Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010845.1 Corchorus olitorius cultivar O-4 contig10877, 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: 11803
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:144 original size:6 final size:6
Alignment explanation
Indices: 126--172 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
116 CCAAGCCAGG
* * *
126 AAAGAA AAA-AA AAAGAA AAGGAA GAGGAA AAAG-A AAAGAA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
172 A
1 A
173 TAAAATAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
5 10 0.29
6 25 0.71
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:169 original size:11 final size:11
Alignment explanation
Indices: 126--172 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
116 CCAAGCCAGG
*
126 AAAGAAAAAAA
1 AAAGAAAAAGA
*
137 AAAGAAAAGGA
1 AAAGAAAAAGA
*
148 AGAGGAAAAAGA
1 A-AAGAAAAAGA
160 AAAGAAAAAGA
1 AAAGAAAAAGA
171 AA
1 AA
173 TAAAATAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
11 21 0.70
12 9 0.30
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAGA
Found at i:3797 original size:11 final size:11
Alignment explanation
Indices: 3781--3856 Score: 68
Period size: 11 Copynumber: 6.9 Consensus size: 11
3771 CGGTTTTCCC
3781 TTCTTTTCTTT
1 TTCTTTTCTTT
*
3792 TTCTTTTTTTT
1 TTCTTTTCTTT
*
3803 TTCTTTT-TTCC
1 TTCTTTTCTT-T
*
3814 TTC-TTCCTTT
1 TTCTTTTCTTT
*
3824 TTCCTTTCTTT
1 TTCTTTTCTTT
3835 TT-TTTCTCTTTT
1 TTCTTT-TC-TTT
3847 TTCTTTTCTT
1 TTCTTTTCTT
3857 CTTGGGCCTT
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
10 9 0.17
11 34 0.64
12 7 0.13
13 3 0.06
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TTCTTTTCTTT
Found at i:3809 original size:7 final size:7
Alignment explanation
Indices: 3781--3859 Score: 54
Period size: 7 Copynumber: 10.7 Consensus size: 7
3771 CGGTTTTCCC
3781 TTCTTTT
1 TTCTTTT
3788 CTT-TTTCT
1 -TTCTTT-T
*
3796 TTTTTTT
1 TTCTTTT
3803 TTCTTTT
1 TTCTTTT
*
3810 TTCCTTCT
1 TT-CTTTT
*
3818 TCCTTTT
1 TTCTTTT
*
3825 TCCTTTCT
1 TTCTTT-T
3833 TT-TTTT
1 TTCTTTT
3839 TCTCTTTT
1 T-TCTTTT
3847 TTCTTTT
1 TTCTTTT
3854 CTTCTT
1 -TTCTT
3860 GGGCCTTGCT
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
6 2 0.03
7 34 0.58
8 23 0.39
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (7 bp):
TTCTTTT
Found at i:3814 original size:48 final size:50
Alignment explanation
Indices: 3756--3856 Score: 129
Period size: 48 Copynumber: 2.1 Consensus size: 50
3746 TCCTTATTTC
3756 CTTTTCTTCCTT-ATCCGGTTTTCCCTTCTTTTCTTTT-TCTTTTTT-TTTT
1 CTTTTCTTCCTTCATCC-GTTTTCCCTTCTTTT-TTTTCTCTTTTTTCTTTT
* * *
3805 CTTTT-TTCCTTCTTCCTTTTTCCTTTCTTTTTTTTCTCTTTTTTCTTTT
1 CTTTTCTTCCTTCATCCGTTTTCCCTTCTTTTTTTTCTCTTTTTTCTTTT
3854 CTT
1 CTT
3857 CTTGGGCCTT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
47 4 0.09
48 27 0.59
49 15 0.33
ACGTcount: A:0.01, C:0.25, G:0.02, T:0.72
Consensus pattern (50 bp):
CTTTTCTTCCTTCATCCGTTTTCCCTTCTTTTTTTTCTCTTTTTTCTTTT
Found at i:8377 original size:2 final size:2
Alignment explanation
Indices: 8362--8396 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
8352 AAAAAGTTTA
*
8362 AT AT AT -T AT CT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8397 TCTAAAACCT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:8950 original size:44 final size:45
Alignment explanation
Indices: 8859--8974 Score: 182
Period size: 44 Copynumber: 2.6 Consensus size: 45
8849 CTCCCGGTAG
8859 GACCTGATTTTGTGTTTTCTTCTTTTCTTTTTTTTTTTTTCCTTT
1 GACCTGATTTTGTGTTTTCTTCTTTTCTTTTTTTTTTTTTCCTTT
8904 GACCTGATTTTGTGTTTTCTTCTTTTC-TTTTTTTTTTTTCCTTT
1 GACCTGATTTTGTGTTTTCTTCTTTTCTTTTTTTTTTTTTCCTTT
** *
8948 GACCTTTTTTTGT-TTTGTTTTCTTTTC
1 GACCTGATTTTGTGTTT-TCTTCTTTTC
8975 ATCATCTTGT
Statistics
Matches: 67, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
43 3 0.04
44 37 0.55
45 27 0.40
ACGTcount: A:0.04, C:0.16, G:0.09, T:0.71
Consensus pattern (45 bp):
GACCTGATTTTGTGTTTTCTTCTTTTCTTTTTTTTTTTTTCCTTT
Found at i:8984 original size:24 final size:24
Alignment explanation
Indices: 8957--9027 Score: 70
Period size: 25 Copynumber: 2.9 Consensus size: 24
8947 TGACCTTTTT
8957 TTGTTTTGTTTTCTTTTCATCATC
1 TTGTTTTGTTTTCTTTTCATCATC
** * * ** *
8981 TTGTTTTACTTTCCTTTAACTTTTT
1 TTGTTTTGTTTTCTTTTCA-TCATC
9006 TTGTTTTGTTTTCTTTTCATCA
1 TTGTTTTGTTTTCTTTTCATCA
9028 CCTAAAATGG
Statistics
Matches: 33, Mismatches: 13, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
24 16 0.48
25 17 0.52
ACGTcount: A:0.10, C:0.15, G:0.07, T:0.68
Consensus pattern (24 bp):
TTGTTTTGTTTTCTTTTCATCATC
Found at i:9213 original size:3 final size:3
Alignment explanation
Indices: 9205--9259 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
9195 TTGTGTAATA
9205 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
9253 TAT TAT T
1 TAT TAT T
9260 TTAAGTTTGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:9653 original size:26 final size:27
Alignment explanation
Indices: 9619--9675 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
9609 TGACATTATC
* *
9619 ATAAGTAATTTTAATAACTATTTCATT
1 ATAAGTAATTTTAATAACAATTTCATG
**
9646 ATAA-TAATTTTGTTAACAATTTCATG
1 ATAAGTAATTTTAATAACAATTTCATG
9672 ATAA
1 ATAA
9676 CAAACCCTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 22 0.85
27 4 0.15
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (27 bp):
ATAAGTAATTTTAATAACAATTTCATG
Found at i:9942 original size:10 final size:10
Alignment explanation
Indices: 9927--9978 Score: 77
Period size: 10 Copynumber: 5.1 Consensus size: 10
9917 AAAAAATAAC
9927 ATATAATTAA
1 ATATAATTAA
9937 ATATAATTAA
1 ATATAATTAA
* *
9947 ATCAAAATTAC
1 AT-ATAATTAA
9958 ATATAATTAA
1 ATATAATTAA
9968 ATATAATTAA
1 ATATAATTAA
9978 A
1 A
9979 GGAAACTGTG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
10 29 0.78
11 8 0.22
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (10 bp):
ATATAATTAA
Found at i:9954 original size:31 final size:31
Alignment explanation
Indices: 9919--9978 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
9909 ATTACATAAA
9919 AAAATAACATATAATTAAATATAATTAAATC
1 AAAATAACATATAATTAAATATAATTAAATC
*
9950 AAAATTACATATAATTAAATATAATTAAA
1 AAAATAACATATAATTAAATATAATTAAA
9979 GGAAACTGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (31 bp):
AAAATAACATATAATTAAATATAATTAAATC
Found at i:9956 original size:21 final size:20
Alignment explanation
Indices: 9931--9978 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
9921 AATAACATAT
9931 AATTAAATATAATTAAATCAA
1 AATTAAATATAATTAAAT-AA
* *
9952 AATTACATATAATTAAATAT
1 AATTAAATATAATTAAATAA
9972 AATTAAA
1 AATTAAA
9979 GGAAACTGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.35
Consensus pattern (20 bp):
AATTAAATATAATTAAATAA
Done.