Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021548.1 Corchorus olitorius cultivar O-4 contig21581, 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: 9091
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:1496 original size:2 final size:2
Alignment explanation
Indices: 1489--1534 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1479 ACAATGTCTT
1489 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1531 CA CA
1 CA CA
1535 GAGGAAAGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1976 original size:23 final size:22
Alignment explanation
Indices: 1950--1993 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1940 CTTGTGATAC
1950 GACTAAATTAGTACATGTATTTT
1 GACTAAATTA-TACATGTATTTT
** *
1973 GACTCTATTATGCATGTATTT
1 GACTAAATTATACATGTATTT
1994 GGTATGTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (22 bp):
GACTAAATTATACATGTATTTT
Found at i:4732 original size:62 final size:61
Alignment explanation
Indices: 4642--4800 Score: 264
Period size: 62 Copynumber: 2.6 Consensus size: 61
4632 CTTTAATTAT
*
4642 TATAATCCGGTCAAAGTTAATCTTAGTTCTTTTAGGTGTAAGGCTTTTTTTCATATATATAAA
1 TATAATCCGGTCAAA-TTAATCTTAGTTCTTTTAGGTGTAAGGC-TATTTTCATATATATAAA
*
4705 TATAATCCGGTCACATTAATCTTAGTTCTTTTAGGTGTAAGGCTATTTTCATATATATAAA
1 TATAATCCGGTCAAATTAATCTTAGTTCTTTTAGGTGTAAGGCTATTTTCATATATATAAA
*
4766 TATAATCCGGTCGAAATTAATCCTAGTTCTTTTAG
1 TATAATCCGGTC-AAATTAATCTTAGTTCTTTTAG
4801 ATATTATAAT
Statistics
Matches: 91, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
61 29 0.32
62 48 0.53
63 14 0.15
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (61 bp):
TATAATCCGGTCAAATTAATCTTAGTTCTTTTAGGTGTAAGGCTATTTTCATATATATAAA
Found at i:4841 original size:50 final size:49
Alignment explanation
Indices: 4781--4881 Score: 148
Period size: 50 Copynumber: 2.0 Consensus size: 49
4771 TCCGGTCGAA
* *
4781 ATTAATCCTAGTTCTTTTAGATATTATAATCCAGTCAAAATTGAAATTTT
1 ATTAATCCTAGTTCTTTTAGATATCATAAT-CAGTCAAAATTGAAAATTT
* **
4831 ATTAATCCTAGTTCTTTTAGCTATCATAATTGGTCAAAATTGAAAATTT
1 ATTAATCCTAGTTCTTTTAGATATCATAATCAGTCAAAATTGAAAATTT
4880 AT
1 AT
4882 ATTTAATTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
49 18 0.39
50 28 0.61
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.44
Consensus pattern (49 bp):
ATTAATCCTAGTTCTTTTAGATATCATAATCAGTCAAAATTGAAAATTT
Found at i:5027 original size:17 final size:17
Alignment explanation
Indices: 5005--5040 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
4995 TTATATATAG
5005 TATAGATAATATAGATA
1 TATAGATAATATAGATA
*
5022 TATAGATATTATAGATA
1 TATAGATAATATAGATA
5039 TA
1 TA
5041 GATAATCCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (17 bp):
TATAGATAATATAGATA
Found at i:5039 original size:9 final size:9
Alignment explanation
Indices: 4995--5039 Score: 56
Period size: 9 Copynumber: 5.1 Consensus size: 9
4985 ATTCTTCTTT
*
4995 TTATATATA
1 TTATAGATA
*
5004 GTATAGATA
1 TTATAGATA
*
5013 ATATAGATA
1 TTATAGATA
5022 -TATAGATA
1 TTATAGATA
5030 TTATAGATA
1 TTATAGATA
5039 T
1 T
5040 AGATAATCCT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
8 8 0.25
9 24 0.75
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (9 bp):
TTATAGATA
Found at i:7660 original size:16 final size:16
Alignment explanation
Indices: 7627--7663 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
7617 CAACATGGTA
*
7627 ATTTTTTTCTAACCAT
1 ATTTTTTTCTAAACAT
*
7643 ATTTTTTTCTAAATAT
1 ATTTTTTTCTAAACAT
7659 ATTTT
1 ATTTT
7664 ATATAGTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.27, C:0.11, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTTTTTCTAAACAT
Found at i:7699 original size:7 final size:7
Alignment explanation
Indices: 7655--7720 Score: 55
Period size: 7 Copynumber: 9.4 Consensus size: 7
7645 TTTTTTCTAA
7655 ATATATT
1 ATATATT
*
7662 TTATA-T
1 ATATATT
*
7668 AGTATAAT
1 A-TATATT
7676 ATATATT
1 ATATATT
* *
7683 GTGATGTT
1 AT-ATATT
7691 ATATATT
1 ATATATT
7698 ATATATT
1 ATATATT
*
7705 ACATATT
1 ATATATT
7712 ATAT-TT
1 ATATATT
7718 ATA
1 ATA
7721 GAAATAATAA
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
6 6 0.13
7 34 0.72
8 7 0.15
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (7 bp):
ATATATT
Found at i:7775 original size:11 final size:11
Alignment explanation
Indices: 7761--7798 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
7751 AATAACAAAG
*
7761 ATATGTATAAT
1 ATATATATAAT
7772 ATATATATAAT
1 ATATATATAAT
7783 ATATATAT-AT
1 ATATATATAAT
7793 ATATAT
1 ATATAT
7799 TATAGTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (11 bp):
ATATATATAAT
Found at i:7777 original size:2 final size:2
Alignment explanation
Indices: 7761--7802 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
7751 AATAACAAAG
*
7761 AT AT GT AT A- AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7800 AT A
1 AT A
7803 GTAATACGGG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 3 0.09
2 32 0.91
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Done.