Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013151.1 Corchorus capsularis cultivar CVL-1 contig13172, 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: 27073
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1860 original size:16 final size:16
Alignment explanation
Indices: 1839--1889 Score: 67
Period size: 16 Copynumber: 3.5 Consensus size: 16
1829 CTGCTCCTTC
1839 TATATTATATATATAA
1 TATATTATATATATAA
1855 TATATTATATATA-AA
1 TATATTATATATATAA
1870 TA-A-TA-ATATATAA
1 TATATTATATATATAA
1883 T-TATTAT
1 TATATTAT
1890 TACTTTGAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
12 5 0.16
13 6 0.19
14 3 0.10
15 4 0.13
16 13 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TATATTATATATATAA
Found at i:1863 original size:14 final size:14
Alignment explanation
Indices: 1846--1889 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
1836 TTCTATATTA
1846 TATATATAATATAT
1 TATATATAATATAT
1860 TATATATAA-ATAAT
1 TATATATAATAT-AT
*
1874 AATATATAAT-TAT
1 TATATATAATATAT
1887 TAT
1 TAT
1890 TACTTTGAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 6 0.23
14 20 0.77
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TATATATAATATAT
Found at i:11536 original size:77 final size:78
Alignment explanation
Indices: 11444--11595 Score: 288
Period size: 77 Copynumber: 2.0 Consensus size: 78
11434 CATGTTGTCT
*
11444 AATGCTTATATATATATATATATATATAAGAAAATTTTTATACAAGGGAATAATATATATACACA
1 AATGCTTAGATATATATATATATATATAAGAAAATTTTTATACAAGGGAATAATATATATACACA
11509 CACATGGAGGCCA
66 CACATGGAGGCCA
11522 AATG-TTAGATATATATATATATATATAAGAAAATTTTTATACAAGGGAATAATATATATACACA
1 AATGCTTAGATATATATATATATATATAAGAAAATTTTTATACAAGGGAATAATATATATACACA
11586 CACATGGAGG
66 CACATGGAGG
11596 AAATAGTCAA
Statistics
Matches: 73, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
77 69 0.95
78 4 0.05
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.32
Consensus pattern (78 bp):
AATGCTTAGATATATATATATATATATAAGAAAATTTTTATACAAGGGAATAATATATATACACA
CACATGGAGGCCA
Found at i:11926 original size:3 final size:3
Alignment explanation
Indices: 11918--11955 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
11908 AAAATTCATG
11918 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
11956 GCTTCATTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:19012 original size:1 final size:1
Alignment explanation
Indices: 19008--19033 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
18998 CAAAAATCAG
19008 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
19034 ATTTATACTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:21708 original size:27 final size:27
Alignment explanation
Indices: 21657--21708 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
21647 TACTCAACTT
* **
21657 TTCCTACTCCTTTACATTACCAAACAA
1 TTCCTACTCCTTAACAACACCAAACAA
*
21684 TTCCTACTCCTTAACAACACTAAAC
1 TTCCTACTCCTTAACAACACCAAAC
21709 TACACCAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (27 bp):
TTCCTACTCCTTAACAACACCAAACAA
Found at i:23817 original size:30 final size:30
Alignment explanation
Indices: 23776--23852 Score: 109
Period size: 30 Copynumber: 2.6 Consensus size: 30
23766 GAGGATAAGG
*
23776 TTACTCTAGAAGAGTCCACTCTTGAAAAAA
1 TTACTCTAGAAGAGTCCACTCCTGAAAAAA
* * *
23806 TTACTCCAGAAGAGTCCACTCCTGAAGAGA
1 TTACTCTAGAAGAGTCCACTCCTGAAAAAA
*
23836 TCACTCTAGAAGAGTCC
1 TTACTCTAGAAGAGTCC
23853 GTAGGCATGA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (30 bp):
TTACTCTAGAAGAGTCCACTCCTGAAAAAA
Found at i:23826 original size:15 final size:15
Alignment explanation
Indices: 23808--23852 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
23798 TGAAAAAATT
23808 ACTCCAGAAGAGTCC
1 ACTCCAGAAGAGTCC
*
23823 ACTCCTGAAGAGAT-C
1 ACTCCAGAAGAG-TCC
*
23838 ACTCTAGAAGAGTCC
1 ACTCCAGAAGAGTCC
23853 GTAGGCATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 1 0.04
15 23 0.92
16 1 0.04
ACGTcount: A:0.33, C:0.29, G:0.20, T:0.18
Consensus pattern (15 bp):
ACTCCAGAAGAGTCC
Found at i:26384 original size:33 final size:33
Alignment explanation
Indices: 26309--26431 Score: 115
Period size: 33 Copynumber: 3.7 Consensus size: 33
26299 AGACAAAGGA
* * *
26309 TCGCGTGGCTGGTTGTGGCCGGGCATGGCCGA-G
1 TCGCGTGGCCGGTTGTGGCCGGACATGTCC-ATG
** * *
26342 TCGTTTGGCCGGTTGTAGCCGGCCATGTCCATG
1 TCGCGTGGCCGGTTGTGGCCGGACATGTCCATG
*
26375 TCGCGTGGCCGG-TGATGGCTGGACATGTCCATG
1 TCGCGTGGCCGGTTG-TGGCCGGACATGTCCATG
*
26408 TCGCGTGGCCAGTCTTGTGGCCGG
1 TCGCGTGGCC-G-GTTGTGGCCGG
26432 TGTTGCGCGG
Statistics
Matches: 72, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
32 3 0.04
33 60 0.83
34 1 0.01
35 6 0.08
36 2 0.03
ACGTcount: A:0.08, C:0.26, G:0.41, T:0.25
Consensus pattern (33 bp):
TCGCGTGGCCGGTTGTGGCCGGACATGTCCATG
Done.