Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017275.1 Corchorus olitorius cultivar O-4 contig17308, 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: 21753
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:140 original size:50 final size:50
Alignment explanation
Indices: 1--142 Score: 257
Period size: 50 Copynumber: 2.8 Consensus size: 50
* *
1 AGGCTTTTCCACAAGCCAAACTCATTTCCATACGAGTCAATTATCAACAT
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTATCAACAT
51 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTATCAACAT
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTATCAACAT
*
101 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGGGTCAGTT
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTT
143 CAAGCCTTGG
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 89 1.00
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (50 bp):
AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTATCAACAT
Found at i:187 original size:69 final size:69
Alignment explanation
Indices: 99--299 Score: 285
Period size: 69 Copynumber: 2.9 Consensus size: 69
89 AGTTATCAAC
*
99 ATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGGGTCAGTTCAAGCCTTGGTTCCATCCAAG
1 ATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGGGTCAGTTCAAGCATTGGTTCCATCCAAG
164 CCAT
66 CCAT
* * * *
168 ATAGGCTTTTCCACCAGCCAAACTCGTTTCCATACGGGTCGGTTCAAGCATTGGTTCTATCTAAG
1 ATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGGGTCAGTTCAAGCATTGGTTCCATCCAAG
233 CCAT
66 CCAT
* * * * * * * *
237 ATAGACTTTTCCATAAGCCGAACTCGTTTCCATGCGAGTCAGTTTAAACATCGGTTCCATCCA
1 ATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGGGTCAGTTCAAGCATTGGTTCCATCCA
300 TACAGCAGTG
Statistics
Matches: 115, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
69 115 1.00
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.29
Consensus pattern (69 bp):
ATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGGGTCAGTTCAAGCATTGGTTCCATCCAAG
CCAT
Found at i:5756 original size:188 final size:188
Alignment explanation
Indices: 5430--5867 Score: 761
Period size: 188 Copynumber: 2.3 Consensus size: 188
5420 TTTACATTGG
* * *
5430 TAAGTCTTTCGGGCACAATTTCAGAAACCTCCAGGTACTAATTCTGATAAGTCCTCCGGGCAATT
1 TAAGTCCTTCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATT
*
5495 GATAAAACCTCCGGGTACATTTGATTTCATCGAGTTTTTCAGCAAAGATTCATGTTTAAGTTTAA
66 GATAAAACCTCCGGGTACATTTGATTTCATCAAGTTTTTCAGCAAAGATTCATGTTTAAGTTTAA
5560 AATCCTTGGTCAAGGTCTCTATTCAGAGTTTACATTGGTAAGTCCTCCGGGCAACTGA
131 AATCCTTGGTCAAGGTCTCTATTCAGAGTTTACATTGGTAAGTCCTCCGGGCAACTGA
*
5618 TAAGTCCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATT
1 TAAGTCCTTCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATT
* *
5683 GATAAAACCTTCGGGTACCATTTGATTTCATCAAG-TTTTCATCAAAGATTCATGTTTAAGTTTA
66 GATAAAACCTCCGGGTA-CATTTGATTTCATCAAGTTTTTCAGCAAAGATTCATGTTTAAGTTTA
*
5747 AAATCCTTGGTCAAGGTCTCTATTCAGAGTTTACATTGGTAAGTTCTCCGGGCAACTGA
130 AAATCCTTGGTCAAGGTCTCTATTCAGAGTTTACATTGGTAAGTCCTCCGGGCAACTGA
* * *
5806 TAAGTCCTTCGGGCAAAATTTCAGAAACCTCTGGGTATTAATTCTGATAAATCCTCCGGGCA
1 TAAGTCCTTCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCA
5868 GTTCATATTT
Statistics
Matches: 237, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
188 221 0.93
189 16 0.07
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (188 bp):
TAAGTCCTTCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATT
GATAAAACCTCCGGGTACATTTGATTTCATCAAGTTTTTCAGCAAAGATTCATGTTTAAGTTTAA
AATCCTTGGTCAAGGTCTCTATTCAGAGTTTACATTGGTAAGTCCTCCGGGCAACTGA
Found at i:5942 original size:39 final size:39
Alignment explanation
Indices: 5898--6024 Score: 123
Period size: 39 Copynumber: 3.3 Consensus size: 39
5888 TTATTTTATC
* * *
5898 ATTGCTTTATGATTC-AATTCCGATCATGATTTTAGGATT
1 ATTGCTTTATCAGTCTAATTCCAATCATGA-TTTAGGATT
* *
5937 ATTGCTTTATCAGTCTTATTCCAATCCTGATTTAGGATT
1 ATTGCTTTATCAGTCTAATTCCAATCATGATTTAGGATT
* * * * * *
5976 ATTGCTTTATCAGT-TTATTTCGATCCTGGTTTAGGATC
1 ATTGCTTTATCAGTCTAATTCCAATCATGATTTAGGATT
*
6014 ATTCCTTTATC
1 ATTGCTTTATC
6025 GCTTTATTTT
Statistics
Matches: 77, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
38 30 0.39
39 36 0.47
40 11 0.14
ACGTcount: A:0.22, C:0.17, G:0.14, T:0.47
Consensus pattern (39 bp):
ATTGCTTTATCAGTCTAATTCCAATCATGATTTAGGATT
Found at i:6003 original size:38 final size:38
Alignment explanation
Indices: 5928--6061 Score: 162
Period size: 38 Copynumber: 3.5 Consensus size: 38
5918 CGATCATGAT
* *
5928 TTTAGGATTATTGCTTTATCAGTCTTATTCCAATCCTGA
1 TTTAGGATCATTGCTTTATCAGT-TTATTTCAATCCTGA
* * *
5967 TTTAGGATTATTGCTTTATCAGTTTATTTCGATCCTGG
1 TTTAGGATCATTGCTTTATCAGTTTATTTCAATCCTGA
* * *
6005 TTTAGGATCATTCCTTTATC-GCTTTATTTTAATCCTGG
1 TTTAGGATCATTGCTTTATCAG-TTTATTTCAATCCTGA
*
6043 TTGAGGATCATTGCTTTAT
1 TTTAGGATCATTGCTTTAT
6062 TTTAATCCTG
Statistics
Matches: 85, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
37 1 0.01
38 61 0.72
39 23 0.27
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.49
Consensus pattern (38 bp):
TTTAGGATCATTGCTTTATCAGTTTATTTCAATCCTGA
Found at i:6059 original size:30 final size:30
Alignment explanation
Indices: 6025--6358 Score: 425
Period size: 30 Copynumber: 11.0 Consensus size: 30
6015 TTCCTTTATC
*
6025 GCTTTATTTTAATCCTGGTTGAGGATCATT
1 GCTTTATTTTAATCCTGGTTTAGGATCATT
6055 GCTTTATTTTAATCCTGGTTTAGGATCATT
1 GCTTTATTTTAATCCTGGTTTAGGATCATT
*
6085 GCTTTATTTTAATCCTGGTTGAGGATCATT
1 GCTTTATTTTAATCCTGGTTTAGGATCATT
* * * * *
6115 GCTTAATGAGTTAATCCTAGTTTACGATTATT
1 GCTTTAT--TTTAATCCTGGTTTAGGATCATT
**
6147 GCTTTATTACAATCCTGGTTTAGGATCATT
1 GCTTTATTTTAATCCTGGTTTAGGATCATT
* *
6177 GCTTTATTTTAATCGTGGTTGAGGATCATT
1 GCTTTATTTTAATCCTGGTTTAGGATCATT
* * *
6207 GCTTTATGAGTTAATCCTGGTTTAGGATCGTC
1 GCTTTAT--TTTAATCCTGGTTTAGGATCATT
* * * *
6239 GGTTTATTTAAATCCTGGTTGAGGATCACT
1 GCTTTATTTTAATCCTGGTTTAGGATCATT
* *
6269 GCTTTATTTTAATCCTGGTTGAGGATCCTT
1 GCTTTATTTTAATCCTGGTTTAGGATCATT
*
6299 GCTTTATTTTAATCCTGATTTAGGATCATT
1 GCTTTATTTTAATCCTGGTTTAGGATCATT
* *
6329 GCTTTATCTTAATCCTGGTTTAGGCTCATT
1 GCTTTATTTTAATCCTGGTTTAGGATCATT
6359 ACTTCATCAG
Statistics
Matches: 259, Mismatches: 41, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
30 211 0.81
32 48 0.19
ACGTcount: A:0.21, C:0.14, G:0.19, T:0.46
Consensus pattern (30 bp):
GCTTTATTTTAATCCTGGTTTAGGATCATT
Found at i:6162 original size:92 final size:92
Alignment explanation
Indices: 6033--6402 Score: 455
Period size: 92 Copynumber: 4.0 Consensus size: 92
6023 TCGCTTTATT
* *
6033 TTAATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGGTTTAGGATCATTGCTTTATTTTAAT
1 TTAATCCTGGTTTAGGATCATTGCTTTATTATAATCCTGGTTTAGGATCATTGCTTTATTTTAAT
*
6098 CCTGGTTGAGGATCATTGCTTAATGAG
66 CCTGGTTGAGGATCATTGCTTTATGAG
* * * *
6125 TTAATCCTAGTTTACGATTATTGCTTTATTACAATCCTGGTTTAGGATCATTGCTTTATTTTAAT
1 TTAATCCTGGTTTAGGATCATTGCTTTATTATAATCCTGGTTTAGGATCATTGCTTTATTTTAAT
*
6190 CGTGGTTGAGGATCATTGCTTTATGAG
66 CCTGGTTGAGGATCATTGCTTTATGAG
* * * * *
6217 TTAATCCTGGTTTAGGATCGTCGGTTTATT-TAAATCCTGGTTGAGGATCACTGCTTTATTTTAA
1 TTAATCCTGGTTTAGGATCATTGCTTTATTAT-AATCCTGGTTTAGGATCATTGCTTTATTTTAA
* *
6281 TCCTGGTTGAGGATCCTTGCTTTAT--T
65 TCCTGGTTGAGGATCATTGCTTTATGAG
* * * * *
6307 TTAATCCTGATTTAGGATCATTGCTTTATCT-TAATCCTGGTTTAGGCTCATTACTTCATCAGTT
1 TTAATCCTGGTTTAGGATCATTGCTTTAT-TATAATCCTGGTTTAGGATCATTGCTTTAT--TTT
* *
6371 AATCC--GATGTAGGATTATTGCTTTATGAG
63 AATCCTGGTTG-AGGATCATTGCTTTATGAG
6400 TTA
1 TTA
6403 TATTTCAATC
Statistics
Matches: 237, Mismatches: 34, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
90 50 0.21
91 16 0.07
92 168 0.71
93 3 0.01
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (92 bp):
TTAATCCTGGTTTAGGATCATTGCTTTATTATAATCCTGGTTTAGGATCATTGCTTTATTTTAAT
CCTGGTTGAGGATCATTGCTTTATGAG
Found at i:6253 original size:122 final size:121
Alignment explanation
Indices: 6020--6396 Score: 438
Period size: 122 Copynumber: 3.1 Consensus size: 121
6010 GATCATTCCT
*
6020 TTATCGCTTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGGTTTAGGATCATT
1 TTATTGCTTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGGTTTAGGATCATT
* * * *
6085 GCTTTATTTTAATCCTGGTTGAGGATCATTGCTTAATGAGTTAATCCTAGTTTACGA
66 GCTTTATCTTAATCCTGGTTTAGGATCATCGCTT-ATGAGTTAATCCTAGTTGACGA
** * * *
6142 TTATTGCTTTATTACAATCCTGGTTTAGGATCATTGCTTTATTTTAATCGTGGTTGAGGATCATT
1 TTATTGCTTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGGTTTAGGATCATT
* * * * * *
6207 GCTTTATGAGTTAATCCTGGTTTAGGATCGTCGGTT-T-ATTTAAATCCTGGTTGAGGA
66 GCTTTAT--CTTAATCCTGGTTTAGGATCATCGCTTATGAGTT-AATCCTAGTTGACGA
* * * *
6264 TCACTGCTTTATTTTAATCCTGGTTGAGGATCCTTGCTTTATTTTAATCCTGATTTAGGATCATT
1 TTATTGCTTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGGTTTAGGATCATT
* ** * * *
6329 GCTTTATCTTAATCCTGGTTTAGGCTCATTACTTCATCAGTTAATCC--GATGTAGGA
66 GCTTTATCTTAATCCTGGTTTAGGATCATCGCTT-ATGAGTTAATCCTAGTTG-ACGA
6385 TTATTGCTTTAT
1 TTATTGCTTTAT
6397 GAGTTATATT
Statistics
Matches: 214, Mismatches: 34, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
120 24 0.11
121 17 0.08
122 148 0.69
123 3 0.01
124 22 0.10
ACGTcount: A:0.21, C:0.15, G:0.19, T:0.45
Consensus pattern (121 bp):
TTATTGCTTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGGTTTAGGATCATT
GCTTTATCTTAATCCTGGTTTAGGATCATCGCTTATGAGTTAATCCTAGTTGACGA
Found at i:6424 original size:39 final size:38
Alignment explanation
Indices: 6371--6514 Score: 110
Period size: 39 Copynumber: 4.0 Consensus size: 38
6361 TTCATCAGTT
* *
6371 AATCCGATGTAGGATTATTGCTTTATGAGTTATATTTC
1 AATCCGATTTAGGATTATTGCTTTATCAGTTATATTTC
** *
6409 AATCCTGATTTAGGATTATCAC-TT-T-AGTT-TATTTG
1 AATCC-GATTTAGGATTATTGCTTTATCAGTTATATTTC
*
6444 AAT-C---TT--GATCATTGCTTTATCAGTTATATTTC
1 AATCCGATTTAGGATTATTGCTTTATCAGTTATATTTC
* * * *
6476 AATCCTGATTTAGGACTATTGTTTTGTCAGTTTTATTTC
1 AATCC-GATTTAGGATTATTGCTTTATCAGTTATATTTC
6515 GATCTTGGTA
Statistics
Matches: 81, Mismatches: 13, Indels: 23
0.69 0.11 0.20
Matches are distributed among these distances:
28 6 0.07
29 2 0.02
30 3 0.04
31 4 0.05
32 8 0.10
33 1 0.01
34 1 0.01
35 8 0.10
36 4 0.05
37 3 0.04
38 7 0.09
39 34 0.42
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.49
Consensus pattern (38 bp):
AATCCGATTTAGGATTATTGCTTTATCAGTTATATTTC
Found at i:8972 original size:17 final size:17
Alignment explanation
Indices: 8946--8983 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
8936 ACACCACAGG
*
8946 ATCAAGAGTCAACAAAA
1 ATCAAAAGTCAACAAAA
*
8963 ATCAAAAGTCAACAAAG
1 ATCAAAAGTCAACAAAA
8980 ATCA
1 ATCA
8984 TCATTGTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.58, C:0.18, G:0.11, T:0.13
Consensus pattern (17 bp):
ATCAAAAGTCAACAAAA
Found at i:14913 original size:17 final size:17
Alignment explanation
Indices: 14891--14923 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
14881 GACAAGGGAG
14891 CGAAAATTAGTCAAATA
1 CGAAAATTAGTCAAATA
14908 CGAAAATTAGTCAAAT
1 CGAAAATTAGTCAAAT
14924 GCTAGAGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (17 bp):
CGAAAATTAGTCAAATA
Found at i:17843 original size:90 final size:90
Alignment explanation
Indices: 17479--18052 Score: 817
Period size: 91 Copynumber: 6.3 Consensus size: 90
17469 GTTCTTGTTT
* * * * * * * *
17479 ATTCGATGAATTAATTTGATGCAGTGCAATATTTCTTCAAGATCGGAATTCAGTGAGCTCGGTGT
1 ATTCGGTGAATCAAGTTGATGCGGTGCATTATTTCTTCAAGATTGG-ATTCGGTGAGCTCGGTGC
* **
17544 AGCAAATTTTCAAACAGTTCAAAATG
65 AGCACATTTTCAAACAGTTCAGGATG
* *
17570 ATTCGGTGAATCAAGTTAATGCGGTGCATTATTTTCTTCAAGATTGGATTCGGTGAGCTCGGTGT
1 ATTCGGTGAATCAAGTTGATGCGGTGCATTA-TTTCTTCAAGATTGGATTCGGTGAGCTCGGTGC
17635 AGCACATTTTCAAACAGTTCAGGATG
65 AGCACATTTTCAAACAGTTCAGGATG
* *
17661 ATTCGGTGAATCAAGTTGATGCGGTGCATTTTTTTCTTCAAAATTGGATTCGGTGAGCAT-GGTG
1 ATTCGGTGAATCAAGTTGATGCGGTGCA-TTATTTCTTCAAGATTGGATTCGGTGAGC-TCGGTG
17725 CAGCACATTTTCAAACAGTTCAGGATG
64 CAGCACATTTTCAAACAGTTCAGGATG
*
17752 ATTCGGTGAATCAAGTTGATGCGGTGCATTATTTCTTCAAGATTGGATTTGGTGAGCTCGGTGCA
1 ATTCGGTGAATCAAGTTGATGCGGTGCATTATTTCTTCAAGATTGGATTCGGTGAGCTCGGTGCA
*
17817 GCACATTTTTAAACAGTTCAGGATG
66 GCACATTTTCAAACAGTTCAGGATG
* * * * * *
17842 ATCCGGTGAATCAAGTCGATGCAGTACATTATTTTATTCAAGATTGGATTCGGTGAGCTCAGTGC
1 ATTCGGTGAATCAAGTTGATGCGGTGCATTA-TTTCTTCAAGATTGGATTCGGTGAGCTCGGTGC
*
17907 AACACATTTTCAAACAGTTCAGGATG
65 AGCACATTTTCAAACAGTTCAGGATG
*
17933 ATTCGGTGAATCAAGTTGATGCGGTGCATTATTTCTTCAAGATTGGATTCAGTGAGCTCGGTGCA
1 ATTCGGTGAATCAAGTTGATGCGGTGCATTATTTCTTCAAGATTGGATTCGGTGAGCTCGGTGCA
* *
17998 TCACATTTTCAAACAGTTTAGGATG
66 GCACATTTTCAAACAGTTCAGGATG
* * * *
18023 ATTCGGTGGATCTAGCTAATGCGGTGCATT
1 ATTCGGTGAATCAAGTTGATGCGGTGCATT
18053 CGGTTTTAGG
Statistics
Matches: 437, Mismatches: 41, Indels: 11
0.89 0.08 0.02
Matches are distributed among these distances:
89 1 0.00
90 163 0.37
91 256 0.59
92 17 0.04
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (90 bp):
ATTCGGTGAATCAAGTTGATGCGGTGCATTATTTCTTCAAGATTGGATTCGGTGAGCTCGGTGCA
GCACATTTTCAAACAGTTCAGGATG
Found at i:17851 original size:181 final size:181
Alignment explanation
Indices: 17479--18052 Score: 828
Period size: 181 Copynumber: 3.2 Consensus size: 181
17469 GTTCTTGTTT
* * * * * * *
17479 ATTCGATGAATTAATTTGATGCAGTGCAATA-TTTCTTCAAGATCGGAATTCAGTGAGCTCGGTG
1 ATTCGGTGAATCAAGTTGATGCGGTGCATTATTTTCTTCAAGATTGG-ATTCGGTGAGCTCGGTG
* * ** *
17543 TAGCAAATTTTCAAACAGTTCAAAATGATTCGGTGAATCAAGTTAATGCGGTGCATTATTTTCTT
65 CAGCACATTTTCAAACAGTTCAGGATGATTCGGTGAATCAAGTTGATGCGGTGCATTA-TTTCTT
*
17608 CAAGATTGGATTCGGTGAGCTCGGTGTAGCACATTTTCAAACAGTTCAGGATG
129 CAAGATTGGATTCGGTGAGCTCGGTGCAGCACATTTTCAAACAGTTCAGGATG
* *
17661 ATTCGGTGAATCAAGTTGATGCGGTGCATTTTTTTCTTCAAAATTGGATTCGGTGAGCAT-GGTG
1 ATTCGGTGAATCAAGTTGATGCGGTGCATTATTTTCTTCAAGATTGGATTCGGTGAGC-TCGGTG
17725 CAGCACATTTTCAAACAGTTCAGGATGATTCGGTGAATCAAGTTGATGCGGTGCATTATTTCTTC
65 CAGCACATTTTCAAACAGTTCAGGATGATTCGGTGAATCAAGTTGATGCGGTGCATTATTTCTTC
* *
17790 AAGATTGGATTTGGTGAGCTCGGTGCAGCACATTTTTAAACAGTTCAGGATG
130 AAGATTGGATTCGGTGAGCTCGGTGCAGCACATTTTCAAACAGTTCAGGATG
* * * * * *
17842 ATCCGGTGAATCAAGTCGATGCAGTACATTATTTTATTCAAGATTGGATTCGGTGAGCTCAGTGC
1 ATTCGGTGAATCAAGTTGATGCGGTGCATTATTTTCTTCAAGATTGGATTCGGTGAGCTCGGTGC
*
17907 AACACATTTTCAAACAGTTCAGGATGATTCGGTGAATCAAGTTGATGCGGTGCATTATTTCTTCA
66 AGCACATTTTCAAACAGTTCAGGATGATTCGGTGAATCAAGTTGATGCGGTGCATTATTTCTTCA
* * *
17972 AGATTGGATTCAGTGAGCTCGGTGCATCACATTTTCAAACAGTTTAGGATG
131 AGATTGGATTCGGTGAGCTCGGTGCAGCACATTTTCAAACAGTTCAGGATG
* * * *
18023 ATTCGGTGGATCTAGCTAATGCGGTGCATT
1 ATTCGGTGAATCAAGTTGATGCGGTGCATT
18053 CGGTTTTAGG
Statistics
Matches: 350, Mismatches: 39, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
180 1 0.00
181 243 0.69
182 92 0.26
183 14 0.04
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (181 bp):
ATTCGGTGAATCAAGTTGATGCGGTGCATTATTTTCTTCAAGATTGGATTCGGTGAGCTCGGTGC
AGCACATTTTCAAACAGTTCAGGATGATTCGGTGAATCAAGTTGATGCGGTGCATTATTTCTTCA
AGATTGGATTCGGTGAGCTCGGTGCAGCACATTTTCAAACAGTTCAGGATG
Found at i:18222 original size:18 final size:18
Alignment explanation
Indices: 18199--18234 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
18189 AGTTGTAGAC
18199 ACATTACTT-TTAGGTTCT
1 ACATTA-TTGTTAGGTTCT
18217 ACATTATTGTTAGGTTCT
1 ACATTATTGTTAGGTTCT
18235 GTTTGGATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 15 0.88
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.50
Consensus pattern (18 bp):
ACATTATTGTTAGGTTCT
Found at i:19556 original size:21 final size:21
Alignment explanation
Indices: 19531--19571 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
19521 TTAGAAACCC
19531 TAGTACCACTTAG-ATCCAATT
1 TAGTACCACTT-GTATCCAATT
19552 TAGTACCACTTGTATCCAAT
1 TAGTACCACTTGTATCCAAT
19572 AGGGCTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34
Consensus pattern (21 bp):
TAGTACCACTTGTATCCAATT
Done.