 12.22 0.00 0.00 5.54
187 218 1.198759 TGGTGGTGGCTTCCTAGGAC 61.199 60.000 12.22 0.00 0.00 3.85
191 222 1.904771 CGATGGTGGTGGCTTCCTA 59.095 57.895 1.63 0.00 0.00 2.94
226 257 1.076777 AAGTGTGGTGGCTGCTTGT 60.077 52.632 0.00 0.00 0.00 3.16
228 259 0.820891 CTCAAGTGTGGTGGCTGCTT 60.821 55.000 0.00 0.00 0.00 3.91
243 274 1.335496 TCACGACATGACGACACTCAA 59.665 47.619 23.72 0.00 37.03 3.02
255 286 3.315142 ATGCCAGGCGTCACGACAT 62.315 57.895 5.45 0.00 37.34 3.06
313 344 2.656069 TTCTCTAGCGTGGTGGGGC 61.656 63.158 0.00 0.00 0.00 5.80
318 349 1.469308 CTCTTCGTTCTCTAGCGTGGT 59.531 52.381 0.00 0.00 0.00 4.16
324 355 1.671845 CGGGGACTCTTCGTTCTCTAG 59.328 57.143 0.00 0.00 0.00 2.43
325 356 1.747709 CGGGGACTCTTCGTTCTCTA 58.252 55.000 0.00 0.00 0.00 2.43
330 361 2.920912 TGGCGGGGACTCTTCGTT 60.921 61.111 0.00 0.00 0.00 3.85
351 382 4.143333 AAGCCCGGTCATCGTCGG 62.143 66.667 0.00 0.00 45.29 4.79
353 384 2.582498 CGAAGCCCGGTCATCGTC 60.582 66.667 1.34 0.00 37.11 4.20
401 432 2.955246 AGGCTCCTCCCTCCTCCA 60.955 66.667 0.00 0.00 34.51 3.86
402 433 2.445654 CAGGCTCCTCCCTCCTCC 60.446 72.222 0.00 0.00 31.24 4.30
403 434 2.445654 CCAGGCTCCTCCCTCCTC 60.446 72.222 0.00 0.00 31.24 3.71
404 435 4.814041 GCCAGGCTCCTCCCTCCT 62.814 72.222 3.29 0.00 31.24 3.69
482 515 5.486526 TCAACCAGATTTTGTTTGCTTTGT 58.513 33.333 0.00 0.00 29.97 2.83
546 579 3.494251 GTGCAAGAAACATGGCGAAAATT 59.506 39.130 0.00 0.00 0.00 1.82
553 586 4.557942 CCGTGCAAGAAACATGGC 57.442 55.556 0.00 0.00 37.38 4.40
555 588 0.109597 GAGGCCGTGCAAGAAACATG 60.110 55.000 0.00 0.00 0.00 3.21
565 600 1.666023 GCTTAAGTTTTGAGGCCGTGC 60.666 52.381 4.02 0.00 0.00 5.34
620 655 4.158384 GTTGTAAATTGACCGAGCACATG 58.842 43.478 0.00 0.00 0.00 3.21
623 658 2.550606 TGGTTGTAAATTGACCGAGCAC 59.449 45.455 0.00 0.00 36.22 4.40
675 711 3.450457 AGAGCCTGAAGTAACCATCTCAG 59.550 47.826 0.00 0.00 0.00 3.35
958 1042 2.674420 CAAGGAGGGAATGGCAATGAT 58.326 47.619 0.00 0.00 0.00 2.45
990 1096 4.143333 CTGGCCATTGCTGCTGCC 62.143 66.667 5.51 13.50 44.27 4.85
1095 1202 2.146061 GGAGGAGATGGGGAGCAGG 61.146 68.421 0.00 0.00 0.00 4.85
1101 1213 2.115337 AAGATCAGGAGGAGATGGGG 57.885 55.000 0.00 0.00 0.00 4.96
1122 1234 3.425162 TTTGCTTCTTCTTCCTCCTCC 57.575 47.619 0.00 0.00 0.00 4.30
1125 1237 5.307926 CAGAATTTGCTTCTTCTTCCTCC 57.692 43.478 0.00 0.00 41.60 4.30
1139 1251 5.542616 AGAAGACGATCTTGCAGAATTTG 57.457 39.130 5.20 0.00 36.73 2.32
1190 1361 6.795098 TCGAGCTGTAGCAGAAATTAAAAA 57.205 33.333 6.65 0.00 45.16 1.94
1192 1363 6.985188 ATTCGAGCTGTAGCAGAAATTAAA 57.015 33.333 15.14 0.00 45.16 1.52
1194 1365 6.985188 AAATTCGAGCTGTAGCAGAAATTA 57.015 33.333 15.14 0.00 45.16 1.40
1195 1366 5.886960 AAATTCGAGCTGTAGCAGAAATT 57.113 34.783 15.14 11.73 45.16 1.82
1196 1367 5.886960 AAAATTCGAGCTGTAGCAGAAAT 57.113 34.783 15.14 7.52 45.16 2.17
1197 1368 5.470098 AGAAAAATTCGAGCTGTAGCAGAAA 59.530 36.000 15.14 3.93 40.94 2.52
1199 1370 4.389992 CAGAAAAATTCGAGCTGTAGCAGA 59.610 41.667 6.65 2.53 37.97 4.26
1200 1371 4.153117 ACAGAAAAATTCGAGCTGTAGCAG 59.847 41.667 6.65 0.06 37.98 4.24
1201 1372 4.065088 ACAGAAAAATTCGAGCTGTAGCA 58.935 39.130 6.65 0.00 37.98 3.49
1204 1375 5.758296 ACTTGACAGAAAAATTCGAGCTGTA 59.242 36.000 0.00 0.00 39.68 2.74
1205 1376 4.576463 ACTTGACAGAAAAATTCGAGCTGT 59.424 37.500 0.00 0.00 42.03 4.40
1206 1377 5.100751 ACTTGACAGAAAAATTCGAGCTG 57.899 39.130 0.00 0.00 34.02 4.24
1207 1378 5.757850 AACTTGACAGAAAAATTCGAGCT 57.242 34.783 0.00 0.00 34.02 4.09
1208 1379 6.812481 AAAACTTGACAGAAAAATTCGAGC 57.188 33.333 0.00 0.00 34.02 5.03
1239 1411 9.309274 ATCGCGCAGATAAAATTCGTCAGAATT 62.309 37.037 8.75 1.09 46.33 2.17
1240 1412 7.932854 ATCGCGCAGATAAAATTCGTCAGAAT 61.933 38.462 8.75 0.00 42.32 2.40
1277 1450 6.759272 ACAAACAGAGCACTTATTAGAGACA 58.241 36.000 0.00 0.00 0.00 3.41
1278 1451 7.659652 AACAAACAGAGCACTTATTAGAGAC 57.340 36.000 0.00 0.00 0.00 3.36
1312 1485 1.893801 GTCGATACCGGATCCTCCAAT 59.106 52.381 9.46 0.00 35.91 3.16
1357 1530 1.221414 GTGAGTTGAGAGGTGTGTGC 58.779 55.000 0.00 0.00 0.00 4.57
1404 1577 2.001812 TTCAGTGAGATTCAGCGAGC 57.998 50.000 0.00 0.00 0.00 5.03
1407 1580 5.793952 CAGAAAATTTCAGTGAGATTCAGCG 59.206 40.000 9.18 0.00 0.00 5.18
1431 1604 3.006247 GCTCCATCCAACAGAGAGAAAC 58.994 50.000 0.00 0.00 0.00 2.78
1436 1610 1.552337 GTCTGCTCCATCCAACAGAGA 59.448 52.381 0.00 0.00 39.69 3.10
1614 1788 8.135529 GCAAACAAGGAAAGTAGAAATACTTGT 58.864 33.333 0.00 0.00 46.12 3.16
1615 1789 8.352942 AGCAAACAAGGAAAGTAGAAATACTTG 58.647 33.333 1.65 0.00 39.93 3.16
1742 1917 6.378280 TGAAAGAATCAAGGAGGATAAAAGGC 59.622 38.462 0.00 0.00 34.30 4.35
1759 1937 8.729805 TTGGTGCATAAAAAGTTTGAAAGAAT 57.270 26.923 0.00 0.00 0.00 2.40
1857 2040 6.670695 AAAATTTAGTGATGCCCAGAAACT 57.329 33.333 0.00 0.00 0.00 2.66
1888 2072 6.843069 TTAAGCCACAAAATTCAGCTTTTC 57.157 33.333 0.41 0.00 40.76 2.29
1893 2078 9.943163 TTTTAAAATTAAGCCACAAAATTCAGC 57.057 25.926 0.00 0.00 0.00 4.26
1920 2139 5.356426 ACAGCCACAAAATCCAGTTTTTAC 58.644 37.500 0.00 0.00 37.93 2.01
2016 2235 4.037923 CAGGTCAACCAGTGCAATTTTAGT 59.962 41.667 1.33 0.00 38.89 2.24
2025 2244 1.656441 CAAGCAGGTCAACCAGTGC 59.344 57.895 1.33 3.72 37.43 4.40
2030 2249 0.610232 ATGAGCCAAGCAGGTCAACC 60.610 55.000 7.28 0.00 40.61 3.77
2039 2258 8.084073 TCATAAGCAATTAATTATGAGCCAAGC 58.916 33.333 15.48 0.00 41.28 4.01
2114 2343 7.752239 CAGTTCAGGTATTTAAGATTTGTGCTG 59.248 37.037 0.00 0.00 0.00 4.41
2147 2378 0.813821 GCCTCTGATTTGGCTGGAAC 59.186 55.000 0.00 0.00 45.26 3.62
2148 2379 3.271250 GCCTCTGATTTGGCTGGAA 57.729 52.632 0.00 0.00 45.26 3.53
2155 2393 5.006386 AGTAGAAACTTGGCCTCTGATTTG 58.994 41.667 3.32 0.00 29.00 2.32
2198 2436 9.855021 AATAAATAGGAAAAGATCAACAAACCG 57.145 29.630 0.00 0.00 0.00 4.44
2244 2485 1.202639 CCTTGTGGTGTGTAGCAGTCA 60.203 52.381 0.00 0.00 34.49 3.41
2298 2539 0.804989 GGGTGTTGAAGATCTTGGCG 59.195 55.000 14.00 0.00 0.00 5.69
2319 2560 0.035881 TCTCCTCAGCTGCAACCTTG 59.964 55.000 9.47 0.00 0.00 3.61
2381 2673 5.468072 ACAACTCTTAGATGAAACACTGCAG 59.532 40.000 13.48 13.48 0.00 4.41
2425 2721 4.571372 TGTGTTCTCACGTGTGTATGTA 57.429 40.909 16.51 0.00 46.49 2.29
2457 2753 9.688592 GTGGTGTGGTACTTATCTATATTGTAC 57.311 37.037 0.00 0.00 34.48 2.90
2458 2754 9.423964 TGTGGTGTGGTACTTATCTATATTGTA 57.576 33.333 0.00 0.00 0.00 2.41
2459 2755 8.202137 GTGTGGTGTGGTACTTATCTATATTGT 58.798 37.037 0.00 0.00 0.00 2.71
2470 2766 2.021457 GCAAAGTGTGGTGTGGTACTT 58.979 47.619 0.00 0.00 35.06 2.24
2482 2778 4.828939 TCTTTTCCATCTGATGCAAAGTGT 59.171 37.500 24.80 0.00 33.83 3.55
2555 2855 7.438564 TCTGTCTGTATCTGCTAGAGTAGTAG 58.561 42.308 0.00 0.00 39.51 2.57
2558 2858 7.561021 TTTCTGTCTGTATCTGCTAGAGTAG 57.439 40.000 0.00 0.00 0.00 2.57
2559 2859 7.415765 GCTTTTCTGTCTGTATCTGCTAGAGTA 60.416 40.741 0.00 0.00 0.00 2.59
2560 2860 6.627065 GCTTTTCTGTCTGTATCTGCTAGAGT 60.627 42.308 0.00 0.00 0.00 3.24
2561 2861 5.748152 GCTTTTCTGTCTGTATCTGCTAGAG 59.252 44.000 0.00 0.00 0.00 2.43
2562 2862 5.420421 AGCTTTTCTGTCTGTATCTGCTAGA 59.580 40.000 0.00 0.00 0.00 2.43
2563 2863 5.659463 AGCTTTTCTGTCTGTATCTGCTAG 58.341 41.667 0.00 0.00 0.00 3.42
2564 2864 5.667539 AGCTTTTCTGTCTGTATCTGCTA 57.332 39.130 0.00 0.00 0.00 3.49
2601 2903 3.230976 ACCTCCAAATTTTGTGGTCCTC 58.769 45.455 9.56 0.00 37.43 3.71
2619 2921 9.574516 GATATAAGGATACAAATGTGGAAACCT 57.425 33.333 0.00 0.00 41.41 3.50
2640 2942 5.768662 AGTGCTCTAACCGTAAGCAGATATA 59.231 40.000 0.00 0.00 45.99 0.86
2641 2943 4.585162 AGTGCTCTAACCGTAAGCAGATAT 59.415 41.667 0.00 0.00 45.99 1.63
2843 3195 6.279513 ACTGTGGACAAATTTCAGTTCAAA 57.720 33.333 4.17 0.00 36.17 2.69
2851 3203 3.882888 TCAGTGGACTGTGGACAAATTTC 59.117 43.478 6.68 0.00 44.12 2.17
2855 3229 2.421388 CCTTCAGTGGACTGTGGACAAA 60.421 50.000 6.68 0.00 44.12 2.83
2908 3287 3.778265 AGTATGGTCCCTGCACAAAATT 58.222 40.909 0.00 0.00 0.00 1.82
3079 3475 2.029110 CCAAGCCTAGATAGCAGAGCTC 60.029 54.545 5.27 5.27 40.44 4.09
3087 3483 1.539065 CGCACACCCAAGCCTAGATAG 60.539 57.143 0.00 0.00 0.00 2.08
3088 3484 0.464036 CGCACACCCAAGCCTAGATA 59.536 55.000 0.00 0.00 0.00 1.98
3089 3485 1.221840 CGCACACCCAAGCCTAGAT 59.778 57.895 0.00 0.00 0.00 1.98
3090 3486 1.476845 TTCGCACACCCAAGCCTAGA 61.477 55.000 0.00 0.00 0.00 2.43
3097 3493 1.974265 TCAGAAATTCGCACACCCAA 58.026 45.000 0.00 0.00 0.00 4.12
3190 3596 1.004080 CACCCACAGCTGGTCTGAG 60.004 63.158 19.93 0.19 45.72 3.35
3193 3599 3.958860 GCCACCCACAGCTGGTCT 61.959 66.667 19.93 0.00 35.46 3.85
3251 3657 6.000219 AGGCTCCAATAATACATTGCAGTAG 59.000 40.000 0.00 0.00 0.00 2.57
3256 3662 3.815401 ACGAGGCTCCAATAATACATTGC 59.185 43.478 9.32 0.00 0.00 3.56
3257 3663 6.035005 CGATACGAGGCTCCAATAATACATTG 59.965 42.308 9.32 0.00 0.00 2.82
3258 3664 6.100004 CGATACGAGGCTCCAATAATACATT 58.900 40.000 9.32 0.00 0.00 2.71
3259 3665 5.651530 CGATACGAGGCTCCAATAATACAT 58.348 41.667 9.32 0.00 0.00 2.29
3269 3679 0.872021 CAGTTGCGATACGAGGCTCC 60.872 60.000 9.32 0.00 0.00 4.70
3271 3681 0.179134 GTCAGTTGCGATACGAGGCT 60.179 55.000 0.00 0.00 0.00 4.58
3272 3682 0.179134 AGTCAGTTGCGATACGAGGC 60.179 55.000 0.00 0.00 0.00 4.70
3279 3689 2.027745 ACCAGATTCAGTCAGTTGCGAT 60.028 45.455 0.00 0.00 0.00 4.58
3303 3713 2.852143 GCAGCATCAACCGATCGAATTG 60.852 50.000 18.66 19.49 0.00 2.32
3308 3728 0.807275 TCTGCAGCATCAACCGATCG 60.807 55.000 9.47 8.51 0.00 3.69
3312 3732 0.463295 ATCCTCTGCAGCATCAACCG 60.463 55.000 9.47 0.00 0.00 4.44
3452 3877 1.482621 CGATGGCCGTCTTGATCACG 61.483 60.000 22.53 3.68 36.99 4.35
3680 4105 0.806868 TCATGGAGGTGACGACGTAC 59.193 55.000 0.00 0.00 0.00 3.67
3721 4146 1.303643 TGGTCGCTCAGAGCTCAGA 60.304 57.895 20.39 12.99 46.86 3.27
3722 4147 1.139308 CTGGTCGCTCAGAGCTCAG 59.861 63.158 20.39 18.51 46.86 3.35
3723 4148 2.999485 GCTGGTCGCTCAGAGCTCA 61.999 63.158 20.39 13.77 46.86 4.26
3724 4149 2.202730 GCTGGTCGCTCAGAGCTC 60.203 66.667 20.39 5.27 46.86 4.09
3725 4150 2.993840 TGCTGGTCGCTCAGAGCT 60.994 61.111 20.39 0.00 46.86 4.09
3726 4151 2.508887 CTGCTGGTCGCTCAGAGC 60.509 66.667 12.94 12.94 46.92 4.09
3727 4152 2.508887 GCTGCTGGTCGCTCAGAG 60.509 66.667 8.65 0.00 40.11 3.35
3744 4169 2.406616 GCGGTGTGGTAGGCATTGG 61.407 63.158 0.00 0.00 0.00 3.16
3746 4171 2.045340 GGCGGTGTGGTAGGCATT 60.045 61.111 0.00 0.00 0.00 3.56
3751 4176 4.789075 CGTCCGGCGGTGTGGTAG 62.789 72.222 27.32 6.71 36.85 3.18
3758 4183 2.985282 TAAGTGTCGTCCGGCGGT 60.985 61.111 27.32 6.20 41.72 5.68
3759 4184 2.202570 CTAAGTGTCGTCCGGCGG 60.203 66.667 22.51 22.51 41.72 6.13
3761 4186 2.508663 GGCTAAGTGTCGTCCGGC 60.509 66.667 0.00 0.00 0.00 6.13
3762 4187 1.139095 GAGGCTAAGTGTCGTCCGG 59.861 63.158 0.00 0.00 0.00 5.14
3764 4189 0.099082 CGAGAGGCTAAGTGTCGTCC 59.901 60.000 0.00 0.00 0.00 4.79
3765 4190 1.085091 TCGAGAGGCTAAGTGTCGTC 58.915 55.000 0.00 0.00 32.49 4.20
3766 4191 0.803740 GTCGAGAGGCTAAGTGTCGT 59.196 55.000 0.00 0.00 32.49 4.34
3786 4215 1.066587 GCCACCCTCGATCGAGAAG 59.933 63.158 39.64 31.43 44.53 2.85
3787 4216 2.423898 GGCCACCCTCGATCGAGAA 61.424 63.158 39.64 10.77 44.53 2.87
3805 4234 9.325150 GAAACATTTTGCAGAAATCAATCAATG 57.675 29.630 0.00 0.00 32.30 2.82
3813 4242 5.888412 ACACGAAACATTTTGCAGAAATC 57.112 34.783 0.00 0.00 0.00 2.17
3826 4255 4.422546 AAGAAACGGAAAACACGAAACA 57.577 36.364 0.00 0.00 34.93 2.83
3835 4264 4.081917 AGACCTTGCAAAAGAAACGGAAAA 60.082 37.500 0.00 0.00 0.00 2.29
3841 4270 3.902150 GGCTAGACCTTGCAAAAGAAAC 58.098 45.455 0.00 0.00 34.51 2.78
3861 4290 1.106944 AGACACGCCCCAAAAACAGG 61.107 55.000 0.00 0.00 0.00 4.00
3914 4352 6.492007 ACATTATTTTCAGAGCACACTGAG 57.508 37.500 7.95 0.00 45.63 3.35
3922 4360 7.370383 TGAGGAAACAACATTATTTTCAGAGC 58.630 34.615 0.00 0.00 31.94 4.09
3945 4386 8.423349 GTTCCATGATTTCATTTATGGGAATGA 58.577 33.333 10.65 0.00 42.58 2.57
3952 4393 8.252417 TCACAAGGTTCCATGATTTCATTTATG 58.748 33.333 0.00 0.00 33.61 1.90
3973 4414 3.033368 TCGAACGGAATCACATCACAA 57.967 42.857 0.00 0.00 0.00 3.33
3974 4415 2.734276 TCGAACGGAATCACATCACA 57.266 45.000 0.00 0.00 0.00 3.58
3975 4416 3.000322 GTGATCGAACGGAATCACATCAC 60.000 47.826 17.66 12.54 42.01 3.06
3976 4417 3.186909 GTGATCGAACGGAATCACATCA 58.813 45.455 17.66 6.37 42.01 3.07
3977 4418 3.186909 TGTGATCGAACGGAATCACATC 58.813 45.455 19.85 5.63 45.61 3.06
3978 4419 3.245518 TGTGATCGAACGGAATCACAT 57.754 42.857 19.85 0.00 45.61 3.21
3987 4428 1.660104 TGCATGACATGTGATCGAACG 59.340 47.619 16.62 0.00 0.00 3.95
4054 4504 4.835615 TCAATTTTGTTGGGCTTAGGCTAA 59.164 37.500 6.80 6.80 38.73 3.09
4055 4505 4.219725 GTCAATTTTGTTGGGCTTAGGCTA 59.780 41.667 5.62 0.00 38.73 3.93
4056 4506 3.006859 GTCAATTTTGTTGGGCTTAGGCT 59.993 43.478 5.62 0.00 38.73 4.58
4057 4507 3.325870 GTCAATTTTGTTGGGCTTAGGC 58.674 45.455 0.00 0.00 37.82 3.93
4058 4508 3.005367 ACGTCAATTTTGTTGGGCTTAGG 59.995 43.478 0.00 0.00 0.00 2.69
4059 4509 4.237349 ACGTCAATTTTGTTGGGCTTAG 57.763 40.909 0.00 0.00 0.00 2.18
4060 4510 4.363999 CAACGTCAATTTTGTTGGGCTTA 58.636 39.130 0.00 0.00 39.36 3.09
4061 4511 3.194062 CAACGTCAATTTTGTTGGGCTT 58.806 40.909 0.00 0.00 39.36 4.35
4083 4533 4.639171 GCACGGCCGGTTTGGTTG 62.639 66.667 31.76 17.74 41.21 3.77
4084 4534 4.887190 AGCACGGCCGGTTTGGTT 62.887 61.111 31.76 8.32 41.21 3.67
4103 4573 0.169230 CAGAGAGACGGACAAGGACG 59.831 60.000 0.00 0.00 0.00 4.79
4124 4594 1.725973 GCGACGCTTGCCTCAAAAC 60.726 57.895 13.73 0.00 0.00 2.43
4190 4660 6.777782 AGGGAAGATAAGATAAGATGCCTTG 58.222 40.000 0.00 0.00 33.94 3.61
4193 4676 5.415221 CGAGGGAAGATAAGATAAGATGCC 58.585 45.833 0.00 0.00 0.00 4.40
4281 4770 1.801178 GGAAAGAGAAAGGTGTGCGAG 59.199 52.381 0.00 0.00 0.00 5.03
4282 4771 1.872237 CGGAAAGAGAAAGGTGTGCGA 60.872 52.381 0.00 0.00 0.00 5.10
4283 4772 0.512952 CGGAAAGAGAAAGGTGTGCG 59.487 55.000 0.00 0.00 0.00 5.34
4284 4773 0.875059 CCGGAAAGAGAAAGGTGTGC 59.125 55.000 0.00 0.00 0.00 4.57
4285 4774 2.143925 GTCCGGAAAGAGAAAGGTGTG 58.856 52.381 5.23 0.00 0.00 3.82
4286 4775 1.270147 CGTCCGGAAAGAGAAAGGTGT 60.270 52.381 5.23 0.00 0.00 4.16
4287 4776 1.429463 CGTCCGGAAAGAGAAAGGTG 58.571 55.000 5.23 0.00 0.00 4.00
4288 4777 0.320508 GCGTCCGGAAAGAGAAAGGT 60.321 55.000 5.23 0.00 0.00 3.50
4289 4778 1.352156 CGCGTCCGGAAAGAGAAAGG 61.352 60.000 5.23 0.00 0.00 3.11
4290 4779 2.070861 CGCGTCCGGAAAGAGAAAG 58.929 57.895 5.23 0.00 0.00 2.62
4291 4780 4.255126 CGCGTCCGGAAAGAGAAA 57.745 55.556 5.23 0.00 0.00 2.52
4313 4820 1.293179 AAAAAGCAGGAATGGCGGC 59.707 52.632 0.00 0.00 36.08 6.53
4336 4843 3.642705 AGCTGAAATTCCAACTTTTCGC 58.357 40.909 0.00 0.00 35.15 4.70
4356 4863 2.350522 CTCCTTGTTCCGTCCATGAAG 58.649 52.381 0.00 0.00 0.00 3.02
4417 4925 1.576356 GATGGAGAAGCATCGACCAC 58.424 55.000 11.67 4.83 38.79 4.16
4420 4928 0.598680 CCGGATGGAGAAGCATCGAC 60.599 60.000 0.00 0.00 37.49 4.20
4439 4947 1.063642 CCCTCCCTTTTCTCCCATTCC 60.064 57.143 0.00 0.00 0.00 3.01
4467 4975 3.787676 TGCGCCGTGAGCATTTCG 61.788 61.111 4.18 0.00 44.04 3.46
4489 4997 5.528690 ACTTTGGTGGATGTATCGATCAATG 59.471 40.000 0.00 11.51 35.92 2.82
4505 5013 1.679153 ACTTTGGCGGTAACTTTGGTG 59.321 47.619 0.00 0.00 0.00 4.17
4639 5147 4.663166 TGGTGTTGACGTTTTGTATGTTG 58.337 39.130 0.00 0.00 0.00 3.33
4640 5148 4.966965 TGGTGTTGACGTTTTGTATGTT 57.033 36.364 0.00 0.00 0.00 2.71
4642 5150 6.820470 ATTTTGGTGTTGACGTTTTGTATG 57.180 33.333 0.00 0.00 0.00 2.39
4643 5151 6.814146 ACAATTTTGGTGTTGACGTTTTGTAT 59.186 30.769 0.00 0.00 0.00 2.29
4674 5186 3.248266 GCCACATGCTTTCAGTTTGATC 58.752 45.455 0.00 0.00 36.87 2.92
4679 5193 2.756760 CCTATGCCACATGCTTTCAGTT 59.243 45.455 0.00 0.00 42.00 3.16


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

AutoCloner maintained by Alex Coulton.