Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013874.1 Corchorus olitorius cultivar O-4 contig13907, 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: 40157
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3626 original size:43 final size:43
Alignment explanation
Indices: 3579--3906 Score: 353
Period size: 41 Copynumber: 7.8 Consensus size: 43
3569 ATAAGGAGAA
3579 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTATAATAGAG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTATAATAGAG
*
3622 ATGCC-CATGTGTTATATATGTGTTTGGGGACTTTGAT-ATA-A-
1 ATGCCTC-TGTGTTATATATGTGTTTGAGGACTTT-ATAATAGAG
3663 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTATAATAGAG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTATAATAGAG
* *
3706 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGAT-ATA-A-
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTT-ATAATAGAG
* * *
3747 ATGCCTCTGTGTTATATATGTGTTTCAGGACTTTGTAATAAAG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTATAATAGAG
* * * * *
3790 GTGCCCCTATG-T-TATATGTGTTTGGGGACTTGGAT-ATAG-G
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTT-TATAATAGAG
*
3830 -TGTCTCTGTGTTATATATGTGTTTGAGGACTTT-TGGAATAGA-
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTAT--AATAGAG
* *
3872 ATTGTCC-ATGTGTTATATATGTGTTTGGGGACTTT
1 A-TG-CCTCTGTGTTATATATGTGTTTGAGGACTTT
3907 TTGGTTATTG
Statistics
Matches: 241, Mismatches: 24, Indels: 39
0.79 0.08 0.13
Matches are distributed among these distances:
39 8 0.03
40 5 0.02
41 106 0.44
42 12 0.05
43 77 0.32
44 32 0.13
45 1 0.00
ACGTcount: A:0.23, C:0.10, G:0.25, T:0.42
Consensus pattern (43 bp):
ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTATAATAGAG
Found at i:3671 original size:84 final size:84
Alignment explanation
Indices: 3577--3906 Score: 497
Period size: 84 Copynumber: 3.9 Consensus size: 84
3567 CCATAAGGAG
3577 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTATAATAGAGATGCCCATGTGTTATATATG
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTATAATAGAGATGCCCATGTGTTATATATG
3642 TGTTTGGGGACTTTGATAT
66 TGTTTGGGGACTTTGATAT
*
3661 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTATAATAGAGATGCCCCTGTGTTATATATG
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTATAATAGAGATGCCCATGTGTTATATATG
3726 TGTTTGGGGACTTTGATAT
66 TGTTTGGGGACTTTGATAT
* * * * * *
3745 AAATGCCTCTGTGTTATATATGTGTTTCAGGACTTTGTAATAAAGGTGCCCCTATG-T-TATATG
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTATAATAGAGATGCCCATGTGTTATATATG
*
3808 TGTTTGGGGACTTGGATAT
66 TGTTTGGGGACTTTGATAT
** * *
3827 AGGTGTCTCTGTGTTATATATGTGTTTGAGGACTTT-TGGAATAGA-ATTGTCCATGTGTTATAT
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTAT--AATAGAGA-TGCCCATGTGTTATAT
3890 ATGTGTTTGGGGACTTT
63 ATGTGTTTGGGGACTTT
3907 TTGGTTATTG
Statistics
Matches: 224, Mismatches: 17, Indels: 9
0.90 0.07 0.04
Matches are distributed among these distances:
81 1 0.00
82 56 0.25
83 13 0.06
84 135 0.60
85 19 0.08
ACGTcount: A:0.23, C:0.10, G:0.25, T:0.42
Consensus pattern (84 bp):
AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTATAATAGAGATGCCCATGTGTTATATATG
TGTTTGGGGACTTTGATAT
Found at i:4314 original size:12 final size:14
Alignment explanation
Indices: 4291--4327 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
4281 TAAAATAAAC
4291 TAAAATGAAAAA-A
1 TAAAATGAAAAATA
4304 TAAAA-GAAAAATA
1 TAAAATGAAAAATA
*
4317 TAAAGTGAAAA
1 TAAAATGAAAA
4328 TATTTGTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 6 0.29
13 10 0.48
14 5 0.24
ACGTcount: A:0.73, C:0.00, G:0.11, T:0.16
Consensus pattern (14 bp):
TAAAATGAAAAATA
Found at i:9306 original size:1 final size:1
Alignment explanation
Indices: 9300--9329 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
9290 GATCTGATTC
9300 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
9330 CATGGACTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:13676 original size:2 final size:2
Alignment explanation
Indices: 13669--13711 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
13659 ATAGTTTGAT
13669 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
13711 T
1 T
13712 TTGTGGTCTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:18687 original size:21 final size:22
Alignment explanation
Indices: 18661--18707 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
18651 TATGGTATGA
18661 AAAATTT-ATAGGGAGATTAAC
1 AAAATTTAATAGGGAGATTAAC
* *
18682 AAAATTTAATAGGGAGGTTATC
1 AAAATTTAATAGGGAGATTAAC
18704 AAAA
1 AAAA
18708 AATCGTAAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.49, C:0.04, G:0.19, T:0.28
Consensus pattern (22 bp):
AAAATTTAATAGGGAGATTAAC
Found at i:18798 original size:42 final size:44
Alignment explanation
Indices: 18727--18845 Score: 109
Period size: 42 Copynumber: 2.7 Consensus size: 44
18717 GAGATTGATT
* * * * * *
18727 AAAATTTCATCGGAAGGTTTATTAAAATTTTATAGT-TAGGTTATC
1 AAAATTTCATAGG-ATGTTTATCACAATTTTATAATGTA-ATTATC
* **
18772 AAAATTTCA-GGGA-GTTTATCACAATTTCGTAATGTAATTATC
1 AAAATTTCATAGGATGTTTATCACAATTTTATAATGTAATTATC
*
18814 AAAATTTCATAGGATGATTATCACAATTTTAT
1 AAAATTTCATAGGATGTTTATCACAATTTTAT
18846 TTCATTGAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
42 29 0.48
43 6 0.10
44 16 0.27
45 9 0.15
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.40
Consensus pattern (44 bp):
AAAATTTCATAGGATGTTTATCACAATTTTATAATGTAATTATC
Found at i:18814 original size:22 final size:21
Alignment explanation
Indices: 18787--18842 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
18777 TTCAGGGAGT
*
18787 TTATCACAATTTCGTA-ATGTAA
1 TTATCACAATTTCATAGATG--A
*
18809 TTATCAAAATTTCATAGGATGA
1 TTATCACAATTTCATA-GATGA
18831 TTATCACAATTT
1 TTATCACAATTT
18843 TATTTCATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 26 0.90
24 3 0.10
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (21 bp):
TTATCACAATTTCATAGATGA
Found at i:20402 original size:17 final size:17
Alignment explanation
Indices: 20380--20416 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
20370 CAATATCTGC
20380 TTTAAACTGTTTCTTAT
1 TTTAAACTGTTTCTTAT
*
20397 TTTAAACTTTTTCTTAT
1 TTTAAACTGTTTCTTAT
20414 TTT
1 TTT
20417 GTTTCTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.11, G:0.03, T:0.65
Consensus pattern (17 bp):
TTTAAACTGTTTCTTAT
Found at i:21789 original size:17 final size:16
Alignment explanation
Indices: 21737--21785 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
21727 CACCCTCCAA
*
21737 ATCACTAGTGATCTAAG
1 ATCACCAGTGATC-AAG
*
21754 ATCAGCAGTGATGCAAG
1 ATCACCAGTGAT-CAAG
*
21771 ATCACCGGTGATCAA
1 ATCACCAGTGATCAA
21786 AGATTACTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 3 0.11
17 23 0.85
18 1 0.04
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.22
Consensus pattern (16 bp):
ATCACCAGTGATCAAG
Found at i:22207 original size:17 final size:16
Alignment explanation
Indices: 22167--22209 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
22157 CGTGTAATCT
*
22167 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
*
22183 TTGCATCACTGGTGATT
1 TTG-ATCACTGGTGATC
22200 TTAGATCACT
1 TT-GATCACT
22210 AATGATCTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 3 0.13
17 19 0.83
18 1 0.04
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:24114 original size:11 final size:11
Alignment explanation
Indices: 24098--24122 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
24088 TGCGCCAAAT
24098 AAAAAAGAAAA
1 AAAAAAGAAAA
24109 AAAAAAGAAAA
1 AAAAAAGAAAA
24120 AAA
1 AAA
24123 GAAAAACCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:26505 original size:34 final size:34
Alignment explanation
Indices: 26439--26523 Score: 125
Period size: 34 Copynumber: 2.4 Consensus size: 34
26429 TTCCTCTATC
*
26439 AGTTGAACTTCTATCATTTTTTTTCTCCTTAGGGAA
1 AGTTGAACTTCTAT--TTGTTTTTCTCCTTAGGGAA
* *
26475 AGTTGAACCTCTATTTGTTTTTCTCTTTAGGGAA
1 AGTTGAACTTCTATTTGTTTTTCTCCTTAGGGAA
26509 AGTTGAACTTCTATT
1 AGTTGAACTTCTATT
26524 ATTAATTGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
34 32 0.71
36 13 0.29
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.47
Consensus pattern (34 bp):
AGTTGAACTTCTATTTGTTTTTCTCCTTAGGGAA
Found at i:29332 original size:15 final size:15
Alignment explanation
Indices: 29314--29355 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
29304 TGGAAACTTC
*
29314 TTCGATTGTCTCAG-A
1 TTCGATTATCTC-GTA
29329 TTCGATTATCTCGTA
1 TTCGATTATCTCGTA
*
29344 TTCGATTTTCTC
1 TTCGATTATCTC
29356 TTCATTCATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 1 0.04
15 23 0.96
ACGTcount: A:0.17, C:0.21, G:0.14, T:0.48
Consensus pattern (15 bp):
TTCGATTATCTCGTA
Found at i:33296 original size:28 final size:29
Alignment explanation
Indices: 33265--33328 Score: 76
Period size: 31 Copynumber: 2.2 Consensus size: 29
33255 TATGGGATTT
*
33265 ATTTGTTCCAAAA-AAAGTTAAGGGGCCA
1 ATTTGTCCCAAAAGAAAGTTAAGGGGCCA
* *
33293 ATTTGTCCCAAAATGGATAGTTAAGGGGCTA
1 ATTTGTCCCAAAA--GAAAGTTAAGGGGCCA
33324 ATTTG
1 ATTTG
33329 GGTATTAAGC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 12 0.40
31 18 0.60
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.30
Consensus pattern (29 bp):
ATTTGTCCCAAAAGAAAGTTAAGGGGCCA
Found at i:38241 original size:18 final size:19
Alignment explanation
Indices: 38208--38243 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
38198 TGAAGATTTA
38208 TTGAAGATAAATTGAAGAT
1 TTGAAGATAAATTGAAGAT
*
38227 TTGAAGAT-GATTGAAGA
1 TTGAAGATAAATTGAAGA
38244 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.25, T:0.31
Consensus pattern (19 bp):
TTGAAGATAAATTGAAGAT
Found at i:38782 original size:21 final size:21
Alignment explanation
Indices: 38753--38794 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
38743 GCCTACTTAG
*
38753 AATTGGAGATAATTTTCAGCA
1 AATTAGAGATAATTTTCAGCA
38774 AATTAGAGATAATTTTCAGCA
1 AATTAGAGATAATTTTCAGCA
38795 CTATAAATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (21 bp):
AATTAGAGATAATTTTCAGCA
Done.