Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014984.1 Corchorus olitorius cultivar O-4 contig15017, 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: 22023
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:3375 original size:25 final size:25
Alignment explanation
Indices: 3330--3384 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
3320 TTTTGAACTC
* *
3330 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATAT
*
3355 ATTATTTATT-TAATAATATATATAT
1 ATTATTTATTAT-ATAAAATATATAT
3380 ATTAT
1 ATTAT
3385 ATCTAAGATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 1 0.04
25 25 0.96
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATAT
Found at i:3754 original size:13 final size:13
Alignment explanation
Indices: 3736--3767 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
3726 AACAGATTTT
3736 CAGAAGTGCTTTC
1 CAGAAGTGCTTTC
*
3749 CAGAAGTGTTTTC
1 CAGAAGTGCTTTC
3762 CAGAAG
1 CAGAAG
3768 CACTTTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (13 bp):
CAGAAGTGCTTTC
Found at i:4365 original size:22 final size:22
Alignment explanation
Indices: 4337--4381 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
4327 TGGGCGCCAA
*
4337 ATCGTCTGTCAGGAGCCGGTAG
1 ATCGTCTGCCAGGAGCCGGTAG
*
4359 ATCGTCTGCCGGGAGCCGGTAG
1 ATCGTCTGCCAGGAGCCGGTAG
4381 A
1 A
4382 AAGAGCTCTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.24, G:0.38, T:0.20
Consensus pattern (22 bp):
ATCGTCTGCCAGGAGCCGGTAG
Found at i:4795 original size:2 final size:2
Alignment explanation
Indices: 4788--4824 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
4778 AAGTAGCTTT
4788 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4825 ACATGTGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:7878 original size:11 final size:11
Alignment explanation
Indices: 7835--7872 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
7825 TTCCTATATA
*
7835 AAATAAATTAT
1 AAATTAATTAT
7846 CAAA-TAATTAT
1 -AAATTAATTAT
7857 AAATTAATTAT
1 AAATTAATTAT
7868 AAATT
1 AAATT
7873 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:9937 original size:11 final size:10
Alignment explanation
Indices: 9890--9939 Score: 82
Period size: 10 Copynumber: 4.9 Consensus size: 10
9880 GGATAAGATA
9890 GAAAACAGAG
1 GAAAACAGAG
*
9900 AAAAACAGAG
1 GAAAACAGAG
9910 GAAAACAGAG
1 GAAAACAGAG
9920 GAAAACAGAG
1 GAAAACAGAG
9930 GAAAAACAGA
1 G-AAAACAGA
9940 CCAGTAAGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
10 29 0.78
11 8 0.22
ACGTcount: A:0.64, C:0.10, G:0.26, T:0.00
Consensus pattern (10 bp):
GAAAACAGAG
Found at i:11696 original size:146 final size:142
Alignment explanation
Indices: 11466--11860 Score: 382
Period size: 146 Copynumber: 2.7 Consensus size: 142
11456 TAAAGAAACT
* * * * *
11466 AGAAACATGACGATTGTTGCTTCTAATATTATCTCGTATTGTAGATAAGGTTTTCTAGATTAGA-
1 AGAAGCATGACGATTGTTGCTTCTAATATTATCTCGTACTATAGACAA-ATTTTCTAGATTAGAT
* * * * * *
11530 TTCTCGACTGGAATACCTCAAATATTGTTCTCTCTCCATCCCTTTCTTTTTCCTGAGAAATATCC
65 TTTTAGACTGGAGTAACTCAAATATTGTTCTCTCTCC--CCC-TT-TTTTTCC-AAAAAATATCC
*
11595 ATGTCC-AATGGAACAAA
125 ATGTCCTAAAGGAACAAA
* *
11612 AGAAGCATGATGATTGTTGCTTCTAATATTATCTCGTACTATAAACAAATTTTCTAGATTAGATT
1 AGAAGCATGACGATTGTTGCTTCTAATATTATCTCGTACTATAGACAAATTTTCTAGATTAGATT
* * * *
11677 TTTAGACTGGAGTAACTCAAATCTCTCTCTCTCTCTCCCCCTTTTTTTCCAAAAAATATTCGTGT
66 TTTAGACTGGAGTAACTCAAATAT-TGT-TCTCTCTCCCCCTTTTTTTCCAAAAAATATCCATGT
*
11742 CCATTAAAGGAACTAA
129 CC--TAAAGGAACAAA
* * * * * ** *
11758 AGAAGTATGACAATTATCGCTTCTAATATTTTCTCGTACCCTAGACATAATTTTCTAAATTAGAT
1 AGAAGCATGACGATTGTTGCTTCTAATATTATCTCGTACTATAGACA-AATTTTCTAGATTAGAT
** * *
11823 TTTTAGAACTAAAGT-ACACAAATATCGTTCTCTCTCCC
65 TTTTAG-ACTGGAGTAACTCAAATATTGTTCTCTCTCCC
11861 TTTTTTATGC
Statistics
Matches: 206, Mismatches: 35, Indels: 17
0.80 0.14 0.07
Matches are distributed among these distances:
143 13 0.06
144 7 0.03
145 26 0.13
146 113 0.55
147 32 0.16
148 15 0.07
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (142 bp):
AGAAGCATGACGATTGTTGCTTCTAATATTATCTCGTACTATAGACAAATTTTCTAGATTAGATT
TTTAGACTGGAGTAACTCAAATATTGTTCTCTCTCCCCCTTTTTTTCCAAAAAATATCCATGTCC
TAAAGGAACAAA
Found at i:14211 original size:87 final size:91
Alignment explanation
Indices: 14063--14240 Score: 231
Period size: 87 Copynumber: 2.0 Consensus size: 91
14053 AAATACCTTC
* * * **
14063 CTTTTATTATTTTATTTCCGGTACATAAGATGTTGATAATGTCGACTAAGTTCCTAAAAC-A-A-
1 CTTTTATTATTTTATTTCCCGTACATAAGATGCTGAAAATGTCGACTAAACTCCTAAAACAACAC
* *
14125 CATCTTCAATGTTTTATTCAAGCAAT
66 CACCTTAAATGTTTTATTCAAGCAAT
*
14151 CTTTTATTATTTT-TTTCCCGTACATAAG-TCGCTGAAAATGTCGACTAAACTCCTAGAACAACA
1 CTTTTATTATTTTATTTCCCGTACATAAGAT-GCTGAAAATGTCGACTAAACTCCTAAAACAACA
*
14214 CCACCTTAAATGTTTTGTTCAAGCAAT
65 CCACCTTAAATGTTTTATTCAAGCAAT
14241 GACAGGAGTT
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
86 1 0.01
87 38 0.49
88 14 0.18
89 1 0.01
90 23 0.30
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.38
Consensus pattern (91 bp):
CTTTTATTATTTTATTTCCCGTACATAAGATGCTGAAAATGTCGACTAAACTCCTAAAACAACAC
CACCTTAAATGTTTTATTCAAGCAAT
Found at i:14271 original size:3 final size:3
Alignment explanation
Indices: 14263--14287 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
14253 AAGTTCCTCT
14263 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
14288 AAACATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:15738 original size:1 final size:1
Alignment explanation
Indices: 15734--15763 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
15724 AACAGAGGGG
15734 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
15764 AGCACATATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:17176 original size:31 final size:31
Alignment explanation
Indices: 17141--17302 Score: 113
Period size: 31 Copynumber: 5.4 Consensus size: 31
17131 TTAGATTAAT
17141 TGCTCAAATAAGGGCCTAATGTTTGTCAAAA
1 TGCTCAAATAAGGGCCTAATGTTTGTCAAAA
* * **
17172 TGCTCAAATAAGGG-CTCGATCTTT-T-AATT
1 TGCTCAAATAAGGGCCT-AATGTTTGTCAAAA
* * *
17201 TGGC-CAAATAAGAGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAATGTTTGTCAAAA
* ** * **
17232 TGCTCAAATAAGGACCCGATCTTT-T-AATT
1 TGCTCAAATAAGGGCCTAATGTTTGTCAAAA
* *
17261 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAATGTTTGTCAAAA
17292 TGCTCAAATAA
1 TGCTCAAATAA
17303 AGGTCTGACA
Statistics
Matches: 93, Mismatches: 28, Indels: 20
0.66 0.20 0.14
Matches are distributed among these distances:
29 34 0.37
30 13 0.14
31 46 0.49
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.28
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAATGTTTGTCAAAA
Found at i:17210 original size:60 final size:60
Alignment explanation
Indices: 17145--17302 Score: 271
Period size: 60 Copynumber: 2.6 Consensus size: 60
17135 ATTAATTGCT
* * * *
17145 CAAATAAGGGCCTAATGTTTGTCAAAATGCTCAAATAAGGGCTCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGACCCGATCTTTTAATTTGGC
*
17205 CAAATAAGAGCCTAACGTTTGCCAAAATGCTCAAATAAGGACCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGACCCGATCTTTTAATTTGGC
17265 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAA
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAA
17303 AGGTCTGACA
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 92 1.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGACCCGATCTTTTAATTTGGC
Found at i:17420 original size:29 final size:29
Alignment explanation
Indices: 17380--17480 Score: 89
Period size: 29 Copynumber: 3.4 Consensus size: 29
17370 GCAAACGTTA
*
17380 GGCCTTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGGCCAAATTAAAAGATCG
* ** **
17409 GGTCCTTATTTGAG-CATTTTCAATAACG-TTA
1 GGCCCTTATTTG-GCCAAATT-AA-AA-GATCG
*
17440 GACCCTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGGCCAAATTAAAAGATCG
17469 GGCCCTTATTTG
1 GGCCCTTATTTG
17481 AGCATTTTCA
Statistics
Matches: 53, Mismatches: 13, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
28 1 0.02
29 28 0.53
30 6 0.11
31 17 0.32
32 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (29 bp):
GGCCCTTATTTGGCCAAATTAAAAGATCG
Found at i:17428 original size:60 final size:60
Alignment explanation
Indices: 17349--17511 Score: 240
Period size: 60 Copynumber: 2.7 Consensus size: 60
17339 ACTGATGCCA
* * *
17349 GGCCCTTATTTGAGTATTTTGGC-A-AACGTTAGGCCTTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTT--CAATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCG
*
17409 GGTCCTTATTTGAGCATTTTCAATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTCAATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCG
* *
17469 GGCCCTTATTTGAGCATTTTCAATAATGTTAGGCCCTTATTTG
1 GGCCCTTATTTGAGCATTTTCAATAACGTTAGACCCTTATTTG
17512 AGCAATTAGC
Statistics
Matches: 94, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
58 1 0.01
59 1 0.01
60 92 0.98
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (60 bp):
GGCCCTTATTTGAGCATTTTCAATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCG
Found at i:17450 original size:31 final size:30
Alignment explanation
Indices: 17412--17515 Score: 106
Period size: 31 Copynumber: 3.4 Consensus size: 30
17402 AAGATCGGGT
*
17412 CCTTATTTGAGCATTTTCAATAACGTTAGAC
1 CCTTATTTGAGCATTTTCAATAA-GTTAGGC
** **
17443 CCTTATTTG-GCCAAATT-AA-AAGATCGGGC
1 CCTTATTTGAG-CATTTTCAATAAG-TTAGGC
17472 CCTTATTTGAGCATTTTCAATAATGTTAGGC
1 CCTTATTTGAGCATTTTCAATAA-GTTAGGC
17503 CCTTATTTGAGCA
1 CCTTATTTGAGCA
17516 ATTAGCCTTC
Statistics
Matches: 58, Mismatches: 9, Indels: 12
0.73 0.11 0.15
Matches are distributed among these distances:
28 1 0.02
29 18 0.31
30 6 0.10
31 32 0.55
32 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (30 bp):
CCTTATTTGAGCATTTTCAATAAGTTAGGC
Done.