Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017475.1 Corchorus olitorius cultivar O-4 contig17508, 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: 13719
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:3060 original size:29 final size:30
Alignment explanation
Indices: 3023--3087 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
3013 GGTTGGTATC
*
3023 AATTT-TTTTTCAAAA-AGGTTCATAAGCA
1 AATTTCTTTTTCAAAAGAGGATCATAAGCA
* *
3051 AGTTTCTTTTTTAAAAGAGGATCATAAGCA
1 AATTTCTTTTTCAAAAGAGGATCATAAGCA
3081 AATTTCT
1 AATTTCT
3088 CTTGTCAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 4 0.13
29 9 0.29
30 18 0.58
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Consensus pattern (30 bp):
AATTTCTTTTTCAAAAGAGGATCATAAGCA
Found at i:4124 original size:11 final size:11
Alignment explanation
Indices: 4108--4150 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
4098 CTAAAAAAAA
4108 TTTATATATAT
1 TTTATATATAT
4119 TTTATATATAT
1 TTTATATATAT
** *
4130 CATAAATATAT
1 TTTATATATAT
4141 TTTATATATA
1 TTTATATATA
4151 ATCATAATCT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (11 bp):
TTTATATATAT
Found at i:4141 original size:22 final size:23
Alignment explanation
Indices: 4113--4157 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
4103 AAAAATTTAT
4113 ATATATTTTATATAT-ATCATAA
1 ATATATTTTATATATAATCATAA
4135 ATATATTTTATATATAATCATAA
1 ATATATTTTATATATAATCATAA
4158 TCTGTCGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (23 bp):
ATATATTTTATATATAATCATAA
Found at i:4302 original size:18 final size:19
Alignment explanation
Indices: 4268--4303 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
4258 GCTTGACCTT
*
4268 GGTCGGTTTTTGGCGGTTC
1 GGTCGGTTTTGGGCGGTTC
4287 GGTCGG-TTTGGGCGGTT
1 GGTCGGTTTTGGGCGGTT
4304 TAAACCGCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.00, C:0.14, G:0.47, T:0.39
Consensus pattern (19 bp):
GGTCGGTTTTGGGCGGTTC
Found at i:8434 original size:3 final size:3
Alignment explanation
Indices: 8428--8478 Score: 50
Period size: 3 Copynumber: 16.3 Consensus size: 3
8418 CATTTTAAAT
* *
8428 TAA TAA TAA TTAA TAA TTA -AA TAA TTAA TAA TAA TTAA AAA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA -TAA TAA TAA -TAA TAA TAA TAA
8475 TAA T
1 TAA T
8479 TGGTGCCGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
2 1 0.03
3 30 0.75
4 9 0.22
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:8443 original size:7 final size:7
Alignment explanation
Indices: 8431--8479 Score: 50
Period size: 7 Copynumber: 7.1 Consensus size: 7
8421 TTTAAATTAA
8431 TAATAAT
1 TAATAAT
8438 TAATAAT
1 TAATAAT
8445 TAAATAAT
1 T-AATAAT
8453 TAATAA-
1 TAATAAT
8459 TAATTAA-
1 TAA-TAAT
*
8466 AAATAA-
1 TAATAAT
8472 TAATAAT
1 TAATAAT
8479 T
1 T
8480 GGTGCCGCCC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
6 11 0.30
7 19 0.51
8 7 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
TAATAAT
Found at i:8453 original size:25 final size:26
Alignment explanation
Indices: 8425--8479 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 26
8415 TAACATTTTA
* *
8425 AATTAATAATAATTAATAATTA-AAT
1 AATTAATAATAATTAAAAATAATAAT
8450 AATTAATAATAATTAAAAATAATAAT
1 AATTAATAATAATTAAAAATAATAAT
8476 AATT
1 AATT
8480 GGTGCCGCCC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 20 0.74
26 7 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
AATTAATAATAATTAAAAATAATAAT
Found at i:11157 original size:39 final size:39
Alignment explanation
Indices: 11103--11184 Score: 164
Period size: 39 Copynumber: 2.1 Consensus size: 39
11093 GTTTCAACCC
11103 AATATTAATTTTGCATATTGTACCATACCACCATTTATG
1 AATATTAATTTTGCATATTGTACCATACCACCATTTATG
11142 AATATTAATTTTGCATATTGTACCATACCACCATTTATG
1 AATATTAATTTTGCATATTGTACCATACCACCATTTATG
11181 AATA
1 AATA
11185 AATGTGTTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.40
Consensus pattern (39 bp):
AATATTAATTTTGCATATTGTACCATACCACCATTTATG
Found at i:11212 original size:27 final size:27
Alignment explanation
Indices: 11182--11283 Score: 133
Period size: 27 Copynumber: 4.0 Consensus size: 27
11172 CCATTTATGA
11182 ATAAATGTGTTCAAGCCATCTGGTATC
1 ATAAATGTGTTCAAGCCATCTGGTATC
11209 ATAAATGTGTTCAAGCCATCTGGTATC
1 ATAAATGTGTTCAAGCCATCTGGTATC
* * **
11236 ATAAATGT-TT-ATG--GT-AAGTATC
1 ATAAATGTGTTCAAGCCATCTGGTATC
11258 ATAAATGTGTTCAAGCCATCTGGTAT
1 ATAAATGTGTTCAAGCCATCTGGTAT
11284 TCGTCAATTC
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
22 13 0.21
23 3 0.05
24 2 0.03
25 2 0.03
26 3 0.05
27 39 0.63
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (27 bp):
ATAAATGTGTTCAAGCCATCTGGTATC
Done.