Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013218.1 Corchorus olitorius cultivar O-4 contig13251, 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: 40831
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--35 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36 TTCCAACCCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9130 original size:2 final size:2
Alignment explanation
Indices: 9123--9154 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
9113 ATTGTGGTGA
9123 AT AT 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 AT AT
9155 GTTAACACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10892 original size:18 final size:18
Alignment explanation
Indices: 10866--10901 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
10856 AAAATACAAA
10866 CAAGGTCTAGATAATCAT
1 CAAGGTCTAGATAATCAT
*
10884 CAAGTTCTAGATAATCAT
1 CAAGGTCTAGATAATCAT
10902 TCCTTTACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.31
Consensus pattern (18 bp):
CAAGGTCTAGATAATCAT
Found at i:13392 original size:25 final size:25
Alignment explanation
Indices: 13342--13387 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
13332 TAGCACGTAT
*
13342 TATTATTATTATTAATCAATTTTTA
1 TATTACTATTATTAATCAATTTTTA
13367 TATTACTATTATT-AT-AATTTT
1 TATTACTATTATTAATCAATTTT
13388 GTTATCATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 2 0.10
25 12 0.60
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (25 bp):
TATTACTATTATTAATCAATTTTTA
Found at i:14830 original size:9 final size:9
Alignment explanation
Indices: 14818--14842 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
14808 GTAAAACATC
14818 AAACAAACA
1 AAACAAACA
14827 AAACAAACA
1 AAACAAACA
14836 AAACAAA
1 AAACAAA
14843 GCAACCATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (9 bp):
AAACAAACA
Found at i:16333 original size:41 final size:41
Alignment explanation
Indices: 16282--16376 Score: 118
Period size: 41 Copynumber: 2.3 Consensus size: 41
16272 AGAAAAATAA
* *
16282 GGACCAAATTGAATCAAATAGTGACTAGAATCCTAAATCAG
1 GGACCAAATTGAATCAAATAGTAAATAGAATCCTAAATCAG
* * * * *
16323 GGACTAAATTGTATCAAATATTAAATTGAATCCTAAATTAG
1 GGACCAAATTGAATCAAATAGTAAATAGAATCCTAAATCAG
*
16364 GGACCATATTGAA
1 GGACCAAATTGAA
16377 CACGGAAACA
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (41 bp):
GGACCAAATTGAATCAAATAGTAAATAGAATCCTAAATCAG
Found at i:19319 original size:27 final size:28
Alignment explanation
Indices: 19288--19361 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 28
19278 AAGTGAACCT
*
19288 AAAATGACCAAAATGCCCTTAGA-CATG
1 AAAATGACCAAAATGCCCCTAGATCATG
* * * **
19315 CAAATGACTAAAATGCCCCTGGATTTTG
1 AAAATGACCAAAATGCCCCTAGATCATG
19343 AAAATGACCAAAATGCCCC
1 AAAATGACCAAAATGCCCC
19362 CTGGTTGATC
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
27 19 0.50
28 19 0.50
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTAGATCATG
Found at i:33045 original size:13 final size:13
Alignment explanation
Indices: 33027--33053 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
33017 TTGTTGTTCC
33027 TGTCATTGATATG
1 TGTCATTGATATG
33040 TGTCATTGATATG
1 TGTCATTGATATG
33053 T
1 T
33054 TTTTATGATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.22, T:0.48
Consensus pattern (13 bp):
TGTCATTGATATG
Found at i:33304 original size:21 final size:21
Alignment explanation
Indices: 33278--33319 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
33268 CAAACTCTTA
33278 ACTACCGCCGAAATCCCGCGG
1 ACTACCGCCGAAATCCCGCGG
33299 ACTACCGCCGAAATCCCGCGG
1 ACTACCGCCGAAATCCCGCGG
33320 CAAGACGTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.43, G:0.24, T:0.10
Consensus pattern (21 bp):
ACTACCGCCGAAATCCCGCGG
Found at i:36404 original size:60 final size:59
Alignment explanation
Indices: 36310--36473 Score: 240
Period size: 59 Copynumber: 2.8 Consensus size: 59
36300 GCTAATTGCT
36310 CAAATAAGGGCCTAACGTTTGTC-AAAATGCTCAAATAAGGGTCTGATCTTTCAATTTAGC
1 CAAATAAGGGCCTAACG-TTGTCGAAAATGCTCAAATAAGGGTCTGATCTTTCAA-TTAGC
* * * * * *
36370 TAAATAAGGGTCTAACGTTGTCGAAAATGCTCAAATAAGGGCCTGGTCTTTTAATTGGC
1 CAAATAAGGGCCTAACGTTGTCGAAAATGCTCAAATAAGGGTCTGATCTTTCAATTAGC
*
36429 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGTCTG
1 CAAATAAGGGCCTAACGTTGTCGAAAATGCTCAAATAAGGGTCTG
36474 GCGTCGAAAA
Statistics
Matches: 93, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
59 50 0.54
60 43 0.46
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (59 bp):
CAAATAAGGGCCTAACGTTGTCGAAAATGCTCAAATAAGGGTCTGATCTTTCAATTAGC
Found at i:36608 original size:60 final size:59
Alignment explanation
Indices: 36513--36675 Score: 229
Period size: 60 Copynumber: 2.7 Consensus size: 59
36503 CTGACGGCAG
* * *
36513 GCCCTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGA
1 GCCCTTATTTGAGCTTTTTGGCA-AACATTAGGCCCTTATTTGGCCAAATTAAAAGAT-GA
* *
36573 GCCCTTATTTGAGCTTTTTGGCAAACATTAAGCCCTTATTTGGCCAAATTAAAAGATTA
1 GCCCTTATTTGAGCTTTTTGGCAAACATTAGGCCCTTATTTGGCCAAATTAAAAGATGA
*
36632 GACCCTTATTTGAGCATTTTTGACAAACATTAGGCCCTTATTTG
1 G-CCCTTATTTGAGC-TTTTTGGCAAACATTAGGCCCTTATTTG
36676 AGTAATTAGC
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
59 2 0.02
60 64 0.69
61 27 0.29
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.36
Consensus pattern (59 bp):
GCCCTTATTTGAGCTTTTTGGCAAACATTAGGCCCTTATTTGGCCAAATTAAAAGATGA
Found at i:36641 original size:29 final size:30
Alignment explanation
Indices: 36540--36643 Score: 92
Period size: 29 Copynumber: 3.5 Consensus size: 30
36530 TTCGATAACG
36540 TTAG-GCCCTTATTTGGCCAAATTAAAAGA
1 TTAGAGCCCTTATTTGGCCAAATTAAAAGA
* *** * *
36569 -TCGAGCCCTTATTTGAG-CTTTTTGGCAAACA
1 TTAGAGCCCTTATTTG-GCCAAATT--AAAAGA
36600 TTA-AGCCCTTATTTGGCCAAATTAAAAGA
1 TTAGAGCCCTTATTTGGCCAAATTAAAAGA
36629 TTAGA-CCCTTATTTG
1 TTAGAGCCCTTATTTG
36644 AGCATTTTTG
Statistics
Matches: 56, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
28 2 0.04
29 31 0.55
30 3 0.05
31 19 0.34
32 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (30 bp):
TTAGAGCCCTTATTTGGCCAAATTAAAAGA
Found at i:39923 original size:18 final size:18
Alignment explanation
Indices: 39882--39927 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
39872 CACTAGAAAT
*
39882 TTAATAATAATTATTCAA
1 TTAATAATTATTATTCAA
** *
39900 AAAATAATTATTATTTAA
1 TTAATAATTATTATTCAA
39918 TTAATAATTA
1 TTAATAATTA
39928 ATTAATTTCA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
TTAATAATTATTATTCAA
Done.