Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017315.1 Corchorus olitorius cultivar O-4 contig17348, 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: 33085
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Found at i:6834 original size:184 final size:184
Alignment explanation
Indices: 6525--6860 Score: 609
Period size: 184 Copynumber: 1.8 Consensus size: 184
6515 ATCTTCTTGC
* *
6525 CCAATCAACCTCATGAGGTCTGAGGGTAGTTCTGAATCATCCGTATATTCCTCAGTTGAATCATT
1 CCAATCAACCTCATGAGGTCTGAGGGTACTTCTGAATCATCCGCATATTCCTCAGTTGAATCATT
*
6590 GTTACACACAGGACCATTGAAATCAGTTGCAGATTTATCTGGTTCGTCTTTGCATTCATCGTCAG
66 GTTACACACAGGACCATTGAAATCAGTTGCAGATTTATCCGGTTCGTCTTTGCATTCATCGTCAG
6655 TTGGCCTGAGAAAGACATAGCATATTCCGATGAAAGATATAGCATATTCTCAGG
131 TTGGCCTGAGAAAGACATAGCATATTCCGATGAAAGATATAGCATATTCTCAGG
*
6709 CCAATCAATCTCATGAGGTCTGAGGGTACTTCTGAATCATCCGCATATTCCTCAGTTGAATCATT
1 CCAATCAACCTCATGAGGTCTGAGGGTACTTCTGAATCATCCGCATATTCCTCAGTTGAATCATT
* *
6774 GTTACACACAGGACCATTGAAATCAGTTGCAGATTTATCCGGTTTGTCTTTGCATTCATCGTTAG
66 GTTACACACAGGACCATTGAAATCAGTTGCAGATTTATCCGGTTCGTCTTTGCATTCATCGTCAG
*
6839 TTGGCCTGAGAAAGATATAGCA
131 TTGGCCTGAGAAAGACATAGCA
6861 AGATATATAT
Statistics
Matches: 145, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
184 145 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.32
Consensus pattern (184 bp):
CCAATCAACCTCATGAGGTCTGAGGGTACTTCTGAATCATCCGCATATTCCTCAGTTGAATCATT
GTTACACACAGGACCATTGAAATCAGTTGCAGATTTATCCGGTTCGTCTTTGCATTCATCGTCAG
TTGGCCTGAGAAAGACATAGCATATTCCGATGAAAGATATAGCATATTCTCAGG
Found at i:14065 original size:22 final size:22
Alignment explanation
Indices: 14039--14091 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
14029 GATTAAAACT
14039 AACAATTAA-AATTAACT-AAGAA
1 AACAATTAAGAA--AACTAAAGAA
* *
14061 AACAATCAAGAAAATTAAAGAA
1 AACAATTAAGAAAACTAAAGAA
14083 AACAATTAA
1 AACAATTAA
14092 TAAGAAAGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 3 0.12
22 21 0.81
23 2 0.08
ACGTcount: A:0.66, C:0.09, G:0.06, T:0.19
Consensus pattern (22 bp):
AACAATTAAGAAAACTAAAGAA
Found at i:24788 original size:33 final size:33
Alignment explanation
Indices: 24746--24859 Score: 115
Period size: 33 Copynumber: 3.5 Consensus size: 33
24736 CTAATTTGAG
* *
24746 TGTTGTTTGCAATGACACGAAATATGTTTTAGA
1 TGTTGTTTGCGATGACACTAAATATGTTTTAGA
* **
24779 TGTTGTTTGCGATGATACTAAA-ACTAATTT-GA
1 TGTTGTTTGCGATGACACTAAATA-TGTTTTAGA
* * *
24811 GTGTTGTTTGTGATGACACTAAATCTGTTTTAGG
1 -TGTTGTTTGCGATGACACTAAATATGTTTTAGA
*
24845 TGTTGTTTGTGATGA
1 TGTTGTTTGCGATGA
24860 AACAAATTCT
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
32 3 0.05
33 62 0.94
34 1 0.02
ACGTcount: A:0.25, C:0.08, G:0.24, T:0.43
Consensus pattern (33 bp):
TGTTGTTTGCGATGACACTAAATATGTTTTAGA
Found at i:24842 original size:66 final size:66
Alignment explanation
Indices: 24736--24859 Score: 194
Period size: 66 Copynumber: 1.9 Consensus size: 66
24726 AATTCTGAAC
24736 CTAATTTGAGTGTTGTTTGCAATGACACGAAATATGTTTTAGATGTTGTTTGCGATGATACTAAA
1 CTAATTTGAGTGTTGTTTGCAATGACACGAAATATGTTTTAGATGTTGTTTGCGATGATACTAAA
24801 A
66 A
** * * * *
24802 CTAATTTGAGTGTTGTTTGTGATGACACTAAATCTGTTTTAGGTGTTGTTTGTGATGA
1 CTAATTTGAGTGTTGTTTGCAATGACACGAAATATGTTTTAGATGTTGTTTGCGATGA
24860 AACAAATTCT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 52 1.00
ACGTcount: A:0.26, C:0.08, G:0.23, T:0.43
Consensus pattern (66 bp):
CTAATTTGAGTGTTGTTTGCAATGACACGAAATATGTTTTAGATGTTGTTTGCGATGATACTAAA
A
Found at i:24871 original size:33 final size:32
Alignment explanation
Indices: 24806--24910 Score: 106
Period size: 33 Copynumber: 3.2 Consensus size: 32
24796 CTAAAACTAA
*
24806 TTTGAGTGTTGTTTGTGATGACACTAAA-TCTGT
1 TTTG-GTGTTGTTTGTGATGAAAC-AAATTCTGT
24839 TTTAGGTGTTGTTTGTGATGAAACAAATTCTGT
1 TTT-GGTGTTGTTTGTGATGAAACAAATTCTGT
* ** *
24872 TTTGGATGCTAATTGTGATGAAAACAAA-TCTAT
1 TTTGG-TGTTGTTTGTGATG-AAACAAATTCTGT
24905 TTTGGT
1 TTTGGT
24911 TTATCATAGC
Statistics
Matches: 63, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
32 6 0.10
33 49 0.78
34 8 0.13
ACGTcount: A:0.26, C:0.08, G:0.23, T:0.44
Consensus pattern (32 bp):
TTTGGTGTTGTTTGTGATGAAACAAATTCTGT
Found at i:26677 original size:21 final size:21
Alignment explanation
Indices: 26663--26742 Score: 142
Period size: 21 Copynumber: 3.8 Consensus size: 21
26653 ATTGGAACAA
26663 GTTCCAAGCTCATTGGAGAAG
1 GTTCCAAGCTCATTGGAGAAG
*
26684 GTTCCATGCTCATTGGAGAAG
1 GTTCCAAGCTCATTGGAGAAG
26705 GTTCCAAGCTCATTGGAGAAG
1 GTTCCAAGCTCATTGGAGAAG
*
26726 GTTTCAAGCTCATTGGA
1 GTTCCAAGCTCATTGGA
26743 ATTGCCTAAG
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.28
Consensus pattern (21 bp):
GTTCCAAGCTCATTGGAGAAG
Found at i:28205 original size:21 final size:22
Alignment explanation
Indices: 28161--28213 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
28151 CCAAAGTCGC
* *
28161 GCCACTACCGGCCATTCACCGT
1 GCCACCACCGGCCATGCACCGT
28183 GCCACCACCGGCCATGC-CCGT
1 GCCACCACCGGCCATGCACCGT
*
28204 GCCATCACCG
1 GCCACCACCG
28214 TTGATGATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 13 0.46
22 15 0.54
ACGTcount: A:0.17, C:0.49, G:0.21, T:0.13
Consensus pattern (22 bp):
GCCACCACCGGCCATGCACCGT
Done.