Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021647.1 Corchorus olitorius cultivar O-4 contig21680, 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: 49022
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:781 original size:12 final size:12
Alignment explanation
Indices: 764--797 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
754 CTTAGCCTAG
*
764 GCGCTGGGCCAT
1 GCGCTGGCCCAT
776 GCGCTGGCCCAT
1 GCGCTGGCCCAT
788 GCGCCTGGCC
1 GCG-CTGGCC
798 TAGGCGCTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.06, C:0.41, G:0.38, T:0.15
Consensus pattern (12 bp):
GCGCTGGCCCAT
Found at i:828 original size:36 final size:36
Alignment explanation
Indices: 758--892 Score: 227
Period size: 36 Copynumber: 3.7 Consensus size: 36
748 CCCAAGCTTA
*
758 GCCTAGGCGC-TGGGCCATGCGCTGGCCCATGCGCCTG
1 GCCTAGGCGCTTGGGCC--GCGCTGGCCCGTGCGCCTG
*
795 GCCTAGGCGCTTGGGCCGCGCTGGCCCGCGCGCCTG
1 GCCTAGGCGCTTGGGCCGCGCTGGCCCGTGCGCCTG
831 GCCTAGGCGCTTGGGCCGCGCTGGCCCGTGCGCCTG
1 GCCTAGGCGCTTGGGCCGCGCTGGCCCGTGCGCCTG
867 GCCTAGGCGCTTGGGCCGCGCTGGCC
1 GCCTAGGCGCTTGGGCCGCGCTGGCC
893 TAGCGTTTGT
Statistics
Matches: 94, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
36 78 0.83
37 10 0.11
38 6 0.06
ACGTcount: A:0.04, C:0.39, G:0.41, T:0.16
Consensus pattern (36 bp):
GCCTAGGCGCTTGGGCCGCGCTGGCCCGTGCGCCTG
Found at i:9791 original size:38 final size:36
Alignment explanation
Indices: 9740--9819 Score: 99
Period size: 38 Copynumber: 2.2 Consensus size: 36
9730 TAACAATTAA
* *
9740 AATTAACTAAGAAAGCAATCAAGA-AAATTAATGAAAAC
1 AATTAAATAAGAAAGCAAT-AA-ATAAACTAA-GAAAAC
*
9778 AATTAAATAAGAAAGCAGTAAATAAACTAAGAAAAC
1 AATTAAATAAGAAAGCAATAAATAAACTAAGAAAAC
9814 AATTAA
1 AATTAA
9820 GAAAACCCTC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 13 0.34
37 8 0.21
38 17 0.45
ACGTcount: A:0.62, C:0.09, G:0.10, T:0.19
Consensus pattern (36 bp):
AATTAAATAAGAAAGCAATAAATAAACTAAGAAAAC
Found at i:13368 original size:14 final size:15
Alignment explanation
Indices: 13342--13371 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
13332 CTAAGTTCAA
13342 TCCTTGTTTATTTAT
1 TCCTTGTTTATTTAT
13357 TCCTTG-TTATTTAT
1 TCCTTGTTTATTTAT
13371 T
1 T
13372 TTTCCTAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.13, C:0.13, G:0.07, T:0.67
Consensus pattern (15 bp):
TCCTTGTTTATTTAT
Found at i:15012 original size:22 final size:22
Alignment explanation
Indices: 14987--15065 Score: 77
Period size: 22 Copynumber: 3.4 Consensus size: 22
14977 AATTGCAGGA
14987 CAACTTCGGCCCAGAACTTGTT
1 CAACTTCGGCCCAGAACTTGTT
** * *
15009 CAACTTCGGGACAGAAGTTGATGCGGA
1 CAACTTCGGCCCAGAACTTG-T----T
15036 CAACTTCGGCCCAGAACTTGTT
1 CAACTTCGGCCCAGAACTTGTT
15058 CAACTTCG
1 CAACTTCG
15066 AGACATAAGT
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
22 25 0.57
23 1 0.02
26 1 0.02
27 17 0.39
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (22 bp):
CAACTTCGGCCCAGAACTTGTT
Found at i:15044 original size:49 final size:49
Alignment explanation
Indices: 14984--15077 Score: 170
Period size: 49 Copynumber: 1.9 Consensus size: 49
14974 AAGAATTGCA
*
14984 GGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGACAGAAGTTGATGC
1 GGACAACTTCGGCCCAGAACTTGTTCAACTTCGAGACAGAAGTTGATGC
*
15033 GGACAACTTCGGCCCAGAACTTGTTCAACTTCGAGACATAAGTTG
1 GGACAACTTCGGCCCAGAACTTGTTCAACTTCGAGACAGAAGTTG
15078 TTGTGGAAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.23
Consensus pattern (49 bp):
GGACAACTTCGGCCCAGAACTTGTTCAACTTCGAGACAGAAGTTGATGC
Found at i:25815 original size:8 final size:8
Alignment explanation
Indices: 25792--25826 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
25782 TTGAGATAAT
25792 TCTTCAATA
1 TCTTCAA-A
25801 TTCTTCAAA
1 -TCTTCAAA
25810 TCTTCAAA
1 TCTTCAAA
25818 TCTTCAAA
1 TCTTCAAA
25826 T
1 T
25827 TATCTTCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 17 0.68
9 1 0.04
10 7 0.28
ACGTcount: A:0.34, C:0.23, G:0.00, T:0.43
Consensus pattern (8 bp):
TCTTCAAA
Found at i:26077 original size:12 final size:13
Alignment explanation
Indices: 26052--26077 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
26042 ATCATAAAAA
26052 TAGGGTCTTTTTT
1 TAGGGTCTTTTTT
26065 TAGGGTCTTTTTT
1 TAGGGTCTTTTTT
26078 GGCTCGATCA
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:0.08, C:0.08, G:0.23, T:0.62
Consensus pattern (13 bp):
TAGGGTCTTTTTT
Found at i:33692 original size:19 final size:18
Alignment explanation
Indices: 33659--33694 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
33649 TTGAAATTAT
33659 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
33677 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
33695 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Done.