Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1231
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: 31767
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Found at i:1021 original size:22 final size:20
Alignment explanation
Indices: 996--1052 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
986 GCTATGGAAA
996 TGTATCGATACATGCTTATAAT
1 TGTATCGATACAT--TTATAAT
* * *
1018 TGTATCGATGCATTTCTCAT
1 TGTATCGATACATTTATAAT
1038 TGTATCGATACATTT
1 TGTATCGATACATTT
1053 TTGGGTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 19 0.61
22 12 0.39
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44
Consensus pattern (20 bp):
TGTATCGATACATTTATAAT
Found at i:2709 original size:9 final size:10
Alignment explanation
Indices: 2683--2713 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
2673 CATTCCTTCC
2683 CATAAAAACA
1 CATAAAAACA
2693 CATAAAAACA
1 CATAAAAACA
2703 CATAAAAACA
1 CATAAAAACA
2713 C
1 C
2714 TTTCTCCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.68, C:0.23, G:0.00, T:0.10
Consensus pattern (10 bp):
CATAAAAACA
Found at i:6982 original size:26 final size:27
Alignment explanation
Indices: 6925--6982 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 27
6915 CACCATCGGG
*
6925 GATACTCTAACCTCGTTATTTTTGAAAG
1 GATACTCTAACCTCG-TATTTTTGAAAA
6953 GATACTCTAACCTCG-ATTTTAT-AAAA
1 GATACTCTAACCTCGTATTTT-TGAAAA
6979 GATA
1 GATA
6983 AATCGATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 12 0.43
27 1 0.04
28 15 0.54
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.36
Consensus pattern (27 bp):
GATACTCTAACCTCGTATTTTTGAAAA
Found at i:7077 original size:53 final size:50
Alignment explanation
Indices: 7001--7208 Score: 181
Period size: 53 Copynumber: 4.1 Consensus size: 50
6991 TAGAATTTAA
* *
7001 TATATAATA-TTTTTAATTTTTTATTATTTTTAAATAGTAATTTAAAATGTT
1 TATAAAATATTTTTTAA-TTTTTATTATTTTTAAATAGTAATTTAAGAT-TT
* * * *
7052 GTATAAAATATTTTTTAATATTTTATCATTTTTAATTTGTAATTTGAGATTT
1 -TATAAAATATTTTTTAAT-TTTTATTATTTTTAAATAGTAATTTAAGATTT
* ** *
7104 AATATAAAATATTTTTTAATCTTTTA-T-TTTCTAAATAAAAATTCAAGATTT
1 --TATAAAATATTTTTTAAT-TTTTATTATTTTTAAATAGTAATTTAAGATTT
* * * * *
7155 AATATAATTTTTTTTAATTTTTAGTATTTTT-AATAGTAATTTGAGATTT
1 TATAAAATATTTTTTAATTTTTATTATTTTTAAATAGTAATTTAAGATTT
*
7204 AATAA
1 TATAA
7209 GATTGTTTAA
Statistics
Matches: 126, Mismatches: 25, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
48 5 0.04
49 34 0.27
50 4 0.03
51 17 0.13
52 11 0.09
53 55 0.44
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (50 bp):
TATAAAATATTTTTTAATTTTTATTATTTTTAAATAGTAATTTAAGATTT
Found at i:7197 original size:100 final size:105
Alignment explanation
Indices: 6995--7207 Score: 260
Period size: 100 Copynumber: 2.1 Consensus size: 105
6985 TCGATTTAGA
* * * ** * *
6995 ATTTAATATATAATATTTTTAATTTTTTATTATTTTTAAATAGTAATTTAAAATGTTGTATAAAA
1 ATTTAATATAAAATATTTTTAATCTTTTATTATTTCTAAATAAAAATTCAAAATGTTGAATAAAA
*
7060 TATTTTTTAATATTTTATCATTTTTAATTTGTAATTTGAG
66 TATTTTTTAATATTTTATCATTTTTAATTAGTAATTTGAG
* *
7100 ATTTAATATAAAATATTTTTTAATCTTTTA-T-TTTCTAAATAAAAATTCAAGAT-TT-AATATA
1 ATTTAATATAAAATA-TTTTTAATCTTTTATTATTTCTAAATAAAAATTCAAAATGTTGAATAAA
*
7161 ATTTTTTTTAAT-TTTTAGT-ATTTTTAA-TAGTAATTTGAG
65 ATATTTTTTAATATTTTA-TCATTTTTAATTAGTAATTTGAG
7200 ATTTAATA
1 ATTTAATA
7208 AGATTGTTTA
Statistics
Matches: 95, Mismatches: 11, Indels: 9
0.83 0.10 0.08
Matches are distributed among these distances:
100 19 0.20
101 13 0.14
102 16 0.17
103 2 0.02
104 17 0.18
105 15 0.16
106 13 0.14
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (105 bp):
ATTTAATATAAAATATTTTTAATCTTTTATTATTTCTAAATAAAAATTCAAAATGTTGAATAAAA
TATTTTTTAATATTTTATCATTTTTAATTAGTAATTTGAG
Found at i:8682 original size:13 final size:12
Alignment explanation
Indices: 8650--8680 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
8640 ATATTAATGA
8650 ATTTTTTAAAAT
1 ATTTTTTAAAAT
8662 ATTTTTTAAAAT
1 ATTTTTTAAAAT
8674 ATTTTTT
1 ATTTTTT
8681 TAGATGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATTTTTTAAAAT
Found at i:8996 original size:39 final size:38
Alignment explanation
Indices: 8916--9038 Score: 122
Period size: 39 Copynumber: 3.2 Consensus size: 38
8906 AGGATATAGA
* * * **
8916 TTTTATTGGAATCTAAACAATGGTTACTAACGCATGAATT
1 TTTTATTGGAATCCAAATAAT-GTGACTAATACATG-ATT
**
8956 TTTTATTGGAATTTAAA-AGATGTGACTAATACATAGATT
1 TTTTATTGGAATCCAAATA-ATGTGACTAATACAT-GATT
* *
8995 TTTTATTGGAATCCAAATAATGTGACTAATATATGAAT
1 TTTTATTGGAATCCAAATAATGTGACTAATACATGATT
9033 TTTTAT
1 TTTTAT
9039 AGAAATCCTA
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
38 9 0.12
39 43 0.60
40 20 0.28
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (38 bp):
TTTTATTGGAATCCAAATAATGTGACTAATACATGATT
Found at i:9059 original size:38 final size:38
Alignment explanation
Indices: 8971--9060 Score: 101
Period size: 38 Copynumber: 2.3 Consensus size: 38
8961 TTGGAATTTA
* * *
8971 AAAGATGTGACTAATACATAGATTTTTTATTGGAATCC
1 AAAGATGTGACTAATACATAGAATTTTTATAGAAATCC
* *
9009 AAATAATGTGACTAATATAT-GAATTTTTATAGAAATCC
1 AAA-GATGTGACTAATACATAGAATTTTTATAGAAATCC
*
9047 TAAAGATATGACTA
1 -AAAGATGTGACTA
9061 TTGTATAGAT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
38 26 0.60
39 17 0.40
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (38 bp):
AAAGATGTGACTAATACATAGAATTTTTATAGAAATCC
Found at i:9966 original size:20 final size:20
Alignment explanation
Indices: 9941--10047 Score: 81
Period size: 20 Copynumber: 4.8 Consensus size: 20
9931 TTCTACCCAG
9941 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* *
9961 ATGTATCGATACATGTATGC-
1 ATGTATCGATACAT-TTTTCA
*
9981 ATGTATCAATACATTCTGTTTTCTACCCA
1 ATGTATCGATACA-----TTTT-T---CA
10010 GATGTATCGATACATTTTTCA
1 -ATGTATCGATACATTTTTCA
10031 ATGTATCGATACATTTT
1 ATGTATCGATACATTTT
10048 GTTTTTTTAC
Statistics
Matches: 69, Mismatches: 6, Indels: 24
0.70 0.06 0.24
Matches are distributed among these distances:
20 43 0.62
21 5 0.07
24 3 0.04
25 5 0.07
28 1 0.01
30 12 0.17
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:10004 original size:70 final size:70
Alignment explanation
Indices: 9910--10044 Score: 243
Period size: 70 Copynumber: 1.9 Consensus size: 70
9900 ATGAACAATA
* *
9910 CATGTATCGATACATTTTATTTTCTACCCAGATGTATCGATACATTTTTCAATGTATCGATACAT
1 CATGTATCAATACATTCTATTTTCTACCCAGATGTATCGATACATTTTTCAATGTATCGATACAT
9975 GTATG
66 GTATG
*
9980 CATGTATCAATACATTCTGTTTTCTACCCAGATGTATCGATACATTTTTCAATGTATCGATACAT
1 CATGTATCAATACATTCTATTTTCTACCCAGATGTATCGATACATTTTTCAATGTATCGATACAT
10045 TTTGTTTTTT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 62 1.00
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.41
Consensus pattern (70 bp):
CATGTATCAATACATTCTATTTTCTACCCAGATGTATCGATACATTTTTCAATGTATCGATACAT
GTATG
Found at i:10074 original size:51 final size:50
Alignment explanation
Indices: 9961--10095 Score: 200
Period size: 51 Copynumber: 2.7 Consensus size: 50
9951 ACATTTTTCA
* * *
9961 ATGTATCGATACATGTATGC-ATGTATCAATACATTCTGTTTTCTACCCAG
1 ATGTATCGATACAT-TTTTCAATGTATCGATACATTCTGTTTTCTACCCAG
* *
10011 ATGTATCGATACATTTTTCAATGTATCGATACATTTTGTTTTTTTACCCAG
1 ATGTATCGATACATTTTTCAATGTATCGATACATTCTG-TTTTCTACCCAG
10062 ATGTATCGATACATTTTTCAATGTATCGATACAT
1 ATGTATCGATACATTTTTCAATGTATCGATACAT
10096 CTAGTTAATT
Statistics
Matches: 78, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
49 3 0.04
50 30 0.38
51 45 0.58
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (50 bp):
ATGTATCGATACATTTTTCAATGTATCGATACATTCTGTTTTCTACCCAG
Found at i:28134 original size:2 final size:2
Alignment explanation
Indices: 28127--28159 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
28117 ATTACTTGCA
*
28127 TG TG TG TG TG TG TG TG TG TG TG TG CG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
28160 AAATATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.03, G:0.48, T:0.48
Consensus pattern (2 bp):
TG
Found at i:29548 original size:12 final size:13
Alignment explanation
Indices: 29529--29560 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
29519 TTAGGCCTTG
29529 AGAAAAAGAAAAA
1 AGAAAAAGAAAAA
29542 A-AAAAAGAAAAA
1 AGAAAAAGAAAAA
29554 AGAAAAA
1 AGAAAAA
29561 AAGAAGCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AGAAAAAGAAAAA
Done.