Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015124.1 Corchorus capsularis cultivar CVL-1 contig15145, 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: 10272
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:3588 original size:8 final size:8
Alignment explanation
Indices: 3575--3604 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
3565 CAAATTAATT
3575 TTCAATAC
1 TTCAATAC
*
3583 TTCAATCC
1 TTCAATAC
3591 TTCAATAC
1 TTCAATAC
3599 TTCAAT
1 TTCAAT
3605 TTATATCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.40
Consensus pattern (8 bp):
TTCAATAC
Found at i:3646 original size:8 final size:8
Alignment explanation
Indices: 3624--3839 Score: 61
Period size: 8 Copynumber: 26.2 Consensus size: 8
3614 AATAATCTCT
3624 TTCTTCAA
1 TTCTTCAA
* *
3632 CTATTCAA
1 TTCTTCAA
*
3640 TGCTTCAA
1 TTCTTCAA
* *
3648 ATCTTCCA
1 TTCTTCAA
*
3656 TTATTCAA
1 TTCTTCAA
3664 TTCTTCAA
1 TTCTTCAA
*
3672 TACTTCAA
1 TTCTTCAA
3680 -T-TT--A
1 TTCTTCAA
*
3684 TCTCTTCGA
1 T-TCTTCAA
3693 TTCTTCAA
1 TTCTTCAA
*
3701 TTATTCAA
1 TTCTTCAA
* *
3709 TACTTTGATCCA
1 T--TCT--TCAA
3721 TCTCTTCAA
1 T-TCTTCAA
* * *
3730 CTCCTCCA
1 TTCTTCAA
*
3738 TTATTCAA
1 TTCTTCAA
*
3746 ATCTTCAA
1 TTCTTCAA
*
3754 TTATTCAA
1 TTCTTCAA
3762 TAT-TTCAATTA
1 T-TCTTC-A--A
3773 TTTCTTCAA
1 -TTCTTCAA
**
3782 TTCTTTGA
1 TTCTTCAA
3790 TTACTT--A
1 TT-CTTCAA
3797 TTGCTTCAA
1 TT-CTTCAA
*
3806 TTTTTCAA
1 TTCTTCAA
3814 TTAC-TCAA
1 TT-CTTCAA
*
3822 TGCTTCAA
1 TTCTTCAA
3830 TTCTTCAA
1 TTCTTCAA
3838 TT
1 TT
3840 TACTTCAATG
Statistics
Matches: 150, Mismatches: 38, Indels: 40
0.66 0.17 0.18
Matches are distributed among these distances:
4 1 0.01
6 3 0.02
7 9 0.06
8 107 0.71
9 14 0.09
10 2 0.01
11 6 0.04
12 8 0.05
ACGTcount: A:0.27, C:0.23, G:0.03, T:0.47
Consensus pattern (8 bp):
TTCTTCAA
Found at i:3724 original size:37 final size:37
Alignment explanation
Indices: 3649--3754 Score: 97
Period size: 37 Copynumber: 2.9 Consensus size: 37
3639 ATGCTTCAAA
* * * **
3649 TCTTCCATTATTCAATTCTTCAATACTTCAATTTATC
1 TCTTCAATTCTTCAATTATTCAATACTTCAATCCATC
* **
3686 TCTTCGATTCTTCAATTATTCAATACTTTGATCCATC
1 TCTTCAATTCTTCAATTATTCAATACTTCAATCCATC
* * *
3723 TCTTCAACTCCTCCATTATTCAA-ATCTTCAAT
1 TCTTCAATTCTTCAATTATTCAATA-CTTCAAT
3755 TATTCAATAT
Statistics
Matches: 55, Mismatches: 13, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
36 1 0.02
37 54 0.98
ACGTcount: A:0.26, C:0.26, G:0.02, T:0.45
Consensus pattern (37 bp):
TCTTCAATTCTTCAATTATTCAATACTTCAATCCATC
Found at i:3797 original size:24 final size:25
Alignment explanation
Indices: 3770--3844 Score: 84
Period size: 24 Copynumber: 3.1 Consensus size: 25
3760 AATATTTCAA
* *
3770 TTATTTCTTCAATTCTTT-GATTAC
1 TTATTGCTTCAATTCTTTCAATTAC
3794 TTATTGCTTCAATT-TTTCAATTAC
1 TTATTGCTTCAATTCTTTCAATTAC
* *
3818 TCAATGCTTCAATTC-TTCAATTTAC
1 TTATTGCTTCAATTCTTTCAA-TTAC
3843 TT
1 TT
3845 CAATGACCCA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
23 3 0.07
24 35 0.81
25 5 0.12
ACGTcount: A:0.24, C:0.19, G:0.04, T:0.53
Consensus pattern (25 bp):
TTATTGCTTCAATTCTTTCAATTAC
Found at i:3920 original size:58 final size:59
Alignment explanation
Indices: 3825--3955 Score: 144
Period size: 58 Copynumber: 2.3 Consensus size: 59
3815 TACTCAATGC
* * * * *
3825 TTCAAT-TCTTCAATTTACTTCAATGACCCAGGGTGGT-CTTTCTTCGTTTCTTCAATTA
1 TTCAATGTCTTCAATTTACTTCAATGACACAGGATGGTCCTTCCTCCG-TTCCTCAATTA
* * *
3883 TTCAATGT-TTCAATTTGCTTCAATGATACATGATGGTCCTTCCTCCGTTCCTCAATTA
1 TTCAATGTCTTCAATTTACTTCAATGACACAGGATGGTCCTTCCTCCGTTCCTCAATTA
*
3941 TTCAATG-CCTCAATT
1 TTCAATGTCTTCAATT
3956 CCAAATTTTC
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
58 53 0.87
59 8 0.13
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.43
Consensus pattern (59 bp):
TTCAATGTCTTCAATTTACTTCAATGACACAGGATGGTCCTTCCTCCGTTCCTCAATTA
Found at i:3979 original size:14 final size:14
Alignment explanation
Indices: 3962--4176 Score: 97
Period size: 14 Copynumber: 16.0 Consensus size: 14
3952 AATTCCAAAT
*
3962 TTTCAATGCTTCAA
1 TTTCAATTCTTCAA
3976 TTTCAATTCTTCAA
1 TTTCAATTCTTCAA
*
3990 ATTCAA-TC--C--
1 TTTCAATTCTTCAA
*
3999 -TCCAATGT-TTCAA
1 TTTCAAT-TCTTCAA
*
4012 TTTCAATTCCTCAA
1 TTTCAATTCTTCAA
**
4026 TGTTTCAAGGCTTCAA
1 --TTTCAATTCTTCAA
4042 TTTCAATTCTTCAA
1 TTTCAATTCTTCAA
*
4056 ATTCAA-TC--C--
1 TTTCAATTCTTCAA
*
4065 -TTCAGTGT-TTCAA
1 TTTCAAT-TCTTCAA
4078 TTTCAATTCTTCAA
1 TTTCAATTCTTCAA
* * *
4092 ATTCAAATCTTGAA
1 TTTCAATTCTTCAA
*
4106 CGTTTCAATTC--AATA
1 --TTTCAATTCTTCA-A
* *
4121 TTTCAATGCTTCAG
1 TTTCAATTCTTCAA
4135 TTTCAATTCTTCAA
1 TTTCAATTCTTCAA
4149 TGCTTCAA--CTTCAA
1 T--TTCAATTCTTCAA
4163 TTTCAATTCTTCAA
1 TTTCAATTCTTCAA
4177 ATTCCAAACG
Statistics
Matches: 150, Mismatches: 24, Indels: 54
0.66 0.11 0.24
Matches are distributed among these distances:
8 8 0.05
10 2 0.01
11 4 0.03
12 5 0.03
13 14 0.09
14 92 0.61
15 2 0.01
16 23 0.15
ACGTcount: A:0.29, C:0.22, G:0.06, T:0.43
Consensus pattern (14 bp):
TTTCAATTCTTCAA
Found at i:3988 original size:22 final size:21
Alignment explanation
Indices: 3934--4055 Score: 81
Period size: 22 Copynumber: 5.5 Consensus size: 21
3924 CCTCCGTTCC
*
3934 TCAATTATTCAATGCCTCAATT
1 TCAATT-TTCAATGCTTCAATT
*
3956 CCAAATTTTCAATGCTTCAATT
1 TC-AATTTTCAATGCTTCAATT
*
3978 TCAATTCTTCAA--ATTCAATCCT
1 TCAATT-TTCAATGCTTCAAT--T
*
4000 CCAATGTTTCAAT--TTCAATT
1 TCAAT-TTTCAATGCTTCAATT
*
4020 CCTCAATGTTTCAAGGCTTCAATT
1 --TCAAT-TTTCAATGCTTCAATT
4044 TCAATTCTTCAA
1 TCAATT-TTCAA
4056 ATTCAATCCT
Statistics
Matches: 82, Mismatches: 7, Indels: 22
0.74 0.06 0.20
Matches are distributed among these distances:
20 7 0.09
21 5 0.06
22 58 0.71
23 5 0.06
24 7 0.09
ACGTcount: A:0.30, C:0.24, G:0.05, T:0.41
Consensus pattern (21 bp):
TCAATTTTCAATGCTTCAATT
Found at i:4011 original size:66 final size:66
Alignment explanation
Indices: 3949--4086 Score: 208
Period size: 66 Copynumber: 2.1 Consensus size: 66
3939 TATTCAATGC
*
3949 CTCAATTCC-AAAT-TTTCAATGCTTCAATTTCAATTCTTCAAATTCAATCCTCCAATGTTTCAA
1 CTCAATTCCTAAATGTTTCAAGGCTTCAATTTCAATTCTTCAAATTCAATCCTCCAATGTTTCAA
4012 T
66 T
* * * *
4013 TTCAATTCCTCAATGTTTCAAGGCTTCAATTTCAATTCTTCAAATTCAATCCTTCAGTGTTTCAA
1 CTCAATTCCTAAATGTTTCAAGGCTTCAATTTCAATTCTTCAAATTCAATCCTCCAATGTTTCAA
4078 T
66 T
*
4079 TTCAATTC
1 CTCAATTC
4087 TTCAAATTCA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
64 8 0.12
65 3 0.04
66 56 0.84
ACGTcount: A:0.29, C:0.24, G:0.05, T:0.42
Consensus pattern (66 bp):
CTCAATTCCTAAATGTTTCAAGGCTTCAATTTCAATTCTTCAAATTCAATCCTCCAATGTTTCAA
T
Found at i:4068 original size:22 final size:22
Alignment explanation
Indices: 3977--4091 Score: 96
Period size: 22 Copynumber: 5.2 Consensus size: 22
3967 ATGCTTCAAT
3977 TTCAAT-TCTTCAAATTCAATCC
1 TTCAATGT-TTCAAATTCAATCC
* *
3999 TCCAATGTTTCAATTTCAATTCC
1 TTCAATGTTTCAAATTCAA-TCC
*
4022 -TCAATGTTTCAAGGCTTCAAT--
1 TTCAATGTTTCAA--ATTCAATCC
4043 TTCAAT-TCTTCAAATTCAATCC
1 TTCAATGT-TTCAAATTCAATCC
* * *
4065 TTCAGTGTTTCAATTTCAATTC
1 TTCAATGTTTCAAATTCAATCC
4087 TTCAA
1 TTCAA
4092 ATTCAAATCT
Statistics
Matches: 75, Mismatches: 9, Indels: 18
0.74 0.09 0.18
Matches are distributed among these distances:
20 6 0.08
21 1 0.01
22 57 0.76
23 6 0.08
24 5 0.07
ACGTcount: A:0.29, C:0.23, G:0.05, T:0.43
Consensus pattern (22 bp):
TTCAATGTTTCAAATTCAATCC
Found at i:4111 original size:36 final size:36
Alignment explanation
Indices: 3963--4119 Score: 168
Period size: 36 Copynumber: 4.6 Consensus size: 36
3953 ATTCCAAATT
*
3963 TTCAATGCTTCAATTTCAATTCTTCAAATTCAATCC
1 TTCAATGTTTCAATTTCAATTCTTCAAATTCAATCC
* **
3999 TCCAATGTTTCAATTTCAATTC--C----TCAATGT
1 TTCAATGTTTCAATTTCAATTCTTCAAATTCAATCC
* *
4029 TTCAAGGCTTCAATTTCAATTCTTCAAATTCAATCC
1 TTCAATGTTTCAATTTCAATTCTTCAAATTCAATCC
*
4065 TTCAGTGTTTCAATTTCAATTCTTCAAATTCAAAT-C
1 TTCAATGTTTCAATTTCAATTCTTCAAATTC-AATCC
* *
4101 TTGAACGTTTCAA-TTCAAT
1 TTCAATGTTTCAATTTCAAT
4120 ATTTCAATGC
Statistics
Matches: 99, Mismatches: 15, Indels: 15
0.77 0.12 0.12
Matches are distributed among these distances:
30 24 0.24
32 1 0.01
34 1 0.01
35 6 0.06
36 64 0.65
37 3 0.03
ACGTcount: A:0.30, C:0.22, G:0.06, T:0.42
Consensus pattern (36 bp):
TTCAATGTTTCAATTTCAATTCTTCAAATTCAATCC
Found at i:4112 original size:66 final size:65
Alignment explanation
Indices: 3963--4205 Score: 211
Period size: 66 Copynumber: 3.9 Consensus size: 65
3953 ATTCCAAATT
*
3963 TTCAATGCTTCAATTTCAATTCTTCAAATTCAATCCTCCAATGTTTCAATTTCAATTCCTCAATG
1 TTCAAAGCTTCAATTTCAATTCTTCAAATTCAATCCTCCAATGTTTCAATTTCAATTCCTCAA-G
*
4028 T
65 A
* * * *
4029 TTCAAGGCTTCAATTTCAATTCTTCAAATTCAATCCTTCAGTGTTTCAATTTCAATTCTTCAA-A
1 TTCAAAGCTTCAATTTCAATTCTTCAAATTCAATCCTCCAATGTTTCAATTTCAATTCCTCAAGA
* * * ** * * * *
4093 TTCAAATCTTGAA---C--GT-TTC-AATTCAATATTTCAATGCTTCAGTTTCAATTCTTCAATG
1 TTCAAAGCTTCAATTTCAATTCTTCAAATTCAATCCTCCAATGTTTCAATTTCAATTCCTCAA-G
*
4151 C
65 A
* * *
4152 TTC-AA-CTTCAATTTCAATTCTTCAAATTCCAAACGT-CAATGTTTCGATTTCAAT
1 TTCAAAGCTTCAATTTCAATTCTTCAAATT-CAATCCTCCAATGTTTCAATTTCAAT
4206 ATGTCAATGC
Statistics
Matches: 144, Mismatches: 23, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
57 37 0.26
58 5 0.03
59 4 0.03
60 1 0.01
61 1 0.01
62 1 0.01
63 3 0.02
64 29 0.20
65 4 0.03
66 59 0.41
ACGTcount: A:0.30, C:0.22, G:0.06, T:0.42
Consensus pattern (65 bp):
TTCAAAGCTTCAATTTCAATTCTTCAAATTCAATCCTCCAATGTTTCAATTTCAATTCCTCAAGA
Found at i:4139 original size:22 final size:22
Alignment explanation
Indices: 4077--4272 Score: 145
Period size: 22 Copynumber: 9.0 Consensus size: 22
4067 CAGTGTTTCA
* *
4077 ATTTCAATTCTTCAAATTCAA-
1 ATTTCAATGCTTCAATTTCAAT
* * *
4098 ATCTTGAACGTTTCAA-TTCAAT
1 AT-TTCAATGCTTCAATTTCAAT
*
4120 ATTTCAATGCTTCAGTTTCAAT
1 ATTTCAATGCTTCAATTTCAAT
*
4142 -TCTTCAATGCTTCAACTTC-A-
1 AT-TTCAATGCTTCAATTTCAAT
* *
4162 ATTTCAATTCTTCAAATTCCAA-
1 ATTTCAATGCTTC-AATTTCAAT
** * *
4184 ACGTCAATGTTTCGATTTCAAT
1 ATTTCAATGCTTCAATTTCAAT
*
4206 ATGTCAATGCTTCAGATTTCAAT
1 ATTTCAATGCTTCA-ATTTCAAT
*
4229 ATGTCAATGCTTCAATTTCAAT
1 ATTTCAATGCTTCAATTTCAAT
* *
4251 -TCTTCCACGCTTCAATTTCAAT
1 AT-TTCAATGCTTCAATTTCAAT
4273 TCTTCGAATT
Statistics
Matches: 140, Mismatches: 25, Indels: 19
0.76 0.14 0.10
Matches are distributed among these distances:
20 10 0.07
21 30 0.21
22 78 0.56
23 22 0.16
ACGTcount: A:0.30, C:0.21, G:0.07, T:0.41
Consensus pattern (22 bp):
ATTTCAATGCTTCAATTTCAAT
Found at i:4307 original size:20 final size:20
Alignment explanation
Indices: 4239--4292 Score: 72
Period size: 22 Copynumber: 2.6 Consensus size: 20
4229 ATGTCAATGC
* *
4239 TTCAATTTCAATTCTTCCACGC
1 TTCAATTTCAATTCTTCGA--A
4261 TTCAATTTCAATTCTTCGAA
1 TTCAATTTCAATTCTTCGAA
4281 TTCAATTTCAAT
1 TTCAATTTCAAT
4293 GTTTTGATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 12 0.40
22 18 0.60
ACGTcount: A:0.28, C:0.24, G:0.04, T:0.44
Consensus pattern (20 bp):
TTCAATTTCAATTCTTCGAA
Found at i:4981 original size:15 final size:15
Alignment explanation
Indices: 4946--4980 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
4936 GCTGACTTAC
4946 TAAAAATAAAATAAA
1 TAAAAATAAAATAAA
4961 TAAAAATAAAA-AAA
1 TAAAAATAAAATAAA
4975 TAAAAA
1 TAAAAA
4981 AACAATTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
TAAAAATAAAATAAA
Found at i:8353 original size:7 final size:7
Alignment explanation
Indices: 8338--8369 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
8328 AAATCAAATC
8338 AAATCAA
1 AAATCAA
*
8345 AATTCAA
1 AAATCAA
8352 AAATCAA
1 AAATCAA
8359 AAATCAA
1 AAATCAA
8366 AAAT
1 AAAT
8370 TTTTCATCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.69, C:0.12, G:0.00, T:0.19
Consensus pattern (7 bp):
AAATCAA
Done.