Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023639.1 Corchorus olitorius cultivar O-4 contig23672, 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: 20767
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Found at i:3992 original size:13 final size:13
Alignment explanation
Indices: 3974--4004 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
3964 AGATTCCCAT
3974 AAAATGAAAAATG
1 AAAATGAAAAATG
3987 AAAATGAAAAATG
1 AAAATGAAAAATG
4000 AAAAT
1 AAAAT
4005 AAAGGCACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.13, T:0.16
Consensus pattern (13 bp):
AAAATGAAAAATG
Found at i:4004 original size:6 final size:7
Alignment explanation
Indices: 3974--4003 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
3964 AGATTCCCAT
3974 AAAATGA
1 AAAATGA
3981 AAAATG-
1 AAAATGA
3987 AAAATGA
1 AAAATGA
3994 AAAATGA
1 AAAATGA
4001 AAA
1 AAA
4004 TAAAGGCACT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (7 bp):
AAAATGA
Found at i:4429 original size:15 final size:15
Alignment explanation
Indices: 4390--4429 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
4380 ATTTAAAAAA
*
4390 AAAATCAAAAAGATC
1 AAAATCAAAAAAATC
**
4405 AAAAAAAAAAAAATC
1 AAAATCAAAAAAATC
4420 AAAATCAAAA
1 AAAATCAAAA
4430 TCAAAATAAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.78, C:0.10, G:0.03, T:0.10
Consensus pattern (15 bp):
AAAATCAAAAAAATC
Found at i:6154 original size:69 final size:69
Alignment explanation
Indices: 6056--6296 Score: 410
Period size: 69 Copynumber: 3.5 Consensus size: 69
6046 CCGAATGCTT
*
6056 TAGGCTTTTCCACAAGCGAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTTCATCCAAGC
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTTCATCCAAGC
6121 CATA
66 CATA
* *
6125 TAGGCTTTTCAACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTTTATCCAAGC
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTTCATCCAAGC
6190 CATA
66 CATA
* *
6194 TAGGCTTTTCCACAAGCCAAACTCATTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGC
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTTCATCCAAGC
6259 CATA
66 CATA
* * *
6263 TAGGTTTTTCCACAAGCCGAATTCGTTTCCATAC
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATAC
6297 AAATCAAGCC
Statistics
Matches: 161, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 161 1.00
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.31
Consensus pattern (69 bp):
TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTTCATCCAAGC
CATA
Found at i:6684 original size:170 final size:170
Alignment explanation
Indices: 6343--6761 Score: 634
Period size: 170 Copynumber: 2.5 Consensus size: 170
6333 CTTATTCCAT
* *
6343 TTGATAAAACCTCCGGGTATCATTTCATTTTATCAAGTTTTTCATCAAAAATTCATGTTTAAGTT
1 TTGATAAAACCTCCGGGTATCATTTCATTTCATCAAGTTTTTCATCAAAGATTCATGTTTAAGTT
* *
6408 TAAAATCCTTGTTCAAGG-TCTCGATTCAAAGTTTGCATTGGTAAGTCCTCCGGGCACAAATTCA
66 TAAAATCCTTGTTTAAGGTTCTCGATTCAAAGTTTCCATTGGTAAGTCCTCCGGGCACAAATTCA
*
6472 GAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGAGCAA
131 GAAACCCCCGGGTATTAATTCTGATAAGTCCTCCGAGCAA
* *
6512 TTGATAAAACCTCCGGGTATCATTCCATTCCATCAAGTTTTTCATCAAAGATTCATGTTTAAGTT
1 TTGATAAAACCTCCGGGTATCATTTCATTTCATCAAGTTTTTCATCAAAGATTCATGTTTAAGTT
* ** *
6577 TAAAACCCTTGTTTAAGGTTC-CTTTTTCAGAGTTTCCATTGGTAAGTCCTCCGGGCACAAATTC
66 TAAAATCCTTGTTTAAGGTTCTC-GATTCAAAGTTTCCATTGGTAAGTCCTCCGGGCACAAATTC
*
6641 AGAAACCCCCGGGTATTAATTCTGATAAGTCCTCCGGGCAA
130 AGAAACCCCCGGGTATTAATTCTGATAAGTCCTCCGAGCAA
* * * *
6682 TTGGTAAAGCCTCCGGGTACCATTTCATTTCATCATGTTTTTCA--AAAG-TTCATGTTTAAG-T
1 TTGATAAAACCTCCGGGTATCATTTCATTTCATCAAGTTTTTCATCAAAGATTCATGTTTAAGTT
*
6743 TAAAATCTTTGTTTAAGGT
66 TAAAATCCTTGTTTAAGGT
6762 CTCATTTCAG
Statistics
Matches: 228, Mismatches: 20, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
166 18 0.08
167 12 0.05
168 4 0.02
169 78 0.34
170 116 0.51
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (170 bp):
TTGATAAAACCTCCGGGTATCATTTCATTTCATCAAGTTTTTCATCAAAGATTCATGTTTAAGTT
TAAAATCCTTGTTTAAGGTTCTCGATTCAAAGTTTCCATTGGTAAGTCCTCCGGGCACAAATTCA
GAAACCCCCGGGTATTAATTCTGATAAGTCCTCCGAGCAA
Found at i:6901 original size:30 final size:30
Alignment explanation
Indices: 6865--7514 Score: 877
Period size: 30 Copynumber: 21.4 Consensus size: 30
6855 GGATCATTGC
* *
6865 ATCATTGCTTGATTTCAATCCTGTTTGAGG
1 ATCATTGCTTTATTTTAATCCTGTTTGAGG
*
6895 ATCATTGCTTTATTTTAATCCTATTTGAGG
1 ATCATTGCTTTATTTTAATCCTGTTTGAGG
* *
6925 ATCATCGCTTTATTTTAACCCTGTTTGAGG
1 ATCATTGCTTTATTTTAATCCTGTTTGAGG
* ** * *
6955 ATCATCGCTCCATTTTAATCCTTTTTTAGG
1 ATCATTGCTTTATTTTAATCCTGTTTGAGG
* *
6985 ATCATCGCTTCTTTTTTAATCCTGTTTGAGG
1 ATCATTGCTT-TATTTTAATCCTGTTTGAGG
* *
7016 ATCTTTGCTTTGTTTTAATCCTGTTTGAGG
1 ATCATTGCTTTATTTTAATCCTGTTTGAGG
* *
7046 ATCACTGCTTTGTTTTAATCCTGTTTGAGG
1 ATCATTGCTTTATTTTAATCCTGTTTGAGG
*
7076 ATCACTGCTTTATTTTAATCCTGTTTGAGG
1 ATCATTGCTTTATTTTAATCCTGTTTGAGG
*
7106 ATCATTGCTTTATTCAATTTAATCCTGTCTGAGG
1 ATCATTGCTTTA-T---TTTAATCCTGTTTGAGG
* *
7140 ATCTTTGCTTTATGTTTAATCCTGGTTGAGG
1 ATCATTGCTTTAT-TTTAATCCTGTTTGAGG
* *
7171 ATCATAGCTTTATTTTAATCCTGGTTGAGG
1 ATCATTGCTTTATTTTAATCCTGTTTGAGG
* * * *
7201 ATCATAGCTTTATTTTTATCCTGGTTAAGG
1 ATCATTGCTTTATTTTAATCCTGTTTGAGG
7231 ATCATTGCTTTATTTTAATCCTGTTTGAGG
1 ATCATTGCTTTATTTTAATCCTGTTTGAGG
7261 ATCATTGCTTTATTTTAATCCTGTTTGAGG
1 ATCATTGCTTTATTTTAATCCTGTTTGAGG
7291 ATCATTGCTTTATGTTTAATCCTGTTTGAGG
1 ATCATTGCTTTAT-TTTAATCCTGTTTGAGG
* * * *
7322 ATCATAGCTTTATTTTTATCCTGGTTAAGG
1 ATCATTGCTTTATTTTAATCCTGTTTGAGG
* * *
7352 ATCATTGCTTCATTTTACTCCTGGTTGAGG
1 ATCATTGCTTTATTTTAATCCTGTTTGAGG
* *
7382 ATCATTGCTTTGTTTTAATCCTGATTGAGG
1 ATCATTGCTTTATTTTAATCCTGTTTGAGG
*
7412 ATCATTGCTTTATTTTAATCCTGGTTGAGG
1 ATCATTGCTTTATTTTAATCCTGTTTGAGG
* *
7442 ATCATTGCTTTGTTTTAATCCTGGTTGAGG
1 ATCATTGCTTTATTTTAATCCTGTTTGAGG
* *
7472 ATCATTGCTTTATTTTAATCATGGTTGAGG
1 ATCATTGCTTTATTTTAATCCTGTTTGAGG
7502 ATCATTGCTTTAT
1 ATCATTGCTTTAT
7515 CAGATTATTG
Statistics
Matches: 560, Mismatches: 54, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
30 452 0.81
31 80 0.14
33 1 0.00
34 27 0.05
ACGTcount: A:0.20, C:0.15, G:0.18, T:0.47
Consensus pattern (30 bp):
ATCATTGCTTTATTTTAATCCTGTTTGAGG
Found at i:7353 original size:151 final size:151
Alignment explanation
Indices: 6865--7514 Score: 881
Period size: 151 Copynumber: 4.3 Consensus size: 151
6855 GGATCATTGC
* * * * **
6865 ATCATTGCTTGATTTCAATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTATTTGAGGATCAT
1 ATCATAGCTTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGGTTGAGGATCAT
* * * ** * * *
6930 CGCTTTATTTTAACCCTGTTTGAGGATCATCGCTCCATTTTAATCCTTTTTTAGGATCATCGCTT
66 TGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTT
* *
6995 CT-TTTTTAATCCTGTTTGAGG
131 -TATGTTTAATCCTGGTTGAGG
* * * * * * * *
7016 ATCTTTGCTTTGTTTTAATCCTGTTTGAGGATCACTGCTTTGTTTTAATCCTGTTTGAGGATCAC
1 ATCATAGCTTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGGTTGAGGATCAT
* *
7081 TGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTATTCAATTTAATCCTGTCTGAGGATCTTT
66 TGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTA-T---TTTAATCCTGTTTGAGGATCATT
7146 GCTTTATGTTTAATCCTGGTTGAGG
127 GCTTTATGTTTAATCCTGGTTGAGG
* * *
7171 ATCATAGCTTTATTTTAATCCTGGTTGAGGATCATAGCTTTATTTTTATCCTGGTTAAGGATCAT
1 ATCATAGCTTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGGTTGAGGATCAT
7236 TGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTT
66 TGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTT
*
7301 TATGTTTAATCCTGTTTGAGG
131 TATGTTTAATCCTGGTTGAGG
* * * *
7322 ATCATAGCTTTATTTTTATCCTGGTTAAGGATCATTGCTTCATTTTACTCCTGGTTGAGGATCAT
1 ATCATAGCTTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGGTTGAGGATCAT
* * *
7387 TGCTTTGTTTTAATCCTGATTGAGGATCATTGCTTTATTTTAATCCTGGTTGAGGATCATTGCTT
66 TGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTT
*
7452 TGT-TTTAATCCTGGTTGAGG
131 TATGTTTAATCCTGGTTGAGG
* *
7472 ATCATTGCTTTATTTTAATCATGGTTGAGGATCATTGCTTTAT
1 ATCATAGCTTTATTTTAATCCTGGTTGAGGATCATTGCTTTAT
7515 CAGATTATTG
Statistics
Matches: 443, Mismatches: 51, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
150 54 0.12
151 256 0.58
152 1 0.00
154 2 0.00
155 130 0.29
ACGTcount: A:0.20, C:0.15, G:0.18, T:0.47
Consensus pattern (151 bp):
ATCATAGCTTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGGTTGAGGATCAT
TGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTT
TATGTTTAATCCTGGTTGAGG
Found at i:17617 original size:48 final size:48
Alignment explanation
Indices: 17497--17620 Score: 160
Period size: 49 Copynumber: 2.5 Consensus size: 48
17487 TTTCCTGCAC
* * *
17497 TTTTCTCAATTTTTACAACAAAATTGAATCTTTATTTTTCCTTGCACCT
1 TTTTCTCAATTTTTA-AACAAAATTGAATATTTACTTTTCATTGCACCT
*
17546 TTTTCTCAATTTTTAAGACAAAATTGAATATTTACTTTTCATTGC-GCT
1 TTTTCTCAATTTTTAA-ACAAAATTGAATATTTACTTTTCATTGCACCT
* *
17594 TTTTATCAATTTTTATACAAAAATTGA
1 TTTTCTCAATTTTTAAAC-AAAATTGA
17621 TTGGCACGCT
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
47 2 0.03
48 25 0.37
49 40 0.60
ACGTcount: A:0.31, C:0.15, G:0.06, T:0.48
Consensus pattern (48 bp):
TTTTCTCAATTTTTAAACAAAATTGAATATTTACTTTTCATTGCACCT
Found at i:19988 original size:33 final size:33
Alignment explanation
Indices: 19941--20021 Score: 92
Period size: 33 Copynumber: 2.5 Consensus size: 33
19931 GTGTTTTAGA
* *
19941 TGTTGTTTGCGATGATACTAAACCTAATTTGA-G
1 TGTTGTTTGTGATGACACTAAACCT-ATTTGAGG
* * *
19974 TGTTGTTTGTGATGACACTAAATCTGTTTTAGG
1 TGTTGTTTGTGATGACACTAAACCTATTTGAGG
*
20007 TATTGTTTGTGATGA
1 TGTTGTTTGTGATGA
20022 AACAAATTCT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
32 4 0.10
33 37 0.90
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.44
Consensus pattern (33 bp):
TGTTGTTTGTGATGACACTAAACCTATTTGAGG
Done.