Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold593
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: 24706
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 424 characters in sequence are not A, C, G, or T
Found at i:1100 original size:10 final size:9
Alignment explanation
Indices: 1071--1256 Score: 68
Period size: 9 Copynumber: 20.6 Consensus size: 9
1061 AAAATAATTT
1071 AAAATTCATA
1 AAAATT-ATA
1081 AAAA-TATA
1 AAAATTATA
*
1089 AAAATTATT
1 AAAATTATA
*
1098 AAAACT-TA
1 AAAATTATA
1106 AAAA-TATTA
1 AAAATTA-TA
*
1115 AAATTTATA
1 AAAATTATA
*
1124 TAAACTTATA
1 -AAAATTATA
1134 AAAATCTA-A
1 AAAAT-TATA
*
1143 TAAATTATGA
1 AAAATTAT-A
*
1153 AGAA-T-TA
1 AAAATTATA
*
1160 AATATGTATA
1 AAAAT-TATA
1170 AAAATCT-TA
1 AAAAT-TATA
1179 AAAACTTATAA
1 AAAA-TTAT-A
*
1190 AAAATCATA
1 AAAATTATA
* *
1199 ATAATAAT-
1 AAAATTATA
*
1207 AAAA-TATT
1 AAAATTATA
1215 AAAATTGATA
1 AAAATT-ATA
* *
1225 TTAACTTATA
1 -AAAATTATA
*
1235 ACAATTATA
1 AAAATTATA
*
1244 AAAAATA-A
1 AAAATTATA
1252 AAAAT
1 AAAAT
1257 AAAAAATAAA
Statistics
Matches: 131, Mismatches: 27, Indels: 38
0.67 0.14 0.19
Matches are distributed among these distances:
7 6 0.05
8 27 0.21
9 53 0.40
10 36 0.27
11 9 0.07
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (9 bp):
AAAATTATA
Found at i:1116 original size:26 final size:27
Alignment explanation
Indices: 1079--1150 Score: 80
Period size: 26 Copynumber: 2.7 Consensus size: 27
1069 TTAAAATTCA
1079 TAAAAATA-TAAAAATTATTA-AAACT
1 TAAAAATATTAAAAATTATTATAAACT
*
1104 TAAAAATATTAAAATTTA-TATAAACT
1 TAAAAATATTAAAAATTATTATAAACT
1130 TATAAAA-ATCTAATAAATTAT
1 TA-AAAATAT-TAA-AAATTAT
1151 GAAGAATTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
25 10 0.26
26 17 0.44
27 7 0.18
28 5 0.13
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (27 bp):
TAAAAATATTAAAAATTATTATAAACT
Found at i:1260 original size:6 final size:7
Alignment explanation
Indices: 1241--1268 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
1231 TATAACAATT
1241 ATAAAAA
1 ATAAAAA
1248 ATAAAAA
1 ATAAAAA
1255 ATAAAAA
1 ATAAAAA
1262 ATAAAAA
1 ATAAAAA
1269 CTTGAACTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
ATAAAAA
Found at i:4853 original size:9 final size:9
Alignment explanation
Indices: 4839--5035 Score: 84
Period size: 9 Copynumber: 20.8 Consensus size: 9
4829 TCAAGTAAAT
4839 TTTTTATAA
1 TTTTTATAA
4848 TTTTTATAA
1 TTTTTATAA
*
4857 GTTTTTATGATT
1 -TTTTTAT-A-A
*
4869 TTTTTATGA
1 TTTTTATAA
*
4878 TTTTGATAA
1 TTTTTATAA
4887 GTTTTTA-AGA
1 -TTTTTATA-A
4897 TTTTTA-AA
1 TTTTTATAA
4905 TATGGTTTATTAA
1 T-T--TTTA-TAA
4918 -TTTTATTAA
1 TTTTTA-TAA
*
4927 -TTTTATTAT
1 TTTTTA-TAA
4936 TTTATTATAA
1 TTT-TTATAA
4946 TTTTTATAA
1 TTTTTATAA
*
4955 GTTTATATCAA
1 -TTTTTAT-AA
4966 -TTTTAGT-A
1 TTTTTA-TAA
4974 TTTTTA-AA
1 TTTTTATAA
* *
4982 TTTTAATAC
1 TTTTTATAA
**
4991 TTTCAATAA
1 TTTTTATAA
* *
5000 TATTTTTTAT
1 T-TTTTATAA
5010 TTTTTAATAA
1 TTTTT-ATAA
*
5020 TTTTTATGA
1 TTTTTATAA
5029 TTTTTAT
1 TTTTTAT
5036 GAGAAAATAT
Statistics
Matches: 147, Mismatches: 21, Indels: 40
0.71 0.10 0.19
Matches are distributed among these distances:
8 9 0.06
9 79 0.54
10 39 0.27
11 18 0.12
13 2 0.01
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:4863 original size:19 final size:19
Alignment explanation
Indices: 4839--4969 Score: 74
Period size: 20 Copynumber: 6.7 Consensus size: 19
4829 TCAAGTAAAT
4839 TTTTTATAATTTTTATAAG
1 TTTTTATAATTTTTATAAG
* * *
4858 TTTTTATGATTTTTTTATG
1 TTTTTATAATTTTTATAAG
* *
4877 ATTTTGATAAGTTTT-TAAG
1 -TTTTTATAATTTTTATAAG
4896 ATTTTTA-AATATGGTTTATTAA-
1 -TTTTTATAAT-T--TTTA-TAAG
* *
4918 -TTTTATTAA-TTTTATTAT
1 TTTTTA-TAATTTTTATAAG
4936 TTTATTATAATTTTTATAAG
1 TTT-TTATAATTTTTATAAG
*
4956 TTTATATCAATTTT
1 TTTTTAT-AATTTT
4970 AGTATTTTTA
Statistics
Matches: 86, Mismatches: 13, Indels: 25
0.69 0.10 0.20
Matches are distributed among these distances:
17 2 0.02
18 6 0.07
19 34 0.40
20 36 0.42
21 3 0.03
22 2 0.02
23 3 0.03
ACGTcount: A:0.30, C:0.01, G:0.07, T:0.63
Consensus pattern (19 bp):
TTTTTATAATTTTTATAAG
Found at i:4874 original size:30 final size:30
Alignment explanation
Indices: 4838--4901 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
4828 TTCAAGTAAA
* *
4838 TTTTTTATAATTTTTATAAGTTTTTATGAT
1 TTTTTTATAATTTTGATAAGTTTTTAAGAT
*
4868 TTTTTTATGATTTTGATAAGTTTTTAAGAT
1 TTTTTTATAATTTTGATAAGTTTTTAAGAT
4898 TTTT
1 TTTT
4902 AAATATGGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (30 bp):
TTTTTTATAATTTTGATAAGTTTTTAAGAT
Found at i:5032 original size:19 final size:19
Alignment explanation
Indices: 4837--5034 Score: 58
Period size: 20 Copynumber: 10.4 Consensus size: 19
4827 TTTCAAGTAA
* *
4837 ATTTTTTATAATTTTTATA
1 ATTTTTAATAATTTTTATG
*
4856 AGTTTTT-ATGATTTTTTTATG
1 A-TTTTTAAT-A-ATTTTTATG
* *
4877 A-TTTTGATAAGTTTTTAAG
1 ATTTTTAATAA-TTTTTATG
* *
4896 ATTTTTAA-ATATGGTTTATT
1 ATTTTTAATA-AT-TTTTATG
* * *
4916 AATTTTATTAA-TTTTATT
1 ATTTTTAATAATTTTTATG
*
4934 ATTTTATTATAATTTTTAT-
1 ATTTT-TAATAATTTTTATG
**
4953 AAGTTTATATCAA-TTTTA-G
1 ATTTTTA-AT-AATTTTTATG
*
4972 TATTTTT-A-AATTTTAAT-
1 -ATTTTTAATAATTTTTATG
* * *
4989 ACTTTCAATAATATTTT-TT
1 ATTTTTAATAAT-TTTTATG
5008 ATTTTTTAATAATTTTTATG
1 A-TTTTTAATAATTTTTATG
5028 ATTTTTA
1 ATTTTTA
5035 TGAGAAAATA
Statistics
Matches: 130, Mismatches: 26, Indels: 46
0.64 0.13 0.23
Matches are distributed among these distances:
16 6 0.05
17 5 0.04
18 16 0.12
19 46 0.35
20 48 0.37
21 9 0.07
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.62
Consensus pattern (19 bp):
ATTTTTAATAATTTTTATG
Found at i:12343 original size:22 final size:22
Alignment explanation
Indices: 12315--12362 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
12305 TTATAATGTT
12315 AATTAAAAGTAAAATCATTTCA
1 AATTAAAAGTAAAATCATTTCA
12337 AATTAAAAGTAAAATCATTTCA
1 AATTAAAAGTAAAATCATTTCA
12359 AATT
1 AATT
12363 TATCTTACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.33
Consensus pattern (22 bp):
AATTAAAAGTAAAATCATTTCA
Found at i:18801 original size:22 final size:23
Alignment explanation
Indices: 18742--18808 Score: 61
Period size: 22 Copynumber: 3.0 Consensus size: 23
18732 TACCATTTTC
*
18742 AATAATATT-ATTTATTAACATTT
1 AATAATATTAATTTATT-TCATTT
* *
18765 AAGTACT-TTAGTTTATTTC-TTT
1 AA-TAATATTAATTTATTTCATTT
18787 AATAATATTAATTTATTT-ATTT
1 AATAATATTAATTTATTTCATTT
18809 TAAATAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
21 3 0.09
22 18 0.51
23 5 0.14
24 9 0.26
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.57
Consensus pattern (23 bp):
AATAATATTAATTTATTTCATTT
Found at i:22471 original size:21 final size:21
Alignment explanation
Indices: 22421--22471 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
22411 ATGGCAGTGG
*
22421 GAGTGATGCAAGTAGCTGAGA
1 GAGTGATGGAAGTAGCTGAGA
*
22442 AAGTGATGGAAG-AGGCTGAGA
1 GAGTGATGGAAGTA-GCTGAGA
22463 GAGTGATGG
1 GAGTGATGG
22472 GATAGACTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.33, C:0.06, G:0.43, T:0.18
Consensus pattern (21 bp):
GAGTGATGGAAGTAGCTGAGA
Done.