Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015540.1 Corchorus olitorius cultivar O-4 contig15573, 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: 50031
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:658 original size:31 final size:31
Alignment explanation
Indices: 615--685 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
605 CCCCAAAATA
615 TTAGGGACTGATTTGAGCCGATTTTGCAACG
1 TTAGGGACTGATTTGAGCCGATTTTGCAACG
* *
646 TTAGGGATTGATTTGAGCTGATTTTGCAACG
1 TTAGGGACTGATTTGAGCCGATTTTGCAACG
*
677 TTAGTGACT
1 TTAGGGACT
686 TAATTAAGCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.23, C:0.13, G:0.28, T:0.37
Consensus pattern (31 bp):
TTAGGGACTGATTTGAGCCGATTTTGCAACG
Found at i:900 original size:20 final size:21
Alignment explanation
Indices: 877--916 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
867 CCTTGATATA
*
877 TAAAAT-ATGACCTTTTGGGC
1 TAAAATCATGACCTATTGGGC
897 TAAAATCCATGACCTATTGG
1 TAAAAT-CATGACCTATTGG
917 AGTGGTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (21 bp):
TAAAATCATGACCTATTGGGC
Found at i:5323 original size:31 final size:31
Alignment explanation
Indices: 5288--5358 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
5278 TGTTCTTAAG
**
5288 CTCAAATTGAGCATTTTTTGAAATG-TTTAGA
1 CTCAAATTGAGCAACTTTTGAAA-GATTTAGA
5319 CTCAAATTGAGCAACTTTTGAAAGATTTAGA
1 CTCAAATTGAGCAACTTTTGAAAGATTTAGA
5350 CTCAAATTG
1 CTCAAATTG
5359 GTGATTTAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 1 0.03
31 36 0.97
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (31 bp):
CTCAAATTGAGCAACTTTTGAAAGATTTAGA
Found at i:5536 original size:18 final size:18
Alignment explanation
Indices: 5513--5549 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
5503 TTCAGTTTAA
5513 AGGTTTAGATTCAAATTG
1 AGGTTTAGATTCAAATTG
5531 AGGTTTAGATTCAAATTG
1 AGGTTTAGATTCAAATTG
5549 A
1 A
5550 ACAAGTTGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.05, G:0.22, T:0.38
Consensus pattern (18 bp):
AGGTTTAGATTCAAATTG
Found at i:6253 original size:15 final size:15
Alignment explanation
Indices: 6233--6262 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6223 GAGTTCAGTG
*
6233 GGCTTGGCGCCTCTA
1 GGCTTGGCGACTCTA
6248 GGCTTGGCGACTCTA
1 GGCTTGGCGACTCTA
6263 CCCGTCAAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.30, G:0.33, T:0.27
Consensus pattern (15 bp):
GGCTTGGCGACTCTA
Found at i:8899 original size:11 final size:11
Alignment explanation
Indices: 8883--8910 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
8873 TCTACTTGTG
8883 CGTAGCAAGTC
1 CGTAGCAAGTC
8894 CGTAGCAAGTC
1 CGTAGCAAGTC
8905 CGTAGC
1 CGTAGC
8911 TAAATGTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.25, C:0.29, G:0.29, T:0.18
Consensus pattern (11 bp):
CGTAGCAAGTC
Found at i:9167 original size:33 final size:33
Alignment explanation
Indices: 9120--9187 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
9110 ATAGGAATAT
*
9120 GTTCGTAGCCATACGAATAAGCGATCGTAGCTA
1 GTTCATAGCCATACGAATAAGCGATCGTAGCTA
9153 GTTCATAGCCATACGAATAAGCGATCGTAGCTA
1 GTTCATAGCCATACGAATAAGCGATCGTAGCTA
9186 GT
1 GT
9188 CCGTAGCAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.25
Consensus pattern (33 bp):
GTTCATAGCCATACGAATAAGCGATCGTAGCTA
Found at i:10704 original size:23 final size:24
Alignment explanation
Indices: 10673--10718 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
10663 GTACCTTTAT
10673 TTAACAAATCAATTTAAG-AATTAC
1 TTAACAAATCAA-TTAAGTAATTAC
*
10697 TTAA-AAATTAATTAAGTAATTA
1 TTAACAAATCAATTAAGTAATTA
10719 GGGGAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 11 0.55
24 4 0.20
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (24 bp):
TTAACAAATCAATTAAGTAATTAC
Found at i:14398 original size:14 final size:16
Alignment explanation
Indices: 14364--14398 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
14354 GGGAAGGCCA
14364 ATTTTGGGAGCTGATG
1 ATTTTGGGAGCTGATG
14380 ATTTT-GGAGCTGA-G
1 ATTTTGGGAGCTGATG
14394 ATTTT
1 ATTTT
14399 TGGCAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.32
15 8 0.42
16 5 0.26
ACGTcount: A:0.20, C:0.06, G:0.31, T:0.43
Consensus pattern (16 bp):
ATTTTGGGAGCTGATG
Found at i:21237 original size:31 final size:31
Alignment explanation
Indices: 21201--21270 Score: 122
Period size: 31 Copynumber: 2.3 Consensus size: 31
21191 TAAACCCTAA
21201 AACGTTAGGAATTGATTTGAGCCGATTTTGC
1 AACGTTAGGAATTGATTTGAGCCGATTTTGC
* *
21232 AACGTTAGGGATTGATTTGAGCTGATTTTGC
1 AACGTTAGGAATTGATTTGAGCCGATTTTGC
21263 AACGTTAG
1 AACGTTAG
21271 AGACTGAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.26, C:0.11, G:0.27, T:0.36
Consensus pattern (31 bp):
AACGTTAGGAATTGATTTGAGCCGATTTTGC
Found at i:23217 original size:1 final size:1
Alignment explanation
Indices: 23211--23235 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
23201 CTTATCTGCT
23211 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
23236 CATACAGAAA
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:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:38203 original size:33 final size:33
Alignment explanation
Indices: 38139--38206 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
38129 AAACTATTTG
*
38139 ACCACTTGATTTTAACAAAGTCAGACTTTAGTT
1 ACCACTTGATTTTAACAAAGTAAGACTTTAGTT
* * *
38172 ACCACTTTATTTTACCAGAGTTAAGAC-TTAGTT
1 ACCACTTGATTTTAACAAAG-TAAGACTTTAGTT
38205 AC
1 AC
38207 TACTATCTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 25 0.83
34 5 0.17
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (33 bp):
ACCACTTGATTTTAACAAAGTAAGACTTTAGTT
Found at i:38888 original size:22 final size:22
Alignment explanation
Indices: 38860--38906 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
38850 TACTTTTTAT
38860 ATTTTAAACAATCCAAACAAGG
1 ATTTTAAACAATCCAAACAAGG
38882 ATTTTAAACAATCCAAACAAGG
1 ATTTTAAACAATCCAAACAAGG
38904 ATT
1 ATT
38907 GATCCTTCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.49, C:0.17, G:0.09, T:0.26
Consensus pattern (22 bp):
ATTTTAAACAATCCAAACAAGG
Found at i:43229 original size:20 final size:22
Alignment explanation
Indices: 43204--43248 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
43194 TGAAAGCTCT
43204 AATTGATT-A-ATATGAAAACC
1 AATTGATTAATATATGAAAACC
43224 AATTGATTAATATATGAAAACC
1 AATTGATTAATATATGAAAACC
43246 AAT
1 AAT
43249 AGAGTAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 8 0.35
21 1 0.04
22 14 0.61
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (22 bp):
AATTGATTAATATATGAAAACC
Found at i:43256 original size:22 final size:22
Alignment explanation
Indices: 43213--43256 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
43203 TAATTGATTA
* *
43213 ATATGAAAACCAATTGATTAAT
1 ATATGAAAACCAATAGAGTAAT
43235 ATATGAAAACCAATAGAGTAAT
1 ATATGAAAACCAATAGAGTAAT
43257 TCATGGACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.52, C:0.09, G:0.11, T:0.27
Consensus pattern (22 bp):
ATATGAAAACCAATAGAGTAAT
Done.