Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01002492.1 Corchorus capsularis cultivar CVL-1 contig02499, 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, 885
Length: 1475
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Found at i:147 original size:49 final size:50
Alignment explanation
Indices: 94--273 Score: 175
Period size: 49 Copynumber: 3.3 Consensus size: 50
84 TTTTAATTTC
94 TAATT-ATTTTTGAAATTTAGAAATTTCATCATTATTGATTATTATATGA
1 TAATTCATTTTTGAAATTTAGAAATTTCATCATTATTGATTATTATATGA
* *
143 TAATTAATTATTATATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTGATTATTATAT
1 TAATTCA-T-TT-T-TG--AA---A-TTTAGAAA--T-----TTCATCATTATTGATTATTATAT
208 GA
49 GA
210 TAATTCATTTTTGAAATTTAG-AATTTCATCATTATTGATTATTATATGA
1 TAATTCATTTTTGAAATTTAGAAATTTCATCATTATTGATTATTATATGA
259 TAATTCATTTTTGAA
1 TAATTCATTTTTGAA
274 TGATGATTTT
Statistics
Matches: 110, Mismatches: 3, Indels: 36
0.74 0.02 0.24
Matches are distributed among these distances:
49 45 0.41
50 1 0.01
51 1 0.01
52 2 0.02
53 1 0.01
54 3 0.03
56 4 0.04
57 4 0.04
58 1 0.01
59 1 0.01
60 7 0.06
61 2 0.02
62 1 0.01
63 2 0.02
64 1 0.01
65 2 0.02
66 1 0.01
67 31 0.28
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51
Consensus pattern (50 bp):
TAATTCATTTTTGAAATTTAGAAATTTCATCATTATTGATTATTATATGA
Found at i:154 original size:18 final size:18
Alignment explanation
Indices: 131--165 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
121 ATCATTATTG
131 ATTATTATATGATAATTA
1 ATTATTATATGATAATTA
149 ATTATTATATGATAATT
1 ATTATTATATGATAATT
166 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:188 original size:21 final size:21
Alignment explanation
Indices: 164--238 Score: 69
Period size: 21 Copynumber: 3.2 Consensus size: 21
154 TATATGATAA
164 TTCATTTTTGAAATTTAGAAT
1 TTCATTTTTGAAATTTAGAAT
* *
185 TTCATCATTATTGATTATTATATGATAA
1 TTCAT--TT-TTGA-AATT-TA-GA-AT
213 TTCATTTTTGAAATTTAGAAT
1 TTCATTTTTGAAATTTAGAAT
234 TTCAT
1 TTCAT
239 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:193 original size:24 final size:24
Alignment explanation
Indices: 165--247 Score: 82
Period size: 24 Copynumber: 3.4 Consensus size: 24
155 ATATGATAAT
*
165 TCATTTTTGAAATTTAGAATTTCA
1 TCATTATTGAAATTTAGAATTTCA
* *
189 TCATTATTGATTATTATATGATAATTCA
1 TCATTATTGA-AATT-TA-GA-ATTTCA
217 T--TT-TTGAAATTTAGAATTTCA
1 TCATTATTGAAATTTAGAATTTCA
238 TCATTATTGA
1 TCATTATTGA
248 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:217 original size:25 final size:25
Alignment explanation
Indices: 189--272 Score: 77
Period size: 25 Copynumber: 3.4 Consensus size: 25
179 TAGAATTTCA
189 TCATTATTGATTATTATATGATAAT
1 TCATTATTGATTATTATATGATAAT
* * *
214 TCATTTTTGA-AATT-TA-GA-ATTT
1 TCATTATTGATTATTATATGATA-AT
236 CATCATTATTGATTATTATATGATAAT
1 --TCATTATTGATTATTATATGATAAT
*
263 TCATTTTTGA
1 TCATTATTGA
273 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:1126 original size:17 final size:18
Alignment explanation
Indices: 1106--1147 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
1096 TATTTAAAAG
*
1106 TAAATATA-CGATAAATA
1 TAAATATATCAATAAATA
1123 TAAATA-ATCAATAAATA
1 TAAATATATCAATAAATA
1140 TAAATATA
1 TAAATATA
1148 AATAATCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 20 0.91
18 1 0.05
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (18 bp):
TAAATATATCAATAAATA
Found at i:1142 original size:23 final size:23
Alignment explanation
Indices: 1116--1177 Score: 106
Period size: 23 Copynumber: 2.6 Consensus size: 23
1106 TAAATATACG
1116 ATAAATATAAATAATCAATAAAT
1 ATAAATATAAATAATCAATAAAT
1139 ATAAATATAAATAATCAATAAAT
1 ATAAATATAAATAATCAATAAAT
1162 ATAAATAAATAAATAA
1 ATAAAT--ATAAATAA
1178 AAGGCCACTC
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
23 29 0.78
25 8 0.22
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (23 bp):
ATAAATATAAATAATCAATAAAT
Done.