Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009766.1 Corchorus capsularis cultivar CVL-1 contig09787, 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: 52135
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:219 original size:3 final size:3
Alignment explanation
Indices: 205--234 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
195 AGTACATATG
*
205 ATA ATG ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
235 TGTCAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:23556 original size:2 final size:2
Alignment explanation
Indices: 23549--23583 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
23539 GGCGATTTGA
23549 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
23584 AAGTTAGCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25554 original size:19 final size:18
Alignment explanation
Indices: 25530--25574 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
25520 ACTAACCGAG
25530 AAACCGAAAAAACCGATCA
1 AAACCGAAAAAACCGA-CA
** *
25549 AAACCGATGAAACCGACT
1 AAACCGAAAAAACCGACA
25567 AAACCGAA
1 AAACCGAA
25575 TTGTATCGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.53, C:0.27, G:0.13, T:0.07
Consensus pattern (18 bp):
AAACCGAAAAAACCGACA
Found at i:26775 original size:60 final size:59
Alignment explanation
Indices: 26682--26842 Score: 241
Period size: 59 Copynumber: 2.7 Consensus size: 59
26672 TGCTAATTGC
* * * *
26682 TCAAATAAGGGTCTAACGTTTGTCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGG
1 TCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCC-CATCTTTGAATTTGG
* *
26742 TCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAAGACCCATCTTTGAATTTGG
1 TCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCATCTTTGAATTTGG
* *
26801 CCAAATAAGGGCCTAACGTTTACCAAAATGCTCAAATAAGGG
1 TCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGG
26843 TCTGTCTCAC
Statistics
Matches: 91, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
59 51 0.56
60 40 0.44
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (59 bp):
TCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCATCTTTGAATTTGG
Found at i:26910 original size:31 final size:29
Alignment explanation
Indices: 26872--27100 Score: 162
Period size: 31 Copynumber: 7.6 Consensus size: 29
26862 AAACTGACAC
26872 TAGGCCCTTATTTGAGCATTTTCGATAACGT
1 TAGGCCCTTATTTGAGCATTTT-GA-AACGT
* ** *
26903 TAGGCCCTTATTTGACCAAATT-AAAAGAT
1 TAGGCCCTTATTTGAGCATTTTGAAACG-T
**
26932 CGGGCCCTTATTTGAGCATTTTCGATAACGT
1 TAGGCCCTTATTTGAGCATTTT-GA-AACGT
** *
26963 TAGGCCCTTATTTG-GCCAAATT-AAAAGAT
1 TAGGCCCTTATTTGAG-CATTTTGAAACG-T
* *
26992 CAGACCCTTATTTGAGCATTTTCGATAACGT
1 TAGGCCCTTATTTGAGCATTTT-GA-AACGT
** * *
27023 TAGGCCCTTATTT-AGCAAAATT-AAAAGA
1 TAGGCCCTTATTTGAGC-ATTTTGAAACGT
*
27051 TCGAGCCCTTATTTGAGCATTTTGGCAAACGT
1 TAG-GCCCTTATTTGAGCATTTT-G-AAACGT
27083 TAGGCCCTTATTTGAGCA
1 TAGGCCCTTATTTGAGCA
27101 ATTAGCCTTT
Statistics
Matches: 150, Mismatches: 32, Indels: 32
0.70 0.15 0.15
Matches are distributed among these distances:
28 11 0.07
29 51 0.34
30 8 0.05
31 68 0.45
32 12 0.08
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (29 bp):
TAGGCCCTTATTTGAGCATTTTGAAACGT
Found at i:26967 original size:60 final size:60
Alignment explanation
Indices: 26874--27097 Score: 362
Period size: 60 Copynumber: 3.7 Consensus size: 60
26864 ACTGACACTA
26874 GGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCG
* *
26934 GGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCA
1 GGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCG
* *
26994 GACCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTT-AGCAAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGA-CCAAATTAAAAGATCG
* *
27054 AGCCCTTATTTGAGCATTTTGGCA-AACGTTAGGCCCTTATTTGA
1 GGCCCTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTTGA
27098 GCAATTAGCC
Statistics
Matches: 152, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
60 150 0.99
61 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (60 bp):
GGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCG
Found at i:29253 original size:30 final size:30
Alignment explanation
Indices: 29213--29317 Score: 131
Period size: 30 Copynumber: 3.5 Consensus size: 30
29203 TAACAGCCAG
*
29213 CTGTAAATCCTGCGGCACTGGAACATCTGT
1 CTGTAAATCCTGCGGCAGTGGAACATCTGT
* * * *
29243 CTGTACATCCTGCGGCAGAGGATCATCAGT
1 CTGTAAATCCTGCGGCAGTGGAACATCTGT
*
29273 TTGTAAATCCTGCGGCAGTGGAACATCTG-
1 CTGTAAATCCTGCGGCAGTGGAACATCTGT
*
29302 CTTGTACATCCTGCGG
1 C-TGTAAATCCTGCGG
29318 TGGAGCTGAA
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
30 62 1.00
ACGTcount: A:0.22, C:0.26, G:0.26, T:0.27
Consensus pattern (30 bp):
CTGTAAATCCTGCGGCAGTGGAACATCTGT
Found at i:32892 original size:11 final size:11
Alignment explanation
Indices: 32878--32915 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
32868 ATTCATAACA
32878 AATTTATAATT
1 AATTTATAATT
32889 AATTTATAATT
1 AATTTATAATT
32900 -ATTTGATAATT
1 AATTT-ATAATT
*
32911 TATTT
1 AATTT
32916 TCTATGGGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:35940 original size:16 final size:16
Alignment explanation
Indices: 35921--36021 Score: 62
Period size: 16 Copynumber: 6.3 Consensus size: 16
35911 CCGTCCAATT
35921 CGAGACCCAAATGACC
1 CGAGACCCAAATGACC
* *
35937 CGAGACCCGAACGACC
1 CGAGACCCAAATGACC
* *
35953 CGTA-ACTCAGATGACC
1 CG-AGACCCAAATGACC
* *
35969 CGTA-ACCTAAGTGACC
1 CG-AGACCCAAATGACC
**
35985 CGAGACCCGTATGACC
1 CGAGACCCAAATGACC
* * * *
36001 TGAAACCCGAATAACC
1 CGAGACCCAAATGACC
36017 CGAGA
1 CGAGA
36022 AGTTAACCCG
Statistics
Matches: 63, Mismatches: 20, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
15 1 0.02
16 61 0.97
17 1 0.02
ACGTcount: A:0.34, C:0.35, G:0.21, T:0.11
Consensus pattern (16 bp):
CGAGACCCAAATGACC
Found at i:36632 original size:42 final size:42
Alignment explanation
Indices: 36562--36643 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
36552 TGTTGACACA
* *
36562 TACCCCACATGATAATTAATTATGTATTTAATATTCAAAACC
1 TACCCCACATGATAATCAATTATATATTTAATATTCAAAACC
* *
36604 TACCTCACCTGATAATCAATTATATATTTAATATTCAAAA
1 TACCCCACATGATAATCAATTATATATTTAATATTCAAAA
36644 TTAATATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.41, C:0.18, G:0.04, T:0.37
Consensus pattern (42 bp):
TACCCCACATGATAATCAATTATATATTTAATATTCAAAACC
Found at i:36917 original size:16 final size:16
Alignment explanation
Indices: 36871--36917 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
36861 CCCGTCCAAC
36871 CCGAAACCCGGTA-GAT
1 CCGAAACCC-GTATGAT
* *
36887 CCGAGACCCGAATGAT
1 CCGAAACCCGTATGAT
*
36903 CCGAAACTCGTATGA
1 CCGAAACCCGTATGA
36918 CCCTAGACCC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.32, C:0.30, G:0.23, T:0.15
Consensus pattern (16 bp):
CCGAAACCCGTATGAT
Found at i:37138 original size:12 final size:12
Alignment explanation
Indices: 37121--37159 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
37111 CGTTTGATTT
37121 TACCGTATGTTA
1 TACCGTATGTTA
* *
37133 TACCGTCTGATTT
1 TACCGTATG-TTA
37146 TACCGTATGTTA
1 TACCGTATGTTA
37158 TA
1 TA
37160 TTGTTTAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.23, C:0.18, G:0.15, T:0.44
Consensus pattern (12 bp):
TACCGTATGTTA
Found at i:37143 original size:25 final size:25
Alignment explanation
Indices: 37105--37159 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
37095 AAAATACTTT
* *
37105 TTATGCCGTTTGATTTTACCGTATG
1 TTATACCGTCTGATTTTACCGTATG
37130 TTATACCGTCTGATTTTACCGTATG
1 TTATACCGTCTGATTTTACCGTATG
37155 TTATA
1 TTATA
37160 TTGTTTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.47
Consensus pattern (25 bp):
TTATACCGTCTGATTTTACCGTATG
Found at i:37151 original size:13 final size:13
Alignment explanation
Indices: 37110--37154 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
37100 ACTTTTTATG
*
37110 CCGTTTGATTTTA
1 CCGTATGATTTTA
*
37123 CCGTATG-TTATA
1 CCGTATGATTTTA
*
37135 CCGTCTGATTTTA
1 CCGTATGATTTTA
37148 CCGTATG
1 CCGTATG
37155 TTATATTGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.44
Consensus pattern (13 bp):
CCGTATGATTTTA
Found at i:38888 original size:31 final size:29
Alignment explanation
Indices: 38821--38880 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 29
38811 TTCAATTTTG
38821 TACTCA-AAAAATGATCAATTAGACCCTA
1 TACTCACAAAAATGATCAATTAGACCCTA
* *
38849 TACTCACAAAATTGAGTCAATATAGTCCCTA
1 TACTCACAAAAATGA-TCAAT-TAGACCCTA
38880 T
1 T
38881 TTTCACAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 6 0.22
29 7 0.26
30 5 0.19
31 9 0.33
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.28
Consensus pattern (29 bp):
TACTCACAAAAATGATCAATTAGACCCTA
Found at i:41119 original size:31 final size:29
Alignment explanation
Indices: 41081--41168 Score: 86
Period size: 29 Copynumber: 3.0 Consensus size: 29
41071 GAGGCTAAAT
**
41081 AATCAATTCAGGATATAACGTTTGCTTGAAA
1 AATCAATTCAGGATATAACGTTT-C-AAAAA
**
41112 AATCAATTTGGGATATAACGTTTCAAAAA
1 AATCAATTCAGGATATAACGTTTCAAAAA
* * * *
41141 AATCTATTCAAGATATAACATTACAAAA
1 AATCAATTCAGGATATAACGTTTCAAAA
41169 GAGTAACAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
29 25 0.53
30 1 0.02
31 21 0.45
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.31
Consensus pattern (29 bp):
AATCAATTCAGGATATAACGTTTCAAAAA
Found at i:42815 original size:30 final size:29
Alignment explanation
Indices: 42738--42815 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
42728 ACCTTCTCGT
* ***
42738 AACGTTATATCCTGAATAGTTTTTTTTGA
1 AACGTTATATCCTGAATTGTTTTTCAGGA
**
42767 AACGTTATATCCCAAATTGTTTTTCAGGCA
1 AACGTTATATCCTGAATTGTTTTTCAGG-A
42797 AACGTTATATCCTGAATTG
1 AACGTTATATCCTGAATTG
42816 GTTATTTAGC
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 22 0.55
30 18 0.45
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.41
Consensus pattern (29 bp):
AACGTTATATCCTGAATTGTTTTTCAGGA
Done.