Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019131.1 Corchorus olitorius cultivar O-4 contig19164, 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: 72319
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1730 original size:17 final size:17
Alignment explanation
Indices: 1710--1745 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1700 ATTGCATCAA
1710 GTTAGATTTTGCTACAT
1 GTTAGATTTTGCTACAT
1727 GTTAGATTTTGCTACAT
1 GTTAGATTTTGCTACAT
1744 GT
1 GT
1746 CATGTAACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.11, G:0.19, T:0.47
Consensus pattern (17 bp):
GTTAGATTTTGCTACAT
Found at i:3862 original size:16 final size:18
Alignment explanation
Indices: 3831--3865 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
3821 GTCGAAAACA
3831 TGATCATCTGCTTCCTTT
1 TGATCATCTGCTTCCTTT
3849 TGATC-TCT-CTTCCTTT
1 TGATCATCTGCTTCCTTT
3865 T
1 T
3866 TTGCCTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 3 0.18
18 5 0.29
ACGTcount: A:0.09, C:0.29, G:0.09, T:0.54
Consensus pattern (18 bp):
TGATCATCTGCTTCCTTT
Found at i:9747 original size:24 final size:24
Alignment explanation
Indices: 9715--9763 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
9705 GACTAAGGCT
9715 CCGTTTAGTAGAGCAGTGTGATAG
1 CCGTTTAGTAGAGCAGTGTGATAG
9739 CCGTTTAGTAGAGCAGTGTGATAG
1 CCGTTTAGTAGAGCAGTGTGATAG
9763 C
1 C
9764 GGTGTGTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.14, G:0.33, T:0.29
Consensus pattern (24 bp):
CCGTTTAGTAGAGCAGTGTGATAG
Found at i:32457 original size:2 final size:2
Alignment explanation
Indices: 32450--32495 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
32440 ACTTGGTCTA
32450 AT AT AT 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 AT AT AT
32492 AT AT
1 AT AT
32496 GAAGTAGAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36843 original size:15 final size:15
Alignment explanation
Indices: 36823--36853 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
36813 CTGATGGTGT
36823 ATTGTATAATTTGCC
1 ATTGTATAATTTGCC
36838 ATTGTATAATTTGCC
1 ATTGTATAATTTGCC
36853 A
1 A
36854 AAAGGAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (15 bp):
ATTGTATAATTTGCC
Found at i:51976 original size:61 final size:61
Alignment explanation
Indices: 51904--52062 Score: 309
Period size: 61 Copynumber: 2.6 Consensus size: 61
51894 TGTAGACTTG
*
51904 AATCAATAATATTTGTTTGATCGAGTGGAATGAGTTCAATGTCTTCATTGTAATTAGAATA
1 AATCAACAATATTTGTTTGATCGAGTGGAATGAGTTCAATGTCTTCATTGTAATTAGAATA
51965 AATCAACAATATTTGTTTGATCGAGTGGAATGAGTTCAATGTCTTCATTGTAATTAGAATA
1 AATCAACAATATTTGTTTGATCGAGTGGAATGAGTTCAATGTCTTCATTGTAATTAGAATA
52026 AATCAACAATATTTGTTTGATCGAGTGGAATGAGTTC
1 AATCAACAATATTTGTTTGATCGAGTGGAATGAGTTC
52063 TATATGCCAA
Statistics
Matches: 97, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
61 97 1.00
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (61 bp):
AATCAACAATATTTGTTTGATCGAGTGGAATGAGTTCAATGTCTTCATTGTAATTAGAATA
Found at i:54160 original size:14 final size:13
Alignment explanation
Indices: 54141--54179 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
54131 AAATTGTAAA
54141 ATTTAAAAAATTT
1 ATTTAAAAAATTT
* *
54154 CATTTAAGAAATAT
1 -ATTTAAAAAATTT
54168 ATTTAAAAAATT
1 ATTTAAAAAATT
54180 CTAATATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (13 bp):
ATTTAAAAAATTT
Found at i:54384 original size:127 final size:127
Alignment explanation
Indices: 54165--54423 Score: 346
Period size: 127 Copynumber: 2.0 Consensus size: 127
54155 ATTTAAGAAA
54165 TATATTTAAAAAATTCTAATATATATAAGTTCTTAAAATAAAATAATAAAATGGTAAAAATAAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTCTTAAAATAAAATAATAAAATGGTAAAAAT---A
* * *
54230 TAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAA
63 CA-GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATAAAA
54295 G
127 G
* * * *
54296 TATATTTAAAAAATTCTAATATATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT
1 TATATTTAAAAAATTC---TA-ATATATATAAGTTCTTAAAATAAAATAATAAAATGGTAAAAAT
*
54361 -CA-TA-AA-GATATTAGATTTAATTAAATAAAATTAGAGTTTTTAGTTGAATAAAACTATAAAA
62 ACAGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATAAAA
54422 G
127 G
54423 T
1 T
54424 TTAAACAATG
Statistics
Matches: 116, Mismatches: 8, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
127 54 0.47
128 2 0.02
129 2 0.02
131 17 0.15
134 2 0.02
135 39 0.34
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.37
Consensus pattern (127 bp):
TATATTTAAAAAATTCTAATATATATAAGTTCTTAAAATAAAATAATAAAATGGTAAAAATACAG
TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATAAAAG
Found at i:54762 original size:29 final size:29
Alignment explanation
Indices: 54729--54788 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
54719 CTATTCCCTT
54729 TAATCCTATATGTATAATCTATTAAACTC
1 TAATCCTATATGTATAATCTATTAAACTC
54758 TAATCCTATATGTATAATCTATTAAACTC
1 TAATCCTATATGTATAATCTATTAAACTC
54787 TA
1 TA
54789 CTGACTATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.38, C:0.17, G:0.03, T:0.42
Consensus pattern (29 bp):
TAATCCTATATGTATAATCTATTAAACTC
Found at i:58927 original size:24 final size:24
Alignment explanation
Indices: 58895--58945 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
58885 GATTGGATTA
58895 ACTCCAAATCAAATTCAATAGCTT
1 ACTCCAAATCAAATTCAATAGCTT
58919 ACTCCAAATCAAATTCAATAGCTT
1 ACTCCAAATCAAATTCAATAGCTT
58943 ACT
1 ACT
58946 GAGATTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.25, G:0.04, T:0.29
Consensus pattern (24 bp):
ACTCCAAATCAAATTCAATAGCTT
Found at i:59100 original size:64 final size:64
Alignment explanation
Indices: 58981--59106 Score: 200
Period size: 64 Copynumber: 2.0 Consensus size: 64
58971 TATCCGTTTC
*
58981 CGTCTTAATGATAAACGATATACGGTTAATTCTATTTGAACATGCCCGGCACAATACTTATATA
1 CGTCTTAATGATAAACGATATACGGTTAATTCTATTCGAACATGCCCGGCACAATACTTATATA
* * *
59045 CGTCTTAATGATAAACGATATACTGTTAATTCTATTCGAATA-GCCTCGGCCCAATACTTATA
1 CGTCTTAATGATAAACGATATACGGTTAATTCTATTCGAACATGCC-CGGCACAATACTTATA
59107 GAGATGAAAG
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
63 3 0.05
64 54 0.95
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (64 bp):
CGTCTTAATGATAAACGATATACGGTTAATTCTATTCGAACATGCCCGGCACAATACTTATATA
Found at i:72275 original size:35 final size:35
Alignment explanation
Indices: 72235--72306 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
72225 TTTCATCTGC
*
72235 AAACAACTTATCACAAAGAGAGAAAAAGAGAGAGA
1 AAACAACTTATCACAAAGAGAAAAAAAGAGAGAGA
*
72270 AAACAACTTATCACAGAGAGAAAAAAAGAGAGAGA
1 AAACAACTTATCACAAAGAGAAAAAAAGAGAGAGA
72305 AA
1 AA
72307 GAGATGGAGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.61, C:0.11, G:0.19, T:0.08
Consensus pattern (35 bp):
AAACAACTTATCACAAAGAGAAAAAAAGAGAGAGA
Found at i:72293 original size:33 final size:34
Alignment explanation
Indices: 72235--72302 Score: 111
Period size: 33 Copynumber: 2.0 Consensus size: 34
72225 TTTCATCTGC
*
72235 AAACAACTTATCACAAAGAGAGAAAAAGAGAGAGA
1 AAACAACTTATCAC-AAGAGAGAAAAAAAGAGAGA
72270 AAACAACTTATCAC-AGAGAGAAAAAAAGAGAGA
1 AAACAACTTATCACAAGAGAGAAAAAAAGAGAGA
72303 GAAAGAGATG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 18 0.56
35 14 0.44
ACGTcount: A:0.60, C:0.12, G:0.19, T:0.09
Consensus pattern (34 bp):
AAACAACTTATCACAAGAGAGAAAAAAAGAGAGA
Done.