Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010377.1 Corchorus olitorius cultivar O-4 contig10409, 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: 2870
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Found at i:1674 original size:22 final size:21
Alignment explanation
Indices: 1645--1690 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
1635 TTTCGAGAAC
*
1645 CCTTTTAT-AAATTTTTTTTAA
1 CCTTTTATGAAA-TTTTGTTAA
1666 CCTTCTTATGAAATTTTGTTAA
1 CCTT-TTATGAAATTTTGTTAA
1688 CCT
1 CCT
1691 CCCTAAGGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 4 0.18
22 15 0.68
23 3 0.14
ACGTcount: A:0.26, C:0.15, G:0.04, T:0.54
Consensus pattern (21 bp):
CCTTTTATGAAATTTTGTTAA
Found at i:1865 original size:22 final size:22
Alignment explanation
Indices: 1840--1886 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1830 GAATTGTTAG
* * *
1840 TAATCACACTCTGAAATTTTGA
1 TAATAACACTATGAAATTTGGA
*
1862 TAATAATACTATGAAATTTGGA
1 TAATAACACTATGAAATTTGGA
1884 TAA
1 TAA
1887 ACCTTCCTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.36
Consensus pattern (22 bp):
TAATAACACTATGAAATTTGGA
Found at i:1987 original size:22 final size:22
Alignment explanation
Indices: 1959--2099 Score: 72
Period size: 22 Copynumber: 6.7 Consensus size: 22
1949 TGATAACTAC
1959 AAATTTTGATAACCTCATTATG
1 AAATTTTGATAACCTCATTATG
1981 AAATTTTG-T----T-ATGTA--
1 AAATTTTGATAACCTCAT-TATG
* * *
1996 AAATTTTGATCTACAT-ACTATG
1 AAATTTTGAT-AACCTCATTATG
*
2018 GAATTTTGATAACCCTC-TTATG
1 AAATTTTGATAA-CCTCATTATG
* * *
2040 AAATTTTGA-AAACTAAACTATG
1 AAATTTTGATAACCT-CATTATG
*
2062 AAATTTTGATAACTTTCA-TATG
1 AAATTTTGATAAC-CTCATTATG
*
2084 AAATTTTGATATCCTC
1 AAATTTTGATAACCTC
2100 CCTGAAATTT
Statistics
Matches: 90, Mismatches: 14, Indels: 31
0.67 0.10 0.23
Matches are distributed among these distances:
15 8 0.09
16 3 0.03
17 3 0.03
20 4 0.04
21 8 0.09
22 60 0.67
23 3 0.03
24 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (22 bp):
AAATTTTGATAACCTCATTATG
Found at i:2250 original size:22 final size:22
Alignment explanation
Indices: 2222--2609 Score: 153
Period size: 22 Copynumber: 17.5 Consensus size: 22
2212 CACATTTTGA
* *
2222 AAATTTTGATAACCTTTTTATG
1 AAATTTTGATAACCTCTCTATG
2244 AAATTTTGATAACCTCTCTATG
1 AAATTTTGATAACCTCTCTATG
** ** *
2266 AAATGGTG-TTGCCCCTCTATG
1 AAATTTTGATAACCTCTCTATG
*
2287 AAATTTTGATATA-TTCAT-TATG
1 AAATTTTGATA-ACCTC-TCTATG
* * * *
2309 TAATTTTTATAACCTCGCTTTG
1 AAATTTTGATAACCTCTCTATG
* *
2331 AAATTTTGATAACAAT-ACTATG
1 AAATTTTGATAAC-CTCTCTATG
2353 AAATTTTGATAATCCGATCTCTATG
1 AAATTTTGATAA-CC--TCTCTATG
* * * *
2378 AAATTTCGATGATCACTCTATG
1 AAATTTTGATAACCTCTCTATG
* *
2400 -GA-TTTGATAACCT-TCTATC
1 AAATTTTGATAACCTCTCTATG
*
2419 AAATTTTGGT-A-CTC-CTTATG
1 AAATTTTGATAACCTCTC-TATG
*
2439 AAATTGAGACTTTTATAACCT-TCATATG
1 AAA-T-----TTTGATAACCTCTC-TATG
* * **
2467 AAATTTTGATAACCACACTAAA
1 AAATTTTGATAACCTCTCTATG
* * * *
2489 AAATTTTAATAACCACACTATA
1 AAATTTTGATAACCTCTCTATG
*
2511 AAATTTTGATAA-CTTTCCTATG
1 AAATTTTGATAACCTCT-CTATG
*
2533 AAATATT-AGTAACCTC-CTTATG
1 AAATTTTGA-TAACCTCTC-TATG
* * *
2555 AAATTTTGTTAACCACACTATG
1 AAATTTTGATAACCTCTCTATG
*
2577 -AATTCTT-ATAACCTCGT-TAGG
1 AAATT-TTGATAACCTC-TCTATG
*
2598 ATATTTTGATAA
1 AAATTTTGATAA
2610 TCTATTTGAT
Statistics
Matches: 269, Mismatches: 63, Indels: 68
0.67 0.16 0.17
Matches are distributed among these distances:
19 8 0.03
20 15 0.06
21 42 0.16
22 164 0.61
23 7 0.03
24 2 0.01
25 15 0.06
26 4 0.01
27 2 0.01
28 10 0.04
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.40
Consensus pattern (22 bp):
AAATTTTGATAACCTCTCTATG
Found at i:2651 original size:22 final size:22
Alignment explanation
Indices: 2616--2658 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2606 ATAATCTATT
**
2616 TGATAACCTTACTATAAAATTG
1 TGATAACCACACTATAAAATTG
*
2638 TGATAACCACACTATGAAATT
1 TGATAACCACACTATAAAATT
2659 TCAATAACCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (22 bp):
TGATAACCACACTATAAAATTG
Done.