Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019062.1 Corchorus olitorius cultivar O-4 contig19095, 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: 27993
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.35
Found at i:1118 original size:24 final size:25
Alignment explanation
Indices: 1072--1122 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
1062 ATTGGAGTAT
*
1072 TTATTTATCTTGTTGCTTAATTTTA
1 TTATTTATCTTGTTGATTAATTTTA
* *
1097 TTATTT-TCTTGTTTATTTATTTTA
1 TTATTTATCTTGTTGATTAATTTTA
1121 TT
1 TT
1123 GTTCACATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.71
Consensus pattern (25 bp):
TTATTTATCTTGTTGATTAATTTTA
Found at i:6088 original size:24 final size:25
Alignment explanation
Indices: 6042--6092 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
6032 ATTGGAGTAT
*
6042 TTATTTATCTTGTTGCTTAATTTTA
1 TTATTTATCTTGTTGATTAATTTTA
* *
6067 TTATTT-TCTTGTTTATTTATTTTA
1 TTATTTATCTTGTTGATTAATTTTA
6091 TT
1 TT
6093 GTTCACATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.71
Consensus pattern (25 bp):
TTATTTATCTTGTTGATTAATTTTA
Found at i:15268 original size:29 final size:30
Alignment explanation
Indices: 15211--15279 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
15201 TAAACCCTCC
*
15211 ATTTTGTCCTACTTTGTCAAACTTTGAGGGCT
1 ATTTTGTCCTA--TTGTCAAACTTCGAGGGCT
* *
15243 ATTTTGTCCTA-TGTCAAAGTTCGAGGTCT
1 ATTTTGTCCTATTGTCAAACTTCGAGGGCT
15272 ATTTTGTC
1 ATTTTGTC
15280 TATCAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 23 0.68
32 11 0.32
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.45
Consensus pattern (30 bp):
ATTTTGTCCTATTGTCAAACTTCGAGGGCT
Found at i:25128 original size:2 final size:2
Alignment explanation
Indices: 25107--25142 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
25097 AATAATCCAC
25107 TA TA -A TA TA TA -A TA TA -A 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
25143 TATTTTTAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.10
2 28 0.90
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:26287 original size:15 final size:16
Alignment explanation
Indices: 26262--26291 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
26252 AATAATTATT
26262 TTTAGATTATAATATA
1 TTTAGATTATAATATA
26278 TTTA-ATTATAATAT
1 TTTAGATTATAATAT
26292 TATTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGATTATAATATA
Found at i:27965 original size:331 final size:329
Alignment explanation
Indices: 26655--27972 Score: 1320
Period size: 331 Copynumber: 4.0 Consensus size: 329
26645 ATCACCAAAC
* * * * *
26655 CAAATCTCAGCAACATTGGATTTAAGAATTTGTTTTTACGAGTATCTGAATCTTATTTCGATTTA
1 CAAATCTCAGCCACATAGGATTTAAGAATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTA
* * * * *** *
26720 ATTAAAAATTAATTTAGAAAAAATAAGAAATATGGTATTAAAAGCGTGAAAAG-CCTTCCAATCT
66 ATTAGAAATTAA-TT-CAAAAAATATGAAAAACAATATTAAAAGCGTGAAAAGCCCTT-CAATAT
* * * * * * *
26784 TTTTGGCGTTCAATTAAATA-CTTTTATAAGTATTTTAGCCAAAAATTGAGGATAA-ATTTTTTG
128 TTTTGGCATTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGA-AATATCTTTCG
* * * * * * * * *
26847 TGTTAATTTTTACAAAATTTTAGCCGAAATAGTGTACTAACCATCACGGCTTTTGGTTAAAAGCG
192 GGTCAATTTTTACAAAATTTTAGCCAAAATCGTGTAATAACCATCACAGTTTTTGGCTAAAAACG
* * *
26912 CGTTCCAGGGACCCGCCTCAATTTTACATGATTTTTGGC-TCTGAGACT-ACTTAAAATATCTAT
257 CGTTCCA--GACCCGCCTCAGTTTTGCATGATTTTTGGCTTC-GAGACTCA-TTGAAATATCTAT
* *
26975 ATTCATCT-AAT
318 ACTCATATAAAT
* * *
26986 CAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAAG-ATATGAATCTTGTTTCGATTT
1 CAAATCTCAGCCACATAGGATTTAAGAATTTGTTTTTAC-AAGCATCTGAATCTTGTTTCGATTT
* ** **
27050 AATTAGAAATTAATTCAAAAAATAGGAAAAACAATATTAGAAA-CGTCCAAAGCCCTTCAACCTT
65 AATTAGAAATTAATTCAAAAAATATGAAAAACAATATTA-AAAGCGTGAAAAGCCCTTCAATATT
* * *
27114 TTTGGCGTTGAAATATATATTTTTTATGAGTATTTTAG-CAAATAATTGAGGAAATATCTTTCGA
129 TTTGGCATTGAATTATATATTTTTTATGAGTATTTTAGCCAAA-AATTGAGGAAATATCTTTCGG
* * * *
27178 GTCAATTTTTGCAAAATTTTAACCAAAATCGTGTAATAACCATCACAGTTTTTAGCTAAAAAAGC
193 GTCAATTTTTACAAAATTTTAGCCAAAATCGTGTAATAACCATCACAGTTTTTGGCTAAAAACGC
*** * * * * * *
27243 GTTCCAGATCCTAACTTAGTTTTGCATAATTTTTGG-TGTCAAGACTCCTTGAGATATCCATAC-
258 GTTCCAGA-CCCGCCTCAGTTTTGCATGATTTTTGGCT-TCGAGACTCATTGAAATATCTATACT
27306 CATATTCATCTAAT
321 CATA-T-A---AAT
* *
27320 CAAATCTTAGCCACATTA-GATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTT
1 CAAATCTCAGCCACA-TAGGATTTAAGAATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTT
* * * *
27384 AATTAGAAATTAATTCAGACTAAATGTGAAAAACAATATTAAAAGCGTGAAAAGTCCTCCAATAT
65 AATTAGAAATTAATTCA-A-AAAATATGAAAAACAATATTAAAAGCGTGAAAAGCCCTTCAATAT
* * * * * *
27449 TTTTGG-AGTTAAATTATATATATTTTATGAGTATTTCATCCAAAAATTGAGGAAAAATTTTTCG
128 TTTTGGCA-TTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCG
* *
27513 GAT-AATTTTTTTACAAAATTTTAGCCAAAATCGTGTAGTAACCATCACAGTTTTTGGCTAAAAA
192 GGTCAA--TTTTTACAAAATTTTAGCCAAAATCGTGTAATAACCATCACAGTTTTTGGCTAAAAA
* ** * * ** *
27577 TGCGTTTCGGGACCCCGGCTCAG-TTTGTATGATTTTTGGCGCCGAGACTCCTTGAAATATCTAT
255 CGCG-TTCCAGA-CCCGCCTCAGTTTTGCATGATTTTTGGCTTCGAGACTCATTGAAATATCTAT
27641 ACTCATATAAAT
318 ACTCATATAAAT
* * * *
27653 -AAATCTTAGCCACATAGCATTTAAGGATTTGTTTTTACAAGCATTTGAATCTTGTTTCGATTTA
1 CAAATCTCAGCCACATAGGATTTAAGAATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTA
** * * *
27717 ATTAGAAATTAATTCGGGAAAATATGAAAAACGATATTAAAAGTGTGAACAGCCCTTCAATATTT
66 ATTAGAAATTAATTC-AAAAAATATGAAAAACAATATTAAAAGCGTGAAAAGCCCTTCAATATTT
* * * *
27782 TTGGCATTGAATTATATATTTTTTATGAGTATTGTGGCTAAAAATTCAGGAAATTATCTTTCGGG
130 TTGGCATTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAA-TATCTTTCGGG
* * *
27847 TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCAC-GATTTTTGGCTAAAAACGC
194 TCAATTTTTACAAAATTTTAGCCAAAATCGTGTAATAACCATCACAG-TTTTTGGCTAAAAACGC
* ** * * * *
27911 GTTCCAGAACCGGTTCAGTTTTGCATGTTTTTTTGCTTCGAAAACTCATTGAAATATATATA
258 GTTCCAGACCCGCCTCAGTTTTGCATGATTTTTGGCTTCG-AGACTCATTGAAATATCTATA
27973 TATATATATA
Statistics
Matches: 818, Mismatches: 133, Indels: 72
0.80 0.13 0.07
Matches are distributed among these distances:
328 5 0.01
329 98 0.12
330 123 0.15
331 225 0.28
332 84 0.10
333 7 0.01
334 74 0.09
335 7 0.01
336 84 0.10
337 96 0.12
338 15 0.02
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (329 bp):
CAAATCTCAGCCACATAGGATTTAAGAATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTA
ATTAGAAATTAATTCAAAAAATATGAAAAACAATATTAAAAGCGTGAAAAGCCCTTCAATATTTT
TGGCATTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTC
AATTTTTACAAAATTTTAGCCAAAATCGTGTAATAACCATCACAGTTTTTGGCTAAAAACGCGTT
CCAGACCCGCCTCAGTTTTGCATGATTTTTGGCTTCGAGACTCATTGAAATATCTATACTCATAT
AAAT
Found at i:27971 original size:2 final size:2
Alignment explanation
Indices: 27964--27993 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
27954 ACTCATTGAA
27964 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
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.