Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013737.1 Corchorus olitorius cultivar O-4 contig13770, 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: 45042
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:6196 original size:19 final size:18
Alignment explanation
Indices: 6144--6196 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
6134 CTAAATCTGT
* *
6144 TTAGTTTTAGTCTTAGGT
1 TTAGTTTTAGTTTTAGGG
6162 TTAG-TTTAGTCGTTTAGGG
1 TTAGTTTTAGT--TTTAGGG
6181 TTAGTTTTAGGTTTTA
1 TTAGTTTTA-GTTTTA
6197 ACTTTTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
17 6 0.21
18 4 0.14
19 13 0.45
20 4 0.14
21 2 0.07
ACGTcount: A:0.17, C:0.04, G:0.25, T:0.55
Consensus pattern (18 bp):
TTAGTTTTAGTTTTAGGG
Found at i:9992 original size:20 final size:20
Alignment explanation
Indices: 9967--10005 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
9957 ATTTGTAAAT
*
9967 AAAGATTGAATTTTTAAGTG
1 AAAGATTGAATCTTTAAGTG
9987 AAAGATTGAATCTTTAAGT
1 AAAGATTGAATCTTTAAGT
10006 TTAAGTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.03, G:0.18, T:0.38
Consensus pattern (20 bp):
AAAGATTGAATCTTTAAGTG
Found at i:10410 original size:21 final size:21
Alignment explanation
Indices: 10384--10423 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
10374 CTTCAATTTG
10384 AAAATTAAGATT-TTGAGTTTA
1 AAAATT-AGATTCTTGAGTTTA
*
10405 AAAATTTGATTCTTGAGTT
1 AAAATTAGATTCTTGAGTT
10424 GATTCAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.45
Consensus pattern (21 bp):
AAAATTAGATTCTTGAGTTTA
Found at i:11567 original size:170 final size:169
Alignment explanation
Indices: 11080--11704 Score: 853
Period size: 170 Copynumber: 3.7 Consensus size: 169
11070 TTTTATACCA
* *
11080 AAAATGCCCCTTCCCGGTCGGAAGGTCCTTGTTTTCATTTCC-AAAATGCCCCTTCCTGGTTGGA
1 AAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTTCCAAAAATGCCCCTTCCTGGTTGGA
* *
11144 AGGTCCCTGTTTTCATTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCAT-TTC-C
66 AGGTCCTTGTTTTCATTTTCAAAAATGCCCCTTCCTGGTTGGAAGGT-CCT-TATTC-TCTTCTC
** *
11207 AAAAATGCCCCTTCCCAGTTGGAAGGTCCCTGTTTTCATTTCC
128 AAAAATG-CCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTTCC
* * * *
11250 AAAAACGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCCTTTTCAAAAAAATGCCCCTTCCTAGTT
1 -AAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTT-CATTTC-CAAAAATGCCCCTTCCTGGTT
* * * * * *
11315 GGAAGGTCCTTATTCTC-TTCTCAAAAATGCCCCTTCCTGGTTGGAAGGTCTTTATTGTCTTTTC
63 GGAAGGTCCTTGTTTTCATTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTATTCTCTTCTC
**
11379 AAAAATGCCCAACCTGGTTGGAAGGTCCTTGTTTTCATTTCC
128 AAAAATGCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTTCC
*
11421 AAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCATTTCCAAAAATGCCCCTTCCTGGTTGGA
1 AAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTTCCAAAAATGCCCCTTCCTGGTTGGA
* * *
11486 AGGTCCTTGTTTTCTTTTTAAAAAATGCACCTTCCTGGTTGGAAGGTCCTTATTCTCTTCTCAAA
66 AGGTCCTTGTTTTCATTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTATTCTCTTCTCAAA
* * * * *
11551 AATGTCCCTTCCTGGTTGGAAGGTCTTTATTGTCTTTTCA
131 AATG-CCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTTCC
**
11591 AAAATGCCCCTTCCTGGTTGGAAGGTTTTTGTTTTCATTTCCAAAAATGCCCCTTCCTGGTTGGA
1 AAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTTCCAAAAATGCCCCTTCCTGGTTGGA
* * *
11656 AGGTCCTTGTTTTCATTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCC
66 AGGTCCTTGTTTTCATTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCC
11705 CAGTTTTCCT
Statistics
Matches: 399, Mismatches: 48, Indels: 15
0.86 0.10 0.03
Matches are distributed among these distances:
168 34 0.09
169 53 0.13
170 167 0.42
171 67 0.17
172 15 0.04
173 31 0.08
174 32 0.08
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (169 bp):
AAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTTCCAAAAATGCCCCTTCCTGGTTGGA
AGGTCCTTGTTTTCATTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTATTCTCTTCTCAAA
AATGCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTTCC
Found at i:11712 original size:43 final size:43
Alignment explanation
Indices: 11077--11704 Score: 833
Period size: 43 Copynumber: 14.7 Consensus size: 43
11067 TTCTTTTATA
* *
11077 CCAAAAATGCCCCTTCCCGGTCGGAAGGTCCTTGTTTTCATTT
1 CCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTT
*
11120 CC-AAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCATTT
1 CCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTT
* *
11162 TCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCATTT
1 CCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTT
** *
11205 CCAAAAATGCCCCTTCCCAGTTGGAAGGTCCCTGTTTTCATTT
1 CCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTT
* *
11248 CCAAAAACGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCCTTTT
1 CCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTT-CATTT
* * * *
11292 CAAAAAAATGCCCCTTCCTAGTTGGAAGGTCCTTATTCTC--TT
1 C-CAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTT
* * *
11334 CTCAAAAATGCCCCTTCCTGGTTGGAAGGTCTTTATTGTC-TTT
1 C-CAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTT
* **
11377 TCAAAAATG-CCCAACCTGGTTGGAAGGTCCTTGTTTTCATTT
1 CCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTT
*
11419 CC-AAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCATTT
1 CCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTT
*
11461 CCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCTTTT
1 CCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTT
** * * *
11504 TAAAAAATGCACCTTCCTGGTTGGAAGGTCCTTATTCTC--TT
1 CCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTT
* * * *
11545 CTCAAAAATGTCCCTTCCTGGTTGGAAGGTCTTTATTGTC-TTT
1 C-CAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTT
* **
11588 TCAAAAATGCCCCTTCCTGGTTGGAAGGTTTTTGTTTTCATTT
1 CCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTT
11631 CCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTT
1 CCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTT
* *
11674 CCAAAAATGCCCCTTCCCGGTCGGAAGGTCC
1 CCAAAAATGCCCCTTCCTGGTTGGAAGGTCC
11705 CAGTTTTCCT
Statistics
Matches: 520, Mismatches: 55, Indels: 20
0.87 0.09 0.03
Matches are distributed among these distances:
41 32 0.06
42 186 0.36
43 264 0.51
44 6 0.01
45 32 0.06
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (43 bp):
CCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTT
Found at i:11783 original size:41 final size:41
Alignment explanation
Indices: 11726--11841 Score: 146
Period size: 40 Copynumber: 2.9 Consensus size: 41
11716 CGATAATTCT
* *
11726 CAGTTTGCCCTTCCTCATCGTAAGGTATTGTTTAAG-TTCAC
1 CAGTTTGCCCTTCCTCATCGAAAGGTGTTGTTTAAGATT-AC
* * *
11767 CAGTTTGTCTTTCCTCATCGAAAGGTGTTGTTT-AGATTTC
1 CAGTTTGCCCTTCCTCATCGAAAGGTGTTGTTTAAGATTAC
* *
11807 CAATTTGCCCTTCCTCATCGGAAGGTGTTGTTTAA
1 CAGTTTGCCCTTCCTCATCGAAAGGTGTTGTTTAA
11842 AGCCCATTCT
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
40 32 0.50
41 32 0.50
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.41
Consensus pattern (41 bp):
CAGTTTGCCCTTCCTCATCGAAAGGTGTTGTTTAAGATTAC
Found at i:11970 original size:40 final size:40
Alignment explanation
Indices: 11857--11949 Score: 168
Period size: 40 Copynumber: 2.3 Consensus size: 40
11847 ATTCTTTCCA
11857 TTTTGCCCTTCCCCACCGGAAGGTGTTGATTTCATTCCCG
1 TTTTGCCCTTCCCCACCGGAAGGTGTTGATTTCATTCCCG
**
11897 TTTTGCCCTTCCCCACCGGAAGGTGTTGATTTCATTCTTG
1 TTTTGCCCTTCCCCACCGGAAGGTGTTGATTTCATTCCCG
11937 TTTTGCCCTTCCC
1 TTTTGCCCTTCCC
11950 GGTCGGAAGG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.11, C:0.32, G:0.18, T:0.39
Consensus pattern (40 bp):
TTTTGCCCTTCCCCACCGGAAGGTGTTGATTTCATTCCCG
Found at i:14428 original size:27 final size:28
Alignment explanation
Indices: 14380--14432 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
14370 CTTACCCTTA
* *
14380 TCTTCTTATTTTTCGTTCTTTTTCTTTT
1 TCTTCTTATTTTTAGTTATTTTTCTTTT
*
14408 TCTT-TTATTTTTATTTATTTTTCTT
1 TCTTCTTATTTTTAGTTATTTTTCTT
14433 AGTTACTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.08, C:0.13, G:0.02, T:0.77
Consensus pattern (28 bp):
TCTTCTTATTTTTAGTTATTTTTCTTTT
Found at i:28746 original size:16 final size:17
Alignment explanation
Indices: 28721--28762 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
28711 TACCCTTATC
28721 TTTTTATTTTTC-GTTA
1 TTTTTATTTTTCTGTTA
* *
28737 TTTTTCTTTTTCTTTTA
1 TTTTTATTTTTCTGTTA
28754 TTTTTATTT
1 TTTTTATTT
28763 ATTTTTCTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.10, C:0.07, G:0.02, T:0.81
Consensus pattern (17 bp):
TTTTTATTTTTCTGTTA
Found at i:36946 original size:31 final size:31
Alignment explanation
Indices: 36908--36977 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
36898 GGCAGATGCT
36908 GCCGCTGCCGCACCAGGCAGTGCATCAAGCA
1 GCCGCTGCCGCACCAGGCAGTGCATCAAGCA
*
36939 GCCGCTGCCGCACGAGGCAGTGCATCAAGCA
1 GCCGCTGCCGCACCAGGCAGTGCATCAAGCA
36970 GCCGCTGC
1 GCCGCTGC
36978 TGCTTCCATG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.20, C:0.39, G:0.31, T:0.10
Consensus pattern (31 bp):
GCCGCTGCCGCACCAGGCAGTGCATCAAGCA
Found at i:41811 original size:21 final size:20
Alignment explanation
Indices: 41778--41820 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
41768 CTTTAGGAGT
*
41778 GCAAGAGAGATTTCAAAGGAA
1 GCAAGAGACATTTCAAA-GAA
* *
41799 GCAAGAGCCATTTCCAAGAA
1 GCAAGAGACATTTCAAAGAA
41819 GC
1 GC
41821 TACAATTCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.42, C:0.19, G:0.26, T:0.14
Consensus pattern (20 bp):
GCAAGAGACATTTCAAAGAA
Done.