Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020115.1 Corchorus olitorius cultivar O-4 contig20148, 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: 28392
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2074 original size:7 final size:7
Alignment explanation
Indices: 2062--2112 Score: 50
Period size: 7 Copynumber: 7.0 Consensus size: 7
2052 TGATCTCTCC
2062 TTCTTTT
1 TTCTTTT
2069 TTCTTTTT
1 TTC-TTTT
*
2077 TTTTTTT
1 TTCTTTT
2084 TTCTAATTT
1 TTCT--TTT
2093 TTCTTTT
1 TTCTTTT
*
2100 GTCTTTT
1 TTCTTTT
2107 TT-TTTT
1 TTCTTTT
2113 CTCATGAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
6 4 0.11
7 20 0.54
8 6 0.16
9 7 0.19
ACGTcount: A:0.04, C:0.10, G:0.02, T:0.84
Consensus pattern (7 bp):
TTCTTTT
Found at i:2085 original size:15 final size:15
Alignment explanation
Indices: 2065--2112 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
2055 TCTCTCCTTC
2065 TTTTTTCTTTTTTTT
1 TTTTTTCTTTTTTTT
* *
2080 TTTTTTCTAATTTTTC
1 TTTTTTCT-TTTTTTT
*
2096 TTTTGTCTTTTTTTT
1 TTTTTTCTTTTTTTT
2111 TT
1 TT
2113 CTCATGAGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 15 0.56
16 12 0.44
ACGTcount: A:0.04, C:0.08, G:0.02, T:0.85
Consensus pattern (15 bp):
TTTTTTCTTTTTTTT
Found at i:3068 original size:52 final size:52
Alignment explanation
Indices: 2999--3255 Score: 417
Period size: 52 Copynumber: 5.0 Consensus size: 52
2989 GGGAACTTTC
* * *
2999 CCTAAATTGAACGCTTTGAAAACCTGATGGGAACTTTCCCACTTTGAAAAGA
1 CCTAAATTGAACACTTTGAAAACTTGTTGGGAACTTTCCCACTTTGAAAAGA
* * *
3051 CCTAAATTGGACACTTTGAAGACTTGTTGGGAACTTTCCCACTTCGAAAAGA
1 CCTAAATTGAACACTTTGAAAACTTGTTGGGAACTTTCCCACTTTGAAAAGA
3103 CCTAAATTGAACACTTTGAAAACTTGTTGGGAACTTTCCCACTTTGAAAAGA
1 CCTAAATTGAACACTTTGAAAACTTGTTGGGAACTTTCCCACTTTGAAAAGA
*
3155 CCTAAACTGAACACTTTGAAAACTTGTTGGGAAC-TTCCCACTTTGAAAAGA
1 CCTAAATTGAACACTTTGAAAACTTGTTGGGAACTTTCCCACTTTGAAAAGA
* * *
3206 CCAAAATTGAACACTTTAAAAATTTGTTGGGAACTTTCCCACTTTGAAAA
1 CCTAAATTGAACACTTTGAAAACTTGTTGGGAACTTTCCCACTTTGAAAA
3256 CTTTGAAGGA
Statistics
Matches: 190, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
51 47 0.25
52 143 0.75
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (52 bp):
CCTAAATTGAACACTTTGAAAACTTGTTGGGAACTTTCCCACTTTGAAAAGA
Found at i:6795 original size:37 final size:36
Alignment explanation
Indices: 6709--6831 Score: 113
Period size: 36 Copynumber: 3.2 Consensus size: 36
6699 TTTGTGTCTG
*
6709 CGTTTTTAATCTGAAAAAAAAAAAATTTCTTTTCAGTTTTC
1 CGTTTTT--TCTGAAAAAAAAAAAATTT-TTGT--GTTTTC
6750 TGCGTTTTTTCTGAAAAAAAAAAAATTTTTGTGTTTTC
1 --CGTTTTTTCTGAAAAAAAAAAAATTTTTGTGTTTTC
** * *
6788 CGTTTTTTCTTTAAAAAAAAAATTGTTTTGT-TTCTTG
1 CGTTTTTTCTGAAAAAAAAAAAAT-TTTTGTGTT-TTC
6825 CGTTTTT
1 CGTTTTT
6832 AATTTGCGTT
Statistics
Matches: 73, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
36 23 0.32
37 15 0.21
38 6 0.08
40 3 0.04
41 19 0.26
43 7 0.10
ACGTcount: A:0.30, C:0.10, G:0.11, T:0.50
Consensus pattern (36 bp):
CGTTTTTTCTGAAAAAAAAAAAATTTTTGTGTTTTC
Found at i:8713 original size:5 final size:6
Alignment explanation
Indices: 8687--8726 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
8677 AACATGTTAA
** *
8687 TTTTCT TTTTAG TTTTGT TTTTCT TTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
8727 TGGATTTCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.03, C:0.10, G:0.05, T:0.82
Consensus pattern (6 bp):
TTTTCT
Found at i:9201 original size:16 final size:15
Alignment explanation
Indices: 9159--9206 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
9149 CTCCATTTAC
*
9159 TTTTTCTTTGCATTG-
1 TTTTGCTTTG-ATTGA
*
9174 TTTTGCTCTGATTGA
1 TTTTGCTTTGATTGA
9189 TTATTGCTTTGATTGA
1 TT-TTGCTTTGATTGA
9205 TT
1 TT
9207 GCCTATTCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 4 0.14
15 10 0.36
16 14 0.50
ACGTcount: A:0.12, C:0.10, G:0.17, T:0.60
Consensus pattern (15 bp):
TTTTGCTTTGATTGA
Found at i:9361 original size:129 final size:129
Alignment explanation
Indices: 9199--9456 Score: 516
Period size: 129 Copynumber: 2.0 Consensus size: 129
9189 TTATTGCTTT
9199 GATTGATTGCCTATTCCTTGATTTGAATTAGTTGTTTGTATTTCTTTTCTATGTTTTCTATGCTT
1 GATTGATTGCCTATTCCTTGATTTGAATTAGTTGTTTGTATTTCTTTTCTATGTTTTCTATGCTT
9264 TGATTTAGATCTTTATTATGACTTATGCTATGATTGCCATGATATATGCTTTGAATTGCTTGAA
66 TGATTTAGATCTTTATTATGACTTATGCTATGATTGCCATGATATATGCTTTGAATTGCTTGAA
9328 GATTGATTGCCTATTCCTTGATTTGAATTAGTTGTTTGTATTTCTTTTCTATGTTTTCTATGCTT
1 GATTGATTGCCTATTCCTTGATTTGAATTAGTTGTTTGTATTTCTTTTCTATGTTTTCTATGCTT
9393 TGATTTAGATCTTTATTATGACTTATGCTATGATTGCCATGATATATGCTTTGAATTGCTTGAA
66 TGATTTAGATCTTTATTATGACTTATGCTATGATTGCCATGATATATGCTTTGAATTGCTTGAA
9457 TTGCTTGATT
Statistics
Matches: 129, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
129 129 1.00
ACGTcount: A:0.21, C:0.12, G:0.16, T:0.51
Consensus pattern (129 bp):
GATTGATTGCCTATTCCTTGATTTGAATTAGTTGTTTGTATTTCTTTTCTATGTTTTCTATGCTT
TGATTTAGATCTTTATTATGACTTATGCTATGATTGCCATGATATATGCTTTGAATTGCTTGAA
Found at i:9652 original size:25 final size:25
Alignment explanation
Indices: 9618--9666 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
9608 TAGAGAGTCT
9618 GCATGCATCATAATCTTAAAATATG
1 GCATGCATCATAATCTTAAAATATG
9643 GCATGCATCATAATCTTAAAATAT
1 GCATGCATCATAATCTTAAAATAT
9667 ACCATAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (25 bp):
GCATGCATCATAATCTTAAAATATG
Found at i:17402 original size:22 final size:23
Alignment explanation
Indices: 17376--17421 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
17366 TCATCCGTCC
17376 TTTCATC-TTC-TTTTTCTTTTCT
1 TTTCATCATTCATTTTT-TTTTCT
17398 TTTCATCATTCATTTTTTTTTCT
1 TTTCATCATTCATTTTTTTTTCT
17421 T
1 T
17422 CCTGTTTGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.32
23 10 0.45
24 5 0.23
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.72
Consensus pattern (23 bp):
TTTCATCATTCATTTTTTTTTCT
Found at i:17527 original size:33 final size:34
Alignment explanation
Indices: 17488--17560 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 34
17478 AGGCCCGCGC
*
17488 GCTGCCCAGCTAGCCAGCAGCGCGGCACAGCG-T
1 GCTGCCCAGCTAGCCAGCAGCGCGGCACAACGCT
* * *
17521 GCTGCCCAGGTGGCCAGCAGCGCGGCCCAACGCT
1 GCTGCCCAGCTAGCCAGCAGCGCGGCACAACGCT
17555 GCTGCC
1 GCTGCC
17561 TGGCCTGGCA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
33 28 0.80
34 7 0.20
ACGTcount: A:0.15, C:0.41, G:0.34, T:0.10
Consensus pattern (34 bp):
GCTGCCCAGCTAGCCAGCAGCGCGGCACAACGCT
Found at i:22037 original size:17 final size:16
Alignment explanation
Indices: 22015--22050 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
22005 GGGTACAAAA
22015 ATAGTATATAAAAATAT
1 ATAGTATAT-AAAATAT
*
22032 ATAGTATATATAATAT
1 ATAGTATATAAAATAT
22048 ATA
1 ATA
22051 ATAGGAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.39
Consensus pattern (16 bp):
ATAGTATATAAAATAT
Found at i:26854 original size:1 final size:1
Alignment explanation
Indices: 26848--26879 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
26838 CCGAAAATTT
26848 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
26880 GCGGAATCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:28164 original size:98 final size:98
Alignment explanation
Indices: 28048--28227 Score: 308
Period size: 99 Copynumber: 1.8 Consensus size: 98
28038 ATAAATTTTT
* *
28048 AAATTAAAATGGTAAAAATAAAATAATTATAAA-ATATTGAATTTAATTAAATGAAAATAGAGTT
1 AAATTAAAATGGTAAAAATAAAATAATTATAAAGATATTAAATTTAATTAAATAAAAATAGAGTT
28112 TTTAGTAGAATAAAACTGTATATTTTGAAAAAA
66 TTTAGTAGAATAAAACTGTATATTTTGAAAAAA
* *
28145 AAATGTAAAATGGTAAAAATAAAGTAATTATAAAGATATTAAATTTAATTGAATAAAAATAGAGT
1 AAAT-TAAAATGGTAAAAATAAAATAATTATAAAGATATTAAATTTAATTAAATAAAAATAGAGT
28210 TTTTAGTAGAATAAAACT
65 TTTTAGTAGAATAAAACT
28228 ATAATAGTTA
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
97 4 0.05
98 28 0.36
99 45 0.58
ACGTcount: A:0.54, C:0.01, G:0.11, T:0.33
Consensus pattern (98 bp):
AAATTAAAATGGTAAAAATAAAATAATTATAAAGATATTAAATTTAATTAAATAAAAATAGAGTT
TTTAGTAGAATAAAACTGTATATTTTGAAAAAA
Found at i:28305 original size:32 final size:32
Alignment explanation
Indices: 28264--28324 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
28254 AAATATGTTT
*
28264 GAAAAATAAGGATATAATGGTCGATTCAATTA
1 GAAAAATAAGGATATAATAGTCGATTCAATTA
*
28296 GAAAAATAAGGGTATAATAGTCGATTCAA
1 GAAAAATAAGGATATAATAGTCGATTCAA
28325 AAGTTTTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.48, C:0.07, G:0.20, T:0.26
Consensus pattern (32 bp):
GAAAAATAAGGATATAATAGTCGATTCAATTA
Found at i:28355 original size:2 final size:2
Alignment explanation
Indices: 28348--28382 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
28338 CTCGTACTTT
28348 TA TA TA TA GTA 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 TA TA
28383 ATAATCAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Done.