Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_259 ID=scaffold_259-JGI_221_v2.0
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: 8878
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.27
Found at i:283 original size:23 final size:23
Alignment explanation
Indices: 253--300 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
243 ATTCAGCCAA
*
253 AGAGATATTCAAAGAAAG-AAGGC
1 AGAGATATGCAAAG-AAGCAAGGC
*
276 AGAGATATGCAGAGAAGCAAGGC
1 AGAGATATGCAAAGAAGCAAGGC
299 AG
1 AG
301 TCGACGCTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 19 0.86
ACGTcount: A:0.48, C:0.10, G:0.31, T:0.10
Consensus pattern (23 bp):
AGAGATATGCAAAGAAGCAAGGC
Found at i:7673 original size:26 final size:26
Alignment explanation
Indices: 7635--7685 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
7625 GCCCACACAC
* *
7635 CAATATTGCAGCATAGTTGCCAGTAA
1 CAATATCGCAGCAGAGTTGCCAGTAA
*
7661 CAATATCGTAGCAGAGTTGCCAGTA
1 CAATATCGCAGCAGAGTTGCCAGTA
7686 CAGTATGTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (26 bp):
CAATATCGCAGCAGAGTTGCCAGTAA
Found at i:7718 original size:27 final size:27
Alignment explanation
Indices: 7680--7746 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
7670 AGCAGAGTTG
7680 CCAGTA-CAGTATGTATGGCAAAGCCA
1 CCAGTATCAGTATGTATGGCAAAGCCA
*
7706 CCAGTATCAGTATGTGTGGCAAAGCCA
1 CCAGTATCAGTATGTATGGCAAAGCCA
7733 CCAGTATCAGTATG
1 CCAGTATCAGTATG
7747 AGTGCGGCAG
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
26 6 0.15
27 33 0.85
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.22
Consensus pattern (27 bp):
CCAGTATCAGTATGTATGGCAAAGCCA
Found at i:7955 original size:26 final size:26
Alignment explanation
Indices: 7926--8154 Score: 216
Period size: 26 Copynumber: 8.7 Consensus size: 26
7916 ACGGTCATTC
7926 TACCCTTCGAGGGTATTTCAGTAATT
1 TACCCTTCGAGGGTATTTCAGTAATT
*
7952 TACCCTCCGA-GGTA-TTCAGGTAAATTT
1 TACCCTTCGAGGGTATTTCA-GT-AA-TT
* *
7979 TACCCTTTGAGAGTATTTCAGTAATT
1 TACCCTTCGAGGGTATTTCAGTAATT
* *
8005 TTCCCATCGAGGGTATTTCAGTAATT
1 TACCCTTCGAGGGTATTTCAGTAATT
* * *
8031 TACCCATAGAGGGTATTTCAATAATT
1 TACCCTTCGAGGGTATTTCAGTAATT
* *
8057 TACCC-TCTAGGGGTATTTCGGTAATTTT
1 TACCCTTCGA-GGGTATTTCAGTAA--TT
* * *
8085 TACCCTTTGTGGGTATTTCAATAATT
1 TACCCTTCGAGGGTATTTCAGTAATT
8111 TACCC-TCTG-GGGCTATTTCAGTAATT
1 TACCCTTC-GAGGG-TATTTCAGTAATT
* *
8137 TTCCCATCGAGGGTATTT
1 TACCCTTCGAGGGTATTT
8155 TGTAAATTTA
Statistics
Matches: 167, Mismatches: 23, Indels: 26
0.77 0.11 0.12
Matches are distributed among these distances:
24 4 0.02
25 12 0.07
26 105 0.63
27 17 0.10
28 24 0.14
29 5 0.03
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (26 bp):
TACCCTTCGAGGGTATTTCAGTAATT
Found at i:8057 original size:79 final size:80
Alignment explanation
Indices: 7926--8117 Score: 207
Period size: 79 Copynumber: 2.4 Consensus size: 80
7916 ACGGTCATTC
* * * *
7926 TACCCTTCGAGGGTATTTCAGTAATTTACCCTCCGAGGTATTCAGGTAAATTTTACCCT-TTGAG
1 TACCCATCGAGGGTATTTCAGTAATTTACCCTCAGAGGTATTCAGATAAA-TTTACCCTCTAG-G
7990 AGTATTTCAGTAA-TTT
64 AGTATTTCAGTAATTTT
8006 T-CCCATCGAGGGTATTTCAGTAATTTACCCAT-AGAGGGTATTTCA-AT-AATTTACCCTCTAG
1 TACCCATCGAGGGTATTTCAGTAATTTACCC-TCAGA-GGTA-TTCAGATAAATTTACCCTCTAG
* *
8067 GGGTATTTCGGTAATTTT
63 GAGTATTTCAGTAATTTT
* * * *
8085 TACCCTTTGTGGGTATTTCAATAATTTACCCTC
1 TACCCATCGAGGGTATTTCAGTAATTTACCCTC
8118 TGGGGCTATT
Statistics
Matches: 95, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
78 20 0.21
79 39 0.41
80 32 0.34
81 4 0.04
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.39
Consensus pattern (80 bp):
TACCCATCGAGGGTATTTCAGTAATTTACCCTCAGAGGTATTCAGATAAATTTACCCTCTAGGAG
TATTTCAGTAATTTT
Found at i:8109 original size:54 final size:54
Alignment explanation
Indices: 7926--8154 Score: 240
Period size: 52 Copynumber: 4.3 Consensus size: 54
7916 ACGGTCATTC
* * * * *
7926 TACCCTTCGAGGGTATTTCAGTAATTTACCCTC-CGAGGTA-TTCAGGTAAATTT
1 TACCCTTTGAGGGTATTTCAATAATTTACCCTCTAGGGGTATTTCA-GTAATTTT
* * * *
7979 TACCCTTTGAGAGTATTTCAGTAATTTTCCCATCGA-GGGTATTTCAGTAA--TT
1 TACCCTTTGAGGGTATTTCAATAATTTACCC-TCTAGGGGTATTTCAGTAATTTT
* * *
8031 TACCCATAGAGGGTATTTCAATAATTTACCCTCTAGGGGTATTTCGGTAATTTT
1 TACCCTTTGAGGGTATTTCAATAATTTACCCTCTAGGGGTATTTCAGTAATTTT
*
8085 TACCCTTTGTGGGTATTTCAATAATTTACCCTCT-GGGGCTATTTCAGTAA-TTT
1 TACCCTTTGAGGGTATTTCAATAATTTACCCTCTAGGGG-TATTTCAGTAATTTT
* *
8138 T-CCCATCGAGGGTATTT
1 TACCCTTTGAGGGTATTT
8155 TGTAAATTTA
Statistics
Matches: 150, Mismatches: 19, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
51 3 0.02
52 54 0.36
53 36 0.24
54 53 0.35
55 4 0.03
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (54 bp):
TACCCTTTGAGGGTATTTCAATAATTTACCCTCTAGGGGTATTTCAGTAATTTT
Found at i:8110 original size:106 final size:105
Alignment explanation
Indices: 7934--8154 Score: 295
Period size: 106 Copynumber: 2.1 Consensus size: 105
7924 TCTACCCTTC
* *
7934 GAGGGTATTTCAGTAATTTACCCTCCGAGGTATTCAGGTAAATTTTACCCTTTGAGAGTATTTCA
1 GAGGGTATTTCAATAATTTACCCTCAGAGGTATTCAGGTAAATTTTACCCTTTGAGAGTATTTCA
* *
7999 GTAATTTTCCCATC-GAGGG-TATTTCAGTAATTTACCCATA
66 ATAATTTACCC-TCTG-GGGCTATTTCAGTAATTTACCCATA
* * * *
8039 GAGGGTATTTCAATAATTTACCCTCTAGGGGTATTTC-GGTAATTTTTACCCTTTGTGGGTATTT
1 GAGGGTATTTCAATAATTTACCCTC-AGAGGTA-TTCAGGTAAATTTTACCCTTTGAGAGTATTT
* *
8103 CAATAATTTACCCTCTGGGGCTATTTCAGTAATTTTCCCATC
64 CAATAATTTACCCTCTGGGGCTATTTCAGTAATTTACCCATA
8145 GAGGGTATTT
1 GAGGGTATTT
8155 TGTAAATTTA
Statistics
Matches: 102, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
105 29 0.28
106 70 0.69
107 3 0.03
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Consensus pattern (105 bp):
GAGGGTATTTCAATAATTTACCCTCAGAGGTATTCAGGTAAATTTTACCCTTTGAGAGTATTTCA
ATAATTTACCCTCTGGGGCTATTTCAGTAATTTACCCATA
Done.