Multiple sequence alignment - TraesCS2A01G186100

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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 TraesCS2A01G186100 chr2A 100.000 3608 0 0 1 3608 147543948 147540341 0.000000e+00 6663.0
1 TraesCS2A01G186100 chr2A 85.424 1969 258 15 1108 3052 148155482 148157445 0.000000e+00 2019.0
2 TraesCS2A01G186100 chr2A 77.977 1621 315 30 987 2589 43282259 43280663 0.000000e+00 977.0
3 TraesCS2A01G186100 chr2A 75.776 1610 330 44 1013 2589 43304838 43303256 0.000000e+00 758.0
4 TraesCS2A01G186100 chr2A 72.660 940 227 26 1973 2896 75635019 75634094 5.900000e-73 285.0
5 TraesCS2A01G186100 chr2B 94.437 2283 117 9 949 3225 211187254 211189532 0.000000e+00 3504.0
6 TraesCS2A01G186100 chr2B 86.030 1990 255 12 1078 3052 210932678 210930697 0.000000e+00 2113.0
7 TraesCS2A01G186100 chr2B 76.848 1529 305 30 1090 2589 67081708 67080200 0.000000e+00 817.0
8 TraesCS2A01G186100 chr2B 90.984 488 25 8 407 893 211186761 211187230 1.090000e-179 640.0
9 TraesCS2A01G186100 chr2B 79.898 786 150 6 1092 1873 67353874 67353093 1.450000e-158 569.0
10 TraesCS2A01G186100 chr2B 89.196 398 26 7 3215 3607 211189881 211190266 7.010000e-132 481.0
11 TraesCS2A01G186100 chr2B 93.214 280 11 6 140 415 211186392 211186667 4.340000e-109 405.0
12 TraesCS2A01G186100 chr2B 94.400 125 7 0 1 125 211186212 211186336 3.680000e-45 193.0
13 TraesCS2A01G186100 chr2B 87.342 79 10 0 3351 3429 749686209 749686287 1.380000e-14 91.6
14 TraesCS2A01G186100 chr2B 89.655 58 6 0 996 1053 210932726 210932669 1.390000e-09 75.0
15 TraesCS2A01G186100 chr2D 85.592 1985 260 16 1089 3052 153003039 153001060 0.000000e+00 2058.0
16 TraesCS2A01G186100 chr2D 91.394 918 45 10 140 1046 153328831 153329725 0.000000e+00 1227.0
17 TraesCS2A01G186100 chr2D 78.297 1562 294 32 994 2534 38238995 38237458 0.000000e+00 965.0
18 TraesCS2A01G186100 chr2D 76.449 1605 329 35 1013 2589 38442067 38440484 0.000000e+00 824.0
19 TraesCS2A01G186100 chr2D 73.402 782 188 18 1973 2743 75754964 75755736 1.280000e-69 274.0
20 TraesCS2A01G186100 chr2D 93.600 125 8 0 1 125 153328651 153328775 1.710000e-43 187.0
21 TraesCS2A01G186100 chr7B 96.875 32 1 0 3007 3038 151152290 151152321 2.000000e-03 54.7
22 TraesCS2A01G186100 chr7D 100.000 28 0 0 600 627 8988449 8988476 7.000000e-03 52.8


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 TraesCS2A01G186100 chr2A 147540341 147543948 3607 True 6663.0 6663 100.0000 1 3608 1 chr2A.!!$R4 3607
1 TraesCS2A01G186100 chr2A 148155482 148157445 1963 False 2019.0 2019 85.4240 1108 3052 1 chr2A.!!$F1 1944
2 TraesCS2A01G186100 chr2A 43280663 43282259 1596 True 977.0 977 77.9770 987 2589 1 chr2A.!!$R1 1602
3 TraesCS2A01G186100 chr2A 43303256 43304838 1582 True 758.0 758 75.7760 1013 2589 1 chr2A.!!$R2 1576
4 TraesCS2A01G186100 chr2A 75634094 75635019 925 True 285.0 285 72.6600 1973 2896 1 chr2A.!!$R3 923
5 TraesCS2A01G186100 chr2B 210930697 210932726 2029 True 1094.0 2113 87.8425 996 3052 2 chr2B.!!$R3 2056
6 TraesCS2A01G186100 chr2B 211186212 211190266 4054 False 1044.6 3504 92.4462 1 3607 5 chr2B.!!$F2 3606
7 TraesCS2A01G186100 chr2B 67080200 67081708 1508 True 817.0 817 76.8480 1090 2589 1 chr2B.!!$R1 1499
8 TraesCS2A01G186100 chr2B 67353093 67353874 781 True 569.0 569 79.8980 1092 1873 1 chr2B.!!$R2 781
9 TraesCS2A01G186100 chr2D 153001060 153003039 1979 True 2058.0 2058 85.5920 1089 3052 1 chr2D.!!$R3 1963
10 TraesCS2A01G186100 chr2D 38237458 38238995 1537 True 965.0 965 78.2970 994 2534 1 chr2D.!!$R1 1540
11 TraesCS2A01G186100 chr2D 38440484 38442067 1583 True 824.0 824 76.4490 1013 2589 1 chr2D.!!$R2 1576
12 TraesCS2A01G186100 chr2D 153328651 153329725 1074 False 707.0 1227 92.4970 1 1046 2 chr2D.!!$F2 1045
13 TraesCS2A01G186100 chr2D 75754964 75755736 772 False 274.0 274 73.4020 1973 2743 1 chr2D.!!$F1 770

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
670 819 0.527565 GAAATGTGTTGCGAGGCCAT 59.472 50.0 5.01 0.0 0.00 4.40 F
1971 2185 0.376152 GCATCGGAGTGTGCATCTTG 59.624 55.0 0.00 0.0 39.26 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2602 2829 0.544833 TAGACGGGGTTGCCTTACCA 60.545 55.0 0.00 0.00 40.09 3.25 R
2991 3218 0.520827 CACCTACGCTCGTCGAGAAC 60.521 60.0 26.11 8.07 41.67 3.01 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
60 61 7.444703 AAGATATAGGAAGGAAAGAAGTGCT 57.555 36.000 0.00 0.00 0.00 4.40
79 80 3.259374 TGCTGGACTTCAAAACCAAAACA 59.741 39.130 0.00 0.00 33.14 2.83
131 132 8.180317 ACTAAACAAACACAAAAATACTGCAC 57.820 30.769 0.00 0.00 0.00 4.57
133 134 7.608308 AAACAAACACAAAAATACTGCACAT 57.392 28.000 0.00 0.00 0.00 3.21
134 135 6.826893 ACAAACACAAAAATACTGCACATC 57.173 33.333 0.00 0.00 0.00 3.06
135 136 6.572519 ACAAACACAAAAATACTGCACATCT 58.427 32.000 0.00 0.00 0.00 2.90
136 137 6.476380 ACAAACACAAAAATACTGCACATCTG 59.524 34.615 0.00 0.00 0.00 2.90
138 139 5.762045 ACACAAAAATACTGCACATCTGAC 58.238 37.500 0.00 0.00 0.00 3.51
197 241 7.312657 ACTGCACATCTGACTTACAAATATG 57.687 36.000 0.00 0.00 0.00 1.78
214 258 8.758633 ACAAATATGTATTCCGCATCTACTAC 57.241 34.615 0.00 0.00 38.24 2.73
262 306 3.852286 TGACACGGTGGTATATGTTGTC 58.148 45.455 13.48 0.00 0.00 3.18
306 352 8.812513 TCATTTCATGAATAGATGTTGGAGTT 57.187 30.769 9.40 0.00 36.11 3.01
486 635 1.065102 GACTCGCGTCTTGCCTATACA 59.935 52.381 5.77 0.00 42.08 2.29
528 677 9.747898 ACTACATAAGGTTATTTGGTGATTTGA 57.252 29.630 0.00 0.00 0.00 2.69
616 765 1.816224 GGAAATTTCTAGCCCGTGCAA 59.184 47.619 17.42 0.00 41.13 4.08
670 819 0.527565 GAAATGTGTTGCGAGGCCAT 59.472 50.000 5.01 0.00 0.00 4.40
727 876 6.120905 CCCCATTAATGCATTTCATTTCCAA 58.879 36.000 18.75 3.23 42.48 3.53
858 1007 3.545624 GCTGAGAATTCGCTGTATGCAAG 60.546 47.826 15.44 2.17 43.06 4.01
863 1012 5.178797 AGAATTCGCTGTATGCAAGTACTT 58.821 37.500 1.12 1.12 43.06 2.24
869 1018 3.448686 CTGTATGCAAGTACTTCCTCCG 58.551 50.000 4.77 0.00 0.00 4.63
872 1021 2.961526 TGCAAGTACTTCCTCCGATC 57.038 50.000 4.77 0.00 0.00 3.69
874 1023 1.536284 GCAAGTACTTCCTCCGATCCG 60.536 57.143 4.77 0.00 0.00 4.18
921 1077 7.985752 ACGGATAGTAGTAGAAATTTTGGGAAG 59.014 37.037 0.00 0.00 0.00 3.46
946 1102 6.426937 GCTATAACCAAAGAGAGTGTGTTTCA 59.573 38.462 0.00 0.00 0.00 2.69
958 1114 2.163412 GTGTGTTTCACTGTTTCCTGCA 59.837 45.455 1.72 0.00 43.13 4.41
989 1145 2.328099 GGCTCGTCCTGCAAAGTGG 61.328 63.158 0.00 0.00 0.00 4.00
999 1155 1.277557 CTGCAAAGTGGTAGGAGAGCT 59.722 52.381 0.00 0.00 0.00 4.09
1006 1162 4.744795 AGTGGTAGGAGAGCTATGTTTG 57.255 45.455 0.00 0.00 0.00 2.93
1116 1281 3.103911 GACGGTCGGCAGTTCACG 61.104 66.667 0.00 0.00 0.00 4.35
1678 1874 4.838152 CGGTGACCATGGCTCCCG 62.838 72.222 18.57 18.57 0.00 5.14
1900 2102 4.069232 CCAAGCCACGCTCGAGGA 62.069 66.667 15.58 0.00 38.25 3.71
1906 2120 2.279120 CACGCTCGAGGATCCTGC 60.279 66.667 22.02 15.90 0.00 4.85
1971 2185 0.376152 GCATCGGAGTGTGCATCTTG 59.624 55.000 0.00 0.00 39.26 3.02
1998 2218 1.468565 CGGCGTCTCAAGTATTCCGAA 60.469 52.381 0.00 0.00 37.79 4.30
2129 2350 1.203994 CGGAAGTGTGTACAGGGGTAG 59.796 57.143 0.00 0.00 0.00 3.18
2279 2500 4.323477 TTACTGCCGGCGCAAGGT 62.323 61.111 23.90 16.65 46.66 3.50
2366 2590 2.767536 CAGGTACACTGGATTGGCG 58.232 57.895 0.00 0.00 43.70 5.69
2460 2687 0.389817 TCCACCGAGATGTGAAAGCG 60.390 55.000 0.00 0.00 38.55 4.68
2580 2807 2.124151 GGCACCATGGGCTACCTG 60.124 66.667 18.09 4.95 37.76 4.00
2592 2819 1.382146 CTACCTGGCCCCCGAGTTA 60.382 63.158 0.00 0.00 0.00 2.24
2600 2827 1.623542 GCCCCCGAGTTAGGACACAT 61.624 60.000 0.00 0.00 0.00 3.21
2602 2829 0.902531 CCCCGAGTTAGGACACATGT 59.097 55.000 0.00 0.00 0.00 3.21
2605 2832 1.275291 CCGAGTTAGGACACATGTGGT 59.725 52.381 28.64 14.83 34.19 4.16
2635 2862 0.179171 CGTCTACCGATGTGTTCGCT 60.179 55.000 0.00 0.00 46.71 4.93
2667 2894 3.614092 TCCTTCTGGAAATCATCTGTGC 58.386 45.455 0.00 0.00 39.87 4.57
2681 2908 1.926511 CTGTGCACGGAGGCCAATTC 61.927 60.000 21.59 0.00 0.00 2.17
2764 2991 2.161855 GGTCTGATTGTTGATGTGGCA 58.838 47.619 0.00 0.00 0.00 4.92
2778 3005 5.748402 TGATGTGGCAGATACAAGAATTCT 58.252 37.500 0.88 0.88 0.00 2.40
2779 3006 5.587443 TGATGTGGCAGATACAAGAATTCTG 59.413 40.000 9.17 6.08 39.87 3.02
2912 3139 3.003763 ACAAGCTCCTCCCGGACC 61.004 66.667 0.73 0.00 34.92 4.46
2921 3148 4.608774 TCCCGGACCTGTCACCGT 62.609 66.667 0.73 0.00 46.53 4.83
2929 3156 0.036732 ACCTGTCACCGTCGTACCTA 59.963 55.000 0.00 0.00 0.00 3.08
2990 3217 1.277842 ACCAGAACGTGATGCCATACA 59.722 47.619 0.00 0.00 0.00 2.29
2991 3218 1.935873 CCAGAACGTGATGCCATACAG 59.064 52.381 0.00 0.00 0.00 2.74
3110 3340 6.672266 ATGGAAGTTCCGATGTATCTATGT 57.328 37.500 17.13 0.00 40.17 2.29
3118 3348 7.284716 AGTTCCGATGTATCTATGTTGTACTCA 59.715 37.037 0.00 0.00 0.00 3.41
3139 3369 8.485976 ACTCATTTTACTAGAAATGTCTGCTC 57.514 34.615 13.64 0.00 43.89 4.26
3145 3375 5.474578 ACTAGAAATGTCTGCTCTTGTGA 57.525 39.130 0.00 0.00 35.12 3.58
3194 3424 8.165239 TCAGGATTATATAAACACACCAATGC 57.835 34.615 0.00 0.00 0.00 3.56
3195 3425 7.998383 TCAGGATTATATAAACACACCAATGCT 59.002 33.333 0.00 0.00 0.00 3.79
3197 3427 7.998383 AGGATTATATAAACACACCAATGCTGA 59.002 33.333 0.00 0.00 0.00 4.26
3198 3428 8.796475 GGATTATATAAACACACCAATGCTGAT 58.204 33.333 0.00 0.00 0.00 2.90
3199 3429 9.831737 GATTATATAAACACACCAATGCTGATC 57.168 33.333 0.00 0.00 0.00 2.92
3200 3430 8.978874 TTATATAAACACACCAATGCTGATCT 57.021 30.769 0.00 0.00 0.00 2.75
3202 3432 8.978874 ATATAAACACACCAATGCTGATCTAA 57.021 30.769 0.00 0.00 0.00 2.10
3204 3434 5.633830 AACACACCAATGCTGATCTAAAG 57.366 39.130 0.00 0.00 0.00 1.85
3205 3435 4.655963 ACACACCAATGCTGATCTAAAGT 58.344 39.130 0.00 0.00 0.00 2.66
3206 3436 4.456911 ACACACCAATGCTGATCTAAAGTG 59.543 41.667 0.00 0.00 0.00 3.16
3208 3438 4.012374 CACCAATGCTGATCTAAAGTGGT 58.988 43.478 7.95 7.95 38.65 4.16
3209 3439 4.012374 ACCAATGCTGATCTAAAGTGGTG 58.988 43.478 11.61 0.00 36.77 4.17
3210 3440 4.012374 CCAATGCTGATCTAAAGTGGTGT 58.988 43.478 0.00 0.00 0.00 4.16
3212 3442 5.396484 CAATGCTGATCTAAAGTGGTGTTG 58.604 41.667 0.00 0.00 0.00 3.33
3224 3813 5.986501 AAGTGGTGTTGTTTTGTTTAGGA 57.013 34.783 0.00 0.00 0.00 2.94
3231 3820 6.401688 GGTGTTGTTTTGTTTAGGAAACTTGC 60.402 38.462 3.92 0.00 43.67 4.01
3235 3824 7.971183 TGTTTTGTTTAGGAAACTTGCTTTT 57.029 28.000 3.92 0.00 43.67 2.27
3248 3837 4.190772 ACTTGCTTTTGTTGATGGTTTGG 58.809 39.130 0.00 0.00 0.00 3.28
3250 3839 4.686191 TGCTTTTGTTGATGGTTTGGAT 57.314 36.364 0.00 0.00 0.00 3.41
3255 3844 5.747951 TTTGTTGATGGTTTGGATTTTGC 57.252 34.783 0.00 0.00 0.00 3.68
3275 3864 1.195448 CGGTGATCTTGTGCAAGTGTC 59.805 52.381 11.17 10.87 39.38 3.67
3292 3881 1.146041 TCACGCTGGTTTGAGCTGT 59.854 52.632 0.00 0.00 36.77 4.40
3315 3904 1.202245 GCGTGCAGTTGGTTCAGAAAA 60.202 47.619 0.00 0.00 0.00 2.29
3363 3952 5.956563 TCTAGTTTTCTTCCTCCTATCCGTT 59.043 40.000 0.00 0.00 0.00 4.44
3367 3956 3.967467 TCTTCCTCCTATCCGTTAGGT 57.033 47.619 8.16 0.00 46.73 3.08
3368 3957 5.393068 TTCTTCCTCCTATCCGTTAGGTA 57.607 43.478 8.16 0.00 46.73 3.08
3385 3975 6.402226 CGTTAGGTATCCTTTTGAGTTTCTGC 60.402 42.308 0.00 0.00 34.61 4.26
3396 3986 2.225467 GAGTTTCTGCTGCTCTTGGTT 58.775 47.619 0.00 0.00 0.00 3.67
3410 4000 3.357203 TCTTGGTTTGTAAACTGTGGCA 58.643 40.909 7.36 0.00 38.89 4.92
3445 4035 0.395724 ATCCATGGCCTTTTCGTCCC 60.396 55.000 6.96 0.00 0.00 4.46
3446 4036 1.304052 CCATGGCCTTTTCGTCCCA 60.304 57.895 3.32 0.00 0.00 4.37
3447 4037 0.684153 CCATGGCCTTTTCGTCCCAT 60.684 55.000 3.32 0.00 38.56 4.00
3496 4086 7.873719 TGAACCAAGAAAATAGTCAGTTTCA 57.126 32.000 1.13 0.00 40.39 2.69
3506 4096 6.697641 AATAGTCAGTTTCAGTCCCCTAAA 57.302 37.500 0.00 0.00 0.00 1.85
3517 4107 2.089201 GTCCCCTAAATTTGTCACCGG 58.911 52.381 0.00 0.00 0.00 5.28
3522 4112 0.961358 TAAATTTGTCACCGGGCCCG 60.961 55.000 37.99 37.99 39.44 6.13
3523 4113 2.700407 AAATTTGTCACCGGGCCCGA 62.700 55.000 45.44 24.18 42.83 5.14
3524 4114 3.622060 ATTTGTCACCGGGCCCGAG 62.622 63.158 45.44 34.23 42.83 4.63
3529 4119 4.090588 CACCGGGCCCGAGCTAAA 62.091 66.667 45.44 0.00 42.83 1.85
3530 4120 4.091939 ACCGGGCCCGAGCTAAAC 62.092 66.667 45.44 2.05 42.83 2.01
3531 4121 4.851179 CCGGGCCCGAGCTAAACC 62.851 72.222 45.44 1.15 42.83 3.27
3532 4122 4.851179 CGGGCCCGAGCTAAACCC 62.851 72.222 41.82 0.00 42.83 4.11
3533 4123 3.408853 GGGCCCGAGCTAAACCCT 61.409 66.667 5.69 0.00 39.73 4.34
3534 4124 2.189784 GGCCCGAGCTAAACCCTC 59.810 66.667 0.00 0.00 39.73 4.30
3535 4125 2.189784 GCCCGAGCTAAACCCTCC 59.810 66.667 0.00 0.00 35.50 4.30
3536 4126 2.666098 GCCCGAGCTAAACCCTCCA 61.666 63.158 0.00 0.00 35.50 3.86
3537 4127 1.522569 CCCGAGCTAAACCCTCCAG 59.477 63.158 0.00 0.00 0.00 3.86
3538 4128 1.265454 CCCGAGCTAAACCCTCCAGT 61.265 60.000 0.00 0.00 0.00 4.00
3539 4129 1.481871 CCGAGCTAAACCCTCCAGTA 58.518 55.000 0.00 0.00 0.00 2.74
3540 4130 2.040178 CCGAGCTAAACCCTCCAGTAT 58.960 52.381 0.00 0.00 0.00 2.12
3558 4148 8.331931 TCCAGTATAAAACAAGATATCTGGGT 57.668 34.615 11.91 1.31 39.91 4.51
3593 4186 3.238597 TGGTTTTGCTGAAATAGGGCTT 58.761 40.909 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 4.524714 TGACTGTTTTGGTTTTGAAGTCCA 59.475 37.500 0.00 0.00 33.29 4.02
67 68 6.970043 TCGTCTTTATGACTGTTTTGGTTTTG 59.030 34.615 0.00 0.00 43.25 2.44
79 80 6.702329 ACATTCTTTCCTCGTCTTTATGACT 58.298 36.000 0.00 0.00 43.25 3.41
125 126 4.280929 TGTAACTACAGTCAGATGTGCAGT 59.719 41.667 0.00 0.00 34.56 4.40
126 127 4.809673 TGTAACTACAGTCAGATGTGCAG 58.190 43.478 0.00 0.00 34.56 4.41
127 128 4.809673 CTGTAACTACAGTCAGATGTGCA 58.190 43.478 8.46 0.00 46.51 4.57
197 241 6.897259 TTTTGTGTAGTAGATGCGGAATAC 57.103 37.500 0.00 0.00 0.00 1.89
314 360 4.763594 AAAACCGTAACAAATGTTTGCG 57.236 36.364 3.85 9.41 41.79 4.85
324 370 7.218228 TCTGTAGAGATGTAAAACCGTAACA 57.782 36.000 0.00 0.00 0.00 2.41
444 593 9.343539 GAGTCTCTGTATTTGCCCTTATTTATT 57.656 33.333 0.00 0.00 0.00 1.40
528 677 7.819900 GTGATCTCCAAACACAGAGTACTAAAT 59.180 37.037 0.00 0.00 35.06 1.40
538 687 5.835257 ACAAATTGTGATCTCCAAACACAG 58.165 37.500 0.00 0.00 43.62 3.66
616 765 1.073548 AACCCGTTACCCGTGCATT 59.926 52.632 0.00 0.00 33.66 3.56
621 770 0.037046 GTCATCAACCCGTTACCCGT 60.037 55.000 0.00 0.00 33.66 5.28
622 771 0.248289 AGTCATCAACCCGTTACCCG 59.752 55.000 0.00 0.00 0.00 5.28
623 772 2.498885 ACTAGTCATCAACCCGTTACCC 59.501 50.000 0.00 0.00 0.00 3.69
624 773 3.881937 ACTAGTCATCAACCCGTTACC 57.118 47.619 0.00 0.00 0.00 2.85
625 774 7.269477 ACTATACTAGTCATCAACCCGTTAC 57.731 40.000 0.00 0.00 32.47 2.50
670 819 8.314021 AGTGTGATGTCTACAAATCTACAATGA 58.686 33.333 0.00 0.00 0.00 2.57
698 847 7.860649 AATGAAATGCATTAATGGGGTCTAT 57.139 32.000 13.39 0.00 45.16 1.98
727 876 2.997986 CGCGTTTGACCAAACTACCTAT 59.002 45.455 19.48 0.00 46.21 2.57
858 1007 4.759183 AGTAATACGGATCGGAGGAAGTAC 59.241 45.833 7.35 3.93 0.00 2.73
863 1012 3.559069 ACAAGTAATACGGATCGGAGGA 58.441 45.455 7.35 0.00 0.00 3.71
917 1073 5.582665 CACACTCTCTTTGGTTATAGCTTCC 59.417 44.000 0.00 0.00 0.00 3.46
918 1074 6.166982 ACACACTCTCTTTGGTTATAGCTTC 58.833 40.000 0.00 0.00 0.00 3.86
921 1077 6.426937 TGAAACACACTCTCTTTGGTTATAGC 59.573 38.462 0.00 0.00 0.00 2.97
946 1102 1.103398 GCTGTGGTGCAGGAAACAGT 61.103 55.000 15.46 0.00 45.14 3.55
989 1145 4.688021 CTGGACAAACATAGCTCTCCTAC 58.312 47.826 0.00 0.00 0.00 3.18
999 1155 3.146066 GTGGTGAAGCTGGACAAACATA 58.854 45.455 0.00 0.00 0.00 2.29
1006 1162 2.633860 CCAAGTGGTGAAGCTGGAC 58.366 57.895 0.00 0.00 0.00 4.02
1893 2095 1.411977 ACAATCTGCAGGATCCTCGAG 59.588 52.381 12.69 10.75 32.76 4.04
1906 2120 1.797046 CGCTATAGGCAGCACAATCTG 59.203 52.381 1.04 0.00 41.88 2.90
2034 2254 8.836413 TGAAACAATTCTTTGTAAGAGAATCGT 58.164 29.630 0.36 0.00 45.30 3.73
2082 2303 2.025605 TCCTACTCCGAGCAGGTTCTTA 60.026 50.000 13.53 0.00 41.99 2.10
2129 2350 1.294659 CTTGTCAGGCTTGCGGAGTC 61.295 60.000 0.00 0.00 0.00 3.36
2366 2590 6.431234 ACCTCTGATTATGTGAAACCTTTGAC 59.569 38.462 0.00 0.00 34.36 3.18
2460 2687 3.194062 GCTGTCTAGGAGAACATTGCTC 58.806 50.000 0.00 0.00 0.00 4.26
2580 2807 2.686106 TGTCCTAACTCGGGGGCC 60.686 66.667 0.00 0.00 0.00 5.80
2586 2813 2.743636 ACCACATGTGTCCTAACTCG 57.256 50.000 23.79 8.10 0.00 4.18
2592 2819 1.064003 TGCCTTACCACATGTGTCCT 58.936 50.000 23.79 8.86 0.00 3.85
2600 2827 2.400269 GACGGGGTTGCCTTACCACA 62.400 60.000 3.32 0.00 41.96 4.17
2602 2829 0.544833 TAGACGGGGTTGCCTTACCA 60.545 55.000 0.00 0.00 40.09 3.25
2605 2832 1.606885 CGGTAGACGGGGTTGCCTTA 61.607 60.000 0.00 0.00 39.42 2.69
2635 2862 1.073125 TCCAGAAGGAATGCACCGAAA 59.927 47.619 0.00 0.00 42.23 3.46
2661 2888 2.410322 AATTGGCCTCCGTGCACAGA 62.410 55.000 18.64 10.47 0.00 3.41
2662 2889 1.926511 GAATTGGCCTCCGTGCACAG 61.927 60.000 18.64 5.51 0.00 3.66
2667 2894 1.243342 TTGCTGAATTGGCCTCCGTG 61.243 55.000 3.32 0.00 0.00 4.94
2681 2908 1.388888 CTGTTTCGCTCGTTTTGCTG 58.611 50.000 0.00 0.00 0.00 4.41
2747 2974 4.637091 TGTATCTGCCACATCAACAATCAG 59.363 41.667 0.00 0.00 0.00 2.90
2764 2991 5.983333 ACCCATCCAGAATTCTTGTATCT 57.017 39.130 4.86 0.00 0.00 1.98
2778 3005 1.916874 TGTCCGGATTAAACCCATCCA 59.083 47.619 7.81 0.00 40.46 3.41
2779 3006 2.721425 TGTCCGGATTAAACCCATCC 57.279 50.000 7.81 0.00 37.45 3.51
2912 3139 1.467035 GCTTAGGTACGACGGTGACAG 60.467 57.143 0.00 0.00 0.00 3.51
2921 3148 2.738643 GCATGCTGAAGCTTAGGTACGA 60.739 50.000 11.37 0.00 42.66 3.43
2929 3156 2.869636 CTCCAGCATGCTGAAGCTT 58.130 52.632 42.21 8.53 46.30 3.74
2990 3217 0.673022 ACCTACGCTCGTCGAGAACT 60.673 55.000 26.11 8.96 41.67 3.01
2991 3218 0.520827 CACCTACGCTCGTCGAGAAC 60.521 60.000 26.11 8.07 41.67 3.01
3078 3308 6.884832 ACATCGGAACTTCCATAGTCAATTA 58.115 36.000 8.59 0.00 35.91 1.40
3118 3348 8.725148 CACAAGAGCAGACATTTCTAGTAAAAT 58.275 33.333 0.00 0.00 0.00 1.82
3134 3364 9.932699 CATAAGAAAGATAAATCACAAGAGCAG 57.067 33.333 0.00 0.00 0.00 4.24
3188 3418 4.012374 ACACCACTTTAGATCAGCATTGG 58.988 43.478 0.00 0.00 0.00 3.16
3194 3424 6.795399 ACAAAACAACACCACTTTAGATCAG 58.205 36.000 0.00 0.00 0.00 2.90
3195 3425 6.767524 ACAAAACAACACCACTTTAGATCA 57.232 33.333 0.00 0.00 0.00 2.92
3197 3427 8.194769 CCTAAACAAAACAACACCACTTTAGAT 58.805 33.333 0.00 0.00 0.00 1.98
3198 3428 7.393796 TCCTAAACAAAACAACACCACTTTAGA 59.606 33.333 0.00 0.00 0.00 2.10
3199 3429 7.540299 TCCTAAACAAAACAACACCACTTTAG 58.460 34.615 0.00 0.00 0.00 1.85
3200 3430 7.463961 TCCTAAACAAAACAACACCACTTTA 57.536 32.000 0.00 0.00 0.00 1.85
3202 3432 5.986501 TCCTAAACAAAACAACACCACTT 57.013 34.783 0.00 0.00 0.00 3.16
3204 3434 6.160684 AGTTTCCTAAACAAAACAACACCAC 58.839 36.000 5.42 0.00 43.79 4.16
3205 3435 6.347859 AGTTTCCTAAACAAAACAACACCA 57.652 33.333 5.42 0.00 43.79 4.17
3206 3436 6.401688 GCAAGTTTCCTAAACAAAACAACACC 60.402 38.462 5.42 0.00 43.79 4.16
3208 3438 6.459923 AGCAAGTTTCCTAAACAAAACAACA 58.540 32.000 5.42 0.00 43.79 3.33
3209 3439 6.961359 AGCAAGTTTCCTAAACAAAACAAC 57.039 33.333 5.42 0.00 43.79 3.32
3210 3440 7.971183 AAAGCAAGTTTCCTAAACAAAACAA 57.029 28.000 5.42 0.00 43.79 2.83
3212 3442 7.802738 ACAAAAGCAAGTTTCCTAAACAAAAC 58.197 30.769 5.42 0.00 43.79 2.43
3224 3813 5.123661 CCAAACCATCAACAAAAGCAAGTTT 59.876 36.000 0.00 0.00 0.00 2.66
3231 3820 6.200808 GCAAAATCCAAACCATCAACAAAAG 58.799 36.000 0.00 0.00 0.00 2.27
3235 3824 3.388308 CGCAAAATCCAAACCATCAACA 58.612 40.909 0.00 0.00 0.00 3.33
3248 3837 2.253603 GCACAAGATCACCGCAAAATC 58.746 47.619 0.00 0.00 0.00 2.17
3250 3839 1.028130 TGCACAAGATCACCGCAAAA 58.972 45.000 0.00 0.00 0.00 2.44
3255 3844 1.195448 GACACTTGCACAAGATCACCG 59.805 52.381 16.95 1.46 40.79 4.94
3275 3864 0.882042 AGACAGCTCAAACCAGCGTG 60.882 55.000 0.00 0.00 44.82 5.34
3292 3881 1.153269 TGAACCAACTGCACGCAGA 60.153 52.632 25.09 0.00 46.30 4.26
3315 3904 1.413445 TGCAACAATCAGGCAAAGCTT 59.587 42.857 0.00 0.00 34.05 3.74
3340 3929 5.855740 ACGGATAGGAGGAAGAAAACTAG 57.144 43.478 0.00 0.00 0.00 2.57
3363 3952 6.173339 CAGCAGAAACTCAAAAGGATACCTA 58.827 40.000 0.00 0.00 31.13 3.08
3367 3956 4.655963 AGCAGCAGAAACTCAAAAGGATA 58.344 39.130 0.00 0.00 0.00 2.59
3368 3957 3.494332 AGCAGCAGAAACTCAAAAGGAT 58.506 40.909 0.00 0.00 0.00 3.24
3385 3975 4.498009 CCACAGTTTACAAACCAAGAGCAG 60.498 45.833 1.27 0.00 39.71 4.24
3454 4044 6.795590 TGGTTCAAAAGTCCAGGGATTATAA 58.204 36.000 0.00 0.00 0.00 0.98
3456 4046 5.269554 TGGTTCAAAAGTCCAGGGATTAT 57.730 39.130 0.00 0.00 0.00 1.28
3506 4096 3.622060 CTCGGGCCCGGTGACAAAT 62.622 63.158 42.36 0.00 40.25 2.32
3517 4107 2.189784 GAGGGTTTAGCTCGGGCC 59.810 66.667 2.00 0.00 39.73 5.80
3522 4112 6.412214 TGTTTTATACTGGAGGGTTTAGCTC 58.588 40.000 0.00 0.00 0.00 4.09
3523 4113 6.382919 TGTTTTATACTGGAGGGTTTAGCT 57.617 37.500 0.00 0.00 0.00 3.32
3524 4114 6.882678 TCTTGTTTTATACTGGAGGGTTTAGC 59.117 38.462 0.00 0.00 0.00 3.09
3527 4117 9.628500 GATATCTTGTTTTATACTGGAGGGTTT 57.372 33.333 0.00 0.00 0.00 3.27
3529 4119 8.432805 CAGATATCTTGTTTTATACTGGAGGGT 58.567 37.037 1.33 0.00 0.00 4.34
3530 4120 7.880195 CCAGATATCTTGTTTTATACTGGAGGG 59.120 40.741 1.33 0.00 43.12 4.30
3531 4121 7.880195 CCCAGATATCTTGTTTTATACTGGAGG 59.120 40.741 1.33 0.00 43.12 4.30
3532 4122 8.432805 ACCCAGATATCTTGTTTTATACTGGAG 58.567 37.037 1.33 0.00 43.12 3.86
3533 4123 8.331931 ACCCAGATATCTTGTTTTATACTGGA 57.668 34.615 1.33 0.00 43.12 3.86
3534 4124 8.210946 TGACCCAGATATCTTGTTTTATACTGG 58.789 37.037 1.33 0.00 41.06 4.00
3535 4125 9.784531 ATGACCCAGATATCTTGTTTTATACTG 57.215 33.333 1.33 0.00 0.00 2.74
3539 4129 9.170890 TCCTATGACCCAGATATCTTGTTTTAT 57.829 33.333 1.33 3.49 0.00 1.40
3540 4130 8.429641 GTCCTATGACCCAGATATCTTGTTTTA 58.570 37.037 1.33 0.15 35.34 1.52
3551 4141 2.747177 TCAACGTCCTATGACCCAGAT 58.253 47.619 0.00 0.00 38.32 2.90
3558 4148 3.438781 GCAAAACCATCAACGTCCTATGA 59.561 43.478 6.36 0.00 0.00 2.15
3563 4153 1.606668 TCAGCAAAACCATCAACGTCC 59.393 47.619 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.