Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021952.1 Corchorus olitorius cultivar O-4 contig21985, 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: 19982
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:133 original size:18 final size:18
Alignment explanation
Indices: 98--134 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
88 TAATTAAAAT
*
98 TTAAAATTTCCAACTTAA
1 TTAAAATTTCCAAATTAA
*
116 TTAAAATTTCTAAATTAA
1 TTAAAATTTCCAAATTAA
134 T
1 T
135 ATAGAGGTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (18 bp):
TTAAAATTTCCAAATTAA
Found at i:517 original size:28 final size:29
Alignment explanation
Indices: 464--520 Score: 107
Period size: 28 Copynumber: 2.0 Consensus size: 29
454 GTAAGTTTGG
464 CATAAGATTTAATTTTTTTTTGGCACCAA
1 CATAAGATTTAATTTTTTTTTGGCACCAA
493 CATAAGATTTAA-TTTTTTTTGGCACCAA
1 CATAAGATTTAATTTTTTTTTGGCACCAA
521 TATATATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 16 0.57
29 12 0.43
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.44
Consensus pattern (29 bp):
CATAAGATTTAATTTTTTTTTGGCACCAA
Found at i:8059 original size:16 final size:16
Alignment explanation
Indices: 8040--8074 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
8030 AAATTAACTT
8040 TTAAACCCGAAATCAA
1 TTAAACCCGAAATCAA
8056 TTAAACCCGAAATCAA
1 TTAAACCCGAAATCAA
8072 TTA
1 TTA
8075 GAAGTTCCGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.49, C:0.23, G:0.06, T:0.23
Consensus pattern (16 bp):
TTAAACCCGAAATCAA
Found at i:9928 original size:25 final size:25
Alignment explanation
Indices: 9894--9942 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
9884 CCAAACAATC
9894 TTGAGCACTCTCGCTCGGTCTCTAA
1 TTGAGCACTCTCGCTCGGTCTCTAA
9919 TTGAGCACTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCGCTCGGTCTCTA
9943 CAAACTAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.14, C:0.33, G:0.20, T:0.33
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCGGTCTCTAA
Found at i:11866 original size:48 final size:48
Alignment explanation
Indices: 11823--11935 Score: 133
Period size: 48 Copynumber: 2.3 Consensus size: 48
11813 CAAGTTCGGA
11823 TCATTTTGGATTC-GAGTCATTTCAGG-TTCGGATCATTTCAAGTTCAAG
1 TCATTTTGGATTCGGA-TCATTT-AGGATTCGGATCATTTCAAGTTCAAG
* * *
11871 TCATTTTGGGTTCGGATCATTTAGGATTCGGATCATTT-TAGATCATAGG
1 TCATTTTGGATTCGGATCATTTAGGATTCGGATCATTTCAAGTTCA-A-G
*
11920 TCATTTTGGTTTCGGA
1 TCATTTTGGATTCGGA
11936 GATTGGGCAG
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
47 8 0.14
48 31 0.54
49 18 0.32
ACGTcount: A:0.21, C:0.14, G:0.23, T:0.42
Consensus pattern (48 bp):
TCATTTTGGATTCGGATCATTTAGGATTCGGATCATTTCAAGTTCAAG
Found at i:11890 original size:16 final size:16
Alignment explanation
Indices: 11816--11909 Score: 75
Period size: 16 Copynumber: 5.9 Consensus size: 16
11806 TGTTAATCAA
11816 GTTCGGATCATTTTGG
1 GTTCGGATCATTTTGG
* **
11832 ATTC-GAGTCATTTCAG
1 GTTCGGA-TCATTTTGG
***
11848 GTTCGGATCATTTCAA
1 GTTCGGATCATTTTGG
*
11864 GTTC-AAGTCATTTTGG
1 GTTCGGA-TCATTTTGG
*
11880 GTTCGGATCATTTAGG
1 GTTCGGATCATTTTGG
*
11896 ATTCGGATCATTTT
1 GTTCGGATCATTTT
11910 AGATCATAGG
Statistics
Matches: 61, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
15 3 0.05
16 55 0.90
17 3 0.05
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.41
Consensus pattern (16 bp):
GTTCGGATCATTTTGG
Found at i:11909 original size:32 final size:32
Alignment explanation
Indices: 11816--11911 Score: 115
Period size: 32 Copynumber: 3.0 Consensus size: 32
11806 TGTTAATCAA
* *
11816 GTTCGGATCATTTTGGATTCGAGTCATTTCAG
1 GTTCGGATCATTTAGGATTCGAGTCATTTTAG
* * *
11848 GTTCGGATCATTTCAAG-TTCAAGTCATTTTGG
1 GTTCGGATCATTT-AGGATTCGAGTCATTTTAG
11880 GTTCGGATCATTTAGGATTCG-GATCATTTTAG
1 GTTCGGATCATTTAGGATTCGAG-TCATTTTAG
11912 ATCATAGGTC
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
31 3 0.06
32 49 0.92
33 1 0.02
ACGTcount: A:0.21, C:0.15, G:0.24, T:0.41
Consensus pattern (32 bp):
GTTCGGATCATTTAGGATTCGAGTCATTTTAG
Found at i:14566 original size:30 final size:31
Alignment explanation
Indices: 14523--14593 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 31
14513 CCATACAAGT
*
14523 CCCTCTACTTACAAAAA-TGGATCAGTTTGGTC
1 CCCTCTACTTACAAAAACT--ATCAATTTGGTC
14555 CCCT-TAC-TACAAAAACTATCAATTTGGT-
1 CCCTCTACTTACAAAAACTATCAATTTGGTC
14583 CCCTCTACTTA
1 CCCTCTACTTA
14594 TAATTTGGTG
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
28 4 0.11
29 13 0.37
30 10 0.29
31 4 0.11
32 4 0.11
ACGTcount: A:0.30, C:0.28, G:0.10, T:0.32
Consensus pattern (31 bp):
CCCTCTACTTACAAAAACTATCAATTTGGTC
Found at i:14881 original size:31 final size:32
Alignment explanation
Indices: 14845--14965 Score: 94
Period size: 31 Copynumber: 3.9 Consensus size: 32
14835 ATATATAATC
14845 AATTGACAGATTTTGTTAAGTAGAGGGACTC-
1 AATTGACAGATTTTGTTAAGTAGAGGGACTCA
* * **
14876 AATTGATACCAAATTG-TAAGTAGAGGGAC-CA
1 AATTGACA-GATTTTGTTAAGTAGAGGGACTCA
14907 AATTGACAG--TTT-TTATAGTAGAGGGAC-CA
1 AATTGACAGATTTTGTTA-AGTAGAGGGACTCA
**** *
14936 AATTGATTTTTTTTTTTAAGTAGAGGGACT
1 AATTGACAGATTTTGTTAAGTAGAGGGACT
14966 TGTACGGTAT
Statistics
Matches: 72, Mismatches: 10, Indels: 15
0.74 0.10 0.15
Matches are distributed among these distances:
28 4 0.06
29 19 0.26
30 1 0.01
31 41 0.57
32 7 0.10
ACGTcount: A:0.34, C:0.09, G:0.23, T:0.34
Consensus pattern (32 bp):
AATTGACAGATTTTGTTAAGTAGAGGGACTCA
Found at i:14948 original size:29 final size:31
Alignment explanation
Indices: 14892--14964 Score: 96
Period size: 29 Copynumber: 2.4 Consensus size: 31
14882 TACCAAATTG
14892 TAAGTAGAGGGACCAAATTGA-CAGTTTTTA
1 TAAGTAGAGGGACCAAATTGATCAGTTTTTA
*** *
14922 T-AGTAGAGGGACCAAATTGATTTTTTTTTT
1 TAAGTAGAGGGACCAAATTGATCAGTTTTTA
14952 TAAGTAGAGGGAC
1 TAAGTAGAGGGAC
14965 TTGTACGGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 19 0.51
30 7 0.19
31 11 0.30
ACGTcount: A:0.33, C:0.08, G:0.25, T:0.34
Consensus pattern (31 bp):
TAAGTAGAGGGACCAAATTGATCAGTTTTTA
Found at i:17434 original size:19 final size:20
Alignment explanation
Indices: 17392--17438 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
17382 GTTTTACAAG
* *
17392 GATTCAAAAAGTTTTCAGTC
1 GATTGAAAAAATTTTCAGTC
*
17412 GATTGAAAAAATTTT-AGTT
1 GATTGAAAAAATTTTCAGTC
17431 GATTGAAA
1 GATTGAAA
17439 TTCAACCAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.36
Consensus pattern (20 bp):
GATTGAAAAAATTTTCAGTC
Found at i:18235 original size:29 final size:29
Alignment explanation
Indices: 18200--18266 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
18190 CGTCAACAGT
18200 CAAATAAGCTCCTGAACTT-CAATTTTGAC
1 CAAATAAGCTCCTGAA-TTACAATTTTGAC
* * *
18229 CAAATAAACTTCTGAATTACCAATTTTGGC
1 CAAATAAGCTCCTGAATTA-CAATTTTGAC
18259 CAAATAAG
1 CAAATAAG
18267 ATCTTCTGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 2 0.06
29 14 0.44
30 16 0.50
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (29 bp):
CAAATAAGCTCCTGAATTACAATTTTGAC
Found at i:18589 original size:29 final size:30
Alignment explanation
Indices: 18526--18591 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
18516 AGCAGAAAGA
* *
18526 CTTATTTGGCCAAAATTGGTAGTTCAGGGT
1 CTTATTTGGCCAAAATTGGAAGTTCAGAGT
* *
18556 TTTATTTGGTCAAAATT-GAAGTTCATGAG-
1 CTTATTTGGCCAAAATTGGAAGTTCA-GAGT
18585 CTTATTT
1 CTTATTT
18592 AACCGTTAGC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 13 0.43
30 17 0.57
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (30 bp):
CTTATTTGGCCAAAATTGGAAGTTCAGAGT
Done.