Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023999.1 Corchorus olitorius cultivar O-4 contig24032, 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: 3886
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.29
Found at i:541 original size:35 final size:37
Alignment explanation
Indices: 502--578 Score: 88
Period size: 35 Copynumber: 2.1 Consensus size: 37
492 AGAAGGAGCT
*
502 AAAAAC-CGGACCTAAAATAGAAAGAGGT-A-AAAAAA
1 AAAAACTCGG-CCTAAAACAGAAAGAGGTCAGAAAAAA
* *
537 AAAAACTTGGCCTAAAACAGAGAGAGGTCAGAAAAAA
1 AAAAACTCGGCCTAAAACAGAAAGAGGTCAGAAAAAA
*
574 GAAAA
1 AAAAA
579 TAAATAAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
35 22 0.63
36 3 0.09
37 10 0.29
ACGTcount: A:0.60, C:0.12, G:0.19, T:0.09
Consensus pattern (37 bp):
AAAAACTCGGCCTAAAACAGAAAGAGGTCAGAAAAAA
Found at i:1479 original size:58 final size:58
Alignment explanation
Indices: 1410--1876 Score: 765
Period size: 58 Copynumber: 8.0 Consensus size: 58
1400 TTAAAACAAA
*
1410 ATCTTATCTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTT
1 ATCTTGTCTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTT
1468 ATCTTGTCTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTT
1 ATCTTGTCTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTT
*
1526 ATCTTGTCTTAAAATCCTGCTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTT
1 ATCTTGTCTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTT
* *
1584 ATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTTCAATTCAAAATCTC
1 ATCTTGTCTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAG-TTTTCAATTCAAAATCTT
* * * * *
1643 ATTTTGTTTTAAAATCCTGTTCTAGGTTTCTGTTAGAGAGTTTTCAATTCAAAATCTC
1 ATCTTGTCTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTT
* *
1701 ATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATT
1 ATCTTGTCTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTT
* *
1759 ATCTTG-CTTCAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTTAAAATATT
1 ATCTTGTCTT-AAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTT
* * *
1817 ATCTTGTTTTAAAATCCTGTTCGAGGTCTCCGTTAGAGAGTTTTCAATTTAAAATCTT
1 ATCTTGTCTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTT
1875 AT
1 AT
1877 TTTGGTCGAG
Statistics
Matches: 388, Mismatches: 18, Indels: 6
0.94 0.04 0.01
Matches are distributed among these distances:
57 2 0.01
58 330 0.85
59 56 0.14
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (58 bp):
ATCTTGTCTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTT
Found at i:1763 original size:233 final size:232
Alignment explanation
Indices: 1418--1880 Score: 802
Period size: 233 Copynumber: 2.0 Consensus size: 232
1408 AAATCTTATC
*
1418 TTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCTTGTCTTAAAAT
1 TTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTCATCTTGTCTTAAAAT
*
1483 CCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCTTGTCTT-AAAATCCTGCT
66 CCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATTATCTTG-CTTCAAAATCCTGCT
*
1547 CGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCTTGTTTTAAAATCCTGTTCGAGGTC
130 CGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATTATCTTGTTTTAAAATCCTGTTCGAGGTC
*
1612 TCTGTTAGAGAGTTTTTCAATTCAAAATCTCATTTTGTT
195 TCCGTTAGAGAG-TTTTCAATTCAAAATCTCATTTTGTT
* * *
1651 TTAAAATCCTGTTCTAGGTTTCTGTTAGAGAGTTTTCAATTCAAAATCTCATCTTGTTTTAAAAT
1 TTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTCATCTTGTCTTAAAAT
*
1716 CCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATTATCTTGCTTCAAAATCCTGTTC
66 CCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATTATCTTGCTTCAAAATCCTGCTC
*
1781 GAGGTCTCTGTTAGAGAGTTTTCAATTTAAAATATTATCTTGTTTTAAAATCCTGTTCGAGGTCT
131 GAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATTATCTTGTTTTAAAATCCTGTTCGAGGTCT
* *
1846 CCGTTAGAGAGTTTTCAATTTAAAATCTTATTTTG
196 CCGTTAGAGAGTTTTCAATTCAAAATCTCATTTTG
1881 GTCGAGATCT
Statistics
Matches: 218, Mismatches: 11, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
232 25 0.11
233 193 0.89
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.43
Consensus pattern (232 bp):
TTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTCATCTTGTCTTAAAAT
CCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATTATCTTGCTTCAAAATCCTGCTC
GAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATTATCTTGTTTTAAAATCCTGTTCGAGGTCT
CCGTTAGAGAGTTTTCAATTCAAAATCTCATTTTGTT
Found at i:2210 original size:29 final size:29
Alignment explanation
Indices: 2150--2312 Score: 120
Period size: 29 Copynumber: 5.6 Consensus size: 29
2140 TGAATCCATA
* * * *
2150 GGCATTTTGGTCATTTTTTGTACATCCGAG
1 GGCATTTTGGTCATTTTTAGCATATTC-AG
*
2180 GGCATTTTGGTCATTTTTAGCATATTTAGG
1 GGCATTTTGGTCATTTTTAGCATATTCA-G
* *
2210 GGCATTTTGGGTCATTTTGTA-CAT-CTGAG
1 GGCATTTT-GGTCATTTT-TAGCATATTCAG
* * *
2239 GGCATTTTAGTC-TTTTTTGCACATTCAG
1 GGCATTTTGGTCATTTTTAGCATATTCAG
* * *
2267 GAGAATTTTGGTCA-TTTTCGCATATCCAGG
1 G-GCATTTTGGTCATTTTTAGCATATTCA-G
2297 GGCATTTTGGTC-TTTT
1 GGCATTTTGGTCATTTT
2313 ATTCTTAGCT
Statistics
Matches: 106, Mismatches: 18, Indels: 19
0.74 0.13 0.13
Matches are distributed among these distances:
26 1 0.01
27 6 0.06
28 7 0.07
29 43 0.41
30 35 0.33
31 12 0.11
32 2 0.02
ACGTcount: A:0.18, C:0.15, G:0.23, T:0.44
Consensus pattern (29 bp):
GGCATTTTGGTCATTTTTAGCATATTCAG
Done.