Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009527.1 Corchorus olitorius cultivar O-4 contig09559, 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: 5233
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Found at i:599 original size:28 final size:28
Alignment explanation
Indices: 563--665 Score: 161
Period size: 28 Copynumber: 3.7 Consensus size: 28
553 AAGTGAACCT
*
563 AAAATGACCAAAATGCCCCCTAGGTGTA
1 AAAATGACCAAAATGCCCCCTAAGTGTA
*
591 AAAATGACCAAAATGCCCTCTAAGTGTA
1 AAAATGACCAAAATGCCCCCTAAGTGTA
** *
619 AAAATGACCAAAATGCCCTTTAAGTGTG
1 AAAATGACCAAAATGCCCCCTAAGTGTA
647 AAAATGACCAAAATGCCCC
1 AAAATGACCAAAATGCCCC
666 TAGATGACCC
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 70 1.00
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.19
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCCTAAGTGTA
Found at i:950 original size:22 final size:22
Alignment explanation
Indices: 745--1155 Score: 203
Period size: 22 Copynumber: 18.5 Consensus size: 22
735 TACAATACCA
* *
745 CTATGAAATTTTGGTAATCACAT
1 CTATGAAATTTTGATAACCAC-T
* * *
768 -TTTGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAACCACT
* * *
789 TTATGAAATTTTGATAAGCTCT
1 CTATGAAATTTTGATAACCACT
** * * *
811 CTACAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAACCACT
*
833 CTATGAAATTTTGATAATCACAT
1 CTATGAAATTTTGATAACCAC-T
* * *
856 -TATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAACCACT
* * *
877 CTTTGAAATTTTGATAACAACA
1 CTATGAAATTTTGATAACCACT
*
899 CTACGAAATTTTGATAATCCAATCT
1 CTATGAAATTTTGATAA-CC-A-CT
*
924 CTATGAAATTTTGATAATCACT
1 CTATGAAATTTTGATAACCACT
** *
946 CTATGTGA-TTTGATAACC-TT
1 CTATGAAATTTTGATAACCACT
* * ***
966 CTATCAAATTTTGGT-ATTGCT
1 CTATGAAATTTTGATAACCACT
* *
987 -TATGAAATTGAGACCTTTATAACC-TT
1 CTATGAAATT------TTGATAACCACT
*
1013 CATATGAAATTTTGATAACCACA
1 C-TATGAAATTTTGATAACCACT
* *
1036 CTA-AAAATTTTTGATAACCACA
1 CTATGAAA-TTTTGATAACCACT
** *
1058 CTAAAAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCACT
* *
1080 CTATGAAATTTTGATAACCTCC
1 CTATGAAATTTTGATAACCACT
* * * *
1102 CCATGAAA-TATCAGTAACCTC-
1 CTATGAAATTTTGA-TAACCACT
* *
1123 CTAATGAAATTTTGTTAACCACA
1 CT-ATGAAATTTTGATAACCACT
1146 CTATGAAATT
1 CTATGAAATT
1156 CTTATAAGCT
Statistics
Matches: 295, Mismatches: 69, Indels: 49
0.71 0.17 0.12
Matches are distributed among these distances:
20 15 0.05
21 23 0.08
22 212 0.72
23 12 0.04
24 2 0.01
25 17 0.06
26 4 0.01
27 1 0.00
28 9 0.03
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACT
Found at i:1302 original size:22 final size:23
Alignment explanation
Indices: 1252--1334 Score: 91
Period size: 22 Copynumber: 3.7 Consensus size: 23
1242 ACATTCCTAA
* *
1252 GAAATTTTAATAACCCGATCCA-AT
1 GAAATTTTGATAA-CC-TTCCACAT
1276 GAAATTTTGATAACCTTCC-CAT
1 GAAATTTTGATAACCTTCCACAT
*
1298 GAAATTTTGATAA-CTTCCATAT
1 GAAATTTTGATAACCTTCCACAT
*
1320 GAAATTTTGGTAACC
1 GAAATTTTGATAACC
1335 ACACTATGGA
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
21 5 0.10
22 32 0.62
23 3 0.06
24 12 0.23
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (23 bp):
GAAATTTTGATAACCTTCCACAT
Found at i:1342 original size:22 final size:21
Alignment explanation
Indices: 1274--1353 Score: 74
Period size: 22 Copynumber: 3.7 Consensus size: 21
1264 ACCCGATCCA
*
1274 ATGAAATTTTGATAACCTTC-CC
1 ATGAAATTTTGATAACC--CACT
1296 ATGAAATTTTGATAACTTCCA-T
1 ATGAAATTTTGATAAC--CCACT
*
1318 ATGAAATTTTGGTAACCACACT
1 ATGAAATTTTGATAACC-CACT
*
1340 ATGGAATTTTGATA
1 ATGAAATTTTGATA
1354 TAATAACCAT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 1 0.02
21 2 0.04
22 45 0.92
24 1 0.02
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (21 bp):
ATGAAATTTTGATAACCCACT
Found at i:1348 original size:44 final size:43
Alignment explanation
Indices: 1270--1353 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 43
1260 AATAACCCGA
*
1270 TCCAATGAAATTTTGATAACCTTCCCATGAAATTTTGATAACT
1 TCCAATGAAATTTTGATAACCTACCCATGAAATTTTGATAACT
* * *
1313 TCCATATGAAATTTTGGTAACC-ACACTATGGAATTTTGATA
1 TCCA-ATGAAATTTTGATAACCTAC-CCATGAAATTTTGATA
1354 TAATAACCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
43 5 0.14
44 30 0.86
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.37
Consensus pattern (43 bp):
TCCAATGAAATTTTGATAACCTACCCATGAAATTTTGATAACT
Found at i:1587 original size:20 final size:20
Alignment explanation
Indices: 1549--1587 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1539 TATTGACATT
1549 TAAAAAATTGAAATTAAAAG
1 TAAAAAATTGAAATTAAAAG
*
1569 TAAAATATT-AAATTCAAAA
1 TAAAAAATTGAAATT-AAAA
1588 AATAATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
TAAAAAATTGAAATTAAAAG
Found at i:4050 original size:61 final size:60
Alignment explanation
Indices: 3968--4089 Score: 190
Period size: 61 Copynumber: 2.0 Consensus size: 60
3958 ACGTGCGTTA
* * ** *
3968 TACGTGACCCAATATGTTTAAATTAAATGAAAATTAAAATCTTAAGTATATTACTAATTT
1 TACGTGAACCAATATGTTTAAATTAAATAAAAATTAAAATCTTAAACATACTACTAATTT
4028 TACGTGCAACCAATATGTTTAAATTAAATAAAAATTAAAATCTTAAACATACTACTAATTT
1 TACGTG-AACCAATATGTTTAAATTAAATAAAAATTAAAATCTTAAACATACTACTAATTT
4089 T
1 T
4090 GTCGTGAAGA
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
60 6 0.11
61 50 0.89
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.37
Consensus pattern (60 bp):
TACGTGAACCAATATGTTTAAATTAAATAAAAATTAAAATCTTAAACATACTACTAATTT
Done.