Multiple sequence alignment - TraesCS6A01G118300

Loading Multiple Alignment...

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 TraesCS6A01G118300 chr6A 100.000 3170 0 0 1 3170 89301554 89304723 0.000000e+00 5854.0
1 TraesCS6A01G118300 chr6A 79.602 201 36 2 1319 1518 109135963 109136159 4.260000e-29 139.0
2 TraesCS6A01G118300 chr6D 87.172 2627 165 84 144 2721 72404680 72407183 0.000000e+00 2826.0
3 TraesCS6A01G118300 chr6D 90.263 380 26 7 2791 3169 72407337 72407706 1.320000e-133 486.0
4 TraesCS6A01G118300 chr6D 80.100 201 35 2 1319 1518 90922941 90923137 9.160000e-31 145.0
5 TraesCS6A01G118300 chr6B 85.714 2534 189 84 679 3141 147055761 147058192 0.000000e+00 2514.0
6 TraesCS6A01G118300 chr6B 83.022 536 37 29 210 696 147055215 147055745 1.350000e-118 436.0
7 TraesCS6A01G118300 chr6B 82.915 199 14 10 16 202 147054922 147055112 9.100000e-36 161.0
8 TraesCS6A01G118300 chr6B 85.714 98 12 2 1408 1504 48074720 48074816 5.590000e-18 102.0
9 TraesCS6A01G118300 chr3D 71.364 887 176 52 1153 2009 95840280 95839442 3.270000e-35 159.0
10 TraesCS6A01G118300 chr3D 87.629 97 10 2 1409 1504 170659602 170659697 9.290000e-21 111.0
11 TraesCS6A01G118300 chr3D 75.532 188 43 2 1316 1503 170558163 170557979 4.360000e-14 89.8
12 TraesCS6A01G118300 chr3A 71.396 888 171 62 1154 2009 113922422 113921586 4.230000e-34 156.0
13 TraesCS6A01G118300 chr3A 87.629 97 10 2 1409 1504 208222051 208222146 9.290000e-21 111.0
14 TraesCS6A01G118300 chr7D 78.218 202 37 3 1319 1518 478370583 478370779 4.290000e-24 122.0
15 TraesCS6A01G118300 chr3B 76.842 190 39 3 1316 1504 245964149 245963964 5.590000e-18 102.0
16 TraesCS6A01G118300 chr3B 85.417 96 14 0 1153 1248 146706994 146706899 2.010000e-17 100.0
17 TraesCS6A01G118300 chr3B 93.333 60 4 0 1445 1504 245969767 245969708 4.360000e-14 89.8
18 TraesCS6A01G118300 chr4B 76.263 198 42 4 1314 1510 139399340 139399533 2.010000e-17 100.0
19 TraesCS6A01G118300 chr4B 76.263 198 42 4 1314 1510 139472485 139472678 2.010000e-17 100.0
20 TraesCS6A01G118300 chr4B 76.263 198 42 4 1314 1510 139510933 139511126 2.010000e-17 100.0
21 TraesCS6A01G118300 chr2D 71.463 410 101 12 1100 1504 55630231 55629833 9.360000e-16 95.3
22 TraesCS6A01G118300 chr5D 91.667 60 5 0 1451 1510 393801779 393801720 2.030000e-12 84.2
23 TraesCS6A01G118300 chr4A 74.872 195 44 4 1317 1510 478219500 478219310 2.030000e-12 84.2
24 TraesCS6A01G118300 chr4A 74.227 194 45 4 1317 1509 478339829 478339640 3.390000e-10 76.8
25 TraesCS6A01G118300 chr4D 75.000 184 43 2 1314 1497 97605460 97605640 7.290000e-12 82.4
26 TraesCS6A01G118300 chr4D 74.242 198 46 4 1314 1510 97720835 97721028 9.430000e-11 78.7
27 TraesCS6A01G118300 chr5B 88.636 44 5 0 179 222 469493490 469493447 2.000000e-03 54.7


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 TraesCS6A01G118300 chr6A 89301554 89304723 3169 False 5854 5854 100.000000 1 3170 1 chr6A.!!$F1 3169
1 TraesCS6A01G118300 chr6D 72404680 72407706 3026 False 1656 2826 88.717500 144 3169 2 chr6D.!!$F2 3025
2 TraesCS6A01G118300 chr6B 147054922 147058192 3270 False 1037 2514 83.883667 16 3141 3 chr6B.!!$F2 3125

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
100 101 0.108138 GTCTGGCTTATCGGCTGTGT 60.108 55.0 0.0 0.0 39.32 3.72 F
925 1149 0.235926 GCAGTTTCTGTCACCGCTTC 59.764 55.0 0.0 0.0 33.43 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1553 1791 0.388520 GCACGTTGGGGAAGAATTGC 60.389 55.0 0.00 0.00 34.72 3.56 R
2796 3163 0.323542 ACCACTTCTCGATCGAGGGT 60.324 55.0 37.28 32.18 42.20 4.34 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
17 18 4.805132 TGGATTTGGGGATTGGCC 57.195 55.556 0.00 0.00 0.00 5.36
18 19 1.381056 TGGATTTGGGGATTGGCCG 60.381 57.895 0.00 0.00 37.63 6.13
49 50 0.912486 AGGCCAAAGGTAAGCTCGAT 59.088 50.000 5.01 0.00 0.00 3.59
51 52 1.406887 GGCCAAAGGTAAGCTCGATCA 60.407 52.381 0.00 0.00 0.00 2.92
60 61 9.226345 CAAAGGTAAGCTCGATCATTTTATTTC 57.774 33.333 0.00 0.00 0.00 2.17
62 63 6.486993 AGGTAAGCTCGATCATTTTATTTCCC 59.513 38.462 0.00 0.00 0.00 3.97
68 69 5.666462 TCGATCATTTTATTTCCCTGTCGA 58.334 37.500 0.00 0.00 32.76 4.20
82 83 1.296715 GTCGACCCAGCATTGAGGT 59.703 57.895 3.51 0.00 36.31 3.85
83 84 0.741221 GTCGACCCAGCATTGAGGTC 60.741 60.000 3.51 9.66 45.49 3.85
96 97 0.687757 TGAGGTCTGGCTTATCGGCT 60.688 55.000 0.00 0.00 39.32 5.52
98 99 0.978146 AGGTCTGGCTTATCGGCTGT 60.978 55.000 0.00 0.00 39.32 4.40
99 100 0.811616 GGTCTGGCTTATCGGCTGTG 60.812 60.000 0.00 0.00 39.32 3.66
100 101 0.108138 GTCTGGCTTATCGGCTGTGT 60.108 55.000 0.00 0.00 39.32 3.72
101 102 0.613260 TCTGGCTTATCGGCTGTGTT 59.387 50.000 0.00 0.00 39.32 3.32
102 103 1.009829 CTGGCTTATCGGCTGTGTTC 58.990 55.000 0.00 0.00 39.32 3.18
103 104 0.613260 TGGCTTATCGGCTGTGTTCT 59.387 50.000 0.00 0.00 39.32 3.01
104 105 1.828595 TGGCTTATCGGCTGTGTTCTA 59.171 47.619 0.00 0.00 39.32 2.10
140 141 6.352516 AGGTCAGCTCGATCTTTTCATTTAT 58.647 36.000 0.00 0.00 26.82 1.40
159 172 1.610363 TGTGCCGTGCCTGATAAAAA 58.390 45.000 0.00 0.00 0.00 1.94
169 182 4.437390 GTGCCTGATAAAAATCAGACACGG 60.437 45.833 15.74 3.52 46.49 4.94
287 399 4.327898 TGATGTACTTTAACGGACGATTGC 59.672 41.667 0.00 0.00 0.00 3.56
350 462 1.222661 GACCGAACCCCACCATACC 59.777 63.158 0.00 0.00 0.00 2.73
351 463 1.539372 ACCGAACCCCACCATACCA 60.539 57.895 0.00 0.00 0.00 3.25
352 464 0.917333 ACCGAACCCCACCATACCAT 60.917 55.000 0.00 0.00 0.00 3.55
455 576 1.873591 CACCAGAAAGAACCAACCGAG 59.126 52.381 0.00 0.00 0.00 4.63
456 577 1.202770 ACCAGAAAGAACCAACCGAGG 60.203 52.381 0.00 0.00 0.00 4.63
512 646 3.482783 GCGTTGCCACTCTCGCTC 61.483 66.667 0.00 0.00 44.28 5.03
513 647 3.175240 CGTTGCCACTCTCGCTCG 61.175 66.667 0.00 0.00 0.00 5.03
514 648 2.049063 GTTGCCACTCTCGCTCGT 60.049 61.111 0.00 0.00 0.00 4.18
515 649 1.664965 GTTGCCACTCTCGCTCGTT 60.665 57.895 0.00 0.00 0.00 3.85
516 650 1.372997 TTGCCACTCTCGCTCGTTC 60.373 57.895 0.00 0.00 0.00 3.95
517 651 2.082629 TTGCCACTCTCGCTCGTTCA 62.083 55.000 0.00 0.00 0.00 3.18
518 652 1.153745 GCCACTCTCGCTCGTTCAT 60.154 57.895 0.00 0.00 0.00 2.57
519 653 1.142778 GCCACTCTCGCTCGTTCATC 61.143 60.000 0.00 0.00 0.00 2.92
520 654 0.526524 CCACTCTCGCTCGTTCATCC 60.527 60.000 0.00 0.00 0.00 3.51
552 702 2.958576 GGTCGCCGGCATTTTTCA 59.041 55.556 28.98 0.00 0.00 2.69
556 706 0.891449 TCGCCGGCATTTTTCAAGGA 60.891 50.000 28.98 8.36 0.00 3.36
585 736 1.764571 TTTGGACCTCGACCACCCAG 61.765 60.000 0.00 0.00 37.13 4.45
587 738 4.083862 GACCTCGACCACCCAGCC 62.084 72.222 0.00 0.00 0.00 4.85
590 741 4.436998 CTCGACCACCCAGCCGAC 62.437 72.222 0.00 0.00 0.00 4.79
607 758 1.646189 GACTCCGATTCAACCAGAGC 58.354 55.000 0.00 0.00 0.00 4.09
661 842 3.509184 ACCGTCCACCTTTTAGACTCTAC 59.491 47.826 0.00 0.00 0.00 2.59
662 843 3.762823 CCGTCCACCTTTTAGACTCTACT 59.237 47.826 0.00 0.00 0.00 2.57
663 844 4.946157 CCGTCCACCTTTTAGACTCTACTA 59.054 45.833 0.00 0.00 0.00 1.82
881 1105 2.735126 CGAGCCACAATAATTGGTTGCC 60.735 50.000 5.59 0.00 36.40 4.52
902 1126 2.747855 AAGCAAGCGCCACTAGCC 60.748 61.111 2.29 0.00 39.83 3.93
914 1138 0.320771 CACTAGCCACGGCAGTTTCT 60.321 55.000 11.35 0.00 44.88 2.52
915 1139 0.320771 ACTAGCCACGGCAGTTTCTG 60.321 55.000 11.35 0.00 44.88 3.02
916 1140 0.320771 CTAGCCACGGCAGTTTCTGT 60.321 55.000 11.35 0.00 44.88 3.41
917 1141 0.320421 TAGCCACGGCAGTTTCTGTC 60.320 55.000 11.35 0.00 44.88 3.51
918 1142 1.891919 GCCACGGCAGTTTCTGTCA 60.892 57.895 2.36 0.00 35.60 3.58
919 1143 1.941812 CCACGGCAGTTTCTGTCAC 59.058 57.895 2.44 0.00 35.60 3.67
920 1144 1.507141 CCACGGCAGTTTCTGTCACC 61.507 60.000 2.44 0.00 35.60 4.02
921 1145 1.594293 ACGGCAGTTTCTGTCACCG 60.594 57.895 10.85 10.85 39.37 4.94
922 1146 2.946762 GGCAGTTTCTGTCACCGC 59.053 61.111 0.00 0.00 35.96 5.68
923 1147 1.598130 GGCAGTTTCTGTCACCGCT 60.598 57.895 0.00 0.00 35.96 5.52
924 1148 1.166531 GGCAGTTTCTGTCACCGCTT 61.167 55.000 0.00 0.00 35.96 4.68
925 1149 0.235926 GCAGTTTCTGTCACCGCTTC 59.764 55.000 0.00 0.00 33.43 3.86
931 1155 1.444553 CTGTCACCGCTTCCGAGTC 60.445 63.158 0.00 0.00 36.29 3.36
975 1204 3.917760 CCTCCGATCGGGTGGCTC 61.918 72.222 32.79 0.00 42.26 4.70
1025 1254 4.452733 CTTCCCCTCCGTGTCCGC 62.453 72.222 0.00 0.00 0.00 5.54
1061 1290 1.003573 GACCCATCCTCCTCCTGGT 59.996 63.158 0.00 0.00 34.23 4.00
1062 1291 1.003573 ACCCATCCTCCTCCTGGTC 59.996 63.158 0.00 0.00 34.23 4.02
1063 1292 1.768077 CCCATCCTCCTCCTGGTCC 60.768 68.421 0.00 0.00 34.23 4.46
1067 1302 2.905676 ATCCTCCTCCTGGTCCTGGC 62.906 65.000 9.96 0.00 34.23 4.85
1180 1415 4.451150 TCATGTCGCAGGCCGTCC 62.451 66.667 0.00 0.00 38.35 4.79
1260 1495 2.874780 GTACGCGTCTCCAGCACG 60.875 66.667 18.63 0.00 40.35 5.34
1261 1496 3.359523 TACGCGTCTCCAGCACGT 61.360 61.111 18.63 0.00 39.54 4.49
1262 1497 2.911484 TACGCGTCTCCAGCACGTT 61.911 57.895 18.63 0.00 39.54 3.99
1264 1499 3.470567 GCGTCTCCAGCACGTTCG 61.471 66.667 0.00 0.00 39.54 3.95
1268 1503 1.007734 TCTCCAGCACGTTCGTGTC 60.008 57.895 22.85 16.06 38.31 3.67
1269 1504 2.022129 CTCCAGCACGTTCGTGTCC 61.022 63.158 22.85 10.18 38.31 4.02
1270 1505 3.403057 CCAGCACGTTCGTGTCCG 61.403 66.667 22.85 13.15 38.31 4.79
1274 1509 2.917901 CACGTTCGTGTCCGTGTG 59.082 61.111 15.81 0.00 46.87 3.82
1275 1510 1.586826 CACGTTCGTGTCCGTGTGA 60.587 57.895 15.81 0.00 46.87 3.58
1276 1511 1.139308 ACGTTCGTGTCCGTGTGAA 59.861 52.632 0.00 0.00 35.69 3.18
1278 1513 0.433492 CGTTCGTGTCCGTGTGAATC 59.567 55.000 0.00 0.00 35.01 2.52
1279 1514 1.493772 GTTCGTGTCCGTGTGAATCA 58.506 50.000 0.00 0.00 35.01 2.57
1280 1515 1.455786 GTTCGTGTCCGTGTGAATCAG 59.544 52.381 0.00 0.00 35.01 2.90
1281 1516 0.955905 TCGTGTCCGTGTGAATCAGA 59.044 50.000 0.00 0.00 35.01 3.27
1282 1517 1.544246 TCGTGTCCGTGTGAATCAGAT 59.456 47.619 0.00 0.00 35.01 2.90
1287 1522 1.757118 TCCGTGTGAATCAGATCCCTC 59.243 52.381 0.00 0.00 0.00 4.30
1304 1539 2.229784 CCCTCTGACTGAATTGGTTTGC 59.770 50.000 0.00 0.00 0.00 3.68
1315 1550 1.927487 TTGGTTTGCATGATGGCTCT 58.073 45.000 0.00 0.00 34.04 4.09
1316 1551 1.927487 TGGTTTGCATGATGGCTCTT 58.073 45.000 0.00 0.00 34.04 2.85
1317 1552 1.820519 TGGTTTGCATGATGGCTCTTC 59.179 47.619 0.00 0.00 34.04 2.87
1536 1774 2.063378 CAGCCCCTCTCTCTCCACC 61.063 68.421 0.00 0.00 0.00 4.61
1541 1779 2.055042 CCTCTCTCTCCACCCCACG 61.055 68.421 0.00 0.00 0.00 4.94
1571 1809 1.247567 AGCAATTCTTCCCCAACGTG 58.752 50.000 0.00 0.00 0.00 4.49
1573 1811 0.243636 CAATTCTTCCCCAACGTGCC 59.756 55.000 0.00 0.00 0.00 5.01
1595 1833 2.159517 GGCCATGAATGAAACACTCGTC 60.160 50.000 0.00 0.00 0.00 4.20
1596 1834 2.474526 GCCATGAATGAAACACTCGTCG 60.475 50.000 0.00 0.00 0.00 5.12
1597 1835 2.736721 CCATGAATGAAACACTCGTCGT 59.263 45.455 0.00 0.00 0.00 4.34
1953 2191 0.595567 CCAACGAGTTCGACAACGGA 60.596 55.000 8.72 0.00 43.02 4.69
2022 2260 1.600916 GCTCTTCAACAACGGGGCT 60.601 57.895 0.00 0.00 0.00 5.19
2103 2341 0.533755 CCTCCATGATCAACCTCGGC 60.534 60.000 0.00 0.00 0.00 5.54
2145 2383 3.160047 AGCGGGGAGATCAGGCTG 61.160 66.667 8.58 8.58 31.74 4.85
2164 2402 3.696051 GCTGGATTGCAGGAAAGTCAATA 59.304 43.478 7.33 0.00 31.30 1.90
2220 2462 9.998106 GTATACATATTGGAAGGAGTAACATGT 57.002 33.333 0.00 0.00 0.00 3.21
2309 2554 8.804743 GCAATTAGTGAGTTGATTGATTCATTG 58.195 33.333 0.00 0.00 33.34 2.82
2314 2559 8.344446 AGTGAGTTGATTGATTCATTGATTGA 57.656 30.769 0.00 0.00 33.34 2.57
2315 2560 8.967918 AGTGAGTTGATTGATTCATTGATTGAT 58.032 29.630 0.00 0.00 33.34 2.57
2355 2600 8.260114 TGATGATGATGAAGTTGTAGAGCTTTA 58.740 33.333 0.00 0.00 0.00 1.85
2390 2641 8.524487 GGAAGATATCTGACGTAACCATTATCT 58.476 37.037 5.86 0.00 0.00 1.98
2399 2650 9.737427 CTGACGTAACCATTATCTATATGATCC 57.263 37.037 0.00 0.00 36.65 3.36
2446 2723 2.333926 CACATTGCAGATTTGGTGCTG 58.666 47.619 0.00 0.00 41.78 4.41
2451 2728 2.153645 TGCAGATTTGGTGCTGTAGTG 58.846 47.619 0.00 0.00 41.78 2.74
2452 2729 1.135575 GCAGATTTGGTGCTGTAGTGC 60.136 52.381 0.00 0.00 37.96 4.40
2453 2730 2.430465 CAGATTTGGTGCTGTAGTGCT 58.570 47.619 0.00 0.00 0.00 4.40
2454 2731 3.599343 CAGATTTGGTGCTGTAGTGCTA 58.401 45.455 0.00 0.00 0.00 3.49
2455 2732 3.372206 CAGATTTGGTGCTGTAGTGCTAC 59.628 47.826 2.60 2.60 36.63 3.58
2456 2733 3.261897 AGATTTGGTGCTGTAGTGCTACT 59.738 43.478 10.28 0.00 37.00 2.57
2457 2734 3.485463 TTTGGTGCTGTAGTGCTACTT 57.515 42.857 10.28 0.00 37.00 2.24
2458 2735 3.485463 TTGGTGCTGTAGTGCTACTTT 57.515 42.857 10.28 0.00 37.00 2.66
2459 2736 4.610605 TTGGTGCTGTAGTGCTACTTTA 57.389 40.909 10.28 0.00 37.00 1.85
2483 2760 1.060698 GCGATCAGTAGCGTGGAAAAC 59.939 52.381 0.00 0.00 36.72 2.43
2489 2766 4.385825 TCAGTAGCGTGGAAAACTTGAAT 58.614 39.130 0.00 0.00 0.00 2.57
2506 2783 7.129457 ACTTGAATCTAACAGCAGATCCATA 57.871 36.000 0.00 0.00 34.08 2.74
2511 2788 3.906218 TCTAACAGCAGATCCATAGCCAT 59.094 43.478 0.00 0.00 0.00 4.40
2513 2790 3.589951 ACAGCAGATCCATAGCCATTT 57.410 42.857 0.00 0.00 0.00 2.32
2517 2794 4.340097 CAGCAGATCCATAGCCATTTCAAA 59.660 41.667 0.00 0.00 0.00 2.69
2518 2795 5.010719 CAGCAGATCCATAGCCATTTCAAAT 59.989 40.000 0.00 0.00 0.00 2.32
2519 2796 5.010719 AGCAGATCCATAGCCATTTCAAATG 59.989 40.000 2.80 2.80 0.00 2.32
2520 2797 5.221382 GCAGATCCATAGCCATTTCAAATGT 60.221 40.000 9.31 0.00 0.00 2.71
2521 2798 6.444633 CAGATCCATAGCCATTTCAAATGTC 58.555 40.000 9.31 0.00 0.00 3.06
2522 2799 5.537674 AGATCCATAGCCATTTCAAATGTCC 59.462 40.000 9.31 0.19 0.00 4.02
2523 2800 4.608269 TCCATAGCCATTTCAAATGTCCA 58.392 39.130 9.31 0.00 0.00 4.02
2524 2801 5.022122 TCCATAGCCATTTCAAATGTCCAA 58.978 37.500 9.31 0.00 0.00 3.53
2525 2802 5.662208 TCCATAGCCATTTCAAATGTCCAAT 59.338 36.000 9.31 0.00 0.00 3.16
2526 2803 5.987347 CCATAGCCATTTCAAATGTCCAATC 59.013 40.000 9.31 0.00 0.00 2.67
2527 2804 6.407187 CCATAGCCATTTCAAATGTCCAATCA 60.407 38.462 9.31 0.00 0.00 2.57
2528 2805 5.080969 AGCCATTTCAAATGTCCAATCAG 57.919 39.130 9.31 0.00 0.00 2.90
2529 2806 4.529377 AGCCATTTCAAATGTCCAATCAGT 59.471 37.500 9.31 0.00 0.00 3.41
2530 2807 4.628333 GCCATTTCAAATGTCCAATCAGTG 59.372 41.667 9.31 0.00 0.00 3.66
2531 2808 5.786311 CCATTTCAAATGTCCAATCAGTGT 58.214 37.500 9.31 0.00 0.00 3.55
2532 2809 5.636121 CCATTTCAAATGTCCAATCAGTGTG 59.364 40.000 9.31 0.00 0.00 3.82
2533 2810 4.852134 TTCAAATGTCCAATCAGTGTGG 57.148 40.909 0.00 0.00 37.51 4.17
2551 2828 4.331717 GTGTGGGTGACATTATTTACTCGG 59.668 45.833 0.00 0.00 36.78 4.63
2557 2834 4.565564 GTGACATTATTTACTCGGACGCTT 59.434 41.667 0.00 0.00 0.00 4.68
2561 2838 5.063060 ACATTATTTACTCGGACGCTTGTTC 59.937 40.000 0.00 0.00 0.00 3.18
2562 2839 1.411394 TTTACTCGGACGCTTGTTCG 58.589 50.000 0.00 0.00 46.28 3.95
2590 2868 3.842925 TTGGGCCAGCTCAACCGAC 62.843 63.158 6.23 0.00 30.47 4.79
2591 2869 4.021925 GGGCCAGCTCAACCGACT 62.022 66.667 4.39 0.00 0.00 4.18
2593 2871 1.448013 GGCCAGCTCAACCGACTAC 60.448 63.158 0.00 0.00 0.00 2.73
2595 2873 1.880894 CCAGCTCAACCGACTACGA 59.119 57.895 0.00 0.00 42.66 3.43
2605 2883 6.397831 TCAACCGACTACGAAATAATTGTG 57.602 37.500 0.00 0.00 42.66 3.33
2608 2886 3.305094 CCGACTACGAAATAATTGTGCGT 59.695 43.478 8.10 8.10 42.66 5.24
2609 2887 4.201647 CCGACTACGAAATAATTGTGCGTT 60.202 41.667 8.26 0.00 42.66 4.84
2610 2888 4.947933 CGACTACGAAATAATTGTGCGTTC 59.052 41.667 8.26 2.20 42.66 3.95
2611 2889 5.443562 CGACTACGAAATAATTGTGCGTTCA 60.444 40.000 8.26 0.00 42.66 3.18
2612 2890 6.417191 ACTACGAAATAATTGTGCGTTCAT 57.583 33.333 8.26 0.00 36.51 2.57
2613 2891 7.513969 CGACTACGAAATAATTGTGCGTTCATA 60.514 37.037 8.26 0.00 42.66 2.15
2614 2892 7.396419 ACTACGAAATAATTGTGCGTTCATAC 58.604 34.615 8.26 0.00 36.51 2.39
2615 2893 6.417191 ACGAAATAATTGTGCGTTCATACT 57.583 33.333 0.00 0.00 0.00 2.12
2638 2916 4.409570 TCATAGTACTCGACAAAAGCGTC 58.590 43.478 0.00 0.00 0.00 5.19
2668 2946 9.135189 ACATATAAATAGCTGGAAAATTGCTGA 57.865 29.630 0.00 0.00 37.62 4.26
2675 2953 1.442520 GAAAATTGCTGAGCGCGCA 60.443 52.632 35.10 14.59 43.27 6.09
2709 2992 2.818274 GTTGGTGGCGATCCCGTC 60.818 66.667 0.00 0.00 41.51 4.79
2721 3004 2.480419 CGATCCCGTCAAGGAATATTGC 59.520 50.000 0.00 0.00 45.00 3.56
2722 3005 1.948104 TCCCGTCAAGGAATATTGCG 58.052 50.000 0.88 0.00 45.00 4.85
2723 3006 0.307760 CCCGTCAAGGAATATTGCGC 59.692 55.000 0.00 0.00 45.00 6.09
2725 3008 1.003545 CCGTCAAGGAATATTGCGCTG 60.004 52.381 9.73 3.86 45.00 5.18
2727 3010 2.537529 CGTCAAGGAATATTGCGCTGTG 60.538 50.000 9.73 0.00 0.00 3.66
2731 3014 2.017049 AGGAATATTGCGCTGTGTTCC 58.983 47.619 23.41 23.41 36.29 3.62
2733 3016 3.118408 AGGAATATTGCGCTGTGTTCCTA 60.118 43.478 28.38 0.00 42.54 2.94
2735 3018 1.651987 TATTGCGCTGTGTTCCTAGC 58.348 50.000 9.73 0.00 36.60 3.42
2740 3023 3.436001 GCTGTGTTCCTAGCGCTAA 57.564 52.632 19.37 2.22 0.00 3.09
2742 3025 2.073816 GCTGTGTTCCTAGCGCTAAAA 58.926 47.619 19.37 12.76 0.00 1.52
2743 3026 2.482721 GCTGTGTTCCTAGCGCTAAAAA 59.517 45.455 19.37 12.39 0.00 1.94
2763 3116 0.401738 ATGGTTGATGGGCGGATAGG 59.598 55.000 0.00 0.00 0.00 2.57
2788 3141 2.754375 GGGAGGGACGAAAAGGCA 59.246 61.111 0.00 0.00 0.00 4.75
2789 3142 1.303282 GGGAGGGACGAAAAGGCAT 59.697 57.895 0.00 0.00 0.00 4.40
2793 3160 0.673644 AGGGACGAAAAGGCATGTCG 60.674 55.000 0.00 0.00 40.56 4.35
2796 3163 1.671850 GGACGAAAAGGCATGTCGAGA 60.672 52.381 9.57 0.00 38.16 4.04
2818 3185 1.532090 CCTCGATCGAGAAGTGGTTCG 60.532 57.143 39.64 19.63 44.53 3.95
2862 3229 4.391869 GGGACTTTTCACCCGACC 57.608 61.111 0.00 0.00 36.56 4.79
2936 3303 7.413877 GCTGATCCATCGATCCAAAAATATCTC 60.414 40.741 0.00 0.00 43.82 2.75
2937 3304 6.881065 TGATCCATCGATCCAAAAATATCTCC 59.119 38.462 0.00 0.00 43.82 3.71
2938 3305 6.439636 TCCATCGATCCAAAAATATCTCCT 57.560 37.500 0.00 0.00 0.00 3.69
2939 3306 6.467677 TCCATCGATCCAAAAATATCTCCTC 58.532 40.000 0.00 0.00 0.00 3.71
3064 3433 2.665165 TCTTGTGGACACCATTTTGCT 58.335 42.857 0.00 0.00 35.28 3.91
3065 3434 2.622942 TCTTGTGGACACCATTTTGCTC 59.377 45.455 0.00 0.00 35.28 4.26
3068 3437 2.964464 TGTGGACACCATTTTGCTCATT 59.036 40.909 0.00 0.00 35.28 2.57
3107 3477 5.296748 CCACTTGTTAAAGTTTGGAATGGG 58.703 41.667 0.00 0.00 44.47 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.381056 CGGCCAATCCCCAAATCCA 60.381 57.895 2.24 0.00 0.00 3.41
1 2 2.796193 GCGGCCAATCCCCAAATCC 61.796 63.158 2.24 0.00 0.00 3.01
2 3 1.402107 ATGCGGCCAATCCCCAAATC 61.402 55.000 2.24 0.00 0.00 2.17
3 4 0.982326 AATGCGGCCAATCCCCAAAT 60.982 50.000 2.24 0.00 0.00 2.32
5 6 2.038651 AATGCGGCCAATCCCCAA 59.961 55.556 2.24 0.00 0.00 4.12
6 7 2.441901 GAATGCGGCCAATCCCCA 60.442 61.111 2.24 0.00 0.00 4.96
7 8 3.226537 GGAATGCGGCCAATCCCC 61.227 66.667 2.24 0.00 35.39 4.81
8 9 1.833934 ATGGAATGCGGCCAATCCC 60.834 57.895 2.24 0.00 39.81 3.85
9 10 1.364901 CATGGAATGCGGCCAATCC 59.635 57.895 2.24 4.76 40.75 3.01
10 11 1.364901 CCATGGAATGCGGCCAATC 59.635 57.895 5.56 0.00 44.97 2.67
11 12 2.799452 GCCATGGAATGCGGCCAAT 61.799 57.895 18.40 0.00 44.97 3.16
12 13 3.459965 GCCATGGAATGCGGCCAA 61.460 61.111 18.40 0.00 44.97 4.52
13 14 4.755507 TGCCATGGAATGCGGCCA 62.756 61.111 18.40 0.00 44.97 5.36
14 15 3.908081 CTGCCATGGAATGCGGCC 61.908 66.667 18.40 0.00 44.97 6.13
15 16 3.908081 CCTGCCATGGAATGCGGC 61.908 66.667 18.40 0.00 44.97 6.53
16 17 3.908081 GCCTGCCATGGAATGCGG 61.908 66.667 18.40 3.58 44.97 5.69
17 18 3.908081 GGCCTGCCATGGAATGCG 61.908 66.667 18.40 0.00 44.97 4.73
18 19 1.901654 TTTGGCCTGCCATGGAATGC 61.902 55.000 18.40 14.55 46.64 3.56
19 20 0.177141 CTTTGGCCTGCCATGGAATG 59.823 55.000 18.40 2.44 46.64 2.67
20 21 0.979187 CCTTTGGCCTGCCATGGAAT 60.979 55.000 18.40 0.00 46.64 3.01
31 32 1.300481 GATCGAGCTTACCTTTGGCC 58.700 55.000 0.00 0.00 0.00 5.36
49 50 4.263550 TGGGTCGACAGGGAAATAAAATGA 60.264 41.667 18.91 0.00 0.00 2.57
51 52 4.270008 CTGGGTCGACAGGGAAATAAAAT 58.730 43.478 18.91 0.00 34.84 1.82
60 61 1.746615 CAATGCTGGGTCGACAGGG 60.747 63.158 18.91 7.18 38.90 4.45
62 63 0.742281 CCTCAATGCTGGGTCGACAG 60.742 60.000 18.91 8.34 41.41 3.51
68 69 1.687612 CCAGACCTCAATGCTGGGT 59.312 57.895 0.00 0.00 44.24 4.51
82 83 0.613260 AACACAGCCGATAAGCCAGA 59.387 50.000 0.00 0.00 0.00 3.86
83 84 1.009829 GAACACAGCCGATAAGCCAG 58.990 55.000 0.00 0.00 0.00 4.85
96 97 0.403655 TTGGCCTGCCATAGAACACA 59.596 50.000 12.40 0.00 46.64 3.72
98 99 1.616725 CCTTTGGCCTGCCATAGAACA 60.617 52.381 24.55 2.30 46.64 3.18
99 100 1.106285 CCTTTGGCCTGCCATAGAAC 58.894 55.000 24.55 0.00 46.64 3.01
100 101 0.704076 ACCTTTGGCCTGCCATAGAA 59.296 50.000 24.55 10.99 46.64 2.10
101 102 0.255890 GACCTTTGGCCTGCCATAGA 59.744 55.000 24.55 9.08 46.64 1.98
102 103 0.034186 TGACCTTTGGCCTGCCATAG 60.034 55.000 18.34 18.34 46.64 2.23
103 104 0.034186 CTGACCTTTGGCCTGCCATA 60.034 55.000 12.40 6.41 46.64 2.74
104 105 1.304713 CTGACCTTTGGCCTGCCAT 60.305 57.895 12.40 0.00 46.64 4.40
140 141 1.610363 TTTTTATCAGGCACGGCACA 58.390 45.000 0.00 0.00 0.00 4.57
159 172 5.722021 AAAATAAAAAGGCCGTGTCTGAT 57.278 34.783 0.00 0.00 0.00 2.90
205 218 5.810074 TGTCTGATTTACCACGTGATACATG 59.190 40.000 19.30 0.71 0.00 3.21
350 462 3.876198 GCGCTGCCCGTGGTAATG 61.876 66.667 0.00 0.00 39.71 1.90
409 523 1.075301 ATTTGGGCCAGGGCATACC 60.075 57.895 16.36 6.45 44.11 2.73
410 524 1.402107 CCATTTGGGCCAGGGCATAC 61.402 60.000 16.36 3.99 44.11 2.39
455 576 0.965363 ATTGTGATCCACCCAACGCC 60.965 55.000 0.00 0.00 32.73 5.68
456 577 0.451783 GATTGTGATCCACCCAACGC 59.548 55.000 0.00 0.00 32.73 4.84
479 613 3.192922 GCACCGCACCGACCATAC 61.193 66.667 0.00 0.00 0.00 2.39
480 614 4.805231 CGCACCGCACCGACCATA 62.805 66.667 0.00 0.00 0.00 2.74
510 644 1.078759 GTGTGCCGAGGATGAACGAG 61.079 60.000 0.00 0.00 0.00 4.18
511 645 1.080093 GTGTGCCGAGGATGAACGA 60.080 57.895 0.00 0.00 0.00 3.85
512 646 2.444624 CGTGTGCCGAGGATGAACG 61.445 63.158 0.00 0.00 39.56 3.95
513 647 2.740714 GCGTGTGCCGAGGATGAAC 61.741 63.158 0.00 0.00 39.56 3.18
514 648 2.434185 GCGTGTGCCGAGGATGAA 60.434 61.111 0.00 0.00 39.56 2.57
515 649 4.794439 CGCGTGTGCCGAGGATGA 62.794 66.667 0.00 0.00 39.56 2.92
539 689 1.798223 GTTTCCTTGAAAAATGCCGGC 59.202 47.619 22.73 22.73 33.14 6.13
552 702 5.278957 CGAGGTCCAAATCAAATGTTTCCTT 60.279 40.000 0.00 0.00 0.00 3.36
556 706 4.022329 GGTCGAGGTCCAAATCAAATGTTT 60.022 41.667 0.00 0.00 0.00 2.83
585 736 1.079405 TGGTTGAATCGGAGTCGGC 60.079 57.895 0.65 0.00 36.95 5.54
587 738 1.914634 CTCTGGTTGAATCGGAGTCG 58.085 55.000 6.12 0.00 34.01 4.18
590 741 1.066573 ACAGCTCTGGTTGAATCGGAG 60.067 52.381 9.92 9.92 39.84 4.63
661 842 4.119556 TCTCCCATCCATAGTCCACTAG 57.880 50.000 0.00 0.00 0.00 2.57
662 843 4.552883 TTCTCCCATCCATAGTCCACTA 57.447 45.455 0.00 0.00 0.00 2.74
663 844 3.421394 TTCTCCCATCCATAGTCCACT 57.579 47.619 0.00 0.00 0.00 4.00
902 1126 1.831389 CGGTGACAGAAACTGCCGTG 61.831 60.000 0.00 0.00 34.37 4.94
914 1138 1.901948 AGACTCGGAAGCGGTGACA 60.902 57.895 0.00 0.00 0.00 3.58
915 1139 1.444553 CAGACTCGGAAGCGGTGAC 60.445 63.158 0.00 0.00 0.00 3.67
916 1140 2.962569 CAGACTCGGAAGCGGTGA 59.037 61.111 0.00 0.00 0.00 4.02
917 1141 2.811317 GCAGACTCGGAAGCGGTG 60.811 66.667 0.00 0.00 0.00 4.94
918 1142 4.421479 CGCAGACTCGGAAGCGGT 62.421 66.667 0.00 0.00 45.83 5.68
921 1145 1.587613 CTAGCGCAGACTCGGAAGC 60.588 63.158 11.47 0.00 0.00 3.86
922 1146 0.524392 CACTAGCGCAGACTCGGAAG 60.524 60.000 11.47 0.00 0.00 3.46
923 1147 1.506718 CACTAGCGCAGACTCGGAA 59.493 57.895 11.47 0.00 0.00 4.30
924 1148 3.052620 GCACTAGCGCAGACTCGGA 62.053 63.158 11.47 0.00 0.00 4.55
925 1149 2.580867 GCACTAGCGCAGACTCGG 60.581 66.667 11.47 0.00 0.00 4.63
975 1204 1.669115 CTTGGCGACCACAGTCCAG 60.669 63.158 0.00 0.00 40.12 3.86
1033 1262 3.148279 GATGGGTCTCGGCCTCGT 61.148 66.667 0.00 0.00 37.69 4.18
1180 1415 3.041940 GGTGCGGGTGTCGTTCAG 61.042 66.667 0.00 0.00 41.72 3.02
1260 1495 1.455786 CTGATTCACACGGACACGAAC 59.544 52.381 0.00 0.00 44.60 3.95
1261 1496 1.338655 TCTGATTCACACGGACACGAA 59.661 47.619 0.00 0.00 44.60 3.85
1262 1497 0.955905 TCTGATTCACACGGACACGA 59.044 50.000 0.00 0.00 44.60 4.35
1264 1499 2.271800 GGATCTGATTCACACGGACAC 58.728 52.381 0.00 0.00 0.00 3.67
1268 1503 1.759445 AGAGGGATCTGATTCACACGG 59.241 52.381 0.00 0.00 0.00 4.94
1269 1504 2.428530 TCAGAGGGATCTGATTCACACG 59.571 50.000 3.88 0.00 41.34 4.49
1270 1505 3.450457 AGTCAGAGGGATCTGATTCACAC 59.550 47.826 10.87 0.00 46.81 3.82
1272 1507 3.703556 TCAGTCAGAGGGATCTGATTCAC 59.296 47.826 10.87 0.00 46.81 3.18
1274 1509 5.549742 ATTCAGTCAGAGGGATCTGATTC 57.450 43.478 10.87 0.32 46.81 2.52
1275 1510 5.397672 CCAATTCAGTCAGAGGGATCTGATT 60.398 44.000 10.87 4.51 46.81 2.57
1276 1511 4.102838 CCAATTCAGTCAGAGGGATCTGAT 59.897 45.833 10.87 0.00 46.81 2.90
1278 1513 3.199508 ACCAATTCAGTCAGAGGGATCTG 59.800 47.826 0.00 0.00 39.00 2.90
1279 1514 3.458831 ACCAATTCAGTCAGAGGGATCT 58.541 45.455 0.00 0.00 0.00 2.75
1280 1515 3.922171 ACCAATTCAGTCAGAGGGATC 57.078 47.619 0.00 0.00 0.00 3.36
1281 1516 4.338879 CAAACCAATTCAGTCAGAGGGAT 58.661 43.478 0.00 0.00 0.00 3.85
1282 1517 3.754965 CAAACCAATTCAGTCAGAGGGA 58.245 45.455 0.00 0.00 0.00 4.20
1287 1522 4.508461 TCATGCAAACCAATTCAGTCAG 57.492 40.909 0.00 0.00 0.00 3.51
1291 1526 2.933906 GCCATCATGCAAACCAATTCAG 59.066 45.455 0.00 0.00 0.00 3.02
1299 1534 1.820519 TGGAAGAGCCATCATGCAAAC 59.179 47.619 0.00 0.00 43.33 2.93
1549 1787 3.016736 ACGTTGGGGAAGAATTGCTATG 58.983 45.455 0.00 0.00 36.31 2.23
1551 1789 2.432444 CACGTTGGGGAAGAATTGCTA 58.568 47.619 0.00 0.00 36.31 3.49
1552 1790 1.247567 CACGTTGGGGAAGAATTGCT 58.752 50.000 0.00 0.00 36.31 3.91
1553 1791 0.388520 GCACGTTGGGGAAGAATTGC 60.389 55.000 0.00 0.00 34.72 3.56
1571 1809 0.458370 GTGTTTCATTCATGGCCGGC 60.458 55.000 21.18 21.18 0.00 6.13
1573 1811 1.202065 CGAGTGTTTCATTCATGGCCG 60.202 52.381 0.00 0.00 0.00 6.13
1576 1814 2.736721 ACGACGAGTGTTTCATTCATGG 59.263 45.455 0.00 0.00 0.00 3.66
1953 2191 2.963782 GGACATGAGGTTCCGGTAGTAT 59.036 50.000 0.00 0.00 0.00 2.12
1962 2200 3.195698 GCGCCGGACATGAGGTTC 61.196 66.667 5.05 0.00 0.00 3.62
2022 2260 3.625897 CGCACCAGGGAGTCCACA 61.626 66.667 12.30 0.00 34.83 4.17
2103 2341 3.414700 GTGAGCGGGCTGACGTTG 61.415 66.667 0.00 0.00 35.98 4.10
2125 2363 4.247380 CCTGATCTCCCCGCTGGC 62.247 72.222 0.00 0.00 0.00 4.85
2145 2383 5.904362 AAGTATTGACTTTCCTGCAATCC 57.096 39.130 0.00 0.00 43.70 3.01
2197 2439 9.747898 AAAACATGTTACTCCTTCCAATATGTA 57.252 29.630 12.39 0.00 34.26 2.29
2198 2440 8.650143 AAAACATGTTACTCCTTCCAATATGT 57.350 30.769 12.39 0.00 36.09 2.29
2200 2442 9.975218 AGTAAAACATGTTACTCCTTCCAATAT 57.025 29.630 12.39 0.00 39.60 1.28
2204 2446 9.802039 AATTAGTAAAACATGTTACTCCTTCCA 57.198 29.630 15.61 0.00 42.14 3.53
2206 2448 9.968743 CGAATTAGTAAAACATGTTACTCCTTC 57.031 33.333 15.61 16.32 42.14 3.46
2207 2449 9.498176 ACGAATTAGTAAAACATGTTACTCCTT 57.502 29.630 15.61 11.07 42.14 3.36
2208 2450 9.498176 AACGAATTAGTAAAACATGTTACTCCT 57.502 29.630 15.61 10.19 42.14 3.69
2220 2462 9.749490 GTCGATTTCATCAACGAATTAGTAAAA 57.251 29.630 0.00 0.00 36.57 1.52
2221 2463 8.105742 CGTCGATTTCATCAACGAATTAGTAAA 58.894 33.333 0.00 0.00 36.57 2.01
2324 2569 9.106070 CTCTACAACTTCATCATCATCATGAAA 57.894 33.333 0.00 0.00 42.53 2.69
2325 2570 7.226128 GCTCTACAACTTCATCATCATCATGAA 59.774 37.037 0.00 0.00 42.53 2.57
2326 2571 6.704937 GCTCTACAACTTCATCATCATCATGA 59.295 38.462 0.00 0.00 43.45 3.07
2327 2572 6.706716 AGCTCTACAACTTCATCATCATCATG 59.293 38.462 0.00 0.00 0.00 3.07
2328 2573 6.828788 AGCTCTACAACTTCATCATCATCAT 58.171 36.000 0.00 0.00 0.00 2.45
2329 2574 6.231258 AGCTCTACAACTTCATCATCATCA 57.769 37.500 0.00 0.00 0.00 3.07
2330 2575 7.551035 AAAGCTCTACAACTTCATCATCATC 57.449 36.000 0.00 0.00 0.00 2.92
2331 2576 8.263640 AGTAAAGCTCTACAACTTCATCATCAT 58.736 33.333 0.00 0.00 0.00 2.45
2332 2577 7.615403 AGTAAAGCTCTACAACTTCATCATCA 58.385 34.615 0.00 0.00 0.00 3.07
2333 2578 9.757227 ATAGTAAAGCTCTACAACTTCATCATC 57.243 33.333 0.00 0.00 0.00 2.92
2335 2580 9.944376 AAATAGTAAAGCTCTACAACTTCATCA 57.056 29.630 0.00 0.00 0.00 3.07
2363 2608 6.732896 AATGGTTACGTCAGATATCTTCCT 57.267 37.500 1.33 0.00 0.00 3.36
2364 2609 8.524487 AGATAATGGTTACGTCAGATATCTTCC 58.476 37.037 1.33 0.00 30.12 3.46
2432 2683 1.135575 GCACTACAGCACCAAATCTGC 60.136 52.381 0.00 0.00 33.80 4.26
2453 2730 4.813161 ACGCTACTGATCGCTACTAAAGTA 59.187 41.667 0.00 0.00 0.00 2.24
2454 2731 3.626670 ACGCTACTGATCGCTACTAAAGT 59.373 43.478 0.00 0.00 0.00 2.66
2455 2732 3.969352 CACGCTACTGATCGCTACTAAAG 59.031 47.826 0.00 0.00 0.00 1.85
2456 2733 3.242969 CCACGCTACTGATCGCTACTAAA 60.243 47.826 0.00 0.00 0.00 1.85
2457 2734 2.289820 CCACGCTACTGATCGCTACTAA 59.710 50.000 0.00 0.00 0.00 2.24
2458 2735 1.871676 CCACGCTACTGATCGCTACTA 59.128 52.381 0.00 0.00 0.00 1.82
2459 2736 0.663688 CCACGCTACTGATCGCTACT 59.336 55.000 0.00 0.00 0.00 2.57
2472 2749 4.819630 TGTTAGATTCAAGTTTTCCACGCT 59.180 37.500 0.00 0.00 0.00 5.07
2483 2760 6.147492 GCTATGGATCTGCTGTTAGATTCAAG 59.853 42.308 8.44 8.43 43.89 3.02
2489 2766 3.308401 TGGCTATGGATCTGCTGTTAGA 58.692 45.455 0.00 0.00 0.00 2.10
2506 2783 4.529377 ACTGATTGGACATTTGAAATGGCT 59.471 37.500 21.87 3.71 0.00 4.75
2511 2788 4.039004 CCCACACTGATTGGACATTTGAAA 59.961 41.667 1.56 0.00 36.02 2.69
2513 2790 3.156293 CCCACACTGATTGGACATTTGA 58.844 45.455 1.56 0.00 36.02 2.69
2517 2794 1.704628 TCACCCACACTGATTGGACAT 59.295 47.619 1.56 0.00 36.02 3.06
2518 2795 1.135960 TCACCCACACTGATTGGACA 58.864 50.000 1.56 0.00 36.02 4.02
2519 2796 1.202758 TGTCACCCACACTGATTGGAC 60.203 52.381 1.56 0.00 36.02 4.02
2520 2797 1.135960 TGTCACCCACACTGATTGGA 58.864 50.000 1.56 0.00 36.02 3.53
2521 2798 2.205022 ATGTCACCCACACTGATTGG 57.795 50.000 0.00 0.00 38.04 3.16
2522 2799 5.902613 AATAATGTCACCCACACTGATTG 57.097 39.130 0.00 0.00 38.04 2.67
2523 2800 7.175104 AGTAAATAATGTCACCCACACTGATT 58.825 34.615 0.00 0.00 38.04 2.57
2524 2801 6.721318 AGTAAATAATGTCACCCACACTGAT 58.279 36.000 0.00 0.00 38.04 2.90
2525 2802 6.121776 AGTAAATAATGTCACCCACACTGA 57.878 37.500 0.00 0.00 38.04 3.41
2526 2803 5.063438 CGAGTAAATAATGTCACCCACACTG 59.937 44.000 0.00 0.00 38.04 3.66
2527 2804 5.175859 CGAGTAAATAATGTCACCCACACT 58.824 41.667 0.00 0.00 38.04 3.55
2528 2805 4.331717 CCGAGTAAATAATGTCACCCACAC 59.668 45.833 0.00 0.00 38.04 3.82
2529 2806 4.223255 TCCGAGTAAATAATGTCACCCACA 59.777 41.667 0.00 0.00 40.18 4.17
2530 2807 4.569564 GTCCGAGTAAATAATGTCACCCAC 59.430 45.833 0.00 0.00 0.00 4.61
2531 2808 4.678574 CGTCCGAGTAAATAATGTCACCCA 60.679 45.833 0.00 0.00 0.00 4.51
2532 2809 3.800506 CGTCCGAGTAAATAATGTCACCC 59.199 47.826 0.00 0.00 0.00 4.61
2533 2810 3.244579 GCGTCCGAGTAAATAATGTCACC 59.755 47.826 0.00 0.00 0.00 4.02
2551 2828 1.421485 CTGCCATCGAACAAGCGTC 59.579 57.895 0.00 0.00 0.00 5.19
2557 2834 1.303236 CCAACCCTGCCATCGAACA 60.303 57.895 0.00 0.00 0.00 3.18
2578 2856 2.060326 TTTCGTAGTCGGTTGAGCTG 57.940 50.000 0.00 0.00 37.69 4.24
2590 2868 7.618442 AGTATGAACGCACAATTATTTCGTAG 58.382 34.615 0.00 0.00 32.71 3.51
2591 2869 7.528481 AGTATGAACGCACAATTATTTCGTA 57.472 32.000 0.00 0.00 32.71 3.43
2593 2871 6.958752 TGAAGTATGAACGCACAATTATTTCG 59.041 34.615 0.00 0.00 0.00 3.46
2595 2873 9.935682 CTATGAAGTATGAACGCACAATTATTT 57.064 29.630 0.00 0.00 0.00 1.40
2605 2883 5.620417 GTCGAGTACTATGAAGTATGAACGC 59.380 44.000 0.00 0.00 40.30 4.84
2608 2886 9.569167 CTTTTGTCGAGTACTATGAAGTATGAA 57.431 33.333 0.00 0.00 40.30 2.57
2609 2887 7.701078 GCTTTTGTCGAGTACTATGAAGTATGA 59.299 37.037 0.00 0.00 40.30 2.15
2610 2888 7.305475 CGCTTTTGTCGAGTACTATGAAGTATG 60.305 40.741 0.00 0.00 40.30 2.39
2611 2889 6.691818 CGCTTTTGTCGAGTACTATGAAGTAT 59.308 38.462 0.00 0.00 40.30 2.12
2612 2890 6.025896 CGCTTTTGTCGAGTACTATGAAGTA 58.974 40.000 0.00 0.00 37.15 2.24
2613 2891 4.857588 CGCTTTTGTCGAGTACTATGAAGT 59.142 41.667 0.00 0.00 39.91 3.01
2614 2892 4.857588 ACGCTTTTGTCGAGTACTATGAAG 59.142 41.667 0.00 0.00 0.00 3.02
2615 2893 4.801891 ACGCTTTTGTCGAGTACTATGAA 58.198 39.130 0.00 0.00 0.00 2.57
2675 2953 2.093075 CCAACTGATCAGAGAGGCACAT 60.093 50.000 29.27 0.00 0.00 3.21
2680 2958 1.406614 GCCACCAACTGATCAGAGAGG 60.407 57.143 29.27 25.10 0.00 3.69
2709 2992 3.429085 GAACACAGCGCAATATTCCTTG 58.571 45.455 11.47 0.00 0.00 3.61
2722 3005 1.722011 TTTAGCGCTAGGAACACAGC 58.278 50.000 17.98 0.00 0.00 4.40
2740 3023 1.638529 TCCGCCCATCAACCATTTTT 58.361 45.000 0.00 0.00 0.00 1.94
2742 3025 2.586425 CTATCCGCCCATCAACCATTT 58.414 47.619 0.00 0.00 0.00 2.32
2743 3026 1.202927 CCTATCCGCCCATCAACCATT 60.203 52.381 0.00 0.00 0.00 3.16
2744 3027 0.401738 CCTATCCGCCCATCAACCAT 59.598 55.000 0.00 0.00 0.00 3.55
2745 3028 1.705002 CCCTATCCGCCCATCAACCA 61.705 60.000 0.00 0.00 0.00 3.67
2746 3029 1.073199 CCCTATCCGCCCATCAACC 59.927 63.158 0.00 0.00 0.00 3.77
2747 3030 1.600916 GCCCTATCCGCCCATCAAC 60.601 63.158 0.00 0.00 0.00 3.18
2769 3122 2.675371 CCTTTTCGTCCCTCCCCC 59.325 66.667 0.00 0.00 0.00 5.40
2776 3129 0.721718 CTCGACATGCCTTTTCGTCC 59.278 55.000 0.00 0.00 34.35 4.79
2793 3160 1.332375 CACTTCTCGATCGAGGGTCTC 59.668 57.143 37.28 0.00 42.20 3.36
2796 3163 0.323542 ACCACTTCTCGATCGAGGGT 60.324 55.000 37.28 32.18 42.20 4.34
2806 3173 2.076863 CCATTCCACGAACCACTTCTC 58.923 52.381 0.00 0.00 0.00 2.87
2807 3174 1.882352 GCCATTCCACGAACCACTTCT 60.882 52.381 0.00 0.00 0.00 2.85
2810 3177 1.303317 GGCCATTCCACGAACCACT 60.303 57.895 0.00 0.00 34.01 4.00
2818 3185 2.046285 CGGTTCAGGGCCATTCCAC 61.046 63.158 6.18 0.00 36.21 4.02
2859 3226 2.828549 AATCCGGCCGCATTGGTC 60.829 61.111 22.85 0.00 41.21 4.02
2862 3229 2.051804 GAGACAATCCGGCCGCATTG 62.052 60.000 34.63 34.63 36.28 2.82
2872 3239 3.633065 ACGGCTAGAACTAGAGACAATCC 59.367 47.826 12.33 2.24 35.21 3.01
2873 3240 4.602995 CACGGCTAGAACTAGAGACAATC 58.397 47.826 12.33 0.00 35.21 2.67
2913 3280 7.108847 AGGAGATATTTTTGGATCGATGGATC 58.891 38.462 0.54 9.09 46.85 3.36
2957 3324 4.508662 CAAGTCTTCACATAGGTCTTCCC 58.491 47.826 0.00 0.00 0.00 3.97
3064 3433 3.153919 GGCAAACTGGACCAACTAATGA 58.846 45.455 0.00 0.00 0.00 2.57
3065 3434 2.890311 TGGCAAACTGGACCAACTAATG 59.110 45.455 0.00 0.00 0.00 1.90
3068 3437 1.493022 AGTGGCAAACTGGACCAACTA 59.507 47.619 0.00 0.00 37.88 2.24
3107 3477 0.246086 CCTGAGTGCTGAGTGACCTC 59.754 60.000 0.00 0.00 38.27 3.85


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

AutoCloner maintained by Alex Coulton.