Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022717.1 Corchorus olitorius cultivar O-4 contig22750, 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: 36648
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Found at i:2727 original size:23 final size:24
Alignment explanation
Indices: 2681--2727 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
2671 ATTGATGTTG
2681 CGGTTTGAAAAAATTTGGTATTGA
1 CGGTTTGAAAAAATTTGGTATTGA
2705 CGGTTTGAAAAAATTTGGT-TTGA
1 CGGTTTGAAAAAATTTGGTATTGA
2728 AAGAAATGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.32, C:0.04, G:0.26, T:0.38
Consensus pattern (24 bp):
CGGTTTGAAAAAATTTGGTATTGA
Found at i:2852 original size:30 final size:30
Alignment explanation
Indices: 2816--2888 Score: 146
Period size: 30 Copynumber: 2.4 Consensus size: 30
2806 TCTAATTGTA
2816 GCCAAATAAGCCCCTTAATTCTTAGAAAAG
1 GCCAAATAAGCCCCTTAATTCTTAGAAAAG
2846 GCCAAATAAGCCCCTTAATTCTTAGAAAAG
1 GCCAAATAAGCCCCTTAATTCTTAGAAAAG
2876 GCCAAATAAGCCC
1 GCCAAATAAGCCC
2889 TTTTCGCAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.40, C:0.26, G:0.14, T:0.21
Consensus pattern (30 bp):
GCCAAATAAGCCCCTTAATTCTTAGAAAAG
Found at i:18522 original size:13 final size:13
Alignment explanation
Indices: 18504--18529 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18494 TAGGTTAAGA
18504 GAGAAAGAGGGAT
1 GAGAAAGAGGGAT
18517 GAGAAAGAGGGAT
1 GAGAAAGAGGGAT
18530 AGGGTTAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.46, T:0.08
Consensus pattern (13 bp):
GAGAAAGAGGGAT
Found at i:24231 original size:31 final size:29
Alignment explanation
Indices: 24165--24244 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
24155 CTCATTTTTG
* * *
24165 AAACGTAAGGGATTAATTTGTCCCGAAAA
1 AAACATAAGGGATTATTTTGTCCCAAAAA
24194 AAACATAAGGGATTATTTTGTCCCAAAAGCA
1 AAACATAAGGGATTATTTTGTCCCAAAA--A
*
24225 AAACATAAGGGATTTTTTTG
1 AAACATAAGGGATTATTTTG
24245 GGTACTTAGC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 25 0.56
31 20 0.44
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (29 bp):
AAACATAAGGGATTATTTTGTCCCAAAAA
Found at i:27194 original size:40 final size:41
Alignment explanation
Indices: 27122--27201 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 41
27112 AATGCACAAG
* *
27122 AATCATTTTTTTTTGGGCTAATTTTGGTTGAATCTGGTAAA
1 AATCACTTTCTTTTGGGCTAATTTTGGTTGAATCTGGTAAA
*
27163 AATCACTTTCTTTTGGG-TAGTTTTGGTTGAATCTGGTAA
1 AATCACTTTCTTTTGGGCTAATTTTGGTTGAATCTGGTAA
27202 GTGTCTAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
40 21 0.58
41 15 0.42
ACGTcount: A:0.23, C:0.09, G:0.21, T:0.47
Consensus pattern (41 bp):
AATCACTTTCTTTTGGGCTAATTTTGGTTGAATCTGGTAAA
Found at i:29125 original size:30 final size:30
Alignment explanation
Indices: 29071--29269 Score: 275
Period size: 30 Copynumber: 6.8 Consensus size: 30
29061 ACCCCAGACG
*
29071 TGCAAAA-TGACCAAAATG-CCCCTGGATA
1 TGCAAAAGTGACTAAAATGTCCCCTGGATA
29099 TGCAAAAGTGACTAAAATGTCCCCTGGATA
1 TGCAAAAGTGACTAAAATGTCCCCTGGATA
* **
29129 TGCAAAAGTGACTAGAATGTCCCCTGGACG
1 TGCAAAAGTGACTAAAATGTCCCCTGGATA
*
29159 TGCAAAA-TGACCAAAATG-CCCCTGGATA
1 TGCAAAAGTGACTAAAATGTCCCCTGGATA
29187 TGCAAAAGTGACTAAAATGTCCCCTGGATA
1 TGCAAAAGTGACTAAAATGTCCCCTGGATA
* **
29217 TGCAAAAGTGACTAGAATGTCCCCTGGACG
1 TGCAAAAGTGACTAAAATGTCCCCTGGATA
*
29247 TGCAAAA-TGACCAAAATG-CCCCT
1 TGCAAAAGTGACTAAAATGTCCCCT
29270 AGACATGAAT
Statistics
Matches: 153, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
28 27 0.18
29 38 0.25
30 88 0.58
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.20
Consensus pattern (30 bp):
TGCAAAAGTGACTAAAATGTCCCCTGGATA
Found at i:29171 original size:88 final size:88
Alignment explanation
Indices: 29067--29269 Score: 406
Period size: 88 Copynumber: 2.3 Consensus size: 88
29057 AAATACCCCA
29067 GACGTGCAAAATGACCAAAATGCCCCTGGATATGCAAAAGTGACTAAAATGTCCCCTGGATATGC
1 GACGTGCAAAATGACCAAAATGCCCCTGGATATGCAAAAGTGACTAAAATGTCCCCTGGATATGC
29132 AAAAGTGACTAGAATGTCCCCTG
66 AAAAGTGACTAGAATGTCCCCTG
29155 GACGTGCAAAATGACCAAAATGCCCCTGGATATGCAAAAGTGACTAAAATGTCCCCTGGATATGC
1 GACGTGCAAAATGACCAAAATGCCCCTGGATATGCAAAAGTGACTAAAATGTCCCCTGGATATGC
29220 AAAAGTGACTAGAATGTCCCCTG
66 AAAAGTGACTAGAATGTCCCCTG
29243 GACGTGCAAAATGACCAAAATGCCCCT
1 GACGTGCAAAATGACCAAAATGCCCCT
29270 AGACATGAAT
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 115 1.00
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.20
Consensus pattern (88 bp):
GACGTGCAAAATGACCAAAATGCCCCTGGATATGCAAAAGTGACTAAAATGTCCCCTGGATATGC
AAAAGTGACTAGAATGTCCCCTG
Found at i:29184 original size:58 final size:59
Alignment explanation
Indices: 29071--29269 Score: 253
Period size: 58 Copynumber: 3.4 Consensus size: 59
29061 ACCCCAGACG
* * *
29071 TGCAAAATGACCAAAATG-CCCCTGGATATGCAAAAGTGACTAAAATGTCCCCTGGATA
1 TGCAAAATGACTAAAATGTCCCCTGGATATGCAAAAGTGACCAAAATGTCCCCTGGACA
* ** *
29129 TGCAAAAGTGACTAGAATGTCCCCTGGACGTGCAAAA-TGACCAAAATG-CCCCTGGATA
1 TGCAAAA-TGACTAAAATGTCCCCTGGATATGCAAAAGTGACCAAAATGTCCCCTGGACA
* * *
29187 TGCAAAAGTGACTAAAATGTCCCCTGGATATGCAAAAGTGACTAGAATGTCCCCTGGACG
1 TGCAAAA-TGACTAAAATGTCCCCTGGATATGCAAAAGTGACCAAAATGTCCCCTGGACA
*
29247 TGCAAAATGACCAAAATG-CCCCT
1 TGCAAAATGACTAAAATGTCCCCT
29270 AGACATGAAT
Statistics
Matches: 124, Mismatches: 13, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
58 56 0.45
59 38 0.31
60 30 0.24
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.20
Consensus pattern (59 bp):
TGCAAAATGACTAAAATGTCCCCTGGATATGCAAAAGTGACCAAAATGTCCCCTGGACA
Found at i:29600 original size:50 final size:50
Alignment explanation
Indices: 29535--29790 Score: 440
Period size: 50 Copynumber: 5.0 Consensus size: 50
29525 CTCTAATATA
* *
29535 TTAAAAGGACCGTCTTCCGCTTATCTTTTAAACTGTCTACCAATTCAATC
1 TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
*
29585 TTGAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
1 TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
*
29635 TTATAAAAAGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
1 -T-TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
29687 TTATAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
1 -T-TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
29739 TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
1 TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
29789 TT
1 TT
29791 GATATCTGGT
Statistics
Matches: 198, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
50 98 0.49
51 2 0.01
52 98 0.49
ACGTcount: A:0.27, C:0.27, G:0.11, T:0.35
Consensus pattern (50 bp):
TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
Found at i:29665 original size:52 final size:51
Alignment explanation
Indices: 29535--29790 Score: 444
Period size: 52 Copynumber: 5.0 Consensus size: 51
29525 CTCTAATATA
* *
29535 TTAAAAGGACCGTCTTCCGCTTATCTTTTAAACTGTCTACCAATTCAATC-
1 TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCT
*
29585 TTGAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCT
1 TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCT
*
29636 TATAAAAAGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCT
1 T-TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCT
29688 TATAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC-
1 T-TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCT
29739 TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCT
1 TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCT
29790 T
1 T
29791 GATATCTGGT
Statistics
Matches: 197, Mismatches: 6, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
50 96 0.49
51 3 0.02
52 98 0.50
ACGTcount: A:0.27, C:0.27, G:0.11, T:0.35
Consensus pattern (51 bp):
TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCT
Done.