Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold228
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: 4123243
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
File 27 of 27
Found at i:4108141 original size:25 final size:26
Alignment explanation
Indices: 4108103--4108155 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
4108093 TATGGATGAA
*
4108103 TTAAATTTTATTAATTTTATTT-TTT
1 TTAAATTTTATTAATTATATTTATTT
4108128 TTAATATTTT-TTAATTATATTTATTT
1 TTAA-ATTTTATTAATTATATTTATTT
4108154 TT
1 TT
4108156 TATTTTGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 15 0.60
26 10 0.40
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (26 bp):
TTAAATTTTATTAATTATATTTATTT
Found at i:4108161 original size:23 final size:25
Alignment explanation
Indices: 4108107--4108161 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
4108097 GATGAATTAA
*
4108107 ATTTTATTAATTTTATTT-TTTTTAAT
1 ATTTT-TTAATTATATTTATTTTT-AT
4108133 ATTTTTTAATTATATTTATTTTT-T
1 ATTTTTTAATTATATTTATTTTTAT
4108157 ATTTT
1 ATTTT
4108162 GAAATAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 6 0.22
25 11 0.41
26 10 0.37
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (25 bp):
ATTTTTTAATTATATTTATTTTTAT
Found at i:4111454 original size:13 final size:14
Alignment explanation
Indices: 4111397--4111454 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
4111387 GTTTTTCTGA
4111397 TTTTCTGGTATATT
1 TTTTCTGGTATATT
4111411 TTTTCT-G-A-ATT
1 TTTTCTGGTATATT
*
4111422 GATTTTCTGGTATGTT
1 --TTTTCTGGTATATT
4111438 TTTTCTGGTAT-TT
1 TTTTCTGGTATATT
4111451 TTTT
1 TTTT
4111455 ATTATTTTCA
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
11 3 0.08
12 1 0.03
13 13 0.34
14 18 0.47
15 1 0.03
16 2 0.05
ACGTcount: A:0.12, C:0.07, G:0.16, T:0.66
Consensus pattern (14 bp):
TTTTCTGGTATATT
Found at i:4112195 original size:28 final size:28
Alignment explanation
Indices: 4112164--4112247 Score: 71
Period size: 28 Copynumber: 2.9 Consensus size: 28
4112154 ATCACTAAAT
4112164 TTTAAAATAATAATAATTAATTAATTAA
1 TTTAAAATAATAATAATTAATTAATTAA
* * * *
4112192 TTT-AAATAAAAATATTTTAATAAATTCA
1 TTTAAAATAATAATA-ATTAATTAATTAA
*
4112220 TTTCAAATGTAATATATAATTGAATTAA
1 TTT-AAA-ATAATA-ATAATT-AATTAA
4112248 AAATAGATTT
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
27 10 0.24
28 16 0.38
30 2 0.05
31 6 0.14
32 8 0.19
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (28 bp):
TTTAAAATAATAATAATTAATTAATTAA
Found at i:4112344 original size:22 final size:23
Alignment explanation
Indices: 4112305--4112350 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
4112295 ATAATAATTT
* *
4112305 AATTTAACAGTAATTAAA-TATA
1 AATTTAACAATAACTAAATTATA
*
4112327 AATTTAAGAATAACTAAATTATA
1 AATTTAACAATAACTAAATTATA
4112350 A
1 A
4112351 TTAAAAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (23 bp):
AATTTAACAATAACTAAATTATA
Found at i:4112352 original size:22 final size:22
Alignment explanation
Indices: 4112300--4112352 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
4112290 ACTTAATAAT
* *
4112300 AATT-TAATTTAACAGTAATTA
1 AATTATAATTTAACAATAACTA
*
4112321 AA-TATAAATTTAAGAATAACTA
1 AATTAT-AATTTAACAATAACTA
4112343 AATTATAATT
1 AATTATAATT
4112353 AAAAATATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 1 0.04
21 3 0.12
22 19 0.73
23 3 0.12
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (22 bp):
AATTATAATTTAACAATAACTA
Found at i:4113582 original size:3 final size:3
Alignment explanation
Indices: 4113576--4113621 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
4113566 TATTAAATGT
4113576 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
4113622 CTTGCCACAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:4114961 original size:20 final size:22
Alignment explanation
Indices: 4114931--4114974 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
4114921 TGATTTCCCG
4114931 TGTGAATGTATCGATACA-ATT
1 TGTGAATGTATCGATACATATT
4114952 TGTG-ATGTATCGATACATATT
1 TGTGAATGTATCGATACATATT
4114973 TG
1 TG
4114975 AAAATATAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (22 bp):
TGTGAATGTATCGATACATATT
Found at i:4115046 original size:13 final size:13
Alignment explanation
Indices: 4115028--4115053 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4115018 CAATTTTTGG
4115028 TGTATCGATACAT
1 TGTATCGATACAT
4115041 TGTATCGATACAT
1 TGTATCGATACAT
4115054 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4115050 original size:33 final size:32
Alignment explanation
Indices: 4115008--4115071 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
4114998 TACAAGCCAA
*
4115008 TGTATCGATACA-ATTTTTGGTGTATCGATACAT
1 TGTATCGATACATA-CTTT-GTGTATCGATACAT
4115041 TGTATCGATACATACTTTGTGTATCGATACA
1 TGTATCGATACATACTTTGTGTATCGATACA
4115072 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.45
33 15 0.52
34 1 0.03
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATACTTTGTGTATCGATACAT
Found at i:4115068 original size:32 final size:33
Alignment explanation
Indices: 4115008--4115071 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
4114998 TACAAGCCAA
*
4115008 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATCTTTGGTGTATCGATACAT
4115041 TGTATCGATAC-ATACTTT-GTGTATCGATACA
1 TGTATCGATACAAT-CTTTGGTGTATCGATACA
4115072 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATCTTTGGTGTATCGATACAT
Found at i:4115988 original size:22 final size:20
Alignment explanation
Indices: 4115962--4116005 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 20
4115952 TTATAGATTA
4115962 AAAAATCAAAGTACAATGCAAAT
1 AAAAA-CAAAGT-CAA-GCAAAT
4115985 AAAAACAAAGTCAAGCAAAT
1 AAAAACAAAGTCAAGCAAAT
4116005 A
1 A
4116006 CTTTAAACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.33
21 3 0.14
22 6 0.29
23 5 0.24
ACGTcount: A:0.64, C:0.14, G:0.09, T:0.14
Consensus pattern (20 bp):
AAAAACAAAGTCAAGCAAAT
Found at i:4117644 original size:13 final size:13
Alignment explanation
Indices: 4117626--4117664 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
4117616 ATAATCCCCC
* *
4117626 TGTATCAATACAG
1 TGTATCGATACAA
4117639 TGTATCGATACAA
1 TGTATCGATACAA
4117652 TGTATCGATACAA
1 TGTATCGATACAA
4117665 AGGAAATGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Done.