Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015210.1 Corchorus olitorius cultivar O-4 contig15243, 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: 7971
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Found at i:6455 original size:53 final size:54
Alignment explanation
Indices: 6327--6465 Score: 210
Period size: 54 Copynumber: 2.6 Consensus size: 54
6317 AAGCCCTGGT
* *
6327 CGGTCTTTCATAGAAGCTTTCAGAGATCTAAGTTGATTTTCAGATGACCCAGTG
1 CGGTCTTTCATAGAAGCTTTCAGAGATCTAAGTTGATCTTAAGATGACCCAGTG
* *
6381 CGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTTAAGA-GA-CCATTTG
1 CGGTCTTTCATAGAAGCTTTCAGAGATCTAAGTTGATCTTAAGATGACCCA-GTG
*
6434 CGGTCTTTAATAGAAGCTTTCAGAGATCTAAG
1 CGGTCTTTCATAGAAGCTTTCAGAGATCTAAG
6466 CCCTGGGCGG
Statistics
Matches: 78, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
52 3 0.04
53 34 0.44
54 41 0.53
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.34
Consensus pattern (54 bp):
CGGTCTTTCATAGAAGCTTTCAGAGATCTAAGTTGATCTTAAGATGACCCAGTG
Found at i:6494 original size:92 final size:93
Alignment explanation
Indices: 6380--6558 Score: 272
Period size: 92 Copynumber: 1.9 Consensus size: 93
6370 ATGACCCAGT
* *
6380 GCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTTAAGA-GA-CCATTTGCGGTCTTTA
1 GCGGTCTTTCATAGAAGCTTTCAGAGATCTAAGTTGATCTTAAGATGACCCA-GTGCGGTCTTTA
6443 ATAGAAGCTTTCAGAGATCTAAGCCCTGG
65 ATAGAAGCTTTCAGAGATCTAAGCCCTGG
* * * *
6472 GCGGTCTTTCATAGAAGCTTTCAGAGATCTAAGTTGATTTTCAGATGACCCAGTGCGGTTTTTCA
1 GCGGTCTTTCATAGAAGCTTTCAGAGATCTAAGTTGATCTTAAGATGACCCAGTGCGGTCTTTAA
*
6537 TAGAAGTTTTCAGAGATCTAAG
66 TAGAAGCTTTCAGAGATCTAAG
6559 TTGATTTTAA
Statistics
Matches: 78, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
92 42 0.54
93 33 0.42
94 3 0.04
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (93 bp):
GCGGTCTTTCATAGAAGCTTTCAGAGATCTAAGTTGATCTTAAGATGACCCAGTGCGGTCTTTAA
TAGAAGCTTTCAGAGATCTAAGCCCTGG
Found at i:6496 original size:146 final size:146
Alignment explanation
Indices: 6227--6607 Score: 683
Period size: 146 Copynumber: 2.6 Consensus size: 146
6217 ACCTTCAAGC
* *
6227 ACCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGATTTAAGTTGATCTTAAGAGACCATTTGCGGT
1 ACCCAGTGCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTTAAGAGACCATTTGCGGT
*
6292 CTTTAATAGAAGCTTTCAGAGATCTAAGCCCTGGTCGGTCTTTCATAGAAGCTTTCAGAGATCTA
66 CTTTAATAGAAGCTTTCAGAGATCTAAGCCCTGGGCGGTCTTTCATAGAAGCTTTCAGAGATCTA
6357 AGTTGATTTTCAGATG
131 AGTTGATTTTCAGATG
6373 ACCCAGTGCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTTAAGAGACCATTTGCGGT
1 ACCCAGTGCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTTAAGAGACCATTTGCGGT
6438 CTTTAATAGAAGCTTTCAGAGATCTAAGCCCTGGGCGGTCTTTCATAGAAGCTTTCAGAGATCTA
66 CTTTAATAGAAGCTTTCAGAGATCTAAGCCCTGGGCGGTCTTTCATAGAAGCTTTCAGAGATCTA
6503 AGTTGATTTTCAGATG
131 AGTTGATTTTCAGATG
* *
6519 ACCCAGTGCGGTTTTTCATAGAAGTTTTCAGAGATCTAAGTTGATTTTAAGATGACC-TTGTGCG
1 ACCCAGTGCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTTAAGA-GACCATT-TGCG
*
6583 GTCTTTCATAGAAGCTTTCAGAGAT
64 GTCTTTAATAGAAGCTTTCAGAGAT
6608 AAGTTGATCT
Statistics
Matches: 227, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
146 195 0.86
147 32 0.14
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.34
Consensus pattern (146 bp):
ACCCAGTGCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTTAAGAGACCATTTGCGGT
CTTTAATAGAAGCTTTCAGAGATCTAAGCCCTGGGCGGTCTTTCATAGAAGCTTTCAGAGATCTA
AGTTGATTTTCAGATG
Found at i:6659 original size:106 final size:107
Alignment explanation
Indices: 6472--6778 Score: 297
Period size: 106 Copynumber: 2.9 Consensus size: 107
6462 TAAGCCCTGG
* *
6472 GCGGTCTTTCATAGAAGCTTTCAGAGATCTAAGTTGATTTTCAGATGACCCAGTGCGGTTTTTCA
1 GCGGTCTTTCATAGAAGCTTTCAGAGA-CTAAGTTGATCTTCAGATGACCCAGTGCGGTCTTTCA
6537 TAGAAGTTTTCAGAGATCTA-AGTTGATTTTAAGATGACCTTGT
65 TAGAAGTTTTCAGAGATC-AGAGTTGATTTTAAGATGACCTTGT
* **
6580 GCGGTCTTTCATAGAAGCTTTCAGAGA-TAAGTTGATCTTCAGATGACTC-GATGTTGTCTTTCA
1 GCGGTCTTTCATAGAAGCTTTCAGAGACTAAGTTGATCTTCAGATGACCCAG-TGCGGTCTTTCA
* *** * *
6643 TAGAAGTTTTTAGAGATCAGAGTTGATCCCCAA-ATGATCTAGT
65 TAGAAGTTTTCAGAGATCAGAGTTGAT-TTTAAGATGACCTTGT
* * * ** * * *
6686 GCGATCATTTCA-AGAAGTTTTCAGTGA-TCAGAGTTGATCCCCAGATGATCTAGTGCGGTCATT
1 GCGGTC-TTTCATAGAAGCTTTCAGAGACT-A-AGTTGATCTTCAGATGACCCAGTGCGGTCTTT
*
6749 C-TAAGAAGTTTTC-GTTGATCAGAGTTGATT
63 CAT-AGAAGTTTTCAG-AGATCAGAGTTGATT
6779 CCAGATGGCC
Statistics
Matches: 165, Mismatches: 25, Indels: 19
0.79 0.12 0.09
Matches are distributed among these distances:
105 2 0.01
106 80 0.48
107 10 0.06
108 72 0.44
109 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (107 bp):
GCGGTCTTTCATAGAAGCTTTCAGAGACTAAGTTGATCTTCAGATGACCCAGTGCGGTCTTTCAT
AGAAGTTTTCAGAGATCAGAGTTGATTTTAAGATGACCTTGT
Found at i:6702 original size:54 final size:54
Alignment explanation
Indices: 6472--6939 Score: 295
Period size: 54 Copynumber: 8.7 Consensus size: 54
6462 TAAGCCCTGG
* * *** *
6472 GCGGTC-TTTCATAGAAGCTTTCAGAGATCTA-AGTTGATTTTCAGATGACCCAGT
1 GCGGTCATTTCA-AGAAGTTTTTAGAGATC-AGAGTTGATCCCCAGATGATCCAGT
* * **** *
6526 GCGGT-TTTTCATAGAAGTTTTCAGAGATCTA-AGTTGATTTTAAGATGA-CCTTGT
1 GCGGTCATTTCA-AGAAGTTTTTAGAGATC-AGAGTTGATCCCCAGATGATCC-AGT
* * ** *
6580 GCGGTC-TTTCATAGAAGCTTTCAGAGAT-A-AGTTGATCTTCAGATGACTCGA-T
1 GCGGTCATTTCA-AGAAGTTTTTAGAGATCAGAGTTGATCCCCAGATGA-TCCAGT
** * *
6632 GTTGTC-TTTCATAGAAGTTTTTAGAGATCAGAGTTGATCCCCAAATGATCTAGT
1 GCGGTCATTTCA-AGAAGTTTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGT
* * * *
6686 GCGATCATTTCAAGAAGTTTTCAGTGATCAGAGTTGATCCCCAGATGATCTAGT
1 GCGGTCATTTCAAGAAGTTTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGT
* * * *
6740 GCGGTCA-TTCTAAGAAG-TTTTCGTTGATCAGAGTTGAT-TCCAGATG-GCCAGT
1 GCGGTCATTTC-AAGAAGTTTTTAG-AGATCAGAGTTGATCCCCAGATGATCCAGT
* * * *
6792 GCGGTCATTCCTATAAG-TTTTAGAGATCAGAGTTGATCCCTAGATGATCCAGT
1 GCGGTCATTTCAAGAAGTTTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGT
* * * * * *
6845 GCGATCA-TTCAAAAGAAGTTTTCAGTGAT-TGAAGTTGATCCCCAGATGAACCGGT
1 GCGGTCATTTC--AAGAAGTTTTTAGAGATCAG-AGTTGATCCCCAGATGATCCAGT
* * **
6900 GCGGTCATTCCATGAAGTTTTTTTATGATCAGAGTTGATC
1 GCGGTCATTTCAAGAAGTTTTTAGA-GATCAGAGTTGATC
6940 TCCTTTCAAG
Statistics
Matches: 339, Mismatches: 54, Indels: 41
0.78 0.12 0.09
Matches are distributed among these distances:
51 13 0.04
52 69 0.20
53 33 0.10
54 171 0.50
55 50 0.15
56 3 0.01
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (54 bp):
GCGGTCATTTCAAGAAGTTTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGT
Found at i:6744 original size:160 final size:159
Alignment explanation
Indices: 6472--6938 Score: 416
Period size: 160 Copynumber: 2.9 Consensus size: 159
6462 TAAGCCCTGG
* *** * * *
6472 GCGGTCTTTCATAGAAGCTTTCAGAGATCTA-AGTTGATTTTCAGATGACCCAGTGCGGT-TTTT
1 GCGGTCTTTCATAGAAG-TTTTAGAGATC-AGAGTTGATCCCCAGATGATCCAGTGCGATCATTT
* **** * *
6535 CATAGAAGTTTTCAGAGATCTA-AGTTGATTTTAAGATGACCTTGTGCGGTCTTTC-ATAGAAGC
64 CA-AGAAGTTTTCAGTGATC-AGAGTTGATCCCCAGATGACCTAGTGCGGTCATTCTA-AGAAGC
*
6598 TTTCAG-AGAT-A-AGTTGATCTTCAGATGACTC-GAT
126 TTTC-GTAGATCAGAGTTGAT-TCCAGATGAC-CAG-T
** * *
6632 GTTGTCTTTCATAGAAGTTTTTAGAGATCAGAGTTGATCCCCAAATGATCTAGTGCGATCATTTC
1 GCGGTCTTTCATAGAAG-TTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGATCATTTC
* *
6697 AAGAAGTTTTCAGTGATCAGAGTTGATCCCCAGATGATCTAGTGCGGTCATTCTAAGAAGTTTTC
65 AAGAAGTTTTCAGTGATCAGAGTTGATCCCCAGATGACCTAGTGCGGTCATTCTAAGAAGCTTTC
* *
6762 GTTGATCAGAGTTGATTCCAGATGGCCAGT
130 GTAGATCAGAGTTGATTCCAGATGACCAGT
* * * *
6792 GCGGTCATTCCTATAAGTTTTAGAGATCAGAGTTGATCCCTAGATGATCCAGTGCGATCA-TTCA
1 GCGGTCTTTCATAGAAGTTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGATCATTTC-
* * * * *
6856 AAAGAAGTTTTCAGTGAT-TGAAGTTGATCCCCAGATGAACC-GGTGCGGTCATTCCATGAAGTT
65 -AAGAAGTTTTCAGTGATCAG-AGTTGATCCCCAGATG-ACCTAGTGCGGTCATTCTAAGAAGCT
**
6919 TTTTTATGATCAGAGTTGAT
127 TTCGTA-GATCAGAGTTGAT
6939 CTCCTTTCAA
Statistics
Matches: 254, Mismatches: 40, Indels: 25
0.80 0.13 0.08
Matches are distributed among these distances:
158 3 0.01
159 44 0.17
160 169 0.67
161 31 0.12
162 7 0.03
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (159 bp):
GCGGTCTTTCATAGAAGTTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGATCATTTCA
AGAAGTTTTCAGTGATCAGAGTTGATCCCCAGATGACCTAGTGCGGTCATTCTAAGAAGCTTTCG
TAGATCAGAGTTGATTCCAGATGACCAGT
Found at i:6846 original size:105 final size:108
Alignment explanation
Indices: 6644--6939 Score: 309
Period size: 106 Copynumber: 2.7 Consensus size: 108
6634 TGTCTTTCAT
* * * * * * * *
6644 AGAAGTTTTTAGAGATCAG-AGTTGATCCCCAAATGATCTAGTGCGATCATTTCAAGAAGTTTTC
1 AGAAGTTTTCAGTGAT-AGAAGTTGATCCCCAGATGAACCAGTGCGGTCATTCCATGAAGTTTT-
* * * *
6708 AGTGATCAGAGTTGATCCCCAGATGATCTAGTGCGGTCATTC-TA
64 AGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGATCATTCAAA
* *
6752 AGAAGTTTTC-GTTGATCAG-AGTTGAT-TCCAGATG-GCCAGTGCGGTCATTCCTAT-AAGTTT
1 AGAAGTTTTCAG-TGAT-AGAAGTTGATCCCCAGATGAACCAGTGCGGTCATTCC-ATGAAGTTT
*
6812 TAGAGATCAGAGTTGATCCCTAGATGATCCAGTGCGATCATTCAAA
63 TAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGATCATTCAAA
* * *
6858 AGAAGTTTTCAGTGATTGAAGTTGATCCCCAGATGAACCGGTGCGGTCATTCCATGAAGTTTTTT
1 AGAAGTTTTCAGTGATAGAAGTTGATCCCCAGATGAACCAGTGCGGTCATTCCATGAAG-TTTTA
*
6923 TATGATCAGAGTTGATC
65 GA-GATCAGAGTTGATC
6940 TCCTTTCAAG
Statistics
Matches: 158, Mismatches: 20, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
105 39 0.25
106 42 0.27
107 18 0.11
108 40 0.25
109 5 0.03
110 14 0.09
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (108 bp):
AGAAGTTTTCAGTGATAGAAGTTGATCCCCAGATGAACCAGTGCGGTCATTCCATGAAGTTTTAG
AGATCAGAGTTGATCCCCAGATGATCCAGTGCGATCATTCAAA
Found at i:6846 original size:159 final size:160
Alignment explanation
Indices: 6650--6938 Score: 431
Period size: 160 Copynumber: 1.8 Consensus size: 160
6640 TCATAGAAGT
*
6650 TTTTAGAGATCAGAGTTGATCCCCAAATGATCTAGTGCGATCATTTC-AAGAAGTTTTCAGTGAT
1 TTTTAGAGATCAGAGTTGATCCCCAAATGATCCAGTGCGATCA-TTCAAAGAAGTTTTCAGTGAT
* * *
6714 CAG-AGTTGATCCCCAGATGATCTAGTGCGGTCATTCTAAGAAGTTTTCGT-TGATCAGAGTTGA
65 -AGAAGTTGATCCCCAGATGAACCAGTGCGGTCATTCCAAGAAGTTTTCGTATGATCAGAGTTGA
6777 TTCCAGATGGCCAGTGCGGTCATTCCTATAAG
129 TTCCAGATGGCCAGTGCGGTCATTCCTATAAG
* *
6809 TTTTAGAGATCAGAGTTGATCCCTAGATGATCCAGTGCGATCATTCAAAAGAAGTTTTCAGTGAT
1 TTTTAGAGATCAGAGTTGATCCCCAAATGATCCAGTGCGATCATTC-AAAGAAGTTTTCAGTGAT
* * * **
6874 TGAAGTTGATCCCCAGATGAACCGGTGCGGTCATTCCATGAAGTTTTTTTATGATCAGAGTTGAT
65 AGAAGTTGATCCCCAGATGAACCAGTGCGGTCATTCCAAGAAGTTTTCGTATGATCAGAGTTGAT
6939 CTCCTTTCAA
Statistics
Matches: 115, Mismatches: 11, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
158 3 0.03
159 41 0.36
160 57 0.50
161 14 0.12
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (160 bp):
TTTTAGAGATCAGAGTTGATCCCCAAATGATCCAGTGCGATCATTCAAAGAAGTTTTCAGTGATA
GAAGTTGATCCCCAGATGAACCAGTGCGGTCATTCCAAGAAGTTTTCGTATGATCAGAGTTGATT
CCAGATGGCCAGTGCGGTCATTCCTATAAG
Found at i:6967 original size:35 final size:35
Alignment explanation
Indices: 6904--7496 Score: 830
Period size: 35 Copynumber: 17.0 Consensus size: 35
6894 ACCGGTGCGG
* * *
6904 TCATTCCATGAAGTTTTTTTATGATCAGAGTTGATC
1 TCATTTCAAGAAG-TTTTGTATGATCAGAGTTGATC
*
6940 TCCTTTCAAGAAGTTTTCGT-TGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTT-GTATGATCAGAGTTGATC
* * *
6975 TCGTTTCAAGAAGTTTTTTATGATCAAAGTTGATC
1 TCATTTCAAGAAGTTTTGTATGATCAGAGTTGATC
* *
7010 TCCTTTCAAGAAGTTTTTTTATGATCAGAGTTGATC
1 TCATTTCAAGAAG-TTTTGTATGATCAGAGTTGATC
*
7046 TCATTCCAAGAAGTTTT-TATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTGTATGATCAGAGTTGATC
7080 TCATTTCAAGAAGTTTT-TATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTGTATGATCAGAGTTGATC
7114 TCATTTCAAGAAGTTTT-TATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTGTATGATCAGAGTTGATC
* *
7148 TCCTTTCAAGAAGTTTTCG-ATTATCAGAGTTGATC
1 TCATTTCAAGAAGTTTT-GTATGATCAGAGTTGATC
7183 TCATTTCAAGAAGTTTT-TATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTGTATGATCAGAGTTGATC
7217 TCATTTCAAGAAGTTTT-TCAATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTGT--ATGATCAGAGTTGATC
* *
7253 TCGTTTCAAGAAGTTTTTTATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTGTATGATCAGAGTTGATC
* *
7288 TAATTTCAAGAAGTTTTCG-AAGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTT-GTATGATCAGAGTTGATC
7323 TCATTTCAAGAAGTTTTG-ATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTGTATGATCAGAGTTGATC
* *
7357 TCGTTTCAAGAAGTTTTTTATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTGTATGATCAGAGTTGATC
*
7392 TCCTTTCAAGAAGTTTTCG-ATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTT-GTATGATCAGAGTTGATC
* *
7427 TCGTTTCAAGAAGTTTTTTATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTGTATGATCAGAGTTGATC
*
7462 TCCTTTCAAGAAGTTTTCG-ATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTT-GTATGATCAGAGTTGATC
7497 CCTAGATGAT
Statistics
Matches: 512, Mismatches: 31, Indels: 29
0.90 0.05 0.05
Matches are distributed among these distances:
34 166 0.32
35 270 0.53
36 75 0.15
37 1 0.00
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.40
Consensus pattern (35 bp):
TCATTTCAAGAAGTTTTGTATGATCAGAGTTGATC
Found at i:6989 original size:19 final size:19
Alignment explanation
Indices: 6932--6989 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
6922 TTATGATCAG
*
6932 AGTTGATCTCCTTTCAAGA
1 AGTTGATCTCGTTTCAAGA
6951 AGTT--T-TCGTTGATC-AG-
1 AGTTGATCTCGTT--TCAAGA
6967 AGTTGATCTCGTTTCAAGA
1 AGTTGATCTCGTTTCAAGA
6986 AGTT
1 AGTT
6990 TTTTATGATC
Statistics
Matches: 31, Mismatches: 1, Indels: 14
0.67 0.02 0.30
Matches are distributed among these distances:
16 8 0.26
17 5 0.16
18 5 0.16
19 13 0.42
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.40
Consensus pattern (19 bp):
AGTTGATCTCGTTTCAAGA
Found at i:7109 original size:174 final size:174
Alignment explanation
Indices: 6913--7496 Score: 933
Period size: 174 Copynumber: 3.4 Consensus size: 174
6903 GTCATTCCAT
* * *
6913 GAAGTTTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGTTGATCAGAGTTGATCTCG
1 GAAG-TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
* * *
6978 TTTCAAGAAGTTTTTTATGATCAAAGTTGATCTCCTTTCAAGAAGTTTTTTTATGATCAGAGTTG
65 TTTCAAGAAGTTTTTGATGATCAGAGTTGATCTCATTTCAAGAAG-TTTTTTATGATCAGAGTTG
* *
7043 ATCTCATTCCAAGAAGTTTTTATGATCAGAGTTGATCTCATTTCAA
129 ATCTCATTTCAAGAAGTTTTTATGATCAGAGTTGATCTCGTTTCAA
* *
7089 GAAG-TTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTT-TATGATCAGAGTTGATCTCCT
1 GAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCAT
* *
7152 TTCAAGAAGTTTTCGATTATCAGAGTTGATCTCATTTCAAGAAG-TTTTTATGATCAGAGTTGAT
66 TTCAAGAAGTTTTTGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATCAGAGTTGAT
7216 CTCATTTCAAGAAGTTTTTCAATGATCAGAGTTGATCTCGTTTCAA
131 CTCATTTCAAGAAGTTTTT--ATGATCAGAGTTGATCTCGTTTCAA
* *
7262 GAAGTTTTTTATGATCAGAGTTGATCTAATTTCAAGAAGTTTTCGAAGATCAGAGTTGATCTCAT
1 GAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCAT
*
7327 TTCAAGAAG-TTTTGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTTTATGATCAGAGTTGAT
66 TTCAAGAAGTTTTTGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATCAGAGTTGAT
* *
7391 CTCCTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAA
131 CTCATTTCAAGAAGTTTT-TATGATCAGAGTTGATCTCGTTTCAA
*
7436 GAAGTTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGATGATCAGAGTTGATC
1 GAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
7497 CCTAGATGAT
Statistics
Matches: 379, Mismatches: 23, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
171 38 0.10
173 85 0.22
174 188 0.50
175 64 0.17
176 4 0.01
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (174 bp):
GAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCAT
TTCAAGAAGTTTTTGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATCAGAGTTGAT
CTCATTTCAAGAAGTTTTTATGATCAGAGTTGATCTCGTTTCAA
Found at i:7531 original size:54 final size:54
Alignment explanation
Indices: 7468--7790 Score: 257
Period size: 53 Copynumber: 5.9 Consensus size: 54
7458 GATCTCCTTT
7468 CAAGAAGTTTTCGATGATCAGAGTTGATCCCTAGATGATCCAGTGCGGTCATTC
1 CAAGAAGTTTTCGATGATCAGAGTTGATCCCTAGATGATCCAGTGCGGTCATTC
* *
7522 CAAGAAGTTTTTCAATGATCCTCAGAGTTGATCCC-AGATGATCCAGTGCGATCATTC
1 CAAGAAG-TTTTCGATGA---TCAGAGTTGATCCCTAGATGATCCAGTGCGGTCATTC
* * * * *
7579 CAAGAAGTTTTTAGA-GATTAGAGTCGATCCC-AGATGATCTAGTGCGGTCTTTC
1 CAAGAAG-TTTTCGATGATCAGAGTTGATCCCTAGATGATCCAGTGCGGTCATTC
* * * * * *
7632 CAAGAAATTTTCAATGATCAGAGTTGAT-CTTCA-ATTGATACAGTACAGTCATTC
1 CAAGAAGTTTTCGATGATCAGAGTTGATCCCT-AGA-TGATCCAGTGCGGTCATTC
* ** ** * ** *
7686 CAAGACGTTTTTTATGATCAGAGTTGATTTTCAATTTGATCCAGTGCGATCATTC
1 CAAGAAGTTTTCGATGATCAGAGTTGA-TCCCTAGATGATCCAGTGCGGTCATTC
* * *
7741 CAAGAAAGGTTTCCG-TGATCA-AGGTTGAAT-CTTAAATGATCCAGTGCGGT
1 CAAG-AA-GTTTTCGATGATCAGA-GTTG-ATCCCTAGATGATCCAGTGCGGT
7791 TGATTAAGAA
Statistics
Matches: 212, Mismatches: 42, Indels: 29
0.75 0.15 0.10
Matches are distributed among these distances:
52 6 0.03
53 49 0.23
54 45 0.21
55 45 0.21
56 14 0.07
57 39 0.18
58 14 0.07
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.32
Consensus pattern (54 bp):
CAAGAAGTTTTCGATGATCAGAGTTGATCCCTAGATGATCCAGTGCGGTCATTC
Found at i:7732 original size:109 final size:107
Alignment explanation
Indices: 7468--7747 Score: 275
Period size: 107 Copynumber: 2.6 Consensus size: 107
7458 GATCTCCTTT
* * *
7468 CAAGAAG-TTTTCGATGATCAGAGTTGATCCCTAGATGATCCAGTGCGGTCATTCCAAGAAGTTT
1 CAAGAAGTTTTTAGA-GATCAGAGTCGATCCC-AGATGATCCAGTGCGGTCATTCCAAGAA-ATT
* *
7532 TTCAATGATCCTCAGAGTTGATCCCAGATGATCCAGTGCGATCATTC
63 TTCAATGA--CTCAGAGTTGATCCCAGATGATACAGTACGATCATTC
* * *
7579 CAAGAAGTTTTTAGAGATTAGAGTCGATCCCAGATGATCTAGTGCGGTCTTTCCAAGAAATTTTC
1 CAAGAAGTTTTTAGAGATCAGAGTCGATCCCAGATGATCCAGTGCGGTCATTCCAAGAAATTTTC
*
7644 AATGA-TCAGAGTTGATCTTCA-ATTGATACAGTAC-AGTCATTC
66 AATGACTCAGAGTTGATC-CCAGA-TGATACAGTACGA-TCATTC
* * * ** *
7686 CAAGACGTTTTTTA-TGATCAGAGTTGATTTTCA-ATTTGATCCAGTGCGATCATTCCAAGAAA
1 CAAGAAG-TTTTTAGAGATCAGAGTCGA-TCCCAGA--TGATCCAGTGCGGTCATTCCAAGAAA
7748 GGTTTCCGTG
Statistics
Matches: 143, Mismatches: 18, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
106 14 0.10
107 34 0.24
108 9 0.06
109 33 0.23
110 26 0.18
111 21 0.15
112 6 0.04
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (107 bp):
CAAGAAGTTTTTAGAGATCAGAGTCGATCCCAGATGATCCAGTGCGGTCATTCCAAGAAATTTTC
AATGACTCAGAGTTGATCCCAGATGATACAGTACGATCATTC
Done.