Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013117.1 Corchorus olitorius cultivar O-4 contig13150, 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: 76483
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:6418 original size:37 final size:37
Alignment explanation
Indices: 6368--6486 Score: 176
Period size: 37 Copynumber: 3.3 Consensus size: 37
6358 CTATGACACA
6368 TAGCTTAAATATATAGCTTATCATGTAAATTCATCCT
1 TAGCTTAAATATATAGCTTATCATGTAAATTCATCCT
6405 TAGCTTAAATATATAGCTTATCATGTAAATTCAT-C-
1 TAGCTTAAATATATAGCTTATCATGTAAATTCATCCT
6440 ---CTTAAATATATAGCTTATCATGTAAATTCATCCAT
1 TAGCTTAAATATATAGCTTATCATGTAAATTCATCC-T
6475 CTAGCTATAAAT
1 -TAGCT-TAAAT
6487 TCACCCCGTA
Statistics
Matches: 74, Mismatches: 0, Indels: 13
0.85 0.00 0.15
Matches are distributed among these distances:
32 31 0.42
33 1 0.01
36 1 0.01
37 34 0.46
39 2 0.03
40 5 0.07
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (37 bp):
TAGCTTAAATATATAGCTTATCATGTAAATTCATCCT
Found at i:6444 original size:32 final size:32
Alignment explanation
Indices: 6371--6472 Score: 159
Period size: 32 Copynumber: 3.0 Consensus size: 32
6361 TGACACATAG
6371 CTTAAATATATAGCTTATCATGTAAATTCATCC
1 CTTAAATATATAGCTTATCATGTAAATTCAT-C
6404 TTAGCTTAAATATATAGCTTATCATGTAAATTCATC
1 ----CTTAAATATATAGCTTATCATGTAAATTCATC
6440 CTTAAATATATAGCTTATCATGTAAATTCATC
1 CTTAAATATATAGCTTATCATGTAAATTCATC
6472 C
1 C
6473 ATCTAGCTAT
Statistics
Matches: 65, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
32 33 0.51
36 1 0.02
37 31 0.48
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.40
Consensus pattern (32 bp):
CTTAAATATATAGCTTATCATGTAAATTCATC
Found at i:8405 original size:45 final size:44
Alignment explanation
Indices: 8355--8443 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 44
8345 ACGGAACAAA
*
8355 GTTTCCTAAGGGCAGGTAGGAAGCAATAACAAAATCCATTAAAAT
1 GTTTCCTAAGGGCAGGTAGGAA-CAATAACAAAATCCATAAAAAT
*
8400 GTTTCCTAAGGGCAGGTAGGAACAATTACAAAATCCATAAAAAT
1 GTTTCCTAAGGGCAGGTAGGAACAATAACAAAATCCATAAAAAT
8444 AATAGAAGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
44 20 0.48
45 22 0.52
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.22
Consensus pattern (44 bp):
GTTTCCTAAGGGCAGGTAGGAACAATAACAAAATCCATAAAAAT
Found at i:11846 original size:2 final size:2
Alignment explanation
Indices: 11839--11872 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
11829 TATTGAAACT
*
11839 AG AG AG AG A- AG AG AC AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
11873 TTTATAGATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.03, G:0.44, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16630 original size:21 final size:19
Alignment explanation
Indices: 16588--16644 Score: 78
Period size: 21 Copynumber: 2.9 Consensus size: 19
16578 GTTTAGTAAT
*
16588 TGTACATATGAGATTATAC
1 TGTACAAATGAGATTATAC
*
16607 TGTACAAATTAGATTAGTTAC
1 TGTACAAATGAGATTA--TAC
16628 TGTACAAATGAGATTAT
1 TGTACAAATGAGATTAT
16645 TAGAGCAGCG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 15 0.45
21 18 0.55
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.37
Consensus pattern (19 bp):
TGTACAAATGAGATTATAC
Found at i:18944 original size:40 final size:44
Alignment explanation
Indices: 18900--18983 Score: 134
Period size: 45 Copynumber: 1.9 Consensus size: 44
18890 AATTCCTATG
* *
18900 TAAT-ATAAATAATAACTAAAATACTTACATTAATTAAATGTAA
1 TAATAATACATAATAACTAAAACACTTACATTAATTAAATGTAA
18943 TAATAATACTATAATAACTAAAACACTTACATTAATTAAAT
1 TAATAATAC-ATAATAACTAAAACACTTACATTAATTAAAT
18984 TCTTAGGTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
43 4 0.11
44 3 0.08
45 30 0.81
ACGTcount: A:0.55, C:0.10, G:0.01, T:0.35
Consensus pattern (44 bp):
TAATAATACATAATAACTAAAACACTTACATTAATTAAATGTAA
Found at i:23193 original size:2 final size:2
Alignment explanation
Indices: 23186--23221 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
23176 CATCACCAGC
23186 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23222 GAAACTAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32770 original size:7 final size:7
Alignment explanation
Indices: 32758--32802 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
32748 AAAAACCATG
32758 AAAAATA
1 AAAAATA
32765 AAAAATA
1 AAAAATA
* *
32772 AGAAAGA
1 AAAAATA
32779 AAAAATA
1 AAAAATA
*
32786 AAAGATA
1 AAAAATA
*
32793 AAAAAGA
1 AAAAATA
32800 AAA
1 AAA
32803 GACCAACCAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (7 bp):
AAAAATA
Found at i:32784 original size:21 final size:21
Alignment explanation
Indices: 32758--32802 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
32748 AAAAACCATG
*
32758 AAAAATAAAAAATAAGAAAGA
1 AAAAATAAAAAATAAAAAAGA
*
32779 AAAAATAAAAGATAAAAAAGA
1 AAAAATAAAAAATAAAAAAGA
32800 AAA
1 AAA
32803 GACCAACCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (21 bp):
AAAAATAAAAAATAAAAAAGA
Found at i:34338 original size:193 final size:193
Alignment explanation
Indices: 34009--34389 Score: 708
Period size: 193 Copynumber: 2.0 Consensus size: 193
33999 AGAGCTTATT
*
34009 AAGCATTTTTTCCTTTTCGGCCTTATAAAGCTTTTTGCTCACCTTATTAATTTTTTTAATCTAAC
1 AAGCATTTTCTCCTTTTCGGCCTTATAAAGCTTTTTGCTCACCTTATTAATTTTTTTAATCTAAC
*
34074 CTTCTTAAGATTTTTAGTAACCGTATTGTGAATTTTAGAAGCCTTATTAAGTTTTTACTAACTTT
66 CTTCTTAAGATTTTTAATAACCGTATTGTGAATTTTAGAAGCCTTATTAAGTTTTTACTAACTTT
* * *
34139 AATTGTTTTTTCAGCACTCTTAGAGATTTTTTGTAACTTTGATAATTTTTAATAATACAAAAA
131 AATTGTTTTTTCAACACTCTTAGAGATTTTTAGTAACCTTGATAATTTTTAATAATACAAAAA
34202 AAGCATTTTCTCCTTTTCGGCCTTATAAAGCTTTTTGCTCACCTTATTAATTTTTTTAATCTAAC
1 AAGCATTTTCTCCTTTTCGGCCTTATAAAGCTTTTTGCTCACCTTATTAATTTTTTTAATCTAAC
*
34267 TTTCTTAAGATTTTTAATAACCGTATTGTGAATTTTAGAAGCCTTATTAAGTTTTTACTAACTTT
66 CTTCTTAAGATTTTTAATAACCGTATTGTGAATTTTAGAAGCCTTATTAAGTTTTTACTAACTTT
34332 AATTGTTTTTTCAACACTCTTAGAGATTTTTAGTAACCTTGATAATTTTTAATAATAC
131 AATTGTTTTTTCAACACTCTTAGAGATTTTTAGTAACCTTGATAATTTTTAATAATAC
34390 TTTTAGTAAC
Statistics
Matches: 182, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
193 182 1.00
ACGTcount: A:0.28, C:0.14, G:0.09, T:0.48
Consensus pattern (193 bp):
AAGCATTTTCTCCTTTTCGGCCTTATAAAGCTTTTTGCTCACCTTATTAATTTTTTTAATCTAAC
CTTCTTAAGATTTTTAATAACCGTATTGTGAATTTTAGAAGCCTTATTAAGTTTTTACTAACTTT
AATTGTTTTTTCAACACTCTTAGAGATTTTTAGTAACCTTGATAATTTTTAATAATACAAAAA
Found at i:34860 original size:21 final size:21
Alignment explanation
Indices: 34828--34874 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
34818 TGTTGTGAAC
* *
34828 TTTTTAATAACCATATTTA-A
1 TTTTTAAAAACCATATTAAGA
*
34848 TTTTTAAGAAACCCTATTAAGA
1 TTTTTAA-AAACCATATTAAGA
34870 TTTTT
1 TTTTT
34875 TTAGAGATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 7 0.32
21 9 0.41
22 6 0.27
ACGTcount: A:0.36, C:0.11, G:0.04, T:0.49
Consensus pattern (21 bp):
TTTTTAAAAACCATATTAAGA
Found at i:35158 original size:3 final size:3
Alignment explanation
Indices: 35150--35292 Score: 236
Period size: 3 Copynumber: 48.0 Consensus size: 3
35140 ACAAATTTTA
** *
35150 AAT AAT AAT AAT AAT AAT AAT AAT ACA- AAT TTT TA- AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT
35194 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
35242 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
35290 AAT
1 AAT
35293 GATGATGATG
Statistics
Matches: 133, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
2 2 0.02
3 130 0.98
4 1 0.01
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:43837 original size:6 final size:6
Alignment explanation
Indices: 43828--43859 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
43818 TATTTTTATT
43828 TTGGAA TTGGAA TTGGAA TTGGAA TTGGAA TT
1 TTGGAA TTGGAA TTGGAA TTGGAA TTGGAA TT
43860 ACTATAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.38
Consensus pattern (6 bp):
TTGGAA
Found at i:45915 original size:14 final size:14
Alignment explanation
Indices: 45896--45930 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
45886 ATTCGCTGAT
45896 GTGGCATGCGACAC
1 GTGGCATGCGACAC
45910 GTGGCATGCGACAC
1 GTGGCATGCGACAC
45924 GTGGCAT
1 GTGGCAT
45931 AAAAATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.20, C:0.26, G:0.37, T:0.17
Consensus pattern (14 bp):
GTGGCATGCGACAC
Found at i:45970 original size:15 final size:15
Alignment explanation
Indices: 45943--45976 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
45933 AAATTAAATA
45943 TTTTTATTATAATATT
1 TTTTTATTATAAT-TT
45959 TTTTTATT-TAATTT
1 TTTTTATTATAATTT
45973 TTTT
1 TTTT
45977 AATAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 4 0.22
16 8 0.44
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTATTATAATTT
Found at i:55528 original size:22 final size:22
Alignment explanation
Indices: 55503--55550 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
55493 CGGCCTGGCG
*
55503 CGGGGAATGGCCGAGTCATGAC
1 CGGGCAATGGCCGAGTCATGAC
* * *
55525 CGGGCTATGGCCTAGTCATGTC
1 CGGGCAATGGCCGAGTCATGAC
55547 CGGG
1 CGGG
55551 TGCCACCGAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.17, C:0.25, G:0.40, T:0.19
Consensus pattern (22 bp):
CGGGCAATGGCCGAGTCATGAC
Found at i:76305 original size:38 final size:38
Alignment explanation
Indices: 76262--76344 Score: 157
Period size: 38 Copynumber: 2.2 Consensus size: 38
76252 TCAATGCATC
*
76262 ATGATCGGAGTTGATTATCACCTTAGATCCCAGGATGT
1 ATGATCGGAGTAGATTATCACCTTAGATCCCAGGATGT
76300 ATGATCGGAGTAGATTATCACCTTAGATCCCAGGATGT
1 ATGATCGGAGTAGATTATCACCTTAGATCCCAGGATGT
76338 ATGATCG
1 ATGATCG
76345 AAACTTCTCC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (38 bp):
ATGATCGGAGTAGATTATCACCTTAGATCCCAGGATGT
Done.