Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011845.1 Corchorus olitorius cultivar O-4 contig11878, 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: 31051
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4799 original size:21 final size:21
Alignment explanation
Indices: 4773--4821 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
4763 GTCTAATATT
4773 AACCTAAGCTTGGCAACACTA
1 AACCTAAGCTTGGCAACACTA
4794 AACCTAAGCTTGGCAACACTA
1 AACCTAAGCTTGGCAACACTA
4815 AACCTAA
1 AACCTAA
4822 TAAACGGTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.41, C:0.29, G:0.12, T:0.18
Consensus pattern (21 bp):
AACCTAAGCTTGGCAACACTA
Found at i:5284 original size:41 final size:42
Alignment explanation
Indices: 5194--5295 Score: 113
Period size: 40 Copynumber: 2.5 Consensus size: 42
5184 AAACTGAATT
*
5194 GGATCTTTCCCTAAATTG--AAAACCTTAAACAAACTTGATG
1 GGATCTTTCCCTAAATTGAAAAAAACTTAAACAAACTTGATG
* ** * *
5234 GGATATTTCCCTAAATTGAAAAAAACTTTGA-AGACTTGGTG
1 GGATCTTTCCCTAAATTGAAAAAAACTTAAACAAACTTGATG
*
5275 GGATCTTTCCC-AATTTGAAAA
1 GGATCTTTCCCTAAATTGAAAA
5296 TCTTTGAAAG
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
40 26 0.50
41 18 0.35
42 8 0.15
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (42 bp):
GGATCTTTCCCTAAATTGAAAAAAACTTAAACAAACTTGATG
Found at i:8441 original size:41 final size:39
Alignment explanation
Indices: 8400--8491 Score: 91
Period size: 41 Copynumber: 2.3 Consensus size: 39
8390 TCTATAAACA
*
8400 AAGACCCAA-ATATATTTAAAACCCATCATATAAAAGCAAC
1 AAGACCCAACATA-AATTAAAACCCATCATA-AAAAGCAAC
* *
8440 AAGGCCCAAGCATAAATTAAAATCCATCATAAAAAG--AC
1 AAGACCCAA-CATAAATTAAAACCCATCATAAAAAGCAAC
*
8478 AAGATCCAAGCATA
1 AAGACCCAA-CATA
8492 CAAACTAAAG
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
38 14 0.31
40 13 0.29
41 15 0.33
42 3 0.07
ACGTcount: A:0.52, C:0.22, G:0.09, T:0.17
Consensus pattern (39 bp):
AAGACCCAACATAAATTAAAACCCATCATAAAAAGCAAC
Found at i:8489 original size:38 final size:40
Alignment explanation
Indices: 8415--8491 Score: 104
Period size: 38 Copynumber: 1.9 Consensus size: 40
8405 CCAAATATAT
*
8415 TTAAAACCCATCATATAAAAGCAACAAGGCCCAAGCATAAA
1 TTAAAACCCATCATATAAAAG-AACAAGACCCAAGCATAAA
* *
8456 TTAAAATCCATCATA-AAAAG-ACAAGATCCAAGCATA
1 TTAAAACCCATCATATAAAAGAACAAGACCCAAGCATA
8492 CAAACTAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
38 14 0.42
40 5 0.15
41 14 0.42
ACGTcount: A:0.52, C:0.22, G:0.09, T:0.17
Consensus pattern (40 bp):
TTAAAACCCATCATATAAAAGAACAAGACCCAAGCATAAA
Found at i:8544 original size:19 final size:19
Alignment explanation
Indices: 8482--8545 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
8472 AAAGACAAGA
* *
8482 TCCAAGCATACAAACTAAAG
1 TCCAAACATA-AATCTAAAG
* *
8502 CCCAAAAATAAAT-TAAGAG
1 TCCAAACATAAATCTAA-AG
*
8521 GCCAAACATAAATCTAAAG
1 TCCAAACATAAATCTAAAG
8540 TCCAAA
1 TCCAAA
8546 TAGGAAAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
18 3 0.09
19 22 0.63
20 10 0.29
ACGTcount: A:0.53, C:0.22, G:0.09, T:0.16
Consensus pattern (19 bp):
TCCAAACATAAATCTAAAG
Found at i:19155 original size:183 final size:183
Alignment explanation
Indices: 18847--19221 Score: 723
Period size: 183 Copynumber: 2.0 Consensus size: 183
18837 GTGCTAGTAT
18847 AAATAGAGAGTTTCTTTATAGGATTTTGTATGCTTGGAGAAAAGATGTAGACTAAAGGTTAGATT
1 AAATAGAGAGTTTCTTTATAGGATTTTGTATGCTTGGAGAAAAGATGTAGACTAAAGGTTAGATT
* *
18912 TGGGCGGAGACACCCCATAGGACAAAAGGATGGTCCTTATGGGTGTGTGTGATTGTTTGGTTTGA
66 TGGGAGGAGACACCCCATAGAACAAAAGGATGGTCCTTATGGGTGTGTGTGATTGTTTGGTTTGA
*
18977 TGTTTGGTTTGTTGATGTGATTGTTGGTTTGTAGAGACCGAACGGGAGTGCTC
131 TGTTTGGTATGTTGATGTGATTGTTGGTTTGTAGAGACCGAACGGGAGTGCTC
19030 AAATAGAGAGTTTCTTTATAGGATTTTGTATGCTTGGAGAAAAGATGTAGACTAAAGGTTAGATT
1 AAATAGAGAGTTTCTTTATAGGATTTTGTATGCTTGGAGAAAAGATGTAGACTAAAGGTTAGATT
19095 TGGGAGGAGACACCCCATAGAACAAAAGGATGGTCCTTATGGGTGTGTGTGATTGTTTGGTTTGA
66 TGGGAGGAGACACCCCATAGAACAAAAGGATGGTCCTTATGGGTGTGTGTGATTGTTTGGTTTGA
19160 TGTTTGGTATGTTGATGTGATTGTTGGTTTGTAGAGACCGAACGGGAGTGCTC
131 TGTTTGGTATGTTGATGTGATTGTTGGTTTGTAGAGACCGAACGGGAGTGCTC
19213 AAATAGAGA
1 AAATAGAGA
19222 CCGAGCGAGA
Statistics
Matches: 189, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
183 189 1.00
ACGTcount: A:0.26, C:0.09, G:0.31, T:0.34
Consensus pattern (183 bp):
AAATAGAGAGTTTCTTTATAGGATTTTGTATGCTTGGAGAAAAGATGTAGACTAAAGGTTAGATT
TGGGAGGAGACACCCCATAGAACAAAAGGATGGTCCTTATGGGTGTGTGTGATTGTTTGGTTTGA
TGTTTGGTATGTTGATGTGATTGTTGGTTTGTAGAGACCGAACGGGAGTGCTC
Found at i:19225 original size:25 final size:25
Alignment explanation
Indices: 19191--19239 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
19181 TGTTGGTTTG
*
19191 TAGAGACCGAACGGGAGTGCTCAAA
1 TAGAGACCGAACGAGAGTGCTCAAA
* *
19216 TAGAGACCGAGCGAGAGTGTTCAA
1 TAGAGACCGAACGAGAGTGCTCAA
19240 GATTGTTTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.18, G:0.33, T:0.14
Consensus pattern (25 bp):
TAGAGACCGAACGAGAGTGCTCAAA
Found at i:20149 original size:128 final size:131
Alignment explanation
Indices: 19923--20175 Score: 354
Period size: 128 Copynumber: 1.9 Consensus size: 131
19913 CATTATTTAA
19923 ACTTTTATAGATTTACTCAACTAAAAAAATCTATTTTTATTTAATTAAATCTAATATCCTTATAA
1 ACTTTTATAGATTTACTCAACTAAAAAAATCTATTTTTATTTAATT-AA-CTAATATCCTTATAA
* *
19988 CTATTTAATTTTTACCATTTTACTATTTTAATT-AAAAAACTTATATATATTAGAATTTTTTAAA
64 CTATTTAATTTTTACCATTTTACTAATTTAATTAAAAAAACTTAGATATATTAGAATTTTTTAAA
20052 TAT
129 TAT
* * * * * *
20055 ACTTTTATTGTTTTACTCAACT-AAAAACTTTATTTTTTATTTAATT-A-TAATATTCTTATACC
1 ACTTTTATAGATTTACTCAACTAAAAAAATCTA-TTTTTATTTAATTAACTAATATCCTTATAAC
*
20117 TAATTT-ATTTTTATCATTTTACTAATTTAATTAAAAAAACTTAGATATATTAGAATTTT
65 T-ATTTAATTTTTACCATTTTACTAATTTAATTAAAAAAACTTAGATATATTAGAATTTT
20176 AAAAATATGT
Statistics
Matches: 109, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
128 38 0.35
129 29 0.27
130 1 0.01
131 8 0.07
132 33 0.30
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.50
Consensus pattern (131 bp):
ACTTTTATAGATTTACTCAACTAAAAAAATCTATTTTTATTTAATTAACTAATATCCTTATAACT
ATTTAATTTTTACCATTTTACTAATTTAATTAAAAAAACTTAGATATATTAGAATTTTTTAAATA
T
Found at i:27684 original size:2 final size:2
Alignment explanation
Indices: 27677--27721 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
27667 GCTTCCAGGT
27677 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
27719 AC A
1 AC A
27722 TATATATATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:27944 original size:13 final size:13
Alignment explanation
Indices: 27926--27952 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
27916 AATTAAGGGT
27926 GATTTTGGTTGGG
1 GATTTTGGTTGGG
27939 GATTTTGGTTGGG
1 GATTTTGGTTGGG
27952 G
1 G
27953 TGATCTTGGC
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:0.07, C:0.00, G:0.48, T:0.44
Consensus pattern (13 bp):
GATTTTGGTTGGG
Found at i:28189 original size:45 final size:44
Alignment explanation
Indices: 28125--28260 Score: 202
Period size: 45 Copynumber: 3.0 Consensus size: 44
28115 ATTGATCGAA
28125 ATTGATAGATTAAGTGTCAAATTGATAAAAAAAAATAAGATAATG
1 ATTGATAGATTAAGTGTCAAATTGAT-AAAAAAAATAAGATAATG
*
28170 ATTGATAGATTAAGTGTCAAATTGAT-AAAAAAACAAGATAATG
1 ATTGATAGATTAAGTGTCAAATTGATAAAAAAAATAAGATAATG
* *
28213 AACTCATTTAGATTAAGTGTCAAATTGATAAAAAAAATAAGATAATG
1 -ATTGA--TAGATTAAGTGTCAAATTGATAAAAAAAATAAGATAATG
28260 A
1 A
28261 ACTCATTTGC
Statistics
Matches: 83, Mismatches: 4, Indels: 7
0.88 0.04 0.07
Matches are distributed among these distances:
43 16 0.19
44 3 0.04
45 26 0.31
46 22 0.27
47 16 0.19
ACGTcount: A:0.52, C:0.04, G:0.15, T:0.29
Consensus pattern (44 bp):
ATTGATAGATTAAGTGTCAAATTGATAAAAAAAATAAGATAATG
Found at i:28227 original size:46 final size:47
Alignment explanation
Indices: 28130--28268 Score: 214
Period size: 47 Copynumber: 3.0 Consensus size: 47
28120 TCGAAATTGA
* *
28130 TAGATTAAGTGTCAAATTGATAAAAAAAAATAAGATAATG-ATTGA--
1 TAGATTAAGTGTCAAATTGAT-AAAAAAAATAAGATAATGAACTCATT
*
28175 TAGATTAAGTGTCAAATTGAT-AAAAAAACAAGATAATGAACTCATT
1 TAGATTAAGTGTCAAATTGATAAAAAAAATAAGATAATGAACTCATT
28221 TAGATTAAGTGTCAAATTGATAAAAAAAATAAGATAATGAACTCATT
1 TAGATTAAGTGTCAAATTGATAAAAAAAATAAGATAATGAACTCATT
28268 T
1 T
28269 GCTCGATTAT
Statistics
Matches: 86, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
43 16 0.19
44 3 0.03
45 21 0.24
46 21 0.24
47 25 0.29
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.29
Consensus pattern (47 bp):
TAGATTAAGTGTCAAATTGATAAAAAAAATAAGATAATGAACTCATT
Found at i:30116 original size:49 final size:48
Alignment explanation
Indices: 30058--30186 Score: 163
Period size: 49 Copynumber: 2.7 Consensus size: 48
30048 TTACATTTCC
** * *
30058 TGCACTTTTTCTCAATTTTTACTACGAAATTGAACTTTT-ATTTTTACT
1 TGCACTTTTTCTCAATTTTTAAGACAAAATTGAACTTTTAATTTTCA-T
*
30106 TGCACCTTTTTCTCAATTTTTAAGACAAAATTGATCTTTTAATTTTCAT
1 TGCA-CTTTTTCTCAATTTTTAAGACAAAATTGAACTTTTAATTTTCAT
* *
30155 TGCACTTTTTATCAATTTTT-TGACAAAATTGA
1 TGCACTTTTTCTCAATTTTTAAGACAAAATTGA
30187 TTGGCACGCT
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
47 11 0.15
48 19 0.26
49 36 0.50
50 6 0.08
ACGTcount: A:0.28, C:0.16, G:0.07, T:0.50
Consensus pattern (48 bp):
TGCACTTTTTCTCAATTTTTAAGACAAAATTGAACTTTTAATTTTCAT
Found at i:30769 original size:18 final size:18
Alignment explanation
Indices: 30726--30772 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
30716 GCAAATCGTG
*
30726 CCGCACCAAGTGGCTGCA
1 CCGCACCAAGTGGCCGCA
**
30744 CCATACCATA-TGGCCGCA
1 CCGCACCA-AGTGGCCGCA
30762 CCGCACCAAGT
1 CCGCACCAAGT
30773 TGCCACACTT
Statistics
Matches: 22, Mismatches: 5, Indels: 4
0.71 0.16 0.13
Matches are distributed among these distances:
17 1 0.05
18 20 0.91
19 1 0.05
ACGTcount: A:0.26, C:0.40, G:0.21, T:0.13
Consensus pattern (18 bp):
CCGCACCAAGTGGCCGCA
Done.