Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1117
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: 55023
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:95 original size:12 final size:13
Alignment explanation
Indices: 76--110 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
66 AGTTTAAAAC
*
76 ATTTTTTTTTCGA
1 ATTTTTTTTTCAA
89 ATTTTTTTTTCAA
1 ATTTTTTTTTCAA
102 ATTTTTTTT
1 ATTTTTTTT
111 ACAATCTCGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.17, C:0.06, G:0.03, T:0.74
Consensus pattern (13 bp):
ATTTTTTTTTCAA
Found at i:4513 original size:13 final size:14
Alignment explanation
Indices: 4495--4533 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
4485 ACTAGCTCTC
4495 TTTTTTTTCACAAT
1 TTTTTTTTCACAAT
4509 TTTTTTTTCACAA-
1 TTTTTTTTCACAAT
4522 TTTTTTTTCACA
1 TTTTTTTTCACA
4534 CTTGATATCC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 12 0.48
14 13 0.52
ACGTcount: A:0.21, C:0.15, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTTTTTCACAAT
Found at i:15471 original size:15 final size:15
Alignment explanation
Indices: 15434--15484 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
15424 TTGAGCAAGA
15434 AAAAGAAAAAGAGAG
1 AAAAGAAAAAGAGAG
* *
15449 -AAACAAAAAGAGTG
1 AAAAGAAAAAGAGAG
*
15463 AAAAGAAAAAGAAAG
1 AAAAGAAAAAGAGAG
15478 AAAAGAA
1 AAAAGAA
15485 TGATGAACGT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 12 0.40
15 18 0.60
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (15 bp):
AAAAGAAAAAGAGAG
Found at i:17904 original size:21 final size:23
Alignment explanation
Indices: 17859--17905 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
17849 TCACCTGCAA
* *
17859 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
17882 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
17903 TAA
1 TAA
17906 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:22970 original size:22 final size:22
Alignment explanation
Indices: 22911--22976 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
22901 GGTATTTGGG
* *
22911 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
22932 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* * *
22954 ATTTGGTATGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
22977 TCAAAAGGAC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
21 19 0.50
22 14 0.37
23 5 0.13
ACGTcount: A:0.30, C:0.03, G:0.30, T:0.36
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:24766 original size:15 final size:15
Alignment explanation
Indices: 24746--24799 Score: 92
Period size: 15 Copynumber: 3.7 Consensus size: 15
24736 TAGCTTCTTC
24746 TTTTTTTTCACGAAA
1 TTTTTTTTCACGAAA
24761 TTTTTTTTCACG-AA
1 TTTTTTTTCACGAAA
*
24775 TTTTTTTTCACGAAT
1 TTTTTTTTCACGAAA
24790 TTTTTTTTCA
1 TTTTTTTTCA
24800 ACTTGATATC
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
14 14 0.38
15 23 0.62
ACGTcount: A:0.20, C:0.13, G:0.06, T:0.61
Consensus pattern (15 bp):
TTTTTTTTCACGAAA
Found at i:24796 original size:14 final size:14
Alignment explanation
Indices: 24746--24796 Score: 93
Period size: 14 Copynumber: 3.6 Consensus size: 14
24736 TAGCTTCTTC
24746 TTTTTTTTCACGAAA
1 TTTTTTTTCACG-AA
24761 TTTTTTTTCACGAA
1 TTTTTTTTCACGAA
24775 TTTTTTTTCACGAA
1 TTTTTTTTCACGAA
24789 TTTTTTTT
1 TTTTTTTT
24797 TCAACTTGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
14 24 0.67
15 12 0.33
ACGTcount: A:0.20, C:0.12, G:0.06, T:0.63
Consensus pattern (14 bp):
TTTTTTTTCACGAA
Found at i:24857 original size:10 final size:10
Alignment explanation
Indices: 24842--24879 Score: 51
Period size: 9 Copynumber: 3.7 Consensus size: 10
24832 AACTAAATTT
24842 TTTTTTTGAA
1 TTTTTTTGAA
24852 TTTTTTTTTG-A
1 --TTTTTTTGAA
24863 TTTTTTTGAA
1 TTTTTTTGAA
24873 TTTTTTT
1 TTTTTTT
24880 TGAAGAAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 8 0.32
10 8 0.32
11 1 0.04
12 8 0.32
ACGTcount: A:0.13, C:0.00, G:0.08, T:0.79
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:24857 original size:11 final size:11
Alignment explanation
Indices: 24841--24883 Score: 63
Period size: 11 Copynumber: 4.0 Consensus size: 11
24831 AAACTAAATT
24841 TTTTTTTTGAA
1 TTTTTTTTGAA
24852 TTTTTTTTTG-A
1 -TTTTTTTTGAA
24863 -TTTTTTTGAA
1 TTTTTTTTGAA
24873 TTTTTTTTGAA
1 TTTTTTTTGAA
24884 GAAACTACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 8 0.28
10 1 0.03
11 11 0.38
12 9 0.31
ACGTcount: A:0.16, C:0.00, G:0.09, T:0.74
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:24857 original size:12 final size:12
Alignment explanation
Indices: 24840--24880 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
24830 GAAACTAAAT
24840 TTTTTTTTTGAA
1 TTTTTTTTTGAA
24852 TTTTTTTTTG-A
1 TTTTTTTTTGAA
24863 --TTTTTTTGAA
1 TTTTTTTTTGAA
24873 TTTTTTTT
1 TTTTTTTT
24881 GAAGAAACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 8 0.31
10 1 0.04
11 1 0.04
12 16 0.62
ACGTcount: A:0.12, C:0.00, G:0.07, T:0.80
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:25895 original size:21 final size:23
Alignment explanation
Indices: 25850--25896 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
25840 TCACCTGCAA
* *
25850 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
25873 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
25894 TAA
1 TAA
25897 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:29500 original size:12 final size:12
Alignment explanation
Indices: 29478--29509 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
29468 CATAAAAATT
29478 TAAACTAAGTAAA
1 TAAA-TAAGTAAA
29491 TAAATAAGTAAA
1 TAAATAAGTAAA
29503 TAAATAA
1 TAAATAA
29510 AAATAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.25
Consensus pattern (12 bp):
TAAATAAGTAAA
Found at i:31723 original size:20 final size:20
Alignment explanation
Indices: 31700--31745 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
31690 CCAGCTCGAA
*
31700 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
31720 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
31740 TTAGCT
1 TTAGCT
31746 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:31727 original size:30 final size:30
Alignment explanation
Indices: 31692--31765 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
31682 AGTTTTTCCC
31692 AGCTCGAATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-ATTGAGCTCA-ATTGAGCTTAATTT
* * *
31722 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGATTGAGCTCAATTGAGCTTAATTT
*
31752 AGCTCGTTTGAGCT
1 AGCTCGATTGAGCT
31766 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 3 0.08
30 36 0.92
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGATTGAGCTCAATTGAGCTTAATTT
Found at i:38921 original size:12 final size:12
Alignment explanation
Indices: 38904--38951 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
38894 ATAGTAGTTT
38904 CTCGAAAAAAAA
1 CTCGAAAAAAAA
38916 CTCGAAAAAAAA
1 CTCGAAAAAAAA
* *
38928 TTCAAAAAAAAA
1 CTCGAAAAAAAA
*
38940 TTCGAAAAAAAA
1 CTCGAAAAAAAA
38952 ACTAGTTTCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.69, C:0.12, G:0.06, T:0.12
Consensus pattern (12 bp):
CTCGAAAAAAAA
Found at i:39036 original size:12 final size:13
Alignment explanation
Indices: 38990--39039 Score: 77
Period size: 13 Copynumber: 3.9 Consensus size: 13
38980 GGATATCAAG
38990 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
39003 TT-TGAAAAAAAAA
1 TTGTG-AAAAAAAA
39016 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
39029 TTGT-AAAAAAA
1 TTGTGAAAAAAA
39040 GAGAGCTAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
12 9 0.26
13 24 0.69
14 2 0.06
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (13 bp):
TTGTGAAAAAAAA
Found at i:41216 original size:22 final size:22
Alignment explanation
Indices: 41188--41231 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
41178 TTTTGAACCA
41188 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
41210 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
41232 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:41568 original size:18 final size:19
Alignment explanation
Indices: 41547--41601 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 19
41537 AAAAGAAACC
41547 GAAAAAGAAACAAAA-ATT-
1 GAAAAAGAAA-AAAAGATTG
41565 GAAAAAGAGAAAAAAGATTG
1 GAAAAAGA-AAAAAAGATTG
*
41585 GAGAAAGAAAAGAAAGA
1 GAAAAAGAAAA-AAAGA
41602 GTGCGAGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
18 12 0.38
19 8 0.25
20 12 0.38
ACGTcount: A:0.69, C:0.02, G:0.22, T:0.07
Consensus pattern (19 bp):
GAAAAAGAAAAAAAGATTG
Found at i:41591 original size:20 final size:21
Alignment explanation
Indices: 41568--41611 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
41558 AAAAATTGAA
*
41568 AAAGAGAAA-AAAGATTG-GAG
1 AAAGA-AAAGAAAGAGTGCGAG
41588 AAAGAAAAGAAAGAGTGCGAG
1 AAAGAAAAGAAAGAGTGCGAG
41609 AAA
1 AAA
41612 CAAGTGTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 3 0.14
20 12 0.57
21 6 0.29
ACGTcount: A:0.61, C:0.02, G:0.30, T:0.07
Consensus pattern (21 bp):
AAAGAAAAGAAAGAGTGCGAG
Found at i:49772 original size:39 final size:40
Alignment explanation
Indices: 49711--49788 Score: 124
Period size: 39 Copynumber: 2.0 Consensus size: 40
49701 GGAATTGTTG
49711 AGACGAGGTTGAGTAGGAAAAAGGC-AAGAGAGCGTGAGT
1 AGACGAGGTTGAGTAGGAAAAAGGCGAAGAGAGCGTGAGT
*
49750 AGACGAGGTTGAGT-GGCTAAAAGGCGAAGAGAGCGTGAG
1 AGACGAGGTTGAGTAGG-AAAAAGGCGAAGAGAGCGTGAG
49789 ACGATTAGAG
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
38 2 0.06
39 21 0.58
40 13 0.36
ACGTcount: A:0.36, C:0.09, G:0.42, T:0.13
Consensus pattern (40 bp):
AGACGAGGTTGAGTAGGAAAAAGGCGAAGAGAGCGTGAGT
Done.