Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016231.1 Corchorus olitorius cultivar O-4 contig16264, 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: 35353
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Found at i:777 original size:15 final size:15
Alignment explanation
Indices: 753--782 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
743 CATTTTTTTG
753 AGTTTAGAATAATTA
1 AGTTTAGAATAATTA
*
768 AGTTTGGAATAATTA
1 AGTTTAGAATAATTA
783 TTTTTTTTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (15 bp):
AGTTTAGAATAATTA
Found at i:836 original size:15 final size:15
Alignment explanation
Indices: 797--864 Score: 91
Period size: 15 Copynumber: 4.3 Consensus size: 15
787 TTTTTGAGGA
797 AAGTTTAGAATAATT
1 AAGTTTAGAATAATT
812 ATCGAGTTTAGAATAATT
1 A---AGTTTAGAATAATT
830 AAGTTTAGAATAATT
1 AAGTTTAGAATAATT
* *
845 GAGTTTAGAATAACT
1 AAGTTTAGAATAATT
860 AAGTT
1 AAGTT
865 CGTTGCATTA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
15 32 0.68
18 15 0.32
ACGTcount: A:0.43, C:0.03, G:0.16, T:0.38
Consensus pattern (15 bp):
AAGTTTAGAATAATT
Found at i:851 original size:30 final size:33
Alignment explanation
Indices: 797--864 Score: 106
Period size: 30 Copynumber: 2.2 Consensus size: 33
787 TTTTTGAGGA
*
797 AAGTTTAGAATAATTATCGAGTTTAGAATAATT
1 AAGTTTAGAATAATTATCGAGTTTAGAATAACT
830 AAGTTTAGAATAA-T-T-GAGTTTAGAATAACT
1 AAGTTTAGAATAATTATCGAGTTTAGAATAACT
860 AAGTT
1 AAGTT
865 CGTTGCATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 19 0.56
31 1 0.03
32 1 0.03
33 13 0.38
ACGTcount: A:0.43, C:0.03, G:0.16, T:0.38
Consensus pattern (33 bp):
AAGTTTAGAATAATTATCGAGTTTAGAATAACT
Found at i:8195 original size:13 final size:13
Alignment explanation
Indices: 8179--8203 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8169 TGCAAAATTA
8179 AATTAATTTAGTG
1 AATTAATTTAGTG
8192 AATTAATTTAGT
1 AATTAATTTAGT
8204 TCGCTAGTCA
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:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
AATTAATTTAGTG
Found at i:19298 original size:21 final size:21
Alignment explanation
Indices: 19259--19298 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19249 AGGAGATGCC
*
19259 AAAGATGCCATTTGATCCATT
1 AAAGATGCCATTAGATCCATT
*
19280 AAAGATGCCATTAGGTCCA
1 AAAGATGCCATTAGATCCA
19299 ATGACAAGAG
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:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (21 bp):
AAAGATGCCATTAGATCCATT
Found at i:21063 original size:30 final size:30
Alignment explanation
Indices: 21027--21083 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
21017 TTATTGTAGC
*
21027 AGAGTCCACTCCTGAAGAGATTACTCCAAA
1 AGAGTCCACTCCTAAAGAGATTACTCCAAA
*
21057 AGAGTCCACTCCTAAAGAGGTTACTCC
1 AGAGTCCACTCCTAAAGAGATTACTCC
21084 GGAAGATTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (30 bp):
AGAGTCCACTCCTAAAGAGATTACTCCAAA
Found at i:22430 original size:16 final size:17
Alignment explanation
Indices: 22404--22437 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
22394 GGGAACAAAT
22404 TTGATTTCTATTTCTAA
1 TTGATTTCTATTTCTAA
*
22421 TTGA-TTCTATTTGTAA
1 TTGATTTCTATTTCTAA
22437 T
1 T
22438 ATTTTTGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.59
Consensus pattern (17 bp):
TTGATTTCTATTTCTAA
Found at i:29040 original size:29 final size:29
Alignment explanation
Indices: 28997--29069 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
28987 TGATTAATGA
* * *
28997 GAATGGTTCAACTTCTTATAGATGTTATG
1 GAATGGTTCATCTTCCTAGAGATGTTATG
29026 GAATGGTTCATCTTCCTAGAGATGTTATG
1 GAATGGTTCATCTTCCTAGAGATGTTATG
29055 GAATGGTTCATCTTC
1 GAATGGTTCATCTTC
29070 ATACATTTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.40
Consensus pattern (29 bp):
GAATGGTTCATCTTCCTAGAGATGTTATG
Found at i:29836 original size:37 final size:37
Alignment explanation
Indices: 29790--29874 Score: 125
Period size: 37 Copynumber: 2.3 Consensus size: 37
29780 TACTTGTTGA
*
29790 AATTTAAATTAAATTTAAAATAGATTTTTATAATCAC
1 AATTCAAATTAAATTTAAAATAGATTTTTATAATCAC
** * *
29827 AATTCAAATTATTTTTAAGATTGATTTTTATAATCAC
1 AATTCAAATTAAATTTAAAATAGATTTTTATAATCAC
29864 AATTCAAATTA
1 AATTCAAATTA
29875 TTATTAAGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (37 bp):
AATTCAAATTAAATTTAAAATAGATTTTTATAATCAC
Found at i:29875 original size:37 final size:37
Alignment explanation
Indices: 29803--29885 Score: 139
Period size: 37 Copynumber: 2.2 Consensus size: 37
29793 TTAAATTAAA
* *
29803 TTTAAAATAGATTTTTATAATCACAATTCAAATTATT
1 TTTAAGATTGATTTTTATAATCACAATTCAAATTATT
29840 TTTAAGATTGATTTTTATAATCACAATTCAAATTATT
1 TTTAAGATTGATTTTTATAATCACAATTCAAATTATT
*
29877 ATTAAGATT
1 TTTAAGATT
29886 TCTGTCTCCT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (37 bp):
TTTAAGATTGATTTTTATAATCACAATTCAAATTATT
Found at i:30003 original size:2 final size:2
Alignment explanation
Indices: 29996--30023 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29986 CTCTTATAGA
29996 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30024 GATTTCAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.