Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020736.1 Corchorus olitorius cultivar O-4 contig20769, 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: 106424
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:655 original size:333 final size:332
Alignment explanation
Indices: 9--769 Score: 1158
Period size: 333 Copynumber: 2.3 Consensus size: 332
1 AAATTTTG
* *
9 AAAACTGACCCG-AAATTTTT-CNCCAGTTTTTGCCACAATACTCACAAAAAATATATAATTCAA
1 AAAACTGACCCGAAAATTTTTCCTCCATTTTTTGCCACAATACTCACAAAAAATATATAATTCAA
*
72 TGCCAAAATAATTGAAGGGTTTTCACGCTTCTAATATCGTCTTTCAAAATTATTCCAAATTAATT
66 TGCCAAAA-AATTGAAGGGTTTTTACGCTTCTAATATCGTCTTTCAAAATTATTCCAAATTAATT
* * * *
137 TTTTAACTAAAATCGAAACATGATTCAGATGCTAGCAAAAACAAATCCTTAAATCCATTGCGGCT
130 TTTCAACTAAAATCGAAACATGATTCAGATGCTAGCAAAAACAAATCATTAAACCCATTGCGACT
* * *
202 GAGATTTGGTTAGATGAATAAAGATATTTCAAGGAGTTTTGGAACAAAAAATAATGCAAAACTGA
195 GAGATTTGGTTAAATGAATAAAGATATTTCAAAGAGTCTTGGAACAAAAAATAATGCAAAACTGA
*
267 GCCGGGGCACCATAGCGCATTTTTAGGCAAAAATCATGATGTAACGTACACGATTTCGGCTAAAA
260 GCCGGGGCACCATAGCGCATTTTTAGCCAAAAATCATGATGTAACGTACACGATTTCGGCTAAAA
332 TTTTTGAA
325 TTTTTGAA
*
340 AAAACTAACCCGAAAATCTTTTCCTCCATTTTTTGCCACAATACTCACAAAAAATATATAATTCA
1 AAAACTGACCCGAAAAT-TTTTCCTCCATTTTTTGCCACAATACTCACAAAAAATATATAATTCA
* * *
405 ATGCCAGAAAGATTGAAGGGTTTTTTACGCTTCTAATATCGTTTTTCAAAATTTTTCCAAATT-A
65 ATGCCA-AAAAATTGAAGGG-TTTTTACGCTTCTAATATCGTCTTTCAAAATTATTCCAAATTAA
* * *
469 TTTTTCAAGT-AAATCGGAACATGATTCAGATGCTCGCAAAAACAAATCATTAAACCCATTGCGA
128 TTTTTCAACTAAAATCGAAACATGATTCAGATGCTAGCAAAAACAAATCATTAAACCCATTGCGA
* * *
533 CTGAGATTTGGTTAAATGAATAAAGATATTTCAAAGAGTCTTGGCACTAAAAATCATGCAAAACT
193 CTGAGATTTGGTTAAATGAATAAAGATATTTCAAAGAGTCTTGGAACAAAAAATAATGCAAAACT
* * * *
598 GAGCCGTGGTC-CCATAGCGCTTTTTTAGCCAAAAATCATGATGGTTA-GTATACGATTTCGGCT
258 GAGCCG-GGGCACCATAGCGCATTTTTAGCCAAAAATCATGAT-GTAACGTACACGATTTCGGCT
661 AAAATTTTTGAA
321 AAAATTTTTGAA
*
673 AAAACTGACCCGAAAATTCTTTCCTCCATTTTTTGCCACAATACTCAC-ATAAATATATAATTCA
1 AAAACTGACCCGAAAATT-TTTCCTCCATTTTTTGCCACAATACTCACAAAAAATATATAATTCA
737 ATGCCAAAAATATTGAAGGGATTTTTACGCTTC
65 ATGCCAAAAA-ATTGAAGGG-TTTTTACGCTTC
770 AAAAAAACTT
Statistics
Matches: 392, Mismatches: 29, Indels: 17
0.89 0.07 0.04
Matches are distributed among these distances:
331 14 0.04
332 47 0.12
333 219 0.56
334 70 0.18
335 42 0.11
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (332 bp):
AAAACTGACCCGAAAATTTTTCCTCCATTTTTTGCCACAATACTCACAAAAAATATATAATTCAA
TGCCAAAAAATTGAAGGGTTTTTACGCTTCTAATATCGTCTTTCAAAATTATTCCAAATTAATTT
TTCAACTAAAATCGAAACATGATTCAGATGCTAGCAAAAACAAATCATTAAACCCATTGCGACTG
AGATTTGGTTAAATGAATAAAGATATTTCAAAGAGTCTTGGAACAAAAAATAATGCAAAACTGAG
CCGGGGCACCATAGCGCATTTTTAGCCAAAAATCATGATGTAACGTACACGATTTCGGCTAAAAT
TTTTGAA
Found at i:884 original size:58 final size:59
Alignment explanation
Indices: 793--907 Score: 223
Period size: 58 Copynumber: 2.0 Consensus size: 59
783 GAAATAAACT
793 TTTTTCTGATGGTTTTTTCACTTTTCACAGCAGCTCTTTCCACACCTCCGGATATCTGG
1 TTTTTCTGATGGTTTTTTCACTTTTCACAGCAGCTCTTTCCACACCTCCGGATATCTGG
852 TTTTT-TGATGGTTTTTTCACTTTTCACAGCAGCTCTTTCCACACCTCCGGATATCT
1 TTTTTCTGATGGTTTTTTCACTTTTCACAGCAGCTCTTTCCACACCTCCGGATATCT
908 TGTGCCAAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
58 51 0.91
59 5 0.09
ACGTcount: A:0.16, C:0.27, G:0.14, T:0.43
Consensus pattern (59 bp):
TTTTTCTGATGGTTTTTTCACTTTTCACAGCAGCTCTTTCCACACCTCCGGATATCTGG
Found at i:13548 original size:13 final size:13
Alignment explanation
Indices: 13532--13558 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13522 CTCTTTAATC
13532 TTCTTCTTTTGCT
1 TTCTTCTTTTGCT
13545 TTCTTCTTTTGCT
1 TTCTTCTTTTGCT
13558 T
1 T
13559 ACATTTTCTA
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:0.00, C:0.22, G:0.07, T:0.70
Consensus pattern (13 bp):
TTCTTCTTTTGCT
Found at i:14245 original size:89 final size:90
Alignment explanation
Indices: 14078--14290 Score: 231
Period size: 89 Copynumber: 2.4 Consensus size: 90
14068 ACTCGAAGTG
* * * * *
14078 GCACCACTATGCCTTTATGCATAATAGGAATGCCACCACATTGTGCCTTTTGCAGCATAATAAGA
1 GCACCATTATACCTTGATGCATAATAGGAATG-CACCACA-TGTGCCTTTTACAGCAAAATAAGA
*
14143 ATTCCCATTACCAACCTT-TATTT-GGAT
64 ATTCCCATTACCAA-CTTCT-TTTCAGAT
* * *
14170 GCACCATTATACCTTGATGTATAATAGGAATGCATCAC-TGTGCCTTTTACTGCAAAATAA-AAT
1 GCACCATTATACCTTGATGCATAATAGGAATGCACCACATGTGCCTTTTACAGCAAAATAAGAAT
*
14233 TTCC-TGTCACCAACTTCTTTTCAGAT
66 TCCCAT-T-ACCAACTTCTTTTCAGAT
*
14259 GCACCATTATACCTTG-TACATAATAGGAATGC
1 GCACCATTATACCTTGATGCATAATAGGAATGC
14291 CATGGTTGTG
Statistics
Matches: 105, Mismatches: 12, Indels: 12
0.81 0.09 0.09
Matches are distributed among these distances:
87 1 0.01
88 27 0.26
89 44 0.42
91 5 0.05
92 28 0.27
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (90 bp):
GCACCATTATACCTTGATGCATAATAGGAATGCACCACATGTGCCTTTTACAGCAAAATAAGAAT
TCCCATTACCAACTTCTTTTCAGAT
Found at i:14791 original size:105 final size:105
Alignment explanation
Indices: 14609--14924 Score: 560
Period size: 105 Copynumber: 3.0 Consensus size: 105
14599 TGTATAATAG
14609 GAATGCCAACATTTGCTCCATTTACTGCATAATAAGAATTCTCATTACAAACTTTAATTCAGACG
1 GAATGCCAACATTTGCTCCATTTACTGCATAATAAGAATTCTCATTACAAACTTTAATTCAGACG
* *
14674 GGATCATTATACCTTAATGTATAATAGGAATGCCACTGTT
66 GCACCATTATACCTTAATGTATAATAGGAATGCCACTGTT
*
14714 GAATGCCAACATTTGCTCCATTTACTGCATAATAAGAATTCTCATTACAAACTTTAATTCAGATG
1 GAATGCCAACATTTGCTCCATTTACTGCATAATAAGAATTCTCATTACAAACTTTAATTCAGACG
14779 GCACCATTATACCTTAATGTATAATAGGAATGCCACTGTT
66 GCACCATTATACCTTAATGTATAATAGGAATGCCACTGTT
* * *
14819 GAATGCCAACATTTGCTCCGTTTACTGCATAATAAGAATGCTCATTACAAACTTTGATTCAGACG
1 GAATGCCAACATTTGCTCCATTTACTGCATAATAAGAATTCTCATTACAAACTTTAATTCAGACG
**
14884 ATACCATTATACCTTAATGTATAATAGGAATGCCACTGTT
66 GCACCATTATACCTTAATGTATAATAGGAATGCCACTGTT
14924 G
1 G
14925 TGAGTTTAGC
Statistics
Matches: 202, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
105 202 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.33
Consensus pattern (105 bp):
GAATGCCAACATTTGCTCCATTTACTGCATAATAAGAATTCTCATTACAAACTTTAATTCAGACG
GCACCATTATACCTTAATGTATAATAGGAATGCCACTGTT
Found at i:27875 original size:29 final size:29
Alignment explanation
Indices: 27831--27892 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
27821 AACTTGTATG
*
27831 ATTTTGACGTTTTGCCCCCTAAACTTT-A
1 ATTTTGACATTTTGCCCCCTAAACTTTCA
* *
27859 ATTTTGGACATTTTGCCCCTTGAACTTTCA
1 ATTTT-GACATTTTGCCCCCTAAACTTTCA
27889 ATTT
1 ATTT
27893 GAAGCCATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 5 0.17
29 19 0.66
30 5 0.17
ACGTcount: A:0.21, C:0.23, G:0.11, T:0.45
Consensus pattern (29 bp):
ATTTTGACATTTTGCCCCCTAAACTTTCA
Found at i:31455 original size:15 final size:15
Alignment explanation
Indices: 31422--31454 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
31412 TCACCCCCAC
*
31422 AAAATAATATAAAAT
1 AAAATAATATAAAAA
31437 AAAATAAT-TAAAAA
1 AAAATAATATAAAAA
31451 AAAA
1 AAAA
31455 AGTATAGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAATAATATAAAAA
Found at i:38462 original size:22 final size:22
Alignment explanation
Indices: 38437--38480 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
38427 TCCTCACCCT
*
38437 CAATTCCTTGCAT-TTCCTTCTC
1 CAATTCCCT-CATCTTCCTTCTC
38459 CAATTCCCTCATCTTCCTTCTC
1 CAATTCCCTCATCTTCCTTCTC
38481 TCCTCTGCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.14, C:0.41, G:0.02, T:0.43
Consensus pattern (22 bp):
CAATTCCCTCATCTTCCTTCTC
Found at i:39950 original size:31 final size:31
Alignment explanation
Indices: 39912--39975 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
39902 GCTGGAACCA
39912 TGATTGAATTATTACGTTTTCGTTTGTAAAG
1 TGATTGAATTATTACGTTTTCGTTTGTAAAG
39943 TGATTGAATTATTACGTTTTCGTTTGTAAAG
1 TGATTGAATTATTACGTTTTCGTTTGTAAAG
39974 TG
1 TG
39976 GGTTCATAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.25, C:0.06, G:0.20, T:0.48
Consensus pattern (31 bp):
TGATTGAATTATTACGTTTTCGTTTGTAAAG
Found at i:65966 original size:92 final size:92
Alignment explanation
Indices: 65862--66045 Score: 359
Period size: 92 Copynumber: 2.0 Consensus size: 92
65852 GTGAAATTTG
65862 AACACAATACATCACAATTCAGACATAAATACACTTACCAATTGAGCTAACAATAGGTGCATTTA
1 AACACAATACATCACAATTCAGACATAAATACACTTACCAATTGAGCTAACAATAGGTGCATTTA
65927 TTATTAATATTTGCTACTCATGAACAT
66 TTATTAATATTTGCTACTCATGAACAT
*
65954 AACACAATACATCACAATTCAGGCATAAATACACTTACCAATTGAGCTAACAATAGGTGCATTTA
1 AACACAATACATCACAATTCAGACATAAATACACTTACCAATTGAGCTAACAATAGGTGCATTTA
66019 TTATTAATATTTGCTACTCATGAACAT
66 TTATTAATATTTGCTACTCATGAACAT
66046 GGTATTGAAA
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 91 1.00
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (92 bp):
AACACAATACATCACAATTCAGACATAAATACACTTACCAATTGAGCTAACAATAGGTGCATTTA
TTATTAATATTTGCTACTCATGAACAT
Found at i:79087 original size:22 final size:22
Alignment explanation
Indices: 79059--79104 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
79049 TTTAGCAAAC
79059 TGCACAAGCGGATCTTGAAGGT
1 TGCACAAGCGGATCTTGAAGGT
*
79081 TGCACAAGCGGGTCTTGAAGGT
1 TGCACAAGCGGATCTTGAAGGT
79103 TG
1 TG
79105 ACATGTGTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.24, C:0.17, G:0.35, T:0.24
Consensus pattern (22 bp):
TGCACAAGCGGATCTTGAAGGT
Found at i:79294 original size:43 final size:43
Alignment explanation
Indices: 79233--79324 Score: 175
Period size: 43 Copynumber: 2.1 Consensus size: 43
79223 AGCAGTTAAA
*
79233 ATTTGAAGCCAATCATTCTAGCTGAGAAACTCTGCCAGGGAGC
1 ATTTGTAGCCAATCATTCTAGCTGAGAAACTCTGCCAGGGAGC
79276 ATTTGTAGCCAATCATTCTAGCTGAGAAACTCTGCCAGGGAGC
1 ATTTGTAGCCAATCATTCTAGCTGAGAAACTCTGCCAGGGAGC
79319 ATTTGT
1 ATTTGT
79325 TTAGGAACTA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (43 bp):
ATTTGTAGCCAATCATTCTAGCTGAGAAACTCTGCCAGGGAGC
Found at i:82962 original size:88 final size:88
Alignment explanation
Indices: 82813--82997 Score: 318
Period size: 88 Copynumber: 2.1 Consensus size: 88
82803 AAAACCCCAA
*
82813 GGGCCCAAGGCGCCCCACGCAAGAGATGGGATTTGATCCCAGGCCCAAGGGAAATCCAATTACTC
1 GGGCCCAAGGCGCCCCACGCAAGAGATGGGATTTGATCCCAGGCCCAAGGGAAATCCAATTAATC
82878 TTTCAATTGAGGACTTAATCAAC
66 TTTCAATTGAGGACTTAATCAAC
*
82901 GGGCCCAAGGCGCCTCACGCAAGAGATGGGATTTGATCCCAGGCCCACA-GGAAATCCAATTAAT
1 GGGCCCAAGGCGCCCCACGCAAGAGATGGGATTTGATCCCAGGCCCA-AGGGAAATCCAATTAAT
* *
82965 CTTTCAATTGAGGGCTTAATCAAT
65 CTTTCAATTGAGGACTTAATCAAC
82989 GGGCCCAAG
1 GGGCCCAAG
82998 CCCAATAAAA
Statistics
Matches: 92, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
88 91 0.99
89 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.25, T:0.19
Consensus pattern (88 bp):
GGGCCCAAGGCGCCCCACGCAAGAGATGGGATTTGATCCCAGGCCCAAGGGAAATCCAATTAATC
TTTCAATTGAGGACTTAATCAAC
Found at i:95817 original size:68 final size:65
Alignment explanation
Indices: 95738--95871 Score: 196
Period size: 68 Copynumber: 2.0 Consensus size: 65
95728 CTTTCAAGAA
* *
95738 TGAGCTTAAAAGAAGGAGAAGCAGCTGCATCCACAATAAGAAAGAGTGCCTCAATAATTGCAAGA
1 TGAGCTTAAAAGAAGGAGAAACAGCTGCATCCAC---AAGAAAGAGTGCCTCAATAACTGCAAGA
95803 AGT
63 AGT
** *
95806 TGAGCTTAAAAGAAGGAGAAACAGCTGCATTGACAAGAGAGAGTGCCTCAATAACTGCAAGAAGT
1 TGAGCTTAAAAGAAGGAGAAACAGCTGCATCCACAAGAAAGAGTGCCTCAATAACTGCAAGAAGT
95871 T
1 T
95872 CTGCTTAATT
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
65 30 0.49
68 31 0.51
ACGTcount: A:0.42, C:0.16, G:0.25, T:0.18
Consensus pattern (65 bp):
TGAGCTTAAAAGAAGGAGAAACAGCTGCATCCACAAGAAAGAGTGCCTCAATAACTGCAAGAAGT
Found at i:95878 original size:65 final size:66
Alignment explanation
Indices: 95740--95879 Score: 192
Period size: 65 Copynumber: 2.1 Consensus size: 66
95730 TTCAAGAATG
* *
95740 AGCTTAAAAGAAGGAGAAGCAGCTGCATCCACAATAAGAAAGAGTGCCTCAATAATTGCAAGAAG
1 AGCTTAAAAGAAGGAGAAACAGCTGCATCCAC-A-AAGAAAGAGTGCCTCAATAACTGCAAGAAG
*
95805 TTG
64 TTC
** *
95808 AGCTTAAAAGAAGGAGAAACAGCTGCATTGAC-AAGAGAGAGTGCCTCAATAACTGCAAGAAGTT
1 AGCTTAAAAGAAGGAGAAACAGCTGCATCCACAAAGAAAGAGTGCCTCAATAACTGCAAGAAGTT
95872 C
66 C
*
95873 TGCTTAA
1 AGCTTAA
95880 TTAGAGTCGG
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
65 36 0.55
68 29 0.45
ACGTcount: A:0.41, C:0.16, G:0.24, T:0.19
Consensus pattern (66 bp):
AGCTTAAAAGAAGGAGAAACAGCTGCATCCACAAAGAAAGAGTGCCTCAATAACTGCAAGAAGTT
C
Found at i:99315 original size:20 final size:20
Alignment explanation
Indices: 99287--99332 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
99277 CACTACATTC
*
99287 TCGAATCACTCACCTTTGTG
1 TCGATTCACTCACCTTTGTG
99307 TCGATTCACTCACCTTTGTG
1 TCGATTCACTCACCTTTGTG
99327 TCGATT
1 TCGATT
99333 TTGAAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.17, C:0.28, G:0.15, T:0.39
Consensus pattern (20 bp):
TCGATTCACTCACCTTTGTG
Found at i:101659 original size:2 final size:2
Alignment explanation
Indices: 101652--101734 Score: 91
Period size: 2 Copynumber: 42.0 Consensus size: 2
101642 AAATATAGTC
*
101652 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
101693 TGA -A TG TA -A AA TA GTC TA TA TA TA TA TA TA TA TA TA TA TA TA
1 T-A TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
101735 AATCATGTGC
Statistics
Matches: 69, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
1 3 0.04
2 65 0.94
3 1 0.01
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:105011 original size:2 final size:2
Alignment explanation
Indices: 105004--105030 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
104994 AATTAATTCC
105004 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
105031 AAGAGATTTA
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
Done.