Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016092.1 Corchorus olitorius cultivar O-4 contig16125, 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: 29205
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Found at i:900 original size:36 final size:36
Alignment explanation
Indices: 853--922 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
843 GAGATTTTGG
* *
853 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
889 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
923 GGTTATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Found at i:2284 original size:58 final size:57
Alignment explanation
Indices: 2193--2301 Score: 148
Period size: 56 Copynumber: 1.9 Consensus size: 57
2183 ATCATGCCTC
2193 GGTCCAAAAACGTCTTTTTTAGGCATCTAATAAAAAAAACATGTCACTCGATAAGTCTT
1 GGTCCAAAAACGTCTTTTTTAGGCATCTAAT--AAAAAACATGTCACTCGATAAGTCTT
* * * * *
2252 GGTCCGAAAGCGT-TTTTTTATGCATCTAATAAAGAACATGTCACTTGATA
1 GGTCCAAAAACGTCTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATA
2302 TTTGATTAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
56 18 0.40
58 16 0.36
59 11 0.24
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (57 bp):
GGTCCAAAAACGTCTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAAGTCTT
Found at i:3715 original size:22 final size:21
Alignment explanation
Indices: 3680--3723 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
3670 ATCTCTGTAA
*
3680 ATTAAATAACCAAATTTTGATG
1 ATTAAATAACCAAAATTT-ATG
* *
3702 ATTAATTAATCAAAATTTATG
1 ATTAAATAACCAAAATTTATG
3723 A
1 A
3724 AAATGAAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.39
Consensus pattern (21 bp):
ATTAAATAACCAAAATTTATG
Found at i:11599 original size:14 final size:14
Alignment explanation
Indices: 11577--11611 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
11567 CCCGGAAAAC
11577 AAACAGAGAAAAAGA
1 AAAC-GAGAAAAAGA
*
11592 AGACGAGAAAAAGA
1 AAACGAGAAAAAGA
11606 AAACGA
1 AAACGA
11612 AAGCAGTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 15 0.83
15 3 0.17
ACGTcount: A:0.69, C:0.09, G:0.23, T:0.00
Consensus pattern (14 bp):
AAACGAGAAAAAGA
Found at i:14256 original size:42 final size:42
Alignment explanation
Indices: 14197--14357 Score: 187
Period size: 42 Copynumber: 4.0 Consensus size: 42
14187 GTGCCAATTG
*
14197 CCAAAGCCAATGTCATCTTCTTCCTAGCTATCTAAGAGTTAT
1 CCAAAGCCAAGGTCATCTTCTTCCTAGCTATCTAAGAGTTAT
*
14239 CCAAAGCCAAGGTCATCTTCTTCCTAACTATCTAAGAGTTAT
1 CCAAAGCCAAGGTCATCTTCTTCCTAGCTATCTAAGAGTTAT
* * **
14281 TC--AG----TGT--T-TTCAAACCTGAGCTATCTAAGAGTTAT
1 CCAAAGCCAAGGTCATCTTC-TTCCT-AGCTATCTAAGAGTTAT
14316 CCAAAGCCAAGGTCATCTTCTTCCTAGCTATCTAAGAGTTAT
1 CCAAAGCCAAGGTCATCTTCTTCCTAGCTATCTAAGAGTTAT
14358 TCAGTGTTTT
Statistics
Matches: 97, Mismatches: 11, Indels: 22
0.75 0.08 0.17
Matches are distributed among these distances:
33 3 0.03
34 4 0.04
35 17 0.18
36 2 0.02
37 2 0.02
40 2 0.02
41 2 0.02
42 58 0.60
43 4 0.04
44 3 0.03
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (42 bp):
CCAAAGCCAAGGTCATCTTCTTCCTAGCTATCTAAGAGTTAT
Found at i:14349 original size:77 final size:77
Alignment explanation
Indices: 14222--14448 Score: 333
Period size: 77 Copynumber: 3.0 Consensus size: 77
14212 TCTTCTTCCT
*
14222 AGCTATCTAAGAGTTATCCAAAGCCAAGGTCATCTTCTTCCTAACTATCTAAGAGTTATTCAGTG
1 AGCTATCTAAGAGTTATCCAAAGCCAAGGTCATCTTCTTCCTAGCTATCTAAGAGTTATTCAGTG
14287 TTTTCAAACCTG
66 TTTTCAAACCTG
14299 AGCTATCTAAGAGTTATCCAAAGCCAAGGTCATCTTCTTCCTAGCTATCTAAGAGTTATTCAGTG
1 AGCTATCTAAGAGTTATCCAAAGCCAAGGTCATCTTCTTCCTAGCTATCTAAGAGTTATTCAGTG
14364 TTTTCAAACCTG
66 TTTTCAAACCTG
* * * *
14376 AACCGGATC---G-GTTAACC---GCCAAGGTCATCTTCTTCCTAGTTATCTAAGAGTTATTCAG
1 -AGC-TATCTAAGAGTTATCCAAAGCCAAGGTCATCTTCTTCCTAGCTATCTAAGAGTTATTCAG
*
14434 TGTTTTCAAGCCTG
64 TGTTTTCAAACCTG
14448 A
1 A
14449 ACTGGATCGG
Statistics
Matches: 142, Mismatches: 6, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
71 1 0.01
72 53 0.37
75 6 0.04
76 1 0.01
77 76 0.54
78 2 0.01
79 3 0.02
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.33
Consensus pattern (77 bp):
AGCTATCTAAGAGTTATCCAAAGCCAAGGTCATCTTCTTCCTAGCTATCTAAGAGTTATTCAGTG
TTTTCAAACCTG
Found at i:14427 original size:72 final size:72
Alignment explanation
Indices: 14244--14465 Score: 304
Period size: 72 Copynumber: 3.0 Consensus size: 72
14234 GTTATCCAAA
* * *
14244 GCCAAGGTCATCTTCTTCCTAACTATCTAAGAGTTATTCAGTGTTTTCAAACCTG-AGC-TATCT
1 GCCAAGGTCATCTTCTTCCTAGCTATCTAAGAGTTATTCAGTGTTTTCAAACCTGAACCGGATC-
*
14307 AAGAGTTATCC
65 --G-GTTAACC
14318 AAAGCCAAGGTCATCTTCTTCCTAGCTATCTAAGAGTTATTCAGTGTTTTCAAACCTGAACCGGA
1 ---GCCAAGGTCATCTTCTTCCTAGCTATCTAAGAGTTATTCAGTGTTTTCAAACCTGAACCGGA
14383 TCGGTTAACC
63 TCGGTTAACC
* * *
14393 GCCAAGGTCATCTTCTTCCTAGTTATCTAAGAGTTATTCAGTGTTTTCAAGCCTGAACTGGATCG
1 GCCAAGGTCATCTTCTTCCTAGCTATCTAAGAGTTATTCAGTGTTTTCAAACCTGAACCGGATCG
14458 GTTAACC
66 GTTAACC
14465 G
1 G
14466 AGAGCCGGAG
Statistics
Matches: 136, Mismatches: 7, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
72 70 0.51
75 6 0.04
76 1 0.01
77 54 0.40
78 2 0.01
79 3 0.02
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (72 bp):
GCCAAGGTCATCTTCTTCCTAGCTATCTAAGAGTTATTCAGTGTTTTCAAACCTGAACCGGATCG
GTTAACC
Found at i:21724 original size:138 final size:135
Alignment explanation
Indices: 21483--21739 Score: 372
Period size: 138 Copynumber: 1.9 Consensus size: 135
21473 TATTTAATCA
* * * * **
21483 AATCCTAATTAAGAAATTTCAAATATATGTTAAGAAAATTCAAATAATCATATAGGAAGAGTATG
1 AATCCAAATTAAGAAAATTCAAATATATGTTAAGAAAATTCAAATAATCATATAAGAAGAGAACA
* *
21548 TTGGTAGGTATGTTAAGAAAATAAGAAAATTAATTAATTCACCCAAAGATTAATAATATTTAATC
66 CTGCTAGGTATGTTAAGAAAATAAGAAAATTAATTAATTCACCCAAAGATTAATAATATTTAATC
21613 AAATT
131 AAATT
*
21618 AATCCAAATTAATAAAATTCAAATATATGTTAAGAAAATTCAAATATTAATCATATAAGAAGAGA
1 AATCCAAATTAAGAAAATTCAAATATATGTTAAGAAAATTC-AA-A-TAATCATATAAGAAGAGA
* *
21683 ACACTGCTAGGTATGTTAAGAAAATAA-AATTATTAATTAATTCAGCCAAAGATTAAT
63 ACACTGCTAGGTATGTTAAGAAAATAAGAA-AATTAATTAATTCACCCAAAGATTAAT
21740 TGAGATATTA
Statistics
Matches: 107, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
135 38 0.36
136 2 0.02
137 3 0.03
138 64 0.60
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (135 bp):
AATCCAAATTAAGAAAATTCAAATATATGTTAAGAAAATTCAAATAATCATATAAGAAGAGAACA
CTGCTAGGTATGTTAAGAAAATAAGAAAATTAATTAATTCACCCAAAGATTAATAATATTTAATC
AAATT
Found at i:28490 original size:2 final size:2
Alignment explanation
Indices: 28483--28511 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
28473 TCTTTTATTT
28483 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28512 TAATTAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.