Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013569.1 Corchorus olitorius cultivar O-4 contig13602, 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: 15072
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Found at i:296 original size:27 final size:27
Alignment explanation
Indices: 266--340 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
256 AATGTACTTG
*
266 AAATGACTAAAATGCCCCTGGACATGT
1 AAATGACTAAAATGCCCCTGGACATGC
* * **
293 AAATGGCCAAAATGCCCCTGGATGTGC
1 AAATGACTAAAATGCCCCTGGACATGC
*
320 AAATGACTGAAATG-CCCTGGA
1 AAATGACTAAAATGCCCCTGGA
341 TGACCCTAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
26 7 0.17
27 33 0.82
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.20
Consensus pattern (27 bp):
AAATGACTAAAATGCCCCTGGACATGC
Found at i:819 original size:16 final size:16
Alignment explanation
Indices: 800--834 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
790 CTTCTTTTTT
800 TTCCCCCATTTTTTCA
1 TTCCCCCATTTTTTCA
816 TTCCCCCATTTTTTCA
1 TTCCCCCATTTTTTCA
832 TTC
1 TTC
835 TTTTATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.37, G:0.00, T:0.51
Consensus pattern (16 bp):
TTCCCCCATTTTTTCA
Found at i:1033 original size:107 final size:105
Alignment explanation
Indices: 861--1091 Score: 265
Period size: 107 Copynumber: 2.2 Consensus size: 105
851 CCTAGTAAAG
* *
861 AATTTTGATTTT-TTTTAAGAGTAAATTATGAAATAAAAGATTTTTATTATAGGGTTTTAGGAAA
1 AATTTTAATTTTATTTTAAGAGTAAATTATGAAATAAAAGATTTTTATAATAGGGTTTTAGGAAA
925 TAAAATACAAAACTAATTTCACTAAATTTAGGCCCA-AATTAA
66 TAAAATACAAAACTAA-TTCACTAAATTTA--CCCAGAATTAA
* * *
967 AATTTTAATTTTATTTTAAGTGTAAATTCCAT-AAATAATA-ATTTATTGTAATAGGGTTTTA-G
1 AATTTTAATTTTATTTTAAGAGTAAATT--ATGAAATAAAAGATTT-TTATAATAGGGTTTTAGG
* * * **
1029 AAATAAAATATATAACTAATTCACTAAGTTTATTCAGAATTAA
63 AAATAAAATACAAAACTAATTCACTAAATTTACCCAGAATTAA
**
1072 AATTAAAATTTTATTTTAAG
1 AATTTTAATTTTATTTTAAG
1092 GGTTAGAAAA
Statistics
Matches: 108, Mismatches: 12, Indels: 11
0.82 0.09 0.08
Matches are distributed among these distances:
104 2 0.02
105 24 0.22
106 23 0.21
107 36 0.33
108 21 0.19
109 2 0.02
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.42
Consensus pattern (105 bp):
AATTTTAATTTTATTTTAAGAGTAAATTATGAAATAAAAGATTTTTATAATAGGGTTTTAGGAAA
TAAAATACAAAACTAATTCACTAAATTTACCCAGAATTAA
Found at i:9699 original size:11 final size:11
Alignment explanation
Indices: 9683--9714 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
9673 TGTTCATGGG
9683 TCGGGCCGGGT
1 TCGGGCCGGGT
9694 TCGGGCCGGGT
1 TCGGGCCGGGT
9705 TCGGGCCGGG
1 TCGGGCCGGG
9715 CCCAAGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.00, C:0.28, G:0.56, T:0.16
Consensus pattern (11 bp):
TCGGGCCGGGT
Found at i:10861 original size:21 final size:21
Alignment explanation
Indices: 10821--10863 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
10811 TTAAAACTAG
10821 TTATTTAAAATATATTTATTAT
1 TTATTTAAAATATA-TTATTAT
10843 TTATTTAATAATATA-TATTAT
1 TTATTTAA-AATATATTATTAT
10864 ATTTAAGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 6 0.30
22 8 0.40
23 6 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTATTTAAAATATATTATTAT
Found at i:10866 original size:23 final size:22
Alignment explanation
Indices: 10821--10868 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 22
10811 TTAAAACTAG
10821 TTATTTAAAATATATTTATTAT
1 TTATTTAAAATATATTTATTAT
10843 TTATTTAATAATATATATTA-TAT
1 TTATTTAA-AATATAT-TTATTAT
10866 TTA
1 TTA
10869 AGATAGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 8 0.33
23 13 0.54
24 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTATTTAAAATATATTTATTAT
Found at i:12690 original size:2 final size:2
Alignment explanation
Indices: 12683--12726 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
12673 TCACCCAAAA
* * *
12683 AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT TT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12725 AT
1 AT
12727 CACATCAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Done.