Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018120.1 Corchorus olitorius cultivar O-4 contig18153, 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: 31479
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:3093 original size:30 final size:29
Alignment explanation
Indices: 3059--3128 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 29
3049 TGCAAAAACC
3059 TTTTTTTTTCGACGCAAAACACAAAACAAT
1 TTTTTTTTTCGACGC-AAACACAAAACAAT
***
3089 TTTTTTTTAT-GACGCAGGGACAAAACAAT
1 TTTTTTTT-TCGACGCAAACACAAAACAAT
3118 TTTCTTTTTTC
1 TTT-TTTTTTC
3129 AAAACGACGC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
29 15 0.44
30 18 0.53
31 1 0.03
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.41
Consensus pattern (29 bp):
TTTTTTTTTCGACGCAAACACAAAACAAT
Found at i:3504 original size:16 final size:15
Alignment explanation
Indices: 3466--3507 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
3456 ACAGAGGTTG
*
3466 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
3481 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
3496 ACTAGAAAACAA
1 AC-AGAAAACAA
3508 AGCAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:4892 original size:11 final size:11
Alignment explanation
Indices: 4876--4906 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
4866 AAATCTTCAA
4876 GTCTTCAAATG
1 GTCTTCAAATG
4887 GTCTTCAAATG
1 GTCTTCAAATG
4898 GTCTTCAAA
1 GTCTTCAAA
4907 CACGAACTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (11 bp):
GTCTTCAAATG
Found at i:7191 original size:14 final size:14
Alignment explanation
Indices: 7172--7201 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
7162 ATAACAAAGC
7172 ATACTTCTGCTCCA
1 ATACTTCTGCTCCA
*
7186 ATACTTCTTCTCCA
1 ATACTTCTGCTCCA
7200 AT
1 AT
7202 GGTAGAAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.33, G:0.03, T:0.40
Consensus pattern (14 bp):
ATACTTCTGCTCCA
Found at i:8565 original size:19 final size:18
Alignment explanation
Indices: 8528--8568 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
8518 CTCTTGAGAT
*
8528 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
8546 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
8565 AATT
1 AATT
8569 AAACTTCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.29, C:0.20, G:0.05, T:0.46
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Found at i:9685 original size:17 final size:18
Alignment explanation
Indices: 9652--9687 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
9642 CTCCTCTTGC
*
9652 ATGAAAACACTTCTTTTT
1 ATGAAAACAATTCTTTTT
9670 ATGAAAACAATT-TTTTT
1 ATGAAAACAATTCTTTTT
9687 A
1 A
9688 ACTCCCCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (18 bp):
ATGAAAACAATTCTTTTT
Found at i:15969 original size:21 final size:21
Alignment explanation
Indices: 15940--16000 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
15930 TCAAAATCAA
* * *
15940 CAAACAAAACCCACATACATT
1 CAAAAAAAATCCACAAACATT
15961 CAAAAAAAATCCACAAACATT
1 CAAAAAAAATCCACAAACATT
*
15982 CAAGAAAAATCCACAAACA
1 CAAAAAAAATCCACAAACA
16001 ATCCACATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.59, C:0.28, G:0.02, T:0.11
Consensus pattern (21 bp):
CAAAAAAAATCCACAAACATT
Found at i:16946 original size:13 final size:13
Alignment explanation
Indices: 16928--16953 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16918 ACTAAGATTG
16928 CAATATTATCCTA
1 CAATATTATCCTA
16941 CAATATTATCCTA
1 CAATATTATCCTA
16954 AGATTCCAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38
Consensus pattern (13 bp):
CAATATTATCCTA
Found at i:18568 original size:49 final size:49
Alignment explanation
Indices: 18511--18611 Score: 159
Period size: 49 Copynumber: 2.1 Consensus size: 49
18501 TGAAGATTTT
* * *
18511 CAATCAAATAAGTTAATCATCCTATTACAATGTTTCTGCCTA-TAAATAA
1 CAATCAAATAAGTTAATCATACTATTACAATATTTCAGCC-ACTAAATAA
18560 CAATCAAATAAGTTAATCATACTATTACAATATTTCAGCCACTAAATAA
1 CAATCAAATAAGTTAATCATACTATTACAATATTTCAGCCACTAAATAA
18609 CAA
1 CAA
18612 ACAATGGCAT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
48 1 0.02
49 47 0.98
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.32
Consensus pattern (49 bp):
CAATCAAATAAGTTAATCATACTATTACAATATTTCAGCCACTAAATAA
Found at i:21614 original size:19 final size:18
Alignment explanation
Indices: 21577--21617 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
21567 CTTTTGAGAT
*
21577 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
21595 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
21614 AATT
1 AATT
21618 AATCTTCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.29, C:0.20, G:0.05, T:0.46
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Found at i:25560 original size:35 final size:35
Alignment explanation
Indices: 25521--25631 Score: 90
Period size: 35 Copynumber: 3.2 Consensus size: 35
25511 AACAATTAAC
25521 AAACCAACAGAACTCAGTCACCAAGAACAAAATAA
1 AAACCAACAGAACTCAGTCACCAAGAACAAAATAA
* *
25556 AAACCAGCACA-AAC-CAGCACAGCCATAGAA-ATAATAA
1 AAACCA--ACAGAACTCAG-TCA-CCA-AGAACAAAATAA
**
25593 GGA--AACAGAA-TCCAGTCACCAAGAACAAAATAA
1 AAACCAACAGAACT-CAGTCACCAAGAACAAAATAA
25626 AAACCA
1 AAACCA
25632 GCACAACCAT
Statistics
Matches: 57, Mismatches: 8, Indels: 22
0.66 0.09 0.25
Matches are distributed among these distances:
32 4 0.07
33 13 0.23
34 4 0.07
35 14 0.25
36 5 0.09
37 13 0.23
38 4 0.07
ACGTcount: A:0.56, C:0.25, G:0.11, T:0.08
Consensus pattern (35 bp):
AAACCAACAGAACTCAGTCACCAAGAACAAAATAA
Found at i:26213 original size:15 final size:17
Alignment explanation
Indices: 26175--26245 Score: 51
Period size: 15 Copynumber: 4.2 Consensus size: 17
26165 AAAGGTTAGG
26175 TATTTATATTACATATA
1 TATTTATATTACATATA
26192 T-TATTATA-TA-ATATA
1 TAT-TTATATTACATATA
* *
26207 TATTTATTTTATTATATA
1 TATTTATATTA-CATATA
*
26225 TTATTTCAGATTA-ATATA
1 -TATTT-ATATTACATATA
26243 TAT
1 TAT
26246 ATTAATATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
15 10 0.23
16 6 0.14
17 9 0.20
18 10 0.23
19 5 0.11
20 4 0.09
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.56
Consensus pattern (17 bp):
TATTTATATTACATATA
Found at i:27207 original size:16 final size:15
Alignment explanation
Indices: 27169--27210 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
27159 ACAGAGGTTG
*
27169 ACAGAAAAAAATTAA
1 ACAGAAAACAATTAA
27184 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
27199 ACTAGAAAACAA
1 AC-AGAAAACAA
27211 AGCAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.69, C:0.12, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:29654 original size:23 final size:22
Alignment explanation
Indices: 29605--29647 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
29595 CACATCAAAG
*
29605 AACAGGCAAGCAATCAAAGTAAT
1 AACAGGCAAGCAA-CAAACTAAT
29628 AACAGGCAAGCAA-AAACTAA
1 AACAGGCAAGCAACAAACTAA
29648 ACTAACATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
23 13 0.68
ACGTcount: A:0.56, C:0.19, G:0.16, T:0.09
Consensus pattern (22 bp):
AACAGGCAAGCAACAAACTAAT
Found at i:29768 original size:21 final size:21
Alignment explanation
Indices: 29742--29791 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
29732 GGAATGGCGA
***
29742 TGGCACGGGCATGGTCGGTGG
1 TGGCACGGGCATAACCGGTGG
*
29763 TGGCACGGGCTTAACCGGTGG
1 TGGCACGGGCATAACCGGTGG
29784 TGGCACGG
1 TGGCACGG
29792 TGAATGGGCG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.12, C:0.22, G:0.48, T:0.18
Consensus pattern (21 bp):
TGGCACGGGCATAACCGGTGG
Done.