Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011376.1 Corchorus capsularis cultivar CVL-1 contig11397, 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: 13789
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Found at i:2844 original size:18 final size:18
Alignment explanation
Indices: 2823--2857 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2813 CACACACAAA
2823 AAAAAGGCCCAACACATG
1 AAAAAGGCCCAACACATG
*
2841 AAAACGGCCCAACACAT
1 AAAAAGGCCCAACACAT
2858 CTCTTCTTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.31, G:0.14, T:0.06
Consensus pattern (18 bp):
AAAAAGGCCCAACACATG
Found at i:3040 original size:35 final size:35
Alignment explanation
Indices: 2944--3042 Score: 135
Period size: 35 Copynumber: 2.8 Consensus size: 35
2934 AACCAAAATA
** * *
2944 CCACATGGCATAAGGGCCTTCATATGCCGTGGTCT
1 CCACATGGCATAAGGATCTTCATATGTCGCGGTCT
* *
2979 GCACATGGCATAAGGATATTCATATGTCGCGGTCT
1 CCACATGGCATAAGGATCTTCATATGTCGCGGTCT
*
3014 CCACATGGCATAAAGATCTTCATATGTCG
1 CCACATGGCATAAGGATCTTCATATGTCG
3043 TAGCACAACA
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 55 1.00
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.27
Consensus pattern (35 bp):
CCACATGGCATAAGGATCTTCATATGTCGCGGTCT
Found at i:3118 original size:17 final size:17
Alignment explanation
Indices: 3096--3130 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3086 CAAAAAATGT
3096 GGACCAAGCCCACTGCG
1 GGACCAAGCCCACTGCG
3113 GGACCAAGCCCACTGCG
1 GGACCAAGCCCACTGCG
3130 G
1 G
3131 AAAACCTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.40, G:0.31, T:0.06
Consensus pattern (17 bp):
GGACCAAGCCCACTGCG
Found at i:4284 original size:52 final size:52
Alignment explanation
Indices: 4203--4305 Score: 161
Period size: 52 Copynumber: 2.0 Consensus size: 52
4193 GGTTTTTCTC
* **
4203 GCAACAACTTCTGTCCCGAAGTTGTACAAGTTCTGGGCCAAAGTTGTCCTGT
1 GCAACAACTTCTGTCCCGAACTTAAACAAGTTCTGGGCCAAAGTTGTCCTGT
* *
4255 GCAACAACTTCTGTCCTGAACTTAAACAAGTTCTGGGCCGAAGTTGTCCTG
1 GCAACAACTTCTGTCCCGAACTTAAACAAGTTCTGGGCCAAAGTTGTCCTG
4306 AAATTCTTGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.28
Consensus pattern (52 bp):
GCAACAACTTCTGTCCCGAACTTAAACAAGTTCTGGGCCAAAGTTGTCCTGT
Found at i:7867 original size:36 final size:37
Alignment explanation
Indices: 7825--7976 Score: 202
Period size: 36 Copynumber: 4.2 Consensus size: 37
7815 CTCTTTTTAG
* *
7825 ATTAAGTTC-TTTATTAACTCCACTTAATTACCCTGA
1 ATTAAGTTCTTTTATTGACGCCACTTAATTACCCTGA
*
7861 ATTAAGTTC-TTTATTGACTCCACTTAATTACCCTGA
1 ATTAAGTTCTTTTATTGACGCCACTTAATTACCCTGA
* *
7897 ATTAAG-TCTTTTATTGACGCTACTTAATTATCCTGA
1 ATTAAGTTCTTTTATTGACGCCACTTAATTACCCTGA
* * * *
7933 ATTAAGTCCTTTTATTGACGCTATTTAATTACCCCGA
1 ATTAAGTTCTTTTATTGACGCCACTTAATTACCCTGA
7970 ATTAAGT
1 ATTAAGT
7977 CTCTAACTTG
Statistics
Matches: 106, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
35 2 0.02
36 71 0.67
37 33 0.31
ACGTcount: A:0.29, C:0.20, G:0.09, T:0.42
Consensus pattern (37 bp):
ATTAAGTTCTTTTATTGACGCCACTTAATTACCCTGA
Found at i:8053 original size:69 final size:68
Alignment explanation
Indices: 7968--8160 Score: 219
Period size: 74 Copynumber: 2.7 Consensus size: 68
7958 TAATTACCCC
*
7968 GAATTAAG-TCTCTAACTTGACTTGATTCCCCTCCTTGGAATCAAGTCCTT-AACTTAATTCCCT
1 GAATTAAGTTCT-TAACTT-ACTT-AATCCCCTCCTTGGAATCAAGTCCTTCAACTTAATTCCCT
8031 TCCTTG
63 TCCTTG
* *
8037 GAATTAAGTTCTTAACTTTACTTAATCCCATTCCTTGGAATCAAGTCCTAAACTCTACTTAATTC
1 GAATTAAGTTCTTAAC-TTACTTAATCCC-CTCCTTGGAATCAAGTCCT----TCAACTTAATTC
8102 CCTTCCTTG
60 CCTTCCTTG
* * *
8111 GAATTAGGTCCTTTACTCTACTTAATCCCCTTCCTTGGAATCAAGTCCTT
1 GAATTAAGTTCTTAACT-TACTTAATCCCC-TCCTTGGAATCAAGTCCTT
8161 TACTCTACTT
Statistics
Matches: 107, Mismatches: 7, Indels: 19
0.80 0.05 0.14
Matches are distributed among these distances:
68 5 0.05
69 34 0.32
70 6 0.06
73 2 0.02
74 60 0.56
ACGTcount: A:0.24, C:0.27, G:0.10, T:0.38
Consensus pattern (68 bp):
GAATTAAGTTCTTAACTTACTTAATCCCCTCCTTGGAATCAAGTCCTTCAACTTAATTCCCTTCC
TTG
Found at i:8113 original size:74 final size:74
Alignment explanation
Indices: 8019--8173 Score: 247
Period size: 74 Copynumber: 2.1 Consensus size: 74
8009 CAAGTCCTTA
* *
8019 ACTTAATTCCCTTCCTTGGAATTAAGTTCTTAACTTTACTTAATCCCATTCCTTGGAATCAAGTC
1 ACTTAATTCCCTTCCTTGGAATTAAGTCCTTAACTCTACTTAATCCCATTCCTTGGAATCAAGTC
8084 CTAAACTCT
66 CTAAACTCT
* * *
8093 ACTTAATTCCCTTCCTTGGAATTAGGTCCTTTACTCTACTTAATCCCCTTCCTTGGAATCAAGTC
1 ACTTAATTCCCTTCCTTGGAATTAAGTCCTTAACTCTACTTAATCCCATTCCTTGGAATCAAGTC
**
8158 CTTTACTCT
66 CTAAACTCT
8167 ACTTAAT
1 ACTTAAT
8174 CCTCTTAGGT
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.25, C:0.27, G:0.08, T:0.40
Consensus pattern (74 bp):
ACTTAATTCCCTTCCTTGGAATTAAGTCCTTAACTCTACTTAATCCCATTCCTTGGAATCAAGTC
CTAAACTCT
Found at i:8172 original size:37 final size:37
Alignment explanation
Indices: 7994--8175 Score: 223
Period size: 37 Copynumber: 5.1 Consensus size: 37
7984 TTGACTTGAT
7994 TCCCC-TCCTTGGAATCAAGTCC-TTA----ACTTAA
1 TCCCCTTCCTTGGAATCAAGTCCTTTACTCTACTTAA
* * * * *
8025 TTCCCTTCCTTGGAATTAAGTTCTTAACTTTACTTAA
1 TCCCCTTCCTTGGAATCAAGTCCTTTACTCTACTTAA
* **
8062 TCCCATTCCTTGGAATCAAGTCCTAAACTCTACTTAA
1 TCCCCTTCCTTGGAATCAAGTCCTTTACTCTACTTAA
* * *
8099 TTCCCTTCCTTGGAATTAGGTCCTTTACTCTACTTAA
1 TCCCCTTCCTTGGAATCAAGTCCTTTACTCTACTTAA
8136 TCCCCTTCCTTGGAATCAAGTCCTTTACTCTACTTAA
1 TCCCCTTCCTTGGAATCAAGTCCTTTACTCTACTTAA
8173 TCC
1 TCC
8176 TCTTAGGTTA
Statistics
Matches: 126, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
31 4 0.03
32 15 0.12
33 2 0.02
37 105 0.83
ACGTcount: A:0.24, C:0.29, G:0.09, T:0.38
Consensus pattern (37 bp):
TCCCCTTCCTTGGAATCAAGTCCTTTACTCTACTTAA
Found at i:8241 original size:36 final size:36
Alignment explanation
Indices: 8166--8244 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 36
8156 TCCTTTACTC
* * *
8166 TACTTAATCCTCTTAGGTTAAGTTTTTGTCTGATCT
1 TACTTAATCATCTTAGGTTAAGTCTTTGTATGATCT
* *
8202 TACTTAATCATCTTTGGATTAAGTCTTTG-ATGATTT
1 TACTTAATCATCTTAGG-TTAAGTCTTTGTATGATCT
8238 TACTTAA
1 TACTTAA
8245 GTCTTGTGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 27 0.73
37 10 0.27
ACGTcount: A:0.24, C:0.14, G:0.13, T:0.49
Consensus pattern (36 bp):
TACTTAATCATCTTAGGTTAAGTCTTTGTATGATCT
Found at i:8352 original size:30 final size:31
Alignment explanation
Indices: 8317--8379 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 31
8307 TGTACCTAAT
8317 TTCCTTCCTTGAAATTAAGTCTGTGC-TTAC
1 TTCCTTCCTTGAAATTAAGTCTGTGCTTTAC
8347 TTCCTTCCTTGAAATTAAGTCTGTGCTTTAC
1 TTCCTTCCTTGAAATTAAGTCTGTGCTTTAC
8378 TT
1 TT
8380 TACCTAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 26 0.81
31 6 0.19
ACGTcount: A:0.19, C:0.22, G:0.13, T:0.46
Consensus pattern (31 bp):
TTCCTTCCTTGAAATTAAGTCTGTGCTTTAC
Found at i:8782 original size:15 final size:17
Alignment explanation
Indices: 8762--8802 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
8752 GGCCCTTTTC
8762 CTTCCT-TTTA-TTCTT
1 CTTCCTCTTTACTTCTT
8777 CTTCCTCTTTACTTTCTT
1 CTTCCTCTTTAC-TTCTT
8795 CTTCCTCT
1 CTTCCTCT
8803 GAAAACCCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.26
16 4 0.17
18 13 0.57
ACGTcount: A:0.05, C:0.34, G:0.00, T:0.61
Consensus pattern (17 bp):
CTTCCTCTTTACTTCTT
Found at i:11165 original size:19 final size:18
Alignment explanation
Indices: 11124--11190 Score: 71
Period size: 19 Copynumber: 3.6 Consensus size: 18
11114 AATTCTTTAG
* *
11124 ATGCAAACCTAAAGTCCA
1 ATGCAAGCCCAAAGTCCA
* *
11142 TATGCAAGCTCAATATTCCA
1 -ATGCAAGCCCAA-AGTCCA
*
11162 ATGCAAGCCCAAAGTCAA
1 ATGCAAGCCCAAAGTCCA
11180 ATGCAAGCCCA
1 ATGCAAGCCCA
11191 TCATGAACCC
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
18 15 0.38
19 20 0.50
20 5 0.12
ACGTcount: A:0.40, C:0.28, G:0.13, T:0.18
Consensus pattern (18 bp):
ATGCAAGCCCAAAGTCCA
Found at i:11293 original size:18 final size:18
Alignment explanation
Indices: 11267--11305 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
11257 TTAAGTACTT
*
11267 AATTCTTCTTTATTAAGC
1 AATTCTTCTTTATTAACC
*
11285 AATTTTTCTTTATTAACC
1 AATTCTTCTTTATTAACC
11303 AAT
1 AAT
11306 GTAAATATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.31, C:0.15, G:0.03, T:0.51
Consensus pattern (18 bp):
AATTCTTCTTTATTAACC
Found at i:11381 original size:15 final size:15
Alignment explanation
Indices: 11358--11395 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
11348 GAAGACATGT
*
11358 AGAAGTGAATAATGA
1 AGAAATGAATAATGA
11373 AGAAATGAATAATGA
1 AGAAATGAATAATGA
11388 AG-AATGAA
1 AGAAATGAA
11396 AGATGCAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.58, C:0.00, G:0.24, T:0.18
Consensus pattern (15 bp):
AGAAATGAATAATGA
Found at i:13152 original size:15 final size:16
Alignment explanation
Indices: 13120--13153 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
13110 AAAGAAGAAT
*
13120 TAAAATTAAATCTAAC
1 TAAAAATAAATCTAAC
13136 TAAAAATAAAT-TAAC
1 TAAAAATAAATCTAAC
13151 TAA
1 TAA
13154 GAAAGCAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (16 bp):
TAAAAATAAATCTAAC
Done.