Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1965
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: 22095
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Found at i:5131 original size:26 final size:26
Alignment explanation
Indices: 5096--5204 Score: 182
Period size: 26 Copynumber: 4.2 Consensus size: 26
5086 ATTGATACAA
5096 ATGATAATGGGTTAGGTAAATGTTCC
1 ATGATAATGGGTTAGGTAAATGTTCC
* * *
5122 ATGACAATGGATTAGGTAAATATTCC
1 ATGATAATGGGTTAGGTAAATGTTCC
5148 ATGATAATGGGTTAGGTAAATGTTCC
1 ATGATAATGGGTTAGGTAAATGTTCC
*
5174 ATGATAATGGTTTAGGTAAATGTTCC
1 ATGATAATGGGTTAGGTAAATGTTCC
5200 ATGAT
1 ATGAT
5205 GGGAATTTCA
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.33, C:0.08, G:0.24, T:0.35
Consensus pattern (26 bp):
ATGATAATGGGTTAGGTAAATGTTCC
Found at i:9046 original size:13 final size:13
Alignment explanation
Indices: 9028--9080 Score: 63
Period size: 13 Copynumber: 4.0 Consensus size: 13
9018 TATATACATC
9028 ATAATAAAAAAAT
1 ATAATAAAAAAAT
*
9041 ATAATAAAAATAT
1 ATAATAAAAAAAT
*
9054 ATATACAAAACAAAT
1 ATA-ATAAAA-AAAT
9069 ATAA-AAAAAAAT
1 ATAATAAAAAAAT
9081 CACGCGGTGG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
12 4 0.11
13 19 0.54
14 6 0.17
15 6 0.17
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.23
Consensus pattern (13 bp):
ATAATAAAAAAAT
Found at i:9499 original size:11 final size:11
Alignment explanation
Indices: 9481--9510 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
9471 GTGTATATTG
9481 TATATATTATA
1 TATATATTATA
*
9492 TTTATATTATA
1 TATATATTATA
9503 TATATATT
1 TATATATT
9511 CTTAATGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATATATTATA
Found at i:9921 original size:16 final size:15
Alignment explanation
Indices: 9897--9931 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
9887 TAATTATTAT
9897 TATTCTAATATTTTGA
1 TATTCTAATATTTT-A
*
9913 TATTTTAATATTTTA
1 TATTCTAATATTTTA
9928 TATT
1 TATT
9932 ATTCACATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (15 bp):
TATTCTAATATTTTA
Found at i:21953 original size:56 final size:56
Alignment explanation
Indices: 21854--21961 Score: 200
Period size: 56 Copynumber: 1.9 Consensus size: 56
21844 TTGTTGTTTC
21854 AAAAAATCAACTCATATTGCGAGAGTGAGTTGAGCCTCGGGACGCTGAGGTATTTT
1 AAAAAATCAACTCATATTGCGAGAGTGAGTTGAGCCTCGGGACGCTGAGGTATTTT
21910 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACGCTGAGGTA
1 AAAAAATCAACTCATATTGCGAGA-GTGAGTTGAGCCTCGGGACGCTGAGGTA
21962 ATTTCAATTT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
56 37 0.73
57 14 0.27
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (56 bp):
AAAAAATCAACTCATATTGCGAGAGTGAGTTGAGCCTCGGGACGCTGAGGTATTTT
Found at i:22011 original size:127 final size:126
Alignment explanation
Indices: 21784--22036 Score: 388
Period size: 127 Copynumber: 2.0 Consensus size: 126
21774 GTTTTATTTC
*
21784 AAAATCAATCATATTGCGAGAGGTGAGTTGAGCCTCGGACACGCTGAGGTATTTCAATTTTTGTT
1 AAAATCAATCATATTGCGAGAGGTGAGTTGAGCCTCGGA-ACGCTGAGGTATTTCAATTTCTGTT
**
21849 GTTTCAAAAAATCAACTCATATTGCGAGAGTGAGTTGAGCCTC-GGGACGCTGAGGTATTTTAA
65 G-TTCAAAAAATCAACTCATATTGCGAGAGTGAGTTGAGCCTCAGACACGC-GAGGTATTTTAA
21912 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG-ACGCTGAGGTAATTTCAATTTCTGT
1 AAAATCAA-TCATATTGCGAGAGGTGAGTTGAGCCTCGGAACGCTGAGGT-ATTTCAATTTCTGT
21976 TG-TCAAAAAAATCAACTCATATTGCGA-AGTGGAGTTGAGCCTCAGACACGCGAGGTATTTT
64 TGTTC-AAAAAATCAACTCATATTGCGAGAGT-GAGTTGAGCCTCAGACACGCGAGGTATTTT
22037 CAATTTCGTT
Statistics
Matches: 117, Mismatches: 3, Indels: 11
0.89 0.02 0.08
Matches are distributed among these distances:
126 5 0.04
127 54 0.46
128 28 0.24
129 30 0.26
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.29
Consensus pattern (126 bp):
AAAATCAATCATATTGCGAGAGGTGAGTTGAGCCTCGGAACGCTGAGGTATTTCAATTTCTGTTG
TTCAAAAAATCAACTCATATTGCGAGAGTGAGTTGAGCCTCAGACACGCGAGGTATTTTAA
Found at i:22031 original size:71 final size:71
Alignment explanation
Indices: 21910--22043 Score: 202
Period size: 71 Copynumber: 1.9 Consensus size: 71
21900 GAGGTATTTT
*
21910 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACGCTGAGGTAATTTCAATTTCTG
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGCACGCTGAGGTAATTTCAATTTCTG
21975 TTGTCA
66 TTGTCA
*
21981 AAAAAATCAACTCATATTGCGA-A-GTGGAGTTGAGCCTCAGACACGC-GAGGTATTTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGT-GAGTTGAGCCTC-G-CACGCTGAGGTAATTTCAATTT
22043 C
63 C
22044 GTTTTTCAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
69 2 0.03
70 13 0.22
71 39 0.67
72 4 0.07
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.28
Consensus pattern (71 bp):
AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGCACGCTGAGGTAATTTCAATTTCTG
TTGTCA
Done.