Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_3680
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: 17608
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:201 original size:41 final size:41
Alignment explanation
Indices: 152--289 Score: 204
Period size: 41 Copynumber: 3.4 Consensus size: 41
142 GACTTTAAGT
* *
152 CTAGCAGGCTAATTGCCGGTGATCTGAATTAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
*
193 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* * * **
234 CTAGCAGGCTACGTGCCGGTGATCTAAATCAGGCTATAAGT
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
275 CTAGCAGGCTAAGTG
1 CTAGCAGGCTAAGTG
290 TCGTTGAATC
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 89 1.00
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:1172 original size:21 final size:20
Alignment explanation
Indices: 1126--1179 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
1116 TTTTGCCAAG
**
1126 TATCGATAAATTTAAATGAA
1 TATCGATAAATTTAAAAAAA
1146 TATCGATAAATTTAAAAAAA
1 TATCGATAAATTTAAAAAAA
*
1166 TTATCGATACATTT
1 -TATCGATAAATTT
1180 TCTGGTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.37
Consensus pattern (20 bp):
TATCGATAAATTTAAAAAAA
Found at i:5187 original size:23 final size:23
Alignment explanation
Indices: 5131--5188 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
5121 GTTCAACTCA
**
5131 GAACATGGCCACAATAAAAACAG
1 GAACATGGCCTTAATAAAAACAG
5154 GAACATGGCCTTAATAAAAACAG
1 GAACATGGCCTTAATAAAAACAG
5177 GAACATGGCCTT
1 GAACATGGCCTT
5189 CATTTGTCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.45, C:0.21, G:0.19, T:0.16
Consensus pattern (23 bp):
GAACATGGCCTTAATAAAAACAG
Found at i:6278 original size:21 final size:21
Alignment explanation
Indices: 6252--6292 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
6242 CGCATTAATT
6252 AAAAATATT-TTTAAATAATAA
1 AAAAATATTATTT-AATAATAA
6273 AAAAATATTATTTAATAATA
1 AAAAATATTATTTAATAATA
6293 TTACATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AAAAATATTATTTAATAATAA
Found at i:6685 original size:89 final size:90
Alignment explanation
Indices: 6533--6791 Score: 357
Period size: 89 Copynumber: 2.8 Consensus size: 90
6523 TGATCGTTCG
6533 TTATTAAATTATATTTATATTAATTATTTTAAATTATATAAATTCATATAAGAAAATTTATTATC
1 TTATTAAATTATATTTATATTAATTATTTTAAATTATATAAATTCATATAAGAAAATTTATTATC
6598 AAGA-ATTTTATG-AAT-TATTA-TA
66 AA-ATATTTTATGAAATATATTATTA
*
6620 TTATTAAATTATATTTATATTGGATTATTTTAAATTATATAAATTTCATATAAGAAAATTTATTA
1 TTATTAAATTATATTTATATT-AATTATTTTAAATTATATAAA-TTCATATAAGAAAATTTATTA
6685 TCAAATATTTTATGAAATAATATTATTA
64 TCAAATATTTTATGAAAT-ATATTATTA
* * *
6713 TTATTAAATTATAATTAATAATAATTTATTTTTAAATTATACAAATTCATATAAGAAAA-TTATT
1 TTATTAAATTAT-ATTTATATTAA-TTA-TTTTAAATTATATAAATTCATATAAGAAAATTTATT
*
6777 AGTTAATATATTTTA
63 A-TCAA-ATATTTTA
6792 AATTTTATTA
Statistics
Matches: 154, Mismatches: 6, Indels: 16
0.88 0.03 0.09
Matches are distributed among these distances:
87 21 0.14
88 21 0.14
89 33 0.21
90 3 0.02
92 5 0.03
93 21 0.14
94 27 0.18
95 23 0.15
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.49
Consensus pattern (90 bp):
TTATTAAATTATATTTATATTAATTATTTTAAATTATATAAATTCATATAAGAAAATTTATTATC
AAATATTTTATGAAATATATTATTA
Found at i:7175 original size:44 final size:45
Alignment explanation
Indices: 7125--7214 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 45
7115 ACCTCTATTC
7125 CATTCAACCAAACACAAGA-TTACTATTACACCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTTACTATTACACCTCTATTCCATTA
*** *
7169 CATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTTACTATTACACCTCTATTCCATTA
7214 C
1 C
7215 GCCTCTAATC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 16 0.39
45 25 0.61
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.32
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTTACTATTACACCTCTATTCCATTA
Found at i:15432 original size:15 final size:15
Alignment explanation
Indices: 15412--15446 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
15402 TTATGTAGGT
15412 TAATATAATAATAAA
1 TAATATAATAATAAA
15427 TAATATAATAATAAA
1 TAATATAATAATAAA
15442 TAATA
1 TAATA
15447 ATAACAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TAATATAATAATAAA
Found at i:15926 original size:20 final size:21
Alignment explanation
Indices: 15901--15945 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
15891 CTAATATTGT
*
15901 ATATATCATATCT-AGATTCC
1 ATATATCATACCTAAGATTCC
*
15921 ATATATCATACCTAAGATTGC
1 ATATATCATACCTAAGATTCC
15942 ATAT
1 ATAT
15946 CCTCGAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.38
Consensus pattern (21 bp):
ATATATCATACCTAAGATTCC
Found at i:16393 original size:130 final size:119
Alignment explanation
Indices: 16235--16515 Score: 362
Period size: 130 Copynumber: 2.3 Consensus size: 119
16225 GACTTGCTGG
*
16235 CTTAAATCTT-CTTCTCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTCCACTACT
1 CTTAAAT-TTGCTTC-CACTATCTTGGAAAGATAAGATTTGCCATCTTTGATCTG-T-C-C-ACT
16299 GCTTAGGGAGATAAGATCTACAATCTTC-ACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTTGG
60 GCTTA-GGAG-TAAG-TCTAC-ATCTTCAACCTACT-CGCTG-TGCTCAGGGAGAC-AGGC-TGG
16363 TGA
117 TGA
16366 CTTAAATTTGCTTCCACTATCTTGGAAAGATAAGATTTGCCATCTTTGATCTGTCCACTGCTTAG
1 CTTAAATTTGCTTCCACTATCTTGGAAAGATAAGATTTGCCATCTTTGATCTGTCCACTGCTTAG
*
16431 GAGTAAGTCTACATCTTCAACCTACTCGCTGTGCTCAGGGAGACAGGCTGGTGG
66 GAGTAAGTCTACATCTTCAACCTACTCGCTGTGCTCAGGGAGACAGGCTGGTGA
16485 CTT-AA-TTG-TTCCACTAT-TTGG-AAGAT-AGATT
1 CTTAAATTTGCTTCCACTATCTTGGAAAGATAAGATT
16516 GTCGTCCTCG
Statistics
Matches: 146, Mismatches: 2, Indels: 22
0.86 0.01 0.13
Matches are distributed among these distances:
113 5 0.03
114 5 0.03
115 4 0.03
116 9 0.06
117 3 0.02
118 2 0.01
119 8 0.05
120 4 0.03
121 13 0.09
122 11 0.08
123 12 0.08
124 4 0.03
125 4 0.03
126 8 0.05
127 1 0.01
128 1 0.01
129 1 0.01
130 40 0.27
131 11 0.08
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (119 bp):
CTTAAATTTGCTTCCACTATCTTGGAAAGATAAGATTTGCCATCTTTGATCTGTCCACTGCTTAG
GAGTAAGTCTACATCTTCAACCTACTCGCTGTGCTCAGGGAGACAGGCTGGTGA
Done.