Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010741.1 Corchorus capsularis cultivar CVL-1 contig10762, 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: 18495
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1181 original size:29 final size:29
Alignment explanation
Indices: 1111--1180 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
1101 ACAAAACGGT
****
1111 CAAATAAGCCCCTGAACTCTAATTGCAGC
1 CAAATAAGCCCCTGAACTCTAAAAAAAGC
1140 CAAATAAGCCCCTGAACTCTTAAAAAAAGC
1 CAAATAAGCCCCTGAACTC-TAAAAAAAGC
1170 CAAATAAGCCC
1 CAAATAAGCCC
1181 TTTTATGATG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 19 0.53
30 17 0.47
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.17
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTCTAAAAAAAGC
Found at i:1647 original size:30 final size:29
Alignment explanation
Indices: 1611--1704 Score: 86
Period size: 29 Copynumber: 3.1 Consensus size: 29
1601 CGTCAGAAAA
1611 GGGCTTATTTGGCCTTTTTTAAGATTTCAG
1 GGGCTTATTTGGCCTTTTTTAAGA-TTCAG
***
1641 GGGCTTATTTGG-CTGCAATT-AGAGTTCAG
1 GGGCTTATTTGGCCT-TTTTTAAGA-TTCAG
1670 GGGCTTATTTGGCCGTTTTGTGTAAG-TTCAG
1 GGGCTTATTTGGCC-TTTT-T-TAAGATTCAG
1701 GGGC
1 GGGC
1705 CTTTTTGAGC
Statistics
Matches: 51, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
29 22 0.43
30 15 0.29
31 11 0.22
32 1 0.02
33 2 0.04
ACGTcount: A:0.16, C:0.14, G:0.31, T:0.39
Consensus pattern (29 bp):
GGGCTTATTTGGCCTTTTTTAAGATTCAG
Found at i:3956 original size:311 final size:311
Alignment explanation
Indices: 3390--4016 Score: 1155
Period size: 311 Copynumber: 2.0 Consensus size: 311
3380 GGGAAGGGGA
*
3390 TCTTTCAGAAGGGCTGTAAGAAAATTATTAGAACAGGCCATCAGACTTCCTTCTGGCATGACAGA
1 TCTTTCAGAAGGGCTATAAGAAAATTATTAGAACAGGCCATCAGACTTCCTTCTGGCATGACAGA
3455 TGGGCTACTGAATCTCCTTTGCGTTCCCTTATTCAAGGCCCTTACAACAAGGATGAGGATGATAT
66 TGGGCTACTGAATCTCCTTTGCGTTCCCTTATTCAAGGCCCTTACAACAAGGATGAGGATGATAT
*
3520 TTCTGTTTCGCATTGTCTCCATCAAAATGGCAGTTGGGATTTGACCAACATCTCTTTCACTTTTC
131 TTCTGTGTCGCATTGTCTCCATCAAAATGGCAGTTGGGATTTGACCAACATCTCTTTCACTTTTC
* *
3585 CTTCTAAGATTGAAGATCTTATCCTTTCTACCGCCTCATCCCCTTTCTCTTCTAGGGAGGATATG
196 CTTCTAAGATTGAAGATCGTATCCTTTCTACCGCCTCATCCCATTTCTCTTCTAGGGAGGATATG
3650 ATTAGTTGGGTCAACTCTTCTTCTGGTGACTTCTCTCTTCAGACAGCTTAT
261 ATTAGTTGGGTCAACTCTTCTTCTGGTGACTTCTCTCTTCAGACAGCTTAT
3701 TCTTTCAGAAGGGCTATAAGAAAATTATTAGAACAGGCCATCAGACTTCCTTCTGGCATGACAGA
1 TCTTTCAGAAGGGCTATAAGAAAATTATTAGAACAGGCCATCAGACTTCCTTCTGGCATGACAGA
3766 TGGGCTACTGAATCTCCTTTGCGTTCCCTTATTCAAGGCCCTTACAACAAGGATGAGGATGATAT
66 TGGGCTACTGAATCTCCTTTGCGTTCCCTTATTCAAGGCCCTTACAACAAGGATGAGGATGATAT
* * *
3831 TTTTGTGTCGTATTGTCTCCATCAAAATGGCAGTTGGGATTTGACCAACATCTCTTTCATTTTTC
131 TTCTGTGTCGCATTGTCTCCATCAAAATGGCAGTTGGGATTTGACCAACATCTCTTTCACTTTTC
* * *
3896 CTTCTGAGATTGAAGATCGTATCCTTTCTACTGCCTCATCCCATTTCTCTTCTGGGGAGGATATG
196 CTTCTAAGATTGAAGATCGTATCCTTTCTACCGCCTCATCCCATTTCTCTTCTAGGGAGGATATG
*
3961 ATTAGTTGGGTTAACTCTTCTTCTGGTGACTTCTCTCTTCAGACAGCTTAT
261 ATTAGTTGGGTCAACTCTTCTTCTGGTGACTTCTCTCTTCAGACAGCTTAT
4012 TCTTT
1 TCTTT
4017 GGCTGTTGAG
Statistics
Matches: 305, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
311 305 1.00
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.36
Consensus pattern (311 bp):
TCTTTCAGAAGGGCTATAAGAAAATTATTAGAACAGGCCATCAGACTTCCTTCTGGCATGACAGA
TGGGCTACTGAATCTCCTTTGCGTTCCCTTATTCAAGGCCCTTACAACAAGGATGAGGATGATAT
TTCTGTGTCGCATTGTCTCCATCAAAATGGCAGTTGGGATTTGACCAACATCTCTTTCACTTTTC
CTTCTAAGATTGAAGATCGTATCCTTTCTACCGCCTCATCCCATTTCTCTTCTAGGGAGGATATG
ATTAGTTGGGTCAACTCTTCTTCTGGTGACTTCTCTCTTCAGACAGCTTAT
Found at i:14052 original size:34 final size:36
Alignment explanation
Indices: 14014--14084 Score: 128
Period size: 34 Copynumber: 2.0 Consensus size: 36
14004 TTGGAATAAT
14014 AGAGAGTCATGGTTTTCAAAAATG-TTT-TTCAAAA
1 AGAGAGTCATGGTTTTCAAAAATGTTTTCTTCAAAA
14048 AGAGAGTCATGGTTTTCAAAAATGTTTTCTTCAAAA
1 AGAGAGTCATGGTTTTCAAAAATGTTTTCTTCAAAA
14084 A
1 A
14085 ATGTTTTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
34 24 0.69
35 3 0.09
36 8 0.23
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (36 bp):
AGAGAGTCATGGTTTTCAAAAATGTTTTCTTCAAAA
Found at i:14124 original size:49 final size:48
Alignment explanation
Indices: 14028--14145 Score: 130
Period size: 49 Copynumber: 2.4 Consensus size: 48
14018 AGTCATGGTT
**** *
14028 TTCAAAAATGTTTTTCAAAAAGAGAGTCATGGTTTTCAAAAATGTTTTC
1 TTCAAAAATGTTTTTC-AAAAGAGAGTCATGGTAAAAAAAAAGGTTTTC
*
14077 TTCAAAAAATGTTTTTCAAAAGAGAGTCATGG-AAAAAAAAAGGGTTTTT
1 TTC-AAAAATGTTTTTCAAAAGAGAGTCATGGTAAAAAAAAA-GGTTTTC
* *
14126 TTCAAAGATGTTCTTCAAAA
1 TTCAAAAATGTTTTTCAAAA
14146 ATAATTTTCG
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
48 20 0.34
49 26 0.44
50 13 0.22
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (48 bp):
TTCAAAAATGTTTTTCAAAAGAGAGTCATGGTAAAAAAAAAGGTTTTC
Found at i:14786 original size:12 final size:12
Alignment explanation
Indices: 14769--14832 Score: 59
Period size: 12 Copynumber: 5.7 Consensus size: 12
14759 TTCCAAGTGC
14769 AATGAAAAAATG
1 AATGAAAAAATG
14781 AATG-AAAAATG
1 AATGAAAAAATG
14792 AA--AAAATAAT-
1 AATGAAAA-AATG
*
14802 AA--ATAAAATG
1 AATGAAAAAATG
14812 AATGAAAAAATG
1 AATGAAAAAATG
14824 AATGGAAAA
1 AAT-GAAAA
14833 GAGCTCTAGG
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
9 3 0.07
10 10 0.23
11 12 0.27
12 14 0.32
13 5 0.11
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (12 bp):
AATGAAAAAATG
Found at i:16031 original size:14 final size:14
Alignment explanation
Indices: 16014--16073 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
16004 ATGCCCCAGT
16014 TTCAATTTCAATTC
1 TTCAATTTCAATTC
** *
16028 TTCAACCTC-AGT-
1 TTCAATTTCAATTC
*
16040 TTCAATTCTTCAATGC
1 TTCAA-T-TTCAATTC
16056 TTCAATTTCAATTC
1 TTCAATTTCAATTC
16070 TTCA
1 TTCA
16074 GCGCTTCAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
12 5 0.15
13 2 0.06
14 20 0.59
15 2 0.06
16 5 0.15
ACGTcount: A:0.27, C:0.25, G:0.03, T:0.45
Consensus pattern (14 bp):
TTCAATTTCAATTC
Found at i:16031 original size:28 final size:27
Alignment explanation
Indices: 15984--16061 Score: 77
Period size: 28 Copynumber: 2.7 Consensus size: 27
15974 TCTTCAATGC
*
15984 TTCAATTCCTCAATTATTCAATGCCCCAGT
1 TTCAATT--TCAATTCTTCAAT-CCCCAGT
*
16014 TTCAATTTCAATTCTTCAA-CCTCAGT
1 TTCAATTTCAATTCTTCAATCCCCAGT
*
16040 TTCAATTCTTCAATGCTTCAAT
1 TTCAA-T-TTCAATTCTTCAAT
16062 TTCAATTCTT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
26 11 0.26
27 1 0.02
28 23 0.55
30 7 0.17
ACGTcount: A:0.27, C:0.27, G:0.05, T:0.41
Consensus pattern (27 bp):
TTCAATTTCAATTCTTCAATCCCCAGT
Found at i:16051 original size:8 final size:8
Alignment explanation
Indices: 16040--16110 Score: 55
Period size: 8 Copynumber: 9.6 Consensus size: 8
16030 CAACCTCAGT
16040 TTCAATTC
1 TTCAATTC
*
16048 TTCAATGC
1 TTCAATTC
16056 TTCAA-T-
1 TTCAATTC
16062 TTCAATTC
1 TTCAATTC
***
16070 TTCAGCGC
1 TTCAATTC
16078 TTCAA-T-
1 TTCAATTC
*
16084 TTCAATAC
1 TTCAATTC
16092 TTCAA-T-
1 TTCAATTC
16098 TTCAATTC
1 TTCAATTC
16106 TTCAA
1 TTCAA
16111 ATTCCAAATG
Statistics
Matches: 48, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
6 15 0.31
7 2 0.04
8 31 0.65
ACGTcount: A:0.28, C:0.24, G:0.04, T:0.44
Consensus pattern (8 bp):
TTCAATTC
Found at i:16067 original size:22 final size:22
Alignment explanation
Indices: 16014--16206 Score: 154
Period size: 22 Copynumber: 8.9 Consensus size: 22
16004 ATGCCCCAGT
16014 TTCAATTTCAATTCTTCAA--C
1 TTCAATTTCAATTCTTCAATGC
* *
16034 CTCAGTTTCAATTCTTCAATGC
1 TTCAATTTCAATTCTTCAATGC
**
16056 TTCAATTTCAATTCTTCAGCGC
1 TTCAATTTCAATTCTTCAATGC
*
16078 TTCAATTTCAATACTTCAAT--
1 TTCAATTTCAATTCTTCAATGC
16098 TTCAATTCTTCAAATTC--CAAATGC
1 TTCAA-T-TTC-AATTCTTC-AATGC
* *
16122 --CAATGCTTCAATCCTTCAATGT
1 TTCAAT--TTCAATTCTTCAATGC
* *
16144 TTCAATTTCAATTTTTCAATGT
1 TTCAATTTCAATTCTTCAATGC
16166 TTCAATTTCAATAT-TTCAATGC
1 TTCAATTTCAAT-TCTTCAATGC
*
16188 TTTAAATTT-AATTCTTCAA
1 -TTCAATTTCAATTCTTCAA
16207 ATTCCAAATG
Statistics
Matches: 141, Mismatches: 16, Indels: 30
0.75 0.09 0.16
Matches are distributed among these distances:
20 22 0.16
21 8 0.06
22 94 0.67
23 13 0.09
24 4 0.03
ACGTcount: A:0.30, C:0.22, G:0.05, T:0.44
Consensus pattern (22 bp):
TTCAATTTCAATTCTTCAATGC
Found at i:16131 original size:36 final size:35
Alignment explanation
Indices: 16050--16133 Score: 89
Period size: 36 Copynumber: 2.3 Consensus size: 35
16040 TTCAATTCTT
** **
16050 CAATGCTTCAATTTCAATTCTTCAGCGCTTCAATTT
1 CAATGCTTCAATTTCAATTCTTCA-CAATTCAATGC
*
16086 CAATACTTCAATTTCAATTCTTCA-AATTCCAAATGC
1 CAATGCTTCAATTTCAATTCTTCACAATT-C-AATGC
16122 CAATGCTTCAAT
1 CAATGCTTCAAT
16134 CCTTCAATGT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
34 2 0.05
35 1 0.03
36 37 0.93
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (35 bp):
CAATGCTTCAATTTCAATTCTTCACAATTCAATGC
Found at i:16147 original size:8 final size:8
Alignment explanation
Indices: 16122--16186 Score: 57
Period size: 8 Copynumber: 8.6 Consensus size: 8
16112 TTCCAAATGC
*
16122 CAATGCTT
1 CAATGTTT
**
16130 CAATCCTT
1 CAATGTTT
16138 CAATGTTT
1 CAATGTTT
16146 CAA--TTT
1 CAATGTTT
*
16152 CAATTTTT
1 CAATGTTT
16160 CAATGTTT
1 CAATGTTT
16168 CAA--TTT
1 CAATGTTT
*
16174 CAATATTT
1 CAATGTTT
16182 CAATG
1 CAATG
16187 CTTTAAATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
6 12 0.25
8 36 0.75
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.46
Consensus pattern (8 bp):
CAATGTTT
Found at i:16234 original size:14 final size:14
Alignment explanation
Indices: 16078--16243 Score: 67
Period size: 14 Copynumber: 11.4 Consensus size: 14
16068 TCTTCAGCGC
*
16078 TTCAATTTCAATAC
1 TTCAATTTCAATAT
16092 TTCAATTTCAAT-T
1 TTCAATTTCAATAT
*
16105 CTTCAAATTCCAA-AT
1 -TTC-AATTTCAATAT
** **
16120 GCCAATGCTTCAATCC
1 TTCAAT--TTCAATAT
16136 TTCAATGTTTC-A-AT
1 TTCAA--TTTCAATAT
*
16150 TTCAATTTTTCAATGT
1 TTCAA--TTTCAATAT
16166 TTCAATTTCAATAT
1 TTCAATTTCAATAT
*
16180 TTCAATGCTTTAA-AT
1 TTCAAT--TTCAATAT
16195 TT-AATTCTTCAA-AT
1 TTCAA-T-TTCAATAT
* *
16209 TCCAAATGTCAATAT
1 TTC-AATTTCAATAT
16224 TTCAATTTCAATAT
1 TTCAATTTCAATAT
*
16238 GTCAAT
1 TTCAAT
16244 GCTTCAATTT
Statistics
Matches: 115, Mismatches: 21, Indels: 32
0.68 0.12 0.19
Matches are distributed among these distances:
13 3 0.03
14 69 0.60
15 24 0.21
16 18 0.16
18 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.04, T:0.44
Consensus pattern (14 bp):
TTCAATTTCAATAT
Found at i:16253 original size:22 final size:22
Alignment explanation
Indices: 16201--16280 Score: 65
Period size: 22 Copynumber: 3.6 Consensus size: 22
16191 AAATTTAATT
* *
16201 CTTCAAATTCCAA-ATGTCAATA
1 CTTC-AATTTCAATATGTCAATG
*
16223 TTTCAATTTCAATATGTCAATG
1 CTTCAATTTCAATATGTCAATG
* * *
16245 CTTCAATTTCGAT-TCTTCCATTG
1 CTTCAATTTCAATAT-GT-CAATG
16268 CTTCAATTTCAAT
1 CTTCAATTTCAAT
16281 TCTTCGAATT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
21 8 0.17
22 23 0.49
23 16 0.34
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.42
Consensus pattern (22 bp):
CTTCAATTTCAATATGTCAATG
Found at i:16292 original size:14 final size:14
Alignment explanation
Indices: 16268--16315 Score: 64
Period size: 14 Copynumber: 3.4 Consensus size: 14
16258 TCTTCCATTG
16268 CTTCAATTTCAATT
1 CTTCAATTTCAATT
16282 CTTCGAA-TTCAATGT
1 CTTC-AATTTCAAT-T
16297 -TTCAATTTCAATT
1 CTTCAATTTCAATT
16310 CTTCAA
1 CTTCAA
16316 AGCCTCCTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
13 3 0.10
14 24 0.80
15 3 0.10
ACGTcount: A:0.29, C:0.21, G:0.04, T:0.46
Consensus pattern (14 bp):
CTTCAATTTCAATT
Done.