Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012715.1 Corchorus capsularis cultivar CVL-1 contig12736, 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: 3382
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Found at i:879 original size:36 final size:36
Alignment explanation
Indices: 828--1086 Score: 131
Period size: 36 Copynumber: 7.2 Consensus size: 36
818 TAAAATAAGT
* *
828 AACTTAAGAAAGACCACCCTGGATCATTCTAAACTG
1 AACTGAAGAAAGACCACCCTCGATCATTCTAAACTG
* * * **
864 AATTGAAGAACGACCACCCTTGATCATTC-CGAC-G
1 AACTGAAGAAAGACCACCCTCGATCATTCTAAACTG
* * * *
898 CAAGCTGAAGAAAGACCACCCTGGGTCA-ACTGAAA-TA
1 -AA-CTGAAGAAAGACCACCCTCGATCATTCT-AAACTG
* ** ***
935 AAATGAAGAGCGACCACCCTCGATCATTCCGGACTG
1 AACTGAAGAAAGACCACCCTCGATCATTCTAAACTG
* *
971 AACTGAAGAATGACCACCCTCGATCATTCT-GAC-G
1 AACTGAAGAAAGACCACCCTCGATCATTCTAAACTG
* * * * *
1005 CAAATTGAAGAAAGAACACCCTGGGTCA-ACTGAAA-T-
1 --AACTGAAGAAAGACCACCCTCGATCATTCT-AAACTG
* * **
1041 AAGCTGAGGAACGACCACCCTCGATCATTCCGAACTG
1 AA-CTGAAGAAAGACCACCCTCGATCATTCTAAACTG
*
1078 AACTTAAGA
1 AACTGAAGA
1087 GCAACCACCT
Statistics
Matches: 161, Mismatches: 46, Indels: 32
0.67 0.19 0.13
Matches are distributed among these distances:
34 4 0.02
35 50 0.31
36 103 0.64
37 4 0.02
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.18
Consensus pattern (36 bp):
AACTGAAGAAAGACCACCCTCGATCATTCTAAACTG
Found at i:960 original size:71 final size:72
Alignment explanation
Indices: 828--997 Score: 204
Period size: 71 Copynumber: 2.4 Consensus size: 72
818 TAAAATAAGT
* * * * *
828 AACTTAAGAAAGACCACCCTGGATCATTCTAAACTGAATTGAAGAACGACCACCCTTGATCATTC
1 AACTGAAGAAAGACCACCCTGGATCATACTAAACTAAAATGAAGAACGACCACCCTCGATCATTC
893 C-GAC-G
66 CGGACTG
* *
898 CAAGCTGAAGAAAGACCACCCTGGGTCA-ACTGAAA-TAAAATGAAGAGCGACCACCCTCGATCA
1 -AA-CTGAAGAAAGACCACCCTGGATCATACT-AAACTAAAATGAAGAACGACCACCCTCGATCA
961 TTCCGGACTG
63 TTCCGGACTG
* *
971 AACTGAAGAATGACCACCCTCGATCAT
1 AACTGAAGAAAGACCACCCTGGATCAT
998 TCTGACGCAA
Statistics
Matches: 84, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
71 53 0.63
72 30 0.36
73 1 0.01
ACGTcount: A:0.36, C:0.28, G:0.18, T:0.18
Consensus pattern (72 bp):
AACTGAAGAAAGACCACCCTGGATCATACTAAACTAAAATGAAGAACGACCACCCTCGATCATTC
CGGACTG
Found at i:1025 original size:107 final size:107
Alignment explanation
Indices: 833--1095 Score: 355
Period size: 107 Copynumber: 2.5 Consensus size: 107
823 TAAGTAACTT
* * ** * *
833 AAGAAAGACCACCCTGGATCATTCTAAACTGAATTGAAGAACGACCACCCTTGATCATTCCGACG
1 AAGAACGACCACCCTCGATCATTCCGAACTGAACTGAAGAACGACCACCCTCGATCATTCCGACG
* *
898 CAAGCTGAAGAAAGACCACCCTGGGTCAACTGAAATAAAATG
66 CAAACTGAAGAAAGAACACCCTGGGTCAACTGAAATAAAATG
* * * *
940 AAGAGCGACCACCCTCGATCATTCCGGACTGAACTGAAGAATGACCACCCTCGATCATTCTGACG
1 AAGAACGACCACCCTCGATCATTCCGAACTGAACTGAAGAACGACCACCCTCGATCATTCCGACG
* **
1005 CAAATTGAAGAAAGAACACCCTGGGTCAACTGAAATAAGCTG
66 CAAACTGAAGAAAGAACACCCTGGGTCAACTGAAATAAAATG
* * * *
1047 AGGAACGACCACCCTCGATCATTCCGAACTGAACTTAAGAGCAACCACC
1 AAGAACGACCACCCTCGATCATTCCGAACTGAACTGAAGAACGACCACC
1096 TTGGGTCATT
Statistics
Matches: 134, Mismatches: 22, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
107 134 1.00
ACGTcount: A:0.36, C:0.28, G:0.19, T:0.17
Consensus pattern (107 bp):
AAGAACGACCACCCTCGATCATTCCGAACTGAACTGAAGAACGACCACCCTCGATCATTCCGACG
CAAACTGAAGAAAGAACACCCTGGGTCAACTGAAATAAAATG
Found at i:1293 original size:35 final size:35
Alignment explanation
Indices: 1266--1349 Score: 152
Period size: 35 Copynumber: 2.4 Consensus size: 35
1256 AATTTGCTAT
1266 AGAAAGATCACCCTAGATTAGCCGAAATTTACTGA
1 AGAAAGATCACCCTAGATTAGCCGAAATTTACTGA
1301 AGAAAGATCACCCTAGATTAGCC-AATATTTACTGA
1 AGAAAGATCACCCTAGATTAGCCGAA-ATTTACTGA
1336 AGAAAGATCACCCT
1 AGAAAGATCACCCT
1350 GGATCAATTA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
34 2 0.04
35 46 0.96
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.23
Consensus pattern (35 bp):
AGAAAGATCACCCTAGATTAGCCGAAATTTACTGA
Found at i:2940 original size:21 final size:21
Alignment explanation
Indices: 2900--2949 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
2890 TTTTCATTCA
2900 TTTTTTTTTTCGCTCTTTTCGT
1 TTTTTTTTTTCGCTCTTTTC-T
2922 TTTTTTTTTTC-CT-TCTTTCT
1 TTTTTTTTTTCGCTCT-TTTCT
*
2942 TTCTTTTT
1 TTTTTTTT
2950 CGAATTTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 9 0.35
21 6 0.23
22 11 0.42
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.78
Consensus pattern (21 bp):
TTTTTTTTTTCGCTCTTTTCT
Done.