Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023913.1 Corchorus olitorius cultivar O-4 contig23946, 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: 71615
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:1419 original size:3 final size:3
Alignment explanation
Indices: 1407--1446 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
1397 AGCGCCAACT
*
1407 TTA TTA -TA TTA TTA TTA TTA TTA -TA TTA TTA -CA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1447 ATATGCATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
2 5 0.16
3 27 0.84
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1420 original size:8 final size:8
Alignment explanation
Indices: 1407--1448 Score: 66
Period size: 8 Copynumber: 5.1 Consensus size: 8
1397 AGCGCCAACT
1407 TTATTATA
1 TTATTATA
1415 TTATTATTA
1 TTATTA-TA
1424 TTATTATA
1 TTATTATA
*
1432 TTATTACA
1 TTATTATA
1440 TTATTATA
1 TTATTATA
1448 T
1 T
1449 ATGCATTTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
8 23 0.74
9 8 0.26
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (8 bp):
TTATTATA
Found at i:4490 original size:1 final size:1
Alignment explanation
Indices: 4484--4519 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
4474 CCTACTTGAA
4484 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4520 CTGGCAGTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:13352 original size:21 final size:21
Alignment explanation
Indices: 13328--13384 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
13318 GAACCCTATT
* *
13328 GGATTCAAGTGGTACAGAATA
1 GGATTTAAGTGGTACAAAATA
13349 GGATTTAAGTGGTACAAAATA
1 GGATTTAAGTGGTACAAAATA
13370 GGATTTAAGTGGTAC
1 GGATTTAAGTGGTAC
13385 TAGGGTTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.37, C:0.07, G:0.28, T:0.28
Consensus pattern (21 bp):
GGATTTAAGTGGTACAAAATA
Found at i:14061 original size:11 final size:11
Alignment explanation
Indices: 14047--14080 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
14037 TAAAGGAAAA
14047 AGCTAGGAAGG
1 AGCTAGGAAGG
14058 AGCTAGGAAGG
1 AGCTAGGAAGG
14069 AGCTAGGAAGG
1 AGCTAGGAAGG
14080 A
1 A
14081 TTCTACTAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.38, C:0.09, G:0.44, T:0.09
Consensus pattern (11 bp):
AGCTAGGAAGG
Found at i:20472 original size:11 final size:11
Alignment explanation
Indices: 20458--20491 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
20448 TAAAGGAAAA
20458 AGCTAGGAAGG
1 AGCTAGGAAGG
20469 AGCTAGGAAGG
1 AGCTAGGAAGG
20480 AGCTAGGAAGG
1 AGCTAGGAAGG
20491 A
1 A
20492 TCCTACTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.38, C:0.09, G:0.44, T:0.09
Consensus pattern (11 bp):
AGCTAGGAAGG
Found at i:22551 original size:30 final size:30
Alignment explanation
Indices: 22515--22577 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
22505 TCTTCAAGGG
*
22515 GGAGGGAGTGATGCGCCCAAGG-CTTATCAT
1 GGAGGGAATGATGCG-CCAAGGACTTATCAT
22545 GGAGGGAATGATGCGCCAAGGACTTATCAT
1 GGAGGGAATGATGCGCCAAGGACTTATCAT
22575 GGA
1 GGA
22578 CTTGAAGATG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 6 0.19
30 25 0.81
ACGTcount: A:0.27, C:0.17, G:0.37, T:0.19
Consensus pattern (30 bp):
GGAGGGAATGATGCGCCAAGGACTTATCAT
Found at i:47080 original size:13 final size:12
Alignment explanation
Indices: 47057--47103 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
47047 AAGTTTATTG
47057 ATAATATATAAT
1 ATAATATATAAT
47069 ATAATAATATAAT
1 ATAAT-ATATAAT
* *
47082 ATAACAT-TATT
1 ATAATATATAAT
47093 ATCAATATATA
1 AT-AATATATA
47104 TAAAGATTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAATATATAAT
Found at i:55684 original size:14 final size:13
Alignment explanation
Indices: 55659--55694 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
55649 GCCCAGCAGG
55659 AAAAAGAAAGAAA
1 AAAAAGAAAGAAA
55672 AAAAAGAAGAGAAA
1 AAAAAGAA-AGAAA
*
55686 GAAAAGAAA
1 AAAAAGAAA
55695 AGGGGAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAGAAA
Found at i:55771 original size:12 final size:12
Alignment explanation
Indices: 55740--55802 Score: 56
Period size: 12 Copynumber: 5.1 Consensus size: 12
55730 AATTGAAAGG
55740 AAAGAAA-AGAAA
1 AAAGAAAGAG-AA
*
55752 AAAAAAAGAGAA
1 AAAGAAAGAGAA
*
55764 AAAGAAAGGGAA
1 AAAGAAAGAGAA
*
55776 AAAGGAAATAAGAA
1 AAA-GAAA-GAGAA
*
55790 AAATAAAGAGAA
1 AAAGAAAGAGAA
55802 A
1 A
55803 TTTGAGAATA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
12 26 0.63
13 9 0.22
14 6 0.15
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (12 bp):
AAAGAAAGAGAA
Found at i:55778 original size:13 final size:13
Alignment explanation
Indices: 55740--55802 Score: 51
Period size: 13 Copynumber: 5.0 Consensus size: 13
55730 AATTGAAAGG
55740 AAAGAAA-AGAAA
1 AAAGAAAGAGAAA
*
55752 AAAAAAAGAG-AA
1 AAAGAAAGAGAAA
*
55764 AAAGAAAGGGAAA
1 AAAGAAAGAGAAA
* *
55777 AAGGAAATA-AGAA
1 AAAGAAAGAGA-AA
*
55790 AAATAAAGAGAAA
1 AAAGAAAGAGAAA
55803 TTTGAGAATA
Statistics
Matches: 38, Mismatches: 9, Indels: 7
0.70 0.17 0.13
Matches are distributed among these distances:
12 17 0.45
13 20 0.53
14 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (13 bp):
AAAGAAAGAGAAA
Found at i:58624 original size:5 final size:5
Alignment explanation
Indices: 58614--58650 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
58604 TGGGTCTTTC
58614 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TA
58651 TTTTTATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAATA
Found at i:59351 original size:3 final size:3
Alignment explanation
Indices: 59345--59408 Score: 119
Period size: 3 Copynumber: 21.3 Consensus size: 3
59335 TAATAATGTT
*
59345 TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
59393 TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA T
59409 ATATACATAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:62245 original size:10 final size:10
Alignment explanation
Indices: 62229--62264 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
62219 TGTTTTATCC
62229 AAATATCCAT
1 AAATATCCAT
*
62239 CAATATCCAT
1 AAATATCCAT
*
62249 AAATATCCGT
1 AAATATCCAT
62259 AAATAT
1 AAATAT
62265 TCAAATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.31
Consensus pattern (10 bp):
AAATATCCAT
Found at i:62726 original size:17 final size:18
Alignment explanation
Indices: 62704--62745 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
62694 TTCATATCAG
* *
62704 ATTTTTTA-TTAGAAAAT
1 ATTTTTTATTTAAAAAAA
*
62721 ATTTTTCATTTAAAAAAA
1 ATTTTTTATTTAAAAAAA
62739 ATTTTTT
1 ATTTTTT
62746 GAAAAAAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (18 bp):
ATTTTTTATTTAAAAAAA
Found at i:62752 original size:15 final size:15
Alignment explanation
Indices: 62732--62764 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
62722 TTTTTCATTT
*
62732 AAAAAAAATTTTTTG
1 AAAAAAAATTCTTTG
62747 AAAAAAAATTCTTTG
1 AAAAAAAATTCTTTG
62762 AAA
1 AAA
62765 TACAAAACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (15 bp):
AAAAAAAATTCTTTG
Found at i:67953 original size:16 final size:16
Alignment explanation
Indices: 67929--67980 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
67919 CTGGACCAAG
*
67929 GCGCGCCAGGCCCAGC
1 GCGCACCAGGCCCAGC
67945 GCGCACCAGGCCCAGC
1 GCGCACCAGGCCCAGC
* *
67961 GC-CAGCTGGCCCAGC
1 GCGCACCAGGCCCAGC
67976 GCGCA
1 GCGCA
67981 GCTGGTCTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
15 13 0.41
16 19 0.59
ACGTcount: A:0.15, C:0.48, G:0.35, T:0.02
Consensus pattern (16 bp):
GCGCACCAGGCCCAGC
Found at i:67984 original size:16 final size:16
Alignment explanation
Indices: 67937--67985 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
67927 AGGCGCGCCA
* *
67937 GGCCCAGCGCGCACCA
1 GGCCCAGCGCGCAGCT
67953 GGCCCAGCGC-CAGCT
1 GGCCCAGCGCGCAGCT
67968 GGCCCAGCGCGCAGCT
1 GGCCCAGCGCGCAGCT
67984 GG
1 GG
67986 TCTTGCGCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 13 0.43
16 17 0.57
ACGTcount: A:0.14, C:0.45, G:0.37, T:0.04
Consensus pattern (16 bp):
GGCCCAGCGCGCAGCT
Found at i:70629 original size:2 final size:2
Alignment explanation
Indices: 70622--70656 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
70612 AGAACAAGTC
70622 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
70657 CTCCTGTCGG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:70841 original size:13 final size:13
Alignment explanation
Indices: 70823--70847 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
70813 TTCAATGTTC
70823 TAAATATTATTTA
1 TAAATATTATTTA
70836 TAAATATTATTT
1 TAAATATTATTT
70848 GGAATTCCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATATTATTTA
Found at i:70959 original size:39 final size:39
Alignment explanation
Indices: 70901--70977 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
70891 CAATCAACTT
70901 TGGACAAATGTCAACAGGAGAAAAGTCAAATACTGAGCA
1 TGGACAAATGTCAACAGGAGAAAAGTCAAATACTGAGCA
* * *
70940 TGGACAAATGTCAGA-AGGAGAAGAGTCAAGTATTGAGC
1 TGGACAAATGTCA-ACAGGAGAAAAGTCAAATACTGAGC
70978 GTACAACAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 33 0.97
40 1 0.03
ACGTcount: A:0.43, C:0.13, G:0.27, T:0.17
Consensus pattern (39 bp):
TGGACAAATGTCAACAGGAGAAAAGTCAAATACTGAGCA
Done.