Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024065.1 Corchorus olitorius cultivar O-4 contig24098, 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: 20780
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:1023 original size:33 final size:33
Alignment explanation
Indices: 970--1050 Score: 83
Period size: 33 Copynumber: 2.5 Consensus size: 33
960 GTGTTTTAGA
* * *
970 TGTTGTTTGCGATGATACTAAACCTAATTTGA-G
1 TGTTATTTGTGATGACACTAAACCT-ATTTGAGG
* * * *
1003 TGTTCTTTGTGATGACACTAAATCTGTTTTAGG
1 TGTTATTTGTGATGACACTAAACCTATTTGAGG
1036 TGTTATTTGTGATGA
1 TGTTATTTGTGATGA
1051 AACAAATAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
32 4 0.10
33 36 0.90
ACGTcount: A:0.23, C:0.10, G:0.22, T:0.44
Consensus pattern (33 bp):
TGTTATTTGTGATGACACTAAACCTATTTGAGG
Found at i:1083 original size:37 final size:37
Alignment explanation
Indices: 1021--1095 Score: 100
Period size: 37 Copynumber: 2.0 Consensus size: 37
1011 GTGATGACAC
* *
1021 TAAATCTGTTTTAGGTGTTATTTGTGATG-AAACAAA
1 TAAATCTGTTTTAGGTGCTAATTGTGATGAAAACAAA
1057 TAAATTCTGTTTT-GGATGCTAATTGTGATGAAAACAAA
1 TAAA-TCTGTTTTAGG-TGCTAATTGTGATGAAAACAAA
1095 T
1 T
1096 CTGTTTTGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 6 0.18
37 20 0.59
38 8 0.24
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.40
Consensus pattern (37 bp):
TAAATCTGTTTTAGGTGCTAATTGTGATGAAAACAAA
Found at i:1104 original size:33 final size:32
Alignment explanation
Indices: 1009--1105 Score: 88
Period size: 37 Copynumber: 2.8 Consensus size: 32
999 TGAGTGTTCT
* * *
1009 TTGTGATG-ACACTAAATCTGTTTTAGGTGTTAT
1 TTGTGATGAAAAC-AAATCTGTTTT-GGTGCTAA
*
1042 TTGTGATGAAACAAATAAATTCTGTTTTGGATGCTAA
1 TTGTGATG--A-AAACAAA-TCTGTTTTGG-TGCTAA
1079 TTGTGATGAAAACAAATCTGTTTTGGT
1 TTGTGATGAAAACAAATCTGTTTTGGT
1106 TGATCATAGC
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
32 1 0.02
33 18 0.34
34 6 0.11
35 1 0.02
36 5 0.09
37 22 0.42
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.41
Consensus pattern (32 bp):
TTGTGATGAAAACAAATCTGTTTTGGTGCTAA
Found at i:1461 original size:36 final size:36
Alignment explanation
Indices: 1410--1478 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
1400 CATTAGAGAA
1410 ATTGAATCCAATCCATATG-GTGTGCGATACAAGTTC
1 ATTGAATCCAATCCATATGTG-GTGCGATACAAGTTC
** *
1446 ATTGAATCCTTTCCATATGTGGTGCGCTACAAG
1 ATTGAATCCAATCCATATGTGGTGCGATACAAG
1479 AAAGGTAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
36 28 0.97
37 1 0.03
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (36 bp):
ATTGAATCCAATCCATATGTGGTGCGATACAAGTTC
Found at i:2934 original size:21 final size:21
Alignment explanation
Indices: 2908--2996 Score: 153
Period size: 21 Copynumber: 4.2 Consensus size: 21
2898 TGCTAGGAGT
2908 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
2929 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
2950 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
*
2971 TCATTGGAG-AAGGTTTCAAGC
1 TCATTGGAGCAA-GTTCCAAGC
2992 TCATT
1 TCATT
2997 AGAATTATCT
Statistics
Matches: 66, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
20 2 0.03
21 64 0.97
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (21 bp):
TCATTGGAGCAAGTTCCAAGC
Found at i:4229 original size:21 final size:21
Alignment explanation
Indices: 4205--4270 Score: 98
Period size: 21 Copynumber: 3.1 Consensus size: 21
4195 ACCAGCCCGT
4205 GCCACCACCATGCCAAGACCG
1 GCCACCACCATGCCAAGACCG
*
4226 GCCATCACCATGCCAAGACCG
1 GCCACCACCATGCCAAGACCG
*
4247 GCCACTC-CCGTGCCAAGACCG
1 GCCAC-CACCATGCCAAGACCG
4268 GCC
1 GCC
4271 TTGCCCGTGC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 40 0.98
22 1 0.02
ACGTcount: A:0.24, C:0.47, G:0.21, T:0.08
Consensus pattern (21 bp):
GCCACCACCATGCCAAGACCG
Found at i:4277 original size:21 final size:20
Alignment explanation
Indices: 4215--4295 Score: 99
Period size: 21 Copynumber: 3.9 Consensus size: 20
4205 GCCACCACCA
*
4215 TGCCAAGACCGGCCATCACCA
1 TGCCAAGACCGGCCATC-CCG
4236 TGCCAAGACCGGCCACTCCCG
1 TGCCAAGACCGGCCA-TCCCG
*
4257 TGCCAAGACCGGCCTTGCCCG
1 TGCCAAGACCGGCCAT-CCCG
**
4278 TGCCACCACCGGCCATCC
1 TGCCAAGACCGGCCATCC
4296 ACGCACCAAC
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.06
21 48 0.91
22 2 0.04
ACGTcount: A:0.20, C:0.47, G:0.22, T:0.11
Consensus pattern (20 bp):
TGCCAAGACCGGCCATCCCG
Found at i:7153 original size:13 final size:13
Alignment explanation
Indices: 7135--7159 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7125 GAGAAGAAAG
7135 AAGTTACTCTTAC
1 AAGTTACTCTTAC
7148 AAGTTACTCTTA
1 AAGTTACTCTTA
7160 TTAGGCCTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (13 bp):
AAGTTACTCTTAC
Found at i:9306 original size:15 final size:15
Alignment explanation
Indices: 9286--9317 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
9276 TAGGGCAAGT
9286 AGGGGTCGATCCCAC
1 AGGGGTCGATCCCAC
9301 AGGGGTCGATCCCAC
1 AGGGGTCGATCCCAC
9316 AG
1 AG
9318 AGAAGGGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.22, C:0.31, G:0.34, T:0.12
Consensus pattern (15 bp):
AGGGGTCGATCCCAC
Found at i:9431 original size:16 final size:15
Alignment explanation
Indices: 9393--9432 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
9383 AGAGGTTGAA
9393 AGAAAACAATTAAAC
1 AGAAAACAATTAAAC
* *
9408 ATAAAACAATTATAC
1 AGAAAACAATTAAAC
9423 TAGAAAACAA
1 -AGAAAACAA
9433 AACAAAGCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.65, C:0.12, G:0.05, T:0.17
Consensus pattern (15 bp):
AGAAAACAATTAAAC
Found at i:15859 original size:21 final size:22
Alignment explanation
Indices: 15829--15878 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
15819 TTTTTTTTTC
* *
15829 AAAAAGACGCAAACACAA-AAA
1 AAAAAAACGCAAAAACAACAAA
*
15850 TAAAAAACGCAAAAACAACAAA
1 AAAAAAACGCAAAAACAACAAA
15872 AAAAAAA
1 AAAAAAA
15879 TTTTTAAGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.76, C:0.16, G:0.06, T:0.02
Consensus pattern (22 bp):
AAAAAAACGCAAAAACAACAAA
Found at i:16192 original size:15 final size:15
Alignment explanation
Indices: 16172--16210 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
16162 AGAGGTTGAA
16172 AGAAAACAATTAAAC-
1 AGAAAACAA-TAAACT
*
16187 AGAAAACAATATACT
1 AGAAAACAATAAACT
16202 AGAAAACAA
1 AGAAAACAA
16211 AACAAAGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.67, C:0.13, G:0.08, T:0.13
Consensus pattern (15 bp):
AGAAAACAATAAACT
Found at i:17012 original size:10 final size:10
Alignment explanation
Indices: 16997--17023 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
16987 TAAAGAGAAT
16997 TATGTGAAGG
1 TATGTGAAGG
17007 TATGTGAAGG
1 TATGTGAAGG
17017 TATGTGA
1 TATGTGA
17024 TCGGTCGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (10 bp):
TATGTGAAGG
Found at i:19637 original size:11 final size:11
Alignment explanation
Indices: 19621--19645 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19611 GGGGAATAAT
19621 CAATCCAAAAA
1 CAATCCAAAAA
19632 CAATCCAAAAA
1 CAATCCAAAAA
19643 CAA
1 CAA
19646 ACAATTTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.28, G:0.00, T:0.08
Consensus pattern (11 bp):
CAATCCAAAAA
Done.