Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2967
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: 20597
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Found at i:350 original size:85 final size:85
Alignment explanation
Indices: 185--352 Score: 313
Period size: 85 Copynumber: 2.0 Consensus size: 85
175 ATCAAACACA
185 ATCAAAGGATTAAAAGCTTAAAAAACCCTAAGGTGATTTCTTTTTTTTTCTTTTTTATTTTAAAT
1 ATCAAAGGATTAAAAGCTTAAAAAACCCTAAGGTGATTTCTTTTTTTTTC-TTTTTATTTTAAAT
250 TCGGTTTTAAGTTTTTTTAAG
65 TCGGTTTTAAGTTTTTTTAAG
271 ATCAAAGGATT-AAAGCTTAAAAAACCCTAAGGTGATTTCTTTTTTTTTC-TTTTATTTTAAATT
1 ATCAAAGGATTAAAAGCTTAAAAAACCCTAAGGTGATTTCTTTTTTTTTCTTTTTATTTTAAATT
334 CGGTTTTAAGTTTTTTTAA
66 CGGTTTTAAGTTTTTTTAA
353 CCTATACATA
Statistics
Matches: 82, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
83 33 0.40
85 38 0.46
86 11 0.13
ACGTcount: A:0.30, C:0.10, G:0.11, T:0.49
Consensus pattern (85 bp):
ATCAAAGGATTAAAAGCTTAAAAAACCCTAAGGTGATTTCTTTTTTTTTCTTTTTATTTTAAATT
CGGTTTTAAGTTTTTTTAAG
Found at i:12719 original size:45 final size:40
Alignment explanation
Indices: 12621--12728 Score: 103
Period size: 41 Copynumber: 2.6 Consensus size: 40
12611 TTATGCTTAA
*
12621 GATGAAAACCCGAAAAGGGCATCTTAAAAAAAAGGGATTAG
1 GATGAAAACCCGAAAAGGGCGTCTTAAAAAAAA-GGATTAG
**
12662 GGCGAAAACCCGAAAAGGGCGTCTTGATTAGTACAAAAA-GATTAG
1 GATGAAAACCCGAAAAGGGCGTCTT-A--A--A-AAAAAGGATTAG
*
12707 GATGAAAACCCG-AGAGGGCGTC
1 GATGAAAACCCGAAAAGGGCGTC
12729 CTAATGAAAC
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
41 22 0.40
42 1 0.02
44 10 0.18
45 16 0.29
46 1 0.02
47 5 0.09
ACGTcount: A:0.42, C:0.16, G:0.28, T:0.15
Consensus pattern (40 bp):
GATGAAAACCCGAAAAGGGCGTCTTAAAAAAAAGGATTAG
Found at i:13623 original size:69 final size:70
Alignment explanation
Indices: 13503--13676 Score: 212
Period size: 69 Copynumber: 2.5 Consensus size: 70
13493 CTTTCCAAGG
**
13503 AAAATCAACTCATATTGCGAG-AGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTT-
1 AAAATCAACTCATATTGCGAGAAG-TGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTA
13566 T-TTTT
65 TGTTTT
** * *
13571 CAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTA
1 -AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTA
13636 TGTTTT
65 TGTTTT
** * *
13642 -AAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
13677 TTTAATTTTT
Statistics
Matches: 92, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
69 85 0.92
70 3 0.03
71 4 0.04
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (70 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTAT
GTTTT
Found at i:14047 original size:77 final size:73
Alignment explanation
Indices: 13694--14027 Score: 442
Period size: 72 Copynumber: 4.5 Consensus size: 73
13684 TTTGTTTTTC
* *
13694 AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
13759 GTTGTTAAA
66 GTT-TTAAA
** *
13768 AAAA--AACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
*
13831 GTTTT-CA
66 GTTTTAAA
* * ** * *
13838 AAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
13903 GTTTTCAAA
66 GTTTT-AAA
* *
13912 AAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTCAATT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTATTTTCAATT
13976 TCTGTTTTTAAAA
63 TCTG-TTTT-AAA
*
13989 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
14028 ATTACACACT
Statistics
Matches: 232, Mismatches: 19, Indels: 14
0.88 0.07 0.05
Matches are distributed among these distances:
70 4 0.02
71 2 0.01
72 119 0.51
73 1 0.00
74 39 0.17
76 24 0.10
77 42 0.18
78 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (73 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
GTTTTAAA
Found at i:14441 original size:88 final size:87
Alignment explanation
Indices: 14246--14491 Score: 298
Period size: 88 Copynumber: 2.8 Consensus size: 87
14236 TGTTTTAATT
*
14246 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACGCCGAGGTATTTTCAATTAAGC-
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACA--CCGAGGTATTTTCAATT--TCT
* * *
14310 CTTTTGATTTCTGTTTTTCAAAAAAA
62 GTTTTCATTTATGTTTTTCAAAAAAA
* *
14336 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACCGAGGTATTTTCCATTTCTGTTT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACCGAGGTATTTTCAATTTCTGTTT
* *
14401 TCATTATTATGTTTTT-GAAAGAA
66 TCA-T-TTATGTTTTTCAAAAAAA
** * ** *
14424 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTAATTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACCGAGGTATTTTCAATTTCTGTTT
14489 TCA
66 TCA
14492 AAATTCAACT
Statistics
Matches: 137, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
86 1 0.01
87 5 0.04
88 82 0.60
89 9 0.07
90 40 0.29
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.35
Consensus pattern (87 bp):
TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACCGAGGTATTTTCAATTTCTGTTT
TCATTTATGTTTTTCAAAAAAA
Found at i:14608 original size:73 final size:72
Alignment explanation
Indices: 14424--14676 Score: 409
Period size: 73 Copynumber: 3.5 Consensus size: 72
14414 TTTGAAAGAA
*
14424 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTAATTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTT
14489 TCAAAAT
66 TCAAAAT
*
14496 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTG-TT
14561 TTCAAAAT
65 TTCAAAAT
* * *
14569 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTG
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTT
*
14634 TCAAAAAAA
66 TC--AAAAT
14643 TCAACTCATATTGCGA-AAAGTGAGTTGAGCCTCA
1 TCAACTCATATTGCGAGAAA-TGAGTTGAGCCTCA
14677 GTTCACATGT
Statistics
Matches: 170, Mismatches: 7, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
72 64 0.38
73 72 0.42
74 34 0.20
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (72 bp):
TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTT
TCAAAAT
Found at i:20123 original size:27 final size:27
Alignment explanation
Indices: 20093--20155 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
20083 CCTACCAAAA
*
20093 AGGCACAACTAGTCGTGCCTGTCAGAT
1 AGGCACAACTAGTCGCGCCTGTCAGAT
* *
20120 AGGCTCAACTAGTTGCGCCTGTCAGAT
1 AGGCACAACTAGTCGCGCCTGTCAGAT
*
20147 AGGCGCAAC
1 AGGCACAAC
20156 ATGTATGTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.21
Consensus pattern (27 bp):
AGGCACAACTAGTCGCGCCTGTCAGAT
Done.