Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011946.1 Corchorus olitorius cultivar O-4 contig11979, 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: 11722
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Found at i:1707 original size:30 final size:30
Alignment explanation
Indices: 1671--1935 Score: 318
Period size: 30 Copynumber: 9.1 Consensus size: 30
1661 TTAACTGATG
* ** *
1671 AAGCAATGATCCTAAAATAGGATTAAAACA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
1701 AAGCAATGATCCT-AGACCAGGA-T----T-
1 AAGCAATGATCCTCA-ACCAGGATTAAAATA
*
1725 AA--AATGATCCTCAACCAGGATTAAAATG
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
1753 GAGCAAAT-ATCCTCAACCAGGATTAAAATA
1 AAGC-AATGATCCTCAACCAGGATTAAAATA
*
1783 AAGCAATGATCCTCAACCATGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* *
1813 AAGCAATGATCCTCAAACAGGATTAAAATG
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* *
1843 AAGCAATGATCCTCAAACATGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
1873 AAGCAATGATCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
1903 AAGCAAAT-ATCCTCAACCAGGATTGAAAATA
1 AAGC-AATGATCCTCAACCAGGATT-AAAATA
1934 AA
1 AA
1936 TTGATAAAAT
Statistics
Matches: 207, Mismatches: 14, Indels: 27
0.83 0.06 0.11
Matches are distributed among these distances:
22 16 0.08
23 2 0.01
24 2 0.01
27 1 0.00
28 1 0.00
29 5 0.02
30 166 0.80
31 14 0.07
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.21
Consensus pattern (30 bp):
AAGCAATGATCCTCAACCAGGATTAAAATA
Found at i:1733 original size:22 final size:22
Alignment explanation
Indices: 1705--1752 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
1695 AAAACAAAGC
1705 AATGATCCT-AGACCAGGATTAA
1 AATGATCCTCA-ACCAGGATTAA
1727 AATGATCCTCAACCAGGATTAA
1 AATGATCCTCAACCAGGATTAA
1749 AATG
1 AATG
1753 GAGCAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 24 0.96
23 1 0.04
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.23
Consensus pattern (22 bp):
AATGATCCTCAACCAGGATTAA
Found at i:2227 original size:37 final size:36
Alignment explanation
Indices: 2147--2505 Score: 321
Period size: 35 Copynumber: 10.3 Consensus size: 36
2137 CAATTTGTGG
* * *
2147 TCAACTGAAATAAACTGCAGAAAAGATCGCCCTAGA
1 TCAACTGAAATAAATTGAAGAAAAGATCGCCCTGGA
* * * *
2183 TCAATTGAAATAAACTGAAGAAAAATATTGCCCTGGA
1 TCAACTGAAATAAATTGAAG-AAAAGATCGCCCTGGA
* * * *
2220 TCCATTGAAATAAATCGAAGAAACGATCGCCCTGGA
1 TCAACTGAAATAAATTGAAGAAAAGATCGCCCTGGA
*
2256 TCAACTGAAATACATTGAAGAAAGAGATCGCCCTGGA
1 TCAACTGAAATAAATTGAAGAAA-AGATCGCCCTGGA
* *
2293 TCAACTGAAATATATTG-AGGAAAGATCGCCCTGGA
1 TCAACTGAAATAAATTGAAGAAAAGATCGCCCTGGA
* *
2328 TCAACTGAAATAAATTGAAG-AAAGACCGCCCTGGG
1 TCAACTGAAATAAATTGAAGAAAAGATCGCCCTGGA
*
2363 TCAACTGAAATAACTTGAAG-AAAGATCGCCCTGGA
1 TCAACTGAAATAAATTGAAGAAAAGATCGCCCTGGA
* * * *
2398 TCAATTAAAATAAACT---GAATA-A----CCTGGA
1 TCAACTGAAATAAATTGAAGAAAAGATCGCCCTGGA
* * * * *
2426 TCAATTAAAATACACTGAA-TAAAGATCGCCCTGGA
1 TCAACTGAAATAAATTGAAGAAAAGATCGCCCTGGA
* * * * * *
2461 TCAACTGAAATAAACTGAA-TAAGGACCACCCTGGG
1 TCAACTGAAATAAATTGAAGAAAAGATCGCCCTGGA
2496 TCAACTGAAA
1 TCAACTGAAA
2506 CGAACTAAAG
Statistics
Matches: 272, Mismatches: 39, Indels: 25
0.81 0.12 0.07
Matches are distributed among these distances:
28 21 0.08
30 2 0.01
31 1 0.00
32 2 0.01
33 2 0.01
35 130 0.48
36 56 0.21
37 58 0.21
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.20
Consensus pattern (36 bp):
TCAACTGAAATAAATTGAAGAAAAGATCGCCCTGGA
Found at i:2275 original size:73 final size:72
Alignment explanation
Indices: 2147--2416 Score: 312
Period size: 73 Copynumber: 3.8 Consensus size: 72
2137 CAATTTGTGG
* * * * *
2147 TCAACTGAAATAAA-CTGCAGAAAAGATCGCCCTAGATCAATTGAAATAAACTGAAGAAAAATAT
1 TCAACTGAAATAAATC-GAAG-AAAGATCGCCCTGGATCAACTGAAATAAATTGAAGAAAAAGAT
*
2211 TGCCCTGGA
64 CGCCCTGGA
* * * *
2220 TCCATTGAAATAAATCGAAGAAACGATCGCCCTGGATCAACTGAAATACATTGAAGAAAGAGATC
1 TCAACTGAAATAAATCGAAGAAA-GATCGCCCTGGATCAACTGAAATAAATTGAAGAAAAAGATC
2285 GCCCTGGA
65 GCCCTGGA
* * * *
2293 TCAACTGAAATATATTGAGGAAAGATCGCCCTGGATCAACTGAAATAAATTGAAG--AAAGACCG
1 TCAACTGAAATAAATCGAAGAAAGATCGCCCTGGATCAACTGAAATAAATTGAAGAAAAAGATCG
*
2356 CCCTGGG
66 CCCTGGA
* * * * *
2363 TCAACTGAAATAACTTGAAGAAAGATCGCCCTGGATCAATTAAAATAAACTGAA
1 TCAACTGAAATAAATCGAAGAAAGATCGCCCTGGATCAACTGAAATAAATTGAA
2417 TAACCTGGAT
Statistics
Matches: 170, Mismatches: 25, Indels: 7
0.84 0.12 0.03
Matches are distributed among these distances:
70 60 0.35
72 34 0.20
73 75 0.44
74 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.20
Consensus pattern (72 bp):
TCAACTGAAATAAATCGAAGAAAGATCGCCCTGGATCAACTGAAATAAATTGAAGAAAAAGATCG
CCCTGGA
Found at i:2432 original size:28 final size:28
Alignment explanation
Indices: 2392--2447 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
2382 GAAAGATCGC
2392 CCTGGATCAATTAAAATAAACTGAATAA
1 CCTGGATCAATTAAAATAAACTGAATAA
*
2420 CCTGGATCAATTAAAATACACTGAATAA
1 CCTGGATCAATTAAAATAAACTGAATAA
2448 AGATCGCCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.48, C:0.16, G:0.11, T:0.25
Consensus pattern (28 bp):
CCTGGATCAATTAAAATAAACTGAATAA
Found at i:2493 original size:98 final size:98
Alignment explanation
Indices: 2322--2499 Score: 232
Period size: 98 Copynumber: 1.8 Consensus size: 98
2312 GAAAGATCGC
* * *
2322 CCTGGATCAACTGAAATAAATTGAAGAAAGACCGCCCTGGGTCAACTGAAATAACTTGAAGAAAG
1 CCTGGATCAACTAAAATAAACTGAAGAAAGACCGCCCTGGATCAACTGAAATAACTTGAAGAAAG
* *
2387 ATCGCCCTGGATCAATTAAAATAAACTGAATAA
66 ACCACCCTGGATCAATTAAAATAAACTGAATAA
* * * * * *
2420 CCTGGATCAATTAAAATACACTGAATAAAGATCGCCCTGGATCAACTGAAATAAAC-TGAATAAG
1 CCTGGATCAACTAAAATAAACTGAAGAAAGACCGCCCTGGATCAACTGAAAT-AACTTGAAGAAA
*
2484 GACCACCCTGGGTCAA
65 GACCACCCTGGATCAA
2500 CTGAAACGAA
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
98 64 0.96
99 3 0.04
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (98 bp):
CCTGGATCAACTAAAATAAACTGAAGAAAGACCGCCCTGGATCAACTGAAATAACTTGAAGAAAG
ACCACCCTGGATCAATTAAAATAAACTGAATAA
Found at i:4245 original size:5 final size:6
Alignment explanation
Indices: 4231--4255 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4221 TCAGGCCAAG
4231 TTTTCT TTTTCT TTTTCT TTTTCT T
1 TTTTCT TTTTCT TTTTCT TTTTCT T
4256 CTTCCGAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTCT
Found at i:6056 original size:19 final size:18
Alignment explanation
Indices: 6023--6058 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
6013 TTGAAATAGA
6023 TCTTCAAAAATCTTCAAG
1 TCTTCAAAAATCTTCAAG
*
6041 TCTTCAAATTATCTTCAA
1 TCTTCAAA-AATCTTCAA
6059 ATGGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (18 bp):
TCTTCAAAAATCTTCAAG
Done.