Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010150.1 Corchorus capsularis cultivar CVL-1 contig10171, 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: 8534
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.31
Found at i:224 original size:52 final size:51
Alignment explanation
Indices: 160--262 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 51
150 GATACTTGTA
*
160 CACTTATGAATTGAAGGCCTATTACTCAGTATTAAATACTTCTATTAACAGC
1 CACTTATGAATTGAAGGCCTATTACTCAGTATTAAATAC-CCTATTAACAGC
212 CACTTATGAATTGAAGGCCTATTACTCAGTATTAAATACCCTATTAACAGC
1 CACTTATGAATTGAAGGCCTATTACTCAGTATTAAATACCCTATTAACAGC
263 AAGGCAATTC
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
51 11 0.22
52 39 0.78
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (51 bp):
CACTTATGAATTGAAGGCCTATTACTCAGTATTAAATACCCTATTAACAGC
Found at i:1318 original size:3 final size:3
Alignment explanation
Indices: 1310--1378 Score: 52
Period size: 3 Copynumber: 22.0 Consensus size: 3
1300 GAACGGGTAG
*
1310 AGA AGA AGA AGA AGA AGA AAA TAGA GAGA A-A A-A AGAA AGAA AGAA
1 AGA AGA AGA AGA AGA AGA AGA -AGA -AGA AGA AGA AG-A AG-A AG-A
* *
1355 ATA AGA AGA AGA GGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA
1379 TAGAGTAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
2 4 0.07
3 37 0.66
4 15 0.27
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:1398 original size:45 final size:48
Alignment explanation
Indices: 1310--1405 Score: 128
Period size: 48 Copynumber: 2.0 Consensus size: 48
1300 GAACGGGTAG
1310 AGAAGAAGAAGAAGAAGAAAATAGAGAGAAAAAAGAAAGAAAG-AAATA
1 AGAAGAAGAAGAAGAAGAAAATAGAGAGAAAAAAG-AAGAAAGAAAATA
* *
1358 AGAAGAAGAGGAAGAAGAAGATAGAGTA-AAAAAAG-A-AAAGAAAATA
1 AGAAGAAGAAGAAGAAGAAAATAGAG-AGAAAAAAGAAGAAAGAAAATA
1404 AG
1 AG
1406 TGGGGAGAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
45 4 0.09
46 8 0.18
48 31 0.70
49 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.26, T:0.05
Consensus pattern (48 bp):
AGAAGAAGAAGAAGAAGAAAATAGAGAGAAAAAAGAAGAAAGAAAATA
Found at i:5765 original size:30 final size:27
Alignment explanation
Indices: 5707--5770 Score: 69
Period size: 30 Copynumber: 2.3 Consensus size: 27
5697 CTAAATTTCC
5707 ATTATTTTAATAATGGAATAATTAAAAT
1 ATTATTTTAATAATGGAAT-ATTAAAAT
5735 ATTATTTAATAATAATGGCAAT-TTAGAAAT
1 ATTATTT--TAATAATGG-AATATTA-AAAT
5765 A-TATTT
1 ATTATTT
5771 GGAAAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
28 7 0.22
29 8 0.25
30 14 0.44
31 3 0.09
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.44
Consensus pattern (27 bp):
ATTATTTTAATAATGGAATATTAAAAT
Found at i:6047 original size:12 final size:12
Alignment explanation
Indices: 6030--6068 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
6020 ATAATTACTC
*
6030 ATATATATATAT
1 ATATATATGTAT
6042 ATATATATGTAT
1 ATATATATGTAT
* *
6054 GTATGTATGTAT
1 ATATATATGTAT
6066 ATA
1 ATA
6069 CTAATTATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (12 bp):
ATATATATGTAT
Found at i:6824 original size:65 final size:65
Alignment explanation
Indices: 6661--6871 Score: 226
Period size: 67 Copynumber: 3.2 Consensus size: 65
6651 TGATTTTTTT
* * * * * * **
6661 AAAAGTCCAATGTTCGAGATCCGAACGGCTATAGTCCGATACGTAAATGGTTGGAGACCCCCGAC
1 AAAAGTCCAA--TTCGAGATCCAAACGGCAATGGTCTGATACGCAAATGGTTGGAAACCCGAGAC
6726 AC
64 AC
* *
6728 AAAAGTCCGATGTTCGAGATCCAAACGGCAATGGTCTGATACACAAATGGTTGGAAACCCGAGAC
1 AAAAGTCC-A-ATTCGAGATCCAAACGGCAATGGTCTGATACGCAAATGGTTGGAAACCCGAGAC
6793 AC
64 AC
* * * *
6795 AAAAGTCCAATACGAGATCCAAACGGCAATGATCTGATATGCAAATGGTT-GAAGACCCGAGAAA
1 AAAAGTCCAATTCGAGATCCAAACGGCAATGGTCTGATACGCAAATGGTTGGAA-ACCCGAGACA
*
6859 G
65 C
*
6860 AAAAGTCTAATT
1 AAAAGTCCAATT
6872 TAGTAAAATT
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
64 3 0.02
65 55 0.45
66 1 0.01
67 62 0.51
68 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.19
Consensus pattern (65 bp):
AAAAGTCCAATTCGAGATCCAAACGGCAATGGTCTGATACGCAAATGGTTGGAAACCCGAGACAC
Done.