Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2238
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: 33527
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4827 original size:10 final size:10
Alignment explanation
Indices: 4778--4840 Score: 63
Period size: 10 Copynumber: 5.8 Consensus size: 10
4768 TTGGAGTAAC
*
4778 AAAAAAATCA
1 AAAAAAATGA
*
4788 AAAAAAATCA
1 AAAAAAATGA
4798 AAAAAAATTGA
1 AAAAAAA-TGA
4809 TTGAAAAAAATGA
1 ---AAAAAAATGA
4822 AAAAAAAGTGA
1 AAAAAAA-TGA
4833 AAAAAAAT
1 AAAAAAAT
4841 CGAGCAAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
10 25 0.53
11 12 0.26
13 3 0.06
14 7 0.15
ACGTcount: A:0.75, C:0.03, G:0.08, T:0.14
Consensus pattern (10 bp):
AAAAAAATGA
Found at i:4839 original size:24 final size:24
Alignment explanation
Indices: 4787--4839 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
4777 CAAAAAAATC
* **
4787 AAAAAAAATCAAAAAAAATTGATT
1 AAAAAAAATCAAAAAAAAGTGAAA
* *
4811 GAAAAAAATGAAAAAAAAGTGAAA
1 AAAAAAAATCAAAAAAAAGTGAAA
4835 AAAAA
1 AAAAA
4840 TCGAGCAAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.75, C:0.02, G:0.09, T:0.13
Consensus pattern (24 bp):
AAAAAAAATCAAAAAAAAGTGAAA
Found at i:4850 original size:34 final size:34
Alignment explanation
Indices: 4777--4852 Score: 93
Period size: 34 Copynumber: 2.2 Consensus size: 34
4767 ATTGGAGTAA
*
4777 CAAAAAAATCAAAAAAAATCAAAAAAAATTGATTG
1 CAAAAAAATCAAAAAAAATCAAAAAAAATCGA-TG
* *
4812 -AAAAAAATGAAAAAAAAGTGAAAAAAAATCGA-G
1 CAAAAAAATCAAAAAAAA-TCAAAAAAAATCGATG
4845 CAAAAAAA
1 CAAAAAAA
4853 AAGAAAAGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
33 1 0.03
34 23 0.64
35 12 0.33
ACGTcount: A:0.72, C:0.07, G:0.09, T:0.12
Consensus pattern (34 bp):
CAAAAAAATCAAAAAAAATCAAAAAAAATCGATG
Found at i:4851 original size:35 final size:34
Alignment explanation
Indices: 4778--4864 Score: 93
Period size: 35 Copynumber: 2.5 Consensus size: 34
4768 TTGGAGTAAC
* * ***
4778 AAAAAAATCAAAAAAAATCAAAAAAAATTGATTG
1 AAAAAAATGAAAAAAAATCAAAAAAAATCGAGCA
*
4812 AAAAAAATGAAAAAAAAGTGAAAAAAAATCGAGCA
1 AAAAAAATGAAAAAAAA-TCAAAAAAAATCGAGCA
*
4847 AAAAAAAAGAAAAGAAAA
1 AAAAAAATGAAAA-AAAA
4865 AAAAAGGTGA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
34 16 0.36
35 24 0.55
36 4 0.09
ACGTcount: A:0.75, C:0.05, G:0.10, T:0.10
Consensus pattern (34 bp):
AAAAAAATGAAAAAAAATCAAAAAAAATCGAGCA
Found at i:10887 original size:21 final size:19
Alignment explanation
Indices: 10860--10935 Score: 52
Period size: 21 Copynumber: 4.0 Consensus size: 19
10850 TTTTCAAGCT
10860 CTCTTTCAATTTCTTTTTC
1 CTCTTTCAATTTCTTTTTC
*
10879 CAATCTTTC--TTT-TTCTT-
1 C--TCTTTCAATTTCTTTTTC
*
10896 CTTTTTCAATTTCTTTTTC
1 CTCTTTCAATTTCTTTTTC
* *
10915 TTTTCTTTCGATTTCTTTTTC
1 --CTCTTTCAATTTCTTTTTC
10936 TCGCTCGCAC
Statistics
Matches: 43, Mismatches: 6, Indels: 14
0.68 0.10 0.22
Matches are distributed among these distances:
15 5 0.12
17 4 0.09
18 8 0.19
19 4 0.09
21 22 0.51
ACGTcount: A:0.09, C:0.22, G:0.01, T:0.67
Consensus pattern (19 bp):
CTCTTTCAATTTCTTTTTC
Found at i:10930 original size:36 final size:36
Alignment explanation
Indices: 10863--10931 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
10853 TCAAGCTCTC
**
10863 TTTCAATTTCTTTTTCCAATCTTTCTTTTTCTTCTT
1 TTTCAATTTCTTTTTCCAATCTTTCGATTTCTTCTT
***
10899 TTTCAATTTCTTTTTCTTTTCTTTCGATTTCTT
1 TTTCAATTTCTTTTTCCAATCTTTCGATTTCTT
10932 TTTCTCGCTC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.10, C:0.20, G:0.01, T:0.68
Consensus pattern (36 bp):
TTTCAATTTCTTTTTCCAATCTTTCGATTTCTTCTT
Found at i:10936 original size:21 final size:21
Alignment explanation
Indices: 10870--10936 Score: 82
Period size: 21 Copynumber: 3.0 Consensus size: 21
10860 CTCTTTCAAT
10870 TTCTTTTTCCAATCTTTCTTTTTC
1 TTCTTTTT-CAA--TTTCTTTTTC
10894 TTCTTTTTCAATTTCTTTTTC
1 TTCTTTTTCAATTTCTTTTTC
*
10915 TT-TTCTTTCGATTTCTTTTTC
1 TTCTT-TTTCAATTTCTTTTTC
10936 T
1 T
10937 CGCTCGCACT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
20 2 0.05
21 28 0.68
23 3 0.07
24 8 0.20
ACGTcount: A:0.07, C:0.21, G:0.01, T:0.70
Consensus pattern (21 bp):
TTCTTTTTCAATTTCTTTTTC
Found at i:11445 original size:20 final size:20
Alignment explanation
Indices: 11399--11445 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
11389 AGCTCGTTTC
*
11399 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
11419 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
11439 CAGCTCA
1 CAGCTCA
11446 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:12974 original size:10 final size:11
Alignment explanation
Indices: 12948--12978 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
12938 GGAAATTTGA
12948 AAAAGAAAATTC
1 AAAA-AAAATTC
12960 AAAAAAAATTC
1 AAAAAAAATTC
12971 AAAAAAAA
1 AAAAAAAA
12979 AATCGAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.77, C:0.06, G:0.03, T:0.13
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:12975 original size:12 final size:12
Alignment explanation
Indices: 12947--12979 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12937 AGGAAATTTG
12947 AAAAAGAAAATTC
1 AAAAA-AAAATTC
12960 -AAAAAAAATTC
1 AAAAAAAAATTC
12971 AAAAAAAAA
1 AAAAAAAAA
12980 ATCGAAGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 7 0.37
12 12 0.63
ACGTcount: A:0.79, C:0.06, G:0.03, T:0.12
Consensus pattern (12 bp):
AAAAAAAAATTC
Found at i:14112 original size:48 final size:48
Alignment explanation
Indices: 14011--14116 Score: 128
Period size: 48 Copynumber: 2.2 Consensus size: 48
14001 GAGTGTCACG
*
14011 GAAAAAGAAATTGAGATTGAAAAAGGATGTGAAAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAAAAAGAGAAAGAAATC
* * *
14059 AAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAA-AGAGA-AAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA--AAAAGAGAAAGAAATC
14107 GAAAAAGAAA
1 GAAAAAGAAA
14117 GAAAAGACAA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
48 38 0.76
49 8 0.16
50 4 0.08
ACGTcount: A:0.60, C:0.02, G:0.24, T:0.14
Consensus pattern (48 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAAAAAGAGAAAGAAATC
Found at i:15831 original size:20 final size:20
Alignment explanation
Indices: 15785--15831 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
15775 AGCTCGTTTC
*
15785 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
15805 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
15825 CAGCTCA
1 CAGCTCA
15832 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:17902 original size:15 final size:17
Alignment explanation
Indices: 17877--17911 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
17867 AATATGTCTT
17877 ATTTAGTTATAAT-TTA
1 ATTTAGTTATAATGTTA
17893 ATTT-GTTATAATGTTA
1 ATTTAGTTATAATGTTA
17909 ATT
1 ATT
17912 AGCATGTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (17 bp):
ATTTAGTTATAATGTTA
Found at i:19000 original size:20 final size:20
Alignment explanation
Indices: 18954--19000 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
18944 AGCTCGTTTC
*
18954 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
18974 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
18994 CAGCTCA
1 CAGCTCA
19001 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:20692 original size:20 final size:19
Alignment explanation
Indices: 20669--20724 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
20659 GTTCATTCAA
20669 CTCAATTTTAGCTCATCGAG
1 CTCAATTTTAGCTCATC-AG
* *
20689 CTCACTCTTAGCTCAATCAG
1 CTCAATTTTAGCTC-ATCAG
20709 CTC-ATTTTAAGCTCAT
1 CTCAATTTT-AGCTCAT
20725 TTGCGTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
19 5 0.17
20 22 0.73
21 3 0.10
ACGTcount: A:0.25, C:0.29, G:0.11, T:0.36
Consensus pattern (19 bp):
CTCAATTTTAGCTCATCAG
Found at i:22796 original size:27 final size:27
Alignment explanation
Indices: 22765--22942 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
22755 TAAATTGTAC
22765 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
22792 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
22818 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
22846 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
22874 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
22901 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
22928 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
22943 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:22879 original size:82 final size:81
Alignment explanation
Indices: 22766--22921 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
22756 AAATTGTACA
* *
22766 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
22830 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
22847 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
22912 TGCGAGTTGA
65 TGCGAATTGA
22922 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:22933 original size:82 final size:81
Alignment explanation
Indices: 22762--22942 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
22752 GATTAAATTG
* *
22762 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
22827 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
22843 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
22907 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
22925 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
22943 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:30877 original size:14 final size:13
Alignment explanation
Indices: 30858--30902 Score: 72
Period size: 13 Copynumber: 3.4 Consensus size: 13
30848 CCGTATGCAA
*
30858 TTTTTTTCAAATT
1 TTTTTTTCAATTT
30871 TTTTTTTCAATTT
1 TTTTTTTCAATTT
30884 TTTTTTCTCAATTT
1 TTTTTT-TCAATTT
30898 TTTTT
1 TTTTT
30903 GATTTTTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
13 18 0.60
14 12 0.40
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTTTCAATTT
Done.