Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014480.1 Corchorus olitorius cultivar O-4 contig14513, 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: 42506
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:179 original size:2 final size:2
Alignment explanation
Indices: 172--213 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
162 ATTTTCTGTG
172 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
214 TGTTATTCAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6932 original size:87 final size:87
Alignment explanation
Indices: 6784--6959 Score: 334
Period size: 87 Copynumber: 2.0 Consensus size: 87
6774 TGACATGAAA
6784 TTAAAATTCTAAAGATATTAGCTAATGTTGGGTTGGTAAATTTTTAAATAAGTAAAATGGAATTC
1 TTAAAATTCTAAAGATATTAGCTAATGTTGGGTTGGTAAATTTTTAAATAAGTAAAATGGAATTC
6849 AATCTGTCATTAATTACCATTG
66 AATCTGTCATTAATTACCATTG
**
6871 TTAAAATTCTAAAGATATTAGCTAATGTTGGGTTGGTAAATTTTTAAATAAGTAACTTGGAATTC
1 TTAAAATTCTAAAGATATTAGCTAATGTTGGGTTGGTAAATTTTTAAATAAGTAAAATGGAATTC
6936 AATCTGTCATTAATTACCATTG
66 AATCTGTCATTAATTACCATTG
6958 TT
1 TT
6960 GCATGGATAG
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (87 bp):
TTAAAATTCTAAAGATATTAGCTAATGTTGGGTTGGTAAATTTTTAAATAAGTAAAATGGAATTC
AATCTGTCATTAATTACCATTG
Found at i:12387 original size:167 final size:172
Alignment explanation
Indices: 12098--12536 Score: 467
Period size: 181 Copynumber: 2.5 Consensus size: 172
12088 ATTTTATTTA
* * * * * *
12098 TCAATGTTTTCTGACAGTGTTATTATGAATATTACCTTTATCATATTTGCAATTAAGAACAAAGG
1 TCAATG-TTTCTAACAATGTTATTATAAATATCACCTTTATCAGATTCGCAATTAAGAACAAAGG
* * *
12163 ATATGTTTGCACAAACACAATCTGTATCATGGGTGACGCTCACGGTCGCCCGCAATTT-T-A-A-
65 ATAAGTTTGCACAAACACAATCTATATCATGGGTGACGCTCACAGTCGCCCGCAATTTATCAGAG
** * * *
12224 ACGCCCTATTGTCTGGGTGTAATGATCCGAAAATCTTGTTTTT
130 ACGCCCTATTGTCTGGGTGTAAAAATCAGAAAATCTCGCTTTT
* * **
12267 TCAATGTTTCTAACAATGTTATTATAAATATCACCTTTATCAGATTCACAA-TAAGAATAAAAAA
1 TCAATGTTTCTAACAATGTTATTATAAATATCACCTTTATCAGATTCGCAATTAAGAACAAAGGA
* *
12331 TAAGTTTGCACAAACACAATCTATATCA-GAGGTGATGCTCACAGTCGCCTGCAATTTCAGAAAT
66 TAAGTTTGCACAAACACAATCTATATCATG-GGTGACGCTCACAGTCGCCCGCAATTT-----AT
* * * * *
12395 CAGGGTTTAGACGCCCTGTTGTGTTGGTTTAAAAATTAGAAAATCTCGCTTTT
125 CA--G---AGACGCCCTATTGTCTGGGTGTAAAAATCAGAAAATCTCGCTTTT
* * *
12448 TGAATGTTTCTAACAATGTTATTATAAATATCACCTTTATTAGGTTCGCAATTAAGAACAAAGGA
1 TCAATGTTTCTAACAATGTTATTATAAATATCACCTTTATCAGATTCGCAATTAAGAACAAAGGA
*
12513 TACGTTTGCACAAACACAATCTAT
66 TAAGTTTGCACAAACACAATCTAT
12537 CTCACGGGCA
Statistics
Matches: 221, Mismatches: 33, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
166 1 0.00
167 60 0.27
168 38 0.17
169 6 0.03
173 1 0.00
174 1 0.00
180 1 0.00
181 80 0.36
182 33 0.15
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34
Consensus pattern (172 bp):
TCAATGTTTCTAACAATGTTATTATAAATATCACCTTTATCAGATTCGCAATTAAGAACAAAGGA
TAAGTTTGCACAAACACAATCTATATCATGGGTGACGCTCACAGTCGCCCGCAATTTATCAGAGA
CGCCCTATTGTCTGGGTGTAAAAATCAGAAAATCTCGCTTTT
Found at i:14144 original size:13 final size:13
Alignment explanation
Indices: 14126--14154 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
14116 AGAATTGAAG
14126 TAATATACCATAT
1 TAATATACCATAT
14139 TAATATACCATAT
1 TAATATACCATAT
14152 TAA
1 TAA
14155 ATTAATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (13 bp):
TAATATACCATAT
Found at i:14852 original size:30 final size:30
Alignment explanation
Indices: 14818--14908 Score: 164
Period size: 30 Copynumber: 3.0 Consensus size: 30
14808 ATTTTTATCT
* *
14818 TGACTTACCTCTTATATCCTCAAATTTTAA
1 TGACTTTCCTCTTATACCCTCAAATTTTAA
14848 TGACTTTCCTCTTATACCCTCAAATTTTAA
1 TGACTTTCCTCTTATACCCTCAAATTTTAA
14878 TGACTTTCCTCTTATACCCTCAAATTTTAA
1 TGACTTTCCTCTTATACCCTCAAATTTTAA
14908 T
1 T
14909 ATCTTACTAA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.27, C:0.25, G:0.03, T:0.44
Consensus pattern (30 bp):
TGACTTTCCTCTTATACCCTCAAATTTTAA
Found at i:16705 original size:51 final size:51
Alignment explanation
Indices: 16657--16797 Score: 228
Period size: 51 Copynumber: 2.8 Consensus size: 51
16647 ATCCGGATCC
* *
16657 TTGTTCCCCATACTCAGGCTTCCTGCCATATCCAGATCCGTACTCGGATTG
1 TTGTTCTCCATACTCAGGTTTCCTGCCATATCCAGATCCGTACTCGGATTG
16708 TTGTTCTCCATACTCAGGTTTCCTGCCATATCCAGATCCGTACTCGGATTG
1 TTGTTCTCCATACTCAGGTTTCCTGCCATATCCAGATCCGTACTCGGATTG
* * * *
16759 TTGTTCTCCATATTCAGGTTTCCGGCCGTACCCAGATCC
1 TTGTTCTCCATACTCAGGTTTCCTGCCATATCCAGATCC
16798 ATATTCCTGG
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 84 1.00
ACGTcount: A:0.17, C:0.32, G:0.18, T:0.33
Consensus pattern (51 bp):
TTGTTCTCCATACTCAGGTTTCCTGCCATATCCAGATCCGTACTCGGATTG
Found at i:16927 original size:54 final size:54
Alignment explanation
Indices: 16814--16956 Score: 155
Period size: 54 Copynumber: 2.6 Consensus size: 54
16804 CTGGGATGCA
* * *
16814 GGCTGCTCAAATTCGGGTCTCCGACCATACCCGGATCCATATTCGGACGAAGGT
1 GGCTGCTCATATTCGGGTCTCCGACCATACCCAGATCCATACTCGGACGAAGGT
* * ** *
16868 TGCTGCTCATATTCTGGTCTCCTG-CCATACCCAGATCCATACTCAGG-CTTATGT
1 GGCTGCTCATATTCGGGTCTCC-GACCATACCCAGATCCATACTC-GGACGAAGGT
* * *
16922 GGCTGCTCATATTCGGGTTTCCGCCCATAGCCAGA
1 GGCTGCTCATATTCGGGTCTCCGACCATACCCAGA
16957 ATCAAACTCC
Statistics
Matches: 74, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
53 1 0.01
54 70 0.95
55 3 0.04
ACGTcount: A:0.20, C:0.31, G:0.22, T:0.27
Consensus pattern (54 bp):
GGCTGCTCATATTCGGGTCTCCGACCATACCCAGATCCATACTCGGACGAAGGT
Found at i:18344 original size:114 final size:114
Alignment explanation
Indices: 18207--18419 Score: 338
Period size: 114 Copynumber: 1.9 Consensus size: 114
18197 ATTTATGTCA
* *
18207 AAGGAATGGATAATTACAAAAAAGGACTCAAGGGTAAGAACTGGCTAGAAACTAATCTAGGGTCT
1 AAGGAAAGGATAATTACAAAAAAGGACTCAAGGGTAAGAACTGGCTAGAAACTAACCTAGGGTCT
18272 TCTCAGTAATTTCGCAAGT-AAGAAGAGACAGAAAATGGCAAAAAAAAGT
66 TCTCAGTAATTTCGCAAGTGAAGAA-AGACAGAAAATGGCAAAAAAAAGT
* *
18321 AAGGAAAGGATAATTACAAAAAAGGGCTCAAGGGTAAGAACTGGTTAGAAACTAACCTAGGGTCT
1 AAGGAAAGGATAATTACAAAAAAGGACTCAAGGGTAAGAACTGGCTAGAAACTAACCTAGGGTCT
* * * *
18386 TTTTAGTAATTTGGCAAGTGAGGAAAGACAGAAA
66 TCTCAGTAATTTCGCAAGTGAAGAAAGACAGAAA
18420 GGGACAAAAA
Statistics
Matches: 90, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
114 86 0.96
115 4 0.04
ACGTcount: A:0.44, C:0.11, G:0.24, T:0.20
Consensus pattern (114 bp):
AAGGAAAGGATAATTACAAAAAAGGACTCAAGGGTAAGAACTGGCTAGAAACTAACCTAGGGTCT
TCTCAGTAATTTCGCAAGTGAAGAAAGACAGAAAATGGCAAAAAAAAGT
Found at i:22717 original size:22 final size:21
Alignment explanation
Indices: 22692--22768 Score: 91
Period size: 22 Copynumber: 3.6 Consensus size: 21
22682 TATTTTTATG
*
22692 AAATTTTGATAACTAACCTATT
1 AAATTTTGATAACT-ACCTATA
* *
22714 AAATTTTGATAACTACCAAATG
1 AAATTTTGATAACTACC-TATA
*
22736 AAATTTTGATAATTACCTATA
1 AAATTTTGATAACTACCTATA
*
22757 AAATTGTGATAA
1 AAATTTTGATAA
22769 ATTCAATAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
21 16 0.33
22 32 0.67
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (21 bp):
AAATTTTGATAACTACCTATA
Found at i:22944 original size:15 final size:15
Alignment explanation
Indices: 22924--22962 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
22914 ATCACACTGA
22924 GTTCCTCCATTCAGC
1 GTTCCTCCATTCAGC
22939 GTTCCTCCATTCAGC
1 GTTCCTCCATTCAGC
*
22954 ATTCCTCCA
1 GTTCCTCCA
22963 CACAACATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.15, C:0.41, G:0.10, T:0.33
Consensus pattern (15 bp):
GTTCCTCCATTCAGC
Found at i:25422 original size:27 final size:26
Alignment explanation
Indices: 25363--25423 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
25353 AATTTCCATG
25363 ATTTTAATAATGAAATAATTAAAATAT
1 ATTTTAATAATGAAAT-ATTAAAATAT
*
25390 -TATTTAATAATAGCAAT-TTAGAAATAT
1 AT-TTTAATAAT-GAAATATTA-AAATAT
25417 ATTTTAA
1 ATTTTAA
25424 AAAAAATACA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
26 4 0.14
27 20 0.69
28 5 0.17
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.43
Consensus pattern (26 bp):
ATTTTAATAATGAAATATTAAAATAT
Found at i:26087 original size:25 final size:24
Alignment explanation
Indices: 26059--26115 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
26049 GTGGATTGTA
*
26059 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTGAAGAATTAA-ACATT
*
26084 AAATAAATTTAAGAATTAAACATT
1 AAATAAATTGAAGAATTAAACATT
26108 AAA-AAATT
1 AAATAAATT
26116 CAAGGCTGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.27
25 17 0.57
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.32
Consensus pattern (24 bp):
AAATAAATTGAAGAATTAAACATT
Found at i:27148 original size:13 final size:13
Alignment explanation
Indices: 27130--27158 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
27120 TCGTATTTTT
27130 ATATATAGTATAG
1 ATATATAGTATAG
27143 ATATATAGTATAG
1 ATATATAGTATAG
27156 ATA
1 ATA
27159 GATATATCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (13 bp):
ATATATAGTATAG
Found at i:42118 original size:15 final size:16
Alignment explanation
Indices: 42098--42128 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
42088 TTATAAAAGC
42098 ATAAGAAT-TAAGCTT
1 ATAAGAATATAAGCTT
42113 ATAAGAATATAAGCTT
1 ATAAGAATATAAGCTT
42129 TTGGAATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.48, C:0.06, G:0.13, T:0.32
Consensus pattern (16 bp):
ATAAGAATATAAGCTT
Done.