Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015347.1 Corchorus olitorius cultivar O-4 contig15380, 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: 20323
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:3419 original size:12 final size:12
Alignment explanation
Indices: 3402--3427 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3392 TCCTATATAC
3402 TAATATTGGATA
1 TAATATTGGATA
3414 TAATATTGGATA
1 TAATATTGGATA
3426 TA
1 TA
3428 TTTTGTGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (12 bp):
TAATATTGGATA
Found at i:14774 original size:17 final size:16
Alignment explanation
Indices: 14728--14777 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
14718 CATGTAATTT
**
14728 TTGATCACCGGTGATC
1 TTGATCACTAGTGATC
* *
14744 TTGATCAGTGGTGATC
1 TTGATCACTAGTGATC
14760 TTAGATCACTAGTGATC
1 TT-GATCACTAGTGATC
14777 T
1 T
14778 AGGGGGTGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 16 0.55
17 13 0.45
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (16 bp):
TTGATCACTAGTGATC
Found at i:14872 original size:2 final size:2
Alignment explanation
Indices: 14865--14904 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
14855 TTTTACAATC
14865 AT AT AT AT 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 AT AT AT AT
14905 TCATCCAACC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16304 original size:330 final size:325
Alignment explanation
Indices: 15701--16477 Score: 877
Period size: 330 Copynumber: 2.4 Consensus size: 325
15691 ATTTTGAAAT
* * * *
15701 AAAAATAGGAAAAATAATATTAGAAGCGTGAAAAAGGCTTTCAATTTTTTTTGCGTTGAATCATA
1 AAAAATAGGAAAAACAATATTAGAAGCGTGAAAAA-CCTTTCAA-TCTTTTTG-GTTGAATTATA
* * *
15766 TATTTTTTATGAGTATTTTCGCTAGAAAC-CGAGGAAAAATCTTTCGGGTCAATGTTTGCAAAAT
63 TAATTTTTATGAGTATTTTAGCTA-AAACTTGAGGAAAAATCTTTCGGGTCAATGTTTGCAAAAT
** * *
15830 TTAGCCGAAATCGTGTACTAACCATCACGGTTTTCGGCTAAAAGTGCATTCTGGGACCCGGCTCA
127 TTAGCCGAAATCGTG-A-TAACCATCACGGTTTTCGGCTAAAAACGCATTATGGGACCCGACTCA
* * *
15895 ATTTTGCATGGTTTTTGGTGCCAAAACTCCTTGAAATATCTATATTCATCTAACCAAATATCAGC
190 ATTTTGCATGATTTTTGGCGCCAAAACTCCTTGAAATATCTATATTCATCTAACCAAATACCAGC
* *
15960 CACATTAGATTTAAGGATTTATTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTA
255 CACATTAGATTTAAGGATTTATTTTTACGAGCATATGAATCTTATTTCGATTTAATTAGAAATTA
16025 ATTCGGAA
320 ATTC--AA
* * *
16033 AAAAATAGGAAAAGCAATATTAGAAGCGTTAAAAACCTTTCAATCTTTTTGATATCGAATTATAT
1 AAAAATAGGAAAAACAATATTAGAAGCGTGAAAAACCTTTCAATCTTTTTGGT-T-GAATTATAT
* * * * *
16098 AATTTTTATGAGTATTTTAGCCAAAACTTGAGGAAATATCTTTTGGGTCATTTTTTTGCAAAATT
64 AATTTTTATGAGTATTTTAGCTAAAACTTGAGGAAAAATCTTTCGGGTCA-ATGTTTGCAAAA-T
** * **
16163 TTAGTTGAAATCGTG-T-ACCATCACGGTTTTTGGCTAAAAACGCATTATAGGG-CCACGACTTT
127 TTAGCCGAAATCGTGATAACCATCACGGTTTTCGGCTAAAAACGCATTAT-GGGACC-CGACTCA
* * * * * * *
16225 GTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTTTATTCATCTAATCGAATCCCAGC
190 ATTTTGCATGATTTTTGGCGCCAAAACTCCTTGAAATATCTATATTCATCTAACCAAATACCAGC
* * *
16290 CACATT-GAATTTAAGGATTTGTTTTTATGTGCATATGAATCTTATTTCGATTTAATTAGAAATT
255 CACATTAG-ATTTAAGGATTTATTTTTACGAGCATATGAATCTTATTTCGATTTAATTAGAAATT
*
16354 AATTCTA
319 AATTCAA
* * * * * *
16361 AAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCC-TCCAATCTTTTTTGGCGTTGAATTTT
1 AAAAATAGGAAAAACAATATTAGAAGCGTGAAAA-ACCTTTCAATC-TTTTT-G-GTTGAATTAT
* * *
16425 AT-ATATTTT-TGAGTATTTTTGCTAAAAATTGAGGAAAAATCTTTCGAGTCAAT
62 ATAAT-TTTTATGAGTATTTTAGCTAAAACTTGAGGAAAAATCTTTCGGGTCAAT
16478 TTTACCATCA
Statistics
Matches: 376, Mismatches: 56, Indels: 31
0.81 0.12 0.07
Matches are distributed among these distances:
327 1 0.00
328 74 0.20
329 51 0.14
330 139 0.37
331 55 0.15
332 42 0.11
333 14 0.04
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (325 bp):
AAAAATAGGAAAAACAATATTAGAAGCGTGAAAAACCTTTCAATCTTTTTGGTTGAATTATATAA
TTTTTATGAGTATTTTAGCTAAAACTTGAGGAAAAATCTTTCGGGTCAATGTTTGCAAAATTTAG
CCGAAATCGTGATAACCATCACGGTTTTCGGCTAAAAACGCATTATGGGACCCGACTCAATTTTG
CATGATTTTTGGCGCCAAAACTCCTTGAAATATCTATATTCATCTAACCAAATACCAGCCACATT
AGATTTAAGGATTTATTTTTACGAGCATATGAATCTTATTTCGATTTAATTAGAAATTAATTCAA
Found at i:20232 original size:72 final size:72
Alignment explanation
Indices: 20143--20281 Score: 233
Period size: 72 Copynumber: 1.9 Consensus size: 72
20133 AAAGACAAGC
* *
20143 CAAGGTGTGAACATTGTCAAAAGATGGGGCACACGAAAGATCAATGTTATGAGATCATTGGATAT
1 CAAGGTGCGAACATTGTCAAAAGATGGGGCACACGAAAGATCAATGCTATGAGATCATTGGATAT
20208 CCTGCTG
66 CCTGCTG
* * *
20215 CAAGGTGCGGACATTGTCAAAAGATGGGGCACATGAAAGATCAGTGCTATGAGATCATTGGATAT
1 CAAGGTGCGAACATTGTCAAAAGATGGGGCACACGAAAGATCAATGCTATGAGATCATTGGATAT
20280 CC
66 CC
20282 CGCAGGATGG
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (72 bp):
CAAGGTGCGAACATTGTCAAAAGATGGGGCACACGAAAGATCAATGCTATGAGATCATTGGATAT
CCTGCTG
Done.