Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1793
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: 27460
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:2546 original size:14 final size:14
Alignment explanation
Indices: 2524--2571 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
2514 ACCTAAACCG
* *
2524 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
2538 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
2552 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
2566 ACCATT
1 ACCATT
2572 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:5029 original size:37 final size:38
Alignment explanation
Indices: 4961--5034 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 38
4951 GCAACTCAGC
* *
4961 ATACGACTCGACTCTCCCCGAGGCGGTTCGTATCACTA
1 ATACGACTCCACTCTCCCCGAGGCGGATCGTATCACTA
**
4999 ATACGACTCCACTCT-TTCGAGGCGGATCGTATCACT
1 ATACGACTCCACTCTCCCCGAGGCGGATCGTATCACT
5035 TTTCTTCTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 18 0.56
38 14 0.44
ACGTcount: A:0.22, C:0.32, G:0.20, T:0.26
Consensus pattern (38 bp):
ATACGACTCCACTCTCCCCGAGGCGGATCGTATCACTA
Found at i:7716 original size:10 final size:11
Alignment explanation
Indices: 7697--7799 Score: 88
Period size: 12 Copynumber: 9.2 Consensus size: 11
7687 TCAAGTAAGT
7697 TTCAAAAAAAA
1 TTCAAAAAAAA
7708 TTCAAAAAAAA
1 TTCAAAAAAAA
7719 TTCAAAAAAAA
1 TTCAAAAAAAA
7730 GTTTCAAATAAAAA
1 --TTCAAA-AAAAA
*
7744 TATGAAAAAAAA
1 T-TCAAAAAAAA
*
7756 TT--AAAAAAG
1 TTCAAAAAAAA
7765 TT--AAAAAAA
1 TTCAAAAAAAA
*
7774 TTTAGAAAAAAA
1 TTCA-AAAAAAA
*
7786 TTAGAAAAAAAA
1 TT-CAAAAAAAA
7798 TT
1 TT
7800 TGAACATTGT
Statistics
Matches: 80, Mismatches: 4, Indels: 15
0.81 0.04 0.15
Matches are distributed among these distances:
9 16 0.20
11 23 0.29
12 25 0.31
13 11 0.14
14 5 0.06
ACGTcount: A:0.69, C:0.04, G:0.05, T:0.22
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:7755 original size:13 final size:12
Alignment explanation
Indices: 7700--7763 Score: 62
Period size: 11 Copynumber: 5.4 Consensus size: 12
7690 AGTAAGTTTC
7700 AAAAAAAATTC-
1 AAAAAAAATTCA
7711 AAAAAAAATTCA
1 AAAAAAAATTCA
*
7723 AAAAAAAGTTTCA
1 AAAAAAA-ATTCA
* *
7736 AATAAAAATAT-G
1 AAAAAAAAT-TCA
7748 AAAAAAAATT-A
1 AAAAAAAATTCA
7759 AAAAA
1 AAAAA
7764 GTTAAAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
11 17 0.39
12 16 0.36
13 11 0.25
ACGTcount: A:0.73, C:0.05, G:0.03, T:0.19
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:7762 original size:35 final size:34
Alignment explanation
Indices: 7693--7796 Score: 110
Period size: 30 Copynumber: 3.1 Consensus size: 34
7683 CTCATCAAGT
7693 AAGTTTCAAAAAAAATTCAAAAAAAATTCAAAAAA
1 AAGTTTCAAAAAAAATTCAAAAAAAATT-AAAAAA
*
7728 AAGTTTCAAATAAAAATATGAAAAAAAATT--AAAA
1 AAGTTTCAAA-AAAAAT-TCAAAAAAAATTAAAAAA
*
7762 AAG-TT--AAAAAAATTTAGAAAAAAATTAGAAAAA
1 AAGTTTCAAAAAAAATTCA-AAAAAAATTA-AAAAA
7795 AA
1 AA
7797 ATTTGAACAT
Statistics
Matches: 61, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
29 2 0.03
30 15 0.25
31 2 0.03
33 8 0.13
34 7 0.11
35 10 0.16
36 6 0.10
37 11 0.18
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.21
Consensus pattern (34 bp):
AAGTTTCAAAAAAAATTCAAAAAAAATTAAAAAA
Found at i:7782 original size:12 final size:11
Alignment explanation
Indices: 7701--7796 Score: 58
Period size: 11 Copynumber: 8.6 Consensus size: 11
7691 GTAAGTTTCA
7701 AAAAAAATTCA-
1 AAAAAAATT-AG
7712 AAAAAAATTCA-
1 AAAAAAATT-AG
**
7723 AAAAAAAGTTTC
1 AAAAAAA-TTAG
*
7735 AAATAAAAATATG
1 AAA-AAAATTA-G
7748 AAAAAAAATT--
1 -AAAAAAATTAG
*
7758 AAAAAAGTTA-
1 AAAAAAATTAG
*
7768 AAAAAATTTAG
1 AAAAAAATTAG
7779 AAAAAAATTAG
1 AAAAAAATTAG
7790 AAAAAAA
1 AAAAAAA
7797 ATTTGAACAT
Statistics
Matches: 70, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
9 8 0.11
10 9 0.13
11 35 0.50
12 6 0.09
13 9 0.13
14 3 0.04
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.20
Consensus pattern (11 bp):
AAAAAAATTAG
Found at i:10926 original size:9 final size:10
Alignment explanation
Indices: 10919--10975 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
10909 AAGAGAAAAC
10919 AAAGAAAAGA
1 AAAGAAAAGA
10929 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
10941 AAAGAAGA-A
1 AAAGAAAAGA
10950 AAAGAAAATGA
1 AAAGAAAA-GA
10961 AATA-AAAAGA
1 AA-AGAAAAGA
10971 AAAGA
1 AAAGA
10976 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:10942 original size:21 final size:20
Alignment explanation
Indices: 10908--10975 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
10898 ACATTCTTGT
10908 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
10929 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
10950 AAAGAAAATGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
10971 AAAGA
1 AAAGA
10976 GAGGCAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 8 0.20
21 27 0.68
22 5 0.12
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:10943 original size:6 final size:5
Alignment explanation
Indices: 10919--10975 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
10909 AAGAGAAAAC
*
10919 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
10966 AAAGA AAAGA
1 AAAGA AAAGA
10976 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:10950 original size:15 final size:14
Alignment explanation
Indices: 10919--10975 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
10909 AAGAGAAAAC
10919 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
10935 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
10950 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
10966 AAAGAAAAGA
1 AAAGAAAAGA
10976 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:11118 original size:30 final size:30
Alignment explanation
Indices: 11044--11125 Score: 80
Period size: 30 Copynumber: 2.7 Consensus size: 30
11034 TTTGAAAAGC
* * *
11044 AAAAA-AAAATGAAAATGAAA-ATGAGATTG
1 AAAAAGAAGATGAAAA-GAAATTTGAGAGTG
*
11073 AAAAAG-AGAACGAAAAGAAATTTGAGAGTG
1 AAAAAGAAG-ATGAAAAGAAATTTGAGAGTG
11103 AAAAAGAAGATGAAAAAGAAATT
1 AAAAAGAAGATG-AAAAGAAATT
11126 GAAACAAAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
29 10 0.23
30 21 0.49
31 12 0.28
ACGTcount: A:0.63, C:0.01, G:0.21, T:0.15
Consensus pattern (30 bp):
AAAAAGAAGATGAAAAGAAATTTGAGAGTG
Found at i:16867 original size:13 final size:14
Alignment explanation
Indices: 16849--16883 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
16839 GGCTGAACCT
16849 ACATAATTAAATA-
1 ACATAATTAAATAG
16862 ACATAATTAAATAG
1 ACATAATTAAATAG
16876 A-ATAATTA
1 ACATAATTA
16884 TTCATATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 20 0.95
14 1 0.05
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (14 bp):
ACATAATTAAATAG
Found at i:17125 original size:21 final size:21
Alignment explanation
Indices: 17101--17141 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
17091 GTAAAAGAAA
*
17101 TGAGCTAAAACGAGCTAAATT
1 TGAGCTAAAACAAGCTAAATT
* *
17122 TGAGCTCAAGCAAGCTAAAT
1 TGAGCTAAAACAAGCTAAAT
17142 CGAGCTCAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (21 bp):
TGAGCTAAAACAAGCTAAATT
Found at i:17148 original size:20 final size:21
Alignment explanation
Indices: 17113--17157 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
17103 AGCTAAAACG
*
17113 AGCTAAATTTGAGCTCAAGCA
1 AGCTAAATTCGAGCTCAAGCA
*
17134 AGCTAAA-TCGAGCTCAAGCG
1 AGCTAAATTCGAGCTCAAGCA
17154 AGCT
1 AGCT
17158 GATTAGAGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (21 bp):
AGCTAAATTCGAGCTCAAGCA
Found at i:17166 original size:20 final size:20
Alignment explanation
Indices: 17113--17167 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
17103 AGCTAAAACG
*
17113 AGCTAAATTTGAGCTCAAGCA
1 AGCTAAA-TAGAGCTCAAGCA
* *
17134 AGCTAAATCGAGCTCAAGCG
1 AGCTAAATAGAGCTCAAGCA
* *
17154 AGCTGATTAGAGCT
1 AGCTAAATAGAGCT
17168 GAATGACGCA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 22 0.76
21 7 0.24
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.22
Consensus pattern (20 bp):
AGCTAAATAGAGCTCAAGCA
Found at i:19866 original size:17 final size:17
Alignment explanation
Indices: 19846--19883 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
19836 CATATTAATA
19846 ACAAATATTAATATAAG
1 ACAAATATTAATATAAG
19863 ACAAATATTAATATAAG
1 ACAAATATTAATATAAG
19880 ACAA
1 ACAA
19884 GTTTAATGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.61, C:0.08, G:0.05, T:0.26
Consensus pattern (17 bp):
ACAAATATTAATATAAG
Found at i:20041 original size:30 final size:30
Alignment explanation
Indices: 19956--20052 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
19946 TAAACTAAAA
* * *
19956 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTAAGCTGAAGT
* * * * *
19986 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTAAGCTGAAGT
20016 TGAGCTAAGGTTTAGCTCGTAAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTAAGCTGAAGT
20045 ATGAGCTA
1 -TGAGCTA
20053 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTAAGCTGAAGT
Found at i:20749 original size:179 final size:179
Alignment explanation
Indices: 20449--20806 Score: 569
Period size: 179 Copynumber: 2.0 Consensus size: 179
20439 CACGGAGTCT
* * *
20449 TCAAGGCATTGTCCTTAGCTCCTCCAACGTCATGAACCTTGTTGTGATCCCAAATGCGTAACACC
1 TCAAGGCATTGTCCTTAGCTCCTCCAACGTCATGAACCTTGTTATCATCCCAAATGCGCAACACC
* *
20514 AATGCAGATAAAGCATCTTGAATTCGCTTGGTTCGAGCTCGATTCATGGGGCCTTTTGGAAGCTC
66 AAGGCAGATAAAGCATCTTGAATTCGCTTGGTTCGAGCTCGAGTCATGGGGCCTTTTGGAAGCTC
*
20579 GATT-GATTCATGATTTGCATTCGAGGATGCCCCAGGCGTGCTCACATCA
131 AATTAG-TTCATGATTTGCATTCGAGGATGCCCCAGGCGTGCTCACATCA
*
20628 TCAAGGCATTGTCCTTAGCTCAC-CCAACGT-ATTGGACCTTGTTATCATCCCAAATGCGCAACA
1 TCAAGGCATTGTCCTTAGCTC-CTCCAACGTCA-TGAACCTTGTTATCATCCCAAATGCGCAACA
* *
20691 CCAAGGCTGATAAAGCATCTTGAATTTGCTTGGTTCGAGCTCGAGTCATGGGGCCTTTTGGAAGC
64 CCAAGGCAGATAAAGCATCTTGAATTCGCTTGGTTCGAGCTCGAGTCATGGGGCCTTTTGGAAGC
* *
20756 TCAATTAGTTCTTGATTTGCATTCGAGGATGCCCCGGGCGTGCTCACATCA
129 TCAATTAGTTCATGATTTGCATTCGAGGATGCCCCAGGCGTGCTCACATCA
20807 CCTACCTAAT
Statistics
Matches: 165, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
178 1 0.01
179 162 0.98
180 2 0.01
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (179 bp):
TCAAGGCATTGTCCTTAGCTCCTCCAACGTCATGAACCTTGTTATCATCCCAAATGCGCAACACC
AAGGCAGATAAAGCATCTTGAATTCGCTTGGTTCGAGCTCGAGTCATGGGGCCTTTTGGAAGCTC
AATTAGTTCATGATTTGCATTCGAGGATGCCCCAGGCGTGCTCACATCA
Done.