Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013993.1 Corchorus olitorius cultivar O-4 contig14026, 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: 29636
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Found at i:1790 original size:22 final size:21
Alignment explanation
Indices: 1748--1794 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1738 CGCAAAAACA
*
1748 AGAAATTTTTTTTTATGACGC
1 AGAAATTTTTTTTTATAACGC
*
1769 AGAAATTTTTTTTTTTCAACGC
1 AGAAATTTTTTTTTAT-AACGC
1791 AGAA
1 AGAA
1795 CACAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.45
Consensus pattern (21 bp):
AGAAATTTTTTTTTATAACGC
Found at i:2260 original size:16 final size:15
Alignment explanation
Indices: 2222--2263 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
2212 AAAGAGGTTG
2222 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
2237 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
2252 ACTAGAAAACAA
1 AC-AGAAAACAA
2264 AACAAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:4310 original size:38 final size:37
Alignment explanation
Indices: 4266--4366 Score: 139
Period size: 39 Copynumber: 2.6 Consensus size: 37
4256 TTAATCGAGC
*
4266 AATTCCGAAAGAAGATTTTGGAAAATAAAAGTTTAGG
1 AATTCCGAAAGAAGATTTTGGAAAATAAAAGTTTAAG
*
4303 TAATTCCGAAAGAAGATTTTGTAAAAATAAAAGTTTAAG
1 -AATTCCGAAAGAAGATTTTG-GAAAATAAAAGTTTAAG
* *
4342 ATATCCCAAAAGAAGATTTTGGAAA
1 A-ATTCCGAAAGAAGATTTTGGAAA
4367 TTAATAAAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
38 24 0.43
39 32 0.57
ACGTcount: A:0.48, C:0.07, G:0.18, T:0.28
Consensus pattern (37 bp):
AATTCCGAAAGAAGATTTTGGAAAATAAAAGTTTAAG
Found at i:9512 original size:28 final size:28
Alignment explanation
Indices: 9480--9582 Score: 161
Period size: 28 Copynumber: 3.7 Consensus size: 28
9470 AGTGCACTTG
* * *
9480 AAATGACCGAAATACCCCTAGATGTGCA
1 AAATGACCAAAATGCCCCTGGATGTGCA
*
9508 AAATGACCAAAATGCTCCTGGATGTGCA
1 AAATGACCAAAATGCCCCTGGATGTGCA
*
9536 AAATGACCAATATGCCCCTGGATGTGCA
1 AAATGACCAAAATGCCCCTGGATGTGCA
9564 AAATGACCAAAATGCCCCT
1 AAATGACCAAAATGCCCCT
9583 CCTTAAGTGA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 68 1.00
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.19
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTGGATGTGCA
Found at i:11110 original size:71 final size:72
Alignment explanation
Indices: 11015--11192 Score: 220
Period size: 71 Copynumber: 2.5 Consensus size: 72
11005 TGTCTTGGTC
* * * * *
11015 ATGGTAGACTGAACCATGGGTTGAGGAAGGCTAGGTAGGAA-ACCTTTGGCTGCCTTTTCCACAT
1 ATGGTAGTCTAAACCATGTGTTGAGGAAGGCTAGGTA-GAAGACCATTGGCTGCCTTTGCCACAT
*
11079 CTTAAT-A
65 ATTAATCA
*
11086 ATGGTAGTCTAAACCATGTGTTGAGGAAGGCTAGGTAGAAGACCATTGGCTGCCTTTGCGACATA
1 ATGGTAGTCTAAACCATGTGTTGAGGAAGGCTAGGTAGAAGACCATTGGCTGCCTTTGCCACATA
*
11151 TTAGTCA
66 TTAATCA
* *
11158 A-GGTAGAT-TAAACCATGTGATGAGGAAAGCTAGGT
1 ATGGTAG-TCTAAACCATGTGTTGAGGAAGGCTAGGT
11193 GAGAGTACTA
Statistics
Matches: 94, Mismatches: 10, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
70 3 0.03
71 88 0.94
72 3 0.03
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.27
Consensus pattern (72 bp):
ATGGTAGTCTAAACCATGTGTTGAGGAAGGCTAGGTAGAAGACCATTGGCTGCCTTTGCCACATA
TTAATCA
Found at i:12091 original size:31 final size:31
Alignment explanation
Indices: 12052--12171 Score: 124
Period size: 31 Copynumber: 4.0 Consensus size: 31
12042 AGGTCTGATG
* **
12052 GCAACGAGCTTTGCTTGTTGAGGATCTGCT-
1 GCAACGAGCTTTGTTTGTCAAGGATCTGCTA
12082 GTCAACGAGCTTTGTTTGTCAAGGATCTGCTA
1 G-CAACGAGCTTTGTTTGTCAAGGATCTGCTA
**
12114 GCAACGAGCTTTGTTTGTCGAA-GCCCTGCT-
1 GCAACGAGCTTTGTTTGTC-AAGGATCTGCTA
* *
12144 G-GA-GAGCTTTGTTTGTCGAGGATCTGCT
1 GCAACGAGCTTTGTTTGTCAAGGATCTGCT
12172 GGAGAGCCCT
Statistics
Matches: 77, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
27 1 0.01
28 20 0.26
29 1 0.01
30 2 0.03
31 50 0.65
32 3 0.04
ACGTcount: A:0.17, C:0.20, G:0.29, T:0.33
Consensus pattern (31 bp):
GCAACGAGCTTTGTTTGTCAAGGATCTGCTA
Found at i:12159 original size:28 final size:28
Alignment explanation
Indices: 12088--12178 Score: 94
Period size: 28 Copynumber: 3.1 Consensus size: 28
12078 TGCTGTCAAC
* *
12088 GAGCTTTGTTTGTC-AAGGATCTGCTAGCAA
1 GAGCTTTGTTTGTCGAA-GACCTGCT-G-GA
*
12118 CGAGCTTTGTTTGTCGAAGCCCTGCTGGA
1 -GAGCTTTGTTTGTCGAAGACCTGCTGGA
* *
12147 GAGCTTTGTTTGTCGAGGATCTGCTGGA
1 GAGCTTTGTTTGTCGAAGACCTGCTGGA
12175 GAGC
1 GAGC
12179 CCTGCTGTGT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
28 29 0.55
29 1 0.02
30 1 0.02
31 20 0.38
32 2 0.04
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.32
Consensus pattern (28 bp):
GAGCTTTGTTTGTCGAAGACCTGCTGGA
Found at i:26331 original size:18 final size:19
Alignment explanation
Indices: 26308--26347 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
26298 TTCTTGAAAT
26308 AATTCTTCA-A-TAGTCTTC
1 AATTCTTCACATTA-TCTTC
26326 AATTCTTCACATTATCTTC
1 AATTCTTCACATTATCTTC
26345 AAT
1 AAT
26348 AAATCTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 9 0.45
19 9 0.45
20 2 0.10
ACGTcount: A:0.30, C:0.23, G:0.03, T:0.45
Consensus pattern (19 bp):
AATTCTTCACATTATCTTC
Found at i:26332 original size:30 final size:30
Alignment explanation
Indices: 26298--26358 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
26288 CAATTCTTGC
* *
26298 TTCTTGAAATAATTCTTCAAT-AGTCTTCAA
1 TTCTTCAAATAA-TCTTCAATAAATCTTCAA
* *
26328 TTCTTCACATTATCTTCAATAAATCTTCAA
1 TTCTTCAAATAATCTTCAATAAATCTTCAA
26358 T
1 T
26359 CACGAACTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.33, C:0.20, G:0.03, T:0.44
Consensus pattern (30 bp):
TTCTTCAAATAATCTTCAATAAATCTTCAA
Done.