Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014212.1 Corchorus olitorius cultivar O-4 contig14245, 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: 12739
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:4677 original size:45 final size:46
Alignment explanation
Indices: 4626--4724 Score: 191
Period size: 45 Copynumber: 2.2 Consensus size: 46
4616 AGTCAACACA
4626 TTATTTTATAAAAATTAGCTTTTTTTTT-GCATCAAAAAAATTAGC
1 TTATTTTATAAAAATTAGCTTTTTTTTTGGCATCAAAAAAATTAGC
4671 TTATTTTATAAAAATTAGCTTTTTTTTTGGCATCAAAAAAATTAGC
1 TTATTTTATAAAAATTAGCTTTTTTTTTGGCATCAAAAAAATTAGC
4717 TTATTTTA
1 TTATTTTA
4725 GTTTGAACTC
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 28 0.53
46 25 0.47
ACGTcount: A:0.36, C:0.08, G:0.07, T:0.48
Consensus pattern (46 bp):
TTATTTTATAAAAATTAGCTTTTTTTTTGGCATCAAAAAAATTAGC
Found at i:5796 original size:3 final size:3
Alignment explanation
Indices: 5790--5826 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
5780 TTCTTTTTTT
* *
5790 TTA TTA TTA TTA TTA TAA TTA TAA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5827 AATAGAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:7994 original size:19 final size:19
Alignment explanation
Indices: 7970--8006 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
7960 CTGTTTAGCA
*
7970 ACTGTACAGATGAGATTAC
1 ACTGTACAAATGAGATTAC
*
7989 ACTGTACAAATTAGATTA
1 ACTGTACAAATGAGATTA
8007 GATACCATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
ACTGTACAAATGAGATTAC
Found at i:8367 original size:26 final size:26
Alignment explanation
Indices: 8318--8394 Score: 138
Period size: 26 Copynumber: 3.0 Consensus size: 26
8308 CTTTCAAATC
*
8318 TCCATATTACTCC-TTTTTTTTTGCA
1 TCCAAATTACTCCTTTTTTTTTTGCA
8343 TCCAAATTACTCCTTTTTTTTTTGCA
1 TCCAAATTACTCCTTTTTTTTTTGCA
8369 TCCAAATTACTCCTTTTTTTTTTGCA
1 TCCAAATTACTCCTTTTTTTTTTGCA
8395 CAAGCACATA
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
25 12 0.24
26 38 0.76
ACGTcount: A:0.18, C:0.23, G:0.04, T:0.55
Consensus pattern (26 bp):
TCCAAATTACTCCTTTTTTTTTTGCA
Found at i:10891 original size:32 final size:31
Alignment explanation
Indices: 10837--10914 Score: 102
Period size: 32 Copynumber: 2.5 Consensus size: 31
10827 GGGTTTGGAC
* * *
10837 TTGAGTCAGGTTTGGTTAAATTTGGGTTAGG
1 TTGATTCAGGTTCGGTTAAATTTGGGTAAGG
10868 TTGATTCAGGTTCGGATTAAATTTGGGTAAGG
1 TTGATTCAGGTTCGG-TTAAATTTGGGTAAGG
* *
10900 TAGATTTAGGTTCGG
1 TTGATTCAGGTTCGG
10915 GTCAATTTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 13 0.32
32 28 0.68
ACGTcount: A:0.22, C:0.05, G:0.33, T:0.40
Consensus pattern (31 bp):
TTGATTCAGGTTCGGTTAAATTTGGGTAAGG
Found at i:10925 original size:32 final size:32
Alignment explanation
Indices: 10854--10925 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
10844 AGGTTTGGTT
* * *
10854 AAATTTGGGTTAGGTTGATTCAGGTTCGGATT
1 AAATTTGGGTAAGGTAGATTCAGGTTCGGATC
* *
10886 AAATTTGGGTAAGGTAGATTTAGGTTCGGGTC
1 AAATTTGGGTAAGGTAGATTCAGGTTCGGATC
*
10918 AATTTTGG
1 AAATTTGG
10926 ATCAGGTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.24, C:0.06, G:0.32, T:0.39
Consensus pattern (32 bp):
AAATTTGGGTAAGGTAGATTCAGGTTCGGATC
Found at i:11218 original size:32 final size:32
Alignment explanation
Indices: 11145--11221 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
11135 GTTTTTTCAA
*
11145 GTTCGGGTTTTATCGGGTTTCAGATTTTTCGG
1 GTTCGGGTTTTTTCGGGTTTCAGATTTTTCGG
* ** *
11177 ATTATGGTTTTTTCGGGTTTGA-ACTTTTTCGG
1 GTTCGGGTTTTTTCGGGTTTCAGA-TTTTTCGG
11209 GTTCGGGTTTTTT
1 GTTCGGGTTTTTT
11222 TGGATTCGGA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
31 1 0.03
32 35 0.97
ACGTcount: A:0.09, C:0.10, G:0.29, T:0.52
Consensus pattern (32 bp):
GTTCGGGTTTTTTCGGGTTTCAGATTTTTCGG
Found at i:11220 original size:16 final size:16
Alignment explanation
Indices: 11130--11221 Score: 60
Period size: 16 Copynumber: 5.8 Consensus size: 16
11120 TAGTATTGAA
**
11130 TTCGGGTTTTTTCAAG
1 TTCGGGTTTTTTCGGG
*
11146 TTCGGGTTTTATCGGG
1 TTCGGGTTTTTTCGGG
* * *
11162 TTTC-AGATTTTTCGGA
1 -TTCGGGTTTTTTCGGG
**
11178 TTATGGTTTTTTCGGG
1 TTCGGGTTTTTTCGGG
* ***
11194 TTTGAACTTTTTCGGG
1 TTCGGGTTTTTTCGGG
11210 TTCGGGTTTTTT
1 TTCGGGTTTTTT
11222 TGGATTCGGA
Statistics
Matches: 54, Mismatches: 20, Indels: 4
0.69 0.26 0.05
Matches are distributed among these distances:
15 2 0.04
16 49 0.91
17 3 0.06
ACGTcount: A:0.10, C:0.11, G:0.27, T:0.52
Consensus pattern (16 bp):
TTCGGGTTTTTTCGGG
Done.