Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold480
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: 956445
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
File 7 of 7
Found at i:921081 original size:12 final size:12
Alignment explanation
Indices: 921007--921083 Score: 61
Period size: 12 Copynumber: 6.5 Consensus size: 12
920997 TAATTTAAAT
921007 ATAATAT-AAAA
1 ATAATATAAAAA
* *
921018 ATAAT-TATAAT
1 ATAATATAAAAA
*
921029 ATTATATAAAATA
1 ATAATATAAAA-A
*
921042 ATTAAAAT-AAAA
1 A-TAATATAAAAA
* *
921054 ATAAAATAAAAT
1 ATAATATAAAAA
921066 ATAATATAAAAA
1 ATAATATAAAAA
921078 ATAATA
1 ATAATA
921084 CAAACACGAT
Statistics
Matches: 51, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
10 1 0.02
11 17 0.33
12 25 0.49
13 4 0.08
14 4 0.08
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
ATAATATAAAAA
Found at i:921083 original size:27 final size:31
Alignment explanation
Indices: 921002--921083 Score: 77
Period size: 32 Copynumber: 2.7 Consensus size: 31
920992 TTATATAATT
921002 TAAATATAATAT-AAAAATAATTATAATATTA
1 TAAATATAATATAAAAAATAA-TATAATATTA
* *
921033 TATAAAATAAT-TAAAATAA-AA-ATAA-AATA
1 TA-AATATAATATAAAA-AATAATATAATATTA
921062 -AAATATAATATAAAAAATAATA
1 TAAATATAATATAAAAAATAATA
921084 CAAACACGAT
Statistics
Matches: 42, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
27 9 0.21
28 8 0.19
29 4 0.10
30 4 0.10
31 3 0.07
32 12 0.29
33 2 0.05
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (31 bp):
TAAATATAATATAAAAAATAATATAATATTA
Found at i:928714 original size:9 final size:9
Alignment explanation
Indices: 928700--928795 Score: 55
Period size: 9 Copynumber: 10.8 Consensus size: 9
928690 CCATATAATT
928700 TTTTTTTCA
1 TTTTTTTCA
928709 TTTTTTTCA
1 TTTTTTTCA
*
928718 --CTTTTCA
1 TTTTTTTCA
928725 TTTTTTTTAACAA
1 -TTTTTTT--C-A
928738 TTTTTTGTCA
1 TTTTTT-TCA
928748 -TTTTTT-A
1 TTTTTTTCA
928755 -TTTTTT-A
1 TTTTTTTCA
928762 TATTTTTT-A
1 T-TTTTTTCA
928771 TTTTTTAT-A
1 TTTTTT-TCA
928780 TTTTTTTCA
1 TTTTTTTCA
*
928789 ATTTTTT
1 TTTTTTT
928796 ATAGAATCAA
Statistics
Matches: 73, Mismatches: 3, Indels: 22
0.74 0.03 0.22
Matches are distributed among these distances:
7 14 0.19
8 7 0.10
9 37 0.51
10 5 0.07
11 1 0.01
12 7 0.10
13 2 0.03
ACGTcount: A:0.17, C:0.07, G:0.01, T:0.75
Consensus pattern (9 bp):
TTTTTTTCA
Found at i:928766 original size:16 final size:16
Alignment explanation
Indices: 928737--928785 Score: 80
Period size: 16 Copynumber: 3.0 Consensus size: 16
928727 TTTTTTAACA
*
928737 ATTTTTTGTCATTTTTT
1 ATTTTTTAT-ATTTTTT
928754 ATTTTTTATATTTTTT
1 ATTTTTTATATTTTTT
928770 ATTTTTTATATTTTTT
1 ATTTTTTATATTTTTT
928786 TCAATTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 23 0.74
17 8 0.26
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (16 bp):
ATTTTTTATATTTTTT
Found at i:933646 original size:13 final size:13
Alignment explanation
Indices: 933628--933669 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
933618 AAATAGTACC
933628 CAATGTATCGATA
1 CAATGTATCGATA
933641 CAATGTATCGATA
1 CAATGTATCGATA
*
933654 CAATGTATTGATA
1 CAATGTATCGATA
933667 CAA
1 CAA
933670 GGAATGTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:933866 original size:29 final size:33
Alignment explanation
Indices: 933816--933885 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 33
933806 AAATAAACAT
* *
933816 AATTCAATCATACAACATAACA-AA-CATC-AA
1 AATTCATTCATACAACAAAACAGAATCATCAAA
933846 AATTCATTCA-ACAACAAAACATGAATCATCAAA
1 AATTCATTCATACAACAAAACA-GAATCATCAAA
933879 AATTCAT
1 AATTCAT
933886 AATATCACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 10 0.29
30 9 0.26
31 2 0.06
32 4 0.12
33 9 0.26
ACGTcount: A:0.54, C:0.21, G:0.01, T:0.23
Consensus pattern (33 bp):
AATTCATTCATACAACAAAACAGAATCATCAAA
Found at i:939952 original size:19 final size:20
Alignment explanation
Indices: 939908--939958 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
939898 CTGCCAATCT
**
939908 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
*
939928 CATGTATCGATGCAATT-AA
1 CATGTATCGATACAATTGAA
939947 CATGTATCGATA
1 CATGTATCGATA
939959 TAATGTATCG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:941254 original size:13 final size:13
Alignment explanation
Indices: 941236--941262 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
941226 TACAATGAAC
941236 ATGTATCGATACA
1 ATGTATCGATACA
941249 ATGTATCGATACA
1 ATGTATCGATACA
941262 A
1 A
941263 AGCATAAGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:946301 original size:13 final size:13
Alignment explanation
Indices: 946261--946313 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
946251 CCGTTACAAG
946261 CAATGTATCGATA
1 CAATGTATCGATA
946274 CAA--T-TC-AT-
1 CAATGTATCGATA
946282 C-ATGTATCGATA
1 CAATGTATCGATA
946294 CAATGTATCGATA
1 CAATGTATCGATA
946307 CAATGTA
1 CAATGTA
946314 CCATGTATCC
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 3 0.09
10 4 0.12
11 3 0.09
12 1 0.03
13 21 0.62
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:946301 original size:33 final size:33
Alignment explanation
Indices: 946261--946329 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
946251 CCGTTACAAG
* *
946261 CAATGTATCGATACAAT-TCATCATGTATCGATA
1 CAATGTATCGATACAATGT-ACCATGTATCCATA
946294 CAATGTATCGATACAATGTACCATGTATCCATA
1 CAATGTATCGATACAATGTACCATGTATCCATA
946327 CAA
1 CAA
946330 ACAGTGATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (33 bp):
CAATGTATCGATACAATGTACCATGTATCCATA
Found at i:946402 original size:19 final size:19
Alignment explanation
Indices: 946358--946413 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
946348 CTGAAAGTTT
**
946358 CATGTATCAATACAATTGTC
1 CATGTATCAATACAA-TGAA
*
946378 CATGTATCTATACAATGAA
1 CATGTATCAATACAATGAA
*
946397 CATGTATCGATACAATG
1 CATGTATCAATACAATG
946414 TATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (19 bp):
CATGTATCAATACAATGAA
Found at i:946416 original size:13 final size:13
Alignment explanation
Indices: 946398--946424 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
946388 TACAATGAAC
946398 ATGTATCGATACA
1 ATGTATCGATACA
946411 ATGTATCGATACA
1 ATGTATCGATACA
946424 A
1 A
946425 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:946455 original size:20 final size:20
Alignment explanation
Indices: 946432--946484 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
946422 CAAAGCATAA
946432 TGTATCGATACATCTGGGTG
1 TGTATCGATACATCTGGGTG
946452 TGTATCGATACATCTGGGTG
1 TGTATCGATACATCTGGGTG
*
946472 TGTATCAATACAT
1 TGTATCGATACAT
946485 TCAAGGGTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATCTGGGTG
Found at i:949258 original size:19 final size:19
Alignment explanation
Indices: 949234--949275 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
949224 TTCAAATGAC
949234 CAAAAATGTCAATTTTGGG
1 CAAAAATGTCAATTTTGGG
*
949253 CAAAAATGTCATTTTTGGG
1 CAAAAATGTCAATTTTGGG
949272 CAAA
1 CAAA
949276 CAAGGTCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (19 bp):
CAAAAATGTCAATTTTGGG
Found at i:949285 original size:20 final size:19
Alignment explanation
Indices: 949234--949285 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
949224 TTCAAATGAC
* *
949234 CAAAAATGTCAATTTTGGG
1 CAAAAAGGTCATTTTTGGG
*
949253 CAAAAATGTCATTTTTGGG
1 CAAAAAGGTCATTTTTGGG
949272 CAAACAAGGTCATT
1 CAAA-AAGGTCATT
949286 AGACAAGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 22 0.73
20 8 0.27
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (19 bp):
CAAAAAGGTCATTTTTGGG
Found at i:955926 original size:14 final size:14
Alignment explanation
Indices: 955909--955939 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
955899 ATATTATATT
*
955909 ATATATATATACAC
1 ATATATACATACAC
955923 ATATATACATACAC
1 ATATATACATACAC
955937 ATA
1 ATA
955940 AAGAAGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (14 bp):
ATATATACATACAC
Done.