Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024423.1 Corchorus olitorius cultivar O-4 contig24456, 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: 2063
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.35
Found at i:950 original size:54 final size:54
Alignment explanation
Indices: 788--950 Score: 245
Period size: 54 Copynumber: 3.0 Consensus size: 54
778 GGAACAGGTG
* * * *
788 TTCAGATGATCTAGTGCGGTCATTCCAACAAGTTTTCAATGGTTAAAGTTGATC
1 TTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATC
* * *
842 CTGAGATGATCCAGTGCAGTCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATC
1 TTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATC
* *
896 TTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCGATGATCAGAGTTGATC
1 TTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATC
950 T
1 T
951 CGTTTCAAGA
Statistics
Matches: 97, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 97 1.00
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.33
Consensus pattern (54 bp):
TTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATC
Found at i:962 original size:35 final size:35
Alignment explanation
Indices: 915--1230 Score: 358
Period size: 35 Copynumber: 9.0 Consensus size: 35
905 TCCAGTGCGG
*
915 TCATTCCAAGAAGTTTTCGATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
* *
950 TCGTTTCAAGAAGTTTTCGGTGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
* * **
985 TCCTTTCAGGAAGTTTTTTATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
* *
1020 TCATTTTCAA-AATGTTTT-TATGGTCAGAGTTGA--
1 TCA-TTTCAAGAA-GTTTTCGATGATCAGAGTTGATC
1053 T--TTTCAAGAAGTTTTCGATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
* *
1086 TCGTTTCAA-AGAGTTTTCGTTGATCAGAGTTGATC
1 TCATTTCAAGA-AGTTTTCGATGATCAGAGTTGATC
** *
1121 TCATTTCAAGAAGTTTTTTATATGGTCAGAGTTGATC
1 TCATTTCAAGAAG--TTTTCGATGATCAGAGTTGATC
* **
1158 TCCTTTCAAGAAGTTTTTTTTATGATCAGAGTTGATC
1 TCATTTCAAGAAG--TTTTCGATGATCAGAGTTGATC
*
1195 TCATTTCAAGAAGTTTTCGATGATCAGAGTCGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
1230 T
1 T
1231 TCACATTGAT
Statistics
Matches: 243, Mismatches: 26, Indels: 24
0.83 0.09 0.08
Matches are distributed among these distances:
30 11 0.05
31 15 0.06
33 2 0.01
34 1 0.00
35 139 0.57
36 11 0.05
37 64 0.26
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.41
Consensus pattern (35 bp):
TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
Found at i:1058 original size:30 final size:31
Alignment explanation
Indices: 1022--1233 Score: 115
Period size: 37 Copynumber: 6.2 Consensus size: 31
1012 AGTTGATCTC
* *
1022 ATTTTCAA-AATGTTTT-TATGGTCAGAGTTG
1 ATTTTCAAGAA-GTTTTCGATGATCAGAGTTG
1052 ATTTTCAAGAAGTTTTCGATGATCAGAGTTG
1 ATTTTCAAGAAGTTTTCGATGATCAGAGTTG
*
1083 ATCTCGTTTCAA-AGAGTTTTCGTTGATCAGAGTTG
1 A--T--TTTCAAGA-AGTTTTCGATGATCAGAGTTG
** *
1118 ATCTCATTTCAAGAAGTTTTTTATATGGTCAGAGTTG
1 A--T--TTTCAAGAAG--TTTTCGATGATCAGAGTTG
**
1155 ATCTCCTTTCAAGAAGTTTTTTTTATGATCAGAGTTG
1 A--T--TTTCAAGAAG--TTTTCGATGATCAGAGTTG
*
1192 ATCTCATTTCAAGAAGTTTTCGATGATCAGAGTCG
1 A--T--TTTCAAGAAGTTTTCGATGATCAGAGTTG
*
1227 ATCTTCA
1 ATTTTCA
1234 CATTGATCCA
Statistics
Matches: 156, Mismatches: 16, Indels: 19
0.82 0.08 0.10
Matches are distributed among these distances:
30 13 0.08
31 19 0.12
33 2 0.01
34 1 0.01
35 56 0.36
36 1 0.01
37 64 0.41
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (31 bp):
ATTTTCAAGAAGTTTTCGATGATCAGAGTTG
Found at i:1101 original size:101 final size:105
Alignment explanation
Indices: 938--1230 Score: 366
Period size: 101 Copynumber: 2.8 Consensus size: 105
928 TTTTCGATGA
* * * *
938 TCAGAGTTGATCTCGTTTCAAGAAGTTTTCGGTGATCAGAGTTGATCTCCTTTCAGGAAGTTTTT
1 TCAGAGTTGA-CTC-TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTC
1003 TATGATCAGAGTTGATCTCATTTTCAA-AA-TGTTTT-TATGG
64 TATGATCAGAGTTGATCTCA-TTTCAAGAAGTGTTTTATATGG
*
1043 TCAGAGTTGA-T-TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAA-AGAGTTTTCG
1 TCAGAGTTGACTCTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGA-AGTTTTC-
*
1105 T-TGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATATGG
64 TATGATCAGAGTTGATCTCATTTCAAGAAGTGTTTTATATGG
**
1146 TCAGAGTTGATCTCCTTTCAAGAAGTTTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTT
1 TCAGAGTTGA-CT-CTTTCAAGAAG--TTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTT
* *
1211 TCGATGATCAGAGTCGATCT
62 TCTATGATCAGAGTTGATCT
1231 TCACATTGAT
Statistics
Matches: 165, Mismatches: 10, Indels: 22
0.84 0.05 0.11
Matches are distributed among these distances:
100 7 0.04
101 64 0.39
102 6 0.04
103 16 0.10
105 11 0.07
107 10 0.06
109 50 0.30
110 1 0.01
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.41
Consensus pattern (105 bp):
TCAGAGTTGACTCTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCTA
TGATCAGAGTTGATCTCATTTCAAGAAGTGTTTTATATGG
Found at i:1101 original size:136 final size:141
Alignment explanation
Indices: 921--1230 Score: 454
Period size: 136 Copynumber: 2.2 Consensus size: 141
911 GCGGTCATTC
921 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTCGGTGATCAGAGTTGATCT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTCGGTGATCAGAGTTGATCT
* * * *
986 CCTTTCAGGAAG-TTTTT-TATGATCAGAGTTGATCTCATTTTCAA-AA-TGTTTTTATGGTCAG
66 CATTTCAAGAAGTTTTTTATATGATCAGAGTTGATCTC-CTTTCAAGAAGTGTTTTTATGATCAG
1047 AGTTGA-T-TTT
130 AGTTGACTATTT
*
1057 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAA-AGAGTTTTCGTTGATCAGAGTTGATC
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGA-AGTTTTCGGTGATCAGAGTTGATC
* *
1121 TCATTTCAAGAAGTTTTTTATATGGTCAGAGTTGATCTCCTTTCAAGAAGTTTTTTTTATGATCA
65 TCATTTCAAGAAGTTTTTTATATGATCAGAGTTGATCTCCTTTCAAGAAG-TGTTTTTATGATCA
1186 GAGTTGATCTCATTT
129 GAGTTGA-CT-ATTT
*
1201 CAAGAAGTTTTCGATGATCAGAGTCGATCT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCT
1231 TCACATTGAT
Statistics
Matches: 156, Mismatches: 8, Indels: 12
0.89 0.05 0.07
Matches are distributed among these distances:
135 1 0.01
136 72 0.46
137 11 0.07
138 20 0.13
140 19 0.12
142 1 0.01
144 32 0.21
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (141 bp):
CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTCGGTGATCAGAGTTGATCT
CATTTCAAGAAGTTTTTTATATGATCAGAGTTGATCTCCTTTCAAGAAGTGTTTTTATGATCAGA
GTTGACTATTT
Done.