Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015021.1 Corchorus olitorius cultivar O-4 contig15054, 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: 35804
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Found at i:1131 original size:22 final size:22
Alignment explanation
Indices: 1087--1131 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1077 ATAATAATTC
*
1087 TTTTAGTAATCTTAAAAGTTTT
1 TTTTAGTAATCTTAAAAGGTTT
* * *
1109 TTTTATTAATTTTATAAGGTTT
1 TTTTAGTAATCTTAAAAGGTTT
1131 T
1 T
1132 AGAAAGCATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.29, C:0.02, G:0.09, T:0.60
Consensus pattern (22 bp):
TTTTAGTAATCTTAAAAGGTTT
Found at i:6118 original size:65 final size:64
Alignment explanation
Indices: 6028--6154 Score: 182
Period size: 65 Copynumber: 2.0 Consensus size: 64
6018 GTAAAAACTA
* *
6028 ACAAAAATCATTTCACTGTAAATGCATGGTCAAACCTCCAAAGAATGATAGTCAAACCTCAAACC
1 ACAAAAAACATTTCACTGTAAATGCATGGTCAAACC-CCAAAGAATGATAGTCAAACCCCAAACC
* * * * *
6093 ACAAAAAACATTTCATTGTAGATGCATGGTCAAACCCTAAAGATTGATAGTTAAACCCCAAA
1 ACAAAAAACATTTCACTGTAAATGCATGGTCAAACCCCAAAGAATGATAGTCAAACCCCAAA
6155 GATTGATAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
64 22 0.40
65 33 0.60
ACGTcount: A:0.43, C:0.22, G:0.12, T:0.23
Consensus pattern (64 bp):
ACAAAAAACATTTCACTGTAAATGCATGGTCAAACCCCAAAGAATGATAGTCAAACCCCAAACC
Found at i:6148 original size:21 final size:21
Alignment explanation
Indices: 6121--6334 Score: 293
Period size: 21 Copynumber: 10.1 Consensus size: 21
6111 TAGATGCATG
* *
6121 GTCAAACCCTAAAGATTGATA
1 GTCAAACCCCAAAGTTTGATA
* *
6142 GTTAAACCCCAAAGATTGATA
1 GTCAAACCCCAAAGTTTGATA
* * *
6163 ATCAAACCCCAAAGTTTGGTT
1 GTCAAACCCCAAAGTTTGATA
*
6184 GTCAAACCCCAAAGTTTTATA
1 GTCAAACCCCAAAGTTTGATA
*
6205 GTCAAACCCCAAAGTTTGATT
1 GTCAAACCCCAAAGTTTGATA
* *
6226 GTAAAACCCCAAAGTTTGATT
1 GTCAAACCCCAAAGTTTGATA
6247 GTCAAACCCCAAAGTTTGATA
1 GTCAAACCCCAAAGTTTGATA
* *
6268 GTCAAACCCCAAAATTTGATT
1 GTCAAACCCCAAAGTTTGATA
*
6289 GTCAAACCCCAAAGTTTGATT
1 GTCAAACCCCAAAGTTTGATA
6310 GTCAAACCCTCAAAGTTTGATA
1 GTCAAACCC-CAAAGTTTGATA
6332 GTC
1 GTC
6335 CACACGTTAA
Statistics
Matches: 172, Mismatches: 20, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
21 158 0.92
22 14 0.08
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (21 bp):
GTCAAACCCCAAAGTTTGATA
Found at i:7686 original size:3 final size:3
Alignment explanation
Indices: 7680--7719 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
7670 TCCCATGATG
* *
7680 ATA ATA ATA ATA GTA ATA ATA ATA AT- ATA ATA ATG ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
7720 TATAGTCATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:7975 original size:15 final size:16
Alignment explanation
Indices: 7944--7982 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
7934 AACGGACTTC
*
7944 TTCTTTTCTTTCTTTT
1 TTCTTTTCTTCCTTTT
7960 TTCTTTT-TTCCTTTT
1 TTCTTTTCTTCCTTTT
*
7975 TCCTTTTC
1 TTCTTTTC
7983 CTCTCTTTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
TTCTTTTCTTCCTTTT
Found at i:8277 original size:29 final size:30
Alignment explanation
Indices: 8203--8289 Score: 86
Period size: 29 Copynumber: 2.9 Consensus size: 30
8193 TATAAAGGCT
* * *
8203 AAAAGTTCAAATATGGGCCTAACCTTTAAGG
1 AAAAGGTCAAATAAGGGTCTAACCTTTAA-G
** *
8234 AAAAGGTCATTTAAGGGTCTAACCTTTCA-
1 AAAAGGTCAAATAAGGGTCTAACCTTTAAG
* *
8263 ATAAGGTCAAATAAGTGTCTAACCTTT
1 AAAAGGTCAAATAAGGGTCTAACCTTT
8290 TCGATTTGGA
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
29 23 0.50
31 23 0.50
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (30 bp):
AAAAGGTCAAATAAGGGTCTAACCTTTAAG
Found at i:16122 original size:261 final size:261
Alignment explanation
Indices: 15644--16142 Score: 750
Period size: 261 Copynumber: 1.9 Consensus size: 261
15634 AAAAGAGAAG
* *
15644 CTTAAAAGAAAACCATAATTTAGTGCTAAAGACAGTCCTGATTTCTTAACAATCTATAATTCTTT
1 CTTAAAAGAAAACCATAATTTAGTGCTAAAGACAGTCCTGATTTCTTAACAATCTATAATGCTCT
* *
15709 AATAATTTAGTGTGTTAGGTAGATATACATACTCGGTGATAACAGAATGGAAAGTAATCATGAGT
66 AATAATTCAGTGTGTTAGGTAAATATACATACTCGGTGATAACAGAATGGAAAGTAATCATGAGT
* **
15774 CAAATTTGTATGGATTATCTCAATTTTCACATGCAATTGAACACCTAGACAGTCTAAATAGTGAC
131 CAAATTTGTATGGATTATCTCAATTTTCACAGGCAATTGAACACCTAGACAGTCTAAATAGCAAC
* * * * *
15839 GCATAATCCACTAAGAGATAATGGATTTTAACACCTGTTTAATTTGAATACAAATTATATCTATT
196 ACATAATCCACTAACAGATAATGGATCTCAACACCAGTTTAATTTGAATACAAATTATATCTATT
15904 A
261 A
* * * * *
15905 CTTAAAGGAAAACCATAGTTCTA-TGCTGAAGACAGTCCTGATTTTTTAGCAATCTATAATGCTC
1 CTTAAAAGAAAACCATAATT-TAGTGCTAAAGACAGTCCTGATTTCTTAACAATCTATAATGCTC
* * *
15969 TAATAATTCAGTGTGTTAGTTAAATATATATACTCGGTGATGACAGAATGGAAAGTAATCATGAG
65 TAATAATTCAGTGTGTTAGGTAAATATACATACTCGGTGATAACAGAATGGAAAGTAATCATGAG
* * *
16034 TCAAATTTGTATGGATTATCTCAATTTTCGCAGGCAATTGGACA-CTCGGACAGTCTAAATAGCA
130 TCAAATTTGTATGGATTATCTCAATTTTCACAGGCAATTGAACACCT-AGACAGTCTAAATAGCA
*
16098 ACACATAATCCACTAACTGATAATGGATCTCAACACCAGTTTAAT
194 ACACATAATCCACTAACAGATAATGGATCTCAACACCAGTTTAAT
16143 GCAAATTGAA
Statistics
Matches: 212, Mismatches: 24, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
260 2 0.01
261 208 0.98
262 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (261 bp):
CTTAAAAGAAAACCATAATTTAGTGCTAAAGACAGTCCTGATTTCTTAACAATCTATAATGCTCT
AATAATTCAGTGTGTTAGGTAAATATACATACTCGGTGATAACAGAATGGAAAGTAATCATGAGT
CAAATTTGTATGGATTATCTCAATTTTCACAGGCAATTGAACACCTAGACAGTCTAAATAGCAAC
ACATAATCCACTAACAGATAATGGATCTCAACACCAGTTTAATTTGAATACAAATTATATCTATT
A
Found at i:35359 original size:23 final size:24
Alignment explanation
Indices: 35332--35383 Score: 88
Period size: 23 Copynumber: 2.2 Consensus size: 24
35322 ATCAAAAATT
35332 CAATGCCAAAGTGTTCGACATGCA
1 CAATGCCAAAGTGTTCGACATGCA
*
35356 -AATGCGAAAGTGTTCGACATGCA
1 CAATGCCAAAGTGTTCGACATGCA
35379 CAATG
1 CAATG
35384 GACACGTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (24 bp):
CAATGCCAAAGTGTTCGACATGCA
Done.