Multiple sequence alignment - TraesCS2D01G031300

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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 TraesCS2D01G031300 chr2D 100.000 3753 0 0 1 3753 12582607 12578855 0.000000e+00 6931.0
1 TraesCS2D01G031300 chr2D 82.592 1551 225 25 1117 2643 12556610 12558139 0.000000e+00 1327.0
2 TraesCS2D01G031300 chr2D 83.529 935 151 3 1691 2623 12551265 12552198 0.000000e+00 870.0
3 TraesCS2D01G031300 chr2B 89.486 3015 245 31 1 2964 19076214 19073221 0.000000e+00 3746.0
4 TraesCS2D01G031300 chr2B 82.053 1549 236 24 1117 2643 18950299 18948771 0.000000e+00 1282.0
5 TraesCS2D01G031300 chr2B 79.299 1768 324 23 1014 2760 19102649 19100903 0.000000e+00 1199.0
6 TraesCS2D01G031300 chr2B 86.923 1040 133 1 1650 2689 18922720 18923756 0.000000e+00 1164.0
7 TraesCS2D01G031300 chr2B 82.386 1056 161 10 1706 2760 19077491 19076460 0.000000e+00 896.0
8 TraesCS2D01G031300 chr2B 81.866 943 162 4 1700 2642 18954877 18953944 0.000000e+00 785.0
9 TraesCS2D01G031300 chr2B 87.087 666 40 12 763 1385 18915067 18915729 0.000000e+00 712.0
10 TraesCS2D01G031300 chr2B 80.522 498 87 6 1128 1620 18955479 18954987 1.270000e-99 374.0
11 TraesCS2D01G031300 chr2B 87.542 297 25 8 2749 3040 18923774 18924063 2.160000e-87 333.0
12 TraesCS2D01G031300 chr2B 82.857 245 36 6 1381 1622 18922416 18922657 8.160000e-52 215.0
13 TraesCS2D01G031300 chr2B 82.449 245 17 17 3125 3344 18924154 18924397 1.380000e-44 191.0
14 TraesCS2D01G031300 chr2B 86.458 96 10 3 3126 3218 19073067 19072972 6.630000e-18 102.0
15 TraesCS2D01G031300 chr2B 96.364 55 2 0 698 752 18914966 18915020 1.440000e-14 91.6
16 TraesCS2D01G031300 chr2B 100.000 38 0 0 721 758 18914926 18914963 1.870000e-08 71.3
17 TraesCS2D01G031300 chr2A 92.730 1458 88 5 184 1628 13040318 13038866 0.000000e+00 2089.0
18 TraesCS2D01G031300 chr2A 83.073 1536 230 21 1125 2643 13013261 13014783 0.000000e+00 1369.0
19 TraesCS2D01G031300 chr2A 87.819 1174 127 8 1653 2820 13038809 13037646 0.000000e+00 1362.0
20 TraesCS2D01G031300 chr2A 79.708 1646 294 22 1134 2760 13068997 13067373 0.000000e+00 1153.0
21 TraesCS2D01G031300 chr2A 83.718 952 155 0 1691 2642 12990989 12991940 0.000000e+00 900.0
22 TraesCS2D01G031300 chr2A 89.904 416 34 6 3341 3753 13037044 13036634 2.570000e-146 529.0
23 TraesCS2D01G031300 chr2A 97.512 201 4 1 1 201 13067128 13066929 3.590000e-90 342.0
24 TraesCS2D01G031300 chr2A 82.822 326 22 15 3046 3344 13037514 13037196 1.030000e-65 261.0
25 TraesCS2D01G031300 chr6A 81.295 278 47 4 1127 1400 553913268 553912992 1.750000e-53 220.0
26 TraesCS2D01G031300 chr6A 81.362 279 45 6 1127 1400 563484792 563485068 1.750000e-53 220.0
27 TraesCS2D01G031300 chr6B 80.287 279 50 4 1126 1400 633730707 633730984 4.910000e-49 206.0
28 TraesCS2D01G031300 chr5B 87.273 55 7 0 3126 3180 485903135 485903189 3.130000e-06 63.9


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 TraesCS2D01G031300 chr2D 12578855 12582607 3752 True 6931.000000 6931 100.000000 1 3753 1 chr2D.!!$R1 3752
1 TraesCS2D01G031300 chr2D 12556610 12558139 1529 False 1327.000000 1327 82.592000 1117 2643 1 chr2D.!!$F2 1526
2 TraesCS2D01G031300 chr2D 12551265 12552198 933 False 870.000000 870 83.529000 1691 2623 1 chr2D.!!$F1 932
3 TraesCS2D01G031300 chr2B 19072972 19077491 4519 True 1581.333333 3746 86.110000 1 3218 3 chr2B.!!$R3 3217
4 TraesCS2D01G031300 chr2B 19100903 19102649 1746 True 1199.000000 1199 79.299000 1014 2760 1 chr2B.!!$R1 1746
5 TraesCS2D01G031300 chr2B 18948771 18955479 6708 True 813.666667 1282 81.480333 1117 2643 3 chr2B.!!$R2 1526
6 TraesCS2D01G031300 chr2B 18922416 18924397 1981 False 475.750000 1164 84.942750 1381 3344 4 chr2B.!!$F2 1963
7 TraesCS2D01G031300 chr2B 18914926 18915729 803 False 291.633333 712 94.483667 698 1385 3 chr2B.!!$F1 687
8 TraesCS2D01G031300 chr2A 13013261 13014783 1522 False 1369.000000 1369 83.073000 1125 2643 1 chr2A.!!$F2 1518
9 TraesCS2D01G031300 chr2A 13036634 13040318 3684 True 1060.250000 2089 88.318750 184 3753 4 chr2A.!!$R1 3569
10 TraesCS2D01G031300 chr2A 12990989 12991940 951 False 900.000000 900 83.718000 1691 2642 1 chr2A.!!$F1 951
11 TraesCS2D01G031300 chr2A 13066929 13068997 2068 True 747.500000 1153 88.610000 1 2760 2 chr2A.!!$R2 2759

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
773 2099 2.614057 CTCAGCAGTCACCTTTCGTTTT 59.386 45.455 0.00 0.0 0.0 2.43 F
1646 5757 0.040958 CATTGGCGCGGATTCTTAGC 60.041 55.000 8.83 0.0 0.0 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2086 6272 0.244450 TTGACATACACGACGGACCC 59.756 55.0 0.00 0.0 0.00 4.46 R
2951 7160 0.036306 AAGAAGGTACACCCGCCTTG 59.964 55.0 0.11 0.0 44.37 3.61 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
137 1415 4.584743 AGAACTGGAACAAAAATCACCCTC 59.415 41.667 0.00 0.00 38.70 4.30
180 1458 3.778954 ATTCTAGGGTGGATTAGCAGC 57.221 47.619 0.00 0.00 0.00 5.25
398 1676 7.139392 TCTTGACCGATAACATCTATCTTTCG 58.861 38.462 0.00 0.00 0.00 3.46
432 1710 9.139174 GAGAATGTTTTATTGTAATGTTGTGGG 57.861 33.333 0.00 0.00 0.00 4.61
585 1871 9.353999 AGTGAGTAAAAACAAAAGAATGAACAC 57.646 29.630 0.00 0.00 0.00 3.32
773 2099 2.614057 CTCAGCAGTCACCTTTCGTTTT 59.386 45.455 0.00 0.00 0.00 2.43
844 2175 6.887368 TGGAGCATTTAATCGACAATATTCG 58.113 36.000 0.00 0.00 40.53 3.34
1201 5269 5.633830 TGATGAAGTTGGCAAAGATCTTC 57.366 39.130 16.94 16.94 36.20 2.87
1279 5354 4.143333 CGTTCCCGCGGTCCTGAT 62.143 66.667 26.12 0.00 0.00 2.90
1328 5403 2.438434 CCACCATTCCTGACGGCC 60.438 66.667 0.00 0.00 0.00 6.13
1479 5590 1.300971 ACGTGTGTCATGGCAGATGC 61.301 55.000 16.01 0.00 41.14 3.91
1480 5591 1.022982 CGTGTGTCATGGCAGATGCT 61.023 55.000 0.00 0.00 41.70 3.79
1496 5607 3.825014 AGATGCTGTCATGAGCTTTTGTT 59.175 39.130 8.27 0.00 39.90 2.83
1529 5640 1.598962 GAGCTCAGTGTGCCTTGCA 60.599 57.895 9.40 0.00 35.60 4.08
1573 5684 1.078708 CGGTTTCATGGGCTACCGT 60.079 57.895 15.79 0.00 46.25 4.83
1604 5715 0.390860 CCTCCTAGACGAGGGCATTG 59.609 60.000 7.07 0.00 46.70 2.82
1625 5736 2.687914 GCCCCTCTCAAAGGTATGCATT 60.688 50.000 3.54 0.00 44.56 3.56
1631 5742 5.963334 CCTCTCAAAGGTATGCATTGCATTG 60.963 44.000 27.73 19.73 42.65 2.82
1637 5748 4.798026 TGCATTGCATTGGCGCGG 62.798 61.111 8.83 0.00 45.35 6.46
1641 5752 1.066257 ATTGCATTGGCGCGGATTC 59.934 52.632 8.83 0.00 45.35 2.52
1642 5753 1.386525 ATTGCATTGGCGCGGATTCT 61.387 50.000 8.83 0.00 45.35 2.40
1644 5755 0.746204 TGCATTGGCGCGGATTCTTA 60.746 50.000 8.83 0.00 45.35 2.10
1646 5757 0.040958 CATTGGCGCGGATTCTTAGC 60.041 55.000 8.83 0.00 0.00 3.09
1648 5759 0.675208 TTGGCGCGGATTCTTAGCAA 60.675 50.000 8.83 0.00 0.00 3.91
1651 5834 1.567504 GCGCGGATTCTTAGCAAGTA 58.432 50.000 8.83 0.00 0.00 2.24
1671 5854 5.370679 AGTAGCATTGCATATGTGTGATGA 58.629 37.500 11.91 0.00 0.00 2.92
1675 5858 3.994204 TTGCATATGTGTGATGATGGC 57.006 42.857 4.29 0.00 0.00 4.40
1785 5968 2.756283 CGCCTCCGAGACTTCCCT 60.756 66.667 0.00 0.00 36.29 4.20
1884 6067 0.107508 CCGCCATCATCCTCAACACT 60.108 55.000 0.00 0.00 0.00 3.55
1899 6082 2.440539 ACACTTTTGACGAGCTCGAT 57.559 45.000 40.58 24.90 43.02 3.59
1903 6086 1.923204 CTTTTGACGAGCTCGATCAGG 59.077 52.381 40.58 24.46 43.02 3.86
1904 6087 0.888619 TTTGACGAGCTCGATCAGGT 59.111 50.000 40.58 18.93 43.02 4.00
1975 6158 0.608035 CCCGCTTAACTTCCTTGCCA 60.608 55.000 0.00 0.00 0.00 4.92
1981 6164 1.909700 TAACTTCCTTGCCAAGCAGG 58.090 50.000 0.00 0.00 40.61 4.85
1984 6167 0.538057 CTTCCTTGCCAAGCAGGTGA 60.538 55.000 0.00 0.00 40.61 4.02
1999 6185 3.700970 TGATTCCTGACGGCGGCA 61.701 61.111 17.61 17.61 0.00 5.69
2052 6238 1.349357 AGCCTTTGGAGAGAAGACCAC 59.651 52.381 0.00 0.00 35.81 4.16
2106 6292 1.134907 GGGTCCGTCGTGTATGTCAAT 60.135 52.381 0.00 0.00 0.00 2.57
2132 6318 2.423373 GGAGCATAACCACCATGTCCAT 60.423 50.000 0.00 0.00 0.00 3.41
2145 6331 1.951209 TGTCCATCCAAGAGCTGGTA 58.049 50.000 0.00 0.00 46.51 3.25
2184 6370 0.949105 CCAACTGCGGCTACGACTTT 60.949 55.000 0.00 0.00 44.60 2.66
2226 6412 1.264749 TAGTGAAGGGTGATGCCGCT 61.265 55.000 0.00 0.00 38.44 5.52
2230 6416 3.925630 AAGGGTGATGCCGCTGTGG 62.926 63.158 2.05 2.05 42.50 4.17
2232 6418 2.267642 GGTGATGCCGCTGTGGTA 59.732 61.111 9.31 4.55 41.21 3.25
2286 6472 2.055042 CCTCCTAGCGAGCTGGTGT 61.055 63.158 7.99 0.00 37.27 4.16
2292 6478 0.391228 TAGCGAGCTGGTGTGAACAA 59.609 50.000 7.99 0.00 0.00 2.83
2426 6612 0.823356 GAGCAGCAAACCAACTCCCA 60.823 55.000 0.00 0.00 0.00 4.37
2473 6659 3.011595 TGGGATGGAAGTTGGTGATGATT 59.988 43.478 0.00 0.00 0.00 2.57
2645 6834 7.614192 TGAGAGTATGTTCAAGGATGTACTACA 59.386 37.037 0.00 0.00 0.00 2.74
2653 6842 0.388294 GGATGTACTACAGACCGCCC 59.612 60.000 0.00 0.00 0.00 6.13
2660 6849 1.033574 CTACAGACCGCCCCTAAGAG 58.966 60.000 0.00 0.00 0.00 2.85
2725 6914 2.814336 GACAGGTTGGGAAGTGTGAATC 59.186 50.000 0.00 0.00 0.00 2.52
2764 6957 2.746904 TGTTGATCCAATAAGGCGTGTG 59.253 45.455 0.00 0.00 37.29 3.82
2765 6958 1.378531 TGATCCAATAAGGCGTGTGC 58.621 50.000 0.00 0.00 41.71 4.57
2821 7016 1.214589 GGCCGTGCGAGAAGTTAGA 59.785 57.895 0.00 0.00 0.00 2.10
2823 7018 0.109226 GCCGTGCGAGAAGTTAGACT 60.109 55.000 0.00 0.00 0.00 3.24
2829 7024 2.800544 TGCGAGAAGTTAGACTTTGTGC 59.199 45.455 0.00 1.15 38.80 4.57
2830 7025 3.060602 GCGAGAAGTTAGACTTTGTGCT 58.939 45.455 0.00 0.00 38.80 4.40
2831 7026 4.235360 GCGAGAAGTTAGACTTTGTGCTA 58.765 43.478 0.00 0.00 38.80 3.49
2832 7027 4.324936 GCGAGAAGTTAGACTTTGTGCTAG 59.675 45.833 0.00 0.00 38.80 3.42
2835 7030 4.838986 AGAAGTTAGACTTTGTGCTAGGGA 59.161 41.667 0.00 0.00 38.80 4.20
2837 7032 5.562298 AGTTAGACTTTGTGCTAGGGAAA 57.438 39.130 0.00 0.00 0.00 3.13
2842 7037 4.520492 AGACTTTGTGCTAGGGAAACAATG 59.480 41.667 0.00 0.00 34.04 2.82
2931 7140 8.732746 ATACTTTGAAAAGAATATGGCTACGT 57.267 30.769 9.71 0.00 39.31 3.57
2950 7159 2.031595 CGTGTATCAGTCGATGGAGAGG 60.032 54.545 0.00 0.00 32.73 3.69
2951 7160 1.957177 TGTATCAGTCGATGGAGAGGC 59.043 52.381 0.00 0.00 32.73 4.70
2956 7165 1.522580 GTCGATGGAGAGGCAAGGC 60.523 63.158 0.00 0.00 0.00 4.35
2958 7167 2.203126 GATGGAGAGGCAAGGCGG 60.203 66.667 0.00 0.00 0.00 6.13
2989 7198 5.103290 TCTTTCAGGAAAACGTGTAATGC 57.897 39.130 0.00 0.00 0.00 3.56
3057 7363 9.706691 GATTTATTTTATCCTACGATCTCACCA 57.293 33.333 0.00 0.00 0.00 4.17
3077 7383 4.952335 ACCAAAAGGGCAGATTCTATTCTG 59.048 41.667 0.00 0.00 44.87 3.02
3081 7387 3.387962 AGGGCAGATTCTATTCTGGTCA 58.612 45.455 3.85 0.00 42.78 4.02
3082 7388 3.979347 AGGGCAGATTCTATTCTGGTCAT 59.021 43.478 3.85 0.00 42.78 3.06
3090 7396 5.512942 TTCTATTCTGGTCATCCCACAAA 57.487 39.130 0.00 0.00 38.72 2.83
3101 7408 5.435291 GTCATCCCACAAATCTCTTCTCAT 58.565 41.667 0.00 0.00 0.00 2.90
3188 7520 1.224075 CAGCAGCAGGACCAATATCG 58.776 55.000 0.00 0.00 0.00 2.92
3204 7537 5.349817 CCAATATCGTGCTGGTCTGATTATC 59.650 44.000 0.00 0.00 0.00 1.75
3212 7545 1.407618 TGGTCTGATTATCGGTGGTCG 59.592 52.381 0.57 0.00 40.90 4.79
3218 7551 3.892522 TGATTATCGGTGGTCGTAATCG 58.107 45.455 0.00 0.00 40.47 3.34
3344 7695 3.305131 CCGCTCCCTTACCAAAAGAAAAC 60.305 47.826 0.00 0.00 0.00 2.43
3359 7865 3.339141 AGAAAACGAAGGGAAGCTCATC 58.661 45.455 0.00 0.00 0.00 2.92
3384 7890 0.535780 ACGCCATACATGCCCATCTG 60.536 55.000 0.00 0.00 0.00 2.90
3399 7905 4.402155 GCCCATCTGTGTGAAAATTATCCA 59.598 41.667 0.00 0.00 0.00 3.41
3400 7906 5.105392 GCCCATCTGTGTGAAAATTATCCAA 60.105 40.000 0.00 0.00 0.00 3.53
3401 7907 6.574073 GCCCATCTGTGTGAAAATTATCCAAA 60.574 38.462 0.00 0.00 0.00 3.28
3443 7949 7.927305 ACGAAGTTTCAGAAGAGTAACTAAC 57.073 36.000 0.00 0.00 37.78 2.34
3444 7950 7.486647 ACGAAGTTTCAGAAGAGTAACTAACA 58.513 34.615 0.00 0.00 37.78 2.41
3452 7958 6.989759 TCAGAAGAGTAACTAACAAATGCACA 59.010 34.615 0.00 0.00 0.00 4.57
3465 7971 5.417811 ACAAATGCACATGTTGTTTCAGAA 58.582 33.333 0.00 0.00 31.52 3.02
3505 8011 2.250485 CGGTACCTATCGTCGGCG 59.750 66.667 10.90 1.15 39.92 6.46
3510 8016 2.002586 GTACCTATCGTCGGCGCTATA 58.997 52.381 3.52 0.00 38.14 1.31
3514 8020 1.736126 CTATCGTCGGCGCTATAGGAA 59.264 52.381 3.52 0.00 38.14 3.36
3516 8022 0.816825 TCGTCGGCGCTATAGGAAGT 60.817 55.000 3.52 0.00 38.14 3.01
3518 8024 1.768510 GTCGGCGCTATAGGAAGTTC 58.231 55.000 7.64 0.00 0.00 3.01
3527 8033 4.580995 CGCTATAGGAAGTTCTGAGGAAGA 59.419 45.833 2.25 0.00 31.46 2.87
3530 8036 7.505258 GCTATAGGAAGTTCTGAGGAAGAAAT 58.495 38.462 2.25 0.00 46.51 2.17
3544 8050 3.181489 GGAAGAAATCTGAGGCAATGCAG 60.181 47.826 7.79 0.00 0.00 4.41
3566 8072 3.589988 CCAGTGCTAGTGGACTAACTTG 58.410 50.000 4.51 0.00 43.08 3.16
3570 8076 4.021016 AGTGCTAGTGGACTAACTTGGAAG 60.021 45.833 0.00 0.00 43.13 3.46
3571 8077 3.901844 TGCTAGTGGACTAACTTGGAAGT 59.098 43.478 0.00 0.00 42.04 3.01
3577 8083 7.407393 AGTGGACTAACTTGGAAGTATAGAC 57.593 40.000 12.06 8.12 38.57 2.59
3582 8088 6.631962 ACTAACTTGGAAGTATAGACTGCAC 58.368 40.000 0.00 0.00 38.57 4.57
3607 8114 6.992123 CACAGAATAAATCACTGCCTACCATA 59.008 38.462 0.00 0.00 35.38 2.74
3613 8120 3.643199 TCACTGCCTACCATATTGCAA 57.357 42.857 0.00 0.00 32.58 4.08
3620 8127 3.499918 GCCTACCATATTGCAAGTGCTAG 59.500 47.826 4.94 7.48 42.66 3.42
3623 8130 6.288294 CCTACCATATTGCAAGTGCTAGTTA 58.712 40.000 4.94 0.00 42.66 2.24
3625 8132 6.624352 ACCATATTGCAAGTGCTAGTTATG 57.376 37.500 4.94 5.44 42.66 1.90
3626 8133 5.532406 ACCATATTGCAAGTGCTAGTTATGG 59.468 40.000 21.62 21.62 40.59 2.74
3655 8162 6.210796 TCATTTGCAATTCTTCAGTCTGTTG 58.789 36.000 0.00 0.00 0.00 3.33
3683 8190 1.603678 GGACCTCGCGTAAACAACAGA 60.604 52.381 5.77 0.00 0.00 3.41
3698 8205 7.775397 AAACAACAGATGAAATGGTTGAAAG 57.225 32.000 10.00 0.00 39.34 2.62
3704 8211 8.652810 ACAGATGAAATGGTTGAAAGAAAAAG 57.347 30.769 0.00 0.00 0.00 2.27
3731 8239 5.964477 ACTTTACCTCCCTGAACATCTATGA 59.036 40.000 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 1288 7.955918 AGCCAACTCTGAAATCATTTTACTTT 58.044 30.769 0.00 0.00 0.00 2.66
13 1291 6.913170 TGAGCCAACTCTGAAATCATTTTAC 58.087 36.000 0.00 0.00 43.85 2.01
137 1415 3.431068 CACGTTAAAGTGGTGCACG 57.569 52.632 11.45 0.00 39.64 5.34
281 1559 2.101415 GGGACCATGCTAAAATTGCTCC 59.899 50.000 0.00 0.00 0.00 4.70
677 1967 5.695851 AATTAACTTTGTGTCTGAGGCTG 57.304 39.130 0.00 0.00 0.00 4.85
773 2099 2.026542 AGATTCTTCAGCCATGCTCACA 60.027 45.455 0.00 0.00 36.40 3.58
957 2304 5.220043 GCTGCGCGTATAGAGTACAATATTG 60.220 44.000 14.01 14.01 0.00 1.90
1187 5255 1.888512 GCAGTGGAAGATCTTTGCCAA 59.111 47.619 15.54 0.80 31.18 4.52
1201 5269 2.115910 TGGAAGCCCTTGCAGTGG 59.884 61.111 0.00 0.00 41.13 4.00
1305 5380 0.321653 GTCAGGAATGGTGGCGAAGT 60.322 55.000 0.00 0.00 0.00 3.01
1469 5580 1.968704 CTCATGACAGCATCTGCCAT 58.031 50.000 0.00 0.00 43.38 4.40
1474 5585 3.418995 ACAAAAGCTCATGACAGCATCT 58.581 40.909 9.38 0.00 42.40 2.90
1479 5590 4.293415 GTCCAAACAAAAGCTCATGACAG 58.707 43.478 5.77 0.00 0.00 3.51
1480 5591 3.243035 CGTCCAAACAAAAGCTCATGACA 60.243 43.478 5.77 0.00 0.00 3.58
1529 5640 2.031163 GGCAGTCCAGAACAGCGT 59.969 61.111 0.00 0.00 41.07 5.07
1573 5684 3.359950 GTCTAGGAGGAACCGGAAGTTA 58.640 50.000 9.46 0.00 44.74 2.24
1625 5736 0.746204 TAAGAATCCGCGCCAATGCA 60.746 50.000 0.00 0.00 37.32 3.96
1631 5742 1.090052 ACTTGCTAAGAATCCGCGCC 61.090 55.000 0.00 0.00 0.00 6.53
1633 5744 1.523095 GCTACTTGCTAAGAATCCGCG 59.477 52.381 0.00 0.00 38.95 6.46
1646 5757 5.488645 TCACACATATGCAATGCTACTTG 57.511 39.130 6.82 1.82 0.00 3.16
1648 5759 5.370679 TCATCACACATATGCAATGCTACT 58.629 37.500 6.82 0.00 0.00 2.57
1651 5834 4.022329 CCATCATCACACATATGCAATGCT 60.022 41.667 6.82 0.00 0.00 3.79
1671 5854 1.135094 AGATCAATCAGACCGGCCAT 58.865 50.000 0.00 0.00 0.00 4.40
1675 5858 1.137675 TGCTCAGATCAATCAGACCGG 59.862 52.381 0.00 0.00 0.00 5.28
1742 5925 3.626996 TTGCTCATCCCCTGTGCCG 62.627 63.158 0.00 0.00 42.41 5.69
1749 5932 2.012902 GCATGTGCTTGCTCATCCCC 62.013 60.000 7.13 0.00 39.57 4.81
1884 6067 1.272490 ACCTGATCGAGCTCGTCAAAA 59.728 47.619 33.33 16.27 40.80 2.44
1938 6121 2.812499 CCGATGGTGTAGACGGGG 59.188 66.667 0.00 0.00 41.41 5.73
1981 6164 3.195698 GCCGCCGTCAGGAATCAC 61.196 66.667 0.00 0.00 41.02 3.06
1984 6167 2.114670 CATTGCCGCCGTCAGGAAT 61.115 57.895 0.00 0.00 41.02 3.01
2022 6208 0.983905 TCCAAAGGCTGGGGCGTATA 60.984 55.000 5.71 0.00 46.44 1.47
2052 6238 0.248843 GGAGCCACTCAAGACAGGAG 59.751 60.000 0.00 0.00 38.36 3.69
2086 6272 0.244450 TTGACATACACGACGGACCC 59.756 55.000 0.00 0.00 0.00 4.46
2094 6280 2.030457 GCTCCCGAAATTGACATACACG 59.970 50.000 0.00 0.00 0.00 4.49
2106 6292 0.693622 TGGTGGTTATGCTCCCGAAA 59.306 50.000 0.00 0.00 0.00 3.46
2184 6370 3.334691 GTCATTCCTCACGATCCACAAA 58.665 45.455 0.00 0.00 0.00 2.83
2208 6394 2.045926 GCGGCATCACCCTTCACT 60.046 61.111 0.00 0.00 33.26 3.41
2286 6472 1.597854 CAGCACCGCCTCTTGTTCA 60.598 57.895 0.00 0.00 0.00 3.18
2426 6612 0.669318 CCACTCCACACACGCGTAAT 60.669 55.000 13.44 0.00 0.00 1.89
2473 6659 4.373116 GACCACCTCTCGGCGCAA 62.373 66.667 10.83 0.00 0.00 4.85
2645 6834 2.359967 GCACTCTTAGGGGCGGTCT 61.360 63.158 0.00 0.00 0.00 3.85
2653 6842 4.698575 GAATTCTACCCAGCACTCTTAGG 58.301 47.826 0.00 0.00 0.00 2.69
2660 6849 2.396590 TTCCGAATTCTACCCAGCAC 57.603 50.000 3.52 0.00 0.00 4.40
2717 6906 4.379186 CCATGCAGAAACTCAGATTCACAC 60.379 45.833 0.00 0.00 0.00 3.82
2725 6914 2.775890 ACAGTCCATGCAGAAACTCAG 58.224 47.619 0.00 0.00 0.00 3.35
2773 6966 2.756760 ACCAAACAATGCTAGCCTCATG 59.243 45.455 13.29 8.32 0.00 3.07
2821 7016 4.215109 ACATTGTTTCCCTAGCACAAAGT 58.785 39.130 0.00 0.00 34.19 2.66
2823 7018 5.596845 GAAACATTGTTTCCCTAGCACAAA 58.403 37.500 25.25 0.00 34.19 2.83
2829 7024 2.159572 CGGCGAAACATTGTTTCCCTAG 60.160 50.000 27.95 18.46 0.00 3.02
2830 7025 1.807742 CGGCGAAACATTGTTTCCCTA 59.192 47.619 27.95 0.00 0.00 3.53
2831 7026 0.596082 CGGCGAAACATTGTTTCCCT 59.404 50.000 27.95 4.17 0.00 4.20
2832 7027 0.594110 TCGGCGAAACATTGTTTCCC 59.406 50.000 27.95 26.27 0.00 3.97
2835 7030 3.634568 TGATTCGGCGAAACATTGTTT 57.365 38.095 27.40 14.42 0.00 2.83
2837 7032 4.261155 CCATATGATTCGGCGAAACATTGT 60.261 41.667 37.85 27.34 36.64 2.71
2842 7037 2.096909 CGACCATATGATTCGGCGAAAC 60.097 50.000 27.40 23.98 0.00 2.78
2905 7114 9.826574 ACGTAGCCATATTCTTTTCAAAGTATA 57.173 29.630 0.00 0.94 37.31 1.47
2929 7138 2.031595 CCTCTCCATCGACTGATACACG 60.032 54.545 0.00 0.00 32.18 4.49
2930 7139 2.287909 GCCTCTCCATCGACTGATACAC 60.288 54.545 0.00 0.00 32.18 2.90
2931 7140 1.957177 GCCTCTCCATCGACTGATACA 59.043 52.381 0.00 0.00 32.18 2.29
2950 7159 2.033602 AAGGTACACCCGCCTTGC 59.966 61.111 0.00 0.00 42.90 4.01
2951 7160 0.036306 AAGAAGGTACACCCGCCTTG 59.964 55.000 0.11 0.00 44.37 3.61
2956 7165 1.621814 TCCTGAAAGAAGGTACACCCG 59.378 52.381 0.00 0.00 38.58 5.28
2958 7167 4.024302 CGTTTTCCTGAAAGAAGGTACACC 60.024 45.833 0.00 0.00 38.58 4.16
2989 7198 5.653769 TCTGAAAAATTCTGCCCCTAGAATG 59.346 40.000 0.00 0.00 44.43 2.67
3031 7299 9.706691 TGGTGAGATCGTAGGATAAAATAAATC 57.293 33.333 0.00 0.00 31.51 2.17
3040 7308 4.344102 CCCTTTTGGTGAGATCGTAGGATA 59.656 45.833 0.00 0.00 38.10 2.59
3041 7309 3.134804 CCCTTTTGGTGAGATCGTAGGAT 59.865 47.826 0.00 0.00 38.10 3.24
3044 7312 2.280628 GCCCTTTTGGTGAGATCGTAG 58.719 52.381 0.00 0.00 38.10 3.51
3057 7363 5.196695 GACCAGAATAGAATCTGCCCTTTT 58.803 41.667 0.00 0.00 44.43 2.27
3077 7383 4.195416 GAGAAGAGATTTGTGGGATGACC 58.805 47.826 0.00 0.00 40.81 4.02
3081 7387 4.386088 CCCATGAGAAGAGATTTGTGGGAT 60.386 45.833 0.85 0.00 46.26 3.85
3082 7388 3.054139 CCCATGAGAAGAGATTTGTGGGA 60.054 47.826 0.85 0.00 46.26 4.37
3090 7396 2.048601 CTGGCTCCCATGAGAAGAGAT 58.951 52.381 0.00 0.00 41.42 2.75
3115 7422 2.123640 GGAGGAGGCTAGTCCGCT 60.124 66.667 3.66 0.00 42.05 5.52
3188 7520 2.205074 CACCGATAATCAGACCAGCAC 58.795 52.381 0.00 0.00 0.00 4.40
3192 7524 1.407618 CGACCACCGATAATCAGACCA 59.592 52.381 0.00 0.00 41.76 4.02
3247 7589 7.329588 ACGGATAAAAATTTGGACCTATGTC 57.670 36.000 0.00 0.00 40.98 3.06
3251 7593 8.866970 ACTTTACGGATAAAAATTTGGACCTA 57.133 30.769 0.00 0.00 29.82 3.08
3344 7695 1.134280 ACCATGATGAGCTTCCCTTCG 60.134 52.381 0.00 0.00 0.00 3.79
3376 7882 4.402155 TGGATAATTTTCACACAGATGGGC 59.598 41.667 0.00 0.00 0.00 5.36
3377 7883 6.528537 TTGGATAATTTTCACACAGATGGG 57.471 37.500 0.00 0.00 0.00 4.00
3420 7926 7.925703 TGTTAGTTACTCTTCTGAAACTTCG 57.074 36.000 0.00 0.00 34.23 3.79
3441 7947 5.417811 TCTGAAACAACATGTGCATTTGTT 58.582 33.333 0.00 2.72 43.61 2.83
3443 7949 5.970140 TTCTGAAACAACATGTGCATTTG 57.030 34.783 0.00 0.00 0.00 2.32
3444 7950 6.050432 ACATTCTGAAACAACATGTGCATTT 58.950 32.000 0.00 0.06 0.00 2.32
3452 7958 5.473162 TCGGATGAACATTCTGAAACAACAT 59.527 36.000 0.00 0.00 0.00 2.71
3505 8011 6.472686 TTCTTCCTCAGAACTTCCTATAGC 57.527 41.667 0.00 0.00 36.51 2.97
3510 8016 5.545723 TCAGATTTCTTCCTCAGAACTTCCT 59.454 40.000 0.00 0.00 41.56 3.36
3514 8020 4.323409 GCCTCAGATTTCTTCCTCAGAACT 60.323 45.833 0.00 0.00 41.56 3.01
3516 8022 3.584406 TGCCTCAGATTTCTTCCTCAGAA 59.416 43.478 0.00 0.00 39.99 3.02
3518 8024 3.623906 TGCCTCAGATTTCTTCCTCAG 57.376 47.619 0.00 0.00 0.00 3.35
3544 8050 1.550976 AGTTAGTCCACTAGCACTGGC 59.449 52.381 3.74 0.00 41.61 4.85
3552 8058 8.334734 AGTCTATACTTCCAAGTTAGTCCACTA 58.665 37.037 0.00 0.00 40.37 2.74
3559 8065 6.531948 GTGTGCAGTCTATACTTCCAAGTTAG 59.468 42.308 0.00 0.97 40.37 2.34
3566 8072 4.720649 TCTGTGTGCAGTCTATACTTCC 57.279 45.455 0.00 0.00 43.05 3.46
3570 8076 8.543774 GTGATTTATTCTGTGTGCAGTCTATAC 58.456 37.037 0.00 0.00 43.05 1.47
3571 8077 8.478066 AGTGATTTATTCTGTGTGCAGTCTATA 58.522 33.333 0.00 0.00 43.05 1.31
3577 8083 4.409570 GCAGTGATTTATTCTGTGTGCAG 58.590 43.478 0.00 0.00 43.87 4.41
3582 8088 5.185454 TGGTAGGCAGTGATTTATTCTGTG 58.815 41.667 0.00 0.00 0.00 3.66
3607 8114 4.881850 GGTACCATAACTAGCACTTGCAAT 59.118 41.667 7.15 0.00 45.16 3.56
3613 8120 6.349300 CAAATGAGGTACCATAACTAGCACT 58.651 40.000 15.94 0.00 0.00 4.40
3620 8127 7.100458 AGAATTGCAAATGAGGTACCATAAC 57.900 36.000 15.94 3.14 0.00 1.89
3623 8130 5.716228 TGAAGAATTGCAAATGAGGTACCAT 59.284 36.000 15.94 0.00 0.00 3.55
3625 8132 5.183904 ACTGAAGAATTGCAAATGAGGTACC 59.816 40.000 1.71 2.73 0.00 3.34
3626 8133 6.150140 AGACTGAAGAATTGCAAATGAGGTAC 59.850 38.462 1.71 0.00 0.00 3.34
3655 8162 2.279502 TACGCGAGGTCCACATGAGC 62.280 60.000 15.93 0.00 41.93 4.26
3683 8190 6.992123 GTCCCTTTTTCTTTCAACCATTTCAT 59.008 34.615 0.00 0.00 0.00 2.57
3721 8229 9.836864 ACATTACACATGTACATCATAGATGTT 57.163 29.630 16.75 1.52 34.67 2.71


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

AutoCloner maintained by Alex Coulton.