Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017741.1 Corchorus olitorius cultivar O-4 contig17774, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 56936
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Found at i:2987 original size:6 final size:6
Alignment explanation
Indices: 2971--3018 Score: 87
Period size: 6 Copynumber: 7.8 Consensus size: 6
2961 GTTCCCATTC
2971 GAAAGAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAA
1 GAAA-AA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAA
3019 CTTGGCCTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
6 37 0.90
7 4 0.10
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:4726 original size:36 final size:35
Alignment explanation
Indices: 4671--5421 Score: 689
Period size: 36 Copynumber: 21.4 Consensus size: 35
4661 GTTGCTAAAT
* *
4671 TTTATTTTAGTTAATCCAGGGCGATCTTCTCTTCAG
1 TTTATTTCAGTTGATCCAGGGCGATCTT-TCTTCAG
* * * *
4707 TTTATTTCAGTTGACCCAGGGCGGTTTTTCTTCAA
1 TTTATTTCAGTTGATCCAGGGCGATCTTTCTTCAG
* *
4742 TTTACTTCAGTTGATCCAGGGCGATCTTCTCTCCAG
1 TTTATTTCAGTTGATCCAGGGCGATCTT-TCTTCAG
* * *
4778 TTTATATCAGTCGATCCAAGGCGATCTTCTCTTCAG
1 TTTATTTCAGTTGATCCAGGGCGATCTT-TCTTCAG
*
4814 TTTATTTCAATTGATCCAGGGCGATCTTCTCTTCAG
1 TTTATTTCAGTTGATCCAGGGCGATCTT-TCTTCAG
* * *
4850 TTTATTTTAATTGATCTAGGGCGATCTTTTCTTCAG
1 TTTATTTCAGTTGATCCAGGGCGATC-TTTCTTCAG
* *
4886 TTTATTTCAGTTGATCCA-TGCGATCTTTATTCAG
1 TTTATTTCAGTTGATCCAGGGCGATCTTTCTTCAG
* * * * * *
4920 TTTATTTTAGTTG-CCCAGGGCGGTCCTTCGTCAA
1 TTTATTTCAGTTGATCCAGGGCGATCTTTCTTCAG
* * * * * *
4954 TTTATTTTAATCGACCCAGGGCGGTCTTTCTTCAC
1 TTTATTTCAGTTGATCCAGGGCGATCTTTCTTCAG
* *
4989 TTTATTTCAGTTGATCCAGGGTGATCTTTCTTTAG
1 TTTATTTCAGTTGATCCAGGGCGATCTTTCTTCAG
* * *
5024 TTTATTTCAATTAATCCAGGGTGATC-TTCATTCAG
1 TTTATTTCAGTTGATCCAGGGCGATCTTTC-TTCAG
* * * * *
5059 TTTATGTCAGTTGATCCAGGGTGATCTCTCCTCAA
1 TTTATTTCAGTTGATCCAGGGCGATCTTTCTTCAG
* * *
5094 TTTACTTC-GCTTGATCCAGGGCGATCTTTTATTCAA
1 TTTATTTCAG-TTGATCCAGGGCGATC-TTTCTTCAG
* * *
5130 TTTATTTTAGTCGATCCAGGGCGATCTTTCCTTCAA
1 TTTATTTCAGTTGATCCAGGGCGATCTTT-CTTCAG
* * * *
5166 TTTATTTTAGTTGACCCAGGGCGGTCATTCTTCAAG
1 TTTATTTCAGTTGATCCAGGGCGATCTTTCTTC-AG
* * *
5202 -TTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAA
1 TTTATTTCAGTTGATCCAGGGCGATCTTTCTTCAG
* * *
5236 TTCATTTCAATTGATCCAGGGCGATCTTACTTCAAG
1 TTTATTTCAGTTGATCCAGGGCGATCTTTCTTC-AG
*
5272 -TTATTTTAGTTGATCCAGGGCGATCTTT-TTCAG
1 TTTATTTCAGTTGATCCAGGGCGATCTTTCTTCAG
* * * *
5305 TTTA---C--TTGACCCAGGGCGATTTTTTCTTTAA
1 TTTATTTCAGTTGATCCAGGGCGA-TCTTTCTTCAG
* * *
5336 TTTATTTCAATGGATCCAGGGCAATCTTTTCTTCAG
1 TTTATTTCAGTTGATCCAGGGCGATC-TTTCTTCAG
* * *
5372 TTTATTTCAATTGATCCAGGGTGATCTTTTTTGCAG
1 TTTATTTCAGTTGATCCAGGGCGATCTTTCTT-CAG
*
5408 TTTATTTCAATTGA
1 TTTATTTCAGTTGA
5422 CCGCAAATTG
Statistics
Matches: 591, Mismatches: 101, Indels: 46
0.80 0.14 0.06
Matches are distributed among these distances:
29 13 0.02
30 4 0.01
31 7 0.01
33 5 0.01
34 53 0.09
35 250 0.42
36 256 0.43
37 3 0.01
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (35 bp):
TTTATTTCAGTTGATCCAGGGCGATCTTTCTTCAG
Found at i:5186 original size:247 final size:246
Alignment explanation
Indices: 4671--5423 Score: 795
Period size: 247 Copynumber: 3.1 Consensus size: 246
4661 GTTGCTAAAT
* * * * * *
4671 TTTATTTTAGTTAATCCAGGGCGATCTTCTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTTTTT
1 TTTATTTTAGTTGACCCAGGGCGGTCAT-TCTTCAATTTATTTCAGTTGACCCAGGGCGGTCTTT
* ** * * *
4736 CTTCAATTTACTTCAGTTGATCCAGGGCGATCTTCTCTCCAGTTTATATCAGTCGATCCAAGGCG
65 CTTCAATTTATTTCAGTTGATCCAGGGCGATCTT-TCTTAAGTTTATTTCAGTTGATCCAGGGCG
* * * * * *
4801 ATCTTCTCTTCAGTTTATTTCAATTGATCCAGGGCGATCTTCTCTTCAGTTTATTTTAATTGATC
129 ATCTTC-ATTCAGTTTATGTCAATTGATCCAGGGCGATCTTCTCCTCAATTTACTTCAATTGATC
* * * * * *
4866 TAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGATCCATGCGATCTTTATTCAG
193 CAGGGCGATCTTTTATTCAATTTATTTCAGTCGATCCAGGCGATCTTTATTCAA
* * * * *
4920 TTTATTTTAGTTG-CCCAGGGCGGTCCTTCGTCAATTTATTTTAATCGACCCAGGGCGGTCTTTC
1 TTTATTTTAGTTGACCCAGGGCGGTCATTCTTCAATTTATTTCAGTTGACCCAGGGCGGTCTTTC
* * * * * *
4984 TTCACTTTATTTCAGTTGATCCAGGGTGATCTTTCTTTAGTTTATTTCAATTAATCCAGGGTGAT
66 TTCAATTTATTTCAGTTGATCCAGGGCGATCTTTCTTAAGTTTATTTCAGTTGATCCAGGGCGAT
* * **
5049 CTTCATTCAGTTTATGTCAGTTGATCCAGGGTGATC-TCTCCTCAATTTACTTCGCTTGATCCAG
131 CTTCATTCAGTTTATGTCAATTGATCCAGGGCGATCTTCTCCTCAATTTACTTCAATTGATCCAG
* *
5113 GGCGATCTTTTATTCAATTTATTTTAGTCGATCCAGGGCGATCTTTCCTTCAA
196 GGCGATCTTTTATTCAATTTATTTCAGTCGATCCA-GGCGATCTTT-ATTCAA
*
5166 TTTATTTTAGTTGACCCAGGGCGGTCATTCTTCAAGTTATTTCAGTTGACCCAGGGCGGTCTTTC
1 TTTATTTTAGTTGACCCAGGGCGGTCATTCTTCAATTTATTTCAGTTGACCCAGGGCGGTCTTTC
* * * *
5231 TTCAATTCATTTCAATTGATCCAGGGCGATCTTACTTCAAG-TTATTTTAGTTGATCCAGGGCGA
66 TTCAATTTATTTCAGTTGATCCAGGGCGATCTTTCTT-AAGTTTATTTCAGTTGATCCAGGGCGA
* * * * * * * *
5295 TCTT-TTTCAGTTTA---C--TTGACCCAGGGCGATTTTTTCTTTAATTTATTTCAATGGATCCA
130 TCTTCATTCAGTTTATGTCAATTGATCCAGGGCGATCTTCTCCTCAATTTACTTCAATTGATCCA
* * * * * * * *
5354 GGGCAATCTTTTCTTCAGTTTATTTCAATTGATCCAGGGTGATCTTTTTTGCAG
195 GGGCGATCTTTTATTCAATTTATTTCAGTCGATCCA-GGCGATCTTTATT-CAA
* *
5408 TTTATTTCAATTGACC
1 TTTATTTTAGTTGACC
5424 GCAAATTGGT
Statistics
Matches: 421, Mismatches: 77, Indels: 19
0.81 0.15 0.04
Matches are distributed among these distances:
241 15 0.04
242 76 0.18
243 1 0.00
244 52 0.12
245 37 0.09
246 54 0.13
247 161 0.38
248 13 0.03
249 12 0.03
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (246 bp):
TTTATTTTAGTTGACCCAGGGCGGTCATTCTTCAATTTATTTCAGTTGACCCAGGGCGGTCTTTC
TTCAATTTATTTCAGTTGATCCAGGGCGATCTTTCTTAAGTTTATTTCAGTTGATCCAGGGCGAT
CTTCATTCAGTTTATGTCAATTGATCCAGGGCGATCTTCTCCTCAATTTACTTCAATTGATCCAG
GGCGATCTTTTATTCAATTTATTTCAGTCGATCCAGGCGATCTTTATTCAA
Found at i:5318 original size:29 final size:28
Alignment explanation
Indices: 5276--5330 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
5266 TTCAAGTTAT
* *
5276 TTTAGTTGATCCAGGGCGATCTTTTTCAG
1 TTTACTTGACCCAGGGCGAT-TTTTTCAG
5305 TTTACTTGACCCAGGGCGATTTTTTC
1 TTTACTTGACCCAGGGCGATTTTTTC
5331 TTTAATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.16, C:0.20, G:0.22, T:0.42
Consensus pattern (28 bp):
TTTACTTGACCCAGGGCGATTTTTTCAG
Found at i:5887 original size:30 final size:30
Alignment explanation
Indices: 5836--6277 Score: 455
Period size: 30 Copynumber: 14.4 Consensus size: 30
5826 ATCATTGCAC
* **
5836 CATTGCTTCATTTCGATCCTGGTTTAGGAT
1 CATTGCTTTATTTTAATCCTGGTTTAGGAT
* * *
5866 CATTACTTTATTTAAATCCTGGTTGAGGATATTTGCTT
1 CATTGCTTTATTTTAATCCTGGTTTAGG--A------T
*
5904 CATTGCTTTGTTTTAATCCT-GTTTGAGGAT
1 CATTGCTTTATTTTAATCCTGGTTT-AGGAT
* *
5934 CGTTGCTTTATTTCAATCCT-GTTTGAGGAT
1 CATTGCTTTATTTTAATCCTGGTTT-AGGAT
* *
5964 CGTTGCTTTGTTTTAATCCT-GTTTGAGGAT
1 CATTGCTTTATTTTAATCCTGGTTT-AGGAT
* *
5994 CATTGTTTTATTTTAATCCTGGTTGAGGAT
1 CATTGCTTTATTTTAATCCTGGTTTAGGAT
*
6024 CGTTGCTTTATTTTAATCCT-GTTTGAGGAT
1 CATTGCTTTATTTTAATCCTGGTTT-AGGAT
6054 CATTGCTTTATTTTAATCCT-GTTTGAGGAT
1 CATTGCTTTATTTTAATCCTGGTTT-AGGAT
6084 CATTGCTTTATTTTAATCCT-GTTTGAGGAT
1 CATTGCTTTATTTTAATCCTGGTTT-AGGAT
* * * *
6114 CCTTACTTTATTTTAATCCTAGTTGAGGAT
1 CATTGCTTTATTTTAATCCTGGTTTAGGAT
* * *
6144 CGTTGCTTTATTTTAATCCTGGTTGAGGAC
1 CATTGCTTTATTTTAATCCTGGTTTAGGAT
* *
6174 CATCGCTTTATTTTTTAATCCTGATTTAGGAT
1 CATTGCTTTA--TTTTAATCCTGGTTTAGGAT
*
6206 CATTGGTTTATTTTAATCCTGGTTTAGGAT
1 CATTGCTTTATTTTAATCCTGGTTTAGGAT
* *
6236 CATTGTTTTATTTTAATCCTGGTTGAGGAT
1 CATTGCTTTATTTTAATCCTGGTTTAGGAT
*
6266 AATTGCTTTATT
1 CATTGCTTTATT
6278 GCTTTGTTTT
Statistics
Matches: 357, Mismatches: 41, Indels: 28
0.84 0.10 0.07
Matches are distributed among these distances:
29 3 0.01
30 297 0.83
31 6 0.02
32 26 0.07
36 1 0.00
37 3 0.01
38 21 0.06
ACGTcount: A:0.19, C:0.14, G:0.18, T:0.49
Consensus pattern (30 bp):
CATTGCTTTATTTTAATCCTGGTTTAGGAT
Found at i:5940 original size:38 final size:38
Alignment explanation
Indices: 5865--5941 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
5855 TGGTTTAGGA
*
5865 TCATTACTTTATTTAAATCCTGGTTGAGGATATTTGCT
1 TCATTACTTTATTTAAATCCTGGTTGAGGATAGTTGCT
* * * * *
5903 TCATTGCTTTGTTTTAATCCTGTTTGAGGATCGTTGCT
1 TCATTACTTTATTTAAATCCTGGTTGAGGATAGTTGCT
5941 T
1 T
5942 TATTTCAATC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.18, C:0.14, G:0.18, T:0.49
Consensus pattern (38 bp):
TCATTACTTTATTTAAATCCTGGTTGAGGATAGTTGCT
Found at i:6004 original size:60 final size:60
Alignment explanation
Indices: 5903--7170 Score: 809
Period size: 60 Copynumber: 21.1 Consensus size: 60
5893 GATATTTGCT
* * *
5903 TCATTGCTTTGTTTTAATCCTGTTTGAGGATCGTTGCTTTATTTCAATCCTGTTTGAGGA
1 TCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGA
* * * *
5963 TCGTTGCTTTGTTTTAATCCTGTTTGAGGATCATTGTTTTATTTTAATCCTGGTTGAGGA
1 TCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGA
*
6023 TCGTTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGA
1 TCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGA
* *
6083 TCATTGCTTTATTTTAATCCTGTTTGAGGATCCTTACTTTATTTTAATCCTAG-TTGAGGA
1 TCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCCT-GTTTGAGGA
* * * *
6143 TCGTTGCTTTATTTTAATCCTGGTTGAGGACCATCGCTTTATTTTTTAATCCTGATTT-AGGA
1 TCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTA--TTTTAATCCTG-TTTGAGGA
* * *
6205 TCATTGGTTTATTTTAATCCTGGTTT-AGGATCATTGTTTTATTTTAATCCTGGTTGAGGA
1 TCATTGCTTTATTTTAATCCT-GTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGA
* * * ** * * * *
6265 TAATTGCTTTATTGCT--T--TGTTTTA--ATCA-TG-TTTGAGGATCATTGCTCTATTTTA--A
1 TCATTGCTTTATT-TTAATCCTGTTTGAGGATCATTGCTTT-A-TTTTAAT-C-CTGTTTGAGGA
* * * ***** * **** * * * *** * **
6320 TC-CTGGTTGAGGACCATCGCTTTATTTTTTAATC-CTGGTTAAGGATCAT--TGCTTT-A-TT
1 TCATTGCTTTATTTTAATC-C--TGTTTGAGGATCATTGCTTTATTTTAATCCTG-TTTGAGGA
* * * * * *** * * *** * * **
6378 TTAAT-CCTGA-TTTAGGATCATTGCTTT-ATTTTAATCCTGGTTTAGGATCAT--TGTTTTATT
1 TCATTGCTTTATTTTA--ATC-CTG-TTTGAGGATCAT--TGCTTTATTTTAATCCTGTTTGAGG
*
6438 T
60 A
* * * *** * * *
6439 TAATCCTGGTTGAGGATCAT--TGCTT-----T-ATTGCTCTATTTTAATCCTGTTTGAGGA
1 TCAT--TGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGA
* * * * * *
6493 TCATTGCTCTATTTTTATCCTGGTTGAGGAT-ATTTGCTATATGTTAATCCTGGCTT-AGGA
1 TCATTGCTTTATTTTAATCCTGTTTGAGGATCA-TTGCTTTATTTTAATCCT-GTTTGAGGA
* * *
6553 TCATTACTTCATTTTAATCCTGTTTGAGGATCATTGTTTTATTTTAATCCTAG-TTGAGGA
1 TCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCCT-GTTTGAGGA
* * *
6613 TCGTTGCTTTATTTTAATCCTGTTTGAGGATCATTGTTTTATTTTAATCCTGATTGAGGA
1 TCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGA
*
6673 TCGTTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGA
1 TCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGA
* * *
6733 TTC-TTGCTTTATTTTAATCCTGGTTGAGGATCGTTGCTTTATTTTAATCCTGGTTGAGGA
1 -TCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGA
* * * *
6793 CCATCGCTTTATTTTTTAATCCTGGTTAAGGATCATTGCTTTATTTTAATCCTGATTT-AGGA
1 TCATTGCTTTA--TTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTG-TTTGAGGA
* *
6855 TCATTGGTTTATTTTAATCCTGGTTT-AGGATCATTGCTTTATTTTAATCCTGGTTGAGGATAA
1 TCATTGCTTTATTTTAATCCT-GTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGG---A
* * * *
6918 TTGCTTTATTGCTTTGTTTTAATCCTGTTTGAGGATCATTGCTCTATTTTTATCCTGGTTGAGGA
1 -T-C---ATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGA
* * * * * * *
6983 T-ATTTGCTATATGTTAATCCTGGCTT-AGGATCATTACTTCATTTTAATCATGTTTTAGGA
1 TCA-TTGCTTTATTTTAATCCT-GTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGA
* * * * * *
7043 TCATTGCTTCATTTTTAATCATGTTTGATGATCATTGCTTCATTTTAATCCCGTTTTAGGA
1 TCATTGCTTTA-TTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGA
* * * *
7104 TCATTGCTTCATTTTAATCCTGGTTGAGGATCATTGCTTTATTTTAATCCAGCTT-AGGA
1 TCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGA
*
7163 TCACTGCT
1 TCATTGCT
7171 CCATCAGTTA
Statistics
Matches: 977, Mismatches: 157, Indels: 149
0.76 0.12 0.12
Matches are distributed among these distances:
52 15 0.02
53 3 0.00
54 23 0.02
55 11 0.01
56 5 0.01
57 12 0.01
58 10 0.01
59 32 0.03
60 620 0.63
61 71 0.07
62 102 0.10
63 13 0.01
64 5 0.01
65 3 0.00
67 4 0.00
68 48 0.05
ACGTcount: A:0.20, C:0.14, G:0.18, T:0.48
Consensus pattern (60 bp):
TCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGA
Found at i:6060 original size:90 final size:90
Alignment explanation
Indices: 5903--7170 Score: 814
Period size: 90 Copynumber: 14.1 Consensus size: 90
5893 GATATTTGCT
* * * *
5903 TCATTGCTTTGTTTTAATCCTGTTTGAGGATCGTTGCTTTATTTCAATCCTGTTTGAGGATCGTT
1 TCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATCATT
* *
5968 GCTTTGTTTTAATCCTGTTTGAGGA
66 GCTTTATTTTAATCCTGGTTGAGGA
* * *
5993 TCATTGTTTTATTTTAATCCTGGTTGAGGATCGTTGCTTTATTTTAATCCTGTTTGAGGATCATT
1 TCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATCATT
*
6058 GCTTTATTTTAATCCTGTTTGAGGA
66 GCTTTATTTTAATCCTGGTTGAGGA
* * *
6083 TCATTGCTTTATTTTAATCCTGTTTGAGGATCCTTACTTTATTTTAATCCTAG-TTGAGGATCGT
1 TCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCCT-GTTTGAGGATCAT
6147 TGCTTTATTTTAATCCTGGTTGAGGA
65 TGCTTTATTTTAATCCTGGTTGAGGA
* * *
6173 CCATCGCTTTATTTTTTAATCCTGATTT-AGGATCATTGGTTTATTTTAATCCTGGTTT-AGGAT
1 TCATTGCTTTA--TTTTAATCCTG-TTTGAGGATCATTGCTTTATTTTAATCCT-GTTTGAGGAT
*
6236 CATTGTTTTATTTTAATCCTGGTTGAGGA
62 CATTGCTTTATTTTAATCCTGGTTGAGGA
* * * ** * * * *
6265 TAATTGCTTTATTGCT--T--TGTTTTA--ATCA-TG-TTTGAGGATCATTGCTCTATTTTA--A
1 TCATTGCTTTATT-TTAATCCTGTTTGAGGATCATTGCTTT-A-TTTTAAT-C-CTGTTTGAGGA
* * * ***** ** ****
6320 TC-CTGGTTGAGGACCATCGCTTTATTTTTTAA
61 TCATTGCTTTATTTTAATC-C--TGGTTGAGGA
* * * *** * ** * * * * * ***
6352 TC-CTGGTTAAGGATCAT--TGCTTT-A-TTTTAAT-CCTGA-TTTAGGATCATTGCTTT-ATTT
1 TCATTGCTTTATTTTAATCCTG-TTTGAGGATCATTGCTTTATTTTA--ATC-CTG-TTTGAGGA
* * *** * * * ***
6409 TAATCCTGGTTTAGGATCAT--TGTTTTATTT
61 TCAT--TGCTTTATTTTAATCCTGGTTGAGGA
* * * *** * * *
6439 TAATCCTGGTTGAGGATCAT--TGCTT-----T-ATTGCTCTATTTTAATCCTGTTTGAGGATCA
1 TCAT--TGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATCA
* *
6496 TTGCTCTATTTTTATCCTGGTTGAGGA
64 TTGCTTTATTTTAATCCTGGTTGAGGA
* * * * *
6523 T-ATTTGCTATATGTTAATCCTGGCTT-AGGATCATTACTTCATTTTAATCCTGTTTGAGGATCA
1 TCA-TTGCTTTATTTTAATCCT-GTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATCA
* *
6586 TTGTTTTATTTTAATCCTAGTTGAGGA
64 TTGCTTTATTTTAATCCTGGTTGAGGA
* * * *
6613 TCGTTGCTTTATTTTAATCCTGTTTGAGGATCATTGTTTTATTTTAATCCTGATTGAGGATCGTT
1 TCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATCATT
*
6678 GCTTTATTTTAATCCTGTTTGAGGA
66 GCTTTATTTTAATCCTGGTTGAGGA
* *
6703 TCATTGCTTTATTTTAATCCTGTTTGAGGATTC-TTGCTTTATTTTAATCCTGGTTGAGGATCGT
1 TCATTGCTTTATTTTAATCCTGTTTGAGGA-TCATTGCTTTATTTTAATCCTGTTTGAGGATCAT
6767 TGCTTTATTTTAATCCTGGTTGAGGA
65 TGCTTTATTTTAATCCTGGTTGAGGA
* * * *
6793 CCATCGCTTTATTTTTTAATCCTGGTTAAGGATCATTGCTTTATTTTAATCCTGATTT-AGGATC
1 TCATTGCTTTA--TTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTG-TTTGAGGATC
* *
6857 ATTGGTTTATTTTAATCCTGGTTTAGGA
63 ATTGCTTTATTTTAATCCTGGTTGAGGA
* *
6885 TCATTGCTTTATTTTAATCCTGGTTGAGGATAATTGCTTTATTGCTTTGTTTTAATCCTGTTTGA
1 TCATTGCTTTATTTTAATCCTGTTTGAGG---A-T-C---ATTGCTTTATTTTAATCCTGTTTGA
* *
6950 GGATCATTGCTCTATTTTTATCCTGGTTGAGGA
58 GGATCATTGCTTTATTTTAATCCTGGTTGAGGA
* * * * * * *
6983 T-ATTTGCTATATGTTAATCCTGGCTT-AGGATCATTACTTCATTTTAATCATGTTTTAGGATCA
1 TCA-TTGCTTTATTTTAATCCT-GTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATCA
* * * *
7046 TTGCTTCATTTTTAATCATGTTTGATGA
64 TTGCTTTA-TTTTAATCCTGGTTGAGGA
* * * * *
7074 TCATTGCTTCATTTTAATCCCGTTTTAGGATCATTGCTTCATTTTAATCCTGGTTGAGGATCATT
1 TCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATCATT
* *
7139 GCTTTATTTTAATCCAGCTT-AGGA
66 GCTTTATTTTAATCCTGGTTGAGGA
*
7163 TCACTGCT
1 TCATTGCT
7171 CCATCAGTTA
Statistics
Matches: 944, Mismatches: 167, Indels: 135
0.76 0.13 0.11
Matches are distributed among these distances:
82 16 0.02
83 7 0.01
84 25 0.03
85 21 0.02
86 17 0.02
87 29 0.03
88 10 0.01
89 20 0.02
90 471 0.50
91 76 0.08
92 163 0.17
93 9 0.01
94 2 0.00
95 2 0.00
97 4 0.00
98 69 0.07
99 3 0.00
ACGTcount: A:0.20, C:0.14, G:0.18, T:0.48
Consensus pattern (90 bp):
TCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATCATT
GCTTTATTTTAATCCTGGTTGAGGA
Found at i:6300 original size:38 final size:38
Alignment explanation
Indices: 6237--6315 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 38
6227 GTTTAGGATC
* * *
6237 ATTGTTTTATTTTAATCCTGGTTGAGGATAATTGCTTT
1 ATTGCTTTATTTTAATCATGGTTGAGGATAATTGCTCT
* * *
6275 ATTGCTTTGTTTTAATCATGTTTGAGGATCATTGCTCT
1 ATTGCTTTATTTTAATCATGGTTGAGGATAATTGCTCT
6313 ATT
1 ATT
6316 TTAATCCTGG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.20, C:0.10, G:0.18, T:0.52
Consensus pattern (38 bp):
ATTGCTTTATTTTAATCATGGTTGAGGATAATTGCTCT
Found at i:6318 original size:30 final size:30
Alignment explanation
Indices: 6275--7170 Score: 950
Period size: 30 Copynumber: 29.2 Consensus size: 30
6265 TAATTGCTTT
* *
6275 ATTGCTTTGTTTTAATCATGTTTGAGGATC
1 ATTGCTTTATTTTAATCCTGTTTGAGGATC
* * *
6305 ATTGCTCTATTTTAATCCTGGTTGAGGACC
1 ATTGCTTTATTTTAATCCTGTTTGAGGATC
* * *
6335 ATCGCTTTATTTTTTAATCCTGGTTAAGGATC
1 ATTGCTTTA--TTTTAATCCTGTTTGAGGATC
6367 ATTGCTTTATTTTAATCCTGATTT-AGGATC
1 ATTGCTTTATTTTAATCCTG-TTTGAGGATC
6397 ATTGCTTTATTTTAATCCTGGTTT-AGGATC
1 ATTGCTTTATTTTAATCCT-GTTTGAGGATC
* *
6427 ATTGTTTTATTTTAATCCTGGTTGAGGATC
1 ATTGCTTTATTTTAATCCTGTTTGAGGATC
6457 ATTGCTTTATTGCTCTATTTTAATCCTGTTTGAGGATC
1 ATTGC-----T--T-TATTTTAATCCTGTTTGAGGATC
* * *
6495 ATTGCTCTATTTTTATCCTGGTTGAGGAT-
1 ATTGCTTTATTTTAATCCTGTTTGAGGATC
* * *
6524 ATTTGCTATATGTTAATCCTGGCTT-AGGATC
1 A-TTGCTTTATTTTAATCCT-GTTTGAGGATC
* *
6555 ATTACTTCATTTTAATCCTGTTTGAGGATC
1 ATTGCTTTATTTTAATCCTGTTTGAGGATC
*
6585 ATTGTTTTATTTTAATCCTAG-TTGAGGATC
1 ATTGCTTTATTTTAATCCT-GTTTGAGGATC
*
6615 GTTGCTTTATTTTAATCCTGTTTGAGGATC
1 ATTGCTTTATTTTAATCCTGTTTGAGGATC
* *
6645 ATTGTTTTATTTTAATCCTGATTGAGGATC
1 ATTGCTTTATTTTAATCCTGTTTGAGGATC
*
6675 GTTGCTTTATTTTAATCCTGTTTGAGGATC
1 ATTGCTTTATTTTAATCCTGTTTGAGGATC
6705 ATTGCTTTATTTTAATCCTGTTTGAGGATTC
1 ATTGCTTTATTTTAATCCTGTTTGAGGA-TC
*
6736 -TTGCTTTATTTTAATCCTGGTTGAGGATC
1 ATTGCTTTATTTTAATCCTGTTTGAGGATC
* * *
6765 GTTGCTTTATTTTAATCCTGGTTGAGGACC
1 ATTGCTTTATTTTAATCCTGTTTGAGGATC
* * *
6795 ATCGCTTTATTTTTTAATCCTGGTTAAGGATC
1 ATTGCTTTA--TTTTAATCCTGTTTGAGGATC
6827 ATTGCTTTATTTTAATCCTGATTT-AGGATC
1 ATTGCTTTATTTTAATCCTG-TTTGAGGATC
*
6857 ATTGGTTTATTTTAATCCTGGTTT-AGGATC
1 ATTGCTTTATTTTAATCCT-GTTTGAGGATC
*
6887 ATTGCTTTATTTTAATCCTGGTTGAGGATAATTGC
1 ATTGCTTTATTTTAATCCTGTTTGAGG---A-T-C
*
6922 TTTATTGCTTTGTTTTAATCCTGTTTGAGGATC
1 ---ATTGCTTTATTTTAATCCTGTTTGAGGATC
* * *
6955 ATTGCTCTATTTTTATCCTGGTTGAGGAT-
1 ATTGCTTTATTTTAATCCTGTTTGAGGATC
* * *
6984 ATTTGCTATATGTTAATCCTGGCTT-AGGATC
1 A-TTGCTTTATTTTAATCCT-GTTTGAGGATC
* * * *
7015 ATTACTTCATTTTAATCATGTTTTAGGATC
1 ATTGCTTTATTTTAATCCTGTTTGAGGATC
* * *
7045 ATTGCTTCATTTTTAATCATGTTTGATGATC
1 ATTGCTTTA-TTTTAATCCTGTTTGAGGATC
* * *
7076 ATTGCTTCATTTTAATCCCGTTTTAGGATC
1 ATTGCTTTATTTTAATCCTGTTTGAGGATC
* *
7106 ATTGCTTCATTTTAATCCTGGTTGAGGATC
1 ATTGCTTTATTTTAATCCTGTTTGAGGATC
* *
7136 ATTGCTTTATTTTAATCCAGCTT-AGGATC
1 ATTGCTTTATTTTAATCCTGTTTGAGGATC
*
7165 ACTGCT
1 ATTGCT
7171 CCATCAGTTA
Statistics
Matches: 747, Mismatches: 80, Indels: 79
0.82 0.09 0.09
Matches are distributed among these distances:
29 28 0.04
30 559 0.75
31 45 0.06
32 54 0.07
33 3 0.00
34 2 0.00
35 3 0.00
37 1 0.00
38 52 0.07
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.48
Consensus pattern (30 bp):
ATTGCTTTATTTTAATCCTGTTTGAGGATC
Found at i:6938 original size:38 final size:38
Alignment explanation
Indices: 6887--6965 Score: 122
Period size: 38 Copynumber: 2.1 Consensus size: 38
6877 GTTTAGGATC
*
6887 ATTGCTTTATTTTAATCCTGGTTGAGGATAATTGCTTT
1 ATTGCTTTATTTTAATCCTGGTTGAGGATAATTGCTCT
* * *
6925 ATTGCTTTGTTTTAATCCTGTTTGAGGATCATTGCTCT
1 ATTGCTTTATTTTAATCCTGGTTGAGGATAATTGCTCT
6963 ATT
1 ATT
6966 TTTATCCTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.19, C:0.13, G:0.18, T:0.51
Consensus pattern (38 bp):
ATTGCTTTATTTTAATCCTGGTTGAGGATAATTGCTCT
Found at i:6975 original size:68 final size:68
Alignment explanation
Indices: 6857--6990 Score: 207
Period size: 68 Copynumber: 2.0 Consensus size: 68
6847 ATTTAGGATC
* *
6857 ATTGGTTTATTTTAATCCTGGTTTAGGATCATTGCTTTATTTTAATCCTGGTTGAGGATAATTGC
1 ATTGCTTTATTTTAATCCTGGTTTAGGATCATTGCTCTATTTTAATCCTGGTTGAGGATAATTGC
6922 TTT
66 TTT
* * *
6925 ATTGCTTTGTTTTAATCCT-GTTTGAGGATCATTGCTCTATTTTTATCCTGGTTGAGGATATTTG
1 ATTGCTTTATTTTAATCCTGGTTT-AGGATCATTGCTCTATTTTAATCCTGGTTGAGGATAATTG
6989 CT
65 CT
6991 ATATGTTAAT
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
67 4 0.07
68 56 0.93
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.50
Consensus pattern (68 bp):
ATTGCTTTATTTTAATCCTGGTTTAGGATCATTGCTCTATTTTAATCCTGGTTGAGGATAATTGC
TTT
Found at i:7000 original size:98 final size:98
Alignment explanation
Indices: 6827--7013 Score: 263
Period size: 98 Copynumber: 1.9 Consensus size: 98
6817 GTTAAGGATC
* * *
6827 ATTGCTTTATTTTAATCCTGATTTAGGATCATTGGTTTATTTTAATCCTGGTTTAGGATCATTGC
1 ATTGCTTTATTTTAATCCTGATTTAGGATCATTGCTCTATTTTAATCCTGGTTGAGGATCATTGC
* *
6892 TTTATTTTAATCCTGG-TTGAGGATAATTGCTTT
66 TATATGTTAATCCTGGCTT-AGGATAATTGCTTT
* *
6925 ATTGCTTTGTTTTAATCCTG-TTTGAGGATCATTGCTCTATTTTTATCCTGGTTGAGGAT-ATTT
1 ATTGCTTTATTTTAATCCTGATTT-AGGATCATTGCTCTATTTTAATCCTGGTTGAGGATCA-TT
6988 GCTATATGTTAATCCTGGCTTAGGAT
64 GCTATATGTTAATCCTGGCTTAGGAT
7014 CATTACTTCA
Statistics
Matches: 79, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
97 4 0.05
98 73 0.92
99 2 0.03
ACGTcount: A:0.20, C:0.12, G:0.19, T:0.49
Consensus pattern (98 bp):
ATTGCTTTATTTTAATCCTGATTTAGGATCATTGCTCTATTTTAATCCTGGTTGAGGATCATTGC
TATATGTTAATCCTGGCTTAGGATAATTGCTTT
Found at i:7792 original size:27 final size:27
Alignment explanation
Indices: 7691--7786 Score: 156
Period size: 27 Copynumber: 3.6 Consensus size: 27
7681 TCTAGGGATG
7691 TTTTGGTCATTTTTACATTCAGGGGCA
1 TTTTGGTCATTTTTACATTCAGGGGCA
7718 TTTTGGTCATTTTTACATTCAGGGGCA
1 TTTTGGTCATTTTTACATTCAGGGGCA
** * *
7745 CATTGGTCATTTTCACATTCAGGGGTA
1 TTTTGGTCATTTTTACATTCAGGGGCA
7772 TTTTGGTCATTTTTA
1 TTTTGGTCATTTTTA
7787 AGTTCACATT
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 62 1.00
ACGTcount: A:0.19, C:0.15, G:0.21, T:0.46
Consensus pattern (27 bp):
TTTTGGTCATTTTTACATTCAGGGGCA
Found at i:15639 original size:80 final size:81
Alignment explanation
Indices: 15338--15654 Score: 474
Period size: 81 Copynumber: 3.9 Consensus size: 81
15328 ATATATGGGT
* * ** * *
15338 AAACGTCTCATTAGGGGACGTTCGCCCTCTTTATTAGTTGCACGGGGACACCATTTTAGGTATTC
1 AAACGTCTCATTAGGGGACGTTCGTCCTCTTTACTAGTTATACGGGGACACCAGTTTAGGTGTTC
* * *
15403 GACCGTGGTAGAGGGA
66 AACCGTTGTAAAGGGA
* * * * *
15419 GAACGTCTCATTAGGGGACATTCCTCCTCTTTATTAGTTATACGGGGACACCAGTTTAGATGTTC
1 AAACGTCTCATTAGGGGACGTTCGTCCTCTTTACTAGTTATACGGGGACACCAGTTTAGGTGTTC
15484 AACCGTTGTAAAGGGA
66 AACCGTTGTAAAGGGA
* *
15500 AAACGTCTCATTAGGAGACGTTCGTCCTCTTTACTAGTTATATGGGGACACCAGTTTAGGTGTTC
1 AAACGTCTCATTAGGGGACGTTCGTCCTCTTTACTAGTTATACGGGGACACCAGTTTAGGTGTTC
15565 AACCGTTGTAAAGGGA
66 AACCGTTGTAAAGGGA
*
15581 AAACGTCTCATTA-GGGACGTTTGTCCTCTTTACTAGTTATACGGGGACACCAGTTTAGGTGTTC
1 AAACGTCTCATTAGGGGACGTTCGTCCTCTTTACTAGTTATACGGGGACACCAGTTTAGGTGTTC
15645 AACCGTTGTA
66 AACCGTTGTA
15655 TATGTATTCG
Statistics
Matches: 214, Mismatches: 22, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
80 58 0.27
81 156 0.73
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (81 bp):
AAACGTCTCATTAGGGGACGTTCGTCCTCTTTACTAGTTATACGGGGACACCAGTTTAGGTGTTC
AACCGTTGTAAAGGGA
Found at i:29101 original size:40 final size:40
Alignment explanation
Indices: 29018--29455 Score: 729
Period size: 40 Copynumber: 11.0 Consensus size: 40
29008 GAATTTAGAT
* * *
29018 AACACTTTCCGGTAGGGATA-GGCAAACT-GGTATCTAAAC
1 AACACCTTCCGGTGGGGA-AGGGCAAACTGGGTATTTAAAC
* *
29057 AACACCTTCCGGTGGGGAAGGGCAAATTGGGTATTTAGAC
1 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
29097 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
1 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
29137 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
1 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
29177 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
1 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
* *
29217 AACACCTTCCGGTGGGGAAGAGCAAACTGGGTATTTAGAC
1 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
* *
29257 AACACCTTCCGGTAGGGAAGGGCAAATTGGGTATTTAAAC
1 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
*
29297 AACACCTTCCGGT-GGGAAGGGCAAACTGGGTATTTAGAC
1 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
*
29336 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTACAC
1 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
* *
29376 AACACCTTTCGGTGGGGAAGGGCAAATTGGGTATTTAAAC
1 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
29416 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
1 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
29456 TAAACAAGAC
Statistics
Matches: 375, Mismatches: 21, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
38 1 0.00
39 60 0.16
40 314 0.84
ACGTcount: A:0.30, C:0.19, G:0.29, T:0.21
Consensus pattern (40 bp):
AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
Found at i:31596 original size:14 final size:14
Alignment explanation
Indices: 31577--31605 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
31567 ATCCAACGAC
31577 TCTCTTTTTTTGTT
1 TCTCTTTTTTTGTT
31591 TCTCTTTTTTTGTT
1 TCTCTTTTTTTGTT
31605 T
1 T
31606 TGCTTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (14 bp):
TCTCTTTTTTTGTT
Found at i:46919 original size:43 final size:43
Alignment explanation
Indices: 46871--46952 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
46861 AAAATTATTG
*
46871 AAATAA-AAAAAATTAATGGAAAAATAAATAA-ATAAATAGAAAA
1 AAATAAGAAAAAA-TAATAGAAAAATAAA-AAGATAAATAGAAAA
* *
46914 AAATAAGTAAAAATAATAGATAAATAAAAAGATAAATAG
1 AAATAAGAAAAAATAATAGAAAAATAAAAAGATAAATAG
46953 GCATATAGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 2 0.06
43 27 0.79
44 5 0.15
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.20
Consensus pattern (43 bp):
AAATAAGAAAAAATAATAGAAAAATAAAAAGATAAATAGAAAA
Found at i:47045 original size:27 final size:27
Alignment explanation
Indices: 47006--47062 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
46996 AAGATAATAG
**
47006 TAAATAATTAGAT-AATAGCTAAATTAA
1 TAAATAAAAAGATAAATAG-TAAATTAA
47033 TAAATAAAAAGATAAATAGTAAATTAA
1 TAAATAAAAAGATAAATAGTAAATTAA
47060 TAA
1 TAA
47063 TAGATAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 22 0.81
28 5 0.19
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (27 bp):
TAAATAAAAAGATAAATAGTAAATTAA
Found at i:48540 original size:53 final size:54
Alignment explanation
Indices: 48442--48766 Score: 382
Period size: 53 Copynumber: 6.1 Consensus size: 54
48432 TTGATCACCT
* ** * * *
48442 TTCTTGGAGTGACCATACTGGATCA-CATTGGAGATCAACTTTGATCATCGAAGAC
1 TTCTTGGAATGACCGCACTGGATCATC-TAGG-GATCAACTCTGATCATCGAAAAC
* * * *
48497 TTCTT-GAACGACCACACTCGATCATCTAGGGATCAACTCTGATC-TCTAAAAAC
1 TTCTTGGAATGACCGCACTGGATCATCTAGGGATCAACTCTGATCATC-GAAAAC
* **
48550 TTCTTGGAATGACCGCACTGGGTCATCTA-GGATCAACTCTGATCAAAGAAAAC
1 TTCTTGGAATGACCGCACTGGATCATCTAGGGATCAACTCTGATCATCGAAAAC
*
48603 TTCTTGGAATGACCGCACTGGATCATCT-GAGATCAACTCTGATCA-CTGAAAAC
1 TTCTTGGAATGACCGCACTGGATCATCTAGGGATCAACTCTGATCATC-GAAAAC
* **
48656 TT-TTGGGAATGACCGCACTGG-TCATCT-GAGATCAACTCTGATCAAAGAAAAC
1 TTCTT-GGAATGACCGCACTGGATCATCTAGGGATCAACTCTGATCATCGAAAAC
48708 TTCTTGGAATGACCGCACTGGATCATCTAGGGATCAACTCTGATCATCG-AAAC
1 TTCTTGGAATGACCGCACTGGATCATCTAGGGATCAACTCTGATCATCGAAAAC
48761 TTCTTG
1 TTCTTG
48767 AAAGGAGATC
Statistics
Matches: 237, Mismatches: 22, Indels: 24
0.84 0.08 0.08
Matches are distributed among these distances:
52 51 0.22
53 126 0.53
54 54 0.23
55 6 0.03
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.27
Consensus pattern (54 bp):
TTCTTGGAATGACCGCACTGGATCATCTAGGGATCAACTCTGATCATCGAAAAC
Found at i:48714 original size:105 final size:107
Alignment explanation
Indices: 48472--48766 Score: 422
Period size: 106 Copynumber: 2.8 Consensus size: 107
48462 GATCACATTG
* ** * * * *
48472 GAGATCAACTTTGATCATCGAAGACTTCTT-GAACGACCACACTCGATCATCTAGGGATCAACTC
1 GAGATCAACTCTGATCAAAGAAAACTTCTTGGAATGACCGCACTGGATCATCTAGGGATCAACTC
*
48536 TGATCTCTAAAAACTTCTTGGAATGACCGCACTGGGTCATCT
66 TGATCACTAAAAACTTCTTGGAATGACCGCACTGGGTCATCT
*
48578 -AGGATCAACTCTGATCAAAGAAAACTTCTTGGAATGACCGCACTGGATCATCT-GAGATCAACT
1 GA-GATCAACTCTGATCAAAGAAAACTTCTTGGAATGACCGCACTGGATCATCTAGGGATCAACT
*
48641 CTGATCACTGAAAACTT-TTGGGAATGACCGCACT-GGTCATCT
65 CTGATCACTAAAAACTTCTT-GGAATGACCGCACTGGGTCATCT
48683 GAGATCAACTCTGATCAAAGAAAACTTCTTGGAATGACCGCACTGGATCATCTAGGGATCAACTC
1 GAGATCAACTCTGATCAAAGAAAACTTCTTGGAATGACCGCACTGGATCATCTAGGGATCAACTC
**
48748 TGATCA-TCGAAACTTCTTG
66 TGATCACTAAAAACTTCTTG
48767 AAAGGAGATC
Statistics
Matches: 170, Mismatches: 13, Indels: 13
0.87 0.07 0.07
Matches are distributed among these distances:
105 70 0.41
106 81 0.48
107 19 0.11
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (107 bp):
GAGATCAACTCTGATCAAAGAAAACTTCTTGGAATGACCGCACTGGATCATCTAGGGATCAACTC
TGATCACTAAAAACTTCTTGGAATGACCGCACTGGGTCATCT
Found at i:48803 original size:35 final size:35
Alignment explanation
Indices: 48739--48911 Score: 258
Period size: 35 Copynumber: 4.9 Consensus size: 35
48729 ATCATCTAGG
48739 GATCAACTCTGATCATCG-AAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGA
*
48773 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGA
* * *
48808 GATCAACTCTGATCTTCAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGA
* ** *
48843 GATCAACTTTGATCATTAAAAACTTCTTGAAAGGG
1 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGA
48878 GATCAACTCTGATCATCGAAAACTTCTATGAAAG
1 GATCAACTCTGATCATCGAAAACTTCT-TGAAAG
48912 ACCACACTGG
Statistics
Matches: 125, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
34 18 0.14
35 101 0.81
36 6 0.05
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (35 bp):
GATCAACTCTGATCATCGAAAACTTCTTGAAAGGA
Found at i:48979 original size:54 final size:54
Alignment explanation
Indices: 48895--49010 Score: 205
Period size: 54 Copynumber: 2.1 Consensus size: 54
48885 TCTGATCATC
* **
48895 GAAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATTTGTTTAGATCTCT
1 GAAAACTTCTATGAAAGACCACACTAGGTCATCTTAAGATCCGTTTAGATCTCT
48949 GAAAACTTCTATGAAAGACCACACTAGGTCATCTTAAGATCCGTTTAGATCTCT
1 GAAAACTTCTATGAAAGACCACACTAGGTCATCTTAAGATCCGTTTAGATCTCT
49003 GAAAACTT
1 GAAAACTT
49011 TAAAAGATCA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 59 1.00
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.31
Consensus pattern (54 bp):
GAAAACTTCTATGAAAGACCACACTAGGTCATCTTAAGATCCGTTTAGATCTCT
Found at i:51058 original size:24 final size:24
Alignment explanation
Indices: 51031--51080 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
51021 TGTCTTTCAT
*
51031 TCATCTGACCTTTGTAATGATGAA
1 TCATCTGACCTTTGTAATGACGAA
51055 TCATCTGACCTTTGTAATGACGAA
1 TCATCTGACCTTTGTAATGACGAA
51079 TC
1 TC
51081 TTGAGCATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (24 bp):
TCATCTGACCTTTGTAATGACGAA
Found at i:55500 original size:41 final size:41
Alignment explanation
Indices: 55455--55547 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 41
55445 TTTCCGTGTT
*
55455 CAATTTAGTCCCTAATTTAGGA-TTCTATTTATTATTTGATA
1 CAATTTAGTCCCTAATTTAGGATTTC-ATTTATTAATTGATA
* * *
55496 CAATTTAGTCTCTAATTTAGTATTTCATTTATTAATTGATT
1 CAATTTAGTCCCTAATTTAGGATTTCATTTATTAATTGATA
*
55537 CAATTTGGTCC
1 CAATTTAGTCC
55548 TTATTTGTCT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 42 0.93
42 3 0.07
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.49
Consensus pattern (41 bp):
CAATTTAGTCCCTAATTTAGGATTTCATTTATTAATTGATA
Done.