Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017828.1 Corchorus olitorius cultivar O-4 contig17861, 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: 37309
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1550 original size:25 final size:25
Alignment explanation
Indices: 1516--1564 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
1506 CCAAACAATC
1516 TTGAGCACTCTCGCTCGGTCTCTAT
1 TTGAGCACTCTCGCTCGGTCTCTAT
*
1541 TTGAGTACTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCGCTCGGTCTCTA
1565 CAAACTAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.12, C:0.31, G:0.20, T:0.37
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCGGTCTCTAT
Found at i:4943 original size:15 final size:15
Alignment explanation
Indices: 4923--4952 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4913 CCAGATACCA
4923 TTGTATATATTTGTT
1 TTGTATATATTTGTT
4938 TTGTATATATTTGTT
1 TTGTATATATTTGTT
4953 AACTACATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.13, T:0.67
Consensus pattern (15 bp):
TTGTATATATTTGTT
Found at i:7096 original size:75 final size:75
Alignment explanation
Indices: 6921--7225 Score: 493
Period size: 75 Copynumber: 4.0 Consensus size: 75
6911 CGCCCTTATT
* *
6921 GCAATCTCTAGCCCGATGATTCAAATCCCCACAGTTATAACACCCGCCGCCGCCGCTGCCTTTCC
1 GCAATCTCTAGCCCGATGATTCAAATCCCCACAGTTATAACA--C-CCGCCGCTGCTGCCGTTCC
6986 TACGATCGTTTCC
63 TACGATCGTTTCC
* *
6999 GCAATCTCTAGCCCGATGATTCAAATCCCCACAGTTATAACACCCACCACTGCTGCCGTTCCTAC
1 GCAATCTCTAGCCCGATGATTCAAATCCCCACAGTTATAACACCCGCCGCTGCTGCCGTTCCTAC
7064 GATCGTTTCC
66 GATCGTTTCC
* * *
7074 GCAATCTTTAGCCCGATGATTCAAATCGCCACAGTTATAACACCCGCCGCTGCTGCCATTCCTAC
1 GCAATCTCTAGCCCGATGATTCAAATCCCCACAGTTATAACACCCGCCGCTGCTGCCGTTCCTAC
*
7139 TATCGTTTCC
66 GATCGTTTCC
* *
7149 GCAATCTCTAGCCCGATGATTCAAATCCCCACAGTTATAACACCCTCCGCTGCTGCCGTTCTTAC
1 GCAATCTCTAGCCCGATGATTCAAATCCCCACAGTTATAACACCCGCCGCTGCTGCCGTTCCTAC
7214 GATCGTTTCC
66 GATCGTTTCC
7224 GC
1 GC
7226 CTCTCCAGCC
Statistics
Matches: 211, Mismatches: 16, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
75 168 0.80
76 1 0.00
78 42 0.20
ACGTcount: A:0.22, C:0.37, G:0.15, T:0.26
Consensus pattern (75 bp):
GCAATCTCTAGCCCGATGATTCAAATCCCCACAGTTATAACACCCGCCGCTGCTGCCGTTCCTAC
GATCGTTTCC
Found at i:19664 original size:2 final size:2
Alignment explanation
Indices: 19652--19686 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
19642 AATCCACCTG
19652 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19687 CACACTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:26635 original size:2 final size:2
Alignment explanation
Indices: 26628--26655 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
26618 TGATTACTGA
26628 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
26656 TTCCTCCTTT
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
Found at i:27058 original size:60 final size:60
Alignment explanation
Indices: 26961--27102 Score: 205
Period size: 60 Copynumber: 2.4 Consensus size: 60
26951 ATGACAGGCT
* *
26961 CTTATTTGAGCATTTTGACAAATGCTAGGTCCTTATTTGGCCAAATTAAAAGACTGAGCC
1 CTTATTTGAGCATTTTGACAAATGCTAGGTCCTTATTTGGCCAAATTAAAAGACTAAACC
* * *
27021 TTTATTTGAGCATTTTGACAAATGTTAGGTTCC-TATTTGGCCAAATTAAAAGATTAAACC
1 CTTATTTGAGCATTTTGACAAATGCTAGG-TCCTTATTTGGCCAAATTAAAAGACTAAACC
* *
27081 CTTATTTAAGTATTTTGACAAA
1 CTTATTTGAGCATTTTGACAAA
27103 CATCAAACCC
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
60 70 0.96
61 3 0.04
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (60 bp):
CTTATTTGAGCATTTTGACAAATGCTAGGTCCTTATTTGGCCAAATTAAAAGACTAAACC
Found at i:34847 original size:56 final size:56
Alignment explanation
Indices: 34775--34886 Score: 190
Period size: 56 Copynumber: 2.0 Consensus size: 56
34765 TTTGTTTCCC
*
34775 TTCACACAATAAATGTTGTAATAAA-CCATATCCCCCTATCTCTAATTAATTATTCT
1 TTCACACAATAAATGTTATAATAAATCC-TATCCCCCTATCTCTAATTAATTATTCT
*
34831 TTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATTCT
1 TTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTAATTAATTATTCT
34887 ACAAAATAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
56 51 0.96
57 2 0.04
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (56 bp):
TTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTAATTAATTATTCT
Found at i:35011 original size:42 final size:42
Alignment explanation
Indices: 34952--35032 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
34942 TAAGGATCAG
34952 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
*
34994 GATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
35033 AAGACTTAGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47
Consensus pattern (42 bp):
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Found at i:36577 original size:56 final size:57
Alignment explanation
Indices: 36470--36581 Score: 174
Period size: 57 Copynumber: 2.0 Consensus size: 57
36460 ATATGTTTCC
* * *
36470 TTTCACACAATAAATGTTATAATAAATCCTATCCCCTCTATCTCTACTTAATTATTT
1 TTTCACACAATAAATATTATAATAAATCATATCCCCACTATCTCTACTTAATTATTT
36527 TTTCACACAATAAATATTAT-ATAAAATCATAT-CCCACTATCTCTACTTAATTATT
1 TTTCACACAATAAATATTATAAT-AAATCATATCCCCACTATCTCTACTTAATTATT
36582 CTACAAAATA
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
56 24 0.47
57 27 0.53
ACGTcount: A:0.37, C:0.21, G:0.01, T:0.41
Consensus pattern (57 bp):
TTTCACACAATAAATATTATAATAAATCATATCCCCACTATCTCTACTTAATTATTT
Found at i:36596 original size:57 final size:57
Alignment explanation
Indices: 36478--36589 Score: 131
Period size: 56 Copynumber: 2.0 Consensus size: 57
36468 CCTTTCACAC
* * * * * * *
36478 AATAAATGTTATAATAAATCCTATCCCCTCTATCTCTACTTAATTATTTTTTCACAC
1 AATAAATATTATAATAAATCATATCCCCACTATCTCTACTTAATTATTTCTACAAAA
36535 AATAAATATTAT-ATAAAATCATAT-CCCACTATCTCTACTTAATTA-TTCTACAAAA
1 AATAAATATTATAAT-AAATCATATCCCCACTATCTCTACTTAATTATTTCTACAAAA
36590 TAAATAATAT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
55 6 0.13
56 22 0.47
57 19 0.40
ACGTcount: A:0.39, C:0.21, G:0.01, T:0.39
Consensus pattern (57 bp):
AATAAATATTATAATAAATCATATCCCCACTATCTCTACTTAATTATTTCTACAAAA
Found at i:36712 original size:42 final size:41
Alignment explanation
Indices: 36649--36733 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 41
36639 TAAGGCTTAG
36649 GATTTGAGTTGAGTATGTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAGTTGAGTATGTCTTAATTTACAAAGAATTTTC-AT
* *
36691 GATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTCAT
1 GATTTGAGTTGAGTATGTCTTAATTTACAAAGAATTTTCAT
36732 GA
1 GA
36734 CTTAGCTAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 4 0.10
42 37 0.90
ACGTcount: A:0.31, C:0.07, G:0.18, T:0.45
Consensus pattern (41 bp):
GATTTGAGTTGAGTATGTCTTAATTTACAAAGAATTTTCAT
Done.