Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021374.1 Corchorus olitorius cultivar O-4 contig21407, 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: 13988
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Found at i:1179 original size:16 final size:16
Alignment explanation
Indices: 1160--1194 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1150 GACCCGAAAA
*
1160 ACCCAAAATCCGAATG
1 ACCCAAAACCCGAATG
*
1176 ACCCAAAACCCGAGTG
1 ACCCAAAACCCGAATG
1192 ACC
1 ACC
1195 TGAAGCCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.37, G:0.14, T:0.09
Consensus pattern (16 bp):
ACCCAAAACCCGAATG
Found at i:1948 original size:22 final size:22
Alignment explanation
Indices: 1923--1968 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
1913 TTTTAGTTGC
* *
1923 GTAAAATTATAAATATAAAATA
1 GTAAAATGATAAAAATAAAATA
1945 GTAAAATGATAAAAATAAAATA
1 GTAAAATGATAAAAATAAAATA
1967 GT
1 GT
1969 TATAAGGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (22 bp):
GTAAAATGATAAAAATAAAATA
Found at i:2523 original size:15 final size:15
Alignment explanation
Indices: 2503--2532 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2493 TGGTATCCTC
2503 CTCCAAATTGGAAAA
1 CTCCAAATTGGAAAA
2518 CTCCAAATTGGAAAA
1 CTCCAAATTGGAAAA
2533 AGGTAGTCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.20, G:0.13, T:0.20
Consensus pattern (15 bp):
CTCCAAATTGGAAAA
Found at i:8026 original size:45 final size:45
Alignment explanation
Indices: 7959--8047 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
7949 AAGCAAATAA
* * *
7959 TTCTACTCCATCTCTAGGTAATTCATCAAAATAAAGGTAATATTC
1 TTCTACTCAATCTCTAGATAATTCATCAAAATAAAGCTAATATTC
*
8004 TTCTCCTCAATCTCTAGATAATTCATCAAAATAAAGCTAATATT
1 TTCTACTCAATCTCTAGATAATTCATCAAAATAAAGCTAATATT
8048 AATTGTTGCT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.36
Consensus pattern (45 bp):
TTCTACTCAATCTCTAGATAATTCATCAAAATAAAGCTAATATTC
Found at i:11247 original size:42 final size:44
Alignment explanation
Indices: 11196--11289 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 44
11186 AGTGCATTAC
*
11196 CTAA-ATTCTA-CC-CCACCTCTAGGTAATTCATCAAAATAAAA
1 CTAATATTCTACCCTCCACCTCTAGATAATTCATCAAAATAAAA
*
11237 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAA
1 CTAATATTCTAC-CCTCCACCTCTAGATAATTCATCAAAATAAAA
11282 CTAATATT
1 CTAATATT
11290 AATTGTTTGC
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
44 2 0.04
45 35 0.74
ACGTcount: A:0.40, C:0.24, G:0.03, T:0.32
Consensus pattern (44 bp):
CTAATATTCTACCCTCCACCTCTAGATAATTCATCAAAATAAAA
Found at i:12130 original size:60 final size:62
Alignment explanation
Indices: 12037--12200 Score: 246
Period size: 60 Copynumber: 2.7 Consensus size: 62
12027 GCTAATTGCT
* * *
12037 CAAATAAGGGCCTAACATT-TGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAA-TTTGGC
1 CAAATAAGGGCCTAACGTTATACAAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTTGGC
* *
12097 CAAATAAGGGCCTAACGTTAT-CGAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTTGGC
1 CAAATAAGGGCCTAACGTTATACAAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTTGGC
*
12158 CAAATAAGGGCCTAACGTTATAAAAAAATGCTCAAAT-AGGGCC
1 CAAATAAGGGCCTAACGTTATACAAAAATGCTCAAATAAGGGCC
12201 TGGCGTCAGT
Statistics
Matches: 95, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
60 49 0.52
61 33 0.35
62 13 0.14
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.26
Consensus pattern (62 bp):
CAAATAAGGGCCTAACGTTATACAAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTTGGC
Found at i:12135 original size:31 final size:29
Alignment explanation
Indices: 12033--12137 Score: 88
Period size: 31 Copynumber: 3.5 Consensus size: 29
12023 TAAGGCTAAT
12033 TGCTCAAATAAGGGCCTAACATTTGCCAAAA
1 TGCTCAAATAAGGGCCTAAC-TTT-CCAAAA
* * * **
12064 TGCTCAAATAAGGGCCCGATCTTT-TAATT
1 TGCTCAAATAAGGG-CCTAACTTTCCAAAA
*
12093 TGGC-CAAATAAGGGCCTAACGTTATCGAAAA
1 T-GCTCAAATAAGGGCCTAAC-TT-TCCAAAA
12124 TGCTCAAATAAGGG
1 TGCTCAAATAAGGG
12138 TCCGATCTTT
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
28 4 0.07
29 15 0.26
30 5 0.09
31 30 0.52
32 4 0.07
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (29 bp):
TGCTCAAATAAGGGCCTAACTTTCCAAAA
Found at i:12278 original size:31 final size:31
Alignment explanation
Indices: 12240--12407 Score: 154
Period size: 31 Copynumber: 5.5 Consensus size: 31
12230 TTTCGACGCC
12240 AGGCCCTTATTTGAGCATTTTGACAAACGTT
1 AGGCCCTTATTTGAGCATTTTGACAAACGTT
** *
12271 AGGCCCTTATTTG-GCCAAATT-A-AAA-GATC
1 AGGCCCTTATTTGAG-CATTTTGACAAACG-TT
*
12300 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTTGACAAACGTT
* ** *
12331 AGGTCCTTATTTG-GCCAAATT-A-AAA-GATC
1 AGGCCCTTATTTGAG-CATTTTGACAAACG-TT
* *
12360 AGACCCTTATTTGAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTTGACAAACGTT
12391 AGGCCCTTATTTGAGCA
1 AGGCCCTTATTTGAGCA
12408 ATTAGCCTAA
Statistics
Matches: 106, Mismatches: 19, Indels: 24
0.71 0.13 0.16
Matches are distributed among these distances:
28 2 0.02
29 40 0.38
30 5 0.05
31 57 0.54
32 2 0.02
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (31 bp):
AGGCCCTTATTTGAGCATTTTGACAAACGTT
Found at i:12312 original size:29 final size:29
Alignment explanation
Indices: 12271--12372 Score: 100
Period size: 29 Copynumber: 3.4 Consensus size: 29
12261 GACAAACGTT
12271 AGGCCCTTATTTGGCCAAATTAAAAGATC
1 AGGCCCTTATTTGGCCAAATTAAAAGATC
** * *
12300 AGGCCCTTATTTGAG-CATTTTGGCAAACG-TT
1 AGGCCCTTATTTG-GCCAAATT---AAAAGATC
*
12331 AGGTCCTTATTTGGCCAAATTAAAAGATC
1 AGGCCCTTATTTGGCCAAATTAAAAGATC
*
12360 AGACCCTTATTTG
1 AGGCCCTTATTTG
12373 AGCATTTTGG
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
28 4 0.07
29 29 0.52
30 2 0.04
31 17 0.30
32 4 0.07
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (29 bp):
AGGCCCTTATTTGGCCAAATTAAAAGATC
Found at i:12332 original size:60 final size:60
Alignment explanation
Indices: 12239--12403 Score: 303
Period size: 60 Copynumber: 2.8 Consensus size: 60
12229 TTTTCGACGC
*
12239 CAGGCCCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
*
12299 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGTCCTTATTTGGCCAAATTAAAAGAT
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
*
12359 CAGACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
12404 AGCAATTAGC
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 101 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (60 bp):
CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
Found at i:13086 original size:2 final size:2
Alignment explanation
Indices: 13079--13107 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
13069 GCAAAATAAC
13079 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13108 ACACAACCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13373 original size:18 final size:17
Alignment explanation
Indices: 13342--13376 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
13332 GAGCCAGTTT
*
13342 AGTTAGTTTGTTGAGTC
1 AGTTAGTTTCTTGAGTC
13359 AGTTCAGTTTCTTGAGTC
1 AGTT-AGTTTCTTGAGTC
13377 GGTTTGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.17, C:0.11, G:0.26, T:0.46
Consensus pattern (17 bp):
AGTTAGTTTCTTGAGTC
Found at i:13952 original size:2 final size:2
Alignment explanation
Indices: 13945--13971 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13935 ATCACATACT
13945 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
13972 TCATTTGACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.