Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013121.1 Corchorus olitorius cultivar O-4 contig13154, 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: 2695
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32
Found at i:101 original size:48 final size:48
Alignment explanation
Indices: 28--175 Score: 215
Period size: 48 Copynumber: 3.0 Consensus size: 48
18 GAAGTTTTAA
*
28 AATAAAATTGCTTTCCATTTATGAGTTCAAGATCAAAATTCGCTTTTC
1 AATAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTC
* * *
76 AATAAAATTGCTTTCCATTCGTGAGTTCAATATCAAAATTTGCTTTTC
1 AATAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTC
* * *
124 AAAGTAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTC
1 -AA-TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTC
174 AA
1 AA
176 AGGACATTGA
Statistics
Matches: 88, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
48 44 0.50
49 4 0.05
50 40 0.45
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (48 bp):
AATAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTC
Found at i:161 original size:50 final size:50
Alignment explanation
Indices: 22--177 Score: 219
Period size: 50 Copynumber: 3.2 Consensus size: 50
12 GAACAAGAAG
* *
22 TTTT-AAAATAAAATTGCTTTCCATTTATGAGTTCAAGATCAAAATTCGC
1 TTTTCAAAGTAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGC
* * *
71 TTTTC-AA-TAAAATTGCTTTCCATTCGTGAGTTCAATATCAAAATTTGC
1 TTTTCAAAGTAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGC
* * *
119 TTTTCAAAGTAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGC
1 TTTTCAAAGTAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGC
169 TTTTCAAAG
1 TTTTCAAAG
178 GACATTGAAG
Statistics
Matches: 94, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
48 42 0.45
49 8 0.09
50 44 0.47
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.38
Consensus pattern (50 bp):
TTTTCAAAGTAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGC
Found at i:932 original size:50 final size:50
Alignment explanation
Indices: 845--1319 Score: 736
Period size: 50 Copynumber: 9.5 Consensus size: 50
835 CCATCCGAAT
* * *
845 ACACAAGCTTTTCCATAAGCCAAACTCGTTTCTATACGAGTTAATTATCA
1 ACACAGGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
* * *
895 ACATAGGCTTTTCCATAAGCCAAACTCATTTCCATACGAGTCACTTATCA
1 ACACAGGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
945 ACACAGGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
1 ACACAGGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
*
995 ACATAGGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
1 ACACAGGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
* *
1045 ACATAGGCTTTTCCATAAGCCAAACTCGTTTCCATATGAGTCAATTATCA
1 ACACAGGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
*
1095 ACACAGGCTTTTCCATAAGCCAAAACTCGTTTACATACGAGTCAATTATCA
1 ACACAGGCTTTTCCATAAGCC-AAACTCGTTTCCATACGAGTCAATTATCA
* * *
1146 ACACAGGCTTTTCCACAAGCCGAACTCATTTCCATACGAGTCAATTATCA
1 ACACAGGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
* * *
1196 ACACAGGCTTTTCCACAAGCCGAGCTCGTTTCCATACGAGTCAATTATCA
1 ACACAGGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
**
1246 ACACAGGCTTTTCCACGAG-CAAACTCGTTTCCATACGTAGTCAATTATCA
1 ACACAGGCTTTTCCATAAGCCAAACTCGTTTCCATACG-AGTCAATTATCA
* * *
1296 ACATAGACTTTTCCACAAGCCAAA
1 ACACAGGCTTTTCCATAAGCCAAA
1320 TTCGAGGATC
Statistics
Matches: 396, Mismatches: 26, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
49 16 0.04
50 329 0.83
51 51 0.13
ACGTcount: A:0.32, C:0.27, G:0.12, T:0.28
Consensus pattern (50 bp):
ACACAGGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
Found at i:1293 original size:251 final size:250
Alignment explanation
Indices: 845--1319 Score: 783
Period size: 251 Copynumber: 1.9 Consensus size: 250
835 CCATCCGAAT
* *
845 ACACAAGCTTTTCCATAAGCCAAACTCGTTTCTATACGAGTTAATTATCAACATAGGCTTTTCCA
1 ACACAAGCTTTTCCATAAGCCAAACTCGTTTCTATACGAGTCAATTATCAACACAGGCTTTTCCA
* * *
910 TAAGCCAAACTCATTTCCATACGAGTCACTTATCAACACAGGCTTTTCCATAAGCCAAACTCGTT
66 CAAGCCAAACTCATTTCCATACGAGTCAATTATCAACACAGGCTTTTCCACAAGCCAAACTCGTT
* *
975 TCCATACGAGTCAATTATCAACATAGGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAAT
131 TCCATACGAGTCAATTATCAACACAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAAT
* *
1040 TATCAACATAGGCTTTTCCATAAGCCAAACTCGTTTCCATATGAGTCAATTATCA
196 TATCAACATAGACTTTTCCACAAGCCAAACTCGTTTCCATATGAGTCAATTATCA
*
1095 ACACAGGCTTTTCCATAAGCCAAAACTCGTTTAC-ATACGAGTCAATTATCAACACAGGCTTTTC
1 ACACAAGCTTTTCCATAAGCC-AAACTCGTTT-CTATACGAGTCAATTATCAACACAGGCTTTTC
* * *
1159 CACAAGCCGAACTCATTTCCATACGAGTCAATTATCAACACAGGCTTTTCCACAAGCCGAGCTCG
64 CACAAGCCAAACTCATTTCCATACGAGTCAATTATCAACACAGGCTTTTCCACAAGCCAAACTCG
*
1224 TTTCCATACGAGTCAATTATCAACACAGGCTTTTCCACGAG-CAAACTCGTTTCCATACGTAGTC
129 TTTCCATACGAGTCAATTATCAACACAGGCTTTTCCACAAGCCAAACTCGTTTCCATACG-AGTC
1288 AATTATCAACATAGACTTTTCCACAAGCCAAA
193 AATTATCAACATAGACTTTTCCACAAGCCAAA
1320 TTCGAGGATC
Statistics
Matches: 208, Mismatches: 14, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
250 38 0.18
251 169 0.81
252 1 0.00
ACGTcount: A:0.32, C:0.27, G:0.12, T:0.28
Consensus pattern (250 bp):
ACACAAGCTTTTCCATAAGCCAAACTCGTTTCTATACGAGTCAATTATCAACACAGGCTTTTCCA
CAAGCCAAACTCATTTCCATACGAGTCAATTATCAACACAGGCTTTTCCACAAGCCAAACTCGTT
TCCATACGAGTCAATTATCAACACAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAAT
TATCAACATAGACTTTTCCACAAGCCAAACTCGTTTCCATATGAGTCAATTATCA
Found at i:1696 original size:28 final size:27
Alignment explanation
Indices: 1598--1700 Score: 93
Period size: 27 Copynumber: 3.7 Consensus size: 27
1588 GGTCATCTAT
* * *
1598 GGGGCATTTTGGGTCATTTTCAAAATCCA
1 GGGGCATTTT-AGTCATTTGC-ACATCCA
*
1627 GGGGCGTTTTAGTCATTTGCACATCCA
1 GGGGCATTTTAGTCATTTGCACATCCA
**
1654 GGGGCA-TTTAGGTCATTTTTACA-CCTA
1 GGGGCATTTTA-GTCATTTGCACATCC-A
1681 GGGGGCATTTTAGTCATTTG
1 -GGGGCATTTTAGTCATTTG
1701 TGCTTCAGGG
Statistics
Matches: 62, Mismatches: 8, Indels: 9
0.78 0.10 0.11
Matches are distributed among these distances:
26 6 0.10
27 22 0.35
28 21 0.34
29 13 0.21
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.36
Consensus pattern (27 bp):
GGGGCATTTTAGTCATTTGCACATCCA
Found at i:1871 original size:19 final size:20
Alignment explanation
Indices: 1824--1875 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
1814 TGTTGTGTTC
*
1824 TTTTGCATATTTGTATCACA
1 TTTTGCATATTTATATCACA
*
1844 TTTTCGCATATTTATCTCACA
1 TTTT-GCATATTTATATCACA
1865 -TTTGCAT-TTTA
1 TTTTGCATATTTA
1876 CATGATCCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 4 0.14
19 4 0.14
20 7 0.24
21 14 0.48
ACGTcount: A:0.23, C:0.17, G:0.08, T:0.52
Consensus pattern (20 bp):
TTTTGCATATTTATATCACA
Done.