Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013004.1 Corchorus olitorius cultivar O-4 contig13037, 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: 7912
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Found at i:3007 original size:27 final size:27
Alignment explanation
Indices: 2959--3021 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
2949 TCATGAGTTG
*
2959 GATGCTGAAATCAACTGGTAAA-AAGAT
1 GATGCTGAAATCAACTGATAAAGAA-AT
*
2986 GATGCTGAAATTGAA-TGATAAAGAAAT
1 GATGCTGAAA-TCAACTGATAAAGAAAT
*
3013 GATCCTGAA
1 GATGCTGAA
3022 CAGGATTCTG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 26 0.84
28 5 0.16
ACGTcount: A:0.44, C:0.10, G:0.22, T:0.24
Consensus pattern (27 bp):
GATGCTGAAATCAACTGATAAAGAAAT
Found at i:3048 original size:40 final size:40
Alignment explanation
Indices: 3001--4369 Score: 1039
Period size: 40 Copynumber: 33.9 Consensus size: 40
2991 TGAAATTGAA
* * *
3001 TGATAAAGAAATGATCCTGAACAGGATTCTGAAATT-CTCT
1 TGATAAAGAAATGATCCTGAGCAGGATTTTGAAATTAAT-T
* * * *
3041 TGATAAAGCAACGATCCTGAGTAGGATTCTGAAATTAATT
1 TGATAAAGAAATGATCCTGAGCAGGATTTTGAAATTAATT
** *
3081 TGATAAAGCGATGATCCTGACCAGGATTTTGAAATTAATT
1 TGATAAAGAAATGATCCTGAGCAGGATTTTGAAATTAATT
* *
3121 TGATAAA-AAGATGATCCTGTGCAGGATTCTGAAATTAATT
1 TGATAAAGAA-ATGATCCTGAGCAGGATTTTGAAATTAATT
* * ***
3161 TGATAAAGCAATGATCCTGTGCAGGATTCCAAAATTAATT
1 TGATAAAGAAATGATCCTGAGCAGGATTTTGAAATTAATT
* * *
3201 TGATAAA-AAGATGATCCTGTGCAGGATTTTGAAATTCACT
1 TGATAAAGAA-ATGATCCTGAGCAGGATTTTGAAATTAATT
* * * *
3241 CGATAAAGCAATGATACTGAGCAGGATTCTGAAATTAATT
1 TGATAAAGAAATGATCCTGAGCAGGATTTTGAAATTAATT
3281 TGATAAA-ACAATGATCCTGAGCAGGATTTTGAAATTAATT
1 TGATAAAGA-AATGATCCTGAGCAGGATTTTGAAATTAATT
* * *
3321 TGATAAA-ACGATGATCCTGTGCAGGATTCTGAAATTAATT
1 TGATAAAGA-AATGATCCTGAGCAGGATTTTGAAATTAATT
* *
3361 TGATAAAGCAATGATCCTGAGCAGGGTTTTGAAATTAATT
1 TGATAAAGAAATGATCCTGAGCAGGATTTTGAAATTAATT
* * * * *
3401 TGATGAAGCAATGATCTTGAGCAGGGTTTTGAAATTAA-C
1 TGATAAAGAAATGATCCTGAGCAGGATTTTGAAATTAATT
* * * * *
3440 TGGTAAAGAAATTATCTTGAGCAGGGTTTTGAAATTAA-C
1 TGATAAAGAAATGATCCTGAGCAGGATTTTGAAATTAATT
* *
3479 TGGTAAAGAAATGATCCTGAGCAGGATTTTGAAATTAA-C
1 TGATAAAGAAATGATCCTGAGCAGGATTTTGAAATTAATT
* * ** *
3518 TGGTTAAGAAATGATCCTGAGCAGGATTTTGAAATCGA-C
1 TGATAAAGAAATGATCCTGAGCAGGATTTTGAAATTAATT
* *
3557 TGGTAAAGAAATGATCATGAGCAGGATTTTGAAATTAATT
1 TGATAAAGAAATGATCCTGAGCAGGATTTTGAAATTAATT
** *
3597 TGATAAA-AAGATGATCCTGAGCAGGATTTTGAAATCGA-C
1 TGATAAAGAA-ATGATCCTGAGCAGGATTTTGAAATTAATT
*
3636 TGGTAAAGAAATGATCCTGAGCAGGATTTTGAAATTAATT
1 TGATAAAGAAATGATCCTGAGCAGGATTTTGAAATTAATT
*
3676 TGATAAA-AAGATGATCCTGAGCAGGAATTTGAAATTAATT
1 TGATAAAGAA-ATGATCCTGAGCAGGATTTTGAAATTAATT
* *
3716 TGATAAAGCAATGATCCTGAGCAGGATTTTGAAATCAATT
1 TGATAAAGAAATGATCCTGAGCAGGATTTTGAAATTAATT
** * *
3756 TGATAAACCAATGATCCGGAGCATGG-TTTTGAAATTAA-C
1 TGATAAAGAAATGATCCTGAGCA-GGATTTTGAAATTAATT
* *
3795 TGGTAAAGAAATGATCCTGAGTAGGATTTTGAAATTAATT
1 TGATAAAGAAATGATCCTGAGCAGGATTTTGAAATTAATT
* *
3835 TGATAAA-AAGATGATCCTGAGCAGGATTCTGAAATTGATT
1 TGATAAAGAA-ATGATCCTGAGCAGGATTTTGAAATTAATT
* * * ** ** **
3875 TGATAAAGCAATTTGAAATCAATTTGATAAAGCAATGATCCT-AAGCATGGTT
1 TGATAAAG-AA-ATG--ATC---CTG----AGC-AGGATTTTGAA-ATTAATT
* * * *** * * ** * ***
3927 T--TGAAATTAACTGGTAAAGA-AATGATCCTGAGCATGGTTT
1 TGAT-AAA-GAAATGATCCTGAGCAGGATTTTGA-AATTAATT
** * * *** * * ** * ** *
3967 TGA-AATTAACTGGTAAAGA-AATGATCCTGAGCAGGATTT
1 TGATAAAGAAATGATCCTGAGCAGGATTTTGA-AATTAATT
** * * * *
4006 TGA-AATTAATTTGATAAAAAGATGATCCTGAGCAAGATTCTGAAATTGATT
1 TGATAAAGAA-ATGA-----------TCCTGAGCAGGATTTTGAAATTAATT
* *
4057 TGATAAAGCAATGATCCTGAGCAGG-TTTTGAAATTAACT
1 TGATAAAGAAATGATCCTGAGCAGGATTTTGAAATTAATT
* * *
4096 AG-TAAAGAAATGATCCTGAGCGGGATTTTGAAATTAA-C
1 TGATAAAGAAATGATCCTGAGCAGGATTTTGAAATTAATT
* * * ** *
4134 TGGTAAATAAATGATCCTGAGCAAGATTTTGAAATCGA-C
1 TGATAAAGAAATGATCCTGAGCAGGATTTTGAAATTAATT
* *
4173 TGGTAAAGAAAATGATCCTGAGCAGAATTTTGAAATTAATT
1 TGATAAAG-AAATGATCCTGAGCAGGATTTTGAAATTAATT
*
4214 TGATAAA-AAGATGATCTTGAGCAGGATTTTGAAATTAATT
1 TGATAAAGAA-ATGATCCTGAGCAGGATTTTGAAATTAATT
4254 TGATAAA-ACAATGATCCTGAGCAGGATTTTGAAATTAATT
1 TGATAAAGA-AATGATCCTGAGCAGGATTTTGAAATTAATT
* *
4294 TGATAAAGCAATGATCCTGAGCAGGGTTTTGAAATTAATT
1 TGATAAAGAAATGATCCTGAGCAGGATTTTGAAATTAATT
* * *
4334 TGATGAAGCAATGATCCTGAGCAGGGTTTTGAAATT
1 TGATAAAGAAATGATCCTGAGCAGGATTTTGAAATT
4370 CACTAATAAA
Statistics
Matches: 1116, Mismatches: 156, Indels: 114
0.81 0.11 0.08
Matches are distributed among these distances:
38 23 0.02
39 322 0.29
40 699 0.63
41 14 0.01
42 4 0.00
44 3 0.00
45 1 0.00
47 2 0.00
48 1 0.00
50 3 0.00
51 22 0.02
52 22 0.02
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.31
Consensus pattern (40 bp):
TGATAAAGAAATGATCCTGAGCAGGATTTTGAAATTAATT
Found at i:3890 original size:13 final size:13
Alignment explanation
Indices: 3872--3910 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
3862 TCTGAAATTG
3872 ATTTGATAAAGCA
1 ATTTGATAAAGCA
*
3885 ATTTG--AAATCA
1 ATTTGATAAAGCA
3896 ATTTGATAAAGCA
1 ATTTGATAAAGCA
3909 AT
1 AT
3911 GATCCTAAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 10 0.45
13 12 0.55
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (13 bp):
ATTTGATAAAGCA
Found at i:4797 original size:144 final size:145
Alignment explanation
Indices: 4490--4927 Score: 736
Period size: 144 Copynumber: 3.0 Consensus size: 145
4480 AGAATGCCCG
* * * ** * *
4490 GAGGACTTGTCAGAATTAATACCTGGAGGTTTCTGAAATTATGCCTGGAGGTCTTA-AGGATGCA
1 GAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATGGTGCCCGGAGGTCTTACA-AATGCA
*
4554 AACTAAACCTTGAGCAAGGTTTTGATTTTGAAATTTAAATGCAACTTTGATTAAAAACTTGATGA
65 AACTCAACCTTGAGCAAGGTTTTGATTTTGAAATTTAAATGCAACTTTGATTAAAAACTTGATGA
4619 AATGAAATGATACCCA
130 AATGAAATGATACCCA
* *
4635 GAGGATTTATCAGAATTAATGCCCGGAGGTTTCTGAAATGGTGCCCGGAGGTCTTACAAATTCAA
1 GAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATGGTGCCCGGAGGTCTTACAAATGCAA
4700 ACTCAACCTTGAGCAAGGTTTTGATTTTG-AATTTAAATGCAACTTTGATTAAAAACTTGATGAA
66 ACTCAACCTTGAGCAAGGTTTTGATTTTGAAATTTAAATGCAACTTTGATTAAAAACTTGATGAA
4764 ATGAAATGATACCCA
131 ATGAAATGATACCCA
*
4779 GAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATGGTGCCCGGAGGTCATACAAATGCAA
1 GAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATGGTGCCCGGAGGTCTTACAAATGCAA
*
4844 ACTCAACCTTGAACAAGGTTTTGATTTTGAAATTTAAATGCAACTTTGATTAAAAACTTGATGAA
66 ACTCAACCTTGAGCAAGGTTTTGATTTTGAAATTTAAATGCAACTTTGATTAAAAACTTGATGAA
*
4909 ATGAAATGATACCCG
131 ATGAAATGATACCCA
4924 GAGG
1 GAGG
4928 TTTCTGAAAT
Statistics
Matches: 276, Mismatches: 15, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
144 140 0.51
145 135 0.49
146 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (145 bp):
GAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATGGTGCCCGGAGGTCTTACAAATGCAA
ACTCAACCTTGAGCAAGGTTTTGATTTTGAAATTTAAATGCAACTTTGATTAAAAACTTGATGAA
ATGAAATGATACCCA
Found at i:5961 original size:13 final size:13
Alignment explanation
Indices: 5943--5982 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
5933 TATCCCCTTC
5943 TTTTTTTGCACCTT
1 TTTTTTTGCA-CTT
5957 TTTTTTTGCACTT
1 TTTTTTTGCACTT
*
5970 TTTTTTTTCACTT
1 TTTTTTTGCACTT
5983 GAAAAGTTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 15 0.60
14 10 0.40
ACGTcount: A:0.07, C:0.17, G:0.05, T:0.70
Consensus pattern (13 bp):
TTTTTTTGCACTT
Found at i:5962 original size:14 final size:14
Alignment explanation
Indices: 5938--5976 Score: 62
Period size: 13 Copynumber: 2.8 Consensus size: 14
5928 AGCTTTATCC
5938 CCTTCTTTTTTTGCA
1 CCTT-TTTTTTTGCA
5953 CCTTTTTTTTTGCA
1 CCTTTTTTTTTGCA
5967 -CTTTTTTTTT
1 CCTTTTTTTTT
5977 TCACTTGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 10 0.42
14 10 0.42
15 4 0.17
ACGTcount: A:0.05, C:0.21, G:0.05, T:0.69
Consensus pattern (14 bp):
CCTTTTTTTTTGCA
Found at i:5977 original size:14 final size:14
Alignment explanation
Indices: 5943--5982 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
5933 TATCCCCTTC
*
5943 TTTTTTTGCACCTT
1 TTTTTTTGCACTTT
5957 TTTTTTTGCACTTT
1 TTTTTTTGCACTTT
5971 TTTTTTT-CACTT
1 TTTTTTTGCACTT
5983 GAAAAGTTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 5 0.20
14 20 0.80
ACGTcount: A:0.07, C:0.17, G:0.05, T:0.70
Consensus pattern (14 bp):
TTTTTTTGCACTTT
Found at i:6321 original size:25 final size:25
Alignment explanation
Indices: 6287--6345 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 25
6277 CAATTTCCAC
*
6287 TTTCATTTTCAATTTTCGCTTCTTT
1 TTTCGTTTTCAATTTTCGCTTCTTT
** * *
6312 TTTCGTTTTCTTTTTTTGCTTTTTT
1 TTTCGTTTTCAATTTTCGCTTCTTT
*
6337 TTTGGTTTT
1 TTTCGTTTT
6346 TGTTTTTTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.05, C:0.14, G:0.08, T:0.73
Consensus pattern (25 bp):
TTTCGTTTTCAATTTTCGCTTCTTT
Found at i:6328 original size:26 final size:26
Alignment explanation
Indices: 6299--6354 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
6289 TCATTTTCAA
*
6299 TTTTCGCTTCTTTTTTCG-TTTTCTT
1 TTTTTGCTTCTTTTTTCGTTTTTCTT
* * *
6324 TTTTTGCTTTTTTTTTGGTTTTTGTT
1 TTTTTGCTTCTTTTTTCGTTTTTCTT
6350 TTTTT
1 TTTTT
6355 TTTGCATATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 15 0.58
26 11 0.42
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.79
Consensus pattern (26 bp):
TTTTTGCTTCTTTTTTCGTTTTTCTT
Found at i:6357 original size:18 final size:18
Alignment explanation
Indices: 6324--6358 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
6314 TCGTTTTCTT
6324 TTTTTGCTTTTTTTTTGG
1 TTTTTGCTTTTTTTTTGG
*
6342 TTTTTGTTTTTTTTTTG
1 TTTTTGCTTTTTTTTTG
6359 CATATTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.03, G:0.14, T:0.83
Consensus pattern (18 bp):
TTTTTGCTTTTTTTTTGG
Done.