Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3248
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: 103944
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:1789 original size:21 final size:23
Alignment explanation
Indices: 1744--1790 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1734 TCACCTGCAA
* *
1744 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
1767 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
1788 TAA
1 TAA
1791 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:7095 original size:15 final size:15
Alignment explanation
Indices: 7075--7130 Score: 78
Period size: 17 Copynumber: 3.7 Consensus size: 15
7065 TAGCTTCTTC
7075 TTTTTTTTCACGAAA
1 TTTTTTTTCACGAAA
*
7090 TTTTTTTTTTCACGAAT
1 --TTTTTTTTCACGAAA
7107 TTTTTTTTCACG-AA
1 TTTTTTTTCACGAAA
7121 TTTTTTTTCA
1 TTTTTTTTCA
7131 ACTTGATATC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
14 11 0.30
15 12 0.32
17 14 0.38
ACGTcount: A:0.20, C:0.12, G:0.05, T:0.62
Consensus pattern (15 bp):
TTTTTTTTCACGAAA
Found at i:7097 original size:17 final size:16
Alignment explanation
Indices: 7075--7128 Score: 92
Period size: 15 Copynumber: 3.4 Consensus size: 16
7065 TAGCTTCTTC
7075 TTTTTTTTCACGAAATT
1 TTTTTTTTCACG-AATT
7092 TTTTTTTTCACGAA-T
1 TTTTTTTTCACGAATT
7107 TTTTTTTTCACGAATT
1 TTTTTTTTCACGAATT
7123 TTTTTT
1 TTTTTT
7129 CAACTTGATA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
15 15 0.42
16 9 0.25
17 12 0.33
ACGTcount: A:0.19, C:0.11, G:0.06, T:0.65
Consensus pattern (16 bp):
TTTTTTTTCACGAATT
Found at i:7187 original size:11 final size:11
Alignment explanation
Indices: 7171--7214 Score: 79
Period size: 11 Copynumber: 4.0 Consensus size: 11
7161 GAAACCAAAT
7171 TTTTTTTTGAA
1 TTTTTTTTGAA
7182 TTTTTTTTGAA
1 TTTTTTTTGAA
7193 TTTTTTTTGAA
1 TTTTTTTTGAA
*
7204 ATTTTTTTGAA
1 TTTTTTTTGAA
7215 GAAAACTACA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 32 1.00
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.70
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:11771 original size:28 final size:28
Alignment explanation
Indices: 11690--11821 Score: 182
Period size: 28 Copynumber: 4.8 Consensus size: 28
11680 CAGTAACTAT
*
11690 ATAATC-AACTCGCACACTTA-TGCTAT
1 ATAATCAAACTCGCACACTTAGTGCTAC
11716 ATAATCAAACTCGCACACTTAGTGGCTAC
1 ATAATCAAACTCGCACACTTAGT-GCTAC
11745 A-AATCAAACTCGCCACACTTAGTGCTAC
1 ATAATCAAACTCG-CACACTTAGTGCTAC
*
11773 AT-CTCAAAACTCGCACACTTAGTGCTAC
1 ATAATC-AAACTCGCACACTTAGTGCTAC
*
11801 ATAATCAAACTTGCACACTTA
1 ATAATCAAACTCGCACACTTA
11822 TCTTTTACAA
Statistics
Matches: 95, Mismatches: 4, Indels: 12
0.86 0.04 0.11
Matches are distributed among these distances:
26 6 0.06
27 14 0.15
28 51 0.54
29 24 0.25
ACGTcount: A:0.36, C:0.29, G:0.10, T:0.26
Consensus pattern (28 bp):
ATAATCAAACTCGCACACTTAGTGCTAC
Found at i:11786 original size:57 final size:55
Alignment explanation
Indices: 11690--11822 Score: 182
Period size: 57 Copynumber: 2.4 Consensus size: 55
11680 CAGTAACTAT
*
11690 ATAATC-AACTCGCACACTTATGCTATATAATCAAACTCGCACACTTAGTGGCTAC
1 ATAATCAAACTCGCACACTTATGCTACATAATCAAACTCGCACACTTAGT-GCTAC
*
11745 A-AATCAAACTCGCCACACTTAGTGCTACAT-CTCAAAACTCGCACACTTAGTGCTAC
1 ATAATCAAACTCG-CACACTTA-TGCTACATAATC-AAACTCGCACACTTAGTGCTAC
*
11801 ATAATCAAACTTGCACACTTAT
1 ATAATCAAACTCGCACACTTAT
11823 CTTTTACAAT
Statistics
Matches: 70, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
54 4 0.06
55 8 0.11
56 24 0.34
57 34 0.49
ACGTcount: A:0.35, C:0.29, G:0.10, T:0.26
Consensus pattern (55 bp):
ATAATCAAACTCGCACACTTATGCTACATAATCAAACTCGCACACTTAGTGCTAC
Found at i:19106 original size:21 final size:21
Alignment explanation
Indices: 19081--19121 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
19071 CACTCCCTCA
*
19081 ATTTTTT-TT-TCTTTTTTTC
1 ATTTTTTGTTCTCTCTTTTTC
19100 ATTTTTTGTTCTCTCTTTTTC
1 ATTTTTTGTTCTCTCTTTTTC
19121 A
1 A
19122 ATCTTTTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 2 0.11
21 10 0.53
ACGTcount: A:0.07, C:0.15, G:0.02, T:0.76
Consensus pattern (21 bp):
ATTTTTTGTTCTCTCTTTTTC
Found at i:21111 original size:13 final size:13
Alignment explanation
Indices: 21093--21125 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
21083 CTTTTTTCAT
*
21093 TTTTTTTCACGAA
1 TTTTTTTCACAAA
21106 TTTTTTTCACAAA
1 TTTTTTTCACAAA
21119 TTTTTTT
1 TTTTTTT
21126 TTCAACTTGA
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:0.21, C:0.12, G:0.03, T:0.64
Consensus pattern (13 bp):
TTTTTTTCACAAA
Found at i:21182 original size:11 final size:11
Alignment explanation
Indices: 21166--21207 Score: 68
Period size: 11 Copynumber: 3.8 Consensus size: 11
21156 AATGGAAACC
21166 ATTTTTTTTGA
1 ATTTTTTTTGA
21177 ATTTTTTTTTG-
1 A-TTTTTTTTGA
21188 ATTTTTTTTGA
1 ATTTTTTTTGA
21199 ATTTTTTTT
1 ATTTTTTTT
21208 TGAAGAAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.31
11 11 0.38
12 9 0.31
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (11 bp):
ATTTTTTTTGA
Found at i:21183 original size:10 final size:10
Alignment explanation
Indices: 21168--21206 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
21158 TGGAAACCAT
21168 TTTTTTTGAA
1 TTTTTTTGAA
*
21178 TTTTTTTTTGAT
1 --TTTTTTTGAA
21190 TTTTTTTGAA
1 TTTTTTTGAA
21200 TTTTTTT
1 TTTTTTT
21207 TTGAAGAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 16 0.64
12 9 0.36
ACGTcount: A:0.13, C:0.00, G:0.08, T:0.79
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:21184 original size:12 final size:12
Alignment explanation
Indices: 21167--21211 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
21157 ATGGAAACCA
21167 TTTTTTTTGAAT
1 TTTTTTTTGAAT
21179 TTTTTTTTG-A-
1 TTTTTTTTGAAT
21189 TTTTTTTTGAAT
1 TTTTTTTTGAAT
21201 TTTTTTTTGAA
1 TTTTTTTTGAA
21212 GAAACTACTA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 9 0.29
11 2 0.06
12 20 0.65
ACGTcount: A:0.16, C:0.00, G:0.09, T:0.76
Consensus pattern (12 bp):
TTTTTTTTGAAT
Found at i:21194 original size:22 final size:22
Alignment explanation
Indices: 21166--21210 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
21156 AATGGAAACC
21166 ATTTTTTTTGAATTTTTTTTTG
1 ATTTTTTTTGAATTTTTTTTTG
21188 ATTTTTTTTGAATTTTTTTTTG
1 ATTTTTTTTGAATTTTTTTTTG
21210 A
1 A
21211 AGAAACTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.16, C:0.00, G:0.09, T:0.76
Consensus pattern (22 bp):
ATTTTTTTTGAATTTTTTTTTG
Found at i:31531 original size:1 final size:1
Alignment explanation
Indices: 31525--31557 Score: 57
Period size: 1 Copynumber: 33.0 Consensus size: 1
31515 ATTGCCTCCA
*
31525 CCCCCCCCCCCCCCCCCCCCCCCCCCCTCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
31558 TTCATGCGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.97, G:0.00, T:0.03
Consensus pattern (1 bp):
C
Found at i:31639 original size:1 final size:1
Alignment explanation
Indices: 31633--31695 Score: 63
Period size: 1 Copynumber: 63.0 Consensus size: 1
31623 CAGGATGGGC
* * * * * * *
31633 GGGGGGGGCGGGTGGGGGGGGTGTGTGGGGCGGGGGGGGGGGGGGGCGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
31696 TCGCGAGATC
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.00, C:0.05, G:0.89, T:0.06
Consensus pattern (1 bp):
G
Found at i:31665 original size:22 final size:21
Alignment explanation
Indices: 31637--31696 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
31627 ATGGGCGGGG
* *
31637 GGGGCGGGTGGGGGGGGTGTGT
1 GGGGCGGG-GGGGGGGGTGGGC
*
31659 GGGGCGGGGGGGGGGGGGGGC
1 GGGGCGGGGGGGGGGGTGGGC
*
31680 GGGGGGGGGGGGGGGGT
1 GGGGCGGGGGGGGGGGT
31697 CGCGAGATCC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
21 25 0.76
22 8 0.24
ACGTcount: A:0.00, C:0.05, G:0.87, T:0.08
Consensus pattern (21 bp):
GGGGCGGGGGGGGGGGTGGGC
Found at i:31667 original size:16 final size:16
Alignment explanation
Indices: 31629--31694 Score: 80
Period size: 16 Copynumber: 4.2 Consensus size: 16
31619 GTATCAGGAT
*
31629 GGGCGGGGGGGGCGGG
1 GGGCGGGGGGGGGGGG
* * * *
31645 TGG-GGGGGGTGTGTG
1 GGGCGGGGGGGGGGGG
31660 GGGCGGGGGGGGGGGG
1 GGGCGGGGGGGGGGGG
31676 GGGCGGGGGGGGGGGG
1 GGGCGGGGGGGGGGGG
31692 GGG
1 GGG
31695 GTCGCGAGAT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
15 11 0.27
16 30 0.73
ACGTcount: A:0.00, C:0.06, G:0.88, T:0.06
Consensus pattern (16 bp):
GGGCGGGGGGGGGGGG
Found at i:32127 original size:13 final size:13
Alignment explanation
Indices: 32109--32142 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
32099 AACTAGCTCT
32109 TTTTTTTTCAAAA
1 TTTTTTTTCAAAA
* *
32122 TTTTTTTGCAACA
1 TTTTTTTTCAAAA
32135 TTTTTTTT
1 TTTTTTTT
32143 TTCATTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.21, C:0.09, G:0.03, T:0.68
Consensus pattern (13 bp):
TTTTTTTTCAAAA
Found at i:40686 original size:16 final size:16
Alignment explanation
Indices: 40665--40707 Score: 70
Period size: 15 Copynumber: 2.8 Consensus size: 16
40655 CTTCTTCTTC
*
40665 TTTTTTTTTTCACGAA
1 TTTTTTTTTTCACAAA
40681 -TTTTTTTTTCACAAA
1 TTTTTTTTTTCACAAA
40696 TTTTTTTTTTCA
1 TTTTTTTTTTCA
40708 ACTTGATATC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 14 0.56
16 11 0.44
ACGTcount: A:0.19, C:0.12, G:0.02, T:0.67
Consensus pattern (16 bp):
TTTTTTTTTTCACAAA
Found at i:40763 original size:11 final size:11
Alignment explanation
Indices: 40747--40779 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
40737 GGAAACCAAT
40747 TTTTTTTTGAA
1 TTTTTTTTGAA
40758 TTTTTTTTGAA
1 TTTTTTTTGAA
40769 TTTTTTTTGAA
1 TTTTTTTTGAA
40780 GAAACTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.73
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:41814 original size:21 final size:23
Alignment explanation
Indices: 41769--41815 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
41759 TCACCTGCAA
* *
41769 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
41792 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
41813 TAA
1 TAA
41816 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:43558 original size:23 final size:22
Alignment explanation
Indices: 43506--43558 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
43496 TCCACGTCTT
*
43506 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
43528 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
43551 TTTCTTTT
1 TTTCTTTT
43559 TCACTCTCAA
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:48692 original size:27 final size:27
Alignment explanation
Indices: 48659--48819 Score: 189
Period size: 27 Copynumber: 6.0 Consensus size: 27
48649 CACATCAAGA
*
48659 AAGAAAAGCCTTTGTGGTGTAATAT-G
1 AAGAAAAGCCTTTGTGGCGTAATATGG
* * *
48685 AAGTAAAAGCCTTTGTGGCATACTATGA
1 AAG-AAAAGCCTTTGTGGCGTAATATGG
* *
48713 AAGAAAAGCCTTTGTAGTGTAATATGG
1 AAGAAAAGCCTTTGTGGCGTAATATGG
**
48740 AAGAAAAGCCTTTGTGATGTAATATGG
1 AAGAAAAGCCTTTGTGGCGTAATATGG
** *
48767 AAGAAAAGTGTTTGTGGCGTAATGTGG
1 AAGAAAAGCCTTTGTGGCGTAATATGG
* *
48794 AAGAAAATCGTTTGTGGCGTAATATG
1 AAGAAAAGCCTTTGTGGCGTAATATG
48820 AAAGGAACAT
Statistics
Matches: 114, Mismatches: 19, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
26 3 0.03
27 108 0.95
28 3 0.03
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.30
Consensus pattern (27 bp):
AAGAAAAGCCTTTGTGGCGTAATATGG
Found at i:48747 original size:54 final size:54
Alignment explanation
Indices: 48657--48823 Score: 210
Period size: 54 Copynumber: 3.1 Consensus size: 54
48647 AACACATCAA
* *
48657 GAAAGAAAAGCCTTTGTGGTGTAATAT-GAAGTAAAAGCCTTTGTGGCATACTAT
1 GAAAGAAAAGCCTTTGTGGTGTAATATGGAAG-AAAAGCCTTTGTGGCGTAATAT
* **
48711 GAAAGAAAAGCCTTTGTAGTGTAATATGGAAGAAAAGCCTTTGTGATGTAATAT
1 GAAAGAAAAGCCTTTGTGGTGTAATATGGAAGAAAAGCCTTTGTGGCGTAATAT
* ** * * * *
48765 GGAAGAAAAGTGTTTGTGGCGTAATGTGGAAGAAAATCGTTTGTGGCGTAATAT
1 GAAAGAAAAGCCTTTGTGGTGTAATATGGAAGAAAAGCCTTTGTGGCGTAATAT
48819 GAAAG
1 GAAAG
48824 GAACATTTGT
Statistics
Matches: 96, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
54 92 0.96
55 4 0.04
ACGTcount: A:0.36, C:0.08, G:0.28, T:0.29
Consensus pattern (54 bp):
GAAAGAAAAGCCTTTGTGGTGTAATATGGAAGAAAAGCCTTTGTGGCGTAATAT
Found at i:53935 original size:22 final size:22
Alignment explanation
Indices: 53892--53934 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
53882 AAGGGCATAA
*
53892 AATGCTCTTTAAAACTCCTTTT
1 AATGATCTTTAAAACTCCTTTT
*
53914 AATGATCTTT-AAGCTCCTTTT
1 AATGATCTTTAAAACTCCTTTT
53935 TTTAACAGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.47
Consensus pattern (22 bp):
AATGATCTTTAAAACTCCTTTT
Found at i:54085 original size:21 final size:23
Alignment explanation
Indices: 54040--54086 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
54030 TCACCTGCAA
* *
54040 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
54063 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
54084 TAA
1 TAA
54087 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:57233 original size:13 final size:13
Alignment explanation
Indices: 57215--57240 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
57205 ACCTGAAAGC
57215 AATTTAATTCATA
1 AATTTAATTCATA
57228 AATTTAATTCATA
1 AATTTAATTCATA
57241 TTAGGACACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTTAATTCATA
Found at i:57654 original size:20 final size:21
Alignment explanation
Indices: 57629--57667 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
57619 TCAAACAAGC
57629 AAATGAGCTCAA-TGAGCTGG
1 AAATGAGCTCAATTGAGCTGG
*
57649 AAATGAGCTGAATTGAGCT
1 AAATGAGCTCAATTGAGCT
57668 CAACGAGCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.23
Consensus pattern (21 bp):
AAATGAGCTCAATTGAGCTGG
Found at i:58941 original size:17 final size:17
Alignment explanation
Indices: 58921--58974 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
58911 CTTCACTCGT
58921 TTTCTTTTCAAACTCTC
1 TTTCTTTTCAAACTCTC
*
58938 TTTCTTTTTCAATCTCAT-
1 TTTC-TTTTCAAACTC-TC
58956 TTTGCTTTTC--ACTCTC
1 TTT-CTTTTCAAACTCTC
58972 TTT
1 TTT
58975 TGTTTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
15 1 0.03
16 6 0.19
17 4 0.13
18 18 0.58
19 2 0.06
ACGTcount: A:0.13, C:0.26, G:0.02, T:0.59
Consensus pattern (17 bp):
TTTCTTTTCAAACTCTC
Found at i:58964 original size:18 final size:18
Alignment explanation
Indices: 58943--58994 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
58933 CTCTCTTTCT
58943 TTTTCAATCTCATTTTGC
1 TTTTCAATCTCATTTTGC
* *
58961 TTTTCACTCTC-TTTTGT
1 TTTTCAATCTCATTTTGC
*
58978 TTTTGAAATCTCATTTT
1 TTTT-CAATCTCATTTT
58995 CATATTTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 9 0.32
18 15 0.54
19 4 0.14
ACGTcount: A:0.15, C:0.19, G:0.06, T:0.60
Consensus pattern (18 bp):
TTTTCAATCTCATTTTGC
Found at i:59008 original size:6 final size:6
Alignment explanation
Indices: 58999--59096 Score: 63
Period size: 6 Copynumber: 15.8 Consensus size: 6
58989 CATTTTCATA
* * * **
58999 TTTTTC TTTTTC AATTTTC TTTTCTTC ATTTTC TTTTTC TCTCAC TTTTTC
1 TTTTTC TTTTTC -TTTTTC -TTT-TTC TTTTTC TTTTTC TTTTTC TTTTTC
* * * **
59050 GTTTTC GTTTTC TTTTT- TGTTTTC TTTTTC TTCTTC ACTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC T-TTTTC TTTTTC TTTTTC TTTTTC TTTTT
59097 TGAATTCATT
Statistics
Matches: 69, Mismatches: 19, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
5 1 0.01
6 55 0.80
7 10 0.14
8 3 0.04
ACGTcount: A:0.05, C:0.19, G:0.03, T:0.72
Consensus pattern (6 bp):
TTTTTC
Found at i:61228 original size:13 final size:13
Alignment explanation
Indices: 61210--61235 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
61200 ACCTGAAAGC
61210 AATTTAATTCATA
1 AATTTAATTCATA
61223 AATTTAATTCATA
1 AATTTAATTCATA
61236 TTAGGACACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTTAATTCATA
Found at i:61650 original size:20 final size:21
Alignment explanation
Indices: 61625--61663 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
61615 TCAAACAAGC
61625 AAATGAGCTCAA-TGAGCTAG
1 AAATGAGCTCAATTGAGCTAG
*
61645 AAATGAGCTGAATTGAGCT
1 AAATGAGCTCAATTGAGCT
61664 CAACGAGCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.23
Consensus pattern (21 bp):
AAATGAGCTCAATTGAGCTAG
Found at i:64178 original size:15 final size:15
Alignment explanation
Indices: 64158--64212 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
64148 ACTCTCCTCA
*
64158 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
64173 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
64188 TTGTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
64202 TTCTTTT-TCTC
1 TTCTTTTCTCTC
64213 GCTCAATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
14 16 0.46
15 19 0.54
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:66310 original size:11 final size:11
Alignment explanation
Indices: 66294--66333 Score: 55
Period size: 12 Copynumber: 3.6 Consensus size: 11
66284 AATACAAACT
66294 TTTTTTTTGAA
1 TTTTTTTTGAA
66305 TTTTTTTTCGAA
1 TTTTTTTT-GAA
*
66317 TTTTTTTCG-A
1 TTTTTTTTGAA
66327 TTTTTTT
1 TTTTTTT
66334 AAATCTCGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 8 0.30
11 9 0.33
12 10 0.37
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.75
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:66310 original size:12 final size:12
Alignment explanation
Indices: 66293--66333 Score: 59
Period size: 11 Copynumber: 3.6 Consensus size: 12
66283 GAATACAAAC
*
66293 TTTTTTTTTGAA
1 TTTTTTTTCGAA
66305 TTTTTTTTCGAA
1 TTTTTTTTCGAA
66317 -TTTTTTTCG-A
1 TTTTTTTTCGAA
66327 TTTTTTT
1 TTTTTTT
66334 AAATCTCGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 1 0.04
11 15 0.56
12 11 0.41
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.76
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:73239 original size:15 final size:15
Alignment explanation
Indices: 73219--73256 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
73209 TAGCTTCTTC
73219 TTTTTTCACAAATTT
1 TTTTTTCACAAATTT
*
73234 TTTTTTCACGAATTT
1 TTTTTTCACAAATTT
73249 TTTTTTCA
1 TTTTTTCA
73257 ACTTGATATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.21, C:0.13, G:0.03, T:0.63
Consensus pattern (15 bp):
TTTTTTCACAAATTT
Found at i:73311 original size:12 final size:12
Alignment explanation
Indices: 73294--73327 Score: 61
Period size: 11 Copynumber: 2.9 Consensus size: 12
73284 ATGGAAACCA
73294 AATTTTTTTTTG
1 AATTTTTTTTTG
73306 AA-TTTTTTTTG
1 AATTTTTTTTTG
73317 AATTTTTTTTT
1 AATTTTTTTTT
73328 TTTTTGAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:73330 original size:17 final size:18
Alignment explanation
Indices: 73308--73343 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
73298 TTTTTTTGAA
73308 TTTTTTTTG-AATTTTTT
1 TTTTTTTTGAAATTTTTT
73325 TTTTTTTTGAAATTTTTT
1 TTTTTTTTGAAATTTTTT
73343 T
1 T
73344 GAAGAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.14, C:0.00, G:0.06, T:0.81
Consensus pattern (18 bp):
TTTTTTTTGAAATTTTTT
Found at i:73340 original size:11 final size:11
Alignment explanation
Indices: 73298--73346 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 11
73288 AAACCAAATT
*
73298 TTTTTTTGAAT
1 TTTTTTTGAAA
73309 TTTTTTTG-AA
1 TTTTTTTGAAA
73319 TTTTTTT----
1 TTTTTTTGAAA
73326 TTTTTTTGAAA
1 TTTTTTTGAAA
73337 TTTTTTTGAA
1 TTTTTTTGAA
73347 GAAACTACTA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
7 7 0.21
10 8 0.24
11 18 0.55
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.73
Consensus pattern (11 bp):
TTTTTTTGAAA
Found at i:74380 original size:21 final size:23
Alignment explanation
Indices: 74335--74381 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
74325 TCACCTGCAA
* *
74335 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
74358 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
74379 TAA
1 TAA
74382 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:77584 original size:19 final size:19
Alignment explanation
Indices: 77557--77649 Score: 88
Period size: 19 Copynumber: 5.1 Consensus size: 19
77547 TTATTCCAGC
*
77557 AACTAAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
77576 AACTTAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
* * *
77595 -A-GTAATTTATTCT-AG--C
1 AACTTAA-TTA-ACTAAGATG
77611 AACTTAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
*
77630 AACTCAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
77649 A
1 A
77650 GTAATTTATT
Statistics
Matches: 59, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
16 2 0.03
17 9 0.15
18 9 0.15
19 39 0.66
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.31
Consensus pattern (19 bp):
AACTTAATTAACTAAGATG
Found at i:77612 original size:54 final size:54
Alignment explanation
Indices: 77547--77672 Score: 225
Period size: 54 Copynumber: 2.3 Consensus size: 54
77537 CAACAATAAA
*
77547 TTATTCCAGCAACTAAATTAACTAAGATGAACTTAATTAACTAAGATGAGTAAT
1 TTATTCCAGCAACTAAATTAACTAAGATGAACTCAATTAACTAAGATGAGTAAT
* *
77601 TTATTCTAGCAACTTAATTAACTAAGATGAACTCAATTAACTAAGATGAGTAAT
1 TTATTCCAGCAACTAAATTAACTAAGATGAACTCAATTAACTAAGATGAGTAAT
77655 TTATTCCAGCAACTAAAT
1 TTATTCCAGCAACTAAAT
77673 ACTTATTCCA
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 67 1.00
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (54 bp):
TTATTCCAGCAACTAAATTAACTAAGATGAACTCAATTAACTAAGATGAGTAAT
Found at i:86211 original size:12 final size:13
Alignment explanation
Indices: 86189--86217 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
86179 AAGTTTTATT
86189 TTTATTTTATTTA
1 TTTATTTTATTTA
86202 TTTA-TTTATTTA
1 TTTATTTTATTTA
86214 TTTA
1 TTTA
86218 CTTAGTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:93441 original size:27 final size:27
Alignment explanation
Indices: 93408--93568 Score: 182
Period size: 27 Copynumber: 6.0 Consensus size: 27
93398 CACATCAAGA
*
93408 AAGAAAAGCCTTTGTGGTGTAATAT-G
1 AAGAAAAGCCTTTGTGGCGTAATATGG
* * *
93434 AAGTAAAAGCCTTTGTGGCATACTATGA
1 AAG-AAAAGCCTTTGTGGCGTAATATGG
* *
93462 AAAAAAAGCCTTTGT-ACTGTAATATGG
1 AAGAAAAGCCTTTGTGGC-GTAATATGG
93489 AAGAAAAGCCTTTGTGGCGTAATATGG
1 AAGAAAAGCCTTTGTGGCGTAATATGG
** *
93516 AAGAAAAGTGTTTGTGGCGTAATGTGG
1 AAGAAAAGCCTTTGTGGCGTAATATGG
***
93543 AAGAAAATTGTTTGTGGCGTAATATG
1 AAGAAAAGCCTTTGTGGCGTAATATG
93569 AAAGGAATGT
Statistics
Matches: 115, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
26 4 0.03
27 108 0.94
28 3 0.03
ACGTcount: A:0.35, C:0.09, G:0.27, T:0.30
Consensus pattern (27 bp):
AAGAAAAGCCTTTGTGGCGTAATATGG
Found at i:100951 original size:15 final size:14
Alignment explanation
Indices: 100924--100953 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
100914 GTTGTAAAGT
100924 TTTATTTTTATTTA
1 TTTATTTTTATTTA
100938 TTTATTTATTATTTA
1 TTTATTT-TTATTTA
100953 T
1 T
100954 ATTCAGTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTTTTATTTA
Done.