Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014297.1 Corchorus olitorius cultivar O-4 contig14330, 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: 2812
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25
Found at i:838 original size:31 final size:31
Alignment explanation
Indices: 791--1261 Score: 699
Period size: 31 Copynumber: 15.7 Consensus size: 31
781 AAATGGAGAA
*
791 ACCTAAAAGTGAACTATATGCTATAACGATAG
1 ACCTAAAA-TGAACTATATGCAATAACGATAG
823 ACCTAAAATGAACTATATGCAATAACGATAG
1 ACCTAAAATGAACTATATGCAATAACGATAG
* *
854 ACCTAGAATGAACTATATGCAATAACAATAG
1 ACCTAAAATGAACTATATGCAATAACGATAG
885 ACCT---A-GAACTATATGCAATAACGATA-
1 ACCTAAAATGAACTATATGCAATAACGATAG
911 ACCT--AA--AACTATATGCAATAACGATAG
1 ACCTAAAATGAACTATATGCAATAACGATAG
* *
938 ACCTAGAATGAACTATATGCAATAAAGATAG
1 ACCTAAAATGAACTATATGCAATAACGATAG
969 ACCT---A-GAACTATATGCAATAACGATAG
1 ACCTAAAATGAACTATATGCAATAACGATAG
996 ACCTAAAATGAACTATATGCAATAACGATAG
1 ACCTAAAATGAACTATATGCAATAACGATAG
*
1027 ACCTAAAATGAACTATATGCAATAACGATAA
1 ACCTAAAATGAACTATATGCAATAACGATAG
1058 ACCT---A-GAACTATATGCAATAACGATAG
1 ACCTAAAATGAACTATATGCAATAACGATAG
1085 ACCTAAAATGAACTATATGCAATAACGATAG
1 ACCTAAAATGAACTATATGCAATAACGATAG
*
1116 ACCTAGAA-GAACTATATGCAATAACGATAG
1 ACCTAAAATGAACTATATGCAATAACGATAG
*
1146 ACCTAAAATGAACTATATGCAATAACGATAA
1 ACCTAAAATGAACTATATGCAATAACGATAG
1177 ACCTAAAATGAACTATATGCAATAACGATAG
1 ACCTAAAATGAACTATATGCAATAACGATAG
* * *
1208 ACCTAAAATGAACTATATGCTATGACGATAA
1 ACCTAAAATGAACTATATGCAATAACGATAG
1239 ACCTAAAAATGAACTATATGCAA
1 ACCT-AAAATGAACTATATGCAA
1262 CAGCCACACT
Statistics
Matches: 407, Mismatches: 16, Indels: 32
0.89 0.04 0.07
Matches are distributed among these distances:
26 24 0.06
27 75 0.18
28 3 0.01
29 2 0.00
30 31 0.08
31 247 0.61
32 25 0.06
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.23
Consensus pattern (31 bp):
ACCTAAAATGAACTATATGCAATAACGATAG
Found at i:985 original size:58 final size:60
Alignment explanation
Indices: 800--1261 Score: 637
Period size: 58 Copynumber: 7.8 Consensus size: 60
790 AACCTAAAAG
*
800 TGAACTATATGCTATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAGAA
1 TGAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCT--AA
*
862 TGAACTATATGCAATAACAATAGACCT---A-GAACTATATGCAATAACGATA-ACCTAA
1 TGAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAA
* *
917 --AACTATATGCAATAACGATAGACCTAGAATGAACTATATGCAATAAAGATAGACCT-A
1 TGAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAA
974 -GAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAAAA
1 TGAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCT--AA
*
1035 TGAACTATATGCAATAACGATAAACCT---A-GAACTATATGCAATAACGATAGACCTAAAA
1 TGAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCT--AA
*
1093 TGAACTATATGCAATAACGATAGACCTAGAA-GAACTATATGCAATAACGATAGACCTAAAA
1 TGAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCT--AA
*
1154 TGAACTATATGCAATAACGATAAACCTAAAATGAACTATATGCAATAACGATAGACCTAAAA
1 TGAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCT--AA
* * *
1216 TGAACTATATGCTATGACGATAAACCTAAAAATGAACTATATGCAA
1 TGAACTATATGCAATAACGATAGACCT-AAAATGAACTATATGCAA
1262 CAGCCACACT
Statistics
Matches: 373, Mismatches: 12, Indels: 29
0.90 0.03 0.07
Matches are distributed among these distances:
53 24 0.06
55 2 0.01
56 1 0.00
57 25 0.07
58 135 0.36
59 2 0.01
61 61 0.16
62 105 0.28
63 18 0.05
ACGTcount: A:0.48, C:0.16, G:0.13, T:0.23
Consensus pattern (60 bp):
TGAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAA
Found at i:1046 original size:89 final size:89
Alignment explanation
Indices: 801--1227 Score: 697
Period size: 89 Copynumber: 4.8 Consensus size: 89
791 ACCTAAAAGT
*
801 GAACTATATGCTATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAGAATGAA
1 GAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAGAATGAA
866 CTATATGCAATAACA-ATAGACCTA
66 CTATATGCAATAA-AGATAGACCTA
890 GAACTATATGCAATAACGATA-ACCT--AA--AACTATATGCAATAACGATAGACCTAGAATGAA
1 GAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAGAATGAA
950 CTATATGCAATAAAGATAGACCTA
66 CTATATGCAATAAAGATAGACCTA
*
974 GAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAAAATGAA
1 GAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAGAATGAA
* *
1039 CTATATGCAATAACGATAAACCTA
66 CTATATGCAATAAAGATAGACCTA
1063 GAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAGAA-GAA
1 GAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAGAATGAA
*
1127 CTATATGCAATAACGATAGACCTAAAA
66 CTATATGCAATAAAGATAGACCT---A
* *
1154 TGAACTATATGCAATAACGATAAACCTAAAATGAACTATATGCAATAACGATAGACCTAAAATGA
1 -GAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAGAATGA
1219 ACTATATGC
65 ACTATATGC
1228 TATGACGATA
Statistics
Matches: 319, Mismatches: 8, Indels: 18
0.92 0.02 0.05
Matches are distributed among these distances:
83 1 0.00
84 76 0.24
85 4 0.01
86 2 0.01
87 2 0.01
88 29 0.09
89 134 0.42
91 1 0.00
92 59 0.18
93 11 0.03
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.23
Consensus pattern (89 bp):
GAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAGAATGAA
CTATATGCAATAAAGATAGACCTA
Found at i:2002 original size:25 final size:25
Alignment explanation
Indices: 1950--2024 Score: 66
Period size: 25 Copynumber: 3.0 Consensus size: 25
1940 AAGATTAATA
*
1950 ATATTAGTTTTAATTTATAATTTAT
1 ATATAAGTTTTAATTTATAATTTAT
* *
1975 ATATAAGTTTTAGTTT-TAATGTTTT
1 ATATAAGTTTTAATTTATAAT-TTAT
2000 ATAATAA-TTTATATATTTAT-ATTTA
1 AT-ATAAGTTT-TA-ATTTATAATTTA
2025 ACATTTATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
24 4 0.10
25 22 0.55
26 8 0.20
27 5 0.12
28 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (25 bp):
ATATAAGTTTTAATTTATAATTTAT
Found at i:2132 original size:19 final size:21
Alignment explanation
Indices: 2108--2146 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2098 ATAAAGTAAA
2108 ACCGACA-AA-ACCGACCGCC
1 ACCGACATAACACCGACCGCC
2127 ACCGACATAACACCGACCGC
1 ACCGACATAACACCGACCGC
2147 TCGGTTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 2 0.11
21 9 0.50
ACGTcount: A:0.36, C:0.46, G:0.15, T:0.03
Consensus pattern (21 bp):
ACCGACATAACACCGACCGCC
Done.