Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017131.1 Corchorus olitorius cultivar O-4 contig17164, 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: 24080
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1323 original size:20 final size:21
Alignment explanation
Indices: 1288--1326 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1278 TTTCCTTTCT
*
1288 TTTCTTTTCTCTTTTCTTTTA
1 TTTCTTTTCACTTTTCTTTTA
1309 TTTCTTTT-ACTTTTCTTT
1 TTTCTTTTCACTTTTCTTT
1327 AAAATTGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTCTTTTCACTTTTCTTTTA
Found at i:3113 original size:20 final size:20
Alignment explanation
Indices: 3088--3129 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
3078 AATAACAGAC
3088 ATGAAAGCATATAATGAAAG
1 ATGAAAGCATATAATGAAAG
*
3108 ATGAAAGCATCTAATGAAAG
1 ATGAAAGCATATAATGAAAG
3128 AT
1 AT
3130 ATAAGGGTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.52, C:0.07, G:0.19, T:0.21
Consensus pattern (20 bp):
ATGAAAGCATATAATGAAAG
Found at i:9237 original size:25 final size:24
Alignment explanation
Indices: 9174--9248 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
9164 TTGAGCAATT
9174 AAAAATAGAGA-AGATATTTTAAAG
1 AAAAATAGAGAGA-ATATTTTAAAG
*
9198 AAAAATAGAGAGAATATTTTAATG
1 AAAAATAGAGAGAATATTTTAAAG
* *
9222 AAAATTTAGAGAGAATATTTGAAAG
1 AAAA-ATAGAGAGAATATTTTAAAG
9247 AA
1 AA
9249 TTATAATTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
24 25 0.56
25 20 0.44
ACGTcount: A:0.56, C:0.00, G:0.17, T:0.27
Consensus pattern (24 bp):
AAAAATAGAGAGAATATTTTAAAG
Found at i:11896 original size:8 final size:7
Alignment explanation
Indices: 11875--12000 Score: 51
Period size: 8 Copynumber: 16.6 Consensus size: 7
11865 TATTATTGAT
11875 TAATTAA
1 TAATTAA
11882 TAATTAA
1 TAATTAA
11889 TGAATTAA
1 T-AATTAA
11897 CTAATTAA
1 -TAATTAA
11905 TTTAA-TAA
1 --TAATTAA
11913 TAATTAAA
1 TAATT-AA
*
11921 TCTATTAA
1 T-AATTAA
*
11929 TAACTTTTCA
1 TAA---TTAA
*
11939 TATTTTAA
1 TA-ATTAA
* *
11947 TAAAATCA
1 T-AATTAA
11955 TAATTAA
1 TAATTAA
11962 TAATTAA
1 TAATTAA
11969 TAA--AA
1 TAATTAA
*
11974 CATATTAA
1 TA-ATTAA
11982 TATATTAA
1 TA-ATTAA
*
11990 TCATTAA
1 TAATTAA
11997 TAAT
1 TAAT
12001 CCTAATTCTT
Statistics
Matches: 90, Mismatches: 15, Indels: 28
0.68 0.11 0.21
Matches are distributed among these distances:
5 3 0.03
6 4 0.04
7 32 0.36
8 38 0.42
9 8 0.09
10 5 0.06
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.43
Consensus pattern (7 bp):
TAATTAA
Found at i:11903 original size:16 final size:15
Alignment explanation
Indices: 11876--11919 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
11866 ATTATTGATT
11876 AATTAATAATTAATG
1 AATTAATAATTAATG
*
11891 AATTAACTAATTAATTT
1 AATTAA-TAATTAA-TG
11908 AA-TAATAATTAA
1 AATTAATAATTAA
11920 ATCTATTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 13 0.50
16 10 0.38
17 3 0.12
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (15 bp):
AATTAATAATTAATG
Found at i:11988 original size:21 final size:23
Alignment explanation
Indices: 11938--11990 Score: 76
Period size: 21 Copynumber: 2.4 Consensus size: 23
11928 ATAACTTTTC
*
11938 ATATTTTAATAAAATCATAATTA
1 ATATATTAATAAAATCATAATTA
11961 ATA-ATTAATAAAA-CAT-ATTA
1 ATATATTAATAAAATCATAATTA
11981 ATATATTAAT
1 ATATATTAAT
11991 CATTAATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 7 0.25
21 9 0.32
22 9 0.32
23 3 0.11
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (23 bp):
ATATATTAATAAAATCATAATTA
Found at i:12063 original size:3 final size:3
Alignment explanation
Indices: 12044--12119 Score: 75
Period size: 3 Copynumber: 25.3 Consensus size: 3
12034 TAACTATTTC
* * * * *
12044 ATA ATA AT- TTA ATTA ATA ATA ATA ATA ACA TTA CTA CATA ATT A-A
1 ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA
12089 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
12120 AACCTAATTA
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
2 2 0.03
3 53 0.88
4 5 0.08
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:12522 original size:86 final size:87
Alignment explanation
Indices: 12377--12540 Score: 287
Period size: 86 Copynumber: 1.9 Consensus size: 87
12367 ACCCACCCCT
12377 CCCGCCGAGATTTCTACCAAACCCGAAATTTTCACGATTTTTTTTGTTTTTTCAAAAAAAAA-AC
1 CCCGCCGAGATTTCTACCAAACCCGAAATTTTCACGATTTTTTTTGTTTTTTCAAAAAAAAAGAC
*
12441 ATATCGGAATTCGTGGTCGCGA
66 ATACCGGAATTCGTGGTCGCGA
*
12463 CCCGCCGAGATTTCTGCCAAACCCGAAATTTTCACGA-TTTTTTTGTTTTTTCAAAAAAAAAAGA
1 CCCGCCGAGATTTCTACCAAACCCGAAATTTTCACGATTTTTTTTGTTTTTTC-AAAAAAAAAGA
12527 CATACCGGAATTCG
65 CATACCGGAATTCG
12541 GAGAAAACTT
Statistics
Matches: 74, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
85 15 0.20
86 45 0.61
87 14 0.19
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.32
Consensus pattern (87 bp):
CCCGCCGAGATTTCTACCAAACCCGAAATTTTCACGATTTTTTTTGTTTTTTCAAAAAAAAAGAC
ATACCGGAATTCGTGGTCGCGA
Found at i:13811 original size:5 final size:5
Alignment explanation
Indices: 13798--13841 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
13788 TAAAAGGACC
* * *
13798 TCCCA TCCCG TCCCA TCCCA TCCCG TCCCA TCCCA TCCCG TCCC
1 TCCCA TCCCA TCCCA TCCCA TCCCA TCCCA TCCCA TCCCA TCCC
13842 TTACTGGTCC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.11, C:0.61, G:0.07, T:0.20
Consensus pattern (5 bp):
TCCCA
Found at i:13818 original size:15 final size:15
Alignment explanation
Indices: 13798--13841 Score: 88
Period size: 15 Copynumber: 2.9 Consensus size: 15
13788 TAAAAGGACC
13798 TCCCATCCCGTCCCA
1 TCCCATCCCGTCCCA
13813 TCCCATCCCGTCCCA
1 TCCCATCCCGTCCCA
13828 TCCCATCCCGTCCC
1 TCCCATCCCGTCCC
13842 TTACTGGTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.11, C:0.61, G:0.07, T:0.20
Consensus pattern (15 bp):
TCCCATCCCGTCCCA
Found at i:21385 original size:130 final size:129
Alignment explanation
Indices: 21157--21390 Score: 362
Period size: 129 Copynumber: 1.8 Consensus size: 129
21147 AAAATACTTT
* * *
21157 TTGAAATTGCGGTTGAAAAATATAAATAATATTTGGTATTACTATCGAAAAATGTGAAGGAGATG
1 TTGAAATTGCGGTTGAAAAATATAAATAATATTTGGTATCACTATCGAAAAATGTGAAGAAGATA
*
21222 AAATATTTAAAAAGGACATTAGTTAACAAGAGAAGAGAAAAAAATATTTAGGACTAGTTTGATA
66 AAATATCTAAAAAGGACATTAGTTAACAAGAGAAGAGAAAAAAATATTTAGGACTAGTTTGATA
* * ** *
21286 TTGAGATTGCGGTTGAAAAATATAATTAATATTTGGTATCGTTATC-AAAAATGTGGTAGAAAGA
1 TTGAAATTGCGGTTGAAAAATATAAATAATATTTGGTATCACTATCGAAAAATGT-GAAG-AAGA
21350 TAAAATATCTAAAAAGGACATTAGTTAACAAGAGAAGAGAA
64 TAAAATATCTAAAAAGGACATTAGTTAACAAGAGAAGAGAA
21391 TATATATATA
Statistics
Matches: 94, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
128 8 0.09
129 44 0.47
130 42 0.45
ACGTcount: A:0.46, C:0.05, G:0.20, T:0.29
Consensus pattern (129 bp):
TTGAAATTGCGGTTGAAAAATATAAATAATATTTGGTATCACTATCGAAAAATGTGAAGAAGATA
AAATATCTAAAAAGGACATTAGTTAACAAGAGAAGAGAAAAAAATATTTAGGACTAGTTTGATA
Found at i:21397 original size:2 final size:2
Alignment explanation
Indices: 21390--21421 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
21380 AGAGAAGAGA
21390 AT 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 AT
21422 GTATTCTTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22947 original size:13 final size:12
Alignment explanation
Indices: 22926--22960 Score: 61
Period size: 13 Copynumber: 2.8 Consensus size: 12
22916 AATATTGTAA
22926 TAATACTATTAT
1 TAATACTATTAT
22938 TAATTACTATTAT
1 TAA-TACTATTAT
22951 TAATACTATT
1 TAATACTATT
22961 TCAATGTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (12 bp):
TAATACTATTAT
Done.