Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01002229.1 Corchorus capsularis cultivar CVL-1 contig02235, 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, 801
Length: 1335
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:143 original size:18 final size:18
Alignment explanation
Indices: 120--154 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
110 ATCATTATTG
120 ATTATTATATGATAATTA
1 ATTATTATATGATAATTA
138 ATTATTATATGATAATT
1 ATTATTATATGATAATT
155 CATTTTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (18 bp):
ATTATTATATGATAATTA
Found at i:177 original size:21 final size:21
Alignment explanation
Indices: 153--227 Score: 69
Period size: 21 Copynumber: 3.2 Consensus size: 21
143 TATATGATAA
153 TTCATTTTTGAAATTTAGAAT
1 TTCATTTTTGAAATTTAGAAT
* *
174 TTCATCATTATTGATTATTATATGATAA
1 TTCAT--TT-TTGA-AATT-TA-GA-AT
202 TTCATTTTTGAAATTTAGAAT
1 TTCATTTTTGAAATTTAGAAT
223 TTCAT
1 TTCAT
228 CATTATTGAT
Statistics
Matches: 43, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
21 11 0.26
22 2 0.05
23 4 0.09
24 7 0.16
25 7 0.16
26 4 0.09
27 2 0.05
28 6 0.14
ACGTcount: A:0.33, C:0.07, G:0.08, T:0.52
Consensus pattern (21 bp):
TTCATTTTTGAAATTTAGAAT
Found at i:182 original size:24 final size:24
Alignment explanation
Indices: 154--236 Score: 82
Period size: 24 Copynumber: 3.4 Consensus size: 24
144 ATATGATAAT
*
154 TCATTTTTGAAATTTAGAATTTCA
1 TCATTATTGAAATTTAGAATTTCA
* *
178 TCATTATTGATTATTATATGATAATTCA
1 TCATTATTGA-AATT-TA-GA-ATTTCA
206 T--TT-TTGAAATTTAGAATTTCA
1 TCATTATTGAAATTTAGAATTTCA
227 TCATTATTGA
1 TCATTATTGA
237 TTATTATATG
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
21 6 0.13
22 2 0.04
23 4 0.09
24 16 0.34
25 7 0.15
26 4 0.09
27 2 0.04
28 6 0.13
ACGTcount: A:0.34, C:0.07, G:0.08, T:0.51
Consensus pattern (24 bp):
TCATTATTGAAATTTAGAATTTCA
Found at i:196 original size:49 final size:49
Alignment explanation
Indices: 138--262 Score: 250
Period size: 49 Copynumber: 2.6 Consensus size: 49
128 ATGATAATTA
138 ATTATTATATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTG
1 ATTATTATATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTG
187 ATTATTATATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTG
1 ATTATTATATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTG
236 ATTATTATATGATAATTCATTTTTGAA
1 ATTATTATATGATAATTCATTTTTGAA
263 TGATGATTTT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 76 1.00
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.51
Consensus pattern (49 bp):
ATTATTATATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTG
Found at i:206 original size:25 final size:25
Alignment explanation
Indices: 178--261 Score: 77
Period size: 25 Copynumber: 3.4 Consensus size: 25
168 TAGAATTTCA
178 TCATTATTGATTATTATATGATAAT
1 TCATTATTGATTATTATATGATAAT
* * *
203 TCATTTTTGA-AATT-TA-GA-ATTT
1 TCATTATTGATTATTATATGATA-AT
225 CATCATTATTGATTATTATATGATAAT
1 --TCATTATTGATTATTATATGATAAT
*
252 TCATTTTTGA
1 TCATTATTGA
262 ATGATGATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 14
0.68 0.11 0.21
Matches are distributed among these distances:
21 1 0.02
22 3 0.07
23 2 0.04
24 12 0.27
25 21 0.47
26 2 0.04
27 3 0.07
28 1 0.02
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.52
Consensus pattern (25 bp):
TCATTATTGATTATTATATGATAAT
Found at i:1115 original size:6 final size:6
Alignment explanation
Indices: 1104--1156 Score: 58
Period size: 6 Copynumber: 9.2 Consensus size: 6
1094 GTAATATACG
* *
1104 ATAAAT ATAAAT AT-CA- ATAAAT ATAAAT ATAAAT AATCAA- ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT -ATAAAT ATAAAT
1150 ATAAAT A
1 ATAAAT A
1157 AATAAATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 2 0.05
5 6 0.15
6 27 0.69
7 4 0.10
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (6 bp):
ATAAAT
Found at i:1125 original size:10 final size:10
Alignment explanation
Indices: 1104--1160 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
1094 GTAATATACG
1104 ATAAATATAA
1 ATAAATATAA
1114 ATATCAATA-AA
1 ATA--AATATAA
1125 TATAAATATAA
1 -ATAAATATAA
*
1136 AT-AAT-CAA
1 ATAAATATAA
1144 ATAAATATAA
1 ATAAATATAA
1154 ATAAATA
1 ATAAATA
1161 AATAAAAGGC
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
8 4 0.10
9 6 0.15
10 18 0.46
11 4 0.10
12 7 0.18
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (10 bp):
ATAAATATAA
Found at i:1149 original size:18 final size:18
Alignment explanation
Indices: 1110--1166 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
1100 TACGATAAAT
*
1110 ATAAATATCAATAAAT--
1 ATAAATATAAATAAATAA
1126 ATAAATATAAAT-AATCAA
1 ATAAATATAAATAAAT-AA
1144 ATAAATATAAATAAATAA
1 ATAAATATAAATAAATAA
1162 ATAAA
1 ATAAA
1167 AGGCCACTCC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
15 3 0.08
16 11 0.31
18 19 0.53
19 3 0.08
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (18 bp):
ATAAATATAAATAAATAA
Found at i:1153 original size:14 final size:14
Alignment explanation
Indices: 1104--1164 Score: 60
Period size: 16 Copynumber: 4.5 Consensus size: 14
1094 GTAATATACG
1104 ATAAATATAAATATCA
1 ATAAATATAAATA--A
1120 ATAAATATAAAT--
1 ATAAATATAAATAA
1132 AT-AA-AT-AATCAA
1 ATAAATATAAAT-AA
1144 ATAAATATAAATAA
1 ATAAATATAAATAA
1158 ATAAATA
1 ATAAATA
1165 AAAGGCCACT
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
9 3 0.08
10 2 0.05
11 2 0.05
12 4 0.10
13 2 0.05
14 11 0.28
15 3 0.08
16 12 0.31
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (14 bp):
ATAAATATAAATAA
Done.