Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008944.1 Corchorus capsularis cultivar CVL-1 contig08965, 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, 754
Length: 1257
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Found at i:797 original size:24 final size:24
Alignment explanation
Indices: 768--912 Score: 77
Period size: 24 Copynumber: 6.0 Consensus size: 24
758 TGTTCAATTC
*
768 GCTTCAATTATTCAATCCTTCAAT
1 GCTTCAATTATTCAATACTTCAAT
* * *
792 GCTTCAATTTTTTTCAAAATAATCTC-TT
1 GCTTCAA--TTATTC--AATACT-TCAAT
* *
820 TCTTCAATTATTCAATGCTTCAAT
1 GCTTCAATTATTCAATACTTCAAT
* * *
844 TCTTCCATTATTCAATTCTTCAAT
1 GCTTCAATTATTCAATACTTCAAT
* *
868 GATTCAATT-TATC--T-CTTCGACT
1 GCTTCAATTAT-TCAATACTTC-AAT
*
890 -CTTTAATTATTCAATACTTCAAT
1 GCTTCAATTATTCAATACTTCAAT
913 TTATTTCTTC
Statistics
Matches: 91, Mismatches: 18, Indels: 25
0.68 0.13 0.19
Matches are distributed among these distances:
21 12 0.13
22 4 0.04
23 6 0.07
24 46 0.51
26 10 0.11
28 11 0.12
29 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.03, T:0.47
Consensus pattern (24 bp):
GCTTCAATTATTCAATACTTCAAT
Found at i:835 original size:8 final size:8
Alignment explanation
Indices: 822--876 Score: 56
Period size: 8 Copynumber: 6.9 Consensus size: 8
812 AATCTCTTTC
822 TTCAATTA
1 TTCAATTA
**
830 TTCAATGC
1 TTCAATTA
*
838 TTCAATTC
1 TTCAATTA
*
846 TTCCATTA
1 TTCAATTA
*
854 TTCAATTC
1 TTCAATTA
*
862 TTCAATGA
1 TTCAATTA
870 TTCAATT
1 TTCAATT
877 TATCTCTTCG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
8 37 1.00
ACGTcount: A:0.29, C:0.20, G:0.04, T:0.47
Consensus pattern (8 bp):
TTCAATTA
Found at i:842 original size:16 final size:16
Alignment explanation
Indices: 822--876 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
812 AATCTCTTTC
* *
822 TTCAATTATTCAATGC
1 TTCAATTCTTCAATGA
* *
838 TTCAATTCTTCCATTA
1 TTCAATTCTTCAATGA
854 TTCAATTCTTCAATGA
1 TTCAATTCTTCAATGA
870 TTCAATT
1 TTCAATT
877 TATCTCTTCG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.29, C:0.20, G:0.04, T:0.47
Consensus pattern (16 bp):
TTCAATTCTTCAATGA
Found at i:915 original size:21 final size:21
Alignment explanation
Indices: 891--930 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
881 TCTTCGACTC
891 TTTAATTATTCAATACTTCAA
1 TTTAATTATTCAATACTTCAA
* * *
912 TTTATTTCTTCAATTCTTC
1 TTTAATTATTCAATACTTC
931 GATCACTTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTAATTATTCAATACTTCAA
Found at i:1024 original size:8 final size:8
Alignment explanation
Indices: 1007--1249 Score: 90
Period size: 8 Copynumber: 33.2 Consensus size: 8
997 AGGGTGGTCT
1007 TTCTTCAA
1 TTCTTCAA
*
1015 TTCTTTAA
1 TTCTTCAA
*
1023 TTATTCAA
1 TTCTTCAA
*
1031 TGCTTCAA
1 TTCTTCAA
*
1039 -T-TT-AT
1 TTCTTCAA
1044 TTCTGGTC-A
1 TTCT--TCAA
*
1053 TTCTTCGA
1 TTCTTCAA
1061 TTC--CAA
1 TTCTTCAA
*
1067 TTTTTCAA
1 TTCTTCAA
1075 -T-TTCAA
1 TTCTTCAA
*
1081 TTCTACAA
1 TTCTTCAA
*
1089 TGCTTCAA
1 TTCTTCAA
1097 -T-TTCAA
1 TTCTTCAA
*
1103 TTATTCAA
1 TTCTTCAA
*
1111 --ATTCAA
1 TTCTTCAA
*
1117 TTCTACAA
1 TTCTTCAA
*
1125 TGT-TCCAA
1 T-TCTTCAA
1133 -T-TTCAA
1 TTCTTCAA
1139 TTCTTCAA
1 TTCTTCAA
* *
1147 -GCCTCAA
1 TTCTTCAA
1154 -T-TTCAA
1 TTCTTCAA
1160 TTC--CAA
1 TTCTTCAA
*
1166 TGCTTCAA
1 TTCTTCAA
1174 -T-TTCAA
1 TTCTTCAA
1180 TTCTTCAA
1 TTCTTCAA
1188 -T-TTCAA
1 TTCTTCAA
** *
1194 CCCTTCAG
1 TTCTTCAA
1202 TGT-TTCAA
1 T-TCTTCAA
1210 TTCTTCAA
1 TTCTTCAA
1218 TTCTTCAA
1 TTCTTCAA
1226 -T-TTCAA
1 TTCTTCAA
1232 TTCTTCAA
1 TTCTTCAA
*
1240 TGCTTCAA
1 TTCTTCAA
1248 TT
1 TT
1250 TCAATTCC
Statistics
Matches: 175, Mismatches: 31, Indels: 58
0.66 0.12 0.22
Matches are distributed among these distances:
5 1 0.01
6 52 0.30
7 18 0.10
8 98 0.56
9 6 0.03
ACGTcount: A:0.28, C:0.22, G:0.05, T:0.46
Consensus pattern (8 bp):
TTCTTCAA
Found at i:1080 original size:6 final size:6
Alignment explanation
Indices: 1069--1193 Score: 61
Period size: 6 Copynumber: 18.0 Consensus size: 6
1059 GATTCCAATT
*
1069 TTTCAA TTTCAA TTCTACAA TGCTTCAA TTTCAA TTATTCAA ATTCAA
1 TTTCAA TTTCAA TT-T-CAA T--TTCAA TTTCAA -T-TTCAA TTTCAA
** *
1117 TTCTACAA TGTTCCAA TTTCAA TTCTTCAA GCCTCAA TTTCAA TTCCAA
1 TT-T-CAA T-TT-CAA TTTCAA -T-TTCAA -TTTCAA TTTCAA TTTCAA
1166 TGCTTCAA TTTCAA TTCTTCAA TTTCAA
1 T--TTCAA TTTCAA -T-TTCAA TTTCAA
1194 CCCTTCAGTG
Statistics
Matches: 94, Mismatches: 10, Indels: 30
0.70 0.07 0.22
Matches are distributed among these distances:
6 42 0.45
7 12 0.13
8 37 0.39
9 2 0.02
10 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.03, T:0.42
Consensus pattern (6 bp):
TTTCAA
Found at i:1175 original size:41 final size:42
Alignment explanation
Indices: 1107--1187 Score: 121
Period size: 41 Copynumber: 1.9 Consensus size: 42
1097 TTTCAATTAT
1107 TCAAATTCAATTCTACAATGTTCCAATTTCAATTCTTCAAGCC
1 TCAAATTCAATTC-ACAATGTTCCAATTTCAATTCTTCAAGCC
*
1150 TCAATTTCAATTC-CAATGCTT-CAATTTCAATTCTTCAA
1 TCAAATTCAATTCACAATG-TTCCAATTTCAATTCTTCAA
1188 TTTCAACCCT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
41 22 0.61
42 2 0.06
43 12 0.33
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.40
Consensus pattern (42 bp):
TCAAATTCAATTCACAATGTTCCAATTTCAATTCTTCAAGCC
Found at i:1190 original size:14 final size:14
Alignment explanation
Indices: 1052--1256 Score: 95
Period size: 14 Copynumber: 14.3 Consensus size: 14
1042 ATTTCTGGTC
* *
1052 ATTCTTCGATTCCA
1 ATTCTTCAATTTCA
*
1066 ATTTTTCAATTTCA
1 ATTCTTCAATTTCA
*
1080 ATTCTACAATGCTTCA
1 ATTCTTCAAT--TTCA
1096 A-T-TTCAATTATTCA
1 ATTCTTCAA-T-TTCA
*
1110 A--ATTCAATTCTACA
1 ATTCTTCAATT-T-CA
*
1124 ATGT-TCCAATTTCA
1 AT-TCTTCAATTTCA
**
1138 ATTCTTCAAGCCTCA
1 ATTCTTCAA-TTTCA
*
1153 A-T-TTCAATTCCA
1 ATTCTTCAATTTCA
*
1165 ATGCTTCAATTTCA
1 ATTCTTCAATTTCA
1179 ATTCTTCAATTTCA
1 ATTCTTCAATTTCA
** *
1193 ACCCTTCAGTGTTTCA
1 ATTCTTCA--ATTTCA
1209 ATTCTTCAATTCTTCA
1 ATTCTTCAA-T-TTCA
1225 A-T-TTCAATTCTTCA
1 ATTCTTCAA-T-TTCA
*
1239 ATGCTTCAATTTCA
1 ATTCTTCAATTTCA
1253 ATTC
1 ATTC
1257 C
Statistics
Matches: 147, Mismatches: 25, Indels: 38
0.70 0.12 0.18
Matches are distributed among these distances:
12 4 0.03
13 8 0.05
14 93 0.63
15 10 0.07
16 32 0.22
ACGTcount: A:0.29, C:0.23, G:0.04, T:0.44
Consensus pattern (14 bp):
ATTCTTCAATTTCA
Found at i:1226 original size:38 final size:36
Alignment explanation
Indices: 1163--1256 Score: 134
Period size: 38 Copynumber: 2.6 Consensus size: 36
1153 ATTTCAATTC
1163 CAATGCTTCAATTTCAATTCTTCAATTTCAACCCTT
1 CAATGCTTCAATTTCAATTCTTCAATTTCAACCCTT
* * **
1199 CAGTGTTTCAATTCTTCAATTCTTCAATTTCAATTCTT
1 CAATGCTTCAA-T-TTCAATTCTTCAATTTCAACCCTT
1237 CAATGCTTCAATTTCAATTC
1 CAATGCTTCAATTTCAATTC
1257 C
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
36 17 0.34
37 2 0.04
38 31 0.62
ACGTcount: A:0.27, C:0.24, G:0.04, T:0.45
Consensus pattern (36 bp):
CAATGCTTCAATTTCAATTCTTCAATTTCAACCCTT
Found at i:1229 original size:22 final size:22
Alignment explanation
Indices: 1204--1256 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
1194 CCCTTCAGTG
*
1204 TTTCAATTCTTCAATTCTTCAA
1 TTTCAATTCTTCAATGCTTCAA
1226 TTTCAATTCTTCAATGCTTCAA
1 TTTCAATTCTTCAATGCTTCAA
1248 TTTCAATTC
1 TTTCAATTC
1257 C
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.26, C:0.23, G:0.02, T:0.49
Consensus pattern (22 bp):
TTTCAATTCTTCAATGCTTCAA
Done.