Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018258.1 Corchorus olitorius cultivar O-4 contig18291, 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: 45636
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:1646 original size:16 final size:16
Alignment explanation
Indices: 1625--1655 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1615 ATCGTTTTTG
*
1625 GTTTTTTTTTTATTTC
1 GTTTTTGTTTTATTTC
1641 GTTTTTGTTTTATTT
1 GTTTTTGTTTTATTT
1656 TTGTTGCGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.06, C:0.03, G:0.10, T:0.81
Consensus pattern (16 bp):
GTTTTTGTTTTATTTC
Found at i:1665 original size:22 final size:23
Alignment explanation
Indices: 1617--1665 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
1607 TGTTTGGCAT
* *
1617 CGTTTTTGGTTTTTTTTTTATTT
1 CGTTTTTGGTTTTATTTTTATTG
*
1640 CGTTTTT-GTTTTATTTTTGTTG
1 CGTTTTTGGTTTTATTTTTATTG
1662 CGTT
1 CGTT
1666 GTCAATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.04, C:0.06, G:0.16, T:0.73
Consensus pattern (23 bp):
CGTTTTTGGTTTTATTTTTATTG
Found at i:3105 original size:12 final size:12
Alignment explanation
Indices: 3076--3108 Score: 52
Period size: 10 Copynumber: 2.9 Consensus size: 12
3066 TATATATAAT
3076 TATAAAATTATG
1 TATAAAATTATG
3088 --TAAAATTATG
1 TATAAAATTATG
3098 TATAAAATTAT
1 TATAAAATTAT
3109 ACATAATTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 10 0.53
12 9 0.47
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (12 bp):
TATAAAATTATG
Found at i:11668 original size:21 final size:21
Alignment explanation
Indices: 11576--11691 Score: 79
Period size: 22 Copynumber: 5.3 Consensus size: 21
11566 TTGATAATTA
** *
11576 CCCTATGAAATTGCCATAAACT
1 CCCTATGAAATT-TTATAACCT
* * *
11598 CCTTATGAAAGTTTGATAACTT
1 CCCTATGAAA-TTTTATAACCT
**
11620 AACTATGAAATTTTAATGAACCT
1 CCCTATGAAATTTT-AT-AACCT
*
11643 TCCTATGAAATTTTATAACCT
1 CCCTATGAAATTTTATAACCT
* * *
11664 CCCTATAAAATTTTGTTAATCT
1 CCCTATGAAATTTT-ATAACCT
11686 CCCTAT
1 CCCTAT
11692 AACTTTTTTA
Statistics
Matches: 74, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
21 20 0.27
22 36 0.49
23 18 0.24
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (21 bp):
CCCTATGAAATTTTATAACCT
Found at i:11690 original size:22 final size:21
Alignment explanation
Indices: 11622--11693 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
11612 GATAACTTAA
* *
11622 CTATGAAATTTTAATGAACCTTC
1 CTATAAAATTTT-AT-AACCTCC
*
11645 CTATGAAATTTTATAACCTCC
1 CTATAAAATTTTATAACCTCC
* *
11666 CTATAAAATTTTGTTAATCTCC
1 CTATAAAATTTT-ATAACCTCC
11688 CTATAA
1 CTATAA
11694 CTTTTTTATA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
21 17 0.39
22 15 0.34
23 12 0.27
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.40
Consensus pattern (21 bp):
CTATAAAATTTTATAACCTCC
Found at i:12288 original size:2 final size:2
Alignment explanation
Indices: 12281--12332 Score: 65
Period size: 2 Copynumber: 27.0 Consensus size: 2
12271 GAGAAGAAGA
*
12281 AT AT AT AT AT AT AT AT AT AT GAT AT -T AA AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT
12322 AT AT AT A- AT AT
1 AT AT AT AT AT AT
12333 TGTCGGTGGG
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
1 3 0.07
2 39 0.89
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12321 original size:27 final size:28
Alignment explanation
Indices: 12280--12333 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 28
12270 AGAGAAGAAG
*
12280 AATATATATATATATATATATGATATTA
1 AATATATATATATATATATATAATATTA
12308 AATATAT-TATATATATATATAATATT
1 AATATATATATATATATATATAATATT
12334 GTCGGTGGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 18 0.72
28 7 0.28
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (28 bp):
AATATATATATATATATATATAATATTA
Found at i:13049 original size:18 final size:19
Alignment explanation
Indices: 13020--13072 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 19
13010 AGAAGTTCAA
*
13020 AACTTTTGTTCAAAAAAGT
1 AACTTTTTTTCAAAAAAGT
*
13039 -ATTTTTTTTC-AAAAAGT
1 AACTTTTTTTCAAAAAAGT
*
13056 AACCTTTTTTCAAAAAA
1 AACTTTTTTTCAAAAAA
13073 AAGGTTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 7 0.25
18 16 0.57
19 5 0.18
ACGTcount: A:0.42, C:0.11, G:0.06, T:0.42
Consensus pattern (19 bp):
AACTTTTTTTCAAAAAAGT
Found at i:14049 original size:2 final size:2
Alignment explanation
Indices: 14042--14070 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
14032 AGAAGAATCT
14042 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
14071 GTGTCACGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16380 original size:11 final size:11
Alignment explanation
Indices: 16366--16390 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16356 ACTAGACCAA
16366 TATCTATATAC
1 TATCTATATAC
16377 TATCTATATAC
1 TATCTATATAC
16388 TAT
1 TAT
16391 ATAAGTCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (11 bp):
TATCTATATAC
Found at i:16659 original size:39 final size:40
Alignment explanation
Indices: 16603--16683 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
16593 TTTAATTCCT
16603 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
16643 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
16682 AT
1 AT
16684 TCTTAGGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:17036 original size:204 final size:200
Alignment explanation
Indices: 16794--17202 Score: 737
Period size: 201 Copynumber: 2.0 Consensus size: 200
16784 TTCCTTAATA
*
16794 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
1 ATAAATAAATCAGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
*
16859 ATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATAGT
66 ATTTAATAAATCAACCACTAATGTTCAACT-ATTTTTTTTGGTATAGTT-T-TATATATAATAAT
*
16924 AATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATT
128 AATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAAATAATAACATT
16989 CACCATTG
193 CACCATTG
16997 ATAAATAAATCAGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCAGATC-TTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
17062 AATTTAATAAATCAACCACTAATGTTCAACTATTTTTTTTGGTATAGTTTTATATATAATAATAA
65 AATTTAATAAATCAACCACTAATGTTCAACTATTTTTTTTGGTATAGTTTTATATATAATAATAA
* *
17127 TGTTTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAAATAATAACATTCC
130 TGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAAATAATAACATTCA
17192 CCATTG
195 CCATTG
17198 ATAAA
1 ATAAA
17203 GTTATTAAGC
Statistics
Matches: 200, Mismatches: 5, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
201 87 0.44
202 1 0.00
203 33 0.17
204 79 0.40
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (200 bp):
ATAAATAAATCAGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
ATTTAATAAATCAACCACTAATGTTCAACTATTTTTTTTGGTATAGTTTTATATATAATAATAAT
GTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAAATAATAACATTCAC
CATTG
Found at i:27691 original size:45 final size:45
Alignment explanation
Indices: 27637--27726 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
27627 AATAGTACTC
*
27637 CCAACTAACATGAATTTGTGAACCTTTTGCTTGTCCAAATTGACT
1 CCAACTAACATGAATTTGTGAACCTTTTGCTTGTCCAAAATGACT
27682 CCAACTAACATGAATTTGTGAACCTTTTGCTTGTCCAAAATGACT
1 CCAACTAACATGAATTTGTGAACCTTTTGCTTGTCCAAAATGACT
27727 TGGTCCATTG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.34
Consensus pattern (45 bp):
CCAACTAACATGAATTTGTGAACCTTTTGCTTGTCCAAAATGACT
Found at i:38823 original size:48 final size:45
Alignment explanation
Indices: 38771--38864 Score: 143
Period size: 48 Copynumber: 2.0 Consensus size: 45
38761 AGCGTGAGTT
* *
38771 GTCAGGCAATTCTGATAGGAGGCATCGTGATGAGAAGGAGCGGGACTG
1 GTCAGGCAACTCGGATAGGAGGCATCGTGAT--G-AGGAGCGGGACTG
38819 GTCAGGCAACTCGGATAGGAGGCATCGTGATGAGGAGCGGGACTG
1 GTCAGGCAACTCGGATAGGAGGCATCGTGATGAGGAGCGGGACTG
38864 G
1 G
38865 GATAGATCTG
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
45 14 0.32
46 1 0.02
48 29 0.66
ACGTcount: A:0.26, C:0.16, G:0.41, T:0.17
Consensus pattern (45 bp):
GTCAGGCAACTCGGATAGGAGGCATCGTGATGAGGAGCGGGACTG
Done.