Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016811.1 Corchorus olitorius cultivar O-4 contig16844, 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: 4233
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.28
Found at i:471 original size:1 final size:1
Alignment explanation
Indices: 465--495 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
455 AAAAGGAGTT
465 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
496 CTGGGCCTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:525 original size:36 final size:36
Alignment explanation
Indices: 485--591 Score: 142
Period size: 36 Copynumber: 3.0 Consensus size: 36
475 AAAAAAAAAA
* *
485 AAAAAAAAAAACTGGGCCTAAAATAGAAAGAGGTTG
1 AAAAAAAAAAACTGGACCTAAAATAGAAAGAGGTCG
* *
521 AAAAACAAAAACAGGACCTAAAATAGAAAGAGGTCG
1 AAAAAAAAAAACTGGACCTAAAATAGAAAGAGGTCG
* * * *
557 GAAAAGAAAGACTGGACCTAAAATAGAGAGAGGTC
1 AAAAAAAAAAACTGGACCTAAAATAGAAAGAGGTC
592 ATAAAAGCTA
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 62 1.00
ACGTcount: A:0.54, C:0.11, G:0.23, T:0.11
Consensus pattern (36 bp):
AAAAAAAAAAACTGGACCTAAAATAGAAAGAGGTCG
Found at i:1474 original size:58 final size:59
Alignment explanation
Indices: 1407--1936 Score: 788
Period size: 59 Copynumber: 9.1 Consensus size: 59
1397 ATTACATTAA
* *
1407 CTTG-TTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTAAATTCAAAATATCTT
1 CTTGATTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATCTT
1465 CTTGATTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATAT-TAT
1 CTTGATTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATCT-T
* *
1524 CTTG-TTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTAAATTCAAAATATCTT
1 CTTGATTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATCTT
*
1582 CTTGATTTAAAAATCCTGTTCGAGGTCTCTGCTAGAGAGTTTTCAATTCAAAATATCTT
1 CTTGATTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATCTT
* * * *
1641 CTTGATTTAAAAATCCTATTTGAGGTCTCTGCTAGAGAGCTTTCAATTCAAAATATCTT
1 CTTGATTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATCTT
*
1700 CTTGATTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCTAAATAT-TAT
1 CTTGATTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATCT-T
* * *
1759 CTTG-TTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAATTTTCAATTCATAATAT-TAT
1 CTTGATTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATCT-T
*
1817 CTTG-TTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATCAT
1 CTTGATTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATCTT
** * * * * *
1875 CTTGCGTT-AAAATCCTATTCGAGGTCTCCGTTAGAGAGTTTTCAATTTAAAATCTTTT
1 CTTGATTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATCTT
1933 CTTG
1 CTTG
1937 GTCGAGATCT
Statistics
Matches: 435, Mismatches: 30, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
58 215 0.49
59 220 0.51
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (59 bp):
CTTGATTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATCTT
Found at i:1590 original size:117 final size:117
Alignment explanation
Indices: 1402--1936 Score: 842
Period size: 117 Copynumber: 4.6 Consensus size: 117
1392 ATCAGATTAC
* *
1402 ATTAACTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTAAATTCAAAATATCTTCT
1 ATTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATCTTCT
1467 TGATTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAAT
66 TGATTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAAT
*
1519 ATTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTAAATTCAAAATATCTTCT
1 ATTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATCTTCT
*
1584 TGATTTAAAAATCCTGTTCGAGGTCTCTGCTAGAGAGTTTTCAATTCAAAAT
66 TGATTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAAT
* * * * *
1636 ATCT-TCTTGATTTAAAAATCCTATTTGAGGTCTCTGCTAGAGAGCTTTCAATTCAAAATATCTT
1 AT-TATCTTG-TTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATCTT
*
1700 CTTGATTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCTAAAT
64 CTTGATTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAAT
* *
1754 ATTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAATTTTCAATTCATAATAT-TATC
1 ATTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATCT-TC
1818 TTG-TTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAAT
65 TTGATTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAAT
* ** * * * * *
1870 ATCATCTTGCGTTAAAATCCTATTCGAGGTCTCCGTTAGAGAGTTTTCAATTTAAAATCTTTTCT
1 ATTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATCTTCT
1935 TG
66 TG
1937 GTCGAGATCT
Statistics
Matches: 386, Mismatches: 27, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
116 105 0.27
117 173 0.45
118 108 0.28
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (117 bp):
ATTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATCTTCT
TGATTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAAT
Found at i:2243 original size:28 final size:28
Alignment explanation
Indices: 2212--2278 Score: 125
Period size: 28 Copynumber: 2.4 Consensus size: 28
2202 ATCTAGGGGT
2212 GTTTTGGTCATCTTGTACATCCAAGGGC
1 GTTTTGGTCATCTTGTACATCCAAGGGC
2240 GTTTTGGTCATCTTGTACATCCAAGGGC
1 GTTTTGGTCATCTTGTACATCCAAGGGC
*
2268 CTTTTGGTCAT
1 GTTTTGGTCAT
2279 TTTTGCACAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (28 bp):
GTTTTGGTCATCTTGTACATCCAAGGGC
Found at i:2306 original size:29 final size:29
Alignment explanation
Indices: 2264--2429 Score: 140
Period size: 29 Copynumber: 5.7 Consensus size: 29
2254 GTACATCCAA
* *
2264 GGGCCTTTTGGTCATTTTTGCACATTCAG
1 GGGCATTTTGGTCATTTTTGCACAATCAG
* * * *
2293 GAGCATTTTAGTCATTTCTGCACAATCCG
1 GGGCATTTTGGTCATTTTTGCACAATCAG
* * * *
2322 GGGCATTTTGATCATTTTT-CACCCACCCG
1 GGGCATTTTGGTCATTTTTGCA-CAATCAG
*
2351 TGGGCATTTTGGTCATTTTCGCAC-ATCCAG
1 -GGGCATTTTGGTCATTTTTGCACAAT-CAG
* * *
2381 GGGCATTTTAGTCGTTTCTGCACAATCTA-
1 GGGCATTTTGGTCATTTTTGCACAATC-AG
*
2410 GGGCGTTTTGGTCATTTTTG
1 GGGCATTTTGGTCATTTTTG
2430 TTTTATTTTT
Statistics
Matches: 107, Mismatches: 24, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
28 2 0.02
29 80 0.75
30 23 0.21
31 2 0.02
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (29 bp):
GGGCATTTTGGTCATTTTTGCACAATCAG
Found at i:2361 original size:88 final size:88
Alignment explanation
Indices: 2264--2428 Score: 249
Period size: 88 Copynumber: 1.9 Consensus size: 88
2254 GTACATCCAA
* * * *
2264 GGGCCTTTTGGTCATTTTTGCACATTCAGGAGCATTTTAGTCATTTCTGCACAATCCGGGGCATT
1 GGGCATTTTGGTCATTTTCGCACATCCAGGAGCATTTTAGTCATTTCTGCACAATCCAGGGCATT
2329 TTGATCATTTTTCACCCACCCGT
66 TTGATCATTTTTCACCCACCCGT
* * * *
2352 GGGCATTTTGGTCATTTTCGCACATCCAGGGGCATTTTAGTCGTTTCTGCACAATCTAGGGCGTT
1 GGGCATTTTGGTCATTTTCGCACATCCAGGAGCATTTTAGTCATTTCTGCACAATCCAGGGCATT
*
2417 TTGGTCATTTTT
66 TTGATCATTTTT
2429 GTTTTATTTT
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
88 68 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (88 bp):
GGGCATTTTGGTCATTTTCGCACATCCAGGAGCATTTTAGTCATTTCTGCACAATCCAGGGCATT
TTGATCATTTTTCACCCACCCGT
Found at i:3419 original size:17 final size:17
Alignment explanation
Indices: 3397--3429 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3387 AAACTCAGAA
3397 AGCAGAGTTCTAAATGC
1 AGCAGAGTTCTAAATGC
3414 AGCAGAGTTCTAAATG
1 AGCAGAGTTCTAAATG
3430 GCAAGGCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.24
Consensus pattern (17 bp):
AGCAGAGTTCTAAATGC
Done.