Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024167.1 Corchorus olitorius cultivar O-4 contig24200, 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: 3877
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:1763 original size:20 final size:20
Alignment explanation
Indices: 1725--1765 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1715 AAAATGAGCA
*
1725 CCAATTTGTAAACCGAATGC
1 CCAATTTGTAAACCAAATGC
*
1745 CCAATTTGTAAATCAAATGC
1 CCAATTTGTAAACCAAATGC
1765 C
1 C
1766 TTTTATTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (20 bp):
CCAATTTGTAAACCAAATGC
Found at i:2314 original size:28 final size:26
Alignment explanation
Indices: 2256--2329 Score: 76
Period size: 28 Copynumber: 2.7 Consensus size: 26
2246 CGGCACTAAG
*
2256 ATGACCACAATGCCCCCCTTGAACCAAAA
1 ATGACCAAAATG--CCCC-TGAACCAAAA
* *
2285 ATGACTATAATGCCCCTGAACCTACAAA
1 ATGACCAAAATGCCCCTGAACC-A-AAA
2313 ATGACCAAAATGCCCCT
1 ATGACCAAAATGCCCCT
2330 ATATGACCCT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
26 6 0.15
27 5 0.13
28 18 0.46
29 10 0.26
ACGTcount: A:0.38, C:0.34, G:0.11, T:0.18
Consensus pattern (26 bp):
ATGACCAAAATGCCCCTGAACCAAAA
Found at i:2578 original size:18 final size:18
Alignment explanation
Indices: 2520--2580 Score: 61
Period size: 17 Copynumber: 3.3 Consensus size: 18
2510 TACTAAAATC
2520 TCTTTTTCTATTTTCTCTCCT
1 TCTTTTTCT-TTTT-T-TCCT
* * *
2541 TCTTCTCCTTTTTTT-TT
1 TCTTTTTCTTTTTTTCCT
2558 TCTTTTTCTTTTTTTCCT
1 TCTTTTTCTTTTTTTCCT
2576 TCTTT
1 TCTTT
2581 CTCCTTCTTG
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
17 14 0.42
18 7 0.21
19 1 0.03
20 4 0.12
21 7 0.21
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.74
Consensus pattern (18 bp):
TCTTTTTCTTTTTTTCCT
Found at i:2763 original size:47 final size:46
Alignment explanation
Indices: 2663--2781 Score: 150
Period size: 47 Copynumber: 2.5 Consensus size: 46
2653 ACTTCTTATA
* * *
2663 AACTCGCGTGGAACCGAGAAAAAGACCAACTTTGTTCACTAAATCAT
1 AACTCGCGTGGAAACGAG-AAAAGACCAACTTTGGTCACTAAATCAC
* *
2710 AGACTCGCATGGAAGCGAGAAAAGACCAACTTTGGTCACTAAAATGC-C
1 A-ACTCGCGTGGAAACGAGAAAAGACCAACTTTGGTCACT-AAAT-CAC
2758 AACTCGCGTGGAAACGAGAAAAGA
1 AACTCGCGTGGAAACGAGAAAAGA
2782 TTACTTGGAT
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
47 42 0.67
48 20 0.32
49 1 0.02
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (46 bp):
AACTCGCGTGGAAACGAGAAAAGACCAACTTTGGTCACTAAATCAC
Found at i:3076 original size:69 final size:68
Alignment explanation
Indices: 2892--3167 Score: 356
Period size: 68 Copynumber: 4.0 Consensus size: 68
2882 CTCATTGAAC
* * * * **
2892 TTGGCTTATGGAAAAG-CTCATGTTGCTTGAATGGAACCAATGCTTGACTGACTCGTATAGAAAC
1 TTGGCTTGTGGAAAAGCCTC-TGCTGCTTGGATGGAACCAAGGCTAAACTGACTCGTATAGAAAC
2956 GAGT
65 GAGT
* * * * * *
2960 TTGGCTCGTGGAAAAGCCCCGGCTGCTTGGATGGAATCAAGGCTAAACGGACTCGTACAGAAACG
1 TTGGCTTGTGGAAAAGCCTCTGCTGCTTGGATGGAACCAAGGCTAAACTGACTCGTATAGAAACG
3025 AGT
66 AGT
* * *
3028 TTGGCTTGTGGAAAAAGCCTCTGCTGCTCGGATGGAACCAAGGCTAAACTGACTCGTGTGGAAAC
1 TTGGCTTGTGG-AAAAGCCTCTGCTGCTTGGATGGAACCAAGGCTAAACTGACTCGTATAGAAAC
3093 GAGT
65 GAGT
* * * *
3097 TTGGCTTGTGGAAAAGCCTCTGCTGCTTGGATGGAACCAAGGCTAAACTAACTAGTGTGGAAACG
1 TTGGCTTGTGGAAAAGCCTCTGCTGCTTGGATGGAACCAAGGCTAAACTGACTCGTATAGAAACG
3162 AGT
66 AGT
3165 TTG
1 TTG
3168 CAAAATTTAT
Statistics
Matches: 182, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
68 120 0.66
69 62 0.34
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.25
Consensus pattern (68 bp):
TTGGCTTGTGGAAAAGCCTCTGCTGCTTGGATGGAACCAAGGCTAAACTGACTCGTATAGAAACG
AGT
Found at i:3160 original size:137 final size:136
Alignment explanation
Indices: 2892--3167 Score: 356
Period size: 137 Copynumber: 2.0 Consensus size: 136
2882 CTCATTGAAC
* * * **
2892 TTGGCTTATGGAAAAGCTCATGTTGCTTGAATGGAACCAATGCTTGACTGACTCGTATAGAAACG
1 TTGGCTTATGGAAAAGCTCATGCTGCTCGAATGGAACCAAGGCTAAACTGACTCGTATAGAAACG
* * *
2957 AGTTTGGCTCGTGGAAAAGCCCCGGCTGCTTGGATGGAATCAAGGCTAAACGGACTCGTACAGAA
66 AGTTTGGCTCGTGGAAAAGCCCCGGCTGCTTGGATGGAACCAAGGCTAAACGAACTAGTACAGAA
3022 ACGAGT
131 ACGAGT
* * * *
3028 TTGGCTTGTGGAAAAAGCCTC-TGCTGCTCGGATGGAACCAAGGCTAAACTGACTCGTGTGGAAA
1 TTGGCTTATGG-AAAAG-CTCATGCTGCTCGAATGGAACCAAGGCTAAACTGACTCGTATAGAAA
* * * * ***
3092 CGAGTTTGGCTTGTGGAAAAGCCTCTGCTGCTTGGATGGAACCAAGGCTAAACTAACTAGTGTGG
64 CGAGTTTGGCTCGTGGAAAAGCCCCGGCTGCTTGGATGGAACCAAGGCTAAACGAACTAGTACAG
3157 AAACGAGT
129 AAACGAGT
3165 TTG
1 TTG
3168 CAAAATTTAT
Statistics
Matches: 119, Mismatches: 19, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
136 10 0.08
137 106 0.89
138 3 0.03
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.25
Consensus pattern (136 bp):
TTGGCTTATGGAAAAGCTCATGCTGCTCGAATGGAACCAAGGCTAAACTGACTCGTATAGAAACG
AGTTTGGCTCGTGGAAAAGCCCCGGCTGCTTGGATGGAACCAAGGCTAAACGAACTAGTACAGAA
ACGAGT
Found at i:3373 original size:16 final size:15
Alignment explanation
Indices: 3334--3375 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
3324 ACAGAGGTTG
3334 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
*
3349 ACGGAAAACAATTAA
1 ACAGAAAACAATTAA
3364 ACTAGAAAACAA
1 AC-AGAAAACAA
3376 AGCAGAGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 16 0.67
16 8 0.33
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.