Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010565.1 Corchorus olitorius cultivar O-4 contig10597, 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, 861
Length: 1436
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Found at i:429 original size:16 final size:16
Alignment explanation
Indices: 408--442 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
398 ACACCGGTTG
*
408 AATACAAACTCTCTCA
1 AATACAAAATCTCTCA
424 AATACAAAATCTCTCA
1 AATACAAAATCTCTCA
440 AAT
1 AAT
443 TTTAGTGCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (16 bp):
AATACAAAATCTCTCA
Found at i:1077 original size:35 final size:35
Alignment explanation
Indices: 1028--1435 Score: 504
Period size: 35 Copynumber: 11.5 Consensus size: 35
1018 ATCAATGTGA
*
1028 AGATCAACTCTGATCATCGAAAACTTCTTGAAATA
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
* **
1063 AGATCAACTTTGATCATAAAAAAAAAAACTTCTTGAAATG
1 AGATCAACTCTGATCAT-----CGAAAACTTCTTGAAATG
* **
1103 AGATCAACTCTGACCATAAAAAAAACTTCTTGAAATG
1 AGATCAACTCTGATCAT--CGAAAACTTCTTGAAATG
* * *
1140 AGATCAACTCTGATCGA-CAAAAACTTCTTAAAAGG
1 AGATCAACTCTGATC-ATCGAAAACTTCTTGAAATG
*
1175 AGATCAACTCTGATCAT-AAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
* *
1209 AGATCAACTCTGATCATTGAAAACTTCTTGAAACG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
*
1244 AGATCAACTCTGATCATTG-AAACTTCTTGAAATG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
*
1278 AGATCAACTCTGATCATAGAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
1313 AGATCAACTCTGATCATACGAAAACTTCTTGAAATGCG
1 AGATCAACTCTGATCAT-CGAAAACTTCTTGAAAT--G
1351 ATGATCAACTCTGATCATCGAAAACTTCTTGAAATG
1 A-GATCAACTCTGATCATCGAAAACTTCTTGAAATG
* *
1387 CGAATCAACTCTGATCATCG-AAACTT-TTG-AAGG
1 AG-ATCAACTCTGATCATCGAAAACTTCTTGAAATG
1420 AGATCAACTCTGATCA
1 AGATCAACTCTGATCA
1436 C
Statistics
Matches: 339, Mismatches: 20, Indels: 31
0.87 0.05 0.08
Matches are distributed among these distances:
32 14 0.04
33 4 0.01
34 68 0.20
35 119 0.35
36 34 0.10
37 34 0.10
38 20 0.06
39 16 0.05
40 30 0.09
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (35 bp):
AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
Found at i:1232 original size:69 final size:69
Alignment explanation
Indices: 1028--1435 Score: 482
Period size: 69 Copynumber: 5.7 Consensus size: 69
1018 ATCAATGTGA
* * * *
1028 AGATCAACTCTGATCATCGAAAACTTCTTGAAATAAGATCAACTTTGATCATAAAAAAAAAAACT
1 AGATCAACTCTGATCAT-AAAAACTTCTTGAAATGAGATCAACTCTGATCAT-----AGAAAACT
*
1093 TCTTGAAATG
60 TCTTGAAAGG
* *
1103 AGATCAACTCTGACCATAAAAAAAACTTCTTGAAATGAGATCAACTCTGATCGACA-AAAACTTC
1 AGATCAACTCTGATCAT---AAAAACTTCTTGAAATGAGATCAACTCTGATC-ATAGAAAACTTC
*
1167 TTAAAAGG
62 TTGAAAGG
*
1175 AGATCAACTCTGATCATAAAAACTTCTTGAAATGAGATCAACTCTGATCATTGAAAACTTCTTGA
1 AGATCAACTCTGATCATAAAAACTTCTTGAAATGAGATCAACTCTGATCATAGAAAACTTCTTGA
*
1240 AACG
66 AAGG
**
1244 AGATCAACTCTGATCATTGAAACTTCTTGAAATGAGATCAACTCTGATCATAGAAAACTTCTTGA
1 AGATCAACTCTGATCATAAAAACTTCTTGAAATGAGATCAACTCTGATCATAGAAAACTTCTTGA
*
1309 AATG
66 AAGG
*
1313 AGATCAACTCTGATCATACGAAAACTTCTTGAAATGCGATGATCAACTCTGATCATCGAAAACTT
1 AGATCAACTCTGATCATA--AAAACTTCTTGAAAT--GA-GATCAACTCTGATCATAGAAAACTT
1378 CTTGAAATGCG
61 CTTGAAA-G-G
** *
1389 A-ATCAACTCTGATCATCGAAACTT-TTG-AAGGAGATCAACTCTGATCA
1 AGATCAACTCTGATCATAAAAACTTCTTGAAATGAGATCAACTCTGATCA
1436 C
Statistics
Matches: 298, Mismatches: 24, Indels: 29
0.85 0.07 0.08
Matches are distributed among these distances:
68 16 0.05
69 130 0.44
71 16 0.05
72 33 0.11
73 9 0.03
74 31 0.10
75 31 0.10
76 2 0.01
77 29 0.10
78 1 0.00
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (69 bp):
AGATCAACTCTGATCATAAAAACTTCTTGAAATGAGATCAACTCTGATCATAGAAAACTTCTTGA
AAGG
Found at i:1408 original size:18 final size:18
Alignment explanation
Indices: 1354--1408 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
1344 AAATGCGATG
1354 ATCAACTCTGATCATCGA
1 ATCAACTCTGATCATCGA
*
1372 A--AACTTCTTGA-AATGCGA
1 ATCAAC-TC-TGATCAT-CGA
1390 ATCAACTCTGATCATCGA
1 ATCAACTCTGATCATCGA
1408 A
1 A
1409 ACTTTTGAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 12
0.67 0.05 0.28
Matches are distributed among these distances:
16 3 0.10
17 4 0.14
18 15 0.52
19 4 0.14
20 3 0.10
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (18 bp):
ATCAACTCTGATCATCGA
Done.