Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023907.1 Corchorus olitorius cultivar O-4 contig23940, 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: 27883
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:10987 original size:95 final size:95
Alignment explanation
Indices: 10824--11014 Score: 364
Period size: 95 Copynumber: 2.0 Consensus size: 95
10814 AATTCGTGGG
10824 AAGAAGCAGCTTGTGTGAATCTGGGTGTCCCCCCTAGAGTGAAATTCAGAATCCCTTTGCATATG
1 AAGAAGCAGCTTGTGTGAATCTGGGTGTCCCCCCTAGAGTGAAATTCAGAATCCCTTTGCATATG
10889 AGAGAGAGAAGTCTCCTTTCCTTAGCTGTA
66 AGAGAGAGAAGTCTCCTTTCCTTAGCTGTA
*
10919 AAGAAGCAGCTTGTGTGAATCTGGGTGTCCCCCCTAGAGTGAAATTCAGAATCGCTTTGCATATG
1 AAGAAGCAGCTTGTGTGAATCTGGGTGTCCCCCCTAGAGTGAAATTCAGAATCCCTTTGCATATG
*
10984 AGAGAGAGAAGTCTTCTTTCCTTAGCTGTA
66 AGAGAGAGAAGTCTCCTTTCCTTAGCTGTA
11014 A
1 A
11015 TTTCTTCCTT
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
95 94 1.00
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.29
Consensus pattern (95 bp):
AAGAAGCAGCTTGTGTGAATCTGGGTGTCCCCCCTAGAGTGAAATTCAGAATCCCTTTGCATATG
AGAGAGAGAAGTCTCCTTTCCTTAGCTGTA
Found at i:12217 original size:15 final size:15
Alignment explanation
Indices: 12163--12218 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 15
12153 ACATTACTTC
12163 TTTT-TATTTTGTAT
1 TTTTGTATTTTGTAT
**
12177 TTTTGCTA-TTTCCAT
1 TTTTG-TATTTTGTAT
* *
12192 TTTTTTTTTTTGTAT
1 TTTTGTATTTTGTAT
12207 TTTTGTATTTTG
1 TTTTGTATTTTG
12219 AGAAATATGT
Statistics
Matches: 31, Mismatches: 8, Indels: 5
0.70 0.18 0.11
Matches are distributed among these distances:
14 5 0.16
15 24 0.77
16 2 0.06
ACGTcount: A:0.11, C:0.05, G:0.09, T:0.75
Consensus pattern (15 bp):
TTTTGTATTTTGTAT
Found at i:14118 original size:94 final size:93
Alignment explanation
Indices: 13968--14313 Score: 346
Period size: 93 Copynumber: 3.8 Consensus size: 93
13958 ACAATTGAGT
* * * *
13968 CTTTGATTGAAAGCTTTGA--TTTTTGAATCAAAATTAACTTGAAAATTG-ATTATTGAATCTTT
1 CTTTGATTTAAAGGTTTGATTTTTTTGAATTAAAATTAACTTGGAAATTGAATT-TTGAATCTTT
14030 TTTAGTCAAGCTTAAGTTGAAAAGTAAAA
65 TTTAGTCAAGCTTAAGTTGAAAAGTAAAA
*
14059 CTTTGATTTAAAGGTTTGATTTTTTTTTAATTAAAATTAACTTGGAAATTGAATTTTGAATCTTT
1 CTTTGATTTAAAGGTTTGA-TTTTTTTGAATTAAAATTAACTTGGAAATTGAATTTTGAATCTTT
* * * * *
14124 TTTAGTTAATCTTTATTTGAAAATTAAAA
65 TTTAGTCAAGCTTAAGTTGAAAAGTAAAA
** * * *
14153 CTTTGATTTAAAGGTTTGATTTTTTTGAATTAAAGCTAACTTGGAAATTGATTTTTGAATCATCT
1 CTTTGATTTAAAGGTTTGATTTTTTTGAATTAAAATTAACTTGGAAATTGAATTTTGAATCTTTT
** * * * * * *
14218 AGAGTCAATCTTGATTTGAAAATTGAAT
66 TTAGTCAAGCTTAAGTTGAAAAGTAAAA
** * * * *
14246 CTTTGATTTAGTGGTTTGA--TTCTTGGATTAAAATTAACTT-GAGATTTG-ATAATTGAATCTT
1 CTTTGATTTAAAGGTTTGATTTTTTTGAATTAAAATTAACTTGGA-AATTGAAT-TTTGAATCTT
14307 TTTTAGT
64 TTTTAGT
14314 TAAGATAGAT
Statistics
Matches: 214, Mismatches: 35, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
90 3 0.01
91 50 0.23
93 79 0.37
94 79 0.37
95 3 0.01
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.46
Consensus pattern (93 bp):
CTTTGATTTAAAGGTTTGATTTTTTTGAATTAAAATTAACTTGGAAATTGAATTTTGAATCTTTT
TTAGTCAAGCTTAAGTTGAAAAGTAAAA
Found at i:14209 original size:93 final size:91
Alignment explanation
Indices: 13950--14313 Score: 381
Period size: 94 Copynumber: 3.9 Consensus size: 91
13940 TGAGTTAAGG
* * ** * * * *
13950 TTAATTTGACAATTGAGTCTTTGATTGAAAGCTTTGATTTTTGAATCAAAATTAACTTGAAAATT
1 TTAATTTGAAAATTAAAACTTTGATTTAAAGGTTTGATTTTTGAATTAAAATTAACTTGGAAATT
*
14015 GATTATTGAATCTTTTTTAGTCAAGC
66 GATTATTGAATCTTTTTTAGTCAATC
* * *
14041 TTAAGTTGAAAAGTAAAACTTTGATTTAAAGGTTTGATTTTTTTTTAATTAAAATTAACTTGGAA
1 TTAATTTGAAAATTAAAACTTTGATTTAAAGGTTTGA---TTTTTGAATTAAAATTAACTTGGAA
*
14106 ATTGAATT-TTGAATCTTTTTTAGTTAATC
63 ATTG-ATTATTGAATCTTTTTTAGTCAATC
* **
14135 TTTATTTGAAAATTAAAACTTTGATTTAAAGGTTTGATTTTTTTGAATTAAAGCTAACTTGGAAA
1 TTAATTTGAAAATTAAAACTTTGATTTAAAGGTTTGA--TTTTTGAATTAAAATTAACTTGGAAA
* * * **
14200 TTGATTTTTGAATCATCTAGAGTCAATC
64 TTGATTATTGAATCTTTTTTAGTCAATC
* * * ** * * *
14228 TTGATTTGAAAATTGAATCTTTGATTTAGTGGTTTGATTCTTGGATTAAAATTAACTT-GAGATT
1 TTAATTTGAAAATTAAAACTTTGATTTAAAGGTTTGATTTTTGAATTAAAATTAACTTGGA-AAT
*
14292 TGATAATTGAATCTTTTTTAGT
65 TGATTATTGAATCTTTTTTAGT
14314 TAAGATAGAT
Statistics
Matches: 227, Mismatches: 40, Indels: 12
0.81 0.14 0.04
Matches are distributed among these distances:
90 2 0.01
91 64 0.28
92 3 0.01
93 76 0.33
94 79 0.35
95 3 0.01
ACGTcount: A:0.33, C:0.06, G:0.15, T:0.46
Consensus pattern (91 bp):
TTAATTTGAAAATTAAAACTTTGATTTAAAGGTTTGATTTTTGAATTAAAATTAACTTGGAAATT
GATTATTGAATCTTTTTTAGTCAATC
Found at i:20946 original size:17 final size:18
Alignment explanation
Indices: 20914--20948 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
20904 TCCTCTTGCA
*
20914 TGAAAGCACTTCTTTTTT
1 TGAAAGCAATTCTTTTTT
20932 TGAAAGCAATT-TTTTTT
1 TGAAAGCAATTCTTTTTT
20949 ACTACCCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.51
Consensus pattern (18 bp):
TGAAAGCAATTCTTTTTT
Found at i:24946 original size:16 final size:17
Alignment explanation
Indices: 24925--24959 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
24915 AGCTTCCTAG
24925 AAAAAACTCAAAA-AAA
1 AAAAAACTCAAAAGAAA
24941 AAAAAACTCAAAAGAAA
1 AAAAAACTCAAAAGAAA
24958 AA
1 AA
24960 TTGTTAGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.80, C:0.11, G:0.03, T:0.06
Consensus pattern (17 bp):
AAAAAACTCAAAAGAAA
Found at i:25167 original size:28 final size:28
Alignment explanation
Indices: 25100--25169 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
25090 TTATGATGCA
25100 AAAACTCTTTTTTTTCTTTTCAAAAACGC
1 AAAACT-TTTTTTTTCTTTTCAAAAACGC
* **
25129 AACACAATTTTTTTTT-AATT-AAAAACGC
1 AA-A-ACTTTTTTTTTCTTTTCAAAAACGC
25157 AAAACTTTTTTTT
1 AAAACTTTTTTTT
25170 ATGACGCAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
26 9 0.26
27 1 0.03
28 10 0.29
29 4 0.11
30 9 0.26
31 2 0.06
ACGTcount: A:0.36, C:0.16, G:0.03, T:0.46
Consensus pattern (28 bp):
AAAACTTTTTTTTTCTTTTCAAAAACGC
Found at i:25541 original size:15 final size:16
Alignment explanation
Indices: 25517--25556 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
25507 AGAGGTTGAA
*
25517 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
25532 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
25548 AGAAAACAA
1 AGAAAACAA
25557 AGCAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Done.