Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017514.1 Corchorus olitorius cultivar O-4 contig17547, 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: 21318
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30
Found at i:6386 original size:21 final size:21
Alignment explanation
Indices: 6345--6387 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
6335 AGATTGAGTG
*
6345 ATATAATTTAACTAAATCTAA
1 ATATAATTTAAATAAATCTAA
*
6366 ATATGATTTAAATCAAA-CTAA
1 ATATAATTTAAAT-AAATCTAA
6387 A
1 A
6388 ATTAAACATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.35
Consensus pattern (21 bp):
ATATAATTTAAATAAATCTAA
Found at i:6633 original size:25 final size:25
Alignment explanation
Indices: 6527--6620 Score: 83
Period size: 25 Copynumber: 4.0 Consensus size: 25
6517 CAAAAAATGA
*
6527 CATGACATGAAACCCAAACCCTAAC
1 CATGACATGAAAGCCAAACCCTAAC
*
6552 CATGAAATG--A--CAAACCCTAA-
1 CATGACATGAAAGCCAAACCCTAAC
* * * * *
6572 -GTAAGATGAAGGCTAAACCCTAAC
1 CATGACATGAAAGCCAAACCCTAAC
6596 CATGACATGAAAGCCAAACCCTAAC
1 CATGACATGAAAGCCAAACCCTAAC
6621 ATGTCATCTA
Statistics
Matches: 52, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
19 5 0.10
21 10 0.19
23 10 0.19
25 27 0.52
ACGTcount: A:0.45, C:0.29, G:0.13, T:0.14
Consensus pattern (25 bp):
CATGACATGAAAGCCAAACCCTAAC
Found at i:6949 original size:17 final size:18
Alignment explanation
Indices: 6927--6962 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
6917 AAAGGGTAGT
*
6927 TAAAAA-AATTGTTTTCA
1 TAAAAAGAAGTGTTTTCA
6944 TAAAAAGAAGTGTTTTCA
1 TAAAAAGAAGTGTTTTCA
6962 T
1 T
6963 GCAAGAGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (18 bp):
TAAAAAGAAGTGTTTTCA
Found at i:13771 original size:27 final size:28
Alignment explanation
Indices: 13736--13809 Score: 123
Period size: 28 Copynumber: 2.7 Consensus size: 28
13726 GGTCACCTAG
*
13736 GGGGCATTTTGGTCATTTT-TACATTCA
1 GGGGCATTTTGGTCATTTTGCACATTCA
*
13763 GGGGCATTTTGGTCATTTTGCATATTCA
1 GGGGCATTTTGGTCATTTTGCACATTCA
13791 GGGGCATTTTGGTCATTTT
1 GGGGCATTTTGGTCATTTT
13810 AAGTTCACAT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
27 19 0.43
28 25 0.57
ACGTcount: A:0.16, C:0.14, G:0.26, T:0.45
Consensus pattern (28 bp):
GGGGCATTTTGGTCATTTTGCACATTCA
Found at i:16012 original size:22 final size:23
Alignment explanation
Indices: 15987--16029 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
15977 AGTTCATTTT
*
15987 TTTATGCTTTAATGG-TTGAAAG
1 TTTATGCTTTAAGGGCTTGAAAG
*
16009 TTTATGTTTTAAGGGCTTGAA
1 TTTATGCTTTAAGGGCTTGAA
16030 TTGATGCTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.26, C:0.05, G:0.23, T:0.47
Consensus pattern (23 bp):
TTTATGCTTTAAGGGCTTGAAAG
Found at i:18851 original size:35 final size:36
Alignment explanation
Indices: 18805--19408 Score: 536
Period size: 35 Copynumber: 16.6 Consensus size: 36
18795 AAATTCTCAG
*
18805 GAATTCAGATGACTCGGTGTAGCATCTCCAAAG-TC
1 GAATTCAGATGACTCGGTGTAGCATCTCCAAAGATT
* * *
18840 GAATTTAGATGACTCGGTGCAGCATTTCCCAAAGATAGT
1 GAATTCAGATGACTCGGTGTAGCATCT-CCAAAGAT--T
* * *
18879 GGATTCAGATGACTCGGTGTAGCATCTTCAAAG-TC
1 GAATTCAGATGACTCGGTGTAGCATCTCCAAAGATT
* *
18914 GAATTTAGATGACTCGGTGCAGCATCTCCCAAAGATAGT
1 GAATTCAGATGACTCGGTGTAGCATCT-CCAAAGAT--T
* * *
18953 GGATTCAGATGACTC--AGTAGCCTC-CTCAAAGA-T
1 GAATTCAGATGACTCGGTGTAGCATCTC-CAAAGATT
18986 GAATTCAGATGACTCGGTGTAGCATCTCCAAAG-TT
1 GAATTCAGATGACTCGGTGTAGCATCTCCAAAGATT
* *
19021 GAATTCAGATGACTCGGTGTAGCATCTTCTAAGA-T
1 GAATTCAGATGACTCGGTGTAGCATCTCCAAAGATT
*
19056 GAATTCAGATGACTCGGTGTAGCCTC-CTCAAAGA-T
1 GAATTCAGATGACTCGGTGTAGCATCTC-CAAAGATT
* * *
19091 GAATTCAGATGACTCGGTATAGCATCTTCAAAG-TC
1 GAATTCAGATGACTCGGTGTAGCATCTCCAAAGATT
* *
19126 GAATTTAGAT-ATCTCGGTGCAGCATCTCCCAAAGATAGT
1 GAATTCAGATGA-CTCGGTGTAGCATCT-CCAAAGAT--T
* * * *
19165 GGATTCAGATGACTCGGTGTAGCGTCTTCAAAG-TC
1 GAATTCAGATGACTCGGTGTAGCATCTCCAAAGATT
* * * *
19200 AAATTTAGATGACTCGGTGCAGCATTTCCCAAAGATAGT
1 GAATTCAGATGACTCGGTGTAGCATCT-CCAAAGAT--T
* * * * *
19239 GGATTCAAATGACTCGGTGTAGCGTCTTCAAAG-TC
1 GAATTCAGATGACTCGGTGTAGCATCTCCAAAGATT
* *
19274 GAATTTAGATGACTCGGTGCAGCATCTCCCAAAGATAGT
1 GAATTCAGATGACTCGGTGTAGCATCT-CCAAAGAT--T
* * * *
19313 GGATTCAGATGACTCGGTGTAGCGTCTTCAAAG-TC
1 GAATTCAGATGACTCGGTGTAGCATCTCCAAAGATT
* *
19348 GAATTTAGATGACTCGGTGCAGCATCTCCCAAAGATT
1 GAATTCAGATGACTCGGTGTAGCATCT-CCAAAGATT
*
19385 GTAGATTTAGATGACTCGGTGTAG
1 G-A-ATTCAGATGACTCGGTGTAG
19409 TATTTTTGAA
Statistics
Matches: 454, Mismatches: 80, Indels: 66
0.76 0.13 0.11
Matches are distributed among these distances:
33 15 0.03
34 1 0.00
35 242 0.53
36 38 0.08
37 17 0.04
38 21 0.05
39 119 0.26
40 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (36 bp):
GAATTCAGATGACTCGGTGTAGCATCTCCAAAGATT
Found at i:18911 original size:74 final size:74
Alignment explanation
Indices: 18807--19408 Score: 872
Period size: 74 Copynumber: 8.3 Consensus size: 74
18797 ATTCTCAGGA
* *
18807 ATTCAGATGACTCGGTGTAGCATCTCCAAAGTCGAATTTAGATGACTCGGTGCAGCATTTCCCAA
1 ATTCAGATGACTCGGTGTAGCATCTTCAAAGTCGAATTTAGATGACTCGGTGCAGCATCTCCCAA
18872 AGATAGTGG
66 AGATAGTGG
18881 ATTCAGATGACTCGGTGTAGCATCTTCAAAGTCGAATTTAGATGACTCGGTGCAGCATCTCCCAA
1 ATTCAGATGACTCGGTGTAGCATCTTCAAAGTCGAATTTAGATGACTCGGTGCAGCATCTCCCAA
18946 AGATAGTGG
66 AGATAGTGG
* * * * *
18955 ATTCAGATGACTC--AGTAGCCTCCTCAAAGAT-GAATTCAGATGACTCGGTGTAGCATCT-CCA
1 ATTCAGATGACTCGGTGTAGCATCTTCAAAG-TCGAATTTAGATGACTCGGTGCAGCATCTCCCA
*
19016 AAG-T--TGA
65 AAGATAGTGG
* * *
19023 ATTCAGATGACTCGGTGTAGCATCTTCTAAGAT-GAATTCAGATGACTCGGTGTAGC--CTCCTC
1 ATTCAGATGACTCGGTGTAGCATCTTCAAAG-TCGAATTTAGATGACTCGGTGCAGCATCTCC-C
*
19085 AAAG--A-TGA
64 AAAGATAGTGG
*
19093 ATTCAGATGACTCGGTATAGCATCTTCAAAGTCGAATTTAGAT-ATCTCGGTGCAGCATCTCCCA
1 ATTCAGATGACTCGGTGTAGCATCTTCAAAGTCGAATTTAGATGA-CTCGGTGCAGCATCTCCCA
19157 AAGATAGTGG
65 AAGATAGTGG
* * *
19167 ATTCAGATGACTCGGTGTAGCGTCTTCAAAGTCAAATTTAGATGACTCGGTGCAGCATTTCCCAA
1 ATTCAGATGACTCGGTGTAGCATCTTCAAAGTCGAATTTAGATGACTCGGTGCAGCATCTCCCAA
19232 AGATAGTGG
66 AGATAGTGG
* *
19241 ATTCAAATGACTCGGTGTAGCGTCTTCAAAGTCGAATTTAGATGACTCGGTGCAGCATCTCCCAA
1 ATTCAGATGACTCGGTGTAGCATCTTCAAAGTCGAATTTAGATGACTCGGTGCAGCATCTCCCAA
19306 AGATAGTGG
66 AGATAGTGG
*
19315 ATTCAGATGACTCGGTGTAGCGTCTTCAAAGTCGAATTTAGATGACTCGGTGCAGCATCTCCCAA
1 ATTCAGATGACTCGGTGTAGCATCTTCAAAGTCGAATTTAGATGACTCGGTGCAGCATCTCCCAA
* *
19380 AGATTGTAG
66 AGATAGTGG
*
19389 ATTTAGATGACTCGGTGTAG
1 ATTCAGATGACTCGGTGTAG
19409 TATTTTTGAA
Statistics
Matches: 486, Mismatches: 28, Indels: 28
0.90 0.05 0.05
Matches are distributed among these distances:
68 17 0.03
69 3 0.01
70 94 0.19
71 11 0.02
72 42 0.09
73 2 0.00
74 316 0.65
75 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (74 bp):
ATTCAGATGACTCGGTGTAGCATCTTCAAAGTCGAATTTAGATGACTCGGTGCAGCATCTCCCAA
AGATAGTGG
Found at i:19788 original size:28 final size:28
Alignment explanation
Indices: 19749--19911 Score: 218
Period size: 28 Copynumber: 5.8 Consensus size: 28
19739 TGTTTGCACC
*
19749 TCCAGGGACATTTTGGTCATTTAGCATG
1 TCCAGGGGCATTTTGGTCATTTAGCATG
*
19777 TCTAGGGGCATTTTGGTCATTTAGCATG
1 TCCAGGGGCATTTTGGTCATTTAGCATG
* *
19805 TCCAGGGGCAGTTTGGTCATTTTGCATG
1 TCCAGGGGCATTTTGGTCATTTAGCATG
*
19833 TCCAGGGGCATTTTGGTCATTTTGCATG
1 TCCAGGGGCATTTTGGTCATTTAGCATG
* * *
19861 TCAAGGGGCATTTTGGTCATTCTTGCACG
1 TCCAGGGGCATTTTGGTCATT-TAGCATG
** *
19890 TCCAGGGGTTTTTTAGTCATTT
1 TCCAGGGGCATTTTGGTCATTT
19912 CAAGTACATT
Statistics
Matches: 122, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
28 99 0.81
29 23 0.19
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.39
Consensus pattern (28 bp):
TCCAGGGGCATTTTGGTCATTTAGCATG
Found at i:20459 original size:23 final size:24
Alignment explanation
Indices: 20433--20481 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
20423 ACAAAGATGG
20433 TGGTTTT-AC-CCTACATTTACATT
1 TGGTTTTCACTCC-ACATTTACATT
20456 TGGTTTTGCACTCCACATTTACATT
1 TGGTTTT-CACTCCACATTTACATT
20481 T
1 T
20482 TCTTTGGCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 7 0.30
25 14 0.61
26 2 0.09
ACGTcount: A:0.20, C:0.22, G:0.10, T:0.47
Consensus pattern (24 bp):
TGGTTTTCACTCCACATTTACATT
Done.