Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017967.1 Corchorus olitorius cultivar O-4 contig18000, 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: 6661
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Found at i:2939 original size:21 final size:21
Alignment explanation
Indices: 2914--2977 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
2904 TTCCCAATTG
2914 ACATTGAACTTTCCTTGATTC
1 ACATTGAACTTTCCTTGATTC
* * ** *
2935 ACATTCAACATTCC-CAATTA
1 ACATTGAACTTTCCTTGATTC
*
2955 ACATTGAACTTGCCTTGATTC
1 ACATTGAACTTTCCTTGATTC
2976 AC
1 AC
2978 TTTCAACATT
Statistics
Matches: 31, Mismatches: 11, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.30, C:0.27, G:0.08, T:0.36
Consensus pattern (21 bp):
ACATTGAACTTTCCTTGATTC
Found at i:2950 original size:41 final size:41
Alignment explanation
Indices: 2904--3058 Score: 231
Period size: 41 Copynumber: 3.8 Consensus size: 41
2894 CACTTTGAAT
*
2904 TTCCCAATTGACATTGAACTTTCCTTGATTCACATTCAACA
1 TTCCCAATTGACATTGAACTTGCCTTGATTCACATTCAACA
* *
2945 TTCCCAATTAACATTGAACTTGCCTTGATTCACTTTCAACA
1 TTCCCAATTGACATTGAACTTGCCTTGATTCACATTCAACA
* *
2986 TTCCCAATTGACATTGAACTTGCCTT-ATTCTCACATCCAACT
1 TTCCCAATTGACATTGAACTTGCCTTGA-T-TCACATTCAACA
*
3028 TTCCCAATTGACATTGAACTTGCCTTAATTC
1 TTCCCAATTGACATTGAACTTGCCTTGATTC
3059 TCACATCCAA
Statistics
Matches: 104, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
40 1 0.01
41 66 0.63
42 36 0.35
43 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.08, T:0.37
Consensus pattern (41 bp):
TTCCCAATTGACATTGAACTTGCCTTGATTCACATTCAACA
Found at i:3027 original size:22 final size:22
Alignment explanation
Indices: 3002--3068 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 22
2992 ATTGACATTG
3002 AACTTGCCTTATTCTCACATCC
1 AACTTGCCTTATTCTCACATCC
* * * * **
3024 AACTTTCC-CAAT-TGACATTG
1 AACTTGCCTTATTCTCACATCC
3044 AACTTGCCTTAATTCTCACATCC
1 AACTTGCCTT-ATTCTCACATCC
3067 AA
1 AA
3069 AAACATTGAA
Statistics
Matches: 30, Mismatches: 12, Indels: 5
0.64 0.26 0.11
Matches are distributed among these distances:
20 12 0.40
21 2 0.07
22 9 0.30
23 7 0.23
ACGTcount: A:0.28, C:0.31, G:0.06, T:0.34
Consensus pattern (22 bp):
AACTTGCCTTATTCTCACATCC
Found at i:3043 original size:83 final size:84
Alignment explanation
Indices: 2891--3101 Score: 248
Period size: 83 Copynumber: 2.7 Consensus size: 84
2881 TACGCGGCGC
* * * * *
2891 ATTCACTTTGAA-TTTCCCAATTGACATTGAACTTTCCTTGA-T-TCACATTCAACATTCCCAAT
1 ATTCACTTTCAACATTCCCAATTGACATTGAACTTGCCTTAATTCTCACATCCAACATTCCCAAT
*
2953 TAACATTGAACTTGCCTTG
66 TAACATTGAACTTGCCTTA
*
2972 ATTCACTTTCAACATTCCCAATTGACATTGAACTTGCCTT-ATTCTCACATCCAACTTTCCCAAT
1 ATTCACTTTCAACATTCCCAATTGACATTGAACTTGCCTTAATTCTCACATCCAACATTCCCAAT
*
3036 TGACATTGAACTTGCCTTA
66 TAACATTGAACTTGCCTTA
**
3055 ATT--C--TC-ACA-T-CCAA-AAACATTGAACTTGCCTTAATTCTCACATCCAA
1 ATTCACTTTCAACATTCCCAATTGACATTGAACTTGCCTTAATTCTCACATCCAA
3102 AAACATTGAA
Statistics
Matches: 117, Mismatches: 9, Indels: 13
0.84 0.06 0.09
Matches are distributed among these distances:
75 16 0.14
76 18 0.15
77 1 0.01
78 3 0.03
79 2 0.02
81 13 0.11
82 26 0.22
83 38 0.32
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.36
Consensus pattern (84 bp):
ATTCACTTTCAACATTCCCAATTGACATTGAACTTGCCTTAATTCTCACATCCAACATTCCCAAT
TAACATTGAACTTGCCTTA
Found at i:3080 original size:33 final size:33
Alignment explanation
Indices: 3038--3317 Score: 524
Period size: 33 Copynumber: 8.5 Consensus size: 33
3028 TTCCCAATTG
3038 ACATTGAACTTGCCTTAATTCTCACATCCAAAA
1 ACATTGAACTTGCCTTAATTCTCACATCCAAAA
3071 ACATTGAACTTGCCTTAATTCTCACATCCAAAA
1 ACATTGAACTTGCCTTAATTCTCACATCCAAAA
*
3104 ACATTGAACTTGCCTTATTTCTCACATCCAAAA
1 ACATTGAACTTGCCTTAATTCTCACATCCAAAA
3137 ACATTGAACTTGCCTTAATTCTCACATCCAAAA
1 ACATTGAACTTGCCTTAATTCTCACATCCAAAA
3170 ACATTGAACTTGCCTTAATTCTCACATCCAAAA
1 ACATTGAACTTGCCTTAATTCTCACATCCAAAA
3203 ACATTGAACTTGCCTTAATTCTCACATCCAAAA
1 ACATTGAACTTGCCTTAATTCTCACATCCAAAA
*
3236 ACATTGAACTTGCCTTAATTCTCACATCCAACA
1 ACATTGAACTTGCCTTAATTCTCACATCCAAAA
* *
3269 ACATTGAACTTGCCTTAATTCTCATATCCAACA
1 ACATTGAACTTGCCTTAATTCTCACATCCAAAA
3302 ACATTGAACTTGCCTT
1 ACATTGAACTTGCCTT
3318 CACTCACATT
Statistics
Matches: 243, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 243 1.00
ACGTcount: A:0.35, C:0.28, G:0.06, T:0.31
Consensus pattern (33 bp):
ACATTGAACTTGCCTTAATTCTCACATCCAAAA
Found at i:6163 original size:198 final size:198
Alignment explanation
Indices: 5825--6221 Score: 785
Period size: 198 Copynumber: 2.0 Consensus size: 198
5815 TGTAAAGTGT
5825 CATTAAGAAAGCCATAACGGTCACCAAAATCCTAGCTCTAATTCCTTCTGGGGTCTTGGGAGTTT
1 CATTAAGAAAGCCATAACGGTCACCAAAATCCTAGCTCTAATTCCTTCTGGGGTCTTGGGAGTTT
5890 CAGGCAACGTCAATGAACCTGAATTGCAAAACATTTCATTTCTTTAAGCATGTTACAAAAGGTCT
66 CAGGCAACGTCAATGAACCTGAATTGCAAAACATTTCATTTCTTTAAGCATGTTACAAAAGGTCT
5955 AAGCATGCAGGCATCGAAAAAGCTAGGATAATATGAGATTAAGTTTTTAACCTTTAGAAGCAGAA
131 AAGCATGCAGGCATCGAAAAAGCTAGGATAATATGAGATTAAGTTTTTAACCTTTAGAAGCAGAA
6020 GGC
196 GGC
6023 CATTAAGAAAGCCATAACGGTCACCAAAATCCTAGCTCTAATTCCTTCTGGGGTCTTGGGAGTTT
1 CATTAAGAAAGCCATAACGGTCACCAAAATCCTAGCTCTAATTCCTTCTGGGGTCTTGGGAGTTT
*
6088 CAGGCAACGTCAATGAACCTGAATTGCAAAACATTTCATTTCTTTAATCATGTTACAAAAGGTCT
66 CAGGCAACGTCAATGAACCTGAATTGCAAAACATTTCATTTCTTTAAGCATGTTACAAAAGGTCT
6153 AAGCATGCAGGCATCGAAAAAGCTAGGATAATATGAGATTAAGTTTTTAACCTTTAGAAGCAGAA
131 AAGCATGCAGGCATCGAAAAAGCTAGGATAATATGAGATTAAGTTTTTAACCTTTAGAAGCAGAA
6218 GGC
196 GGC
6221 C
1 C
6222 TCAGGAGGGC
Statistics
Matches: 198, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
198 198 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (198 bp):
CATTAAGAAAGCCATAACGGTCACCAAAATCCTAGCTCTAATTCCTTCTGGGGTCTTGGGAGTTT
CAGGCAACGTCAATGAACCTGAATTGCAAAACATTTCATTTCTTTAAGCATGTTACAAAAGGTCT
AAGCATGCAGGCATCGAAAAAGCTAGGATAATATGAGATTAAGTTTTTAACCTTTAGAAGCAGAA
GGC
Done.