Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010027.1 Corchorus olitorius cultivar O-4 contig10059, 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: 1811
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Found at i:710 original size:36 final size:35
Alignment explanation
Indices: 362--774 Score: 324
Period size: 35 Copynumber: 11.6 Consensus size: 35
352 ATTTCAGATG
* * *
362 CTTCAGTTCATTTCAGTTAACCCAGGGCGGTCTTT
1 CTTCAATTTATTTCAGTTGACCCAGGGCGGTCTTT
* *
397 CTTCAATTTATTTCAGTTGACCCAGGGTGGTCCTT
1 CTTCAATTTATTTCAGTTGACCCAGGGCGGTCTTT
* *
432 CTTCAATTTATTTCAATTGACCTAGGGCGGTCTTT
1 CTTCAATTTATTTCAGTTGACCCAGGGCGGTCTTT
* * * * ** *
467 CTTCAATTCATTTCACTTTGATCTAGGATGATCTTTT
1 CTTCAATTTATTTCA-GTTGACCCAGGGCGGTC-TTT
* ** * ** *
504 CTTCATTTTACCTCAGTTGATCCAGGGCGACCCGTT
1 CTTCAATTTATTTCAGTTGACCCAGGGCG-GTCTTT
* *
540 CTTCAGTTTATTTCAAGTTGACCCAGGGTGGTCTTTT
1 CTTCAATTTATTTC-AGTTGACCCAGGGCGGTC-TTT
* * * * * *
577 CATTCAGTTTATGTT-AGTTGATCCGGGGTGATCTCT
1 C-TTCAATTTAT-TTCAGTTGACCCAGGGCGGTCTTT
* * * * * *
613 CCTCAATTTACTCCAGTTGATCCAGCGCGATCTTTT
1 CTTCAATTTATTTCAGTTGACCCAGGGCGGTC-TTT
* * * * *
649 ATTCAATTTATTTCAATCGATCCAGGGCGATCTTT
1 CTTCAATTTATTTCAGTTGACCCAGGGCGGTCTTT
* * *
684 CCTTCAATTTATTTTAGCTGACCCAGGGCGGTCATT
1 -CTTCAATTTATTTCAGTTGACCCAGGGCGGTCTTT
*
720 CTTCAAGTTATTTCAGTTGACCCAGGGCGGTCTTT
1 CTTCAATTTATTTCAGTTGACCCAGGGCGGTCTTT
* *
755 CTTCAATTCATTTCAATTGA
1 CTTCAATTTATTTCAGTTGA
775 TTTAGGGTGA
Statistics
Matches: 300, Mismatches: 68, Indels: 20
0.77 0.18 0.05
Matches are distributed among these distances:
34 1 0.00
35 148 0.49
36 93 0.31
37 46 0.15
38 10 0.03
39 2 0.01
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.40
Consensus pattern (35 bp):
CTTCAATTTATTTCAGTTGACCCAGGGCGGTCTTT
Found at i:837 original size:36 final size:36
Alignment explanation
Indices: 837--978 Score: 189
Period size: 36 Copynumber: 4.0 Consensus size: 36
827 TTCGGTTTAT
837 TTGATCCAGGGCGATATTTTCTTCAGTTCATTTCAA
1 TTGATCCAGGGCGATATTTTCTTCAGTTCATTTCAA
873 TTGATCCAGGGCGATATTTTCTTCAGTTCATTTCAA
1 TTGATCCAGGGCGATATTTTCTTCAGTTCATTTCAA
* *
909 TTGATCCAGGGCGATCTTTTCTTTAGTT--TCTTCAA
1 TTGATCCAGGGCGATATTTTCTTCAGTTCAT-TTCAA
* * * * * *
944 TTTATCCATGGTGATCTTTTCTGCAGTTTATTTCA
1 TTGATCCAGGGCGATATTTTCTTCAGTTCATTTCA
979 GTAGACCGCA
Statistics
Matches: 96, Mismatches: 7, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
34 1 0.01
35 28 0.29
36 66 0.69
37 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.16, T:0.45
Consensus pattern (36 bp):
TTGATCCAGGGCGATATTTTCTTCAGTTCATTTCAA
Found at i:841 original size:31 final size:31
Alignment explanation
Indices: 801--905 Score: 93
Period size: 31 Copynumber: 3.2 Consensus size: 31
791 TTCAAGTTAT
* * * *
801 TTTAGTTGATCGAGGGAGATCTTTTCTTCGG
1 TTTATTTGATCCAGGGAGATATTTTCTTCAG
*
832 TTTATTTGATCCAGGGCGATATTTTCTTCAG
1 TTTATTTGATCCAGGGAGATATTTTCTTCAG
* *
863 TTCATTTCAATTGATCCAGGGCGATATTTTCTTCAG
1 ----TTT-ATTTGATCCAGGGAGATATTTTCTTCAG
*
899 TTCATTT
1 TTTATTT
906 CAATTGATCC
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
31 29 0.48
32 2 0.03
35 3 0.05
36 27 0.44
ACGTcount: A:0.19, C:0.16, G:0.20, T:0.45
Consensus pattern (31 bp):
TTTATTTGATCCAGGGAGATATTTTCTTCAG
Found at i:971 original size:71 final size:71
Alignment explanation
Indices: 837--978 Score: 187
Period size: 71 Copynumber: 2.0 Consensus size: 71
827 TTCGGTTTAT
*
837 TTGATCCAGGGCGATATTTTCTTCAGTTCATTTCAATTGATCCAGGGCGATATTTTCTTCAGTTC
1 TTGATCCAGGGCGATATTTTCTTCAGTTCA-TTCAATTGATCCAGGGCGATATTTTCTGCAGTTC
902 ATTTCAA
65 ATTTCAA
* * * * * * *
909 TTGATCCAGGGCGATCTTTTCTTTAGTTTC-TTCAATTTATCCATGGTGATCTTTTCTGCAGTTT
1 TTGATCCAGGGCGATATTTTCTTCAG-TTCATTCAATTGATCCAGGGCGATATTTTCTGCAGTTC
973 ATTTCA
65 ATTTCA
979 GTAGACCGCA
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
71 34 0.56
72 24 0.39
73 3 0.05
ACGTcount: A:0.20, C:0.19, G:0.16, T:0.45
Consensus pattern (71 bp):
TTGATCCAGGGCGATATTTTCTTCAGTTCATTCAATTGATCCAGGGCGATATTTTCTGCAGTTCA
TTTCAA
Found at i:972 original size:35 final size:36
Alignment explanation
Indices: 383--972 Score: 205
Period size: 35 Copynumber: 16.7 Consensus size: 36
373 TTCAGTTAAC
* * * *
383 CCAGGGCGGTC-TTTCTTCAATTT-ATTTCAGTTGAC
1 CCAGGGCGATCTTTTCTTCAGTTTCA-TTCAATTGAT
* * * *
418 CCAGGGTGGTC-CTTCTTCAATTT-ATTTCAATTGA-
1 CCAGGGCGATCTTTTCTTCAGTTTCA-TTCAATTGAT
* * *
452 CCTAGGGCGGTC-TTTCTTCA-ATTCATTTCACTTTGAT
1 CC-AGGGCGATCTTTTCTTCAGTTTCA-TTCA-ATTGAT
* ** * * *
489 CTAGGATGATCTTTTCTTCA-TTTTACCTCAGTTGAT
1 CCAGGGCGATCTTTTCTTCAGTTTCA-TTCAATTGAT
* ** *
525 CCAGGGCGACCCGTTCTTCAGTTT-ATTTCAAGTTGAC
1 CCAGGGCGATCTTTTCTTCAGTTTCA-TTCAA-TTGAT
* * * *
562 CCAGGGTGGTCTTTTCATTCAGTTT-ATGTTAGTTGAT
1 CCAGGGCGATCTTTTC-TTCAGTTTCAT-TCAATTGAT
* * * * * * *
599 CCGGGGTGATC-TCTCCTCAATTT-ACTCCAGTTGAT
1 CCAGGGCGATCTTTTCTTCAGTTTCA-TTCAATTGAT
* * * *
634 CCAGCGCGATCTTTTATTCAATTT-ATTTCAATCGAT
1 CCAGGGCGATCTTTTCTTCAGTTTCA-TTCAATTGAT
* * * ** *
670 CCAGGGCGATCTTTCCTTCAATTT-ATTTTAGCTGAC
1 CCAGGGCGATCTTTTCTTCAGTTTCA-TTCAATTGAT
* * * *
706 CCAGGGCGGTC-ATTCTTCAAG-TT-ATTTCAGTTGAC
1 CCAGGGCGATCTTTTCTTC-AGTTTCA-TTCAATTGAT
* *
741 CCAGGGCGGTC-TTTCTTCA-ATTCATTTCAATTGAT
1 CCAGGGCGATCTTTTCTTCAGTTTCA-TTCAATTGAT
** * * * * *
776 TTAGGGTGATC-CTACTTCAAG-TT-ATTTTAGTTGAT
1 CCAGGGCGATCTTTTCTTC-AGTTTCA-TTCAATTGAT
* * *
811 CGAGGGAGATCTTTTCTTCGGTTT-A-T---TTGAT
1 CCAGGGCGATCTTTTCTTCAGTTTCATTCAATTGAT
*
842 CCAGGGCGATATTTTCTTCAG-TTCATTTCAATTGAT
1 CCAGGGCGATCTTTTCTTCAGTTTCA-TTCAATTGAT
*
878 CCAGGGCGATATTTTCTTCAG-TTCATTTCAATTGAT
1 CCAGGGCGATCTTTTCTTCAGTTTCA-TTCAATTGAT
* *
914 CCAGGGCGATCTTTTCTTTAGTTTC-TTCAATTTAT
1 CCAGGGCGATCTTTTCTTCAGTTTCATTCAATTGAT
* * *
949 CCATGGTGATCTTTTCTGCAGTTT
1 CCAGGGCGATCTTTTCTTCAGTTT
973 ATTTCAGTAG
Statistics
Matches: 437, Mismatches: 93, Indels: 50
0.75 0.16 0.09
Matches are distributed among these distances:
30 2 0.00
31 23 0.05
33 1 0.00
34 8 0.02
35 178 0.41
36 164 0.38
37 50 0.11
38 11 0.03
ACGTcount: A:0.19, C:0.21, G:0.18, T:0.42
Consensus pattern (36 bp):
CCAGGGCGATCTTTTCTTCAGTTTCATTCAATTGAT
Found at i:1764 original size:30 final size:30
Alignment explanation
Indices: 1196--1749 Score: 759
Period size: 30 Copynumber: 18.5 Consensus size: 30
1186 CATTGCTTCG
* *
1196 TTGCTTTATTTTAATCTTGTTTGAGGATCT
1 TTGCTTTATTTTAATCCTGTTTGAGGATCA
* * *
1226 TTGCTTTGTTTTAATCCTATTTGAGGATCT
1 TTGCTTTATTTTAATCCTGTTTGAGGATCA
* *
1256 TTGCTTTGTTTTAATCCTGTTTGAGGATCG
1 TTGCTTTATTTTAATCCTGTTTGAGGATCA
* *
1286 TTGCTTTATTTTAATCTTGTTTGAGGATCT
1 TTGCTTTATTTTAATCCTGTTTGAGGATCA
* * * *
1316 TTGCTTTGTTTTAACCCTGGTTGAGGATCG
1 TTGCTTTATTTTAATCCTGTTTGAGGATCA
* *
1346 TTGCTTTATCTTAATCCTGTTTGAGGATCG
1 TTGCTTTATTTTAATCCTGTTTGAGGATCA
*
1376 TTGCTTTATTTTAATCCTGTTTGAGGATCT
1 TTGCTTTATTTTAATCCTGTTTGAGGATCA
* *
1406 TTGCTTTGTTTTAATCCTGTTTGAGGATCT
1 TTGCTTTATTTTAATCCTGTTTGAGGATCA
*
1436 TTGCTTCATTTTAATCCTGTTTGAGGATCA
1 TTGCTTTATTTTAATCCTGTTTGAGGATCA
*
1466 TTGCTTCATTTTAATCCTGTTTGAGGATCA
1 TTGCTTTATTTTAATCCTGTTTGAGGATCA
1496 TTGCTTTATTTTAATCCTGTTTGAGGATCA
1 TTGCTTTATTTTAATCCTGTTTGAGGATCA
* *
1526 TTGCTTTATGTTAATCCTGGTTT-AGGATCG
1 TTGCTTTATTTTAATCCT-GTTTGAGGATCA
* * *
1556 TTGCTTTATGTTAATCCTGGTTGAGGATCG
1 TTGCTTTATTTTAATCCTGTTTGAGGATCA
1586 TTGCTTTATTTTAATCCTGTTTGAGGATCA
1 TTGCTTTATTTTAATCCTGTTTGAGGATCA
* *
1616 TTGCTTTATGTTAATCCTGTTTGAGGATAA
1 TTGCTTTATTTTAATCCTGTTTGAGGATCA
* * *
1646 TTTCTTTATGTTAATCATGTTTGAGGATCA
1 TTGCTTTATTTTAATCCTGTTTGAGGATCA
* * *
1676 TTGCTTTATGTTAATCCTGGTTGAGGATCG
1 TTGCTTTATTTTAATCCTGTTTGAGGATCA
* * * *
1706 TTGCTTTATGTTAGTCCTGGTTAAGGATCA
1 TTGCTTTATTTTAATCCTGTTTGAGGATCA
1736 TTGCTTTATTTTAA
1 TTGCTTTATTTTAA
1750 ACTTGGTTTA
Statistics
Matches: 478, Mismatches: 44, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
29 3 0.01
30 471 0.99
31 4 0.01
ACGTcount: A:0.18, C:0.13, G:0.20, T:0.49
Consensus pattern (30 bp):
TTGCTTTATTTTAATCCTGTTTGAGGATCA
Done.