Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020025.1 Corchorus olitorius cultivar O-4 contig20058, 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: 7637
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:2049 original size:18 final size:18
Alignment explanation
Indices: 2028--2074 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
2018 CTTTTCTTCC
*
2028 TTTCTTTTTTTTTAATT-T
1 TTTCTTTTTTATT-ATTAT
2046 TTTCTATTTTTATTATTAT
1 TTTCT-TTTTTATTATTAT
*
2065 TTTATTTTTT
1 TTTCTTTTTT
2075 CAATTCAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 13 0.52
19 12 0.48
ACGTcount: A:0.15, C:0.04, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTCTTTTTTATTATTAT
Found at i:2323 original size:135 final size:135
Alignment explanation
Indices: 2076--2362 Score: 495
Period size: 135 Copynumber: 2.1 Consensus size: 135
2066 TTATTTTTTC
*
2076 AATTCAAAGCACAATGGGTTGGACTTAATAGTAAAGGAAGCAATGCCCAAAAGAAAATGGACCAA
1 AATTCAAAGCACAATGGGTTGGACTTAATAGTAAAGGAAGCAATACCCAAAAGAAAATGGACCAA
* *
2141 GTCCAACAAAACAAGTTTGGGCTTAAATAACTTATTTAAGAATAAATTGAAATAAAAAATCGGGC
66 GTCCAACAAAACAAGTTTGGGCTTAAATAACTTATTGAAGAACAAATTGAAATAAAAAATCGGGC
2206 CAAGA
131 CAAGA
* *
2211 AATTCAAAGCGCAATGGGTTGGGCTTAATAGTAAAGGAAGCAATACCCAAAAGAAAATGGACCAA
1 AATTCAAAGCACAATGGGTTGGACTTAATAGTAAAGGAAGCAATACCCAAAAGAAAATGGACCAA
* *
2276 GTCCAATAAAACAAGTTTGGGCTTAAGTGAA-TTATTGAAGAACAAATTGAAATAAAAAATCGGG
66 GTCCAACAAAACAAGTTTGGGCTTAAAT-AACTTATTGAAGAACAAATTGAAATAAAAAATCGGG
2340 CCAAGA
130 CCAAGA
2346 AATTCAAAGCACAATGG
1 AATTCAAAGCACAATGG
2363 TCTAGGAAAA
Statistics
Matches: 143, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
135 141 0.99
136 2 0.01
ACGTcount: A:0.46, C:0.14, G:0.20, T:0.20
Consensus pattern (135 bp):
AATTCAAAGCACAATGGGTTGGACTTAATAGTAAAGGAAGCAATACCCAAAAGAAAATGGACCAA
GTCCAACAAAACAAGTTTGGGCTTAAATAACTTATTGAAGAACAAATTGAAATAAAAAATCGGGC
CAAGA
Found at i:3861 original size:14 final size:15
Alignment explanation
Indices: 3842--3871 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3832 CAATCAAAGC
3842 AATAAT-CAAGGAAA
1 AATAATGCAAGGAAA
3856 AATAATGCAAGGAAA
1 AATAATGCAAGGAAA
3871 A
1 A
3872 TTAAAGAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13
Consensus pattern (15 bp):
AATAATGCAAGGAAA
Found at i:4255 original size:21 final size:21
Alignment explanation
Indices: 4229--4278 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
4219 GGAATGGCGA
**
4229 TGGCACGGGCATGGCCGGTGG
1 TGGCACGGGCATAACCGGTGG
*
4250 TGGCACGGGCTTAACCGGTGG
1 TGGCACGGGCATAACCGGTGG
4271 TGGCACGG
1 TGGCACGG
4279 TGAATGGGCG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.12, C:0.24, G:0.48, T:0.16
Consensus pattern (21 bp):
TGGCACGGGCATAACCGGTGG
Found at i:4420 original size:42 final size:42
Alignment explanation
Indices: 4369--4459 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
4359 GCCGGTCCTA
* * * *
4369 GCCGGGCATGTGGCTCGGATGAGGCTTG-AGATGGCGGGCATG
1 GCCGGGCATGAGGCGCAGATGAGGCTTGTAG-TGCCGGGCATG
*
4411 GCCGGGCATGAGGCGCAGCTGAGGCTTGTAGTGCCGGGCATG
1 GCCGGGCATGAGGCGCAGATGAGGCTTGTAGTGCCGGGCATG
4453 GCCGGGC
1 GCCGGGC
4460 GTGATACTTG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 41 0.95
43 2 0.05
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.16
Consensus pattern (42 bp):
GCCGGGCATGAGGCGCAGATGAGGCTTGTAGTGCCGGGCATG
Found at i:6927 original size:53 final size:54
Alignment explanation
Indices: 6812--6929 Score: 161
Period size: 53 Copynumber: 2.2 Consensus size: 54
6802 AGAAAAGTTT
*
6812 TTTTTTTTTTTAAATGACGCAAAAATATTTTTTTTTTCGACGCAAAACAAAACAA
1 TTTTTTTTTTT-AATGACGCAAAAATATTGTTTTTTTCGACGCAAAACAAAACAA
**
6867 AATTTTTTTTT-ATGACGCAAAAAT-TTGTTTTTTTCGA-GCAAAACACAAAACAA
1 TTTTTTTTTTTAATGACGCAAAAATATTGTTTTTTTCGACGC-AAA-ACAAAACAA
6920 TTTTTTTTTT
1 TTTTTTTTTT
6930 AGATTAAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
51 2 0.04
52 15 0.27
53 30 0.54
55 9 0.16
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.45
Consensus pattern (54 bp):
TTTTTTTTTTTAATGACGCAAAAATATTGTTTTTTTCGACGCAAAACAAAACAA
Found at i:7288 original size:16 final size:15
Alignment explanation
Indices: 7252--7293 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
7242 ACAGAGGTTG
7252 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
*
7267 ACAGAAAACAATTTA
1 ACAGAAAACAATTAA
7282 ACTAGAAAACAA
1 AC-AGAAAACAA
7294 AGCAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.07, T:0.14
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.