Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021772.1 Corchorus olitorius cultivar O-4 contig21805, 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: 46411
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Found at i:10109 original size:20 final size:20
Alignment explanation
Indices: 10084--10126 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
10074 AAATATTAAG
10084 GGGAGAAAG-GAAGAGAGAGA
1 GGGAGAAAGCGAAG-GAGAGA
*
10104 GGGAGAAAGCGAAGGATAGA
1 GGGAGAAAGCGAAGGAGAGA
10124 GGG
1 GGG
10127 GGATATAGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.44, C:0.02, G:0.51, T:0.02
Consensus pattern (20 bp):
GGGAGAAAGCGAAGGAGAGA
Found at i:11425 original size:15 final size:16
Alignment explanation
Indices: 11400--11433 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
11390 CCAAAACCCT
*
11400 CCCCTTCTCTAGCCCA
1 CCCCTTCTCTACCCCA
11416 CCCC-TCTCTACCCCA
1 CCCCTTCTCTACCCCA
11431 CCC
1 CCC
11434 ATCCCTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.12, C:0.65, G:0.03, T:0.21
Consensus pattern (16 bp):
CCCCTTCTCTACCCCA
Found at i:17281 original size:19 final size:20
Alignment explanation
Indices: 17248--17286 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
17238 TTTTAGAAGT
17248 AATGACTCTTAAGGCATTGC
1 AATGACTCTTAAGGCATTGC
17268 AATGACTC-TAAGGCATTGC
1 AATGACTCTTAAGGCATTGC
17287 CTGCTAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (20 bp):
AATGACTCTTAAGGCATTGC
Found at i:19083 original size:5 final size:5
Alignment explanation
Indices: 19057--19097 Score: 54
Period size: 5 Copynumber: 9.0 Consensus size: 5
19047 ACAAAACATG
19057 ATTTT A-TTT A-TTT -TTTT A-TTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
19098 TTGTTTCAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 14 0.42
5 19 0.58
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:23374 original size:12 final size:12
Alignment explanation
Indices: 23357--23381 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23347 ATTCCAGATT
23357 AGTTAGATTCAA
1 AGTTAGATTCAA
23369 AGTTAGATTCAA
1 AGTTAGATTCAA
23381 A
1 A
23382 TTGTAATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (12 bp):
AGTTAGATTCAA
Found at i:23767 original size:31 final size:31
Alignment explanation
Indices: 23729--23836 Score: 107
Period size: 31 Copynumber: 3.5 Consensus size: 31
23719 TTAGACTAAT
23729 TGCTCAAATAAGGGCCTAACGTTTGCAAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGCAAAAA
* * * **
23760 TGCTCAAATAAGGACCTGATC-TTT--TAATT
1 TGCTCAAATAAGGGCCT-AACGTTTGCAAAAA
*
23789 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGCAAAAA
*
23820 TGCTTAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
23837 GGCGTCGAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 12
0.72 0.13 0.14
Matches are distributed among these distances:
28 2 0.03
29 18 0.30
30 4 0.07
31 34 0.57
32 2 0.03
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTTGCAAAAA
Found at i:23975 original size:60 final size:60
Alignment explanation
Indices: 23876--24038 Score: 229
Period size: 60 Copynumber: 2.7 Consensus size: 60
23866 ACTGACGCCA
** * *
23876 AACCCTTATTTGAGCATTTTTTATAACGTTAGGCTCTTATTTGGCTAAATTAAAAGATCG
1 AACCCTTATTTGAGCATTTTCAATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
* *
23936 AACCCTTATTTGAGCATTTTCAATAACGTTAAGCCCTTATTTGGCCAAATTAACAGATCG
1 AACCCTTATTTGAGCATTTTCAATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
** *
23996 GGCCCTTATTTGAGCATTTTGACA-AACGTTAGGCCCTTATTTG
1 AACCCTTATTTGAGCATTTTCA-ATAACGTTAGGCCCTTATTTG
24039 AGCAATTAGC
Statistics
Matches: 92, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
60 91 0.99
61 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (60 bp):
AACCCTTATTTGAGCATTTTCAATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
Found at i:24034 original size:31 final size:32
Alignment explanation
Indices: 23938--24042 Score: 96
Period size: 31 Copynumber: 3.4 Consensus size: 32
23928 AAAGATCGAA
* * *
23938 CCCTTATTTGAGCATTTTCA-ATAACGTTAAG
1 CCCTTATTTGAGCATTTTAACAGAACGTTAGG
** *
23969 CCCTTATTTG-GCCAAATTAACAGATCG---GG
1 CCCTTATTTGAG-CATTTTAACAGAACGTTAGG
*
23998 CCCTTATTTGAGCATTTTGACA-AACGTTAGG
1 CCCTTATTTGAGCATTTTAACAGAACGTTAGG
24029 CCCTTATTTGAGCA
1 CCCTTATTTGAGCA
24043 ATTAGCCTTA
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
28 3 0.05
29 18 0.31
30 2 0.03
31 31 0.53
32 4 0.07
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (32 bp):
CCCTTATTTGAGCATTTTAACAGAACGTTAGG
Found at i:30812 original size:7 final size:7
Alignment explanation
Indices: 30800--30878 Score: 65
Period size: 7 Copynumber: 11.1 Consensus size: 7
30790 GATTCCAATT
30800 ATTATTA
1 ATTATTA
30807 ATTATTTA
1 ATTA-TTA
30815 ATTATTA
1 ATTATTA
30822 ATTATT-
1 ATTATTA
30828 ATTAGTTTAA
1 ATTA--TT-A
*
30838 ATTGTT-
1 ATTATTA
30844 ATTATTA
1 ATTATTA
30851 ATTA-TA
1 ATTATTA
*
30857 ATTAATA
1 ATTATTA
*
30864 ATAATTA
1 ATTATTA
*
30871 ATAATTA
1 ATTATTA
30878 A
1 A
30879 AAAAAAGGGT
Statistics
Matches: 61, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
6 15 0.25
7 32 0.52
8 11 0.18
10 3 0.05
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (7 bp):
ATTATTA
Found at i:30819 original size:18 final size:18
Alignment explanation
Indices: 30796--30830 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
30786 CCAAGATTCC
30796 AATTATT-ATTAATTATTT
1 AATTATTAATT-ATTATTT
30814 AATTATTAATTATTATT
1 AATTATTAATTATTATT
30831 AGTTTAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
AATTATTAATTATTATTT
Found at i:38576 original size:79 final size:79
Alignment explanation
Indices: 38423--38583 Score: 247
Period size: 79 Copynumber: 2.0 Consensus size: 79
38413 CCTCTTTGGA
*
38423 TCAACTTCTAAATACCAATTCTCATTGTTTAGATTAAGTTAGGAATTTGGAATCAAACTGAATAT
1 TCAACTTCTAAATACCAAGTCTCATTGTTTAGATTAAGTTAGGAATTTGGAATCAAACTGAATAT
38488 ATTGCCCATTATGT
66 ATTGCCCATTATGT
* *
38502 TCAACTTCTAAATACTAAGTCTCATTGTTTAGATTAAGTTTGGAATTTTTGGAATCAAACTG-AT
1 TCAACTTCTAAATACCAAGTCTCATTGTTTAGATTAAGTTAGGAA--TTTGGAATCAAACTGAAT
38566 -TATT-CTCCATTATGT
64 ATATTGC-CCATTATGT
38581 TCA
1 TCA
38584 TCTTAGTATA
Statistics
Matches: 76, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.76
80 2 0.03
81 15 0.20
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.40
Consensus pattern (79 bp):
TCAACTTCTAAATACCAAGTCTCATTGTTTAGATTAAGTTAGGAATTTGGAATCAAACTGAATAT
ATTGCCCATTATGT
Done.