Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1342
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: 61245
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:11102 original size:20 final size:21
Alignment explanation
Indices: 11079--11126 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
11069 AGCTCCGTCC
11079 AGCTCAACTT-AGCTCATTTG
1 AGCTCAACTTCAGCTCATTTG
** *
11099 AGCTC-GTTTCAGCTCGTTTG
1 AGCTCAACTTCAGCTCATTTG
11119 AGCTCAAC
1 AGCTCAAC
11127 CGAGCTTACT
Statistics
Matches: 21, Mismatches: 5, Indels: 3
0.72 0.17 0.10
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33
Consensus pattern (21 bp):
AGCTCAACTTCAGCTCATTTG
Found at i:11143 original size:31 final size:31
Alignment explanation
Indices: 11105--11179 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
11095 TTTGAGCTCG
* **
11105 TTTCAGCTCGTTTGAGCTCAACCGAGCTTAC
1 TTTCAGCTCCTTCAAGCTCAACCGAGCTTAC
11136 TTTCAGCTCCTTCAAGCTCAACCGAGCTTAC
1 TTTCAGCTCCTTCAAGCTCAACCGAGCTTAC
11167 TTTCAGCTCCTTC
1 TTTCAGCTCCTTC
11180 TTTCTTCCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.19, C:0.33, G:0.15, T:0.33
Consensus pattern (31 bp):
TTTCAGCTCCTTCAAGCTCAACCGAGCTTAC
Found at i:14864 original size:15 final size:15
Alignment explanation
Indices: 14844--14891 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
14834 TCAAAGATGG
14844 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
14859 GTTTATGTAGATGGA
1 GTTTATGGATATGAA
*
14874 -TTTATGGATATAAA
1 GTTTATGGATATGAA
14888 GTTT
1 GTTT
14892 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:14871 original size:29 final size:29
Alignment explanation
Indices: 14838--14897 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
14828 AAGGATTCAA
* *
14838 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGATTTATGGATATAAAGTTTATGT
*
14867 AGATGGATTTATGGATATAAAGTTTTTGT
1 AGATGGATTTATGGATATAAAGTTTATGT
14896 AG
1 AG
14898 GTTTGGTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (29 bp):
AGATGGATTTATGGATATAAAGTTTATGT
Found at i:16783 original size:12 final size:11
Alignment explanation
Indices: 16739--16781 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
16729 ACACCTCTCC
16739 TTTTTTTCGAA
1 TTTTTTTCGAA
*
16750 TTTTTTTTGAA
1 TTTTTTTCGAA
*
16761 TTTTTTT-AAA
1 TTTTTTTCGAA
16771 TTTTTTTCGAA
1 TTTTTTTCGAA
16782 ATATTTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.21, C:0.05, G:0.07, T:0.67
Consensus pattern (11 bp):
TTTTTTTCGAA
Found at i:16788 original size:21 final size:21
Alignment explanation
Indices: 16748--16788 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
16738 CTTTTTTTCG
* * *
16748 AATTTTTTTTGAATTTTTTTA
1 AATTTTTTTCGAAATATTTTA
16769 AATTTTTTTCGAAATATTTT
1 AATTTTTTTCGAAATATTTT
16789 TTAATATACT
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:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (21 bp):
AATTTTTTTCGAAATATTTTA
Found at i:19065 original size:20 final size:20
Alignment explanation
Indices: 19042--19089 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
19032 TCCCAACTCG
19042 ATTTAGCTCACATGAGCTCA
1 ATTTAGCTCACATGAGCTCA
***
19062 ATTTAGCTCGTTTGAGCTCA
1 ATTTAGCTCACATGAGCTCA
19082 ATTTAGCT
1 ATTTAGCT
19090 TACTTTAGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.38
Consensus pattern (20 bp):
ATTTAGCTCACATGAGCTCA
Found at i:19069 original size:10 final size:10
Alignment explanation
Indices: 19042--19100 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
19032 TCCCAACTCG
19042 ATTTAGCTCA
1 ATTTAGCTCA
*
19052 CA-TGAGCTCA
1 -ATTTAGCTCA
19062 ATTTAGCTC-
1 ATTTAGCTCA
*
19071 GTTTGAGCTCA
1 ATTT-AGCTCA
*
19082 ATTTAGCTTA
1 ATTTAGCTCA
*
19092 CTTTAGCTC
1 ATTTAGCTC
19101 GTTTGAGCTT
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
9 4 0.11
10 30 0.79
11 4 0.11
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (10 bp):
ATTTAGCTCA
Found at i:19081 original size:30 final size:30
Alignment explanation
Indices: 19038--19109 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
19028 TTTTTCCCAA
19038 CTCGATTT-AGCTCACA-TGAGCTCAATTTAG
1 CTCG-TTTGAGCTCA-ATTGAGCTCAATTTAG
* * *
19068 CTCGTTTGAGCTCAATTTAGCTTACTTTAG
1 CTCGTTTGAGCTCAATTGAGCTCAATTTAG
19098 CTCGTTTGAGCT
1 CTCGTTTGAGCT
19110 TGGCTTAAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 4 0.11
30 33 0.89
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.39
Consensus pattern (30 bp):
CTCGTTTGAGCTCAATTGAGCTCAATTTAG
Found at i:19099 original size:20 final size:20
Alignment explanation
Indices: 19042--19100 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
19032 TCCCAACTCG
* * *
19042 ATTTAGCTCACATGAGCTCA
1 ATTTAGCTTACTTTAGCTCA
19062 ATTTAGC-T-CGTTTGAGCTCA
1 ATTTAGCTTAC-TTT-AGCTCA
19082 ATTTAGCTTACTTTAGCTC
1 ATTTAGCTTACTTTAGCTC
19101 GTTTGAGCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 25 0.78
21 4 0.12
22 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (20 bp):
ATTTAGCTTACTTTAGCTCA
Found at i:20735 original size:16 final size:16
Alignment explanation
Indices: 20696--20736 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
20686 CAAAAAAATC
20696 AAAAAAAA-TTGATTG
1 AAAAAAAATTTGATTG
20711 AAAAAAAATTTGATTG
1 AAAAAAAATTTGATTG
20727 AAAAAAAATT
1 AAAAAAAATT
20737 CAAAAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 8 0.32
16 17 0.68
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (16 bp):
AAAAAAAATTTGATTG
Found at i:21861 original size:18 final size:18
Alignment explanation
Indices: 21835--21920 Score: 64
Period size: 18 Copynumber: 4.6 Consensus size: 18
21825 AAATTGAAAG
*
21835 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
* *
21853 AAAAGAAAAAGAAATCAA
1 AAAAGAAAAAGAAAACGA
** * *
21871 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAACGA
* *
21889 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-CGA
21910 AAAAGAAAAAG
1 AAAAGAAAAAG
21921 CGAAAAAAGA
Statistics
Matches: 50, Mismatches: 15, Indels: 5
0.71 0.21 0.07
Matches are distributed among these distances:
18 31 0.62
19 5 0.10
20 8 0.16
21 6 0.12
ACGTcount: A:0.73, C:0.03, G:0.17, T:0.06
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:21863 original size:6 final size:6
Alignment explanation
Indices: 21831--21920 Score: 58
Period size: 6 Copynumber: 14.7 Consensus size: 6
21821 AAAGAAATTG
* * * **
21831 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATCA-AA AAAGTG
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA A-AAGAA AAAGAA
* * *
21878 AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA AAAGAA AAAG
1 AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA AAAGAA AAAG
21921 CGAAAAAAGA
Statistics
Matches: 63, Mismatches: 16, Indels: 11
0.70 0.18 0.12
Matches are distributed among these distances:
5 4 0.06
6 47 0.75
7 8 0.13
8 4 0.06
ACGTcount: A:0.73, C:0.03, G:0.18, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:21900 original size:14 final size:13
Alignment explanation
Indices: 21881--21918 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
21871 AAAAGTGAGA
21881 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
21893 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
21908 GAAAAAGAAAA
1 GAAAAAGAAAA
21919 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:21915 original size:13 final size:12
Alignment explanation
Indices: 21817--21918 Score: 50
Period size: 12 Copynumber: 8.0 Consensus size: 12
21807 AGAAAGAGAT
*
21817 TGAAAAAGAAAT
1 TGAAAAAGAAAA
21829 TG--AAAGAAAA
1 TGAAAAAGAAAA
*
21839 -CAAAAAGAAAA
1 TGAAAAAGAAAA
*
21850 CGAAAAAGAAAA
1 TGAAAAAGAAAA
*
21862 AGAAATCAA-AAAA
1 TGAAA--AAGAAAA
21875 GTGAGAGAAAAAGAAAA
1 -T----GAAAAAGAAAA
21892 TGAAGAAAAGAAAA
1 TG-A-AAAAGAAAA
21906 TTGAAAAAGAAAA
1 -TGAAAAAGAAAA
21919 AGCGAAAAAA
Statistics
Matches: 71, Mismatches: 5, Indels: 27
0.69 0.05 0.26
Matches are distributed among these distances:
10 7 0.10
11 8 0.11
12 17 0.24
13 14 0.20
14 12 0.17
15 2 0.03
16 3 0.04
17 4 0.06
18 4 0.06
ACGTcount: A:0.72, C:0.03, G:0.18, T:0.08
Consensus pattern (12 bp):
TGAAAAAGAAAA
Found at i:21932 original size:21 final size:21
Alignment explanation
Indices: 21882--21932 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
21872 AAAGTGAGAG
*
21882 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
21903 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
21924 AAAAAGAAA
1 AAAAAGAAA
21933 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:23796 original size:20 final size:20
Alignment explanation
Indices: 23773--23826 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
23763 AGTTTTTCCC
*
23773 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
23793 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
23813 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
23827 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:23808 original size:30 final size:30
Alignment explanation
Indices: 23773--23846 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
23763 AGTTTTTCCC
23773 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
23803 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
23833 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
23847 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:23836 original size:20 final size:20
Alignment explanation
Indices: 23773--23837 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
23763 AGTTTTTCCC
* * * *
23773 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
23793 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
23812 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
23833 AGCTC
1 AGCTC
23838 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:28561 original size:20 final size:20
Alignment explanation
Indices: 28515--28561 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
28505 AGCTCGTTTC
*
28515 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
28535 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
28555 CAGCTCA
1 CAGCTCA
28562 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:30058 original size:10 final size:11
Alignment explanation
Indices: 30043--30072 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
30033 ATTGGAGTAA
30043 AAAAAAAATC-
1 AAAAAAAATCG
30053 AAAAAAAATCG
1 AAAAAAAATCG
30064 AAAAAAAAT
1 AAAAAAAAT
30073 TGATTGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.80, C:0.07, G:0.03, T:0.10
Consensus pattern (11 bp):
AAAAAAAATCG
Found at i:30104 original size:11 final size:11
Alignment explanation
Indices: 30090--30152 Score: 63
Period size: 11 Copynumber: 5.4 Consensus size: 11
30080 AAAAAAAAAA
30090 AAAAAAAAGTG
1 AAAAAAAAGTG
*
30101 AAAAAAAATCGAG
1 AAAAAAAA--GTG
30114 CAAAAAAAAGTG
1 -AAAAAAAAGTG
**
30126 AGAAAAAAAAAG
1 A-AAAAAAAGTG
30138 AAAAAAAAGTG
1 AAAAAAAAGTG
30149 AAAA
1 AAAA
30153 GTCTTGCGAG
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
11 21 0.50
12 11 0.26
13 2 0.05
14 8 0.19
ACGTcount: A:0.75, C:0.03, G:0.16, T:0.06
Consensus pattern (11 bp):
AAAAAAAAGTG
Found at i:30108 original size:48 final size:47
Alignment explanation
Indices: 30041--30152 Score: 140
Period size: 48 Copynumber: 2.4 Consensus size: 47
30031 GTATTGGAGT
* *
30041 AAAAAAAAAA-TCAAAAAAAATCG--AAAAAAAATTGATTGAAAAAAAAA
1 AAAAAAAAAAGTGAAAAAAAATCGACAAAAAAAAGTGA--G-AAAAAAAA
30088 AAAAAAAAAAGTGAAAAAAAATCGAGCAAAAAAAAGTGAGAAAAAAAA
1 AAAAAAAAAAGTGAAAAAAAATCGA-CAAAAAAAAGTGAGAAAAAAAA
*
30136 AGAAAAAAAAGTGAAAA
1 AAAAAAAAAAGTGAAAA
30153 GTCTTGCGAG
Statistics
Matches: 58, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
47 10 0.17
48 36 0.62
49 1 0.02
51 11 0.19
ACGTcount: A:0.76, C:0.04, G:0.12, T:0.09
Consensus pattern (47 bp):
AAAAAAAAAAGTGAAAAAAAATCGACAAAAAAAAGTGAGAAAAAAAA
Found at i:30118 original size:14 final size:13
Alignment explanation
Indices: 30090--30149 Score: 60
Period size: 10 Copynumber: 4.9 Consensus size: 13
30080 AAAAAAAAAA
30090 AAAAAAAAGT--G
1 AAAAAAAAGTGAG
30101 AAAAAAAA-TCGAG
1 AAAAAAAAGT-GAG
30114 CAAAAAAAAGTGAG
1 -AAAAAAAAGTGAG
30128 AAAAAAAA---AG
1 AAAAAAAAGTGAG
30138 AAAAAAAAGTGA
1 AAAAAAAAGTGA
30150 AAAGTCTTGC
Statistics
Matches: 41, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
10 11 0.27
11 8 0.20
13 10 0.24
14 11 0.27
15 1 0.02
ACGTcount: A:0.73, C:0.03, G:0.17, T:0.07
Consensus pattern (13 bp):
AAAAAAAAGTGAG
Found at i:30120 original size:37 final size:37
Alignment explanation
Indices: 30041--30122 Score: 96
Period size: 38 Copynumber: 2.2 Consensus size: 37
30031 GTATTGGAGT
** *
30041 AAAAAAAAAATCAAAAAAAATCGAAAAAAAATTGATTG-
1 AAAAAAAAAAAAAAAAAAAATCGAAAAAAAATCGA--GC
*
30079 AAAAAAAAAAAAAAAAAAAGT-GAAAAAAAATCGAGC
1 AAAAAAAAAAAAAAAAAAAATCGAAAAAAAATCGAGC
30115 AAAAAAAA
1 AAAAAAAA
30123 GTGAGAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
35 1 0.03
36 8 0.21
37 12 0.31
38 18 0.46
ACGTcount: A:0.77, C:0.05, G:0.09, T:0.10
Consensus pattern (37 bp):
AAAAAAAAAAAAAAAAAAAATCGAAAAAAAATCGAGC
Found at i:31251 original size:48 final size:47
Alignment explanation
Indices: 31172--31277 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
31162 GAGTGTCATG
*
31172 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
31220 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
31268 GAAAAAGAAA
1 GAAAAAGAAA
31278 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:32993 original size:20 final size:20
Alignment explanation
Indices: 32947--32984 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
32937 AGCTCGTTTC
*
32947 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
*
32967 CAACTCACTCAAGCTCAA
1 CAGCTCACTCAAGCTCAA
32985 TTTAGCTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.37, G:0.13, T:0.18
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:33873 original size:6 final size:6
Alignment explanation
Indices: 33862--33887 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
33852 GTAAATAAAT
33862 AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AA
33888 CTTTACAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:35285 original size:23 final size:22
Alignment explanation
Indices: 35233--35285 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
35223 TCCACGTCTT
*
35233 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
35255 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
35278 TTTCTTTT
1 TTTCTTTT
35286 TCACTTCAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:35292 original size:24 final size:23
Alignment explanation
Indices: 35243--35292 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
35233 TTTCTTTTGT
*
35243 TTCTTTTTCTAATTCATTTTCTC
1 TTCTTTTTCTAATTCATTTTCAC
*
35266 TTCTTTCTTC-AATTTCTTTTTCAC
1 TTCTTT-TTCTAA-TTCATTTTCAC
35290 TTC
1 TTC
35293 AATCTCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.64
Consensus pattern (23 bp):
TTCTTTTTCTAATTCATTTTCAC
Found at i:37951 original size:28 final size:28
Alignment explanation
Indices: 37915--37970 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
37905 GATTCAAAGT
* *
37915 ATGGGTTTATGGATA-GAAGTTTATGTAG
1 ATGGATTTATGGATATAAAGTTT-TGTAG
37943 ATGGATTTATGGATATAAAGTTTTGTAG
1 ATGGATTTATGGATATAAAGTTTTGTAG
37971 GTTTGGGTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 19 0.76
29 6 0.24
ACGTcount: A:0.30, C:0.00, G:0.29, T:0.41
Consensus pattern (28 bp):
ATGGATTTATGGATATAAAGTTTTGTAG
Found at i:39852 original size:10 final size:10
Alignment explanation
Indices: 39839--39890 Score: 50
Period size: 10 Copynumber: 4.7 Consensus size: 10
39829 TTTCGAATTT
*
39839 TTTTTTTGAA
1 TTTTTTTAAA
39849 TTTTTTTAAA
1 TTTTTTTAAA
39859 TTTTTTTCGAAA
1 TTTTTTT--AAA
39871 TATTTTTTAATA
1 T-TTTTTTAA-A
39883 TCTTTTTT
1 T-TTTTTT
39891 TATCACTACT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
10 16 0.44
11 2 0.06
12 12 0.33
13 6 0.17
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.69
Consensus pattern (10 bp):
TTTTTTTAAA
Found at i:39865 original size:13 final size:13
Alignment explanation
Indices: 39823--39855 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
39813 AACCTTCTCC
39823 TTTTTTTTTCGAA
1 TTTTTTTTTCGAA
*
39836 TTTTTTTTTTGAA
1 TTTTTTTTTCGAA
39849 TTTTTTT
1 TTTTTTT
39856 AAATTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.03, G:0.06, T:0.79
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Found at i:39876 original size:13 final size:12
Alignment explanation
Indices: 39825--39878 Score: 51
Period size: 13 Copynumber: 4.6 Consensus size: 12
39815 CCTTCTCCTT
*
39825 TTTTTTTCGAATT
1 TTTTTTTCGAA-A
*
39838 TTTTTTTTG-AA
1 TTTTTTTCGAAA
39849 TTTTTTT--AAA
1 TTTTTTTCGAAA
39859 TTTTTTTCGAAA
1 TTTTTTTCGAAA
39871 TATTTTTT
1 T-TTTTTT
39879 AATATCTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
10 9 0.26
11 7 0.20
12 5 0.14
13 14 0.40
ACGTcount: A:0.20, C:0.04, G:0.06, T:0.70
Consensus pattern (12 bp):
TTTTTTTCGAAA
Found at i:43885 original size:17 final size:17
Alignment explanation
Indices: 43862--43906 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
43852 CAAAAAAATC
43862 AAAAAAAAATTTGATTG
1 AAAAAAAAATTTGATTG
*
43879 GAAAAAAAATTTGATTG
1 AAAAAAAAATTTGATTG
43896 AAAAAAAAATT
1 AAAAAAAAATT
43907 CAAAAAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.62, C:0.00, G:0.11, T:0.27
Consensus pattern (17 bp):
AAAAAAAAATTTGATTG
Found at i:45090 original size:14 final size:14
Alignment explanation
Indices: 45072--45110 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
45062 AAAGTGAGAA
45072 GAGAAAAGAAAA-T
1 GAGAAAAGAAAATT
45085 GCAGAAAAGAAAATT
1 G-AGAAAAGAAAATT
45100 GA-AAAAGAAAA
1 GAGAAAAGAAAA
45111 AGCGAAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 10 0.42
14 12 0.50
15 2 0.08
ACGTcount: A:0.69, C:0.03, G:0.21, T:0.08
Consensus pattern (14 bp):
GAGAAAAGAAAATT
Found at i:45103 original size:21 final size:21
Alignment explanation
Indices: 45047--45104 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 21
45037 AGAAAACAAA
*
45047 AGAAAAG-AAATTCAAAAAGTG
1 AGAAAAGAAAATT-GAAAAGTG
*
45068 AGAAGAGAAAA--GAAAA-TG
1 AGAAAAGAAAATTGAAAAGTG
45086 CAGAAAAGAAAATTGAAAA
1 -AGAAAAGAAAATTGAAAA
45105 AGAAAAAGCG
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
18 2 0.07
19 14 0.47
21 11 0.37
22 3 0.10
ACGTcount: A:0.66, C:0.03, G:0.21, T:0.10
Consensus pattern (21 bp):
AGAAAAGAAAATTGAAAAGTG
Found at i:45105 original size:27 final size:28
Alignment explanation
Indices: 45075--45131 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
45065 GTGAGAAGAG
*
45075 AAAAGAAAATGC-AGAA-AAGAAAATTGA
1 AAAAGAAAAAGCGA-AACAAGAAAATTGA
45102 AAAAGAAAAAGCGAAACAAGAAAATTGA
1 AAAAGAAAAAGCGAAACAAGAAAATTGA
45130 AA
1 AA
45132 GAGAGCTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 13 0.48
28 14 0.52
ACGTcount: A:0.68, C:0.05, G:0.18, T:0.09
Consensus pattern (28 bp):
AAAAGAAAAAGCGAAACAAGAAAATTGA
Found at i:45111 original size:14 final size:13
Alignment explanation
Indices: 45075--45131 Score: 53
Period size: 14 Copynumber: 4.2 Consensus size: 13
45065 GTGAGAAGAG
45075 AAAAGAAAA-TGCA
1 AAAAGAAAATTG-A
45088 GAAAAGAAAATTGA
1 -AAAAGAAAATTGA
**
45102 AAAAGAAAAAGCGA
1 AAAAG-AAAATTGA
45116 AACAAGAAAATTGA
1 AA-AAGAAAATTGA
45130 AA
1 AA
45132 GAGAGCTTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
13 5 0.14
14 26 0.72
15 5 0.14
ACGTcount: A:0.68, C:0.05, G:0.18, T:0.09
Consensus pattern (13 bp):
AAAAGAAAATTGA
Found at i:51755 original size:20 final size:20
Alignment explanation
Indices: 51709--51755 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
51699 GCTCGTTTCC
*
51709 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
51729 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
51749 CAGCTCA
1 CAGCTCA
51756 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:53255 original size:11 final size:10
Alignment explanation
Indices: 53238--53268 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
53228 ATTTGAGTAA
53238 CAAAAAAAAT
1 CAAAAAAAAT
53248 CAAAAAAAAT
1 CAAAAAAAAT
53258 CGAAAAAAAAT
1 C-AAAAAAAAT
53269 TGATTGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.55
11 9 0.45
ACGTcount: A:0.77, C:0.10, G:0.03, T:0.10
Consensus pattern (10 bp):
CAAAAAAAAT
Found at i:53265 original size:13 final size:13
Alignment explanation
Indices: 53249--53324 Score: 59
Period size: 15 Copynumber: 5.6 Consensus size: 13
53239 AAAAAAAATC
53249 AAAAAAAATCGAA
1 AAAAAAAATCGAA
* *
53262 AAAAAATTGATTGAA
1 AAAAAA--AATCGAA
53277 AAAAAAAATTC-AA
1 AAAAAAAA-TCGAA
53290 AAAAAAAAGT-G-A
1 AAAAAAAA-TCGAA
53302 AAAAAAAATCGAGCA
1 AAAAAAAATCGA--A
53317 AAAAAAAA
1 AAAAAAAA
53325 GGTGAGAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
11 1 0.02
12 10 0.20
13 18 0.36
14 1 0.02
15 20 0.40
ACGTcount: A:0.74, C:0.05, G:0.09, T:0.12
Consensus pattern (13 bp):
AAAAAAAATCGAA
Found at i:53319 original size:15 final size:14
Alignment explanation
Indices: 53249--53341 Score: 56
Period size: 15 Copynumber: 6.7 Consensus size: 14
53239 AAAAAAAATC
53249 AAAAAAAATCGA-A
1 AAAAAAAATCGAGA
* *
53262 AAAAAATTGATTGA-A
1 AAAAAA--AATCGAGA
53277 AAAAAAAATTC-A-A
1 AAAAAAAA-TCGAGA
*
53290 AAAAAAAA--GTGA
1 AAAAAAAATCGAGA
53302 AAAAAAAATCGAGCA
1 AAAAAAAATCGAG-A
53317 AAAAAAAAGGT-GAGA
1 AAAAAAAA--TCGAGA
53332 AAAAAAAATC
1 AAAAAAAATC
53342 AAGTTAAAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 21
0.70 0.07 0.23
Matches are distributed among these distances:
12 9 0.14
13 18 0.29
14 3 0.05
15 29 0.46
16 3 0.05
17 1 0.02
ACGTcount: A:0.71, C:0.05, G:0.12, T:0.12
Consensus pattern (14 bp):
AAAAAAAATCGAGA
Found at i:53334 original size:30 final size:28
Alignment explanation
Indices: 53287--53361 Score: 89
Period size: 30 Copynumber: 2.6 Consensus size: 28
53277 AAAAAAAATT
* *
53287 CAAAAAAAAAAGTGAAAAAAAAATCGAG
1 CAAAAAAAAAGGTGAAAAAAAAATCAAG
53315 CAAAAAAAAAGGTGAGAAAAAAAAATCAAG
1 CAAAAAAAAAGGT--GAAAAAAAAATCAAG
**
53345 TTAAAAAAAA-GTGAAAA
1 CAAAAAAAAAGGTGAAAA
53362 GTCTTGCGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
27 5 0.12
28 12 0.29
29 2 0.05
30 22 0.54
ACGTcount: A:0.71, C:0.05, G:0.15, T:0.09
Consensus pattern (28 bp):
CAAAAAAAAAGGTGAAAAAAAAATCAAG
Found at i:57134 original size:6 final size:6
Alignment explanation
Indices: 57123--57148 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
57113 ATAAATAAAT
57123 AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AA
57149 CTTTACAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:58562 original size:19 final size:20
Alignment explanation
Indices: 58534--58576 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
58524 CTTCAATTTC
58534 TTTTCAC-TTTCAATCTCTT
1 TTTTCACTTTTCAATCTCTT
* *
58553 TTTTCTCTTTTTCATTCTCTT
1 TTTTCAC-TTTTCAATCTCTT
58574 TTT
1 TTT
58577 CTTTTTCCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 6 0.30
21 14 0.70
ACGTcount: A:0.09, C:0.23, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTCACTTTTCAATCTCTT
Found at i:58577 original size:20 final size:20
Alignment explanation
Indices: 58541--58582 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
58531 TTCTTTTCAC
58541 TTTCAATCTCTTTTTTCTCTT
1 TTTCAATCTCTTTTTTCT-TT
*
58562 TTTCATTCTC-TTTTTCTTT
1 TTTCAATCTCTTTTTTCTTT
58581 TT
1 TT
58583 CCTCACTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 7 0.35
21 9 0.45
ACGTcount: A:0.07, C:0.21, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTCAATCTCTTTTTTCTTT
Found at i:60912 original size:14 final size:14
Alignment explanation
Indices: 60893--60924 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
60883 TTAAACTAAG
*
60893 TAAATAAATATAAA
1 TAAATAAATAAAAA
60907 TAAATAAATAAAAA
1 TAAATAAATAAAAA
60921 TAAA
1 TAAA
60925 ACTTTACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (14 bp):
TAAATAAATAAAAA
Found at i:60916 original size:18 final size:19
Alignment explanation
Indices: 60879--60924 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
60869 ATTGCCATAA
* *
60879 AAATTTAAACTAAGTAAAT
1 AAATATAAACTAAATAAAT
60898 AAATATAAA-TAAATAAAT
1 AAATATAAACTAAATAAAT
*
60916 AAAAATAAA
1 AAATATAAA
60925 ACTTTACAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (19 bp):
AAATATAAACTAAATAAAT
Done.