Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022653.1 Corchorus olitorius cultivar O-4 contig22686, 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: 8651
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:2259 original size:26 final size:27
Alignment explanation
Indices: 2206--2264 Score: 75
Period size: 30 Copynumber: 2.1 Consensus size: 27
2196 AGTAGATTAT
2206 TAATATCTTTTCATAATTAACCTCAAAAAA
1 TAATATCTTTTCATAATT-A--TCAAAAAA
*
2236 TAATATCTTTTCATAATT-TTAAAAAA
1 TAATATCTTTTCATAATTATCAAAAAA
2262 TAA
1 TAA
2265 AATATTGGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 10 0.36
30 18 0.64
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (27 bp):
TAATATCTTTTCATAATTATCAAAAAA
Found at i:2419 original size:2 final size:2
Alignment explanation
Indices: 2407--2452 Score: 67
Period size: 2 Copynumber: 23.0 Consensus size: 2
2397 TTCGTGATTT
*
2407 TA TA TA GTA TA TA TA TA TA TA TA TA TA TA -A TA AA TA TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2449 TA TA
1 TA TA
2453 GTTGAATCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 1 0.03
2 37 0.93
3 2 0.05
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:2433 original size:21 final size:20
Alignment explanation
Indices: 2407--2454 Score: 71
Period size: 19 Copynumber: 2.4 Consensus size: 20
2397 TTCGTGATTT
*
2407 TATATAGTATATATATATATA
1 TATATAGTA-ATAAATATATA
2428 TATATA-TAATAAATATATA
1 TATATAGTAATAAATATATA
2447 TATATAGT
1 TATATAGT
2455 TGAATCAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 16 0.64
20 3 0.12
21 6 0.24
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (20 bp):
TATATAGTAATAAATATATA
Found at i:6783 original size:16 final size:16
Alignment explanation
Indices: 6751--6795 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
6741 AAATAAAAGG
* *
6751 AAAGAAGAAGAGAA-A
1 AAAGAATAAAAGAATA
6766 AAAGAAT-AAAGAATA
1 AAAGAATAAAAGAATA
6781 AAAGAATAAAAGAAT
1 AAAGAATAAAAGAAT
6796 TTAAAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 5 0.19
15 14 0.54
16 7 0.27
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (16 bp):
AAAGAATAAAAGAATA
Found at i:6786 original size:8 final size:8
Alignment explanation
Indices: 6751--6795 Score: 58
Period size: 8 Copynumber: 5.9 Consensus size: 8
6741 AAATAAAAGG
*
6751 AAAGAAGA
1 AAAGAATA
*
6759 AGAGAA-A
1 AAAGAATA
6766 AAAGAAT-
1 AAAGAATA
6773 AAAGAATA
1 AAAGAATA
6781 AAAGAATA
1 AAAGAATA
6789 AAAGAAT
1 AAAGAAT
6796 TTAAAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
7 13 0.39
8 20 0.61
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (8 bp):
AAAGAATA
Found at i:7099 original size:21 final size:21
Alignment explanation
Indices: 7073--7115 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
7063 TATATAACAG
*
7073 TCAACATTTGTATTTGTTTAT
1 TCAACATTTATATTTGTTTAT
7094 TCAACATTTATATTTGTTTAT
1 TCAACATTTATATTTGTTTAT
7115 T
1 T
7116 GTCACACTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.09, G:0.07, T:0.58
Consensus pattern (21 bp):
TCAACATTTATATTTGTTTAT
Found at i:7263 original size:41 final size:41
Alignment explanation
Indices: 7214--7296 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
7204 TGTAATTCGC
*
7214 ATTAATAGAATCCTATATGTTATTTTCATCTAATATCATCT
1 ATTAATAGAATCCTATAAGTTATTTTCATCTAATATCATCT
*
7255 ATTAATAGAATCCTATAAGTTATTTTCATCTGATATCATCT
1 ATTAATAGAATCCTATAAGTTATTTTCATCTAATATCATCT
7296 A
1 A
7297 GGAGATTGAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.35, C:0.14, G:0.06, T:0.45
Consensus pattern (41 bp):
ATTAATAGAATCCTATAAGTTATTTTCATCTAATATCATCT
Found at i:7557 original size:16 final size:16
Alignment explanation
Indices: 7518--7638 Score: 90
Period size: 16 Copynumber: 7.6 Consensus size: 16
7508 CGGGCTCGGG
*
7518 CGGGTTCGGGTACTTT
1 CGGGTTCGGGTATTTT
*
7534 -GTGTTCGGGCT-TTTT
1 CGGGTTCGGG-TATTTT
7549 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
* * **
7565 CAGGCTCGGGT-TAAGT
1 CGGGTTCGGGTAT-TTT
*
7581 CGGGTTCGGTTATTTT
1 CGGGTTCGGGTATTTT
*
7597 CGGGCTC-GG-ATTATGT
1 CGGGTTCGGGTATT-T-T
7613 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
*
7629 TGGGTTCGGG
1 CGGGTTCGGG
7639 CTCGGGTCGG
Statistics
Matches: 80, Mismatches: 16, Indels: 18
0.70 0.14 0.16
Matches are distributed among these distances:
14 3 0.04
15 15 0.19
16 55 0.69
17 4 0.05
18 3 0.04
ACGTcount: A:0.07, C:0.15, G:0.38, T:0.40
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:7584 original size:32 final size:32
Alignment explanation
Indices: 7548--7628 Score: 126
Period size: 32 Copynumber: 2.5 Consensus size: 32
7538 TCGGGCTTTT
*
7548 TCGGGTTCGGGTATTTTCAGGCTCGGGTTAAG
1 TCGGGTTCGGGTATTTTCAGGCTCGGATTAAG
* * *
7580 TCGGGTTCGGTTATTTTCGGGCTCGGATTATG
1 TCGGGTTCGGGTATTTTCAGGCTCGGATTAAG
7612 TCGGGTTCGGGTATTTT
1 TCGGGTTCGGGTATTTT
7629 TGGGTTCGGG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.10, C:0.15, G:0.36, T:0.40
Consensus pattern (32 bp):
TCGGGTTCGGGTATTTTCAGGCTCGGATTAAG
Found at i:7805 original size:13 final size:12
Alignment explanation
Indices: 7782--7828 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
7772 AAGTTTATTG
7782 ATAATATATAAT
1 ATAATATATAAT
7794 ATAATAATATAAT
1 ATAAT-ATATAAT
* *
7807 ATAACAT-TATT
1 ATAATATATAAT
7818 ATCAATATATA
1 AT-AATATATA
7829 TAAATATTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAATATATAAT
Found at i:8388 original size:2 final size:2
Alignment explanation
Indices: 8383--8408 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8373 ATATAAGTTT
8383 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
8409 GTAGTTTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.