Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009161.1 Corchorus olitorius cultivar O-4 contig09189, 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, 811
Length: 1353
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:141 original size:57 final size:58
Alignment explanation
Indices: 13--168 Score: 253
Period size: 57 Copynumber: 2.7 Consensus size: 58
3 CAATGCAAAA
*
13 TTGACACAACACGGGGAAATCACTATATTCTATATTCTA-ATTCAAAATTCAAAGAAAAGAC
1 TTGACACAACACGGGGAAATCACTATAAT-TA-ATTCTATATT--AAATTCAAAGAAAAGAC
74 TTGACACAACACGGGGAAATCACTATAATTAATTCTATATT-AATTCAAAGAAAAGAC
1 TTGACACAACACGGGGAAATCACTATAATTAATTCTATATTAAATTCAAAGAAAAGAC
131 TTGACACAACACGGGGAAATCACTATAATTAATTCTAT
1 TTGACACAACACGGGGAAATCACTATAATTAATTCTAT
169 TAAATTGTAT
Statistics
Matches: 93, Mismatches: 1, Indels: 6
0.93 0.01 0.06
Matches are distributed among these distances:
57 54 0.58
59 6 0.06
60 5 0.05
61 28 0.30
ACGTcount: A:0.44, C:0.17, G:0.12, T:0.27
Consensus pattern (58 bp):
TTGACACAACACGGGGAAATCACTATAATTAATTCTATATTAAATTCAAAGAAAAGAC
Found at i:289 original size:55 final size:51
Alignment explanation
Indices: 67--291 Score: 130
Period size: 57 Copynumber: 4.1 Consensus size: 51
57 AAATTCAAAG
* *
67 AAAAGACTTGACACAACACGGGGAAATCACTATAATTAATTCTATATTAATTC
1 AAAAGAATTGACACAACACGGGGAAATCACTAAAATTAATTC--TATTAATTC
* * *
120 AAAGAAAAGACTTGACACAACACGGGGAAATCACTATAATTAATTCTATTAAATTGT
1 ----AAAAGAATTGACACAACACGGGGAAATCACTAAAATTAATTCTATT-AATT-C
* * * * * * * * * ***
177 ATATGAATT--CAAAAGAAGGGCAAATTACTAAAATTCTATATTGTATCAAAAGA
1 AAAAGAATTGACACAACACGGGGAAATCACTAAAA-T-TA-ATTCTAT-TAATTC
*
230 AAAAGAATTGATACAACACGGGGAAATCACTAAAATTCTATATTCTAATTAATTC
1 AAAAGAATTGACACAACACGGGGAAATCACTAAAA-T-TA-ATTCT-ATTAATTC
285 AAAAGAA
1 AAAAGAA
292 AAGAGCTCTA
Statistics
Matches: 131, Mismatches: 28, Indels: 20
0.73 0.16 0.11
Matches are distributed among these distances:
51 18 0.14
52 1 0.01
53 15 0.11
54 8 0.06
55 41 0.31
56 6 0.05
57 42 0.32
ACGTcount: A:0.47, C:0.13, G:0.12, T:0.27
Consensus pattern (51 bp):
AAAAGAATTGACACAACACGGGGAAATCACTAAAATTAATTCTATTAATTC
Found at i:392 original size:12 final size:12
Alignment explanation
Indices: 375--402 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
365 CCCCATTTNT
375 AAAAAAATTAAA
1 AAAAAAATTAAA
387 AAAAAAATTAAA
1 AAAAAAATTAAA
399 AAAA
1 AAAA
403 TTTCAAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAAAATTAAA
Found at i:410 original size:21 final size:22
Alignment explanation
Indices: 374--415 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
364 ACCCCATTTN
374 TAAAAAAATTAAAAAA-AAAAT
1 TAAAAAAATTAAAAAAGAAAAT
**
395 TAAAAAAATTTCAAAAGAAAA
1 TAAAAAAATTAAAAAAGAAAA
416 AGAGCTCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.19
Consensus pattern (22 bp):
TAAAAAAATTAAAAAAGAAAAT
Found at i:828 original size:27 final size:27
Alignment explanation
Indices: 798--877 Score: 74
Period size: 27 Copynumber: 3.0 Consensus size: 27
788 AAATAAATTT
798 AAGAAATTTAAAACACTTAGAAATGAA
1 AAGAAATTTAAAACACTTAGAAATGAA
* * ** **
825 AAGAAGTTTAGAAATGA-AAAGAAAT-TT
1 AAGAAATTTA-AAA-CACTTAGAAATGAA
852 AAGAAATTTAAAACACTTAGAAATGA
1 AAGAAATTTAAAACACTTAGAAATGA
878 GACGGATAAG
Statistics
Matches: 38, Mismatches: 11, Indels: 8
0.67 0.19 0.14
Matches are distributed among these distances:
25 1 0.03
26 9 0.24
27 18 0.47
28 9 0.24
29 1 0.03
ACGTcount: A:0.57, C:0.05, G:0.14, T:0.24
Consensus pattern (27 bp):
AAGAAATTTAAAACACTTAGAAATGAA
Found at i:858 original size:19 final size:18
Alignment explanation
Indices: 814--858 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 18
804 TTTAAAACAC
*
814 TTAGAAATGAAAAGAAGT
1 TTAGAAATGAAAAGAAAT
832 TTAGAAATGAAAAGAAAT
1 TTAGAAATGAAAAGAAAT
850 TTAAGAAAT
1 TT-AGAAAT
859 TTAAAACACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 19 0.76
19 6 0.24
ACGTcount: A:0.58, C:0.00, G:0.18, T:0.24
Consensus pattern (18 bp):
TTAGAAATGAAAAGAAAT
Found at i:1243 original size:15 final size:15
Alignment explanation
Indices: 1223--1253 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1213 TAGTTAACAT
1223 TAACATTAACTATGA
1 TAACATTAACTATGA
1238 TAACATTAACTATGA
1 TAACATTAACTATGA
1253 T
1 T
1254 CATTGTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.35
Consensus pattern (15 bp):
TAACATTAACTATGA
Done.