Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001733.1 Corchorus capsularis cultivar CVL-1 contig01733, 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: 3520
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1411 original size:22 final size:22
Alignment explanation
Indices: 1384--1457 Score: 85
Period size: 22 Copynumber: 3.4 Consensus size: 22
1374 TAGTATGTAG
* *
1384 ATCAAAATATCATAGGGAGATT
1 ATCAAAATATCATAAGGAGGTT
* * *
1406 AACAAAATTTCATAATGAGGTT
1 ATCAAAATATCATAAGGAGGTT
* *
1428 ATCAAAAAATCATACGGAGGTT
1 ATCAAAATATCATAAGGAGGTT
1450 ATCAAAAT
1 ATCAAAAT
1458 TTGTAGTTAT
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.47, C:0.11, G:0.15, T:0.27
Consensus pattern (22 bp):
ATCAAAATATCATAAGGAGGTT
Found at i:1432 original size:44 final size:44
Alignment explanation
Indices: 1356--1459 Score: 120
Period size: 44 Copynumber: 2.4 Consensus size: 44
1346 GCTGGATGAT
* * * * *
1356 GAGATTAACAAAATTTTATAGTATGTAGATCAAAATATCATAGG
1 GAGATTAACAAAATTTCATAATAGGTAGATCAAAAAATCATACG
*
1400 GAGATTAACAAAATTTCATAATGAGGT-TATCAAAAAATCATACG
1 GAGATTAACAAAATTTCATAAT-AGGTAGATCAAAAAATCATACG
* *
1444 GAGGTTATCAAAATTT
1 GAGATTAACAAAATTT
1460 GTAGTTATCA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
44 48 0.94
45 3 0.06
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.31
Consensus pattern (44 bp):
GAGATTAACAAAATTTCATAATAGGTAGATCAAAAAATCATACG
Found at i:1532 original size:20 final size:22
Alignment explanation
Indices: 1486--1539 Score: 78
Period size: 20 Copynumber: 2.5 Consensus size: 22
1476 CATAAGAAAG
1486 TTATC-AAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGA-GT
1508 TTATCAAAATTTTATA-GGA-T
1 TTATCAAAATTTTATAGGGAGT
1528 TTATCAAAATTT
1 TTATCAAAATTT
1540 CATAACGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.42
22 8 0.26
23 10 0.32
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.44
Consensus pattern (22 bp):
TTATCAAAATTTTATAGGGAGT
Found at i:1765 original size:21 final size:22
Alignment explanation
Indices: 1725--1765 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1715 TTCCTTAGGG
* *
1725 AGGTTAACAAAATTTCATAAGA
1 AGGTTAAAAAAAATTCATAAGA
1747 AGGTTAAAAAAAATT-ATAA
1 AGGTTAAAAAAAATTCATAA
1766 AAAGAATCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.56, C:0.05, G:0.12, T:0.27
Consensus pattern (22 bp):
AGGTTAAAAAAAATTCATAAGA
Found at i:1840 original size:22 final size:23
Alignment explanation
Indices: 1792--1845 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
1782 CCATAGTATC
*
1792 ATTATTAAAATTTCATAGAAAGG
1 ATTATAAAAATTTCATAGAAAGG
* **
1815 -TTATCAAAATTTCATA-ATGGG
1 ATTATAAAAATTTCATAGAAAGG
1836 ATTATAAAAA
1 ATTATAAAAA
1846 ATAGTGTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 3 0.12
22 23 0.88
ACGTcount: A:0.48, C:0.06, G:0.11, T:0.35
Consensus pattern (23 bp):
ATTATAAAAATTTCATAGAAAGG
Found at i:1964 original size:2 final size:2
Alignment explanation
Indices: 1959--2039 Score: 93
Period size: 2 Copynumber: 43.5 Consensus size: 2
1949 AGTGTGTGTG
* *
1959 TA TA TA TA TA TA TA GA TA TA TA TA TA TA TA T- TA T- TA GA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1999 TA TA TA TA TA T- TA T- TA GA TA TA TA T- TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2037 TA T
1 TA T
2040 CCTAAATAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
1 6 0.09
2 61 0.91
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1984 original size:20 final size:20
Alignment explanation
Indices: 1959--2031 Score: 107
Period size: 20 Copynumber: 3.8 Consensus size: 20
1949 AGTGTGTGTG
* *
1959 TATATATATATA-TA-GATA
1 TATATATATATATTATTAGA
1977 TATATATATATATTATTAGA
1 TATATATATATATTATTAGA
1997 TATATATATATATTATTAGA
1 TATATATATATATTATTAGA
2017 TATATAT-TATATTAT
1 TATATATATATATTAT
2032 ATATATATCC
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
18 12 0.24
19 10 0.20
20 29 0.57
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (20 bp):
TATATATATATATTATTAGA
Done.