Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019633.1 Corchorus olitorius cultivar O-4 contig19666, 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: 57455
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:5117 original size:30 final size:31
Alignment explanation
Indices: 5062--5119 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
5052 TTGGCCTTTT
* *
5062 TTAAGAGTTCAGGGGCTTAATTTGGCTGCAA
1 TTAAAAGTTCAGGAGCTTAATTTGGCTGCAA
5093 TTAAAAGTTCAGGAGCTT-ATTTGGCTG
1 TTAAAAGTTCAGGAGCTTAATTTGGCTG
5120 TTTTATGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 9 0.36
31 16 0.64
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (31 bp):
TTAAAAGTTCAGGAGCTTAATTTGGCTGCAA
Found at i:5362 original size:30 final size:29
Alignment explanation
Indices: 5289--5364 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
5279 ACTTGTAGCG
* *
5289 TTTGGATATTTTGTCCCC-TCAACTTCAAT
1 TTTGGACATTTTG-CCCCATGAACTTCAAT
5318 TTTGGACATTTTGCCCCATGAACTTCAAT
1 TTTGGACATTTTGCCCCATGAACTTCAAT
*
5347 TTTGAGACGTTTTGCCCC
1 TTTG-GACATTTTGCCCC
5365 CTCAGACTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
28 4 0.10
29 26 0.62
30 12 0.29
ACGTcount: A:0.20, C:0.25, G:0.14, T:0.41
Consensus pattern (29 bp):
TTTGGACATTTTGCCCCATGAACTTCAAT
Found at i:5587 original size:29 final size:29
Alignment explanation
Indices: 5555--5632 Score: 129
Period size: 29 Copynumber: 2.7 Consensus size: 29
5545 GCAAAACGTC
5555 CCAAAATTGAAGTTCAGGGGGTAAAATAT
1 CCAAAATTGAAGTTCAGGGGGTAAAATAT
* * *
5584 CCAAAATTGAAGTTTATGGGGTAAAATGT
1 CCAAAATTGAAGTTCAGGGGGTAAAATAT
5613 CCAAAATTGAAGTTCAGGGG
1 CCAAAATTGAAGTTCAGGGG
5633 ACAAAACATC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.26
Consensus pattern (29 bp):
CCAAAATTGAAGTTCAGGGGGTAAAATAT
Found at i:5638 original size:29 final size:29
Alignment explanation
Indices: 5540--5638 Score: 126
Period size: 29 Copynumber: 3.4 Consensus size: 29
5530 CGTTAACCTG
*
5540 AGGGGGCAAAACGTCCCAAAATTGAAGTTC
1 AGGGGGCAAAATGT-CCAAAATTGAAGTTC
* * *
5570 AGGGGGTAAAATATCCAAAATTGAAGTTT
1 AGGGGGCAAAATGTCCAAAATTGAAGTTC
* *
5599 ATGGGGTAAAATGTCCAAAATTGAAGTTC
1 AGGGGGCAAAATGTCCAAAATTGAAGTTC
*
5628 AGGGGACAAAA
1 AGGGGGCAAAA
5639 CATCTAAATG
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
29 48 0.81
30 11 0.19
ACGTcount: A:0.40, C:0.12, G:0.26, T:0.21
Consensus pattern (29 bp):
AGGGGGCAAAATGTCCAAAATTGAAGTTC
Found at i:7818 original size:31 final size:30
Alignment explanation
Indices: 7780--7943 Score: 126
Period size: 31 Copynumber: 5.4 Consensus size: 30
7770 TTTGGCTAAT
7780 TGCTCAAATAAGGGTCTAACGTTTGTCAAAA
1 TGCTCAAATAAGGGTCTAAC-TTTGTCAAAA
* **
7811 TGCTCAAATAAGGGTCTGATCTTT-T-AATT
1 TGCTCAAATAAGGGTCT-AACTTTGTCAAAA
7840 TGGC-CAAATAAGGGTCTAACATTTG-CTAAAA
1 T-GCTCAAATAAGGGTCTAAC-TTTGTC-AAAA
* **
7871 TGCTCAAATAAGGGTCCAATCTTT-T-AATT
1 TGCTCAAATAAGGGTCTAA-CTTTGTCAAAA
* * *
7900 TGGC-CAAATAAGGGCCTAATGTTTGCCAAAA
1 T-GCTCAAATAAGGGTCTAA-CTTTGTCAAAA
7931 TGCTCAAATAAGG
1 TGCTCAAATAAGG
7944 ACCTGGCATC
Statistics
Matches: 105, Mismatches: 15, Indels: 26
0.72 0.10 0.18
Matches are distributed among these distances:
28 2 0.02
29 39 0.37
30 9 0.09
31 52 0.50
32 3 0.03
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.30
Consensus pattern (30 bp):
TGCTCAAATAAGGGTCTAACTTTGTCAAAA
Found at i:7877 original size:60 final size:60
Alignment explanation
Indices: 7784--7943 Score: 250
Period size: 60 Copynumber: 2.7 Consensus size: 60
7774 GCTAATTGCT
**
7784 CAAATAAGGGTCTAACGTTTG-TCAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGC
1 CAAATAAGGGTCTAACGTTTGCT-AAAATGCTCAAATAAGGGTCCAATCTTTTAATTTGGC
*
7844 CAAATAAGGGTCTAACATTTGCTAAAATGCTCAAATAAGGGTCCAATCTTTTAATTTGGC
1 CAAATAAGGGTCTAACGTTTGCTAAAATGCTCAAATAAGGGTCCAATCTTTTAATTTGGC
* * *
7904 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGG
1 CAAATAAGGGTCTAACGTTTGCTAAAATGCTCAAATAAGG
7944 ACCTGGCATC
Statistics
Matches: 92, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
60 91 0.99
61 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (60 bp):
CAAATAAGGGTCTAACGTTTGCTAAAATGCTCAAATAAGGGTCCAATCTTTTAATTTGGC
Found at i:8149 original size:60 final size:60
Alignment explanation
Indices: 7989--8154 Score: 199
Period size: 60 Copynumber: 2.8 Consensus size: 60
7979 TGACGCCAGG
* * * * ***
7989 CCCTTATTTGAACATTTTTGATAACGTTAAGCCCTTATTTAGCCAAATTAAAAGACCGGG
1 CCCTTATTTGAACATTTTCGATAACGTTAGGCCCTTATTTGGACAAATTAAAAGACCAAA
* ** *
8049 TCCTTATTTGAGTATTTTCGATAACGTTAGGCCCTTATTTGGACAAATTAAAAGATCAAA
1 CCCTTATTTGAACATTTTCGATAACGTTAGGCCCTTATTTGGACAAATTAAAAGACCAAA
* *
8109 CCCTTATTTGAACATTTTACCA-AACGTTAGGCCCTTATTTGAACAA
1 CCCTTATTTGAACATTTT-CGATAACGTTAGGCCCTTATTTGGACAA
8155 TTATCCTTTT
Statistics
Matches: 89, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
60 87 0.98
61 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (60 bp):
CCCTTATTTGAACATTTTCGATAACGTTAGGCCCTTATTTGGACAAATTAAAAGACCAAA
Found at i:10658 original size:110 final size:106
Alignment explanation
Indices: 10491--10711 Score: 336
Period size: 110 Copynumber: 2.0 Consensus size: 106
10481 ATATATATAT
* * *
10491 AAGATCTGCATATATATACATTAAGGAATTCAACAGGAACAAACAAATGCATGCATACAAATAGA
1 AAGATATGCATATATATACATTAAGGAATTCAACAGAAACAAACAAATGCATACATACAAATAGA
10556 TGGATATCCACATTGAAGTTC-ATAGAGTGAGAAACAGAGG
66 TGGATATCCACATTGAAGTTCAATAGAGTGAGAAACAGAGG
* *
10596 AAGATATGCATATATTATACATTAATGAATGAATTCAATAGAAACAAATAAATGCATACATACAA
1 AAGATATGCATATA-TATACATTAA-G---GAATTCAACAGAAACAAACAAATGCATACATACAA
10661 ATAGATGGATATCCACATTGAAGTTCATATAGAGTGAGAAACAGAGG
61 ATAGATGGATATCCACATTGAAGTTCA-ATAGAGTGAGAAACAGAGG
10708 AAGA
1 AAGA
10712 AGAGACAGGG
Statistics
Matches: 104, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
105 13 0.12
106 10 0.10
107 1 0.01
110 57 0.55
112 23 0.22
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.24
Consensus pattern (106 bp):
AAGATATGCATATATATACATTAAGGAATTCAACAGAAACAAACAAATGCATACATACAAATAGA
TGGATATCCACATTGAAGTTCAATAGAGTGAGAAACAGAGG
Found at i:22627 original size:2 final size:2
Alignment explanation
Indices: 22591--22618 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
22581 AGAGAAAGAA
22591 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
22619 CGCGTGTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:32103 original size:2 final size:2
Alignment explanation
Indices: 32096--32121 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
32086 ACACCAAAGA
32096 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
32122 GACCTGAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:33622 original size:11 final size:11
Alignment explanation
Indices: 33598--33632 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
33588 TTGACAGTGC
33598 AACAAAAACAA
1 AACAAAAACAA
* *
33609 AACGAAAACGA
1 AACAAAAACAA
33620 AACAAAAACAA
1 AACAAAAACAA
33631 AA
1 AA
33633 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:47744 original size:16 final size:17
Alignment explanation
Indices: 47723--47766 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
47713 CGGTAGGAGG
47723 AAGGAAATAGGAA-GGA
1 AAGGAAATAGGAAGGGA
*
47739 AAGGAAATAGTAAGGGA
1 AAGGAAATAGGAAGGGA
47756 AAGGAAATAGG
1 AAGGAAATAGG
47767 GAGAAAGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.55, C:0.00, G:0.36, T:0.09
Consensus pattern (17 bp):
AAGGAAATAGGAAGGGA
Found at i:48883 original size:15 final size:16
Alignment explanation
Indices: 48845--48888 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
48835 AACAAAAGAA
* *
48845 CCATCTTCCTTCCTTC
1 CCATCTTCTTTCCTCC
48861 CCAT-TTCTTTCC-CC
1 CCATCTTCTTTCCTCC
48875 CCATCTTCTTTCCT
1 CCATCTTCTTTCCT
48889 TCCTATTTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 5 0.21
15 15 0.62
16 4 0.17
ACGTcount: A:0.07, C:0.48, G:0.00, T:0.45
Consensus pattern (16 bp):
CCATCTTCTTTCCTCC
Found at i:50710 original size:25 final size:24
Alignment explanation
Indices: 50660--50711 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
50650 CCTTGAATTT
* *
50660 TTTAATGTTTAATTCTTAAATTTA
1 TTTAATGTTTAATTATTAAATGTA
*
50684 TTTAATGTCTTAATTATTCAATGTA
1 TTTAATGT-TTAATTATTAAATGTA
50709 TTT
1 TTT
50712 TACAATCCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.58
Consensus pattern (24 bp):
TTTAATGTTTAATTATTAAATGTA
Found at i:53397 original size:18 final size:18
Alignment explanation
Indices: 53376--53412 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
53366 GCAGCCATTT
*
53376 CTGATGATGATGAGGTTG
1 CTGATGATGAAGAGGTTG
53394 CTGATGATGAAGAGGTTG
1 CTGATGATGAAGAGGTTG
53412 C
1 C
53413 GGAGGAGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.08, G:0.38, T:0.30
Consensus pattern (18 bp):
CTGATGATGAAGAGGTTG
Done.