Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020939.1 Corchorus olitorius cultivar O-4 contig20972, 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: 11344
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:1041 original size:2 final size:2
Alignment explanation
Indices: 1034--1059 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1024 ACCATAATTT
1034 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1060 CTAGTTTTAA
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):
TA
Found at i:1150 original size:22 final size:20
Alignment explanation
Indices: 1118--1261 Score: 92
Period size: 22 Copynumber: 6.6 Consensus size: 20
1108 TGATTATTTT
*
1118 TATGAGATTTTGATAACTACTC
1 TATGAAATTTTGATAA-TAC-C
*
1140 TATTAAATTTTGATAATCACGC
1 TATGAAATTTTGATAAT-AC-C
*
1162 TATGAAATTTTAATAATTACC
1 TATGAAATTTTGATAA-TACC
*
1183 TATGAAATTGTGATAA-ACTCC
1 TATGAAATTTTGATAATA--CC
* *
1204 ATATGAAATTTTTATAACCTAAC
1 -TATGAAATTTTGATAA--TACC
* *
1227 TATGAAATTTTAATAAAACTTCC
1 TATGAAATTTTGAT--AA-TACC
1250 TATGAAATTTTG
1 TATGAAATTTTG
1262 TAACCTTCCT
Statistics
Matches: 98, Mismatches: 14, Indels: 19
0.75 0.11 0.15
Matches are distributed among these distances:
19 1 0.01
21 18 0.18
22 60 0.61
23 16 0.16
24 2 0.02
25 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (20 bp):
TATGAAATTTTGATAATACC
Found at i:1232 original size:44 final size:44
Alignment explanation
Indices: 1161--1260 Score: 123
Period size: 43 Copynumber: 2.3 Consensus size: 44
1151 GATAATCACG
* * *
1161 CTATGAAATTTTAATAATTACCTATGAAATTGTGAT-AAAC-TC
1 CTATGAAATTTTAATAACTAACTATGAAATTGTAATAAAACTTC
* *
1203 CATATGAAATTTTTATAACCTAACTATGAAATTTTAATAAAACTTC
1 C-TATGAAATTTTAATAA-CTAACTATGAAATTGTAATAAAACTTC
1249 CTATGAAATTTT
1 CTATGAAATTTT
1261 GTAACCTTCC
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
42 1 0.02
43 15 0.31
44 15 0.31
45 15 0.31
46 3 0.06
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.40
Consensus pattern (44 bp):
CTATGAAATTTTAATAACTAACTATGAAATTGTAATAAAACTTC
Found at i:4029 original size:43 final size:44
Alignment explanation
Indices: 3938--4040 Score: 145
Period size: 43 Copynumber: 2.4 Consensus size: 44
3928 TGAATATTTT
* * **
3938 TATGAAATTTTGATAATTATCCTATTAAATTTTGATAACCACGT
1 TATGAAATTTTGATAATTATCCTATTAAATTGTGATAAACACCA
*
3982 TATGAAATTTTGATAATTA-CCTATTAAATTGTGATAAACTCCA
1 TATGAAATTTTGATAATTATCCTATTAAATTGTGATAAACACCA
*
4025 TATGAAACTTTGATAA
1 TATGAAATTTTGATAA
4041 CCTAACTATG
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 34 0.64
44 19 0.36
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.41
Consensus pattern (44 bp):
TATGAAATTTTGATAATTATCCTATTAAATTGTGATAAACACCA
Found at i:4051 original size:65 final size:64
Alignment explanation
Indices: 3982--4136 Score: 168
Period size: 65 Copynumber: 2.4 Consensus size: 64
3972 ATAACCACGT
*
3982 TATGAAATTTTGATAAT-TACCTATTAAATTGTGATAAACTCCATATGAAACTTTGATAACCTAA
1 TATGAAATTTTGATAATCTACCTATGAAATTGTG-TAAACTCCATATG-AACTTTGATAACCTAA
4046 C
64 C
* * * * ** **
4047 TATGAAATTTTAATAAATCTTCCTATGAAATTGTGTAACCTCCCTATGAGTTTTGATAACCTCCC
1 TATGAAATTTTGAT-AATCTACCTATGAAATTGTGTAAACTCCATATGAACTTTGATAACCTAAC
* * *
4112 TATGATATTTTGTTAATCTCCCTAT
1 TATGAAATTTTGATAATCTACCTAT
4137 AATTTTTTGA
Statistics
Matches: 75, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
64 10 0.13
65 37 0.49
66 14 0.19
67 14 0.19
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.40
Consensus pattern (64 bp):
TATGAAATTTTGATAATCTACCTATGAAATTGTGTAAACTCCATATGAACTTTGATAACCTAAC
Found at i:4094 original size:21 final size:22
Alignment explanation
Indices: 3938--4136 Score: 145
Period size: 22 Copynumber: 9.1 Consensus size: 22
3928 TGAATATTTT
* *
3938 TATGAAATTTTGATAA-TTATCC
1 TATGAAATTTTGATAACCT-CCC
* * **
3960 TATTAAATTTTGATAACCACGT
1 TATGAAATTTTGATAACCTCCC
* *
3982 TATGAAATTTTGATAA-TTACC
1 TATGAAATTTTGATAACCTCCC
* * * *
4003 TATTAAATTGTGATAAACTCCA
1 TATGAAATTTTGATAACCTCCC
* **
4025 TATGAAACTTTGATAACCTAAC
1 TATGAAATTTTGATAACCTCCC
* * *
4047 TATGAAATTTTAATAAATCTTCC
1 TATGAAATTTTGAT-AACCTCCC
*
4070 TATGAAATTGTG-TAACCTCCC
1 TATGAAATTTTGATAACCTCCC
*
4091 TATG-AGTTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCCC
* * *
4112 TATGATATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTCCC
4134 TAT
1 TAT
4137 AATTTTTTGA
Statistics
Matches: 133, Mismatches: 39, Indels: 10
0.73 0.21 0.05
Matches are distributed among these distances:
20 5 0.04
21 37 0.28
22 76 0.57
23 15 0.11
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCC
Found at i:4132 original size:22 final size:21
Alignment explanation
Indices: 4068--4145 Score: 77
Period size: 22 Copynumber: 3.7 Consensus size: 21
4058 AATAAATCTT
* *
4068 CCTATGAAATTGTGTAACCTC
1 CCTATGATATTTTGTAACCTC
*
4089 CCTATGA-GTTTTGATAACCTC
1 CCTATGATATTTTG-TAACCTC
*
4110 CCTATGATATTTTGTTAATCTC
1 CCTATGATATTTTG-TAACCTC
* *
4132 CCTATAATTTTTTG
1 CCTATGATATTTTG
4146 ATACTGTAGT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
20 4 0.08
21 21 0.44
22 23 0.48
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.44
Consensus pattern (21 bp):
CCTATGATATTTTGTAACCTC
Done.