Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016052.1 Corchorus olitorius cultivar O-4 contig16085, 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: 23414
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:783 original size:2 final size:2
Alignment explanation
Indices: 776--813 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
766 CTCATACTTT
*
776 TA TA TA TA GTA TA GA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
814 GCTAAGAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 1 0.03
2 29 0.91
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:796 original size:16 final size:16
Alignment explanation
Indices: 775--814 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
765 ACTCATACTT
775 TTATATATAGTATAGA
1 TTATATATAGTATAGA
*
791 TTATATATA-TATATA
1 TTATATATAGTATAGA
806 -TATATATAG
1 TTATATATAG
815 CTAAGAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 8 0.36
15 5 0.23
16 9 0.41
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (16 bp):
TTATATATAGTATAGA
Found at i:989 original size:16 final size:16
Alignment explanation
Indices: 944--1031 Score: 60
Period size: 16 Copynumber: 5.5 Consensus size: 16
934 TCCGAGCTCA
*
944 AAAAAACTC-GAACCCT
1 AAAAAA-TCAGAACCCG
*
960 AAATAACTCA-AACCCG
1 AAA-AAATCAGAACCCG
976 AAAAAATCAGAACCCG
1 AAAAAATCAGAACCCG
992 -AAAAATCTA-AGACCC-
1 AAAAAATC-AGA-ACCCG
* *
1007 AATAAAACCCGAACCCG
1 AA-AAAATCAGAACCCG
1024 AAAAAATC
1 AAAAAATC
1032 CGAATTCAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 18
0.70 0.07 0.22
Matches are distributed among these distances:
15 13 0.23
16 34 0.60
17 10 0.18
ACGTcount: A:0.53, C:0.28, G:0.08, T:0.10
Consensus pattern (16 bp):
AAAAAATCAGAACCCG
Found at i:1034 original size:16 final size:16
Alignment explanation
Indices: 970--1035 Score: 64
Period size: 16 Copynumber: 4.1 Consensus size: 16
960 AAATAACTCA
*
970 AACCCGAAAAAATCAG
1 AACCCGAAAAAATCCG
**
986 AACCCG-AAAAATCTA
1 AACCCGAAAAAATCCG
*
1001 AGACCC-AATAAAACCCG
1 A-ACCCGAA-AAAATCCG
1018 AACCCGAAAAAATCCG
1 AACCCGAAAAAATCCG
1034 AA
1 AA
1036 TTCAATACTA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
15 8 0.20
16 24 0.60
17 8 0.20
ACGTcount: A:0.53, C:0.29, G:0.11, T:0.08
Consensus pattern (16 bp):
AACCCGAAAAAATCCG
Found at i:1105 original size:16 final size:17
Alignment explanation
Indices: 1084--1116 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1074 AAACAAAATT
*
1084 TTTAT-AATTTAAATAA
1 TTTATAAATATAAATAA
1100 TTTATAAATATAAATAA
1 TTTATAAATATAAATAA
1117 AACAAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTATAAATATAAATAA
Found at i:6851 original size:2 final size:2
Alignment explanation
Indices: 6839--6879 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
6829 GAAAAATCCT
*
6839 CA CA AA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
6880 TTGTTTACCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:8727 original size:32 final size:32
Alignment explanation
Indices: 8671--8739 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
8661 CTGACTCAAG
* * *
8671 CCCGAACCTGAATTAAACTGACCCAAAATTGA
1 CCCGAACCCGAATCAAACTAACCCAAAATTGA
* * *
8703 CCCGAACCCGAATCAACCTAACCCAAATTTTA
1 CCCGAACCCGAATCAAACTAACCCAAAATTGA
8735 CCCGA
1 CCCGA
8740 CCTGACTCAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.38, C:0.35, G:0.10, T:0.17
Consensus pattern (32 bp):
CCCGAACCCGAATCAAACTAACCCAAAATTGA
Found at i:11949 original size:37 final size:40
Alignment explanation
Indices: 11898--11990 Score: 115
Period size: 37 Copynumber: 2.5 Consensus size: 40
11888 AAACCGACCG
*
11898 ATATATATAT-TATATAATTT-TTATTTTTTATATATAAT
1 ATATATATATATATATAATTTGTTATTTTTAATATATAAT
* * *
11936 -TATATCT-TATATAT-ATTTGTTCTTTTTAATTTATAAT
1 ATATATATATATATATAATTTGTTATTTTTAATATATAAT
11973 ATATATATATATATATAA
1 ATATATATATATATATAA
11991 AACAAAACTT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
36 5 0.11
37 26 0.58
38 6 0.13
39 7 0.16
40 1 0.02
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (40 bp):
ATATATATATATATATAATTTGTTATTTTTAATATATAAT
Found at i:19299 original size:7 final size:7
Alignment explanation
Indices: 19289--19314 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
19279 AAATTGATTT
19289 TTTTTTC
1 TTTTTTC
19296 TTTTTTC
1 TTTTTTC
19303 TTTTTTC
1 TTTTTTC
19310 TTTTT
1 TTTTT
19315 CCTTCTCCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:19705 original size:179 final size:180
Alignment explanation
Indices: 19503--19863 Score: 600
Period size: 180 Copynumber: 2.0 Consensus size: 180
19493 TAATGTCATT
19503 TAAGAAATATATTTAAAAAATTCTAATATATCTAA-TTTTTGAATTAAAATAGTAAAATGGTAAA
1 TAAGAAATATATTTAAAAAATTCTAATATATCTAAGTTTTTGAATTAAAATAGTAAAATGGTAAA
** *
19567 AATAAAATAG-TTATAAATATATTAGATTTGATTAAATAAAACTAGAGTTTTTAATTGAGTAAAA
66 AATAAAAT-GTTTATAAATATATTAGATTAAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAA
* * * * * *
19631 TTGTAAAAGTTTAAACAATGGCATTTAAGAAATATATTTGAAAAATAAGGG
130 CTATAAAAATTTAAACAATGACATTTAAGAAATATAATCGAAAAATAAGGG
*
19682 TAAGAAATATATTTAAAAAATTCTAATATATCTAAGTTTTTTAATTAAAATAGTAAAATGGTAAA
1 TAAGAAATATATTTAAAAAATTCTAATATATCTAAGTTTTTGAATTAAAATAGTAAAATGGTAAA
*
19747 AATAAAATGTTTATAAATATATTAGATTAAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAAC
66 AATAAAATGTTTATAAATATATTAGATTAAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAAC
19812 TATAAAAATTTAAACAATGACATTTAAGAAATATAATCGAAAAATAAGGG
131 TATAAAAATTTAAACAATGACATTTAAGAAATATAATCGAAAAATAAGGG
19862 TA
1 TA
19864 TAATCGTCAA
Statistics
Matches: 169, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
179 36 0.21
180 133 0.79
ACGTcount: A:0.51, C:0.03, G:0.11, T:0.35
Consensus pattern (180 bp):
TAAGAAATATATTTAAAAAATTCTAATATATCTAAGTTTTTGAATTAAAATAGTAAAATGGTAAA
AATAAAATGTTTATAAATATATTAGATTAAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAAC
TATAAAAATTTAAACAATGACATTTAAGAAATATAATCGAAAAATAAGGG
Found at i:20352 original size:30 final size:31
Alignment explanation
Indices: 20290--20354 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
20280 GACTAAATAT
*
20290 CAAAAAAATCCCTTATGTTTTTCTTTTGGGA
1 CAAAAAAATCCCTTATGTTTTTCTTATGGGA
*
20321 CAAAAGAATCCCTTATGTTTTT-TTATGGGA
1 CAAAAAAATCCCTTATGTTTTTCTTATGGGA
20351 CAAA
1 CAAA
20355 TTAGTCTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 11 0.34
31 21 0.66
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.38
Consensus pattern (31 bp):
CAAAAAAATCCCTTATGTTTTTCTTATGGGA
Found at i:20514 original size:28 final size:28
Alignment explanation
Indices: 20465--20522 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
20455 GGCTCTTTTT
* *
20465 AAAAACGTAATGGATTAATTTGTCCCAA
1 AAAAACATAAGGGATTAATTTGTCCCAA
* *
20493 AAAAACATAAGGGGTTATTTTGTCCCAA
1 AAAAACATAAGGGATTAATTTGTCCCAA
20521 AA
1 AA
20523 GCAACACATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.28
Consensus pattern (28 bp):
AAAAACATAAGGGATTAATTTGTCCCAA
Done.