Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009224.1 Corchorus capsularis cultivar CVL-1 contig09245, 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: 17063
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:721 original size:20 final size:20
Alignment explanation
Indices: 683--721 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
673 GAATCTTTTG
*
683 TTTTTGTTTTTTTTCTTAAA
1 TTTTTGTTTTCTTTCTTAAA
703 TTTTATGTTTTCTTT-TTAA
1 TTTT-TGTTTTCTTTCTTAA
722 TAGAACTCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.15, C:0.05, G:0.05, T:0.74
Consensus pattern (20 bp):
TTTTTGTTTTCTTTCTTAAA
Found at i:1238 original size:6 final size:6
Alignment explanation
Indices: 1227--1251 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1217 CTGGAGTGTG
1227 GCCTCT GCCTCT GCCTCT GCCTCT G
1 GCCTCT GCCTCT GCCTCT GCCTCT G
1252 AACTCTCTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.48, G:0.20, T:0.32
Consensus pattern (6 bp):
GCCTCT
Found at i:3937 original size:3 final size:3
Alignment explanation
Indices: 3929--3959 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3919 TCAAAAGAAA
3929 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT T
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT T
3960 TTTTTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TGT
Found at i:3964 original size:1 final size:1
Alignment explanation
Indices: 3958--3982 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
3948 GTTGTTGTTG
3958 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
3983 CTGAATTTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:5898 original size:33 final size:33
Alignment explanation
Indices: 5801--5961 Score: 189
Period size: 33 Copynumber: 4.9 Consensus size: 33
5791 AAATAGCCTT
* * *
5801 GCCGCCCTAGTGGGGCGGCTCCGTCATGGCAGA
1 GCCGCCCTAGTGGGGAGGCTCCGCCGTGGCAGA
* * * * *
5834 GTCGTCTTAGTGGGGTGGCT-AGCCGTGGCAGA
1 GCCGCCCTAGTGGGGAGGCTCCGCCGTGGCAGA
* * * *
5866 GCTGTCCTAGTGGGGCGGCTCCGCTGTGGCAGA
1 GCCGCCCTAGTGGGGAGGCTCCGCCGTGGCAGA
*
5899 GCCGCCCAAGTGGGGAGGCTCCGCCGTGGCAGA
1 GCCGCCCTAGTGGGGAGGCTCCGCCGTGGCAGA
*
5932 GCCGCCCCAGTGGGGAGGCTCCGCCGTGGC
1 GCCGCCCTAGTGGGGAGGCTCCGCCGTGGC
5962 TAAGGGCAAA
Statistics
Matches: 108, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
32 25 0.23
33 83 0.77
ACGTcount: A:0.11, C:0.30, G:0.42, T:0.16
Consensus pattern (33 bp):
GCCGCCCTAGTGGGGAGGCTCCGCCGTGGCAGA
Found at i:5911 original size:65 final size:66
Alignment explanation
Indices: 5801--5961 Score: 191
Period size: 65 Copynumber: 2.5 Consensus size: 66
5791 AAATAGCCTT
* * * ** *
5801 GCCGCCCTAGTGGGGCGGCTCCG-TCATGGCAGAGTCGTCTTAGTGGGGTGGCT-AGCCGTGGCA
1 GCCGCCCTAGTGGGGCGGCTCCGCT-GTGGCAGAGCCGCCCAAGTGGGGAGGCTCAGCCGTGGCA
5864 GA
65 GA
* * *
5866 GCTGTCCTAGTGGGGCGGCTCCGCTGTGGCAGAGCCGCCCAAGTGGGGAGGCTCCGCCGTGGCAG
1 GCCGCCCTAGTGGGGCGGCTCCGCTGTGGCAGAGCCGCCCAAGTGGGGAGGCTCAGCCGTGGCAG
5931 A
66 A
* * *
5932 GCCGCCCCAGTGGGGAGGCTCCGCCGTGGC
1 GCCGCCCTAGTGGGGCGGCTCCGCTGTGGC
5962 TAAGGGCAAA
Statistics
Matches: 80, Mismatches: 14, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
65 43 0.54
66 37 0.46
ACGTcount: A:0.11, C:0.30, G:0.42, T:0.16
Consensus pattern (66 bp):
GCCGCCCTAGTGGGGCGGCTCCGCTGTGGCAGAGCCGCCCAAGTGGGGAGGCTCAGCCGTGGCAG
A
Found at i:6384 original size:17 final size:17
Alignment explanation
Indices: 6364--6396 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6354 GCAGCCTATC
6364 ACCTCATACTACCTAGT
1 ACCTCATACTACCTAGT
*
6381 ACCTTATACTACCTAG
1 ACCTCATACTACCTAG
6397 GTACTATGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.33, G:0.06, T:0.30
Consensus pattern (17 bp):
ACCTCATACTACCTAGT
Found at i:6565 original size:21 final size:21
Alignment explanation
Indices: 6541--6601 Score: 97
Period size: 21 Copynumber: 3.0 Consensus size: 21
6531 CAGAAGAGTT
6541 CGCCTTCCTCAGCAAGTAAAA
1 CGCCTTCCTCAGCAAGTAAAA
6562 CGCCTTCCTCAGCAAGT-AAA
1 CGCCTTCCTCAGCAAGTAAAA
* *
6582 TGCCTTCTTCAGCAAGTAAA
1 CGCCTTCCTCAGCAAGTAAA
6602 GCCCGCCAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 18 0.49
21 19 0.51
ACGTcount: A:0.31, C:0.31, G:0.15, T:0.23
Consensus pattern (21 bp):
CGCCTTCCTCAGCAAGTAAAA
Found at i:6588 original size:20 final size:20
Alignment explanation
Indices: 6541--6601 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
6531 CAGAAGAGTT
6541 CGCCTTCCTCAGCAAGTAAAA
1 CGCCTTCCTCAGCAAGT-AAA
6562 CGCCTTCCTCAGCAAGTAAA
1 CGCCTTCCTCAGCAAGTAAA
* *
6582 TGCCTTCTTCAGCAAGTAAA
1 CGCCTTCCTCAGCAAGTAAA
6602 GCCCGCCAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
20 21 0.55
21 17 0.45
ACGTcount: A:0.31, C:0.31, G:0.15, T:0.23
Consensus pattern (20 bp):
CGCCTTCCTCAGCAAGTAAA
Found at i:9872 original size:156 final size:157
Alignment explanation
Indices: 9586--9949 Score: 395
Period size: 156 Copynumber: 2.3 Consensus size: 157
9576 TCATCTCAAA
* * *
9586 CAGACTTAGCATGAAAAACTTATGCTAGTTTTTCAGTTAAGGA-CAGTTTGAGGAGACAAACCAA
1 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACCAGCTTGAGGAGACAAACCAA
* * * * *
9650 CTTCTCTATGCTAGAGAGTTAGGTTTCACTTAGAATTTTTCCCATAGCTTTATGGTGATAATCTA
66 CTTCACCATGCAAGAGAGCTAGGTTTCACTTAGAATTTTTCCCATAGCTTTATGGTGATAAGCTA
* * *
9715 AGTATATTGGTGGAAA-ATCAGCTTCGTT
131 AGTACATTGG-CGAAATATCAGC-TCATT
* * * *
9743 -GGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACCA-CTTGGGGAGAGAAACCTA
1 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACCAGCTTGAGGAGACAAACCAA
* * * * * *
9806 GTTCACCAT-CAAGGGGAGCTCGGTTTTACTTAGAATTTTTTCCATAG-TCTTAT-GTGGATACG
66 CTTCACCATGCAA-GAGAGCTAGGTTTCACTTAGAATTTTTCCCATAGCT-TTATGGT-GATAAG
* * *
9868 CTAAGTCCCTTGGCGAAATTTCAGCTCATT
128 CTAAGTACATTGGCGAAATATCAGCTCATT
*
9898 CAGACTTAGAATG-AAAACTTATGCTAGTTTTTCATTTAAGGA-CAGTTTGAGG
1 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACCAGCTTGAGG
9950 TGAGAAGCTC
Statistics
Matches: 173, Mismatches: 27, Indels: 16
0.80 0.12 0.07
Matches are distributed among these distances:
154 2 0.01
155 47 0.27
156 122 0.71
157 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.34
Consensus pattern (157 bp):
CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACCAGCTTGAGGAGACAAACCAA
CTTCACCATGCAAGAGAGCTAGGTTTCACTTAGAATTTTTCCCATAGCTTTATGGTGATAAGCTA
AGTACATTGGCGAAATATCAGCTCATT
Found at i:12082 original size:2 final size:2
Alignment explanation
Indices: 12075--12105 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12065 CATCAATGGC
12075 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 A
12106 AACCAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12474 original size:69 final size:70
Alignment explanation
Indices: 12391--12530 Score: 255
Period size: 69 Copynumber: 2.0 Consensus size: 70
12381 AGTAGTAATC
* *
12391 ATGTCAAACGTTGATGATGTTGGTTGAGATTAAAATTGTT-AAGAGTTTGTGTTGAATAAAAGAT
1 ATGTCAAACATTGATGAGGTTGGTTGAGATTAAAATTGTTCAAGAGTTTGTGTTGAATAAAAGAT
12455 TATAT
66 TATAT
12460 ATGTCAAACATTGATGAGGTTGGTTGAGATTAAAATTGTTCAAGAGTTTGTGTTGAATAAAAGAT
1 ATGTCAAACATTGATGAGGTTGGTTGAGATTAAAATTGTTCAAGAGTTTGTGTTGAATAAAAGAT
12525 TATAT
66 TATAT
12530 A
1 A
12531 ATATGTTAAT
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
69 38 0.56
70 30 0.44
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.38
Consensus pattern (70 bp):
ATGTCAAACATTGATGAGGTTGGTTGAGATTAAAATTGTTCAAGAGTTTGTGTTGAATAAAAGAT
TATAT
Found at i:13000 original size:49 final size:50
Alignment explanation
Indices: 12921--13017 Score: 151
Period size: 49 Copynumber: 1.9 Consensus size: 50
12911 GTGTTCAGGT
**
12921 CCTACACAAAAATAGATGTAATTATCATATAAAGTTAAAATTAAAAGATCA
1 CCTACACAAAAATA-ATGTAATTATCATATAAAACTAAAATTAAAAGATCA
*
12972 CCTACACAAAAAT-ATGTAATTATTATATAAAACTAAAATTAAAAGA
1 CCTACACAAAAATAATGTAATTATCATATAAAACTAAAATTAAAAGA
13018 AAAGTAAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
49 30 0.70
51 13 0.30
ACGTcount: A:0.55, C:0.11, G:0.06, T:0.28
Consensus pattern (50 bp):
CCTACACAAAAATAATGTAATTATCATATAAAACTAAAATTAAAAGATCA
Found at i:14517 original size:17 final size:17
Alignment explanation
Indices: 14491--14526 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
14481 AAGCCATGTA
*
14491 ATCTTTGATCACCAGTG
1 ATCTTGGATCACCAGTG
*
14508 ATCTTGGATCACTAGTG
1 ATCTTGGATCACCAGTG
14525 AT
1 AT
14527 TTAGGGGGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.36
Consensus pattern (17 bp):
ATCTTGGATCACCAGTG
Found at i:15154 original size:16 final size:16
Alignment explanation
Indices: 15133--15164 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
15123 AGATGCAAAT
*
15133 TTATAATGTAATGTGG
1 TTATAATCTAATGTGG
15149 TTATAATCTAATGTGG
1 TTATAATCTAATGTGG
15165 GTTGTGGGCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.03, G:0.22, T:0.44
Consensus pattern (16 bp):
TTATAATCTAATGTGG
Done.