Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020420.1 Corchorus olitorius cultivar O-4 contig20453, 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: 5863
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:765 original size:26 final size:27
Alignment explanation
Indices: 713--779 Score: 100
Period size: 26 Copynumber: 2.5 Consensus size: 27
703 CAGACTCTGG
* *
713 ATTTTGAGTTTCGAACATGACATGCAA
1 ATTTTGAGTTTTGAACATGAAATGCAA
740 ATTTTGAGTTTTGAA-ATGAAATGCAA
1 ATTTTGAGTTTTGAACATGAAATGCAA
*
766 ATTTTGAATTTTGA
1 ATTTTGAGTTTTGA
780 CTTTTGAGGA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
26 23 0.62
27 14 0.38
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.40
Consensus pattern (27 bp):
ATTTTGAGTTTTGAACATGAAATGCAA
Found at i:1035 original size:33 final size:33
Alignment explanation
Indices: 993--1070 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
983 AGAAACTGTG
* * *
993 GATTTTGAACTTTGAGTTTTGATATGATATGCA
1 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
1026 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
1 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
*
1059 AATTTTGAACTT
1 GATTTTGAACTT
1071 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:1234 original size:54 final size:55
Alignment explanation
Indices: 1123--1379 Score: 226
Period size: 54 Copynumber: 4.7 Consensus size: 55
1113 ATGGAAACAT
* * * *
1123 TTCT-TGGAATGACCGCACCGGGTCAGT-TTAGAGATCAACTCT-GATCATC-GTAAAC
1 TTCTATGGAATGACCACACTGGATCA-TCTTA-AGATCAACT-TAGATC-TCTGAAAAC
* * * *
1178 TTCT-TGGAATGACCACACTGGATCAACTTAAGATCAATTTAGATTTTTGAAAAC
1 TTCTATGGAATGACCACACTGGATCATCTTAAGATCAACTTAGATCTCTGAAAAC
* * * *
1232 TTCTATGGAA-GACCACACAGGGTCATCTGAAGATCAACTTAGACCTCT-AAAAGC
1 TTCTATGGAATGACCACACTGGATCATCTTAAGATCAACTTAGATCTCTGAAAA-C
* * * * *
1286 TTCTGT-GAAAGATCGCACTGGATCATCTAAAGATCAACTTAGATCTCTGAAAAC
1 TTCTATGGAATGACCACACTGGATCATCTTAAGATCAACTTAGATCTCTGAAAAC
* * *
1340 TTCTAT-GTATGACCGCACTGGGTCATCTTAAGATCAACTT
1 TTCTATGGAATGACCACACTGGATCATCTTAAGATCAACTT
1380 TCTAGAGAGA
Statistics
Matches: 166, Mismatches: 29, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
53 9 0.05
54 123 0.74
55 34 0.20
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (55 bp):
TTCTATGGAATGACCACACTGGATCATCTTAAGATCAACTTAGATCTCTGAAAAC
Found at i:1431 original size:20 final size:18
Alignment explanation
Indices: 1411--1452 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1401 CATTTTAAAC
*
1411 ACAAAACATGAATTTTGA
1 ACAAAAAATGAATTTTGA
* *
1429 ACAAGAAATGGATTTTGA
1 ACAAAAAATGAATTTTGA
1447 ACAAAA
1 ACAAAA
1453 TTTTGATAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.52, C:0.10, G:0.14, T:0.24
Consensus pattern (18 bp):
ACAAAAAATGAATTTTGA
Found at i:1532 original size:37 final size:37
Alignment explanation
Indices: 1486--2162 Score: 644
Period size: 37 Copynumber: 18.3 Consensus size: 37
1476 GATTTTGAAG
* *
1486 AGACACCTAAACAGGTACCTTAAATAAGGATTTAATA
1 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
* * ** * * *
1523 AGAAACCTAAACAGGAATTTTGAACAA-GATTTTGATG
1 AGACACCTAAACAGGGACCTTAAATAAGGA-TTTGATA
* *
1560 AGACACCTAAACAGTGACCTTAAATAAGAATTTGATA
1 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
* * * **
1597 AGAAACCTAAACAGGGATCTTAAACAAAAATTTGATA
1 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
1634 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
1 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
* * * * * * * *
1671 AGAAAGCTAAACCGAGATCTTAAACAA-GACTTTAATG
1 AGACACCTAAACAGGGACCTTAAATAAGGA-TTTGATA
* * *
1708 AGACACCTAAATAGGGACCTTAAATAAAGATTTAATA
1 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
* * * * * *
1745 AGAAACCTAAACAGGAATCTTGAACAA-GATTTTGATG
1 AGACACCTAAACAGGGACCTTAAATAAGGA-TTTGATA
* * * ** *
1782 AGACACCTAAACAAGGATCTTGAACCA-GATTTCGATG
1 AGACACCTAAACAGGGACCTTAAATAAGGATTT-GATA
1819 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
1 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
* * *
1856 AGACACCTAAACAGGAACCTTAAATAAGGATTTAATC
1 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
1893 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
1 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
* * * * * * * *
1930 AGAAACCTAACCAGGAATCTTGAACAAGGTTTTGATG
1 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
* *
1967 AGACACCTATACAGGGACCTTAAATAAGGATTTGACA
1 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
* ** * * * * *
2004 AGAAAACCTAAACAGTAATCTTGAACAAGGTTTTGATG
1 AG-ACACCTAAACAGGGACCTTAAATAAGGATTTGATA
*
2042 AGACACCTAAATAGGGACCTTAAATAAGGATTTGATA
1 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
* * * * * * * *
2079 AGAAATCTAAACAGGAATCTTGAACAAGGTTTTGATG
1 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
2116 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
1 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
2153 AGTA-ACCTAA
1 AG-ACACCTAA
2163 TCAGAAATCT
Statistics
Matches: 510, Mismatches: 121, Indels: 18
0.79 0.19 0.03
Matches are distributed among these distances:
36 9 0.02
37 465 0.91
38 36 0.07
ACGTcount: A:0.44, C:0.16, G:0.17, T:0.23
Consensus pattern (37 bp):
AGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
Found at i:3098 original size:87 final size:87
Alignment explanation
Indices: 2946--3189 Score: 407
Period size: 87 Copynumber: 2.8 Consensus size: 87
2936 CAAACCATCT
* * * * * * * *
2946 TCCAATTTGGTCATGTATTGATATTCCCAACTCAACTGATGGTTCTGGACCAGCTTCCCACCTTA
1 TCCAATTTGATCATGCATTGATATTCCCAACTCAATTGATGTTTCTGGATCAGTTTCTCATCTTA
*
3011 AGAAATATTTCTCAAATCTTCC
66 AGAAATATTTCCCAAATCTTCC
3033 TCCAATTTGATCATGCATTGATATTCCCAACTCAATTGATGTTTCTGGATCAGTTTCTCATCTTA
1 TCCAATTTGATCATGCATTGATATTCCCAACTCAATTGATGTTTCTGGATCAGTTTCTCATCTTA
3098 AGAAATATTTCCCAAATCTTCC
66 AGAAATATTTCCCAAATCTTCC
3120 TCCAATTTGATCATGCATTGATATTCCCAACTCAATTGATGTTTCTGGATCAGTTTCTCATCTTA
1 TCCAATTTGATCATGCATTGATATTCCCAACTCAATTGATGTTTCTGGATCAGTTTCTCATCTTA
3185 AGAAA
66 AGAAA
3190 CCTTCAAACA
Statistics
Matches: 148, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 148 1.00
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.37
Consensus pattern (87 bp):
TCCAATTTGATCATGCATTGATATTCCCAACTCAATTGATGTTTCTGGATCAGTTTCTCATCTTA
AGAAATATTTCCCAAATCTTCC
Found at i:3348 original size:27 final size:27
Alignment explanation
Indices: 3310--3374 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 27
3300 AATTTGAACC
*
3310 TTTTTCCTTTTGTATTTTTCTTTCTT-T
1 TTTTTTCTTTTGTATTTTTCTTT-TTCT
*
3337 TTTTTTCTTTTG-CTTTTTCTTTTTCT
1 TTTTTTCTTTTGTATTTTTCTTTTTCT
*
3363 TCTTTT-TTTTGT
1 TTTTTTCTTTTGT
3375 TTAGATTGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
25 7 0.21
26 15 0.45
27 11 0.33
ACGTcount: A:0.02, C:0.14, G:0.05, T:0.80
Consensus pattern (27 bp):
TTTTTTCTTTTGTATTTTTCTTTTTCT
Found at i:4042 original size:13 final size:13
Alignment explanation
Indices: 4008--4078 Score: 83
Period size: 14 Copynumber: 5.3 Consensus size: 13
3998 TTGAAAACTC
4008 AAAACC-TTTTTG
1 AAAACCATTTTTG
4020 AAAACTCATTTTTG
1 AAAAC-CATTTTTG
4034 AAAACCATTTCTTG
1 AAAACCATTT-TTG
4048 AAAA-CAGTTTCTTG
1 AAAACCA-TTT-TTG
*
4062 AAAATCATTTTTG
1 AAAACCATTTTTG
4075 AAAA
1 AAAA
4079 AATCCTTTAT
Statistics
Matches: 54, Mismatches: 0, Indels: 9
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.09
13 15 0.28
14 32 0.59
15 2 0.04
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.38
Consensus pattern (13 bp):
AAAACCATTTTTG
Done.