Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007238.1 Corchorus capsularis cultivar CVL-1 contig07259, 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: 37250
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:869 original size:22 final size:23
Alignment explanation
Indices: 828--871 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
818 AATAAAAATT
828 AAGAGTCAAAATAAATAGTAATC
1 AAGAGTCAAAATAAATAGTAATC
*
851 AAGAGTCAAAGT-AATAGTAAT
1 AAGAGTCAAAATAAATAGTAAT
872 TAAGTGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.55, C:0.07, G:0.16, T:0.23
Consensus pattern (23 bp):
AAGAGTCAAAATAAATAGTAATC
Found at i:1347 original size:14 final size:14
Alignment explanation
Indices: 1328--1421 Score: 56
Period size: 14 Copynumber: 6.9 Consensus size: 14
1318 AATTAAAGGA
1328 AGTAATCAGTAAAG
1 AGTAATCAGTAAAG
* *
1342 AGTAATCGGTAAAA
1 AGTAATCAGTAAAG
** *
1356 AGTAAAAATGGCAAAG
1 AGTAATCA--GTAAAG
*
1372 AG---T-AGTAAAA
1 AGTAATCAGTAAAG
1382 AGTAATCAGGTAAA-
1 AGTAATCA-GTAAAG
1396 AGTAATCAGT-AAG
1 AGTAATCAGTAAAG
1409 AAGTAATCAGTAA
1 -AGTAATCAGTAA
1422 GAAGGTCAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 19
0.67 0.11 0.21
Matches are distributed among these distances:
10 6 0.10
12 3 0.05
13 3 0.05
14 36 0.60
15 6 0.10
16 6 0.10
ACGTcount: A:0.52, C:0.06, G:0.21, T:0.20
Consensus pattern (14 bp):
AGTAATCAGTAAAG
Found at i:1422 original size:14 final size:14
Alignment explanation
Indices: 1375--1425 Score: 77
Period size: 14 Copynumber: 3.6 Consensus size: 14
1365 GGCAAAGAGT
*
1375 AGTAAAAAGTAATC
1 AGTAAGAAGTAATC
1389 AGGTAA-AAGTAATC
1 A-GTAAGAAGTAATC
1403 AGTAAGAAGTAATC
1 AGTAAGAAGTAATC
1417 AGTAAGAAG
1 AGTAAGAAG
1426 GTCAAAAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.11
14 27 0.77
15 4 0.11
ACGTcount: A:0.53, C:0.06, G:0.22, T:0.20
Consensus pattern (14 bp):
AGTAAGAAGTAATC
Found at i:1507 original size:44 final size:42
Alignment explanation
Indices: 1417--1571 Score: 142
Period size: 42 Copynumber: 3.7 Consensus size: 42
1407 AGAAGTAATC
* * *
1417 AGTAAGAAGGTCAAAAATGGTATCAAGTGAAATATGGTATTG
1 AGTAAGAAGGTCAAAAATGGTATAAAGTAAAATATGGTATTA
*
1459 AGTAAGAAGGTCAAAAAATGGTGTAAGAGTAAAATATGGTATTA
1 AGTAAGAAGGTC-AAAAATGGTATAA-AGTAAAATATGGTATTA
* *
1503 AGTAA-AAGAGT-AAAGAACGGTATTAAA-CAAAA-ATGGTATTA
1 AGTAAGAAG-GTCAAA-AATGGTA-TAAAGTAAAATATGGTATTA
* *
1544 AGTAAAAAGAGT-AAAAATGATA-AAAGTA
1 AGTAAGAAG-GTCAAAAATGGTATAAAGTA
1572 GCAAAAGTAA
Statistics
Matches: 96, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
39 3 0.03
40 1 0.01
41 19 0.20
42 28 0.29
43 20 0.21
44 25 0.26
ACGTcount: A:0.51, C:0.03, G:0.23, T:0.23
Consensus pattern (42 bp):
AGTAAGAAGGTCAAAAATGGTATAAAGTAAAATATGGTATTA
Found at i:1534 original size:25 final size:25
Alignment explanation
Indices: 1483--1534 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
1473 AAAATGGTGT
* **
1483 AAGAGTAAAATATGGTATTAAGTAA
1 AAGAGTAAAATACGGTATTAAACAA
1508 AAGAGTAAAGA-ACGGTATTAAACAA
1 AAGAGTAAA-ATACGGTATTAAACAA
1533 AA
1 AA
1535 ATGGTATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 22 0.96
26 1 0.04
ACGTcount: A:0.56, C:0.04, G:0.19, T:0.21
Consensus pattern (25 bp):
AAGAGTAAAATACGGTATTAAACAA
Found at i:22017 original size:40 final size:41
Alignment explanation
Indices: 21953--22033 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 41
21943 GAAACAGATT
21953 ATTATTATATTTTTTTAATGATGGACATATATATATATATA
1 ATTATTATATTTTTTTAATGATGGACATATATATATATATA
*
21994 ATTATTATA-TTTTTTAATGATGGATATATATATATATATA
1 ATTATTATATTTTTTTAATGATGGACATATATATATATATA
22034 TATGTATGTA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
40 30 0.77
41 9 0.23
ACGTcount: A:0.40, C:0.01, G:0.07, T:0.52
Consensus pattern (41 bp):
ATTATTATATTTTTTTAATGATGGACATATATATATATATA
Found at i:22243 original size:26 final size:26
Alignment explanation
Indices: 22206--22255 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
22196 GCCATTAGTT
22206 GCTTATACGCATAATGTAATTTTTTA
1 GCTTATACGCATAATGTAATTTTTTA
*
22232 GCTTATATGCATAATGTAATTTTT
1 GCTTATACGCATAATGTAATTTTT
22256 GACATTAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.10, G:0.12, T:0.48
Consensus pattern (26 bp):
GCTTATACGCATAATGTAATTTTTTA
Found at i:28768 original size:18 final size:18
Alignment explanation
Indices: 28744--28840 Score: 113
Period size: 18 Copynumber: 5.4 Consensus size: 18
28734 GGAACAGAAT
*
28744 CTGTGTTCGGTGTTGGGA
1 CTGTGTTCGGTGCTGGGA
* *
28762 TTGTGTTCGGCGCTGGGA
1 CTGTGTTCGGTGCTGGGA
* *
28780 TTGTGGTCGGTGCTGGGA
1 CTGTGTTCGGTGCTGGGA
* * *
28798 CTATGTTTGATGCTGGGA
1 CTGTGTTCGGTGCTGGGA
*
28816 CTGTATTCGGTGCTGGGA
1 CTGTGTTCGGTGCTGGGA
28834 CTGTGTT
1 CTGTGTT
28841 AACAGGTTGG
Statistics
Matches: 64, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 64 1.00
ACGTcount: A:0.08, C:0.13, G:0.41, T:0.37
Consensus pattern (18 bp):
CTGTGTTCGGTGCTGGGA
Done.