Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024125.1 Corchorus olitorius cultivar O-4 contig24158, 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: 10802
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Found at i:798 original size:36 final size:36
Alignment explanation
Indices: 758--869 Score: 111
Period size: 36 Copynumber: 3.4 Consensus size: 36
748 CTATCTTCGT
758 GAACTGTCTTCAGATTCACTCTTAATCACCTTTTAG
1 GAACTGTCTTCAGATTCACTCTTAATCACCTTTTAG
*
794 GAACTGTCTTCAGA---AC-C-----CATC-TTT-G
1 GAACTGTCTTCAGATTCACTCTTAATCACCTTTTAG
* *
819 TGAACTGTCTTTAGATTCACTCTTAATTACCTTTTAG
1 -GAACTGTCTTCAGATTCACTCTTAATCACCTTTTAG
856 GAACTGTCTTCAGA
1 GAACTGTCTTCAGA
870 ACCCATCTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 24
0.67 0.06 0.27
Matches are distributed among these distances:
25 1 0.02
26 16 0.27
27 3 0.05
29 2 0.03
30 1 0.02
32 1 0.02
33 2 0.03
35 2 0.03
36 30 0.51
37 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.38
Consensus pattern (36 bp):
GAACTGTCTTCAGATTCACTCTTAATCACCTTTTAG
Found at i:1021 original size:58 final size:58
Alignment explanation
Indices: 714--1290 Score: 550
Period size: 58 Copynumber: 9.7 Consensus size: 58
704 TCCAATTCGT
* * * *
714 TCTTAAAACTCTTTTCAGGAACTGTCTTCAGAACCTATCTTCGTGAACTGTCTTCAG-ATTCAC
1 TCTTAAAA-TCTTTT-AGGAACTGTCTTCAGATCC-ATC-T-GTGAGCTGTCTTCAGCCTT-AA
* * * * * * *
777 TCTTAATCACCTTTTAGGAACTGTCTTCAGAACCCATCTTTGTGAACTGTCTTTAG-ATTCAC
1 TCTTAA-AATCTTTTAGGAACTGTCTTCAG-ATCCATC--TGTGAGCTGTCTTCAGCCTT-AA
* * * * ** * * *
839 TCTTAATTACCTTTTAGGAACTGTCTTCAGAACCCATCTTTTTGAATTGTCTTTAG-ATT-C
1 TCTTAA-AATCTTTTAGGAACTGTCTTCAG-ATCCATC--TGTGAGCTGTCTTCAGCCTTAA
* * * * * * * * * ** * *
899 TCTTAAATATCATTCAGGGACTGTCTTCGGGACCCGTCTATGAACCGTCTTCATACTCAC
1 TCTTAAA-ATCTTTTAGGAACTGTCTTC-AGATCCATCTGTGAGCTGTCTTCAGCCTTAA
* *
959 TCTTAAAATATTTTAGGAACTGTCTTCAGATCCATCTGTGAGCTGTCTTCAGTCTTAA
1 TCTTAAAATCTTTTAGGAACTGTCTTCAGATCCATCTGTGAGCTGTCTTCAGCCTTAA
* *
1017 TCTTAAAATCCTTTAGGAACTGTCTTTAGATCCATCTGTGAGCTGTCTTCAGCCTTAA
1 TCTTAAAATCTTTTAGGAACTGTCTTCAGATCCATCTGTGAGCTGTCTTCAGCCTTAA
* *
1075 TCTTAAAATCTTTTAGGAATTGTCTTCAGATTCATCTGTGAGCTGTCTTCAGCCTTAA
1 TCTTAAAATCTTTTAGGAACTGTCTTCAGATCCATCTGTGAGCTGTCTTCAGCCTTAA
* * *
1133 TCTTAAAATCTTTTAGGAACTGTCTTCAGATCCATCCGTGAGCTGTCTTCAGTCTCAA
1 TCTTAAAATCTTTTAGGAACTGTCTTCAGATCCATCTGTGAGCTGTCTTCAGCCTTAA
* *
1191 CCTTAAAATCTTTTAGGAACTGTCTTCAGATCCATCTGTGAGCTGTCTTTAGCCTTAAA
1 TCTTAAAATCTTTTAGGAACTGTCTTCAGATCCATCTGTGAGCTGTCTTCAGCCTT-AA
* *
1250 TCTTAAAATCTTTTAGGAATTGTCTTCAGATCCATTTGTGA
1 TCTTAAAATCTTTTAGGAACTGTCTTCAGATCCATCTGTGA
1291 TTAATTCTTT
Statistics
Matches: 450, Mismatches: 56, Indels: 20
0.86 0.11 0.04
Matches are distributed among these distances:
58 244 0.54
59 57 0.13
60 37 0.08
61 1 0.00
62 94 0.21
63 16 0.04
64 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.39
Consensus pattern (58 bp):
TCTTAAAATCTTTTAGGAACTGTCTTCAGATCCATCTGTGAGCTGTCTTCAGCCTTAA
Found at i:2030 original size:3 final size:3
Alignment explanation
Indices: 2022--2058 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2012 ATATATATAT
2022 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2059 AAAGATGCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:7079 original size:34 final size:34
Alignment explanation
Indices: 7038--7102 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
7028 GTTTCACTAA
7038 AAACCCGCACGGTGACTATCGCCACACGAGGGCT
1 AAACCCGCACGGTGACTATCGCCACACGAGGGCT
*
7072 AAACCCGCACGGTGACTATTGCCACACGAGG
1 AAACCCGCACGGTGACTATCGCCACACGAGG
7103 ACTAGCTACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.28, C:0.34, G:0.26, T:0.12
Consensus pattern (34 bp):
AAACCCGCACGGTGACTATCGCCACACGAGGGCT
Found at i:7990 original size:43 final size:39
Alignment explanation
Indices: 7923--8237 Score: 219
Period size: 39 Copynumber: 7.6 Consensus size: 39
7913 AATTTTTAAC
*
7923 GGGATCTTTCCCCT-AATTGAAAACTTGAAAACAAAAGACTAGAT
1 GGGATCTTT-CCCTAAATT-AAAACTTG--AA-AAAA-ACTGGAT
*** *
7967 GGGATCTTTCCCTAAATTAAAACTTCTGAAAAACTTGAT
1 GGGATCTTTCCCTAAATTAAAACTTGAAAAAAACTGGAT
* *
8006 GGGATCTTTCCCTGAATTAAAACTTTG---AAGACTGGAT
1 GGGATCTTTCCCTAAATTAAAAC-TTGAAAAAAACTGGAT
*
8043 GGGATCTTTCCCTAAATTAAAAAACTTTAAAAAGAAACTGGAT
1 GGGATCTTTCCCTAAATT--AAAAC-TTGAAAA-AAACTGGAT
*** *
8086 GGGATCTTTCCCTAAATTAAAACTTCTGAAAAACTTGAT
1 GGGATCTTTCCCTAAATTAAAACTTGAAAAAAACTGGAT
* * *
8125 AGGATCTTTCCCTGAATTAAAAAAACTTTGAAAAATACTTTGG-T
1 GGGATCTTTCCCTAAATT---AAAAC-TTGAAAAAAAC--TGGAT
* **
8169 GAGATCTTTCCCTAAATTGAAGTCTTTGAAAAAAATACTTTGG-T
1 GGGATCTTTCCCTAAATT-AAAAC-TTG-AAAAAA-AC--TGGAT
8213 GGGATCTTTCCCTAAATTAAAACTT
1 GGGATCTTTCCCTAAATTAAAACTT
8238 CCTTTTGATT
Statistics
Matches: 223, Mismatches: 32, Indels: 34
0.77 0.11 0.12
Matches are distributed among these distances:
37 25 0.11
39 60 0.27
40 10 0.04
41 5 0.02
42 15 0.07
43 52 0.23
44 54 0.24
45 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (39 bp):
GGGATCTTTCCCTAAATTAAAACTTGAAAAAAACTGGAT
Found at i:8015 original size:39 final size:38
Alignment explanation
Indices: 7955--8237 Score: 262
Period size: 39 Copynumber: 6.9 Consensus size: 38
7945 ACTTGAAAAC
*
7955 AAAAGACTAGATGGGATCTTTCCCTAAATTAAAACTTCTG
1 AAAA-ACTTGATGGGATCTTTCCCTAAATTAAAACTT-TG
*
7995 AAAAACTTGATGGGATCTTTCCCTGAATTAAAACTTTG
1 AAAAACTTGATGGGATCTTTCCCTAAATTAAAACTTTG
* * *
8033 -AAGACTGGATGGGATCTTTCCCTAAATTAAAAAACTTTAAA
1 AAAAACTTGATGGGATCTTTCCCTAAATT--AAAACTTT--G
*
8074 AAGAAACTGGATGGGATCTTTCCCTAAATTAAAACTTCTG
1 AA-AAACTTGATGGGATCTTTCCCTAAATTAAAACTT-TG
* *
8114 AAAAACTTGATAGGATCTTTCCCTGAATTAAAAAAACTTTG
1 AAAAACTTGATGGGATCTTTCCCTAAATT---AAAACTTTG
* * **
8155 AAAAATACTTTGGTGAGATCTTTCCCTAAATTGAAGTCTTTG
1 -AAAA-AC-TTGATGGGATCTTTCCCTAAATT-AAAACTTTG
*
8197 AAAAAAATACTTTGGTGGGATCTTTCCCTAAATTAAAACTT
1 ---AAAA-AC-TTGATGGGATCTTTCCCTAAATTAAAACTT
8238 CCTTTTGATT
Statistics
Matches: 207, Mismatches: 21, Indels: 27
0.81 0.08 0.11
Matches are distributed among these distances:
37 25 0.12
38 2 0.01
39 62 0.30
40 6 0.03
41 9 0.04
42 20 0.10
43 33 0.16
44 50 0.24
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.33
Consensus pattern (38 bp):
AAAAACTTGATGGGATCTTTCCCTAAATTAAAACTTTG
Found at i:8088 original size:119 final size:120
Alignment explanation
Indices: 7923--8238 Score: 383
Period size: 119 Copynumber: 2.6 Consensus size: 120
7913 AATTTTTAAC
* *
7923 GGGATCTTTCCCCT-AATTGAAAACTTGAAAACAAAAGACTAGATGGGATCTTTCCCTAAATTAA
1 GGGATCTTT-CCCTAAATTGAAAACTT-TAAA-AAAAGACTGGATGGGATCTTTCCCTAAATTAA
*
7987 AACTTCTGAAAAACTTGATGGGATCTTTCCCTGAATT-AAAACTTTG-AAGAC-TGGAT
63 AACTTCTGAAAAACTTGATAGGATCTTTCCCTGAATTAAAAACTTTGAAAGACTTGG-T
*
8043 GGGATCTTTCCCTAAATTAAAAAACTTTAAAAAGAA-ACTGGATGGGATCTTTCCCTAAATTAAA
1 GGGATCTTTCCCTAAATT-GAAAACTTTAAAAA-AAGACTGGATGGGATCTTTCCCTAAATTAAA
*
8107 ACTTCTGAAAAACTTGATAGGATCTTTCCCTGAATTAAAAAAACTTTGAAAAATACTTTGGT
64 ACTTCTGAAAAACTTGATAGGATCTTTCCCTGAATT--AAAAACTTTG--AAAGAC-TTGGT
* ** *
8169 GAGATCTTTCCCTAAATTGAAGTCTTTGAAAAAAATACTTTGG-TGGGATCTTTCCCTAAATTAA
1 GGGATCTTTCCCTAAATTGAAAACTTT-AAAAAAAGAC--TGGATGGGATCTTTCCCTAAATTAA
8233 AACTTC
63 AACTTC
8239 CTTTTGATTT
Statistics
Matches: 172, Mismatches: 9, Indels: 23
0.84 0.04 0.11
Matches are distributed among these distances:
119 68 0.40
120 18 0.10
121 7 0.04
122 9 0.05
125 12 0.07
126 25 0.15
127 30 0.17
128 3 0.02
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (120 bp):
GGGATCTTTCCCTAAATTGAAAACTTTAAAAAAAGACTGGATGGGATCTTTCCCTAAATTAAAAC
TTCTGAAAAACTTGATAGGATCTTTCCCTGAATTAAAAACTTTGAAAGACTTGGT
Found at i:8177 original size:44 final size:42
Alignment explanation
Indices: 7969--8234 Score: 188
Period size: 44 Copynumber: 6.5 Consensus size: 42
7959 GACTAGATGG
* *
7969 GATCTTTCCCTAAATT--AAAACTTCTG-AAAA-ACTTGATGG
1 GATCTTTCCCTAAATTAAAAAACTT-TGAAAAATACTTGGTGA
* * *
8008 GATCTTTCCCTGAATT--AAAACTTTG---AAGAC-TGGATGG
1 GATCTTTCCCTAAATTAAAAAACTTTGAAAAATACTTGG-TGA
* * *
8045 GATCTTTCCCTAAATTAAAAAACTTTAAAAAGAAAC-TGGATGG
1 GATCTTTCCCTAAATTAAAAAACTTTGAAAA-ATACTTGG-TGA
*
8088 GATCTTTCCCTAAATT--AAAACTTCTG-AAAA-ACTTGAT-A
1 GATCTTTCCCTAAATTAAAAAACTT-TGAAAAATACTTGGTGA
*
8126 GGATCTTTCCCTGAATTAAAAAAACTTTGAAAAATACTTTGGTGA
1 -GATCTTTCCCTAAATT-AAAAAACTTTGAAAAATAC-TTGGTGA
* ** *
8171 GATCTTTCCCTAAATT-GAAGTCTTTGAAAAAAATACTTTGGTGG
1 GATCTTTCCCTAAATTAAAAAACTTTG--AAAAATAC-TTGGTGA
8215 GATCTTTCCCTAAATTAAAA
1 GATCTTTCCCTAAATTAAAA
8235 CTTCCTTTTG
Statistics
Matches: 190, Mismatches: 16, Indels: 36
0.79 0.07 0.15
Matches are distributed among these distances:
36 4 0.02
37 20 0.11
38 2 0.01
39 48 0.25
40 3 0.02
41 12 0.06
42 20 0.11
43 28 0.15
44 50 0.26
45 3 0.02
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (42 bp):
GATCTTTCCCTAAATTAAAAAACTTTGAAAAATACTTGGTGA
Found at i:10629 original size:30 final size:30
Alignment explanation
Indices: 10595--10662 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
10585 CTGTTAATGC
* *
10595 TTATGTGGCT-TTCTGATTACCTGTATTTGA
1 TTATGTGGCTCTT-TGATGACATGTATTTGA
*
10625 TTATGTGGCTCTTTGATGACATGTATTTGT
1 TTATGTGGCTCTTTGATGACATGTATTTGA
10655 TTATGTGG
1 TTATGTGG
10663 AGTTATGGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 32 0.94
31 2 0.06
ACGTcount: A:0.16, C:0.10, G:0.24, T:0.50
Consensus pattern (30 bp):
TTATGTGGCTCTTTGATGACATGTATTTGA
Done.