Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010279.1 Corchorus capsularis cultivar CVL-1 contig10300, 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: 13123
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Found at i:214 original size:27 final size:27
Alignment explanation
Indices: 184--238 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
174 ATTAGTAGTG
184 AAGAGTA-AGAAATGGTGA-TCAGTAAAA
1 AAGAGTACA-AAATGGT-ATTCAGTAAAA
*
211 AAGAGTACAAAGTGGTATTCAGTAAAA
1 AAGAGTACAAAATGGTATTCAGTAAAA
238 A
1 A
239 GGGATAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 1 0.04
27 23 0.92
28 1 0.04
ACGTcount: A:0.51, C:0.05, G:0.24, T:0.20
Consensus pattern (27 bp):
AAGAGTACAAAATGGTATTCAGTAAAA
Found at i:281 original size:26 final size:26
Alignment explanation
Indices: 251--341 Score: 76
Period size: 26 Copynumber: 3.3 Consensus size: 26
241 GATAAAAATG
*
251 GTAAAAAAGAGAAAAAATGGCATTAA
1 GTAAAAAAGAGAAAAAATGGAATTAA
*
277 GTAAAAAAGGAGAGTAAAAAAATAGTAATTAA
1 GT-AAAAA--AGAG--AAAAAAT-GGAATTAA
* * *
309 AT-AAAAAGAGTAAAAATGGTATTAA
1 GTAAAAAAGAGAAAAAATGGAATTAA
334 GTAAAAAA
1 GTAAAAAA
342 TGGTAATTAA
Statistics
Matches: 51, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
25 7 0.14
26 13 0.25
27 5 0.10
28 4 0.08
29 4 0.08
30 4 0.08
31 7 0.14
32 7 0.14
ACGTcount: A:0.63, C:0.01, G:0.18, T:0.19
Consensus pattern (26 bp):
GTAAAAAAGAGAAAAAATGGAATTAA
Found at i:284 original size:28 final size:27
Alignment explanation
Indices: 253--341 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 27
243 TAAAAATGGT
253 AAAAAAGAGAAAAAATGGCATTAAGTAA
1 AAAAAAGAGAAAAAATGG-ATTAAGTAA
* * *
281 AAAAGGAGAGTAAAAAAAT--AGTAATTAA
1 AAAA-AAGAG--AAAAAATGGATTAAGTAA
*
309 ATAAAAAGAGTAAAAATGGTATTAAGTAA
1 A-AAAAAGAGAAAAAATGG-ATTAAGTAA
338 AAAA
1 AAAA
342 TGGTAATTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
26 6 0.13
28 19 0.40
29 15 0.32
31 7 0.15
ACGTcount: A:0.64, C:0.01, G:0.17, T:0.18
Consensus pattern (27 bp):
AAAAAAGAGAAAAAATGGATTAAGTAA
Found at i:284 original size:46 final size:48
Alignment explanation
Indices: 205--296 Score: 118
Period size: 46 Copynumber: 2.0 Consensus size: 48
195 ATGGTGATCA
* * * *
205 GTAAAAAAGAGTACAAAGTGGTATTCAGTAAAAAGG-GA-TAAAAATG
1 GTAAAAAAGAGTAAAAAATGGCATTAAGTAAAAAGGAGAGTAAAAATG
251 GTAAAAAAGAG-AAAAAATGGCATTAAGTAAAAAAGGAGAGTAAAAA
1 GTAAAAAAGAGTAAAAAATGGCATTAAGT-AAAAAGGAGAGTAAAAA
297 AATAGTAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
45 13 0.33
46 18 0.46
47 2 0.05
48 6 0.15
ACGTcount: A:0.58, C:0.03, G:0.23, T:0.16
Consensus pattern (48 bp):
GTAAAAAAGAGTAAAAAATGGCATTAAGTAAAAAGGAGAGTAAAAATG
Found at i:338 original size:16 final size:17
Alignment explanation
Indices: 317--358 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
307 AAATAAAAAG
317 AGTAAAAATGGT-ATTA
1 AGTAAAAATGGTAATTA
333 AGTAAAAAATGGTAATTA
1 AGT-AAAAATGGTAATTA
*
351 AGCAAAAA
1 AGTAAAAA
359 GAGTGAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 3 0.13
17 14 0.61
18 6 0.26
ACGTcount: A:0.57, C:0.02, G:0.17, T:0.24
Consensus pattern (17 bp):
AGTAAAAATGGTAATTA
Found at i:340 original size:17 final size:18
Alignment explanation
Indices: 320--358 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
310 TAAAAAGAGT
*
320 AAAAATGGT-ATTAAGTA
1 AAAAATGGTAATTAAGCA
337 AAAAATGGTAATTAAGCA
1 AAAAATGGTAATTAAGCA
355 AAAA
1 AAAA
359 GAGTGAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.59, C:0.03, G:0.15, T:0.23
Consensus pattern (18 bp):
AAAAATGGTAATTAAGCA
Found at i:7833 original size:3 final size:3
Alignment explanation
Indices: 7827--7876 Score: 59
Period size: 3 Copynumber: 17.0 Consensus size: 3
7817 AGAAGTTATC
* *
7827 GAA GAA GAA -AA TGAA GAT GAA GAA GAA GAA GAA GAA AAA GAA GAA
1 GAA GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
7872 -AA GAA
1 GAA GAA
7877 TGATGAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 34 0.85
4 2 0.05
ACGTcount: A:0.68, C:0.00, G:0.28, T:0.04
Consensus pattern (3 bp):
GAA
Found at i:11391 original size:33 final size:33
Alignment explanation
Indices: 11345--11460 Score: 128
Period size: 33 Copynumber: 3.5 Consensus size: 33
11335 GCGCAACACT
11345 GGCCACAAGACCGGCCACGCGACATGGACATGTCC
1 GGCCAC-A-ACCGGCCACGCGACATGGACATGTCC
* *
11380 GGCCATC-ACCGGCCACGCGACATGCACATGGCC
1 GGCCA-CAACCGGCCACGCGACATGGACATGTCC
* ** *
11413 GGCTACAACCGGCCAAACGAC-TCGACCATGTCC
1 GGCCACAACCGGCCACGCGACATGGA-CATGTCC
11446 GGCCACAACCGGCCA
1 GGCCACAACCGGCCA
11461 AACGATCCTT
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
32 3 0.04
33 60 0.87
35 5 0.07
36 1 0.01
ACGTcount: A:0.25, C:0.41, G:0.26, T:0.09
Consensus pattern (33 bp):
GGCCACAACCGGCCACGCGACATGGACATGTCC
Found at i:12382 original size:9 final size:8
Alignment explanation
Indices: 12354--12390 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
12344 CACCACCTTC
12354 TTCAAAAA
1 TTCAAAAA
12362 TTCAAAAA
1 TTCAAAAA
*
12370 TTCAGAAAC
1 TTCA-AAAA
12379 TTCAAAAA
1 TTCAAAAA
12387 TTCA
1 TTCA
12391 TAGCCGATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
8 19 0.73
9 7 0.27
ACGTcount: A:0.54, C:0.16, G:0.03, T:0.27
Consensus pattern (8 bp):
TTCAAAAA
Done.