Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012653.1 Corchorus olitorius cultivar O-4 contig12686, 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: 76036
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:14 original size:2 final size:2
Alignment explanation
Indices: 9--64 Score: 69
Period size: 2 Copynumber: 28.0 Consensus size: 2
1 TACGTGTG
* * *
9 TA TA TA TA TA TA TA TA TA T- TC TT TCA AA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA
51 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
65 CTTTGAATTA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:84 original size:36 final size:36
Alignment explanation
Indices: 9--85 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
1 TACGTGTG
* * * *
9 TATATATATATATATATATTCTTTCAAATATATATA
1 TATATATATATATATATATACTTTCAAATACAGAAA
* * *
45 TATATATATATATATATATACTTTGAATTACCGAAA
1 TATATATATATATATATATACTTTCAAATACAGAAA
81 TATAT
1 TATAT
86 GGATTTGTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (36 bp):
TATATATATATATATATATACTTTCAAATACAGAAA
Found at i:3088 original size:2 final size:2
Alignment explanation
Indices: 3083--3108 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3073 TTTTTTACTG
3083 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3109 CTTATAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4235 original size:19 final size:19
Alignment explanation
Indices: 4211--4247 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4201 GTATAGTACC
4211 CAATCTAATCTGTACAGTG
1 CAATCTAATCTGTACAGTG
*
4230 CAATCTCATCTGTACAGT
1 CAATCTAATCTGTACAGT
4248 TCCTAAACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (19 bp):
CAATCTAATCTGTACAGTG
Found at i:7926 original size:18 final size:18
Alignment explanation
Indices: 7889--7927 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
7879 CTTAACCGCC
* **
7889 CTCTCTCTCTCTTTTTCT
1 CTCTATCTCTCTTTCACT
7907 CTCTATCTCTCTTTCACT
1 CTCTATCTCTCTTTCACT
7925 CTC
1 CTC
7928 CCCTCCTAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.05, C:0.41, G:0.00, T:0.54
Consensus pattern (18 bp):
CTCTATCTCTCTTTCACT
Found at i:16034 original size:2 final size:2
Alignment explanation
Indices: 16027--16056 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
16017 AATACCGACC
16027 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16057 CCGTGGGCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17155 original size:27 final size:27
Alignment explanation
Indices: 17124--17180 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
17114 TGTCAATATA
17124 CCTACTAACTAAAAGGCCTTTGAGTTT
1 CCTACTAACTAAAAGGCCTTTGAGTTT
17151 CCTACTAACTAAAAGGCCTTTGAGTTT
1 CCTACTAACTAAAAGGCCTTTGAGTTT
17178 CCT
1 CCT
17181 TTACCCACCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (27 bp):
CCTACTAACTAAAAGGCCTTTGAGTTT
Found at i:20962 original size:21 final size:18
Alignment explanation
Indices: 20919--20960 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
20909 ACACGTGTCC
20919 TCGTCGGACCCTGCGCCG
1 TCGTCGGACCCTGCGCCG
20937 TCGTCGGACCCTGCGCCG
1 TCGTCGGACCCTGCGCCG
20955 TCGTCG
1 TCGTCG
20961 TCCTCTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.05, C:0.43, G:0.33, T:0.19
Consensus pattern (18 bp):
TCGTCGGACCCTGCGCCG
Found at i:21167 original size:27 final size:25
Alignment explanation
Indices: 21125--21176 Score: 59
Period size: 27 Copynumber: 2.0 Consensus size: 25
21115 GAAGAGGCAG
* **
21125 AAGCAGAATTGAGAAGGGAAGGAAA
1 AAGCAAAATTGAGAAGACAAGGAAA
21150 AAGCAAAATATGAGGAAGACAAGGAAA
1 AAGCAAAAT-TGA-GAAGACAAGGAAA
21177 GGAAGTGAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 8 0.36
26 3 0.14
27 11 0.50
ACGTcount: A:0.56, C:0.06, G:0.31, T:0.08
Consensus pattern (25 bp):
AAGCAAAATTGAGAAGACAAGGAAA
Found at i:34905 original size:30 final size:30
Alignment explanation
Indices: 34869--34926 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
34859 AATAAGCTAA
*
34869 TAAAATTTGAGGGTATAAGAGAAAAGTCAT
1 TAAAATTTGAGGGTATAAGAAAAAAGTCAT
*
34899 TAAAATTTGAGGGTATGAGAAAAAAGTC
1 TAAAATTTGAGGGTATAAGAAAAAAGTC
34927 GAGATAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.24, T:0.26
Consensus pattern (30 bp):
TAAAATTTGAGGGTATAAGAAAAAAGTCAT
Found at i:35443 original size:22 final size:24
Alignment explanation
Indices: 35408--35456 Score: 68
Period size: 22 Copynumber: 2.1 Consensus size: 24
35398 AATTTCTATT
35408 TATAATATTCATATTCATA-ATATA
1 TATAATATTCATATT-ATATATATA
35432 TATAAT-TT-ATATTATATATATA
1 TATAATATTCATATTATATATATA
35454 TAT
1 TAT
35457 GTATAATAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 3 0.12
22 13 0.54
23 2 0.08
24 6 0.25
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (24 bp):
TATAATATTCATATTATATATATA
Found at i:45450 original size:23 final size:23
Alignment explanation
Indices: 45420--45467 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
45410 ATAGTAATAT
*
45420 GACCATTCAATTTGGAACAGAGG
1 GACCATTCAATTTGAAACAGAGG
*
45443 GACCATTCAATTTGAAACGGAGG
1 GACCATTCAATTTGAAACAGAGG
45466 GA
1 GA
45468 GTATATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (23 bp):
GACCATTCAATTTGAAACAGAGG
Found at i:48862 original size:93 final size:93
Alignment explanation
Indices: 48736--48912 Score: 282
Period size: 93 Copynumber: 1.9 Consensus size: 93
48726 AGTATTTATT
* * *
48736 TATATGATATTAACACTTGTAGCGCAATCTTGCTATCACCACTATTAATTAAAAGCTGGAAATCC
1 TATATGATAATAACAATTCTAGCGCAATCTTGCTATCACCACTATTAATTAAAAGCTGGAAATCC
48801 GAAGTTTTGATTTGTGGTGAAAGACATA
66 GAAGTTTTGATTTGTGGTGAAAGACATA
* * * * *
48829 TATATGATAATAATAATTCTAGTGCAATCTTGCTATCACTACTATTAATTAAAAGCTGTAAATCT
1 TATATGATAATAACAATTCTAGCGCAATCTTGCTATCACCACTATTAATTAAAAGCTGGAAATCC
48894 GAAGTTTTGATTTGTGGTG
66 GAAGTTTTGATTTGTGGTG
48913 GAGGTCTGCA
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (93 bp):
TATATGATAATAACAATTCTAGCGCAATCTTGCTATCACCACTATTAATTAAAAGCTGGAAATCC
GAAGTTTTGATTTGTGGTGAAAGACATA
Found at i:49686 original size:51 final size:51
Alignment explanation
Indices: 49631--49732 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
49621 AGACGGTTAG
49631 TAGAATTTTTTTTTGTCAAATCAAGTAATAATTAGTATTAAATTTATTGAT
1 TAGAATTTTTTTTTGTCAAATCAAGTAATAATTAGTATTAAATTTATTGAT
49682 TAGAATTTTTTTTTGTCAAATCAAGTAATAATTAGTATTAAATTTATTGAT
1 TAGAATTTTTTTTTGTCAAATCAAGTAATAATTAGTATTAAATTTATTGAT
49733 AGCAATTAGG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.49
Consensus pattern (51 bp):
TAGAATTTTTTTTTGTCAAATCAAGTAATAATTAGTATTAAATTTATTGAT
Found at i:54648 original size:3 final size:3
Alignment explanation
Indices: 54640--54669 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
54630 ATATATATAT
54640 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
54670 TACTAGCATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:55094 original size:27 final size:28
Alignment explanation
Indices: 55044--55101 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 28
55034 TAACTCTAAT
* *
55044 AAGTATTTACCTATTACTTTCAAAAATAA
1 AAGTATTTACCTATTAC-TCCAAAAAGAA
55073 AAGTATTTACCTATTA-TCCAAAAAGAA
1 AAGTATTTACCTATTACTCCAAAAAGAA
55100 AA
1 AA
55102 AAAGTATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 11 0.41
29 16 0.59
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.33
Consensus pattern (28 bp):
AAGTATTTACCTATTACTCCAAAAAGAA
Found at i:55103 original size:29 final size:29
Alignment explanation
Indices: 55044--55113 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
55034 TAACTCTAAT
* *
55044 AAGTATTTACCTATTACTTTC-AAAAATAA
1 AAGTATTTACCTATTAC-TCCAAAAAAAAA
55073 AAGTATTTACCTATTA-TCCAAAAAGAAAAA
1 AAGTATTTACCTATTACTCC-AAAA-AAAAA
55103 AAGTATTTACC
1 AAGTATTTACC
55114 ACGTACGTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
27 2 0.06
29 19 0.53
30 15 0.42
ACGTcount: A:0.47, C:0.14, G:0.06, T:0.33
Consensus pattern (29 bp):
AAGTATTTACCTATTACTCCAAAAAAAAA
Found at i:60133 original size:2 final size:2
Alignment explanation
Indices: 60128--60155 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
60118 TATTGTCCCT
60128 TA TA TA 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
60156 ATAACCTAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:63780 original size:2 final size:2
Alignment explanation
Indices: 63773--63811 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
63763 TATAAATGAG
63773 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
63812 GCTCGTAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:66580 original size:4 final size:4
Alignment explanation
Indices: 66571--66607 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
66561 GCATCGATTA
66571 TAAT TAAT TAAT TAAT TAAT T-AT TAAT TAAT TAAT TA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TA
66608 TAATGCTATG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.09
4 29 0.91
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (4 bp):
TAAT
Found at i:66597 original size:15 final size:15
Alignment explanation
Indices: 66571--66608 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
66561 GCATCGATTA
66571 TAATTAATTAATTAAT
1 TAATT-ATTAATTAAT
66587 TAATTATTAATTAAT
1 TAATTATTAATTAAT
66602 TAATTAT
1 TAATTAT
66609 AATGCTATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TAATTATTAATTAAT
Found at i:71931 original size:3 final size:3
Alignment explanation
Indices: 71923--71955 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
71913 CATAGTCGCT
71923 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
71956 AAACTCTTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:71981 original size:12 final size:12
Alignment explanation
Indices: 71923--71985 Score: 63
Period size: 12 Copynumber: 5.0 Consensus size: 12
71913 CATAGTCGCT
*
71923 TTCTTCTTCTTC
1 TTCTTCTTCCTC
*
71935 TTCTTCTTCTTC
1 TTCTTCTTCCTC
71947 TTCTTCTTCAAACTC
1 TTCTTCTTC---CTC
*
71962 TTCCTCTTCCTC
1 TTCTTCTTCCTC
*
71974 ATCTTCTTCCTC
1 TTCTTCTTCCTC
71986 CACATTAGCT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
12 34 0.77
15 10 0.23
ACGTcount: A:0.06, C:0.38, G:0.00, T:0.56
Consensus pattern (12 bp):
TTCTTCTTCCTC
Done.