Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018665.1 Corchorus olitorius cultivar O-4 contig18698, 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: 16310
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:151 original size:16 final size:16
Alignment explanation
Indices: 130--165 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
120 TTAATTGATG
130 TAAATATAATATAAAT
1 TAAATATAATATAAAT
* *
146 TAAATATATTATAATT
1 TAAATATAATATAAAT
162 TAAA
1 TAAA
166 ATTAATTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATATAATATAAAT
Found at i:3546 original size:16 final size:17
Alignment explanation
Indices: 3483--3558 Score: 79
Period size: 16 Copynumber: 4.7 Consensus size: 17
3473 AATTTTGGGT
* *
3483 ACCCGAACCTG-AAATT
1 ACCCGAACCCGAAAATG
* *
3499 ACCCGAATCC--AAACG
1 ACCCGAACCCGAAAATG
3514 ACCCGAACCCGAAAATG
1 ACCCGAACCCGAAAATG
*
3531 ACCCAAACCC-AAAATG
1 ACCCGAACCCGAAAATG
3547 ACCCGAACCCGA
1 ACCCGAACCCGA
3559 TCAACCCGAT
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
15 12 0.24
16 23 0.47
17 14 0.29
ACGTcount: A:0.41, C:0.38, G:0.13, T:0.08
Consensus pattern (17 bp):
ACCCGAACCCGAAAATG
Found at i:5227 original size:15 final size:15
Alignment explanation
Indices: 5173--5229 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
5163 TCCGAACCGT
*
5173 ATGACCCGAAACCGAAA
1 ATGACCCG-AACC-CAA
*
5190 ACGACCC-AACCCAGA
1 ATGACCCGAACCCA-A
5205 ATTGACCCGAACCCAA
1 A-TGACCCGAACCCAA
5221 ATGACCCGA
1 ATGACCCGA
5230 CATTTGAACG
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
14 1 0.03
15 14 0.41
16 7 0.21
17 12 0.35
ACGTcount: A:0.40, C:0.37, G:0.16, T:0.07
Consensus pattern (15 bp):
ATGACCCGAACCCAA
Found at i:7727 original size:376 final size:375
Alignment explanation
Indices: 6992--7752 Score: 1265
Period size: 376 Copynumber: 2.0 Consensus size: 375
6982 TATTATTAAT
*
6992 AAAATATCAAGTGACATGTTTTTTGTTACATGCATAAAAAAAAAGATGTTTTAGGACCAAGCCTT
1 AAAATATCAAGTGACATGTTTTTTGTTACATGCATAAAAAAAAAGACGTTTTAGGACCAAGCCTT
*
7057 ATCGAGTGACATGTTTATTAGTAAATGCATAAAAAAAGACGCTTTAGGACCGAGGCATGATGCTA
66 ATCGAGTGACATGTTTATTAGTAAATGCATAAAAAAAGACGCTTTAGGACCGAAGCATGATGCTA
* *
7122 TCAACAAATTCGACAACTATATATCCTTAATTGATATCTTACATCCTTAGTAAGTAATTAATACT
131 TCAACAAATTCGACAACTATATATCCTTAATTGATATCTGACATCCTTAGTAAGTAATTAATACC
7187 GATTTTTTACATAAGTTAAAAAAAAACTTTAGAGGTTATTAAAAAAGCTACAATGCTATCAATAA
196 GATTTTTTACATAAGTTAAAAAAAAACTTTAGAGGTTATTAAAAAAGCTACAATGCTATCAATAA
* * *
7252 AAATTATGTAACCATAAATCCTTAATAGCTTAAGTAATAAGCAATAAGTAATAAAGAATGATGGT
261 AAATTAAGTAACCATAAATCCTTAATAACTTAAGTAATAAGCAATAAGTAATAAAGAATGATGAT
7317 TACGAATTCTCTTATATAAAATTACAAAAAAAAAAGTTGTAGTGGTTATCCA
326 TACGAATTCTCTTATATAAAATTAC--AAAAAAAAGTTGTAGTGGTTATCCA
* ** *
7369 AAAATATCAAGTGACATGTTTTTTGTTAGATGCAT-AAAAAAAAGACGTTTTAGGACTGAGGCTT
1 AAAATATCAAGTGACATGTTTTTTGTTACATGCATAAAAAAAAAGACGTTTTAGGACCAAGCCTT
* *
7433 ATCGAGTGACATGTTTATTATTAAATGCATACAAAAAGACGCTTTAGGACCGAAGCATGATGCTA
66 ATCGAGTGACATGTTTATTAGTAAATGCATAAAAAAAGACGCTTTAGGACCGAAGCATGATGCTA
7498 TCAACAAATTCGACAACTATATATCCTTAATTGATATCTGACATCCTTAGTAAGTAATTAATACC
131 TCAACAAATTCGACAACTATATATCCTTAATTGATATCTGACATCCTTAGTAAGTAATTAATACC
* *
7563 GATTTTTTACATAAGTT-AAAAAAAACTTTAGAGGTTATTAAAAAGGCTACGATGCTATCAATAA
196 GATTTTTTACATAAGTTAAAAAAAAACTTTAGAGGTTATTAAAAAAGCTACAATGCTATCAATAA
*
7627 AAATTAAGTAACCATATATAAATCCTTAATAACTTAAGTAATAAGCAATAAGTAATAAATAATGA
261 AAATTAAGTAACC----ATAAATCCTTAATAACTTAAGTAATAAGCAATAAGTAATAAAGAATGA
* *
7692 TGATTACGAATTCTCTTATCTAAATTTACAAAAAAAAAAAGTTGTAGTGGTTATCCA
322 TGATTACGAATTCTCTTATATAAAATTAC---AAAAAAAAGTTGTAGTGGTTATCCA
7749 AAAA
1 AAAA
7753 AGTATTTTAT
Statistics
Matches: 361, Mismatches: 18, Indels: 7
0.94 0.05 0.02
Matches are distributed among these distances:
375 57 0.16
376 167 0.46
377 34 0.09
379 72 0.20
380 31 0.09
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (375 bp):
AAAATATCAAGTGACATGTTTTTTGTTACATGCATAAAAAAAAAGACGTTTTAGGACCAAGCCTT
ATCGAGTGACATGTTTATTAGTAAATGCATAAAAAAAGACGCTTTAGGACCGAAGCATGATGCTA
TCAACAAATTCGACAACTATATATCCTTAATTGATATCTGACATCCTTAGTAAGTAATTAATACC
GATTTTTTACATAAGTTAAAAAAAAACTTTAGAGGTTATTAAAAAAGCTACAATGCTATCAATAA
AAATTAAGTAACCATAAATCCTTAATAACTTAAGTAATAAGCAATAAGTAATAAAGAATGATGAT
TACGAATTCTCTTATATAAAATTACAAAAAAAAGTTGTAGTGGTTATCCA
Found at i:16183 original size:30 final size:30
Alignment explanation
Indices: 16143--16202 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
16133 GTTGAGTGTG
16143 ACTGGCTGATATATGAATCTCATAAATCAT
1 ACTGGCTGATATATGAATCTCATAAATCAT
*
16173 ACTGGTTGATATATGAATCTCATAAATCAT
1 ACTGGCTGATATATGAATCTCATAAATCAT
16203 GCCATGAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (30 bp):
ACTGGCTGATATATGAATCTCATAAATCAT
Found at i:16284 original size:2 final size:2
Alignment explanation
Indices: 16273--16310 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
16263 ACACATTACT
16273 TA TA -A 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 TA TA T
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.