Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017744.1 Corchorus olitorius cultivar O-4 contig17777, 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: 9229
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Found at i:1622 original size:47 final size:48
Alignment explanation
Indices: 1516--2334 Score: 930
Period size: 47 Copynumber: 16.5 Consensus size: 48
1506 AAGTAGAAGA
* *
1516 TAATTAAACTAAGTAGTAAAAGAAGAAGAA-ATTTAGTTTAATCCTAAG
1 TAATTAAACTAAGTAGTAAAAGAAGAAGAAGA-TTAGTTTAATTCTAGG
*
1564 TAATTAGACTAAG-AGGTAAAAGAAGAAGAAG-TTAGTTTAATTCTAGG
1 TAATTAAACTAAGTA-GTAAAAGAAGAAGAAGATTAGTTTAATTCTAGG
1611 TAATTAAACTAAGTAGTAAAAGAGGAGGAAATTAGAAGAGATTAGTTTAATTCTAGG
1 TAATTAAACTAAGTAGTAAAAGA--A-G--A--AG-A-AGATTAGTTTAATTCTAGG
1668 TAATTAAACTAAGTAGTAAAAGAGGAGGAAATTAGAAGAGATTAGTTTAATTCTAGG
1 TAATTAAACTAAGTAGTAAAAGA--A-G--A--AG-A-AGATTAGTTTAATTCTAGG
* * *
1725 TGATTAAACTAAGTAGTAAAAGAAGAGGAA-ATTTGTTTAATTCTAGG
1 TAATTAAACTAAGTAGTAAAAGAAGAAGAAGATTAGTTTAATTCTAGG
* *
1772 TAATTAAACTAAGTAGTAAAAGAAGAAGAA-ATTTAGTTTAATCCTAAG
1 TAATTAAACTAAGTAGTAAAAGAAGAAGAAGA-TTAGTTTAATTCTAGG
* *
1820 TAATTAGACTAAG-AGGTAAAAGAAGAAGAAG-TTAGTTTAATTCCAGG
1 TAATTAAACTAAGTA-GTAAAAGAAGAAGAAGATTAGTTTAATTCTAGG
1867 TAATTAAACTAAGTAGTAAAAGAGGAGGAAATTAGAAGAGATTAGTTTAATTCTAGG
1 TAATTAAACTAAGTAGTAAAAGA--A-G--A--AG-A-AGATTAGTTTAATTCTAGG
*
1924 TAATTAAACTAAGTAGTAAAAGAGGAGGAAATTAGACGAGATTAGTTTAATTATAGG
1 TAATTAAACTAAGTAGTAAAAGA--A-G--A--AGA--AGATTAGTTTAATTCTAGG
* * *
1981 TGATTAAACTAAGTAGTAAAAGAAGAGGAA-ATTTGTTTAATTCTAGG
1 TAATTAAACTAAGTAGTAAAAGAAGAAGAAGATTAGTTTAATTCTAGG
*
2028 TAATTAGACTAAGTAGTAAAAGAAGAAG-AGATTAGTTTAATTCTAGG
1 TAATTAAACTAAGTAGTAAAAGAAGAAGAAGATTAGTTTAATTCTAGG
2075 TAATTAAACTAAGTAGTAAAAGAAGAAG-AGATTAGTTTAATTCTAGG
1 TAATTAAACTAAGTAGTAAAAGAAGAAGAAGATTAGTTTAATTCTAGG
* * *
2122 TAATTAAACTAAGTAGTAAGAGAGGATG-AGATTAGTTTAATTCTAGG
1 TAATTAAACTAAGTAGTAAAAGAAGAAGAAGATTAGTTTAATTCTAGG
* *
2169 TAGTTAAACTAGGTAGTAAAAGAAGAAG-AGATTAGTTTAATTCTAGG
1 TAATTAAACTAAGTAGTAAAAGAAGAAGAAGATTAGTTTAATTCTAGG
2216 TAATTAAACTAAGTAGTAAAAGAAGAAG-AGATTAGTTTAATTCTAGG
1 TAATTAAACTAAGTAGTAAAAGAAGAAGAAGATTAGTTTAATTCTAGG
* * * *
2263 TAATTAAACTAAGTGGTAAAAGGAA-AAG-AGATTGGTTTAAGTCTAGA
1 TAATTAAACTAAGTAGTAAAA-GAAGAAGAAGATTAGTTTAATTCTAGG
* *
2310 TAATTAAACTAAGTAGCAGAAGAAG
1 TAATTAAACTAAGTAGTAAAAGAAG
2335 GGAATATTTG
Statistics
Matches: 695, Mismatches: 45, Indels: 63
0.87 0.06 0.08
Matches are distributed among these distances:
46 4 0.01
47 404 0.58
48 74 0.11
49 3 0.00
50 5 0.01
52 4 0.01
54 6 0.01
55 4 0.01
56 5 0.01
57 186 0.27
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.29
Consensus pattern (48 bp):
TAATTAAACTAAGTAGTAAAAGAAGAAGAAGATTAGTTTAATTCTAGG
Found at i:1643 original size:28 final size:28
Alignment explanation
Indices: 1612--1701 Score: 74
Period size: 28 Copynumber: 3.2 Consensus size: 28
1602 AATTCTAGGT
1612 AATTAAACTAAGTAGTAAAAGAGGAGGA
1 AATTAAACTAAGTAGTAAAAGAGGAGGA
* * ** **** *
1640 AATTAGAA-GAGATTAGTTTAATTCTAGGT
1 AATTA-AACTA-AGTAGTAAAAGAGGAGGA
1669 AATTAAACTAAGTAGTAAAAGAGGAGGA
1 AATTAAACTAAGTAGTAAAAGAGGAGGA
1697 AATTA
1 AATTA
1702 GAAGAGATTA
Statistics
Matches: 41, Mismatches: 18, Indels: 6
0.63 0.28 0.09
Matches are distributed among these distances:
28 23 0.56
29 18 0.44
ACGTcount: A:0.49, C:0.03, G:0.22, T:0.26
Consensus pattern (28 bp):
AATTAAACTAAGTAGTAAAAGAGGAGGA
Found at i:1899 original size:28 final size:28
Alignment explanation
Indices: 1868--1957 Score: 74
Period size: 28 Copynumber: 3.2 Consensus size: 28
1858 AATTCCAGGT
1868 AATTAAACTAAGTAGTAAAAGAGGAGGA
1 AATTAAACTAAGTAGTAAAAGAGGAGGA
* * ** **** *
1896 AATTAGAA-GAGATTAGTTTAATTCTAGGT
1 AATTA-AACTA-AGTAGTAAAAGAGGAGGA
1925 AATTAAACTAAGTAGTAAAAGAGGAGGA
1 AATTAAACTAAGTAGTAAAAGAGGAGGA
1953 AATTA
1 AATTA
1958 GACGAGATTA
Statistics
Matches: 41, Mismatches: 18, Indels: 6
0.63 0.28 0.09
Matches are distributed among these distances:
28 23 0.56
29 18 0.44
ACGTcount: A:0.49, C:0.03, G:0.22, T:0.26
Consensus pattern (28 bp):
AATTAAACTAAGTAGTAAAAGAGGAGGA
Found at i:1971 original size:256 final size:255
Alignment explanation
Indices: 1516--2284 Score: 1222
Period size: 256 Copynumber: 3.1 Consensus size: 255
1506 AAGTAGAAGA
1516 TAATTAAACTAAGTAGTAAAAGAAGAAGAAATTTAGTTTAATCCTAAGTAATTAGACTAAGAGGT
1 TAATTAAACTAAGTAGTAAAAGAAGAAGAAATTTAGTTTAATCCTAAGTAATTAGACTAAGAGGT
1581 AAAAGAAGAAGAAGTTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAGGAGGAAATTAG
66 AAAAGAAGAAGAAGTTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAGGAGGAAATTAG
1646 AAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAGGAGGAAATTAGAAGAGATT
131 AAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAGGAGGAAATTAG-AGAGATT
1711 AGTTTAATTCTAGGTGATTAAACTAAGTAGTAAAAGAAGAGGAAATTTGTTTAATTCTAGG
195 AGTTTAATTCTAGGTGATTAAACTAAGTAGTAAAAGAAGAGGAAATTTGTTTAATTCTAGG
1772 TAATTAAACTAAGTAGTAAAAGAAGAAGAAATTTAGTTTAATCCTAAGTAATTAGACTAAGAGGT
1 TAATTAAACTAAGTAGTAAAAGAAGAAGAAATTTAGTTTAATCCTAAGTAATTAGACTAAGAGGT
*
1837 AAAAGAAGAAGAAGTTAGTTTAATTCCAGGTAATTAAACTAAGTAGTAAAAGAGGAGGAAATTAG
66 AAAAGAAGAAGAAGTTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAGGAGGAAATTAG
1902 AAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAGGAGGAAATTAGACGAGATT
131 AAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAGGAGGAAATTAGA-GAGATT
*
1967 AGTTTAATTATAGGTGATTAAACTAAGTAGTAAAAGAAGAGGAAATTTGTTTAATTCTAGG
195 AGTTTAATTCTAGGTGATTAAACTAAGTAGTAAAAGAAGAGGAAATTTGTTTAATTCTAGG
* * * * *
2028 TAATTAGACTAAGTAGTAAAAGAAGAAGAGA-TTAGTTTAATTCTAGGTAATTAAACTAAGTA-G
1 TAATTAAACTAAGTAGTAAAAGAAGAAGAAATTTAGTTTAATCCTAAGTAATTAGACTAAG-AGG
2091 TAAAAGAAGAAG-AGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGT--AAGA-GAGG--A-T
65 TAAAAGAAGAAGAAG-TTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAGGAGGAAATT
* *
2149 ----GAGATTAGTTTAATTCTAGGTAGTTAAACTAGGTAGTAAAAGA--A-G-----A-AGAGAT
129 AGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAGGAGGAAATTAGAGAGAT
* * * *
2201 TAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGATTAGTTTAATTCTAGG
194 TAGTTTAATTCTAGGTGATTAAACTAAGTAGTAAAAGAAGAGGAAATTTGTTTAATTCTAGG
*
2263 TAATTAAACTAAGTGGTAAAAG
1 TAATTAAACTAAGTAGTAAAAG
2285 GAAAAGAGAT
Statistics
Matches: 493, Mismatches: 17, Indels: 27
0.92 0.03 0.05
Matches are distributed among these distances:
235 82 0.17
236 1 0.00
237 1 0.00
242 1 0.00
243 1 0.00
245 41 0.08
249 1 0.00
250 1 0.00
252 4 0.01
253 4 0.01
254 2 0.00
255 72 0.15
256 282 0.57
ACGTcount: A:0.45, C:0.04, G:0.21, T:0.29
Consensus pattern (255 bp):
TAATTAAACTAAGTAGTAAAAGAAGAAGAAATTTAGTTTAATCCTAAGTAATTAGACTAAGAGGT
AAAAGAAGAAGAAGTTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAGGAGGAAATTAG
AAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAGGAGGAAATTAGAGAGATTA
GTTTAATTCTAGGTGATTAAACTAAGTAGTAAAAGAAGAGGAAATTTGTTTAATTCTAGG
Found at i:2799 original size:58 final size:57
Alignment explanation
Indices: 2698--2809 Score: 165
Period size: 58 Copynumber: 1.9 Consensus size: 57
2688 AGCATCATGC
*
2698 CTCGGTCCTAAAACGTCTTTTTTAGACATCTAATAGAAAACATGTCACTCGATAAGT
1 CTCGGTCCGAAAACGTCTTTTTTAGACATCTAATAGAAAACATGTCACTCGATAAGT
*
2755 CTCGGTCCGAAAACGTCTTTTTTTATG-CATCTAATA-AAGAACATGTCACTTGATA
1 CTCGGTCCGAAAACGTC-TTTTTTA-GACATCTAATAGAA-AACATGTCACTCGATA
2810 TTTGATTAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
57 18 0.36
58 31 0.62
59 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (57 bp):
CTCGGTCCGAAAACGTCTTTTTTAGACATCTAATAGAAAACATGTCACTCGATAAGT
Found at i:3369 original size:11 final size:11
Alignment explanation
Indices: 3353--3377 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3343 TTTTTGTACA
3353 AGTTAGAATAT
1 AGTTAGAATAT
3364 AGTTAGAATAT
1 AGTTAGAATAT
3375 AGT
1 AGT
3378 AGCATTCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.20, T:0.36
Consensus pattern (11 bp):
AGTTAGAATAT
Found at i:8103 original size:6 final size:6
Alignment explanation
Indices: 8034--8109 Score: 59
Period size: 6 Copynumber: 12.5 Consensus size: 6
8024 CCAAGCCTGG
* * *
8034 AAAAGA AAAAAA AAGAGAGA GAAAAGA AAAAGGA AAAAGA AAAGGA AAACG-
1 AAAAGA AAAAGA AA-A-AGA -AAAAGA AAAA-GA AAAAGA AAAAGA AAAAGA
*
8085 AAAAG- GAAA-A AAAAGA AAAAGA AAA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAA
8110 TAAAAGAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
5 10 0.18
6 32 0.56
7 10 0.18
8 3 0.05
9 2 0.04
ACGTcount: A:0.78, C:0.01, G:0.21, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:8998 original size:28 final size:28
Alignment explanation
Indices: 8930--9004 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 28
8920 TATGGGCATA
* *
8930 AAATTACCGTTTTACCCTAAGAATGAAT
1 AAATTACAGTTTTACCCTTAGAATGAAT
**
8958 AAATTACCA-TTTTACCCTTAGAA-GGTT
1 AAATTA-CAGTTTTACCCTTAGAATGAAT
*
8985 AAATTTACAGTTTTAACCTT
1 AAA-TTACAGTTTTACCCTT
9005 GTACTTTGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
27 7 0.18
28 31 0.79
29 1 0.03
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.37
Consensus pattern (28 bp):
AAATTACAGTTTTACCCTTAGAATGAAT
Done.