Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015612.1 Corchorus olitorius cultivar O-4 contig15645, 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: 32714
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31
Found at i:5454 original size:19 final size:19
Alignment explanation
Indices: 5430--5470 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
5420 GTTTAGATTA
5430 TTACCTTTCCAAATAATAT
1 TTACCTTTCCAAATAATAT
5449 TTACCTTTCCAAATAATAT
1 TTACCTTTCCAAATAATAT
5468 TTA
1 TTA
5471 ATATCTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.37, C:0.20, G:0.00, T:0.44
Consensus pattern (19 bp):
TTACCTTTCCAAATAATAT
Found at i:9252 original size:7 final size:7
Alignment explanation
Indices: 9240--9273 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
9230 ATAAATGAAC
9240 TATAATT
1 TATAATT
9247 TATAATT
1 TATAATT
9254 TATAATT
1 TATAATT
9261 TATAATT
1 TATAATT
9268 TATAAT
1 TATAAT
9274 CCTCAACTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TATAATT
Found at i:12903 original size:23 final size:23
Alignment explanation
Indices: 12877--12930 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
12867 GTTGAGTTAC
12877 ATGAGTAATATAGTTGGTATAAT
1 ATGAGTAATATAGTTGGTATAAT
*
12900 ATGAGTAATATAGTTTGTATAAT
1 ATGAGTAATATAGTTGGTATAAT
*
12923 ATTAGTAA
1 ATGAGTAA
12931 AATTTTTAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (23 bp):
ATGAGTAATATAGTTGGTATAAT
Found at i:13693 original size:16 final size:16
Alignment explanation
Indices: 13672--13710 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
13662 GTTTAGTCTG
*
13672 AACCTGAAATTACTCA
1 AACCTGAAATTACCCA
*
13688 AACCTGAATTTACCCA
1 AACCTGAAATTACCCA
13704 AACCTGA
1 AACCTGA
13711 GACAACCCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.41, C:0.28, G:0.08, T:0.23
Consensus pattern (16 bp):
AACCTGAAATTACCCA
Found at i:15350 original size:121 final size:127
Alignment explanation
Indices: 15103--15352 Score: 359
Period size: 121 Copynumber: 2.0 Consensus size: 127
15093 TAAGAAATAA
*
15103 ATTTAAAAAATTCTTATATATATAAGTTTTTTAATTAAAATATTAAAATGATAAAAATAAAATAG
1 ATTTAAAAAATTCTTATATATATAAGTTTTTTAATTAAAATAGTAAAATGATAAAAAT---ATA-
* *
15168 GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAAATGTAAAAGTA
62 GTATAAGGATATCAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAAATATAAAAGTA
15233 T
127 T
*
15234 ATTTAAAAAATTC-TA-ATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-TA-TA-
1 ATTTAAAAAATTCTTATATATATAAGTTTTTTAATTAAAATAGTAAAATGATAAAAATATAGTAT
* * *
15294 AA-GATATCAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTGAAACTATAAAAGT
66 AAGGATATCAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAAATATAAAAGT
15353 TTAAACCATG
Statistics
Matches: 112, Mismatches: 7, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
121 52 0.46
122 2 0.02
123 2 0.02
125 2 0.02
129 39 0.35
130 2 0.02
131 13 0.12
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (127 bp):
ATTTAAAAAATTCTTATATATATAAGTTTTTTAATTAAAATAGTAAAATGATAAAAATATAGTAT
AAGGATATCAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAAATATAAAAGTAT
Found at i:20681 original size:43 final size:43
Alignment explanation
Indices: 20616--20701 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
20606 CACCCCTTTC
20616 CTTTCTTCCTACCAAACGCACCAACATTTTATTTGCACTCCAA
1 CTTTCTTCCTACCAAACGCACCAACATTTTATTTGCACTCCAA
*
20659 CTTTCTTCCTACCAAACTCACCAACATTTTATTTGCACTCCAA
1 CTTTCTTCCTACCAAACGCACCAACATTTTATTTGCACTCCAA
20702 ATTTAGGTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.28, C:0.35, G:0.03, T:0.34
Consensus pattern (43 bp):
CTTTCTTCCTACCAAACGCACCAACATTTTATTTGCACTCCAA
Found at i:28280 original size:106 final size:106
Alignment explanation
Indices: 28095--28295 Score: 285
Period size: 106 Copynumber: 1.9 Consensus size: 106
28085 AGATAAAAAA
* * * * * * * *
28095 AAAATTGCAAAGAGTGTTGCACCTTAGAGTTTTAGTTGCATCTTAGGGAGCACTTCCTAAGTGTT
1 AAAATTGCAAAGAGTGTTGCACCTTAGAGCTTTAGTCGCATCTCAGGAAACACCTACTAAGTATT
28160 GCACTTTAAACTTGGGTCGCACCTCAAGAAAATATTGTTTT
66 GCACTTTAAACTTGGGTCGCACCTCAAGAAAATATTGTTTT
* * *
28201 AAAATTGTAAGGAGTGTTGCACCTTAGAGCTTTAGTCGCATCTCAGGAAATACCTACTAAGTATT
1 AAAATTGCAAAGAGTGTTGCACCTTAGAGCTTTAGTCGCATCTCAGGAAACACCTACTAAGTATT
* *
28266 GCACTTTAGACTTGGGTTGCACCTCAAGAA
66 GCACTTTAAACTTGGGTCGCACCTCAAGAA
28296 GTATAATTCT
Statistics
Matches: 82, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
106 82 1.00
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (106 bp):
AAAATTGCAAAGAGTGTTGCACCTTAGAGCTTTAGTCGCATCTCAGGAAACACCTACTAAGTATT
GCACTTTAAACTTGGGTCGCACCTCAAGAAAATATTGTTTT
Found at i:28897 original size:14 final size:14
Alignment explanation
Indices: 28878--28906 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
28868 CGATGCTAAA
28878 GGCATGGTACTCGC
1 GGCATGGTACTCGC
28892 GGCATGGTACTCGC
1 GGCATGGTACTCGC
28906 G
1 G
28907 ATATGGTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.28, G:0.38, T:0.21
Consensus pattern (14 bp):
GGCATGGTACTCGC
Found at i:28912 original size:14 final size:14
Alignment explanation
Indices: 28880--28914 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
28870 ATGCTAAAGG
*
28880 CATGGTACTCGCGG
1 CATGGTACTCGCGA
28894 CATGGTACTCGCGA
1 CATGGTACTCGCGA
*
28908 TATGGTA
1 CATGGTA
28915 TGATATTCGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.20, C:0.23, G:0.31, T:0.26
Consensus pattern (14 bp):
CATGGTACTCGCGA
Found at i:29029 original size:42 final size:40
Alignment explanation
Indices: 28965--29042 Score: 129
Period size: 42 Copynumber: 1.9 Consensus size: 40
28955 TGATGGCATA
28965 TGGTATGGTATTCGACGCTAAAGGCATGGTACTCGCAATG
1 TGGTATGGTATTCGACGCTAAAGGCATGGTACTCGCAATG
*
29005 TGGTGTGGTATTCGCAACGCTAAAGGCATGGTACTCGC
1 TGGTATGGTATTCG--ACGCTAAAGGCATGGTACTCGC
29043 GGCATGGTAC
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
40 13 0.37
42 22 0.63
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (40 bp):
TGGTATGGTATTCGACGCTAAAGGCATGGTACTCGCAATG
Found at i:29258 original size:14 final size:14
Alignment explanation
Indices: 29239--29304 Score: 87
Period size: 14 Copynumber: 4.7 Consensus size: 14
29229 CCTCAATGAC
*
29239 ATGTGGTGTTCGCG
1 ATGTGGTATTCGCG
29253 ATGTGGTATTCGCG
1 ATGTGGTATTCGCG
* *
29267 ATATGGTATTTGCG
1 ATGTGGTATTCGCG
*
29281 ATGTGGTATTTGCG
1 ATGTGGTATTCGCG
*
29295 ATATGGTATT
1 ATGTGGTATT
29305 TGTGTAAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 47 1.00
ACGTcount: A:0.17, C:0.09, G:0.33, T:0.41
Consensus pattern (14 bp):
ATGTGGTATTCGCG
Found at i:29281 original size:28 final size:28
Alignment explanation
Indices: 29250--29306 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
29240 TGTGGTGTTC
29250 GCGATGTGGTATTCGCGATATGGTATTT
1 GCGATGTGGTATTCGCGATATGGTATTT
*
29278 GCGATGTGGTATTTGCGATATGGTATTT
1 GCGATGTGGTATTCGCGATATGGTATTT
29306 G
1 G
29307 TGTAAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.18, C:0.09, G:0.33, T:0.40
Consensus pattern (28 bp):
GCGATGTGGTATTCGCGATATGGTATTT
Found at i:30074 original size:51 final size:51
Alignment explanation
Indices: 30001--30114 Score: 201
Period size: 51 Copynumber: 2.2 Consensus size: 51
29991 GTAATTGGGA
*
30001 GAGGCATGCTAGTACCAGATGTTGGTGATGGGGAAGGAAAAGCAGCAAGAG
1 GAGGCATGCTAGTACCAAATGTTGGTGATGGGGAAGGAAAAGCAGCAAGAG
* *
30052 GAGGCATGCTAGTACCAAATGTTGGTGATGGGGAAGGAAAAGTAGCAGGAG
1 GAGGCATGCTAGTACCAAATGTTGGTGATGGGGAAGGAAAAGCAGCAAGAG
30103 GAGGCATGCTAG
1 GAGGCATGCTAG
30115 GATAGGTCAC
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.32, C:0.11, G:0.39, T:0.17
Consensus pattern (51 bp):
GAGGCATGCTAGTACCAAATGTTGGTGATGGGGAAGGAAAAGCAGCAAGAG
Found at i:30698 original size:33 final size:33
Alignment explanation
Indices: 30660--30727 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
30650 ATCATCAGCA
*
30660 ACCTCTTCAACATGGTCGGTAGCAACTTCCATG
1 ACCTCTTCAACATGGTCGATAGCAACTTCCATG
* *
30693 ACCTCTTCAACATTGTCGATAGTAACTTCCATG
1 ACCTCTTCAACATGGTCGATAGCAACTTCCATG
30726 AC
1 AC
30728 ATGATCCTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.29
Consensus pattern (33 bp):
ACCTCTTCAACATGGTCGATAGCAACTTCCATG
Found at i:31853 original size:2 final size:2
Alignment explanation
Indices: 31848--31894 Score: 69
Period size: 2 Copynumber: 23.5 Consensus size: 2
31838 AAAACTAATA
*
31848 AT AT AT AT AT AGT A- AA AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31890 AT AT A
1 AT AT A
31895 CCTGGCCAAC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
1 1 0.02
2 39 0.93
3 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Done.