Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022462.1 Corchorus olitorius cultivar O-4 contig22495, 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: 126731
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:7613 original size:22 final size:22
Alignment explanation
Indices: 7588--7630 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
7578 AAACATTTAA
7588 ATGAGAATCCAATCCAAACTAG
1 ATGAGAATCCAATCCAAACTAG
*
7610 ATGAGAATCTAATCCAAACTA
1 ATGAGAATCCAATCCAAACTA
7631 AGAAATTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.47, C:0.21, G:0.12, T:0.21
Consensus pattern (22 bp):
ATGAGAATCCAATCCAAACTAG
Found at i:7702 original size:35 final size:34
Alignment explanation
Indices: 7663--7730 Score: 100
Period size: 35 Copynumber: 2.0 Consensus size: 34
7653 CTTAACAAAC
*
7663 TATCAAACAAATTTTCCATGAGATTTGAAACCAAT
1 TATCAAACAAAATTTCCATGAGATTTG-AACCAAT
* *
7698 TATCAAACAAAATTTCCGTGTGATTTGAACCAA
1 TATCAAACAAAATTTCCATGAGATTTGAACCAA
7731 GGATCTAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 6 0.20
35 24 0.80
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (34 bp):
TATCAAACAAAATTTCCATGAGATTTGAACCAAT
Found at i:8037 original size:71 final size:71
Alignment explanation
Indices: 7916--8052 Score: 211
Period size: 71 Copynumber: 1.9 Consensus size: 71
7906 TGTTAATTCG
* * * *
7916 AGTTTTCACAAATTTTGGTAGAGAATCTGTAAGTTCGTCAATTTGGAAAAACTCCACGAAAAAAA
1 AGTTTTCACAAATTTTGATAGAGAATCTGTAAATTCGTCAATCTGAAAAAACTCCACGAAAAAAA
7981 AATCTT
66 AATCTT
* * *
7987 AGTTTTCACAAATTTTGATAGAGAATTTGTAAATTCGTCAATCTGAAAAAACTCTAGGAAAAAAA
1 AGTTTTCACAAATTTTGATAGAGAATCTGTAAATTCGTCAATCTGAAAAAACTCCACGAAAAAAA
8052 A
66 A
8053 TCCATATATC
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
71 59 1.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (71 bp):
AGTTTTCACAAATTTTGATAGAGAATCTGTAAATTCGTCAATCTGAAAAAACTCCACGAAAAAAA
AATCTT
Found at i:10274 original size:10 final size:10
Alignment explanation
Indices: 10259--10284 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
10249 AACATCTAAA
10259 ACCACAGAAT
1 ACCACAGAAT
10269 ACCACAGAAT
1 ACCACAGAAT
10279 ACCACA
1 ACCACA
10285 TAGAAAGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.35, G:0.08, T:0.08
Consensus pattern (10 bp):
ACCACAGAAT
Found at i:15963 original size:21 final size:23
Alignment explanation
Indices: 15923--15965 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
15913 CAACTAAAAT
*
15923 CTAATAATATTTGTTTGTATAAA
1 CTAATAATATTTGTTGGTATAAA
15946 CTAATAAT-TTT-TTGGTATAA
1 CTAATAATATTTGTTGGTATAA
15966 TTTGTATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 3 0.16
23 8 0.42
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49
Consensus pattern (23 bp):
CTAATAATATTTGTTGGTATAAA
Found at i:16993 original size:85 final size:85
Alignment explanation
Indices: 16850--17020 Score: 306
Period size: 85 Copynumber: 2.0 Consensus size: 85
16840 TATTTCATCC
* *
16850 GGTATTCAGGGCTTTGCCCTGACTAATTCAGATTCGACCCACGTCACGCACCTGGTTATGGTGGG
1 GGTATTCAGGGCTTTGCCCTGACTAATTCAGATCCAACCCACGTCACGCACCTGGTTATGGTGGG
16915 TGAGTCTCCCAACAGGGGCA
66 TGAGTCTCCCAACAGGGGCA
* *
16935 GGTATTCAGGGCTTTGTCCTGACTAATTCAGATCCAACCCACGTCACGTACCTGGTTATGGTGGG
1 GGTATTCAGGGCTTTGCCCTGACTAATTCAGATCCAACCCACGTCACGCACCTGGTTATGGTGGG
17000 TGAGTCTCCCAACAGGGGCA
66 TGAGTCTCCCAACAGGGGCA
17020 G
1 G
17021 CTGCGTAAAA
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 82 1.00
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.25
Consensus pattern (85 bp):
GGTATTCAGGGCTTTGCCCTGACTAATTCAGATCCAACCCACGTCACGCACCTGGTTATGGTGGG
TGAGTCTCCCAACAGGGGCA
Found at i:22200 original size:72 final size:72
Alignment explanation
Indices: 22083--22226 Score: 288
Period size: 72 Copynumber: 2.0 Consensus size: 72
22073 GATCTATTCC
22083 CTGTTCTTTCTTCAGGAGCACAGACATTCCCAAATGCAACTTTTGGTTGGGTCAACGTTAAAGAT
1 CTGTTCTTTCTTCAGGAGCACAGACATTCCCAAATGCAACTTTTGGTTGGGTCAACGTTAAAGAT
22148 GTTGCAA
66 GTTGCAA
22155 CTGTTCTTTCTTCAGGAGCACAGACATTCCCAAATGCAACTTTTGGTTGGGTCAACGTTAAAGAT
1 CTGTTCTTTCTTCAGGAGCACAGACATTCCCAAATGCAACTTTTGGTTGGGTCAACGTTAAAGAT
22220 GTTGCAA
66 GTTGCAA
22227 ATGCACACAT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (72 bp):
CTGTTCTTTCTTCAGGAGCACAGACATTCCCAAATGCAACTTTTGGTTGGGTCAACGTTAAAGAT
GTTGCAA
Found at i:26615 original size:24 final size:25
Alignment explanation
Indices: 26585--26632 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
26575 TCTTTTTAGA
*
26585 TTTTTTAGG-AGGATCCAATATTAT
1 TTTTTTAGGAAGGATACAATATTAT
26609 TTTTTTAGGTAAGGATACAATATT
1 TTTTTTAGG-AAGGATACAATATT
26633 CTTTGTTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.43
26 12 0.57
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.46
Consensus pattern (25 bp):
TTTTTTAGGAAGGATACAATATTAT
Found at i:28206 original size:118 final size:118
Alignment explanation
Indices: 27998--28234 Score: 447
Period size: 118 Copynumber: 2.0 Consensus size: 118
27988 TTTTTATAAA
**
27998 ACATTCAAAATTAACTAAGAATTTTCTCTTCTAAATTTTAATATAATAATTTAAACACGAACATA
1 ACATTCAAAATTAACTAAGAATTTTCTCTTCTAAATTTTAATATAATAATTTAAACAAAAACATA
28063 TTATCGATATTAGGATAATATTATCACTATTGTTGCATTGTTATGAACTGAGC
66 TTATCGATATTAGGATAATATTATCACTATTGTTGCATTGTTATGAACTGAGC
*
28116 ACATTCAAAATTAACTAAGAATTTTCTCTTCTAAATTTTAGTATAATAATTTAAACAAAAACATA
1 ACATTCAAAATTAACTAAGAATTTTCTCTTCTAAATTTTAATATAATAATTTAAACAAAAACATA
28181 TTATCGATATTAGGATAATATTATCACTATTGTTGCATTGTTATGAACTGAGC
66 TTATCGATATTAGGATAATATTATCACTATTGTTGCATTGTTATGAACTGAGC
28234 A
1 A
28235 TATCCAACCG
Statistics
Matches: 116, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
118 116 1.00
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (118 bp):
ACATTCAAAATTAACTAAGAATTTTCTCTTCTAAATTTTAATATAATAATTTAAACAAAAACATA
TTATCGATATTAGGATAATATTATCACTATTGTTGCATTGTTATGAACTGAGC
Found at i:32009 original size:28 final size:28
Alignment explanation
Indices: 31978--32035 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
31968 CGTCATGTAC
31978 TTTTTTTTTG-T-CCATTTTTTTCTCTA
1 TTTTTTTTTGATACCATTTTTTTCTCTA
32004 TTTTTTTTTGATACCATTTTTTTCTCTA
1 TTTTTTTTTGATACCATTTTTTTCTCTA
32032 TTTT
1 TTTT
32036 GTTTAACAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 10 0.33
27 1 0.03
28 19 0.63
ACGTcount: A:0.10, C:0.14, G:0.03, T:0.72
Consensus pattern (28 bp):
TTTTTTTTTGATACCATTTTTTTCTCTA
Found at i:42897 original size:64 final size:64
Alignment explanation
Indices: 42826--42954 Score: 231
Period size: 64 Copynumber: 2.0 Consensus size: 64
42816 GTTGTCTTTT
* *
42826 CTTTTTTCTTACTAACCATCTAGTGTTTAGTAATCATATTGGGTCCGACTAATTCGAAATGGAG
1 CTTTTTTCTTACTAACCATCTAGTGTTTAGTAATCACATTGAGTCCGACTAATTCGAAATGGAG
*
42890 CTTTTTTCTTACTAACCATCTAGTGTTTAGTAATCGCATTGAGTCCGACTAATTCGAAATGGAG
1 CTTTTTTCTTACTAACCATCTAGTGTTTAGTAATCACATTGAGTCCGACTAATTCGAAATGGAG
42954 C
1 C
42955 CGCGTTGGAC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (64 bp):
CTTTTTTCTTACTAACCATCTAGTGTTTAGTAATCACATTGAGTCCGACTAATTCGAAATGGAG
Found at i:52915 original size:46 final size:46
Alignment explanation
Indices: 52882--52984 Score: 156
Period size: 46 Copynumber: 2.2 Consensus size: 46
52872 TCAATCTGAC
*
52882 AATCTATAAATCCAAAAATTTATATGTAATAA-TTATTTAATAAATA
1 AATCTATAAATCCAAAAATTTATATGTAATAATTTATTCAAT-AATA
*
52928 AATCTATAAATCCAAAAATTTATATGTAATAA-TTATTTAATAAATA
1 AATCTATAAATCCAAAAATTTATATGTAATAATTTATTCAAT-AATA
52974 AATCTATAAAT
1 AATCTATAAAT
52985 ATTTGTGAAG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 57 1.00
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (46 bp):
AATCTATAAATCCAAAAATTTATATGTAATAATTTATTCAATAATA
Found at i:55408 original size:28 final size:28
Alignment explanation
Indices: 55359--55432 Score: 121
Period size: 28 Copynumber: 2.6 Consensus size: 28
55349 TTAAGGGAGT
* *
55359 AAAATATCCAAAATTAAAATTTAGAGAGC
1 AAAACATCC-AAATCAAAATTTAGAGAGC
55388 AAAACATCCAAATCAAAATTTAGAGAGC
1 AAAACATCCAAATCAAAATTTAGAGAGC
55416 AAAACATCCAAATCAAA
1 AAAACATCCAAATCAAA
55433 CAAATTCAGG
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
28 35 0.81
29 8 0.19
ACGTcount: A:0.57, C:0.16, G:0.08, T:0.19
Consensus pattern (28 bp):
AAAACATCCAAATCAAAATTTAGAGAGC
Found at i:64095 original size:17 final size:16
Alignment explanation
Indices: 64041--64091 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
64031 ATCACCCCTC
*
64041 AGATCACTAGTGATCTA
1 AGATCACCAGTGATC-A
64058 AGATCACCAGTGATGCA
1 AGATCACCAGTGAT-CA
*
64075 AGATCACCGGTGATCA
1 AGATCACCAGTGATCA
64091 A
1 A
64092 AGATTATATG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 3 0.10
17 27 0.87
18 1 0.03
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (16 bp):
AGATCACCAGTGATCA
Found at i:66704 original size:87 final size:87
Alignment explanation
Indices: 66550--66725 Score: 246
Period size: 87 Copynumber: 2.0 Consensus size: 87
66540 CCCCAGCATT
* **
66550 CTCACATTTTCACATGTTTCTATTGAGTCCATAGATCCAAATGGCTGCTTCTGGCTTTCACTAAG
1 CTCACATTTTCACATGTTTCTATTGAGTCCATAGATCCAAATGGCCGCTTCTGGAATTCACTAAG
*
66615 CTTTGGACTT-GTCTTTCTGCTG
66 CTTTGGA-TTAGTCTTTATGCTG
* * * * * *
66637 CTCACATTTTGACATGTTTGTATTGAGTCCATAGATTCAAATGGCCGTTTCTGGAATTGACTGAG
1 CTCACATTTTCACATGTTTCTATTGAGTCCATAGATCCAAATGGCCGCTTCTGGAATTCACTAAG
66702 CTTTGGATTAGTCTTTATGCTG
66 CTTTGGATTAGTCTTTATGCTG
66724 CT
1 CT
66726 GTTTGTGCTA
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
86 2 0.03
87 76 0.97
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.40
Consensus pattern (87 bp):
CTCACATTTTCACATGTTTCTATTGAGTCCATAGATCCAAATGGCCGCTTCTGGAATTCACTAAG
CTTTGGATTAGTCTTTATGCTG
Found at i:71891 original size:2 final size:2
Alignment explanation
Indices: 71876--71945 Score: 59
Period size: 2 Copynumber: 39.0 Consensus size: 2
71866 GACAATAGTG
*
71876 TA TA T- TA T- TA TA TA TA T- TA T- TG TA T- TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
71912 TA -A TA TA TA TA TA TA TA TA TA T- TA T- TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
71946 ATAACTAATA
Statistics
Matches: 57, Mismatches: 1, Indels: 20
0.73 0.01 0.26
Matches are distributed among these distances:
1 9 0.16
2 46 0.81
3 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (2 bp):
TA
Found at i:71903 original size:17 final size:18
Alignment explanation
Indices: 71881--71936 Score: 69
Period size: 19 Copynumber: 3.1 Consensus size: 18
71871 TAGTGTATAT
*
71881 TATTATATATAT-TATTG
1 TATTATATATATATATTA
*
71898 TATTATTATATATATAATA
1 TATTA-TATATATATATTA
71917 TATATATATATATATATTA
1 TAT-TATATATATATATTA
71936 T
1 T
71937 TATAGTATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 5 0.15
18 7 0.21
19 19 0.58
20 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
TATTATATATATATATTA
Found at i:71927 original size:8 final size:8
Alignment explanation
Indices: 71876--71945 Score: 59
Period size: 7 Copynumber: 9.8 Consensus size: 8
71866 GACAATAGTG
71876 TATAT-TA
1 TATATATA
71883 T-TATATA
1 TATATATA
71890 TAT-TAT-
1 TATATATA
*
71896 TGTAT-TA
1 TATATATA
71903 T-TATATA
1 TATATATA
71910 TATA-ATA
1 TATATATA
71917 TATATATA
1 TATATATA
71925 TATATATA
1 TATATATA
71933 T-TAT-TA
1 TATATATA
71939 TAGTATA
1 TA-TATA
71946 ATAACTAATA
Statistics
Matches: 52, Mismatches: 1, Indels: 18
0.73 0.01 0.25
Matches are distributed among these distances:
6 12 0.23
7 22 0.42
8 18 0.35
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (8 bp):
TATATATA
Found at i:78897 original size:2 final size:2
Alignment explanation
Indices: 78892--78917 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
78882 TCTGTAGTTC
78892 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
78918 TAACATTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:80143 original size:23 final size:23
Alignment explanation
Indices: 80117--80162 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
80107 TACCAATTAA
80117 CTAGCCCAATTATCATCAAAACT
1 CTAGCCCAATTATCATCAAAACT
80140 CTAGCCCAATTATCATCAAAACT
1 CTAGCCCAATTATCATCAAAACT
80163 GTTTTTGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.30, G:0.04, T:0.26
Consensus pattern (23 bp):
CTAGCCCAATTATCATCAAAACT
Found at i:87754 original size:23 final size:23
Alignment explanation
Indices: 87710--87754 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
87700 CGTGGACCCC
*
87710 TTCCCTCTCCTCCTCTTCTTCCT
1 TTCCCTCTCCTCCTCGTCTTCCT
*
87733 TTCCCT-TCCTCCCTCGTGTTCC
1 TTCCCTCTCCT-CCTCGTCTTCC
87755 CCACGCGCCG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.00, C:0.51, G:0.04, T:0.44
Consensus pattern (23 bp):
TTCCCTCTCCTCCTCGTCTTCCT
Found at i:106561 original size:55 final size:53
Alignment explanation
Indices: 106494--106604 Score: 177
Period size: 55 Copynumber: 2.1 Consensus size: 53
106484 CTTCCCAAAT
* * *
106494 TAAGTATTGTGGCATGTACCCCTACTATTATTGGCAACTATATAGTAGTTATATA
1 TAAGTACTGTGGCATATACCCCTACTATTATTAGCAAC--TATAGTAGTTATATA
106549 TAAGTACTGTGGCATATACCCCTACTATTATTAGCAACTATAGTAGTTATATA
1 TAAGTACTGTGGCATATACCCCTACTATTATTAGCAACTATAGTAGTTATATA
106602 TAA
1 TAA
106605 TTGTATATAT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
53 18 0.34
55 35 0.66
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.37
Consensus pattern (53 bp):
TAAGTACTGTGGCATATACCCCTACTATTATTAGCAACTATAGTAGTTATATA
Found at i:118702 original size:14 final size:16
Alignment explanation
Indices: 118671--118707 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
118661 CTATAGAATG
118671 TTTTTTTCATGCTCTT
1 TTTTTTTCATGCTCTT
*
118687 TTTTTTTC-T-CTGTT
1 TTTTTTTCATGCTCTT
118701 TTTTTTT
1 TTTTTTT
118708 TCCTCACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 11 0.55
15 1 0.05
16 8 0.40
ACGTcount: A:0.03, C:0.14, G:0.05, T:0.78
Consensus pattern (16 bp):
TTTTTTTCATGCTCTT
Found at i:126445 original size:15 final size:15
Alignment explanation
Indices: 126425--126455 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
126415 GATTAACATG
126425 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
126440 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
126455 T
1 T
126456 AATGTATTGT
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:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (15 bp):
TTTCTATTTGATAGT
Done.