Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012010.1 Corchorus olitorius cultivar O-4 contig12043, 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: 23548
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:14 original size:2 final size:2
Alignment explanation
Indices: 8--55 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1 ACTACTA
8 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
50 CT CT CT
1 CT CT CT
56 ATATATATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:60 original size:2 final size:2
Alignment explanation
Indices: 55--81 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
45 TCTCTCTCTC
55 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 T
82 GGAAAAGTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3306 original size:48 final size:47
Alignment explanation
Indices: 3195--3331 Score: 150
Period size: 49 Copynumber: 2.9 Consensus size: 47
3185 ATCTTTTACA
* ** * * *
3195 TTTCA-TGCACATTTTTCTCATTTTTTACAACAAAAATGAATCTTTAAT
1 TTTCATTGCAC-TTTTTCTCAATTTTT-GTACAAAATTGATTATTTAAT
* *
3243 TTTCCTTGCACCTTTTTCTCAATTTTTGTGACAAAATTGATTATTTATT
1 TTTCATTGCA-CTTTTTCTCAATTTTTGT-ACAAAATTGATTATTTAAT
*
3292 TTTCATTGCACTTTTTATCAATTTTTGTACAAAATTGATT
1 TTTCATTGCACTTTTTCTCAATTTTTGTACAAAATTGATT
3332 GGCACGCTCG
Statistics
Matches: 76, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
47 12 0.16
48 21 0.28
49 42 0.55
50 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.07, T:0.50
Consensus pattern (47 bp):
TTTCATTGCACTTTTTCTCAATTTTTGTACAAAATTGATTATTTAAT
Found at i:12812 original size:15 final size:14
Alignment explanation
Indices: 12789--12818 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
12779 ATAAAAATTA
12789 AATATTTTTATTTT
1 AATATTTTTATTTT
12803 AATATATTTTATTTT
1 AATAT-TTTTATTTT
12818 A
1 A
12819 TTGAAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
AATATTTTTATTTT
Found at i:20274 original size:22 final size:22
Alignment explanation
Indices: 20244--20387 Score: 78
Period size: 22 Copynumber: 6.5 Consensus size: 22
20234 TTCAATGTAG
*
20244 AAATATTGATAACCACATTTTGA
1 AAAT-TTGATAACCACATTATGA
*** *
20267 AAATTTGATAATTTCATCATGA
1 AAATTTGATAACCACATTATGA
*
20289 AAATTCGATAAACTC-CA-TATGA
1 AAATTTGAT-AAC-CACATTATGA
* *
20311 AAATTTGATAACCACACTGTGA
1 AAATTTGATAACCACATTATGA
* * * *
20333 AATTTTGATTATCACACTATG-
1 AAATTTGATAACCACATTATGA
* * * *
20354 AAATTTCGACAACCTCAGTGTGA
1 AAATTT-GATAACCACATTATGA
*
20377 AATTTTGATAA
1 AAATTTGATAA
20388 TCTGCCTATA
Statistics
Matches: 91, Mismatches: 24, Indels: 13
0.71 0.19 0.10
Matches are distributed among these distances:
20 1 0.01
21 10 0.11
22 67 0.74
23 13 0.14
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (22 bp):
AAATTTGATAACCACATTATGA
Found at i:20402 original size:44 final size:43
Alignment explanation
Indices: 20310--20403 Score: 109
Period size: 44 Copynumber: 2.2 Consensus size: 43
20300 ACTCCATATG
* *
20310 AAAATTTGATAACCACACTGTGAAATTTTGATTATCACACTAT
1 AAAATTTGACAACCACACTGTGAAATTTTGATAATCACACTAT
* * * *
20353 GAAATTTCGACAACCTCAGTGTGAAATTTTGATAATCTGC-CTAT
1 AAAATTT-GACAACCACACTGTGAAATTTTGATAATC-ACACTAT
20397 AAAATTT
1 AAAATTT
20404 TAATAATCAC
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
43 6 0.14
44 35 0.83
45 1 0.02
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (43 bp):
AAAATTTGACAACCACACTGTGAAATTTTGATAATCACACTAT
Found at i:20561 original size:21 final size:22
Alignment explanation
Indices: 20535--20582 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
20525 CTCTCTATGT
20535 ATTTTC-GAACCTCTCC-ATAAA
1 ATTTTCAGAACCTC-CCTATAAA
*
20556 ATTTTCATAACCTCCCTATAAA
1 ATTTTCAGAACCTCCCTATAAA
20578 ATTTT
1 ATTTT
20583 GTTAACCTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.33, C:0.25, G:0.02, T:0.40
Consensus pattern (22 bp):
ATTTTCAGAACCTCCCTATAAA
Found at i:20569 original size:22 final size:22
Alignment explanation
Indices: 20542--20609 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
20532 TGTATTTTCG
20542 AACCTCTCC-ATAAAATTTTCAT
1 AACCTC-CCTATAAAATTTTCAT
**
20564 AACCTCCCTATAAAATTTTGTT
1 AACCTCCCTATAAAATTTTCAT
** *
20586 AACCTCCCTAGGAAATTTTGAT
1 AACCTCCCTATAAAATTTTCAT
20608 AA
1 AA
20610 GCACAAATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
21 2 0.05
22 38 0.95
ACGTcount: A:0.35, C:0.24, G:0.06, T:0.35
Consensus pattern (22 bp):
AACCTCCCTATAAAATTTTCAT
Found at i:20664 original size:22 final size:21
Alignment explanation
Indices: 20636--20823 Score: 119
Period size: 22 Copynumber: 8.6 Consensus size: 21
20626 CCTCCCTCCC
*
20636 TATGAAATTTTGTTAACTTTCA
1 TATGAAATTTTGATAAC-TTCA
* *
20658 TATGAAATTTT-ATTAACATCCC
1 TATGAAATTTTGA-TAAC-TTCA
* * **
20680 TAAGAAATTTTGGTAACTTTTT
1 TATGAAATTTTGATAAC-TTCA
* * *
20702 TATGAAATTTTGGTAACCTCTG
1 TATGAAATTTTGATAACTTC-A
*
20724 TATGAAATTTTGATAACTACA
1 TATGAAATTTTGATAACTTCA
* *
20745 CTATGAAGTTTTGATAACCTCTA
1 -TATGAAATTTTGATAACTTC-A
* **
20768 TATGAAATTTTGGTAACCACA
1 TATGAAATTTTGATAACTTCA
20789 CTATGAAATTTTGATAATCTTTC-
1 -TATGAAATTTTGATAA-C-TTCA
*
20812 TATGTAATTTTG
1 TATGAAATTTTG
20824 GTTTGATTGT
Statistics
Matches: 130, Mismatches: 28, Indels: 16
0.75 0.16 0.09
Matches are distributed among these distances:
21 2 0.02
22 125 0.96
23 2 0.02
24 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (21 bp):
TATGAAATTTTGATAACTTCA
Found at i:20728 original size:66 final size:66
Alignment explanation
Indices: 20636--20805 Score: 177
Period size: 66 Copynumber: 2.6 Consensus size: 66
20626 CCTCCCTCCC
* * * * *
20636 TATGAAATTTTGTTAA-CTTTCATATGAAATTTT-ATTAAC-ATCCCTAAGAAATTTTGGTAACT
1 TATGAAATTTTGGTAACCTCT-ATATGAAATTTTGA-TAACTA-CACTAAGAAATTTTGATAACC
* *
20698 TTTT
63 TCTA
* * *
20702 TATGAAATTTTGGTAACCTCTGTATGAAATTTTGATAACTACACTATGAAGTTTTGATAACCTCT
1 TATGAAATTTTGGTAACCTCTATATGAAATTTTGATAACTACACTAAGAAATTTTGATAACCTCT
20767 A
66 A
*
20768 TATGAAATTTTGGTAACCAC-ACTATGAAATTTTGATAA
1 TATGAAATTTTGGTAACCTCTA-TATGAAATTTTGATAA
20806 TCTTTCTATG
Statistics
Matches: 88, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
66 83 0.94
67 5 0.06
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (66 bp):
TATGAAATTTTGGTAACCTCTATATGAAATTTTGATAACTACACTAAGAAATTTTGATAACCTCT
A
Found at i:20731 original size:44 final size:44
Alignment explanation
Indices: 20636--20825 Score: 157
Period size: 44 Copynumber: 4.3 Consensus size: 44
20626 CCTCCCTCCC
* * * **
20636 TATGAAATTTTGTTAACTTTCATATGAAATTTT-ATTAACATCCC
1 TATGAAATTTTGGTAACTTTAATATGAAATTTTGA-TAACCTCTA
* ** * *
20680 TAAGAAATTTTGGTAACTTTTTTATGAAATTTTGGTAACCTCTG
1 TATGAAATTTTGGTAACTTTAATATGAAATTTTGATAACCTCTA
* ** * *
20724 TATGAAATTTTGATAACTACACTATGAAGTTTTGATAACCTCTA
1 TATGAAATTTTGGTAACTTTAATATGAAATTTTGATAACCTCTA
*** * * * *
20768 TATGAAATTTTGGTAACCACACTATGAAATTTTGATAATCTTTC
1 TATGAAATTTTGGTAACTTTAATATGAAATTTTGATAACCTCTA
*
20812 TATGTAATTTTGGT
1 TATGAAATTTTGGT
20826 TTGATTGTCA
Statistics
Matches: 121, Mismatches: 24, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
44 121 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (44 bp):
TATGAAATTTTGGTAACTTTAATATGAAATTTTGATAACCTCTA
Found at i:21427 original size:2 final size:2
Alignment explanation
Indices: 21409--21449 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
21399 ATATTTAAAA
* *
21409 AT AT AA AT AT GAT AT AT AT AT AT AT AT GT 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 AT AT
21450 GAAGAGCTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:22604 original size:2 final size:2
Alignment explanation
Indices: 22597--22622 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
22587 CTTTAATTGA
22597 AT 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
22623 GAAGAGCTAG
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.