Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1230
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: 12949
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Found at i:198 original size:35 final size:35
Alignment explanation
Indices: 159--325 Score: 286
Period size: 35 Copynumber: 4.9 Consensus size: 35
149 TTAATTTTTT
*
159 ATGCCCATCATTCCATGCCTTGATTTTTATATTCC
1 ATGCCCATCATTCCATGCCTTCATTTTTATATTCC
*
194 ATGCCCATCA-TCCAT-CTTTCATTTTT-TATTCC
1 ATGCCCATCATTCCATGCCTTCATTTTTATATTCC
226 ATGCCCATCATTCCATGCCTTCATTTTTATATTCC
1 ATGCCCATCATTCCATGCCTTCATTTTTATATTCC
261 ATGCCCATCATTCCATGCCTTCATTTTTATATTCC
1 ATGCCCATCATTCCATGCCTTCATTTTTATATTCC
*
296 ATTCCCATCATTCCATGCCTTCATTTTTAT
1 ATGCCCATCATTCCATGCCTTCATTTTTAT
326 TTTTTTTTGA
Statistics
Matches: 125, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
32 16 0.13
33 14 0.11
34 15 0.12
35 80 0.64
ACGTcount: A:0.20, C:0.31, G:0.05, T:0.44
Consensus pattern (35 bp):
ATGCCCATCATTCCATGCCTTCATTTTTATATTCC
Found at i:245 original size:67 final size:70
Alignment explanation
Indices: 159--325 Score: 286
Period size: 67 Copynumber: 2.4 Consensus size: 70
149 TTAATTTTTT
* *
159 ATGCCCATCATTCCATGCCTTGATTTTTATATTCCATGCCCATCA-TCCAT-CTTTCATTTTT-T
1 ATGCCCATCATTCCATGCCTTCATTTTTATATTCCATGCCCATCATTCCATGCCTTCATTTTTAT
221 ATTCC
66 ATTCC
226 ATGCCCATCATTCCATGCCTTCATTTTTATATTCCATGCCCATCATTCCATGCCTTCATTTTTAT
1 ATGCCCATCATTCCATGCCTTCATTTTTATATTCCATGCCCATCATTCCATGCCTTCATTTTTAT
291 ATTCC
66 ATTCC
*
296 ATTCCCATCATTCCATGCCTTCATTTTTAT
1 ATGCCCATCATTCCATGCCTTCATTTTTAT
326 TTTTTTTTGA
Statistics
Matches: 94, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
67 44 0.47
68 5 0.05
69 10 0.11
70 35 0.37
ACGTcount: A:0.20, C:0.31, G:0.05, T:0.44
Consensus pattern (70 bp):
ATGCCCATCATTCCATGCCTTCATTTTTATATTCCATGCCCATCATTCCATGCCTTCATTTTTAT
ATTCC
Found at i:5773 original size:20 final size:20
Alignment explanation
Indices: 5748--5868 Score: 82
Period size: 20 Copynumber: 5.5 Consensus size: 20
5738 TTTTAACTAG
5748 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
5768 ATGTATCGATACATCTAGGTAAAAAGACAGA
1 ATGTATCGATACAT-T--G-----A-A-A-A
* *
5799 ATGTATCGATATATTGAAGA
1 ATGTATCGATACATTGAAAA
* * * *
5819 ATATATCGATACATTCATAC
1 ATGTATCGATACATTGAAAA
5839 ATGTATCGATACATT-AAAA
1 ATGTATCGATACATTGAAAA
5858 ATGTATCGATA
1 ATGTATCGATA
5869 TATCTGGGTA
Statistics
Matches: 79, Mismatches: 11, Indels: 23
0.70 0.10 0.20
Matches are distributed among these distances:
19 13 0.16
20 43 0.54
21 1 0.01
22 1 0.01
23 2 0.03
28 2 0.03
29 1 0.01
30 2 0.03
31 14 0.18
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:6826 original size:33 final size:32
Alignment explanation
Indices: 6788--6853 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
6778 CATTGGGTTT
*
6788 AGAAGGGATAATACCAACTTGTGTGGCCTTTAG
1 AGAA-GGATAACACCAACTTGTGTGGCCTTTAG
* ** *
6821 AGAAGGTTGCCACCAACTTGTGTGGGCTTTAG
1 AGAAGGATAACACCAACTTGTGTGGCCTTTAG
6853 A
1 A
6854 AGGGTTACCA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 24 0.86
33 4 0.14
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (32 bp):
AGAAGGATAACACCAACTTGTGTGGCCTTTAG
Found at i:6903 original size:28 final size:28
Alignment explanation
Indices: 6841--7496 Score: 443
Period size: 28 Copynumber: 23.5 Consensus size: 28
6831 CACCAACTTG
* * *
6841 TGTGGGCTTTAGAAGGGTTACCACTGACT
1 TGTGGGCTTT-GAAAGGATGCCACTGACT
* * *
6870 TATGGGCTTTAAAAGGATGCCACTGATT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
** *
6898 TGTGGGCTTCAAAAGG-TGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
6925 TGTAGGCTTCGAAAGGGTGCCACCGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
6953 TAT-GGCTTTGAAAGAGGTTGCCACCGACT
1 TGTGGGCTTTG-AA-AGGATGCCACTGACT
* *
6982 TGTGTGGGTTTCG-AAGGGTGCCACTGACT
1 TGTG-GGCTTT-GAAAGGATGCCACTGACT
* *
7011 TGTGGGTTTTTAAAAGG-TGCCACTGACT
1 TGTGGG-CTTTGAAAGGATGCCACTGACT
*
7039 TATGGGCTTTTGAAAGGATG---CT-AC-
1 TGTGGGC-TTTGAAAGGATGCCACTGACT
7063 --TGGGCTTTTGAAAGGATGCCACT-A--
1 TGTGGGC-TTTGAAAGGATGCCACTGACT
*
7087 ----GGCTTTTGAAAGGTTGCCACTGACT
1 TGTGGGC-TTTGAAAGGATGCCACTGACT
* * *
7112 CGTGGGATTTTTGAAAGGATGCCATTGACT
1 TGTGGG--CTTTGAAAGGATGCCACTGACT
*
7142 CGTGGGCTTTTGAAAGGATGCCACTGACT
1 TGTGGGC-TTTGAAAGGATGCCACTGACT
* * *
7171 CGTGGGCTTTGAAAGGGTGCCACTTACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
7199 TGTGGGCTTTGAAAGAGGTTGCCACCGACTT
1 TGTGGGCTTTG-AA-AGGATGCCACTGAC-T
* *
7230 GTGTGGGCTTTGAAAGGGTGCCACTGATT
1 -TGTGGGCTTTGAAAGGATGCCACTGACT
* *
7259 TGTGGGCTTTTAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
7287 TATGGGCTTTGAAAGGGTGCTACTGAAT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
7315 CGTGGGCTTTTGAAAGGATGCCACTGACT
1 TGTGGGC-TTTGAAAGGATGCCACTGACT
** ** * * *
7344 CAT-GGAATTGGAAGAATGCCACTTACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
7371 TATGGGCTTTAAAAGGGTGCCACTGAAT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
7399 CGTGGGCTTTGAAAAGATACCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
** * * *
7427 CATGGGCTTTGGAAGAATGCCACTCACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
7455 TGTGGGCTTTAAAAGAGGTGTCATTGACT
1 TGTGGGCTTTGAAAG-GATGCCACTGACT
7484 TGTGGGC-TTGAAA
1 TGTGGGCTTTGAAA
7497 AAGGGTCGTA
Statistics
Matches: 507, Mismatches: 90, Indels: 61
0.77 0.14 0.09
Matches are distributed among these distances:
22 38 0.07
23 1 0.00
25 5 0.01
26 2 0.00
27 48 0.09
28 227 0.45
29 118 0.23
30 48 0.09
31 8 0.02
32 12 0.02
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.30
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:7002 original size:86 final size:85
Alignment explanation
Indices: 6861--7301 Score: 233
Period size: 88 Copynumber: 5.3 Consensus size: 85
6851 AGAAGGGTTA
*
6861 CCACTGACTTATGGGCTTT-AAA-AGGATGCCACTGATTTGTGGGCTTCAAAAGGTGCCACTAAC
1 CCACTGACTTATGGGCTTTGAAAGAGGATGCCACCGATTTGTGGGCTTCAAAAGGTGCCACTAAC
*
6924 TTGTAGGCTTCGAAAGGGTG
66 TTGTAGGCTTCGAAAAGGTG
* * * * * *
6944 CCACCGACTTAT-GGCTTTGAAAGAGGTTGCCACCGACTTGTGTGGGTTTCGAAGGGTGCCACTG
1 CCACTGACTTATGGGCTTTGAAAGAGGATGCCACCGA-TT-TGTGGGCTTCAAAAGGTGCCACTA
* * **
7008 ACTTGTGGGTTTTTAAAAGGTG
64 ACTTGTAGGCTTCGAAAAGGTG
* **
7030 CCACTGACTTATGGGCTTTTG-AA-AGGATGCTA-C------TGGGCTTTTGAAAGGATG-C-C-
1 CCACTGACTTATGGGC-TTTGAAAGAGGATGCCACCGATTTGTGGGC-TTCAAAAGG-TGCCACT
*
7083 -AC---TAGGCTTTTG-AAAGGTTG
63 AACTTGTAGGC-TTCGAAAAGG-TG
** * ** * * **
7103 CCACTGACTCGTGGGATTTTTG-AA-AGGATGCCATTGACTCGTGGGCTTTTGAAAGGATGCCAC
1 CCACTGACTTATGGG--CTTTGAAAGAGGATGCCACCGATTTGTGGGC-TTCAAAAGG-TGCCAC
* * * * *
7166 TGACTCGTGGGCTTTGAAAGGGTG
62 TAACTTGTAGGCTTCGAAAAGGTG
* * * * *
7190 CCACTTACTTGTGGGCTTTGAAAGAGGTTGCCACCGACTTGTGTGGGCTTTGAAAGGGTGCCACT
1 CCACTGACTTATGGGCTTTGAAAGAGGATGCCACCGA-TT-TGTGGGC-TTCAAAAGGTGCCACT
* * * ** *
7255 GATTTGTGGGCTTTTAAAGGGTG
63 AACTTGTAGGCTTCGAAAAGGTG
7278 CCACTGACTTATGGGCTTTGAAAG
1 CCACTGACTTATGGGCTTTGAAAG
7302 GGTGCTACTG
Statistics
Matches: 283, Mismatches: 44, Indels: 57
0.74 0.11 0.15
Matches are distributed among these distances:
72 8 0.03
73 18 0.06
74 14 0.05
75 2 0.01
77 5 0.02
78 8 0.03
79 2 0.01
81 18 0.06
82 7 0.02
83 15 0.05
84 11 0.04
85 9 0.03
86 57 0.20
87 34 0.12
88 62 0.22
89 13 0.05
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (85 bp):
CCACTGACTTATGGGCTTTGAAAGAGGATGCCACCGATTTGTGGGCTTCAAAAGGTGCCACTAAC
TTGTAGGCTTCGAAAAGGTG
Found at i:7069 original size:22 final size:22
Alignment explanation
Indices: 7041--7108 Score: 109
Period size: 22 Copynumber: 3.1 Consensus size: 22
7031 CACTGACTTA
*
7041 TGGGCTTTTGAAAGGATGCTAC
1 TGGGCTTTTGAAAGGATGCCAC
7063 TGGGCTTTTGAAAGGATGCCAC
1 TGGGCTTTTGAAAGGATGCCAC
* *
7085 TAGGCTTTTGAAAGGTTGCCAC
1 TGGGCTTTTGAAAGGATGCCAC
7107 TG
1 TG
7109 ACTCGTGGGA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.22, C:0.16, G:0.31, T:0.31
Consensus pattern (22 bp):
TGGGCTTTTGAAAGGATGCCAC
Found at i:7558 original size:13 final size:13
Alignment explanation
Indices: 7513--7579 Score: 52
Period size: 13 Copynumber: 5.2 Consensus size: 13
7503 CGTATTGATG
*
7513 AAAATTTCTTGAC
1 AAAAGTTCTTGAC
7526 -AAAGTT-TTGAC
1 AAAAGTTCTTGAC
*
7537 AAACA-TTCTCGAC
1 AAA-AGTTCTTGAC
7550 AAAAGTTCTTGA-
1 AAAAGTTCTTGAC
*
7562 AGATAATTTCTTGAC
1 A-A-AAGTTCTTGAC
7577 AAA
1 AAA
7580 TGGAAAATTG
Statistics
Matches: 43, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
11 5 0.12
12 11 0.26
13 16 0.37
14 10 0.23
15 1 0.02
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (13 bp):
AAAAGTTCTTGAC
Found at i:8568 original size:11 final size:11
Alignment explanation
Indices: 8554--8587 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
8544 TTCTTTTTTA
8554 TTTTTTTTTGT
1 TTTTTTTTTGT
8565 TTTTTTTTTGGT
1 TTTTTTTTT-GT
*
8577 TTTTGTTTTGT
1 TTTTTTTTTGT
8588 ACGAAGGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (11 bp):
TTTTTTTTTGT
Found at i:8569 original size:12 final size:12
Alignment explanation
Indices: 8554--8586 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
8544 TTCTTTTTTA
8554 TTTTTTTTT-GT
1 TTTTTTTTTGGT
8565 TTTTTTTTTGGT
1 TTTTTTTTTGGT
*
8577 TTTTGTTTTG
1 TTTTTTTTTG
8587 TACGAAGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (12 bp):
TTTTTTTTTGGT
Found at i:12809 original size:13 final size:13
Alignment explanation
Indices: 12791--12817 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12781 TACTCAAATG
12791 TATCGATACATTA
1 TATCGATACATTA
12804 TATCGATACATTA
1 TATCGATACATTA
12817 T
1 T
12818 TCAATGTATC
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:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (13 bp):
TATCGATACATTA
Done.