Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019487.1 Corchorus olitorius cultivar O-4 contig19520, 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: 23360
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:3303 original size:30 final size:31
Alignment explanation
Indices: 3237--3304 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
3227 AGTTTTGTAA
* *
3237 AATTTTTGAAACACCTATTATACCCTTATTT
1 AATTTTTGAAACACCAATTATACCCTTATCT
** *
3268 AATTTTTGAAATGCCAATTATATCCTTA-CT
1 AATTTTTGAAACACCAATTATACCCTTATCT
3298 AATTTTT
1 AATTTTT
3305 AATTTTATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 8 0.25
31 24 0.75
ACGTcount: A:0.32, C:0.16, G:0.04, T:0.47
Consensus pattern (31 bp):
AATTTTTGAAACACCAATTATACCCTTATCT
Found at i:3989 original size:21 final size:21
Alignment explanation
Indices: 3963--4005 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3953 GCTGTCTCAA
**
3963 AAAAGATGGATGGTGCTATTG
1 AAAAGATGGATAATGCTATTG
3984 AAAAGATGGATAATGCTATTG
1 AAAAGATGGATAATGCTATTG
4005 A
1 A
4006 TGGTGCTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.28, T:0.28
Consensus pattern (21 bp):
AAAAGATGGATAATGCTATTG
Found at i:4013 original size:33 final size:33
Alignment explanation
Indices: 3971--4040 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
3961 AAAAAAGATG
3971 GATGGTGCTATTGAAAAGATGGATAATGCTATT
1 GATGGTGCTATTGAAAAGATGGATAATGCTATT
**
4004 GATGGTGCTATTGAAAAGATGGATGGTGCTATT
1 GATGGTGCTATTGAAAAGATGGATAATGCTATT
4037 GATG
1 GATG
4041 TGACGGAAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.30, C:0.06, G:0.31, T:0.33
Consensus pattern (33 bp):
GATGGTGCTATTGAAAAGATGGATAATGCTATT
Found at i:7895 original size:44 final size:47
Alignment explanation
Indices: 7832--7922 Score: 143
Period size: 47 Copynumber: 2.0 Consensus size: 47
7822 TTTGATTTTG
7832 ATTTTGATTTTTATTTAAA-T-TATA-TATATTATATATTATAAAGT
1 ATTTTGATTTTTATTTAAATTATATATTATATTATATATTATAAAGT
* *
7876 ATTTTTATTTTTATTTAAATTATATATTATATTATTTATTATAAAGT
1 ATTTTGATTTTTATTTAAATTATATATTATATTATATATTATAAAGT
7923 GATATATGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
44 18 0.43
45 1 0.02
46 4 0.10
47 19 0.45
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.59
Consensus pattern (47 bp):
ATTTTGATTTTTATTTAAATTATATATTATATTATATATTATAAAGT
Found at i:8376 original size:48 final size:49
Alignment explanation
Indices: 8241--8383 Score: 261
Period size: 48 Copynumber: 2.9 Consensus size: 49
8231 CCTAAAATCT
8241 GTATAAGCCATATTTTCTCAATTAAATTTATATTTTATAAATACTAGATCC
1 GTATAAGCCATATTTTCTCAATTAAATTTA-A-TTTATAAATACTAGATCC
8292 GTATAAGCCATATTTTCTCAATTAAATTTAATTTATAAATACTAGATCC
1 GTATAAGCCATATTTTCTCAATTAAATTTAATTTATAAATACTAGATCC
8341 GTATAAGCCATA-TTTCTCAATTAAATTTAATTTATAAATACTA
1 GTATAAGCCATATTTTCTCAATTAAATTTAATTTATAAATACTA
8384 TATATATATA
Statistics
Matches: 92, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
48 31 0.34
49 30 0.33
50 1 0.01
51 30 0.33
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (49 bp):
GTATAAGCCATATTTTCTCAATTAAATTTAATTTATAAATACTAGATCC
Found at i:11030 original size:5 final size:6
Alignment explanation
Indices: 11012--11054 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
11002 ACAGCGCAAT
* *
11012 AACAAA AACAAA AACAAA AAC-AA AA-AAA CAGAAA AACAAA AAC
1 AACAAA AACAAA AACAAA AACAAA AACAAA AACAAA AACAAA AAC
11055 GATGCCAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
5 7 0.22
6 25 0.78
ACGTcount: A:0.81, C:0.16, G:0.02, T:0.00
Consensus pattern (6 bp):
AACAAA
Found at i:13480 original size:47 final size:47
Alignment explanation
Indices: 13411--13505 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
13401 CATCATATGG
13411 AAATTATATTAAGGGTAATTATTTGATACACATTGGAGTTATATTAA
1 AAATTATATTAAGGGTAATTATTTGATACACATTGGAGTTATATTAA
13458 AAATTATATTAAGGGTAATTATTTGATACACATTGGAGTTATATTAA
1 AAATTATATTAAGGGTAATTATTTGATACACATTGGAGTTATATTAA
13505 A
1 A
13506 GGTAATTATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.41, C:0.04, G:0.15, T:0.40
Consensus pattern (47 bp):
AAATTATATTAAGGGTAATTATTTGATACACATTGGAGTTATATTAA
Found at i:13576 original size:13 final size:13
Alignment explanation
Indices: 13558--13690 Score: 99
Period size: 13 Copynumber: 9.3 Consensus size: 13
13548 AATTATATTA
*
13558 TATTAAGGGTAAT
1 TATTAAAGGTAAT
13571 TATTAAAGGTAAT
1 TATTAAAGGTAAT
13584 TATTGAATATATGG-AAT
1 TATT--A-A-A-GGTAAT
*
13601 TATATTAAGTGTAAT
1 TAT-TAAAG-GTAAT
13616 TATTAAAGGTAAT
1 TATTAAAGGTAAT
13629 TATTAAAGGTAAT
1 TATTAAAGGTAAT
13642 TATTGAATATATGG-AAT
1 TATT--A-A-A-GGTAAT
*
13659 TATATTAAGTGTAAT
1 TAT-TAAAG-GTAAT
13674 TATTAAAGGTAAT
1 TATTAAAGGTAAT
13687 TATT
1 TATT
13691 GAACACATGT
Statistics
Matches: 99, Mismatches: 5, Indels: 32
0.73 0.04 0.24
Matches are distributed among these distances:
13 49 0.49
14 12 0.12
15 16 0.16
16 2 0.02
17 14 0.14
18 6 0.06
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (13 bp):
TATTAAAGGTAAT
Found at i:13603 original size:45 final size:45
Alignment explanation
Indices: 13554--13812 Score: 169
Period size: 45 Copynumber: 5.9 Consensus size: 45
13544 ATGGAATTAT
13554 ATTATATTAAGGGTAATTATTAAAGGTAATTATTGAATATATGGA
1 ATTATATTAAGGGTAATTATTAAAGGTAATTATTGAATATATGGA
*
13599 ATTATATTAAGTGTAATTATTAAAGGTAATTATT--A-A-A-GGTA
1 ATTATATTAAGGGTAATTATTAAAGGTAATTATTGAATATATGG-A
* * *
13640 ATTATTGAATATATGG-AATTATATTAAGTGTAATTATT--A-A-A-GGTA
1 ATTA-T-ATTA-AGGGTAATTAT-TAAAG-GTAATTATTGAATATATGG-A
* * ** *
13685 ATTAT-TGAA---CACATGTATTATATATATACATCATATGGAAT-TAT---
1 ATTATATTAAGGGTA-AT-TATTA-A-AGGTA-AT--TATTGAATATATGGA
13729 ATTATATTAAGGGTAATTATTAAAGGTAATTATTGAATATATGGA
1 ATTATATTAAGGGTAATTATTAAAGGTAATTATTGAATATATGGA
*
13774 ATTATATTAAGTGTAATTATTAAAGGTAATTATTGAATA
1 ATTATATTAAGGGTAATTATTAAAGGTAATTATTGAATA
13813 CATATATTAT
Statistics
Matches: 170, Mismatches: 17, Indels: 54
0.71 0.07 0.22
Matches are distributed among these distances:
39 1 0.01
40 5 0.03
41 20 0.12
42 9 0.05
43 12 0.07
44 18 0.11
45 95 0.56
46 6 0.04
47 3 0.02
48 1 0.01
ACGTcount: A:0.42, C:0.02, G:0.15, T:0.41
Consensus pattern (45 bp):
ATTATATTAAGGGTAATTATTAAAGGTAATTATTGAATATATGGA
Found at i:13737 original size:117 final size:117
Alignment explanation
Indices: 13616--13849 Score: 441
Period size: 117 Copynumber: 2.0 Consensus size: 117
13606 TAAGTGTAAT
13616 TATTAAAGGTAATTATTAAAGGTAATTATTGAATATATGGAATTATATTAAGTGTAATTATTAAA
1 TATTAAAGGTAATTATTAAAGGTAATTATTGAATATATGGAATTATATTAAGTGTAATTATTAAA
*
13681 GGTAATTATTGAACACATGTATTATATATATACATCATATGGAATTATATTA
66 GGTAATTATTGAACACATATATTATATATATACATCATATGGAATTATATTA
*
13733 TATTAAGGGTAATTATTAAAGGTAATTATTGAATATATGGAATTATATTAAGTGTAATTATTAAA
1 TATTAAAGGTAATTATTAAAGGTAATTATTGAATATATGGAATTATATTAAGTGTAATTATTAAA
*
13798 GGTAATTATTGAATACATATATTATATATATACATCATATGGAATTATATTA
66 GGTAATTATTGAACACATATATTATATATATACATCATATGGAATTATATTA
13850 AGGGTAATTA
Statistics
Matches: 114, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
117 114 1.00
ACGTcount: A:0.43, C:0.03, G:0.13, T:0.41
Consensus pattern (117 bp):
TATTAAAGGTAATTATTAAAGGTAATTATTGAATATATGGAATTATATTAAGTGTAATTATTAAA
GGTAATTATTGAACACATATATTATATATATACATCATATGGAATTATATTA
Found at i:13751 original size:13 final size:13
Alignment explanation
Indices: 13733--13807 Score: 62
Period size: 13 Copynumber: 5.3 Consensus size: 13
13723 AATTATATTA
*
13733 TATTAAGGGTAAT
1 TATTAAAGGTAAT
13746 TATTAAAGGTAAT
1 TATTAAAGGTAAT
13759 TATTGAATATATGG-AAT
1 TATT--A-A-A-GGTAAT
*
13776 TATATTAAGTGTAAT
1 TAT-TAAAG-GTAAT
13791 TATTAAAGGTAAT
1 TATTAAAGGTAAT
13804 TATT
1 TATT
13808 GAATACATAT
Statistics
Matches: 51, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
13 26 0.51
14 6 0.12
15 8 0.16
16 1 0.02
17 7 0.14
18 3 0.06
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.43
Consensus pattern (13 bp):
TATTAAAGGTAAT
Found at i:13828 original size:58 final size:57
Alignment explanation
Indices: 13558--13807 Score: 310
Period size: 58 Copynumber: 4.3 Consensus size: 57
13548 AATTATATTA
*
13558 TATTAAGGGTAATTATTAAAGGTAATTATTGAATATATGGAATTATATTAAGTGTAAT
1 TATTAAAGGTAATTATTAAA-GTAATTATTGAATATATGGAATTATATTAAGTGTAAT
13616 TATTAAAGGTAATTATTAAAGGTAATTATTGAATATATGGAATTATATTAAGTGTAAT
1 TATTAAAGGTAATTATTAAA-GTAATTATTGAATATATGGAATTATATTAAGTGTAAT
* * * * * * *
13674 TATTAAAGGTAATTATTGAA-CACATGTATT-ATATATAT--ACATCATATGGAATTATATT
1 TATTAAAGGTAATTATTAAAGTA-AT-TATTGA-ATATATGGA-ATTATAT-TAAGTGTAAT
*
13732 ATATTAAGGGTAATTATTAAAGGTAATTATTGAATATATGGAATTATATTAAGTGTAAT
1 -TATTAAAGGTAATTATTAAA-GTAATTATTGAATATATGGAATTATATTAAGTGTAAT
13791 TATTAAAGGTAATTATT
1 TATTAAAGGTAATTATT
13808 GAATACATAT
Statistics
Matches: 164, Mismatches: 17, Indels: 22
0.81 0.08 0.11
Matches are distributed among these distances:
56 2 0.01
57 9 0.05
58 108 0.66
59 34 0.21
60 9 0.05
61 2 0.01
ACGTcount: A:0.42, C:0.02, G:0.15, T:0.42
Consensus pattern (57 bp):
TATTAAAGGTAATTATTAAAGTAATTATTGAATATATGGAATTATATTAAGTGTAAT
Found at i:16063 original size:78 final size:78
Alignment explanation
Indices: 15825--16129 Score: 537
Period size: 78 Copynumber: 4.0 Consensus size: 78
15815 GTCCCGCACT
*
15825 ACACGATTGTCCAATTCAATCTTAGTTAGAGAATGTGTTAATACATTGGCTTCCTTATTTACAAA
1 ACACGATTGTCCAATTCAATCTTAGTTAGAGAATGTGCTAATACATTGGCTTCCTTATTTACAAA
15890 TTGAAACGTAACC
66 TTGAAACGTAACC
*
15903 ACATGATTGTCCAATTCAATCTTAGTTAGAGAATGTGCTAAT--A--GGCTTCCTTATTTACAAA
1 ACACGATTGTCCAATTCAATCTTAGTTAGAGAATGTGCTAATACATTGGCTTCCTTATTTACAAA
15964 TTGAAACGTAACC
66 TTGAAACGTAACC
*
15977 ACAAGATTGTCCAATTCAATCTTAGTTAGAGAATGTGCTAATACATTGGCTTCCTTATTTACAAA
1 ACACGATTGTCCAATTCAATCTTAGTTAGAGAATGTGCTAATACATTGGCTTCCTTATTTACAAA
16042 TTGAAACGTAACC
66 TTGAAACGTAACC
* *
16055 ACACGATTGTCCAATTCAATCTTAGTTAGAGAATGTGCTAATACATTGGTTTCCCTATTTACAAA
1 ACACGATTGTCCAATTCAATCTTAGTTAGAGAATGTGCTAATACATTGGCTTCCTTATTTACAAA
16120 TTGAAACGTA
66 TTGAAACGTA
16130 CATAAATCAA
Statistics
Matches: 217, Mismatches: 6, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
74 72 0.33
76 2 0.01
78 143 0.66
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (78 bp):
ACACGATTGTCCAATTCAATCTTAGTTAGAGAATGTGCTAATACATTGGCTTCCTTATTTACAAA
TTGAAACGTAACC
Found at i:17388 original size:30 final size:30
Alignment explanation
Indices: 17354--17413 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
17344 TTTTATCTTA
17354 ACTTTCCTCTTATACCCTCAAATTTTAATG
1 ACTTTCCTCTTATACCCTCAAATTTTAATG
*
17384 ACTTTTCTCTTATACCCTCAAATTTTAATG
1 ACTTTCCTCTTATACCCTCAAATTTTAATG
17414 GCTTATTAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.25, G:0.03, T:0.45
Consensus pattern (30 bp):
ACTTTCCTCTTATACCCTCAAATTTTAATG
Done.