Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008481.1 Corchorus capsularis cultivar CVL-1 contig08502, 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: 61341
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2347 original size:30 final size:29
Alignment explanation
Indices: 2251--2351 Score: 112
Period size: 29 Copynumber: 3.4 Consensus size: 29
2241 TAATCTACTA
** * *
2251 TTTTGCCCCCTGAACTTGTAGCGTTTAGACG
1 TTTTGCCCCCTGAACTTCAATC--TTGGACG
* *
2282 TTTTGCCCCCCGAACTTCAATCTTGGACA
1 TTTTGCCCCCTGAACTTCAATCTTGGACG
*
2311 TTTTGCCCCCTGAACTTCAATTTTGGGACG
1 TTTTGCCCCCTGAACTTCAATCTT-GGACG
2341 TTTTGCCCCCT
1 TTTTGCCCCCT
2352 CAACCTAACG
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
29 27 0.45
30 15 0.25
31 18 0.30
ACGTcount: A:0.16, C:0.31, G:0.18, T:0.36
Consensus pattern (29 bp):
TTTTGCCCCCTGAACTTCAATCTTGGACG
Found at i:2488 original size:13 final size:13
Alignment explanation
Indices: 2470--2496 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2460 TGGTCTGACA
2470 TGGCAATGCCACG
1 TGGCAATGCCACG
2483 TGGCAATGCCACG
1 TGGCAATGCCACG
2496 T
1 T
2497 CAGCAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.30, G:0.30, T:0.19
Consensus pattern (13 bp):
TGGCAATGCCACG
Found at i:2577 original size:29 final size:30
Alignment explanation
Indices: 2519--2598 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
2509 GGAGCCGGTT
*
2519 AAGTTGAGGGGGCAAAACGTCCCAAAATTG
1 AAGTTCAGGGGGCAAAACGTCCCAAAATTG
* *
2549 AAGTTCAGGGGGCAAAATGT-CCAAGATTG
1 AAGTTCAGGGGGCAAAACGTCCCAAAATTG
2578 AAGTTC-GGGGGACAAAACGTC
1 AAGTTCAGGGGG-CAAAACGTC
2599 TAAATGCTAC
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
28 5 0.11
29 21 0.48
30 18 0.41
ACGTcount: A:0.35, C:0.16, G:0.31, T:0.17
Consensus pattern (30 bp):
AAGTTCAGGGGGCAAAACGTCCCAAAATTG
Found at i:12960 original size:2 final size:2
Alignment explanation
Indices: 12953--12985 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
12943 AATATAGTGT
12953 TA TA TA TA TA TA TA TA TA TA TA TA -A TA CTA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA T
12986 TGGGTGACGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:20850 original size:11 final size:11
Alignment explanation
Indices: 20830--20864 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
20820 TTGACAGCAC
20830 AACAAAAACAA
1 AACAAAAACAA
*
20841 AACGAAAACAA
1 AACAAAAACAA
20852 AACAAAAACAA
1 AACAAAAACAA
20863 AA
1 AA
20865 AACAGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:25742 original size:12 final size:12
Alignment explanation
Indices: 25725--25749 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25715 GTACTGCCTC
25725 ATTAAATTGAGA
1 ATTAAATTGAGA
25737 ATTAAATTGAGA
1 ATTAAATTGAGA
25749 A
1 A
25750 GTTACGTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (12 bp):
ATTAAATTGAGA
Found at i:26952 original size:16 final size:16
Alignment explanation
Indices: 26931--26964 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
26921 TTTTTTGGCA
26931 TCCATTTCTTCCTAGT
1 TCCATTTCTTCCTAGT
26947 TCCATTTCTTCCTAGT
1 TCCATTTCTTCCTAGT
26963 TC
1 TC
26965 TTACTAGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.12, C:0.32, G:0.06, T:0.50
Consensus pattern (16 bp):
TCCATTTCTTCCTAGT
Found at i:38347 original size:2 final size:2
Alignment explanation
Indices: 38340--38366 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
38330 GAGTAGAAGA
38340 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
38367 AAAATTATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:47932 original size:59 final size:59
Alignment explanation
Indices: 47865--48056 Score: 375
Period size: 59 Copynumber: 3.3 Consensus size: 59
47855 CCTTGATTGT
*
47865 TTTTAATCAATGTTTAAGGTTTTTAATTAATTGCTTCTAAACCCTAAACCCTTAATTAC
1 TTTTAATCAATGTTTAAGGCTTTTAATTAATTGCTTCTAAACCCTAAACCCTTAATTAC
47924 TTTTAATCAATGTTTAAGGCTTTTAATTAATTGCTTCTAAACCCTAAACCCTTAATTAC
1 TTTTAATCAATGTTTAAGGCTTTTAATTAATTGCTTCTAAACCCTAAACCCTTAATTAC
47983 TTTTAATCAATGTTTAAGGCTTTTAATTAATTGCTTCTAAACCCTAAACCCTTAATTAC
1 TTTTAATCAATGTTTAAGGCTTTTAATTAATTGCTTCTAAACCCTAAACCCTTAATTAC
48042 TTTTAATCAATGTTT
1 TTTTAATCAATGTTT
48057 CTCTCGTTGT
Statistics
Matches: 132, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
59 132 1.00
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.44
Consensus pattern (59 bp):
TTTTAATCAATGTTTAAGGCTTTTAATTAATTGCTTCTAAACCCTAAACCCTTAATTAC
Found at i:49267 original size:17 final size:17
Alignment explanation
Indices: 49247--49292 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
49237 ACAGCACAAT
*
49247 AAATAAATTTAAAAATA
1 AAATAAATTTAAAAAGA
49264 AAATAAA--TAAAAAGA
1 AAATAAATTTAAAAAGA
**
49279 AACCAAATTTAAAA
1 AAATAAATTTAAAA
49293 GGACTGACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 12 0.50
17 12 0.50
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.22
Consensus pattern (17 bp):
AAATAAATTTAAAAAGA
Found at i:50812 original size:33 final size:33
Alignment explanation
Indices: 50775--50859 Score: 102
Period size: 31 Copynumber: 2.6 Consensus size: 33
50765 ATGTACCAAT
* * *
50775 AAGTGATATGTGACACGCTACGTGTACAAAAAA
1 AAGTGACATATGACACGCCACGTGTACAAAAAA
*
50808 AAGTGACATATGTCACGCCACGTGTAC--AAAA
1 AAGTGACATATGACACGCCACGTGTACAAAAAA
* *
50839 AAGTGACACATGGCACGCCAC
1 AAGTGACATATGACACGCCAC
50860 TTGCATCAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 23 0.50
33 23 0.50
ACGTcount: A:0.39, C:0.22, G:0.21, T:0.18
Consensus pattern (33 bp):
AAGTGACATATGACACGCCACGTGTACAAAAAA
Found at i:50842 original size:31 final size:31
Alignment explanation
Indices: 50760--50859 Score: 101
Period size: 31 Copynumber: 3.2 Consensus size: 31
50750 GACGTGGCAT
* * * * *
50760 GCCACATGTACCAATAAGTGATATGTGACAC
1 GCCACGTGTACAAAAAAGTGACATATGACAC
* *
50791 GCTACGTGTACAAAAAAAAGTGACATATGTCAC
1 GCCACGTGTAC--AAAAAAGTGACATATGACAC
* *
50824 GCCACGTGTACAAAAAAGTGACACATGGCAC
1 GCCACGTGTACAAAAAAGTGACATATGACAC
50855 GCCAC
1 GCCAC
50860 TTGCATCAAA
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
31 32 0.56
33 25 0.44
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (31 bp):
GCCACGTGTACAAAAAAGTGACATATGACAC
Found at i:50871 original size:31 final size:31
Alignment explanation
Indices: 50805--50907 Score: 109
Period size: 31 Copynumber: 3.3 Consensus size: 31
50795 CGTGTACAAA
* * * *
50805 AAAAAGTGACATATGTCACGCCACGTGTA-C
1 AAAAAGTGACACATGGCACGCCACATGCATC
*
50835 AAAAAAGTGACACATGGCACGCCACTTGCATC
1 -AAAAAGTGACACATGGCACGCCACATGCATC
* * * *
50867 AAAAAGTGAAACATGGCATGCAACATGCTTC
1 AAAAAGTGACACATGGCACGCCACATGCATC
50898 AAAAAGTGAC
1 AAAAAGTGAC
50908 CCGTGGCAAG
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
31 60 0.98
32 1 0.02
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.17
Consensus pattern (31 bp):
AAAAAGTGACACATGGCACGCCACATGCATC
Found at i:51279 original size:5 final size:5
Alignment explanation
Indices: 51263--51313 Score: 86
Period size: 5 Copynumber: 10.4 Consensus size: 5
51253 ACTTTAGAAC
*
51263 ATTAT A-TAT ATTAT ATTAT ATTAT ATTAT ATTGT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
51312 AT
1 AT
51314 ATGTTATGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
4 4 0.09
5 39 0.91
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:52813 original size:17 final size:16
Alignment explanation
Indices: 52791--52829 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
52781 CGCAAAACAC
52791 AAAAAAAGAA-AATAATT
1 AAAAAAA-AATAATAA-T
52808 AAAAAAAAATAATAAT
1 AAAAAAAAATAATAAT
52824 AAAAAA
1 AAAAAA
52830 TTGAAAAGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (16 bp):
AAAAAAAAATAATAAT
Found at i:52827 original size:13 final size:14
Alignment explanation
Indices: 52793--52830 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
52783 CAAAACACAA
52793 AAAAAGAAAATAATT
1 AAAAA-AAAATAATT
52808 AAAAAAAAATAA-T
1 AAAAAAAAATAATT
*
52821 AATAAAAAAT
1 AAAAAAAAAT
52831 TGAAAAGGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.45
14 7 0.32
15 5 0.23
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (14 bp):
AAAAAAAAATAATT
Found at i:52939 original size:13 final size:13
Alignment explanation
Indices: 52923--52952 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
52913 TCGTCTCTTT
52923 CTTTCTCTCTCCA
1 CTTTCTCTCTCCA
*
52936 CTTTCTCTCTCTA
1 CTTTCTCTCTCCA
52949 CTTT
1 CTTT
52953 GGTCTCATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.40, G:0.00, T:0.53
Consensus pattern (13 bp):
CTTTCTCTCTCCA
Found at i:53107 original size:17 final size:16
Alignment explanation
Indices: 53082--53116 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
53072 GCTCTGTTCC
53082 TTTTTTTTTATATAGTT
1 TTTTTTTTTAT-TAGTT
53099 TTTTGTTTTTATTAGTT
1 TTTT-TTTTTATTAGTT
53116 T
1 T
53117 CGGTTTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.14, C:0.00, G:0.09, T:0.77
Consensus pattern (16 bp):
TTTTTTTTTATTAGTT
Found at i:60837 original size:28 final size:28
Alignment explanation
Indices: 60805--60865 Score: 122
Period size: 28 Copynumber: 2.2 Consensus size: 28
60795 CAAGCTATCT
60805 TCAAAATTATGTAGATAACTGTCTGAAC
1 TCAAAATTATGTAGATAACTGTCTGAAC
60833 TCAAAATTATGTAGATAACTGTCTGAAC
1 TCAAAATTATGTAGATAACTGTCTGAAC
60861 TCAAA
1 TCAAA
60866 TTCTGAGTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (28 bp):
TCAAAATTATGTAGATAACTGTCTGAAC
Found at i:61324 original size:2 final size:2
Alignment explanation
Indices: 61312--61340 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
61302 GCCCAATCGG
61312 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
61341 A
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.