Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015998.1 Corchorus olitorius cultivar O-4 contig16031, 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: 3371
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:1149 original size:24 final size:24
Alignment explanation
Indices: 1121--1195 Score: 150
Period size: 24 Copynumber: 3.1 Consensus size: 24
1111 CCGCTCCTAA
1121 AACAAAAGAATGATTTGAACATCG
1 AACAAAAGAATGATTTGAACATCG
1145 AACAAAAGAATGATTTGAACATCG
1 AACAAAAGAATGATTTGAACATCG
1169 AACAAAAGAATGATTTGAACATCG
1 AACAAAAGAATGATTTGAACATCG
1193 AAC
1 AAC
1196 CTCCATCGGG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.51, C:0.13, G:0.16, T:0.20
Consensus pattern (24 bp):
AACAAAAGAATGATTTGAACATCG
Found at i:1386 original size:7 final size:7
Alignment explanation
Indices: 1378--1496 Score: 193
Period size: 7 Copynumber: 17.0 Consensus size: 7
1368 GAGACATGAA
*
1378 TTTTGAA
1 TTTTGAG
*
1385 TTTTGAA
1 TTTTGAG
1392 TTTTGAG
1 TTTTGAG
1399 TTTTGAG
1 TTTTGAG
1406 TTTTGAG
1 TTTTGAG
1413 TTTTGAG
1 TTTTGAG
1420 TTTTGAG
1 TTTTGAG
1427 TTTTGAG
1 TTTTGAG
1434 TTTTGAG
1 TTTTGAG
1441 TTTTGAG
1 TTTTGAG
1448 TTTTGAG
1 TTTTGAG
1455 TTTTGAG
1 TTTTGAG
1462 TTTTGAG
1 TTTTGAG
*
1469 TTTTGAA
1 TTTTGAG
*
1476 TTTTGAA
1 TTTTGAG
*
1483 TTTTGAA
1 TTTTGAG
1490 TTTTGAG
1 TTTTGAG
1497 CAATGAAATG
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 109 1.00
ACGTcount: A:0.18, C:0.00, G:0.24, T:0.57
Consensus pattern (7 bp):
TTTTGAG
Found at i:1677 original size:33 final size:33
Alignment explanation
Indices: 1635--1712 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
1625 AGAAAATGTG
* * *
1635 GATTTTGAACTTTGAGTTTTGATATGATATGCA
1 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
1668 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
1 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
*
1701 AATTTTGAACTT
1 GATTTTGAACTT
1713 CTTAATTAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (33 bp):
GATTTTGAACTTTGAATTTTGAAATGAAATGCA
Found at i:1812 original size:56 final size:54
Alignment explanation
Indices: 1750--2020 Score: 139
Period size: 54 Copynumber: 5.0 Consensus size: 54
1740 AATTCAACCT
** * **
1750 TGATCAT-GGAAATCTTTCTTGGAATGACTGCACTGGGTCAGTTTAGAGATCAACTC
1 TGATCATCGGAAA-C-TTCTTGGAATGACCACACTGGATCAACTTA-AGATCAACTC
*
1806 TGATCATCGTAAACTTCTTGGAATGACCACACTGGATCAACTTAAGATCAACT-
1 TGATCATCGGAAACTTCTTGGAATGACCACACTGGATCAACTTAAGATCAACTC
* ** * * * * *
1859 TAGAT-TTTTGAAAATTCCTATGGAA-GACCACACGGGGTCATCTGAAGATCAACT-
1 T-GATCATCGGAAACTT-CT-TGGAATGACCACACTGGATCAACTTAAGATCAACTC
* ** * * *
1913 TAGACCA-CTAAAAACTTCTAT-GAAAGACCACACTGGGTCATCTTAAGATCAACT-
1 T-GATCATC-GGAAACTTCT-TGGAATGACCACACTGGATCAACTTAAGATCAACTC
* * * * *
1967 TAGATC-TCTGAAAGCTTCTAT-GAAAGACCATACTGGGTCATCTTAAGATCAACT
1 T-GATCATCGGAAA-CTTCT-TGGAATGACCACACTGGATCAACTTAAGATCAACT
2021 TAGACCTCTA
Statistics
Matches: 179, Mismatches: 27, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
53 13 0.07
54 119 0.66
55 35 0.20
56 8 0.04
57 4 0.02
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (54 bp):
TGATCATCGGAAACTTCTTGGAATGACCACACTGGATCAACTTAAGATCAACTC
Found at i:1888 original size:54 final size:54
Alignment explanation
Indices: 1816--2072 Score: 331
Period size: 54 Copynumber: 4.8 Consensus size: 54
1806 TGATCATCGT
* * * ** *
1816 AAACTTCT-TGGAATGACCACACTGGATCAACTTAAGATCAACTTAGATTTTTGA
1 AAACTTCTAT-GAAAGACCACACTGGGTCATCTTAAGATCAACTTAGACCTCTGA
* * * * *
1870 AAA-TTCCTATGGAAGACCACACGGGGTCATCTGAAGATCAACTTAGACCACTAA
1 AAACTT-CTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAGACCTCTGA
*
1924 AAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAGATCTCTGA
1 AAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAGACCTCTGA
* *
1978 AAGCTTCTATGAAAGACCATACTGGGTCATCTTAAGATCAACTTAGACCTCT-A
1 AAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAGACCTCTGA
*
2031 AAAGCTTCTATGAAAGACCACACTAGGTCATCTTAAGATCAA
1 AAA-CTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAA
2073 TTTTCTAGAG
Statistics
Matches: 176, Mismatches: 23, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
53 5 0.03
54 168 0.95
55 3 0.02
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (54 bp):
AAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAGACCTCTGA
Found at i:2019 original size:162 final size:162
Alignment explanation
Indices: 1780--2072 Score: 366
Period size: 162 Copynumber: 1.8 Consensus size: 162
1770 GGAATGACTG
*
1780 CACTGGGTCAGTTTAGAGATCAACTCTGATCATCGTAAACTTCTTGGAATGACCACACTGGATCA
1 CACTGGGTCAGTTTAGAGATCAACTCTGATCATCGTAAACTTCTTGGAAAGACCACACTGGATCA
** * * *
1845 ACTTAAGATCAACTTAGATTTTTGAAAA-TTCCTATGGAAGACCACACGGGGTCATCTGAAGATC
66 ACTTAAGATCAACTTAGACCTCT-AAAACTT-CTATGAAAGACCACACGAGGTCATCTGAAGATC
1909 AACTTAGACCACTAAAAACTTCTATGAAAGACCA
129 AACTTAGACCACTAAAAACTTCTATGAAAGACCA
*
1943 CACTGGGTCA-TCTTA-AGATCAACT-TAGATC-TC-TGAAAGCTTCTAT-GAAAGACCATACTG
1 CACTGGGTCAGT-TTAGAGATCAACTCT-GATCATCGT-AAA-CTTCT-TGGAAAGACCACACTG
* * * *
2002 GGTCATCTTAAGATCAACTTAGACCTCTAAAAGCTTCTATGAAAGACCACACTAGGTCATCTTAA
61 GATCAACTTAAGATCAACTTAGACCTCTAAAA-CTTCTATGAAAGACCACACGAGGTCATCTGAA
2067 GATCAA
125 GATCAA
2073 TTTTCTAGAG
Statistics
Matches: 112, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
160 1 0.01
161 10 0.09
162 85 0.76
163 16 0.14
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (162 bp):
CACTGGGTCAGTTTAGAGATCAACTCTGATCATCGTAAACTTCTTGGAAAGACCACACTGGATCA
ACTTAAGATCAACTTAGACCTCTAAAACTTCTATGAAAGACCACACGAGGTCATCTGAAGATCAA
CTTAGACCACTAAAAACTTCTATGAAAGACCA
Found at i:2177 original size:37 final size:37
Alignment explanation
Indices: 2132--2428 Score: 332
Period size: 37 Copynumber: 8.0 Consensus size: 37
2122 TGAACAAGAA
* * *
2132 AGGGACCTTAAATAAGGATTTGATAAGAAATCTAAAC
1 AGGGACCTTAAACAAGGATTTGATAAGACACCTAAAC
* * *
2169 AGGAACCTTGAACAA-GATTTTGATGAGACACCTAAAC
1 AGGGACCTTAAACAAGGA-TTTGATAAGACACCTAAAC
* * * * *
2206 AAGGATCTTGAACCA-GATTTCGATGAGACACCTAAAC
1 AGGGACCTTAAACAAGGATTT-GATAAGACACCTAAAC
* *
2243 AGGGACCTTAAATAAGGATTTGATAAGACACTTAAAC
1 AGGGACCTTAAACAAGGATTTGATAAGACACCTAAAC
* * *
2280 AGGGACCTTAAATAAGGATTTAATAAGACACCTATAC
1 AGGGACCTTAAACAAGGATTTGATAAGACACCTAAAC
2317 AGGGACCTTAAACAAGGATTTGATAAGACACCTAAAC
1 AGGGACCTTAAACAAGGATTTGATAAGACACCTAAAC
* * * *
2354 AGGAATCTTGAACAA-GATTTTTATGAA-ACACCTAAAC
1 AGGGACCTTAAACAAGGA-TTTGAT-AAGACACCTAAAC
* *
2391 AGGGACCTTAAATAAGGATTTGATTAGACACCTAAAC
1 AGGGACCTTAAACAAGGATTTGATAAGACACCTAAAC
2428 A
1 A
2429 AAAATCTTGA
Statistics
Matches: 220, Mismatches: 33, Indels: 14
0.82 0.12 0.05
Matches are distributed among these distances:
36 8 0.04
37 203 0.92
38 9 0.04
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.23
Consensus pattern (37 bp):
AGGGACCTTAAACAAGGATTTGATAAGACACCTAAAC
Done.