Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014634.1 Corchorus olitorius cultivar O-4 contig14667, 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: 41880
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:14543 original size:11 final size:11
Alignment explanation
Indices: 14527--14562 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
14517 CAAAGGAAAA
14527 AAACAGGGGAG
1 AAACAGGGGAG
*
14538 AAACAGGGGGCG
1 AAACA-GGGGAG
14550 AAACAGGGGAG
1 AAACAGGGGAG
14561 AA
1 AA
14563 CGAAAGTTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.44, C:0.11, G:0.44, T:0.00
Consensus pattern (11 bp):
AAACAGGGGAG
Found at i:16459 original size:15 final size:15
Alignment explanation
Indices: 16439--16470 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
16429 GGTGTAGCCT
*
16439 TGTAGGTTAGTGAAA
1 TGTAGGTTAATGAAA
16454 TGTAGGTTAATGAAA
1 TGTAGGTTAATGAAA
16469 TG
1 TG
16471 AAAGTCCGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (15 bp):
TGTAGGTTAATGAAA
Found at i:17355 original size:17 final size:18
Alignment explanation
Indices: 17335--17370 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
17325 TAAAGCTAGA
*
17335 TAATGTTT-ATCGTTTCT
1 TAATGTTTAATCATTTCT
17352 TAATGTTTAATCATTTCT
1 TAATGTTTAATCATTTCT
17370 T
1 T
17371 TATAATAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.22, C:0.11, G:0.08, T:0.58
Consensus pattern (18 bp):
TAATGTTTAATCATTTCT
Found at i:24656 original size:13 final size:13
Alignment explanation
Indices: 24638--24662 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24628 GGGTTGATAG
24638 AAAACAAAAAAAA
1 AAAACAAAAAAAA
24651 AAAACAAAAAAA
1 AAAACAAAAAAA
24663 GCTTGAAAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAACAAAAAAAA
Found at i:26460 original size:21 final size:21
Alignment explanation
Indices: 26434--26473 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
26424 GTCCTCTGTC
*
26434 TTCACCATCGCCATCACCATT
1 TTCACCATCACCATCACCATT
*
26455 TTCACCTTCACCATCACCA
1 TTCACCATCACCATCACCA
26474 CTATCTCCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.45, G:0.03, T:0.28
Consensus pattern (21 bp):
TTCACCATCACCATCACCATT
Found at i:34959 original size:58 final size:58
Alignment explanation
Indices: 34883--35113 Score: 408
Period size: 58 Copynumber: 4.0 Consensus size: 58
34873 GATGAAATAC
* ** *
34883 CATTAGGGCATTTTCTTAGGGTTCAAGGATTCTGTCCGGTAATCACATTAGTCTTGAT
1 CATTAGGACATTTTCTTAGGGTTCAAGGACCCTGTCCGATAATCACATTAGTCTTGAT
34941 CATTAGGACATTTTCTTAGGGTTCAAGGACCCTGTCCGATAATCACATTAGTCTTGAT
1 CATTAGGACATTTTCTTAGGGTTCAAGGACCCTGTCCGATAATCACATTAGTCTTGAT
34999 CATTAGGACATTTTCTTAGGGTTCAAGGACCCTGTCCGATAATCACATTAGTCTTGAT
1 CATTAGGACATTTTCTTAGGGTTCAAGGACCCTGTCCGATAATCACATTAGTCTTGAT
* *
35057 CATTAGGACATTTTCTTAGGGTTCAAGGATCCTGTCCGGTAATCACATTAGTCTTGA
1 CATTAGGACATTTTCTTAGGGTTCAAGGACCCTGTCCGATAATCACATTAGTCTTGA
35114 CTAATTTGAA
Statistics
Matches: 167, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 167 1.00
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.35
Consensus pattern (58 bp):
CATTAGGACATTTTCTTAGGGTTCAAGGACCCTGTCCGATAATCACATTAGTCTTGAT
Found at i:38820 original size:36 final size:36
Alignment explanation
Indices: 38779--38868 Score: 119
Period size: 36 Copynumber: 2.5 Consensus size: 36
38769 GAAGAGAGAG
*
38779 GCTGCTCGGAGTGAGA-GAGAGAGAGAGGCTGCTGCT
1 GCTGCTCGGAGTCAGAGGA-AGAGAGAGGCTGCTGCT
*
38815 GCTGCTCAGAGTCAGAGGAAGAGAGAGGCTGCTGCT
1 GCTGCTCGGAGTCAGAGGAAGAGAGAGGCTGCTGCT
* * *
38851 ACTGCTCGAATTCAGAGG
1 GCTGCTCGGAGTCAGAGG
38869 GAGAATGAGA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
36 45 0.96
37 2 0.04
ACGTcount: A:0.24, C:0.19, G:0.39, T:0.18
Consensus pattern (36 bp):
GCTGCTCGGAGTCAGAGGAAGAGAGAGGCTGCTGCT
Found at i:40953 original size:20 final size:20
Alignment explanation
Indices: 40924--40962 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40914 TATTTTGGGA
40924 TTTTTATGGATGTTTATGTC
1 TTTTTATGGATGTTTATGTC
* *
40944 TTTTTTTGGATTTTTATGT
1 TTTTTATGGATGTTTATGT
40963 ATATTGGGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.03, G:0.18, T:0.67
Consensus pattern (20 bp):
TTTTTATGGATGTTTATGTC
Done.