Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014034.1 Corchorus olitorius cultivar O-4 contig14067, 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: 30608
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:3449 original size:27 final size:27
Alignment explanation
Indices: 3408--3905 Score: 176
Period size: 30 Copynumber: 16.9 Consensus size: 27
3398 AGGTAAAATC
3408 ATGACAACTTCTGGTGTCAATTGAATT
1 ATGACAACTTCTGGTGTCAATTGAATT
*
3435 ATGACAACTTTTGGTGTCAATTGAATT
1 ATGACAACTTCTGGTGTCAATTGAATT
* ** *
3462 ATGACATCTTCAAGTGTCTATTGGAAATTTAT
1 ATGACAACTTCTGGTGTCAATT-G-AA--T-T
* **
3494 CATGACAAGTTCT-G-GTCAATTGTAAGACC
1 -ATGACAACTTCTGGTGTCAATTG--A-ATT
* *
3523 ATTGACAACTTCTGGTGTCAATTACAAGATC
1 A-TGACAACTTCTGGTGTCAATT--GA-ATT
* **
3554 ATGACAACTTCTGGTGTCAGTTGCAAGAGC
1 ATGACAACTTCTGGTGTCAATTG--A-ATT
**
3584 ATGACAACTTCTGGTGTCAATTGCAAGAGC
1 ATGACAACTTCTGGTGTCAATTG--A-ATT
3614 ATGACAACTTCTGGTGTCAATTGAATT
1 ATGACAACTTCTGGTGTCAATTGAATT
* ** * *
3641 ATGACATCTTCAAGTGTCTACTGGAAATTTAT
1 ATGACAACTTCTGGTGTC-AATTG-AA--T-T
**
3673 CATGACAACTTCT-G-GTCAATTGTAAGACC
1 -ATGACAACTTCTGGTGTCAATTG--A-ATT
**
3702 ATTGACAACTTCTGGTGTCAATTGTAAGAGC
1 A-TGACAACTTCTGGTGTCAATTG--A-ATT
* * **
3733 ATGGCAACTTCTAGTGTCAATTGCAAGAGC
1 ATGACAACTTCTGGTGTCAATTG--A-ATT
* **
3763 ATGGCAACTTCTGGTGTCAATTGCAAGAGC
1 ATGACAACTTCTGGTGTCAATTG--A-ATT
* **
3793 ATGATAACTTCTGGTGTCAATTGCAAAACC
1 ATGACAACTTCTGGTGTCAATTG---AATT
* **
3823 ATGACAACTTCCGGTGTCAATTGCAAGACC
1 ATGACAACTTCTGGTGTCAATTG--A-ATT
* * **
3853 ATGACAATTTATGGTGTCAATTGCAAGACC
1 ATGACAACTTCTGGTGTCAATTG--A-ATT
3883 ATGACAACTTCTGGTGTCAATTG
1 ATGACAACTTCTGGTGTCAATTG
3906 CAAGACCATG
Statistics
Matches: 394, Mismatches: 49, Indels: 53
0.79 0.10 0.11
Matches are distributed among these distances:
27 59 0.15
28 7 0.02
29 27 0.07
30 232 0.59
31 44 0.11
32 6 0.02
33 19 0.05
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (27 bp):
ATGACAACTTCTGGTGTCAATTGAATT
Found at i:3561 original size:30 final size:30
Alignment explanation
Indices: 3494--3931 Score: 503
Period size: 30 Copynumber: 14.7 Consensus size: 30
3484 GGAAATTTAT
* *
3494 CATGACAAGTTCT-G-GTCAATTGTAAGAC
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
* *
3522 CATTGACAACTTCTGGTGTCAATTACAAGAT
1 CA-TGACAACTTCTGGTGTCAATTGCAAGAC
* *
3553 CATGACAACTTCTGGTGTCAGTTGCAAGAG
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
*
3583 CATGACAACTTCTGGTGTCAATTGCAAGAG
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
*
3613 CATGACAACTTCTGGTGTCAATTG--A-AT
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
* * ** * * * * *
3640 TATGACATCTTCAAGTGTCTACTGGAAATTTAT
1 CATGACAACTTCTGGTGTC-AATTGCAA--GAC
*
3673 CATGACAACTTCT-G-GTCAATTGTAAGAC
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
* *
3701 CATTGACAACTTCTGGTGTCAATTGTAAGAG
1 CA-TGACAACTTCTGGTGTCAATTGCAAGAC
* * *
3732 CATGGCAACTTCTAGTGTCAATTGCAAGAG
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
* *
3762 CATGGCAACTTCTGGTGTCAATTGCAAGAG
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
* *
3792 CATGATAACTTCTGGTGTCAATTGCAAAAC
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
*
3822 CATGACAACTTCCGGTGTCAATTGCAAGAC
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
* *
3852 CATGACAATTTATGGTGTCAATTGCAAGAC
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
3882 CATGACAACTTCTGGTGTCAATTGCAAGAC
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
*
3912 CATGACAACTTCTAGTGTCA
1 CATGACAACTTCTGGTGTCA
3932 TTTGGTGATT
Statistics
Matches: 357, Mismatches: 41, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
27 16 0.04
28 9 0.03
29 21 0.06
30 267 0.75
31 31 0.09
32 1 0.00
33 12 0.03
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.29
Consensus pattern (30 bp):
CATGACAACTTCTGGTGTCAATTGCAAGAC
Found at i:3634 original size:90 final size:90
Alignment explanation
Indices: 3407--3931 Score: 527
Period size: 90 Copynumber: 5.9 Consensus size: 90
3397 AAGGTAAAAT
** * **
3407 CATGACAACTTCTGGTGTCAATTG--A-ATTATGACAACTTTTGGTGTCAATTG--A-ATTATGA
1 CATGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGCAAGACCATGA
* * * * * *
3466 CATCTTCAAGTGTCTATTGGAAATTTAT
66 CAACTTCTAGTGTCAATT-GCAA--GAG
* * * *
3494 CATGACAAGTTCT-G-GTCAATTGTAAGACCATTGACAACTTCTGGTGTCAATTACAAGATCATG
1 CATGACAACTTCTGGTGTCAATTGCAAGACCA-TGACAACTTCTGGTGTCAATTGCAAGACCATG
* *
3557 ACAACTTCTGGTGTCAGTTGCAAGAG
65 ACAACTTCTAGTGTCAATTGCAAGAG
* **
3583 CATGACAACTTCTGGTGTCAATTGCAAGAGCATGACAACTTCTGGTGTCAATTG--A-ATTATGA
1 CATGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGCAAGACCATGA
* * * * * * *
3645 CATCTTCAAGTGTCTACTGGAAATTTAT
66 CAACTTCTAGTGTC-AATTGCAA--GAG
* * *
3673 CATGACAACTTCT-G-GTCAATTGTAAGACCATTGACAACTTCTGGTGTCAATTGTAAGAGCATG
1 CATGACAACTTCTGGTGTCAATTGCAAGACCA-TGACAACTTCTGGTGTCAATTGCAAGACCATG
*
3736 GCAACTTCTAGTGTCAATTGCAAGAG
65 ACAACTTCTAGTGTCAATTGCAAGAG
* * * *
3762 CATGGCAACTTCTGGTGTCAATTGCAAGAGCATGATAACTTCTGGTGTCAATTGCAAAACCATGA
1 CATGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGCAAGACCATGA
** *
3827 CAACTTCCGGTGTCAATTGCAAGAC
66 CAACTTCTAGTGTCAATTGCAAGAG
* *
3852 CATGACAATTTATGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGCAAGACCATGA
1 CATGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGCAAGACCATGA
3917 CAACTTCTAGTGTCA
66 CAACTTCTAGTGTCA
3932 TTTGGTGATT
Statistics
Matches: 362, Mismatches: 58, Indels: 33
0.80 0.13 0.07
Matches are distributed among these distances:
85 8 0.02
86 1 0.00
87 30 0.08
88 22 0.06
89 69 0.19
90 159 0.44
91 38 0.10
92 35 0.10
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (90 bp):
CATGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGCAAGACCATGA
CAACTTCTAGTGTCAATTGCAAGAG
Found at i:3704 original size:179 final size:179
Alignment explanation
Indices: 3407--3931 Score: 713
Period size: 179 Copynumber: 2.9 Consensus size: 179
3397 AAGGTAAAAT
** *
3407 CATGACAACTTCTGGTGTCAATTG--A-ATTATGACAACTTTTGGTGTCAATTGAATTATGACAT
1 CATGACAACTTCTGGTGTCAATTGCAAGAGCATGACAACTTCTGGTGTCAATTGAATTATGACAT
* *
3469 CTTCAAGTGTCTATTGGAAATTTATCATGACAAGTTCTGGTCAATTGTAAGACCATTGACAACTT
66 CTTCAAGTGTCTAATGGAAATTTATCATGACAACTTCTGGTCAATTGTAAGACCATTGACAACTT
* * * *
3534 CTGGTGTCAATTACAAGATCATGACAACTTCTGGTGTCAGTTGCAAGAG
131 CTGGTGTCAATTGCAAGACCATGACAACTTCTAGTGTCAATTGCAAGAG
3583 CATGACAACTTCTGGTGTCAATTGCAAGAGCATGACAACTTCTGGTGTCAATTGAATTATGACAT
1 CATGACAACTTCTGGTGTCAATTGCAAGAGCATGACAACTTCTGGTGTCAATTGAATTATGACAT
*
3648 CTTCAAGTGTCTACTGGAAATTTATCATGACAACTTCTGGTCAATTGTAAGACCATTGACAACTT
66 CTTCAAGTGTCTAATGGAAATTTATCATGACAACTTCTGGTCAATTGTAAGACCATTGACAACTT
* * *
3713 CTGGTGTCAATTGTAAGAGCATGGCAACTTCTAGTGTCAATTGCAAGAG
131 CTGGTGTCAATTGCAAGACCATGACAACTTCTAGTGTCAATTGCAAGAG
* * **
3762 CATGGCAACTTCTGGTGTCAATTGCAAGAGCATGATAACTTCTGGTGTCAATTGCAAAACCATGA
1 CATGACAACTTCTGGTGTCAATTGCAAGAGCATGACAACTTCTGGTGTCAATTG---AATTATGA
* ** * * * * * * *
3827 CAACTTCCGGTGTC-AATTGCAA--GACCATGACAATTTATGGTGTCAATTGCAAGACCA-TGAC
63 CATCTTCAAGTGTCTAATGGAAATTTATCATGACAACTTCT-G-GTCAATTGTAAGACCATTGAC
3888 AACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTAGTGTCA
126 AACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTAGTGTCA
3932 TTTGGTGATT
Statistics
Matches: 312, Mismatches: 29, Indels: 12
0.88 0.08 0.03
Matches are distributed among these distances:
176 24 0.08
178 1 0.00
179 204 0.65
180 46 0.15
181 20 0.06
182 17 0.05
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (179 bp):
CATGACAACTTCTGGTGTCAATTGCAAGAGCATGACAACTTCTGGTGTCAATTGAATTATGACAT
CTTCAAGTGTCTAATGGAAATTTATCATGACAACTTCTGGTCAATTGTAAGACCATTGACAACTT
CTGGTGTCAATTGCAAGACCATGACAACTTCTAGTGTCAATTGCAAGAG
Found at i:5037 original size:22 final size:24
Alignment explanation
Indices: 5002--5055 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
4992 ATAAATGTTG
* *
5002 CTGATAA-TCTTCT-CTTTTATCT
1 CTGATAATTCTTCTCCATTTATCA
5024 CTGATAATTC-TCTCCATTTATCA
1 CTGATAATTCTTCTCCATTTATCA
5047 CTTGATAAT
1 C-TGATAAT
5056 ATCTAACCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 10 0.37
23 10 0.37
24 7 0.26
ACGTcount: A:0.24, C:0.22, G:0.06, T:0.48
Consensus pattern (24 bp):
CTGATAATTCTTCTCCATTTATCA
Found at i:9421 original size:66 final size:66
Alignment explanation
Indices: 9333--9464 Score: 201
Period size: 66 Copynumber: 2.0 Consensus size: 66
9323 TATAGTTTTA
* * *
9333 TAACAAAAAATGGCTTCAATGTACCGATTTTTAACGGAAAACGGACTTATGAACATAGATAAAAA
1 TAACAAAAAACGGCTTCAATGTACCGAATTTTAAAGGAAAACGGACTTATGAACATAGATAAAAA
9398 C
66 C
* ** *
9399 TAACGAAAAACGGCTTTGATGTACCGAATTTTAAAGGAAAACGGATTTATGAACATAGATAAAAA
1 TAACAAAAAACGGCTTCAATGTACCGAATTTTAAAGGAAAACGGACTTATGAACATAGATAAAAA
9464 C
66 C
9465 CTTATTTTGG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.24
Consensus pattern (66 bp):
TAACAAAAAACGGCTTCAATGTACCGAATTTTAAAGGAAAACGGACTTATGAACATAGATAAAAA
C
Found at i:12175 original size:15 final size:17
Alignment explanation
Indices: 12155--12191 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
12145 TAATGCTGAA
12155 ATTAA-TTA-AATAATT
1 ATTAATTTAGAATAATT
12170 ATTAATTTTAGAATAATT
1 ATTAA-TTTAGAATAATT
12188 ATTA
1 ATTA
12192 TTATTCCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 5 0.26
17 3 0.16
18 11 0.58
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
ATTAATTTAGAATAATT
Found at i:20770 original size:26 final size:26
Alignment explanation
Indices: 20734--20784 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
20724 ATAGCATAGT
20734 TTCATGAGGCAATAGAAATAAAAAGA
1 TTCATGAGGCAATAGAAATAAAAAGA
20760 TTCATGAGGCAATAGAAATAAAAAG
1 TTCATGAGGCAATAGAAATAAAAAG
20785 TACGTACATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.53, C:0.08, G:0.20, T:0.20
Consensus pattern (26 bp):
TTCATGAGGCAATAGAAATAAAAAGA
Found at i:29410 original size:27 final size:28
Alignment explanation
Indices: 29344--29418 Score: 98
Period size: 27 Copynumber: 2.7 Consensus size: 28
29334 AGGATCACCT
*
29344 AGGGGCATTTTGGTCATTTTCAAAAATCC
1 AGGGGCATTTTGGTCATTTGC-AAAATCC
** *
29373 AGGGGCATTTTGGTCATTTGC-ACGTTC
1 AGGGGCATTTTGGTCATTTGCAAAATCC
29400 AGGGGCATTTTGGTCATTT
1 AGGGGCATTTTGGTCATTT
29419 TAAGTTCACT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 22 0.52
29 20 0.48
ACGTcount: A:0.20, C:0.16, G:0.27, T:0.37
Consensus pattern (28 bp):
AGGGGCATTTTGGTCATTTGCAAAATCC
Done.