Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010436.1 Corchorus capsularis cultivar CVL-1 contig10457, 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: 28979
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:934 original size:18 final size:17
Alignment explanation
Indices: 896--937 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
886 GACTATTATT
* *
896 TATACATAAAAATAGTT
1 TATACATAAAAATAATA
913 TATACATAAAAATTAATA
1 TATACATAAAAA-TAATA
931 TATACAT
1 TATACAT
938 TTTTTATACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (17 bp):
TATACATAAAAATAATA
Found at i:1001 original size:21 final size:21
Alignment explanation
Indices: 977--1018 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
967 AAAAATATGT
977 GTTTAGAAGT-TTACTTTTTAA
1 GTTTAGAAGTATTA-TTTTTAA
*
998 GTTTATAAGTATTATTTTTAA
1 GTTTAGAAGTATTATTTTTAA
1019 AATTTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.55
Consensus pattern (21 bp):
GTTTAGAAGTATTATTTTTAA
Found at i:1024 original size:22 final size:21
Alignment explanation
Indices: 978--1025 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
968 AAAATATGTG
* *
978 TTTAGAAGTTTACTTTTTAAG
1 TTTATAAGTTTACTTTTTAAA
999 TTTATAAGTATTA-TTTTTAAAA
1 TTTATAAGT-TTACTTTTT-AAA
1021 TTTAT
1 TTTAT
1026 TTTGCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.56
Consensus pattern (21 bp):
TTTATAAGTTTACTTTTTAAA
Found at i:4074 original size:124 final size:126
Alignment explanation
Indices: 3838--4079 Score: 380
Period size: 127 Copynumber: 1.9 Consensus size: 126
3828 ATACTTCTAG
* *
3838 TTCTAATTGTTGTTGCAGAAAAATGATTTCAACTTTCATTGTTGTCTCAGTTTTATTTAGAGATT
1 TTCTAATTGTTGTTACAGAAAAATGATTTCAACTTTCATTGTTGTCTCAGTTTTATTTAGAGA-G
* *
3903 ATTTTTTGTTTGTTGGTTGATGATTTGTGGGGCGGTTAGTGAAGATACAGTGGCTTTACTTA
65 ATTTTGTGTTTGTTGGTTGATGATTTGTAGGGCGGTTAGTGAAGATACAGTGGCTTTACTTA
* * *
3965 TTCTAGTTGTTGTTACAGCAAAATGATTTCAACTTTCATTGTTGTCTCAGTTTTATTTTG-G-GA
1 TTCTAATTGTTGTTACAGAAAAATGATTTCAACTTTCATTGTTGTCTCAGTTTTATTTAGAGAGA
* *
4028 TTTTGTGTTTGTTGGTTGATGATTTTTAGGGCGGTTAGTGAAGATACGGTGG
66 TTTTGTGTTTGTTGGTTGATGATTTGTAGGGCGGTTAGTGAAGATACAGTGG
4080 ATTTGCGTGA
Statistics
Matches: 106, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
124 49 0.46
126 1 0.01
127 56 0.53
ACGTcount: A:0.21, C:0.09, G:0.24, T:0.46
Consensus pattern (126 bp):
TTCTAATTGTTGTTACAGAAAAATGATTTCAACTTTCATTGTTGTCTCAGTTTTATTTAGAGAGA
TTTTGTGTTTGTTGGTTGATGATTTGTAGGGCGGTTAGTGAAGATACAGTGGCTTTACTTA
Found at i:8579 original size:11 final size:11
Alignment explanation
Indices: 8563--8587 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
8553 TTCTAAACTT
8563 GAAAAAAAAAA
1 GAAAAAAAAAA
8574 GAAAAAAAAAA
1 GAAAAAAAAAA
8585 GAA
1 GAA
8588 TACAAATGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:26951 original size:18 final size:16
Alignment explanation
Indices: 26928--26961 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 16
26918 ACAATTTTGA
26928 TTCTTTCTTTTTTCTTTT
1 TTCTTT-TTTTTT-TTTT
26946 TTCTTTTTTTTTTTTT
1 TTCTTTTTTTTTTTTT
26962 GCATTACTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 6 0.38
18 6 0.38
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (16 bp):
TTCTTTTTTTTTTTTT
Found at i:26961 original size:7 final size:7
Alignment explanation
Indices: 26931--26960 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
26921 ATTTTGATTC
26931 TTTCTTT
1 TTTCTTT
26938 TTTCTTT
1 TTTCTTT
26945 TTTCTTT
1 TTTCTTT
26952 TTT-TTT
1 TTTCTTT
26958 TTT
1 TTT
26961 TGCATTACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (7 bp):
TTTCTTT
Done.