Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold158
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: 1811518
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 13
Found at i:1759837 original size:18 final size:18
Alignment explanation
Indices: 1759816--1759852 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1759806 CCTTGTAGCG
1759816 AACATCTTTCTTGCTATA
1 AACATCTTTCTTGCTATA
1759834 AACATCTTTCTTGCTATA
1 AACATCTTTCTTGCTATA
1759852 A
1 A
1759853 GATCCATCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.22, G:0.05, T:0.43
Consensus pattern (18 bp):
AACATCTTTCTTGCTATA
Found at i:1760748 original size:24 final size:24
Alignment explanation
Indices: 1760716--1760763 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
1760706 ACCATGTTCC
1760716 TGGCAAACGTCGAAGAACGGATCA
1 TGGCAAACGTCGAAGAACGGATCA
*
1760740 TGGCAAACGTCGAAGAATGGATCA
1 TGGCAAACGTCGAAGAACGGATCA
1760764 CTTTTATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.19, G:0.29, T:0.15
Consensus pattern (24 bp):
TGGCAAACGTCGAAGAACGGATCA
Found at i:1762836 original size:23 final size:25
Alignment explanation
Indices: 1762803--1762848 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
1762793 AATAAAAATT
1762803 AGTCACTAA-TTTTGACAAACAACA
1 AGTCACTAATTTTTGACAAACAACA
1762827 AGTCA-TAATTTTTGACAAACAA
1 AGTCACTAATTTTTGACAAACAA
1762849 AAAAAAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.28
Consensus pattern (25 bp):
AGTCACTAATTTTTGACAAACAACA
Found at i:1763152 original size:17 final size:17
Alignment explanation
Indices: 1763132--1763169 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
1763122 ATAATATCTG
*
1763132 TTAAATATTTAAATTTA
1 TTAAATATTCAAATTTA
1763149 TTAAATATTCAAATTTA
1 TTAAATATTCAAATTTA
1763166 TTAA
1 TTAA
1763170 TTTTTTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAAATATTCAAATTTA
Found at i:1764143 original size:22 final size:22
Alignment explanation
Indices: 1764118--1764165 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
1764108 TTTTGATACG
* *
1764118 AATACGAT-AATATAATTTTTTA
1 AATA-GATAAATAAAATTTTTAA
*
1764140 AATATATAAATAAAATTTTTAA
1 AATAGATAAATAAAATTTTTAA
1764162 AATA
1 AATA
1764166 TAAATATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
AATAGATAAATAAAATTTTTAA
Found at i:1764166 original size:22 final size:22
Alignment explanation
Indices: 1764126--1764167 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1764116 CGAATACGAT
* *
1764126 AATATAATTTTTTAAATATATA
1 AATAAAATTTTTAAAATATATA
1764148 AATAAAATTTTTAAAATATA
1 AATAAAATTTTTAAAATATA
1764168 AATATATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AATAAAATTTTTAAAATATATA
Found at i:1766239 original size:21 final size:19
Alignment explanation
Indices: 1766201--1766243 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
1766191 TATTTAAATA
1766201 TAAATAAAAAATAATTTTT
1 TAAATAAAAAATAATTTTT
* *
1766220 TAAATATATAAATAAATTTT
1 TAAATA-AAAAATAATTTTT
1766240 TAAA
1 TAAA
1766244 AAATAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TAAATAAAAAATAATTTTT
Found at i:1769194 original size:22 final size:22
Alignment explanation
Indices: 1769166--1769220 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
1769156 TGGACATGTT
1769166 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
1769188 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
1769210 AAAAATGCATG
1 AAAAATGCATG
1769221 GTCAAAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (22 bp):
AAAAATGCATGAAACATAATAA
Found at i:1770181 original size:20 final size:20
Alignment explanation
Indices: 1770134--1770208 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
1770124 AAAAAGACAT
*
1770134 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
1770153 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
1770174 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
1770194 AATGTATCGATACAT
1 AATGTATCGATACAT
1770209 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:1770202 original size:40 final size:39
Alignment explanation
Indices: 1770131--1770208 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1770121 GGTAAAAAGA
* *
1770131 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
1770170 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
1770209 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:1770819 original size:32 final size:32
Alignment explanation
Indices: 1770776--1771277 Score: 718
Period size: 32 Copynumber: 15.7 Consensus size: 32
1770766 TTTTTAAAAA
** * *
1770776 AAAAGGG-TGCCACTAACTTATGTGGGCCTTG
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
** *
1770807 AAAAGAATTGCCACCGACTCGTGTGGGCTTTG
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
*
1770839 AAATGGGTTGCCACCGACTTGTGTGGGCTTTG
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
1770871 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
* *
1770903 AAATGGGTTTCCACCGACTTGTGTGGGCTTTG
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
* *
1770935 GAATGGGTTGCCACCGACTTGTGTGGGCTTTG
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
*
1770967 AAATGGGTTGCCACCGACTTGTGTGGGCTTTG
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
* *
1770999 GAATGGGTTGCCACCGACTTGTGTGGGCTTTG
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
* *
1771031 GAATGGGTTGCCACCGACTTGTGTGGGCTTTG
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
*
1771063 AAATGGGTTGCCACCGACTTGTGTGGGCTTTG
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
* *
1771095 GAATGGGTTGCCACCGACTTGTGTGGGCTTTG
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
* * *
1771127 GAATGAGTTGCCACCGACTTGTGTGGGCTTTG
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
*
1771159 AAATGGGTTGCCACCGACTTGTGTGGGCTTTG
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
* *
1771191 GAATGGGTTGCCACCGACTTGTGTGGGCTTTG
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
*
1771223 AAATGGGTTGCCACCGACTTGTGTGGGCTTTG
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
* * * *
1771255 AAATGGGTTACCACTGAGTTGTG
1 AAAAGGGTTGCCACCGACTTGTG
1771278 GTCTTAAAAG
Statistics
Matches: 442, Mismatches: 28, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
31 5 0.01
32 437 0.99
ACGTcount: A:0.17, C:0.19, G:0.34, T:0.30
Consensus pattern (32 bp):
AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
Found at i:1770884 original size:64 final size:64
Alignment explanation
Indices: 1770791--1771277 Score: 812
Period size: 64 Copynumber: 7.6 Consensus size: 64
1770781 GGTGCCACTA
* * * ** *
1770791 ACTTATGTGGGCCTTGAAAAGAATTGCCACCGACTCGTGTGGGCTTTGAAATGGGTTGCCACCG
1 ACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCG
* *
1770855 ACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTTCCACCG
1 ACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCG
*
1770919 ACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCG
1 ACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCG
* *
1770983 ACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCG
1 ACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCG
*
1771047 ACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCG
1 ACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCG
* *
1771111 ACTTGTGTGGGCTTTGGAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCG
1 ACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCG
*
1771175 ACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCG
1 ACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCG
* * *
1771239 ACTTGTGTGGGCTTTGAAATGGGTTACCACTGAGTTGTG
1 ACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTG
1771278 GTCTTAAAAG
Statistics
Matches: 404, Mismatches: 19, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 404 1.00
ACGTcount: A:0.16, C:0.19, G:0.34, T:0.31
Consensus pattern (64 bp):
ACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCG
Found at i:1770947 original size:96 final size:96
Alignment explanation
Indices: 1770814--1771277 Score: 838
Period size: 96 Copynumber: 4.8 Consensus size: 96
1770804 TTGAAAAGAA
* * *
1770814 TTGCCACCGACTCGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGT
1 TTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
*
1770879 TGCCACCGACTTGTGTGGGCTTTGAAATGGG
66 TGCCACCGACTTGTGTGGGCTTTGGAATGGG
*
1770910 TTTCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
1 TTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
1770975 TGCCACCGACTTGTGTGGGCTTTGGAATGGG
66 TGCCACCGACTTGTGTGGGCTTTGGAATGGG
1771006 TTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
1 TTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
1771071 TGCCACCGACTTGTGTGGGCTTTGGAATGGG
66 TGCCACCGACTTGTGTGGGCTTTGGAATGGG
*
1771102 TTGCCACCGACTTGTGTGGGCTTTGGAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
1 TTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
1771167 TGCCACCGACTTGTGTGGGCTTTGGAATGGG
66 TGCCACCGACTTGTGTGGGCTTTGGAATGGG
*
1771198 TTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
1 TTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
* * *
1771263 TACCACTGAGTTGTG
66 TGCCACCGACTTGTG
1771278 GTCTTAAAAG
Statistics
Matches: 356, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
96 356 1.00
ACGTcount: A:0.15, C:0.19, G:0.35, T:0.31
Consensus pattern (96 bp):
TTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
TGCCACCGACTTGTGTGGGCTTTGGAATGGG
Found at i:1771329 original size:27 final size:27
Alignment explanation
Indices: 1771265--1771751 Score: 776
Period size: 27 Copynumber: 17.8 Consensus size: 27
1771255 AAATGGGTTA
* *
1771265 CCACTGAGTTGTGGTCTTAAAAGGGATG
1 CCACGGAGTTGTGGACTTAAAAGGG-TG
1771293 CCACGGAGTTGTGGACTTAAAAGGGTG
1 CCACGGAGTTGTGGACTTAAAAGGGTG
1771320 CCACGGAGTTGTGGACTTAAAAGGGTG
1 CCACGGAGTTGTGGACTTAAAAGGGTG
1771347 CCACGGAGTTGTGGACTTAAAAGGGTG
1 CCACGGAGTTGTGGACTTAAAAGGGTG
* *
1771374 CCACAGAGTTGTGGACTTAAAAGAGTG
1 CCACGGAGTTGTGGACTTAAAAGGGTG
*
1771401 CCACGGAGTTGTGGACTTAAAAAGGTG
1 CCACGGAGTTGTGGACTTAAAAGGGTG
*
1771428 CTACGGAGTTGTGGACTTAAAAGGGTG
1 CCACGGAGTTGTGGACTTAAAAGGGTG
*
1771455 CCACAGAGTTGTGGACTTAAAAGGGTG
1 CCACGGAGTTGTGGACTTAAAAGGGTG
*
1771482 CCACGGAGTTGTGGACTTAAAAGAGATG
1 CCACGGAGTTGTGGACTTAAAAG-GGTG
*
1771510 CCACGGAGTTGTGGACGTAAAAGGGATG
1 CCACGGAGTTGTGGACTTAAAAGGG-TG
*
1771538 CCACGGAGTTGTGGACTTAAAAGGATG
1 CCACGGAGTTGTGGACTTAAAAGGGTG
1771565 CCACGGAGTTGTGGACTTAAAAGGGTG
1 CCACGGAGTTGTGGACTTAAAAGGGTG
1771592 CCACGGAGTTGTGGACTTAAAAGGGTG
1 CCACGGAGTTGTGGACTTAAAAGGGTG
*
1771619 CCACGGAGTTGTGGACTTAAAGAAGGTG
1 CCACGGAGTTGTGGACTTAAA-AGGGTG
* *
1771647 CCACGGAGTTGTGGACTTAATAGAGTG
1 CCACGGAGTTGTGGACTTAAAAGGGTG
*
1771674 CCACGGAGTTGTGGATTTAAAAGGGTG
1 CCACGGAGTTGTGGACTTAAAAGGGTG
* *
1771701 CCACAGAGTTGTGGACTTTAAAAGGATG
1 CCACGGAGTTGTGGAC-TTAAAAGGGTG
1771729 CCACGGAGTTGTGGACTTCAAAA
1 CCACGGAGTTGTGGACTT-AAAA
1771752 AGAAATGCCA
Statistics
Matches: 425, Mismatches: 29, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
27 298 0.70
28 127 0.30
ACGTcount: A:0.28, C:0.15, G:0.34, T:0.23
Consensus pattern (27 bp):
CCACGGAGTTGTGGACTTAAAAGGGTG
Found at i:1771597 original size:82 final size:81
Alignment explanation
Indices: 1771265--1771751 Score: 762
Period size: 82 Copynumber: 5.9 Consensus size: 81
1771255 AAATGGGTTA
* * * *
1771265 CCACTGAGTTGTGGTCTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTT
1 CCACGGAGTTGTGGACTTAAAAGGG-TGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTT
1771330 GTGGACTTAAAAGGGTG
65 GTGGACTTAAAAGGGTG
1771347 CCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA-GAGTGCCACGGAGTT
1 CCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGA-TGCCACGGAGTT
*
1771411 GTGGACTTAAAAAGGTG
65 GTGGACTTAAAAGGGTG
* *
1771428 CTACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTG
1 CCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTTG
*
1771493 TGGACTTAAAAGAGATG
66 TGGACTTAAAAG-GGTG
* *
1771510 CCACGGAGTTGTGGACGTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTT
1 CCACGGAGTTGTGGACTTAAAAGGG-TGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTT
1771575 GTGGACTTAAAAGGGTG
65 GTGGACTTAAAAGGGTG
*
1771592 CCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAGAAGG-TGCCACGGAGT
1 CCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTT-AA-AAGGATGCCACGGAGT
* *
1771656 TGTGGACTTAATAGAGTG
64 TGTGGACTTAAAAGGGTG
*
1771674 CCACGGAGTTGTGGATTTAAAAGGGTGCCACAGAGTTGTGGACTTTAAAAGGATGCCACGGAGTT
1 CCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGAC-TTAAAAGGATGCCACGGAGTT
1771739 GTGGACTTCAAAA
65 GTGGACTT-AAAA
1771752 AGAAATGCCA
Statistics
Matches: 376, Mismatches: 20, Indels: 17
0.91 0.05 0.04
Matches are distributed among these distances:
80 1 0.00
81 147 0.39
82 169 0.45
83 59 0.16
ACGTcount: A:0.28, C:0.15, G:0.34, T:0.23
Consensus pattern (81 bp):
CCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTTG
TGGACTTAAAAGGGTG
Found at i:1779270 original size:22 final size:22
Alignment explanation
Indices: 1779242--1779296 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
1779232 TGGACATGTT
1779242 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
1779264 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
1779286 AAAAATGCATG
1 AAAAATGCATG
1779297 GTCAAAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (22 bp):
AAAAATGCATGAAACATAATAA
Found at i:1780257 original size:20 final size:20
Alignment explanation
Indices: 1780210--1780284 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
1780200 AAAAAGACAT
*
1780210 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
1780229 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
1780250 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
1780270 AATGTATCGATACAT
1 AATGTATCGATACAT
1780285 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:1780278 original size:40 final size:39
Alignment explanation
Indices: 1780207--1780284 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1780197 GGTAAAAAGA
* *
1780207 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
1780246 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
1780285 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:1787131 original size:13 final size:13
Alignment explanation
Indices: 1787110--1787157 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
1787100 TACTAAAATC
*
1787110 ATATTTATATTAG
1 ATATATATATTAG
*
1787123 ATAAATATATTAG
1 ATATATATATTAG
* *
1787136 -TATTTATATTAT
1 ATATATATATTAG
1787148 ATATATATAT
1 ATATATATAT
1787158 ATCAGTATTA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
12 9 0.32
13 19 0.68
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (13 bp):
ATATATATATTAG
Found at i:1787131 original size:30 final size:29
Alignment explanation
Indices: 1787058--1787131 Score: 71
Period size: 30 Copynumber: 2.5 Consensus size: 29
1787048 ATTACTTAAA
1787058 ATATTAGAT-ATATAATAAAATCATATAT
1 ATATTAGATAATATAATAAAATCATATAT
** * *
1787086 ATACCA-ATATTATATACTAAAATCATATTT
1 ATATTAGATA--ATATAATAAAATCATATAT
1787116 ATATTAGATAAATATA
1 ATATTAGAT-AATATA
1787132 TTAGTATTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
27 2 0.06
28 4 0.11
30 26 0.74
31 2 0.06
32 1 0.03
ACGTcount: A:0.51, C:0.07, G:0.03, T:0.39
Consensus pattern (29 bp):
ATATTAGATAATATAATAAAATCATATAT
Found at i:1787141 original size:25 final size:27
Alignment explanation
Indices: 1787107--1787171 Score: 82
Period size: 25 Copynumber: 2.5 Consensus size: 27
1787097 ATATACTAAA
1787107 ATCA-TATTTATATTAGATA-A-ATAT
1 ATCAGTATTTATATTAGATATATATAT
* *
1787131 ATTAGTATTTATATTATATATATATAT
1 ATCAGTATTTATATTAGATATATATAT
1787158 ATCAGTATTATATA
1 ATCAGTATT-TATA
1787172 CATACATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 3 0.09
25 14 0.41
26 1 0.03
27 12 0.35
28 4 0.12
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (27 bp):
ATCAGTATTTATATTAGATATATATAT
Found at i:1787661 original size:2 final size:2
Alignment explanation
Indices: 1787656--1787726 Score: 61
Period size: 2 Copynumber: 35.5 Consensus size: 2
1787646 ACACACACAA
* * * * * *
1787656 AT AT AT AT AT AC AC AT AT AT AT GT GT AT AC AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
1787698 AT AT TT AT AC AC AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1787727 AGCAGATTAT
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1787675 original size:16 final size:16
Alignment explanation
Indices: 1787650--1787698 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
1787640 TTACACACAC
* *
1787650 ACACAAATATATATAT
1 ACACATATATATGTAT
*
1787666 ACACATATATATGTGT
1 ACACATATATATGTAT
*
1787682 ATACATATATATGTAT
1 ACACATATATATGTAT
1787698 A
1 A
1787699 TATTTATACA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (16 bp):
ACACATATATATGTAT
Found at i:1787698 original size:24 final size:24
Alignment explanation
Indices: 1787670--1787725 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
1787660 ATATATACAC
* *
1787670 ATATATATGTGTATACATATATAT
1 ATATATATGTATACACATATATAT
* *
1787694 GTATATATTTATACACATATATAT
1 ATATATATGTATACACATATATAT
1787718 ATATATAT
1 ATATATAT
1787726 AAGCAGATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.46
Consensus pattern (24 bp):
ATATATATGTATACACATATATAT
Found at i:1787722 original size:22 final size:22
Alignment explanation
Indices: 1787670--1787723 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
1787660 ATATATACAC
* *
1787670 ATATATATGTGTATACATATAT
1 ATATATATATGTATACACATAT
* *
1787692 ATGTATATATTTATACACATAT
1 ATATATATATGTATACACATAT
1787714 ATATATATAT
1 ATATATATAT
1787724 ATAAGCAGAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.46
Consensus pattern (22 bp):
ATATATATATGTATACACATAT
Found at i:1789583 original size:21 final size:21
Alignment explanation
Indices: 1789544--1789591 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
1789534 AATTATATTT
*
1789544 TTTCATCCAAAAAATGCATTC-
1 TTTCATCCAAAAAACGCA-TCA
**
1789565 TTTCATCCAACCAACGCATCA
1 TTTCATCCAAAAAACGCATCA
1789586 TTTCAT
1 TTTCAT
1789592 TTAAAGATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.33
Consensus pattern (21 bp):
TTTCATCCAAAAAACGCATCA
Found at i:1789849 original size:16 final size:15
Alignment explanation
Indices: 1789826--1789887 Score: 72
Period size: 15 Copynumber: 4.0 Consensus size: 15
1789816 TCTTGAATTA
*
1789826 TTAAATTTTAATTTT
1 TTAAATTTAAATTTT
1789841 TTAAAATTTAAATATTT
1 TT-AAATTTAAAT-TTT
*
1789858 TT-ATTTTAAATTTTT
1 TTAAATTTAAA-TTTT
1789873 TTAAATTTAAATTTT
1 TTAAATTTAAATTTT
1789888 ATTTTAATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
15 18 0.45
16 17 0.43
17 5 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTAAATTTAAATTTT
Found at i:1789896 original size:17 final size:16
Alignment explanation
Indices: 1789829--1789898 Score: 70
Period size: 16 Copynumber: 4.4 Consensus size: 16
1789819 TGAATTATTA
* **
1789829 AATTTTAATTTTTTAA
1 AATTTAAATTTTTTTT
*
1789845 AATTTAAA-TATTTTT
1 AATTTAAATTTTTTTT
* *
1789860 ATTTTAAATTTTTTTA
1 AATTTAAATTTTTTTT
1789876 AATTTAAATTTTATTTT
1 AATTTAAATTTT-TTTT
1789893 AATTTA
1 AATTTA
1789899 TTTTTATATT
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
15 11 0.26
16 23 0.53
17 9 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
AATTTAAATTTTTTTT
Found at i:1789910 original size:28 final size:28
Alignment explanation
Indices: 1789830--1789912 Score: 89
Period size: 28 Copynumber: 2.9 Consensus size: 28
1789820 GAATTATTAA
*
1789830 ATTTT-AATTTTTTAAAATTTAAATATTTTT
1 ATTTTAAATTTTTTTAAATTT-AA-A-TTTT
1789860 ATTTTAAATTTTTTTAAATTTAAATTTT
1 ATTTTAAATTTTTTTAAATTTAAATTTT
* *
1789888 ATTTTAATTTATTTTTATA-TTAAAT
1 ATTTTAAATT-TTTTTAAATTTAAAT
1789913 ATAATTATTT
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
28 19 0.40
29 8 0.17
30 7 0.15
31 14 0.29
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (28 bp):
ATTTTAAATTTTTTTAAATTTAAATTTT
Found at i:1790568 original size:42 final size:42
Alignment explanation
Indices: 1790522--1790627 Score: 162
Period size: 42 Copynumber: 2.5 Consensus size: 42
1790512 TTTTCAACAC
1790522 GTTATTAAATTATTAAAATTAA-TAATATTTATTTTTTAAAAT
1 GTTATTAAATTATTAAAATTAACT-ATATTTATTTTTTAAAAT
*
1790564 GTTATTTAAA-TATTAAAATTAACTGTATTTATTTTTTAAAAT
1 GTTA-TTAAATTATTAAAATTAACTATATTTATTTTTTAAAAT
*
1790606 ATTATTAAATTATTAAAATTAA
1 GTTATTAAATTATTAAAATTAA
1790628 GGTATTTTGA
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
41 5 0.08
42 48 0.81
43 6 0.10
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (42 bp):
GTTATTAAATTATTAAAATTAACTATATTTATTTTTTAAAAT
Found at i:1790611 original size:19 final size:19
Alignment explanation
Indices: 1790542--1790611 Score: 59
Period size: 19 Copynumber: 3.5 Consensus size: 19
1790532 TATTAAAATT
*
1790542 AATAATATTTATTTTTTAA
1 AATATTATTTATTTTTTAA
* ** *
1790561 AATGTTATTTAAATATTAA
1 AATATTATTTATTTTTTAA
1790580 AATTAACTGTATTTATTTTTTAA
1 AA-T-A-T-TATTTATTTTTTAA
1790603 AATATTATT
1 AATATTATT
1790612 AAATTATTAA
Statistics
Matches: 38, Mismatches: 9, Indels: 8
0.69 0.16 0.15
Matches are distributed among these distances:
19 20 0.53
20 2 0.05
21 1 0.03
22 2 0.05
23 13 0.34
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (19 bp):
AATATTATTTATTTTTTAA
Found at i:1790621 original size:19 final size:20
Alignment explanation
Indices: 1790523--1790624 Score: 57
Period size: 19 Copynumber: 4.9 Consensus size: 20
1790513 TTTCAACACG
1790523 TTATTAAATTATTAAAATTAA
1 TTATTAAATTATTAAAA-TAA
* * * *
1790544 TAATATTTATTTTTTAAAAT-G
1 T--TATTAAATTATTAAAATAA
1790565 TTATTTAAA-TATTAAAATTAA
1 TTA-TTAAATTATTAAAA-TAA
* * *
1790586 CTGTATTTATTTTTTAAAAT-A
1 -T-TATTAAATTATTAAAATAA
1790607 TTATTAAATTATTAAAAT
1 TTATTAAATTATTAAAAT
1790625 TAAGGTATTT
Statistics
Matches: 59, Mismatches: 14, Indels: 18
0.65 0.15 0.20
Matches are distributed among these distances:
19 23 0.39
20 5 0.08
21 3 0.05
22 6 0.10
23 22 0.37
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (20 bp):
TTATTAAATTATTAAAATAA
Found at i:1791576 original size:24 final size:24
Alignment explanation
Indices: 1791549--1791597 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
1791539 TTAATTCATT
*
1791549 AATTTTCCTCAAATTTTGCAGTAA
1 AATTTTCCTCAAATTCTGCAGTAA
*
1791573 AATTTTGCTCAAATTCTGCAGTAA
1 AATTTTCCTCAAATTCTGCAGTAA
1791597 A
1 A
1791598 TTCAGCTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (24 bp):
AATTTTCCTCAAATTCTGCAGTAA
Found at i:1791605 original size:23 final size:24
Alignment explanation
Indices: 1791556--1791610 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
1791546 ATTAATTTTC
* **
1791556 CTCAAATTTTGCAGTAAAATTTTG
1 CTCAAATTCTGCAGTAAAATTCAG
1791580 CTCAAATTCTGCAGT-AAATTCAG
1 CTCAAATTCTGCAGTAAAATTCAG
1791603 CTCAAATT
1 CTCAAATT
1791611 AATTCACTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 14 0.50
24 14 0.50
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (24 bp):
CTCAAATTCTGCAGTAAAATTCAG
Found at i:1792476 original size:26 final size:25
Alignment explanation
Indices: 1792447--1792496 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1792437 AAAATTTTTT
1792447 AATTATTA-AAATATAATTTTAATTAA
1 AATT-TTATAAATATAA-TTTAATTAA
*
1792473 AATTTTATAACTATAATTTAATTA
1 AATTTTATAAATATAATTTAATTA
1792497 CAGGAAGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (25 bp):
AATTTTATAAATATAATTTAATTAA
Found at i:1793247 original size:10 final size:10
Alignment explanation
Indices: 1793232--1793386 Score: 55
Period size: 10 Copynumber: 13.9 Consensus size: 10
1793222 TCCTTGATTG
1793232 TAATAATATT
1 TAATAATATT
1793242 TAATAATATATTT
1 TAAT-A-ATA-TT
*
1793255 TAATATTTAATT
1 TAATA-AT-ATT
*
1793267 TGATAATATT
1 TAATAATATT
1793277 TAATGATATATT
1 TAAT-A-ATATT
*
1793289 TAATAGTATAT
1 TAATAATAT-T
1793300 TAA-ACATATTT
1 TAATA-ATA-TT
*
1793311 TAATATAAAATT
1 T-A-ATAATATT
*
1793323 TAATAATGTAT
1 TAATAATAT-T
1793334 TAA-AATTATTT
1 TAATAA-TA-TT
*
1793345 TAAAAATA-T
1 TAATAATATT
*
1793354 TATTTAATCATAT
1 TA-ATAAT-AT-T
1793367 TAGATAATATT
1 TA-ATAATATT
1793378 TAATAATAT
1 TAATAATAT
1793387 GAAAAATGTT
Statistics
Matches: 111, Mismatches: 14, Indels: 40
0.67 0.08 0.24
Matches are distributed among these distances:
9 3 0.03
10 31 0.28
11 28 0.25
12 31 0.28
13 17 0.15
14 1 0.01
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.48
Consensus pattern (10 bp):
TAATAATATT
Found at i:1793254 original size:12 final size:12
Alignment explanation
Indices: 1793232--1793366 Score: 65
Period size: 12 Copynumber: 11.5 Consensus size: 12
1793222 TCCTTGATTG
1793232 TAATAATATTTAA
1 TAAT-ATATTTAA
1793245 TAATATATTTTAA
1 TAATATA-TTTAA
* *
1793258 T-ATTTAATTTGA
1 TAATAT-ATTTAA
1793270 T-A-ATATTTAA
1 TAATATATTTAA
*
1793280 TGATATATTTAA
1 TAATATATTTAA
*
1793292 TAGTATA-TTAA
1 TAATATATTTAA
1793303 -ACATAT-TTTAA
1 TA-ATATATTTAA
*
1793314 T-ATAAAATTTAA
1 TAAT-ATATTTAA
*
1793326 TAATGTA-TTAA
1 TAATATATTTAA
1793337 -AAT-TATTTTAA
1 TAATATA-TTTAA
*
1793348 AAATATTATTTAA
1 TAATA-TATTTAA
*
1793361 TCATAT
1 TAATAT
1793367 TAGATAATAT
Statistics
Matches: 95, Mismatches: 12, Indels: 31
0.69 0.09 0.22
Matches are distributed among these distances:
9 2 0.02
10 12 0.13
11 22 0.23
12 36 0.38
13 21 0.22
14 2 0.02
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (12 bp):
TAATATATTTAA
Found at i:1793275 original size:15 final size:14
Alignment explanation
Indices: 1793255--1793292 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
1793245 TAATATATTT
1793255 TAATATTTAATTTGA
1 TAATATTTAA-TTGA
1793270 TAATATTTAA-TGA
1 TAATATTTAATTGA
1793283 T-ATATTTAAT
1 TAATATTTAAT
1793293 AGTATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 8 0.36
13 4 0.18
15 10 0.45
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (14 bp):
TAATATTTAATTGA
Found at i:1793313 original size:34 final size:33
Alignment explanation
Indices: 1793275--1793366 Score: 87
Period size: 34 Copynumber: 2.7 Consensus size: 33
1793265 TTTGATAATA
*
1793275 TTTAATGATATATTTAATAGTATATTAAACA-TAT
1 TTTAAT-ATATATTTAATAATATATTAAA-ATTAT
* *
1793309 TTTAATATAAAATTTAATAATGTATTAAAATTAT
1 TTTAATAT-ATATTTAATAATATATTAAAATTAT
* *
1793343 TTTAAAAATATTATTTAATCATAT
1 TTT-AATATA-TATTTAATAATAT
1793367 TAGATAATAT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
33 3 0.06
34 30 0.64
35 14 0.30
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (33 bp):
TTTAATATATATTTAATAATATATTAAAATTAT
Found at i:1793379 original size:55 final size:52
Alignment explanation
Indices: 1793315--1793442 Score: 141
Period size: 53 Copynumber: 2.4 Consensus size: 52
1793305 ATATTTTAAT
* * *
1793315 ATAAAATTTAATAATGTATTAAAATTATTTTAAAAATATTATTTAATCATATTA
1 ATAATATTTAATAAT-TATTAAAAATATTTTAAAAATATTATTTAATAATA-TA
* * *
1793369 GATAATATTTAATAA-TATGAAAAATGTTTTAAAAATATTATTTCATAATATA
1 -ATAATATTTAATAATTATTAAAAATATTTTAAAAATATTATTTAATAATATA
*
1793421 TTAAATATTTAATAATATATTA
1 AT-AATATTTAATAAT-TATTA
1793443 GATTTTTGTC
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
51 1 0.02
52 14 0.23
53 30 0.48
54 4 0.06
55 13 0.21
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (52 bp):
ATAATATTTAATAATTATTAAAAATATTTTAAAAATATTATTTAATAATATA
Found at i:1802121 original size:21 final size:22
Alignment explanation
Indices: 1802095--1802137 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
1802085 CTTTTTGTAC
1802095 TTTAAAATTAAAAA-TTATTTA
1 TTTAAAATTAAAAATTTATTTA
*
1802116 TTTAAATTTAAAAATTTATTTA
1 TTTAAAATTAAAAATTTATTTA
1802138 ATATTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTAAAATTAAAAATTTATTTA
Found at i:1802134 original size:18 final size:19
Alignment explanation
Indices: 1802111--1802148 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
1802101 ATTAAAAATT
1802111 ATTTATTTAA-ATTTAAAA
1 ATTTATTTAATATTTAAAA
1802129 ATTTATTTAATATTTAAAA
1 ATTTATTTAATATTTAAAA
1802148 A
1 A
1802149 AATTTGAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTATTTAATATTTAAAA
Found at i:1802149 original size:21 final size:20
Alignment explanation
Indices: 1802095--1802153 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
1802085 CTTTTTGTAC
* *
1802095 TTTAAAATTAAAAATTATTTA
1 TTTAAATTTAAAAA-AATTTA
1802116 TTTAAATTT--AAAAATTTA
1 TTTAAATTTAAAAAAATTTA
1802134 TTTAATATTTAAAAAAATTT
1 TTTAA-ATTTAAAAAAATTT
1802154 GAACAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 10 0.30
19 7 0.21
21 16 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTAAATTTAAAAAAATTTA
Found at i:1802197 original size:18 final size:18
Alignment explanation
Indices: 1802174--1802218 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
1802164 ATTAAATCTT
1802174 AAAAATAAGATTGAGTAA
1 AAAAATAAGATTGAGTAA
* * * *
1802192 AAAAATAAAATTTATTTA
1 AAAAATAAGATTGAGTAA
1802210 AAAAATAAG
1 AAAAATAAG
1802219 TTAGAGCCTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (18 bp):
AAAAATAAGATTGAGTAA
Found at i:1802302 original size:19 final size:17
Alignment explanation
Indices: 1802278--1802322 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
1802268 TCGAATAAAG
1802278 TATTTTATTATAAAATTT
1 TATTTTATTA-AAAATTT
*
1802296 ATATTTTA-TAATAATTT
1 -TATTTTATTAAAAATTT
1802313 TATTTTATTA
1 TATTTTATTA
1802323 GTTATTAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 7 0.29
17 8 0.33
18 2 0.08
19 7 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTTTATTAAAAATTT
Found at i:1802306 original size:16 final size:16
Alignment explanation
Indices: 1802285--1802320 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
1802275 AAGTATTTTA
1802285 TTATAA-AATTTATATT
1 TTATAATAATTT-TATT
1802301 TTATAATAATTTTATT
1 TTATAATAATTTTATT
1802317 TTAT
1 TTAT
1802321 TAGTTATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATAATAATTTTATT
Found at i:1802419 original size:33 final size:31
Alignment explanation
Indices: 1802382--1802444 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
1802372 TTTAAAAGAA
1802382 TATTAACAAA-AAAATTAATAAAATATATTTAAT
1 TATTAA-AAATAAAATT-A-AAAATATATTTAAT
*
1802415 TATTAAAAATTAAATTAAAAATATATTTAA
1 TATTAAAAATAAAATTAAAAATATATTTAA
1802445 AAAATAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 13 0.46
32 4 0.14
33 11 0.39
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (31 bp):
TATTAAAAATAAAATTAAAAATATATTTAAT
Found at i:1804180 original size:15 final size:16
Alignment explanation
Indices: 1804154--1804195 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
1804144 GGTACTATTT
1804154 TAATTT-TTTTAAATA
1 TAATTTATTTTAAATA
1804169 T-ATTTATTTTAAATA
1 TAATTTATTTTAAATA
1804184 TAATTTTATTTT
1 TAA-TTTATTTT
1804196 TATACACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 4 0.17
15 11 0.46
16 1 0.04
17 8 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TAATTTATTTTAAATA
Found at i:1805371 original size:19 final size:21
Alignment explanation
Indices: 1805347--1805386 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
1805337 ATATTAAAAA
1805347 TTATTTTTAT-ATT-AATTTT
1 TTATTTTTATAATTAAATTTT
1805366 TTATTTTTATAATTAAATTTT
1 TTATTTTTATAATTAAATTTT
1805387 AATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.53
20 3 0.16
21 6 0.32
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
TTATTTTTATAATTAAATTTT
Found at i:1806664 original size:12 final size:12
Alignment explanation
Indices: 1806644--1806676 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
1806634 AAATAATTAA
1806644 ATAATTAAAGTG
1 ATAATTAAAGTG
*
1806656 ATAACTAAAGTG
1 ATAATTAAAGTG
1806668 ATAATTAAA
1 ATAATTAAA
1806677 ATTCTAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.55, C:0.03, G:0.12, T:0.30
Consensus pattern (12 bp):
ATAATTAAAGTG
Found at i:1808760 original size:22 final size:22
Alignment explanation
Indices: 1808734--1808794 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 22
1808724 TTGTATAATA
1808734 AATTAAAAAATTATTTAAATTT
1 AATTAAAAAATTATTTAAATTT
* *
1808756 AATT-ATAAATATATATAAATTT
1 AATTAAAAAAT-TATTTAAATTT
* *
1808778 -TTTAAAAAAAT-TTTAAA
1 AATTAAAAAATTATTTAAA
1808795 AAATAAAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
20 5 0.16
21 8 0.26
22 18 0.58
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AATTAAAAAATTATTTAAATTT
Found at i:1809024 original size:29 final size:30
Alignment explanation
Indices: 1808975--1809032 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
1808965 GACAAAGTGC
* *
1808975 TGTTAATTTTTAAATAGATTATTAAAATAA
1 TGTTAATTTTAAAATAAATTATTAAAATAA
1809005 TGTTAA-TTTAAAATAAATTATTAAAATA
1 TGTTAATTTTAAAATAAATTATTAAAATA
1809033 TTATTGTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 20 0.77
30 6 0.23
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (30 bp):
TGTTAATTTTAAAATAAATTATTAAAATAA
Found at i:1809976 original size:2 final size:2
Alignment explanation
Indices: 1809969--1810000 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1809959 TGTATGTATG
*
1809969 TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1810001 ATTTTGTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1810597 original size:9 final size:9
Alignment explanation
Indices: 1810534--1810618 Score: 52
Period size: 10 Copynumber: 9.4 Consensus size: 9
1810524 AGTTGATTAC
1810534 TATTTAA-A
1 TATTTAATA
*
1810542 TATATTAAAA
1 TAT-TTAATA
*
1810552 TATTTATATT
1 TATTTA-ATA
1810562 TATTTAATA
1 TATTTAATA
* *
1810571 TGTTTTAAAA
1 T-ATTTAATA
1810581 TA-TT--TA
1 TATTTAATA
1810587 TATTTAATA
1 TATTTAATA
1810596 TATTTAAATA
1 TATTT-AATA
* *
1810606 TACTAAATA
1 TATTTAATA
1810615 TATT
1 TATT
1810619 AAAATATGTT
Statistics
Matches: 59, Mismatches: 10, Indels: 15
0.70 0.12 0.18
Matches are distributed among these distances:
6 3 0.05
7 2 0.03
8 5 0.08
9 24 0.41
10 25 0.42
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (9 bp):
TATTTAATA
Found at i:1810607 original size:10 final size:10
Alignment explanation
Indices: 1810534--1810630 Score: 61
Period size: 9 Copynumber: 10.6 Consensus size: 10
1810524 AGTTGATTAC
1810534 TATTTAAATA
1 TATTTAAATA
1810544 TA-TTAAA-A
1 TATTTAAATA
* *
1810552 TATTTATATT
1 TATTTAAATA
1810562 TATTT-AATA
1 TATTTAAATA
*
1810571 TGTTTTAAA-A
1 T-ATTTAAATA
1810581 TA-TT---TA
1 TATTTAAATA
1810587 TATTT-AATA
1 TATTTAAATA
1810596 TATTTAAATA
1 TATTTAAATA
*
1810606 TA-CTAAATA
1 TATTTAAATA
*
1810615 TATTAAAATA
1 TATTTAAATA
*
1810625 TGTTTA
1 TATTTA
1810631 TATTGTAAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
6 3 0.05
7 2 0.03
8 5 0.08
9 27 0.41
10 27 0.41
11 2 0.03
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (10 bp):
TATTTAAATA
Found at i:1810912 original size:29 final size:29
Alignment explanation
Indices: 1810871--1810929 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 29
1810861 GATGAATTAT
1810871 TTTTTCTTACATTCAG-TAAAAGTAATGCA
1 TTTTTCTTACATTCAGTTAAAA-TAATGCA
1810900 TTTTTCTTACATTCAGTTAAAATAATGCA
1 TTTTTCTTACATTCAGTTAAAATAATGCA
1810929 T
1 T
1810930 ATGAAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 24 0.83
30 5 0.17
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.44
Consensus pattern (29 bp):
TTTTTCTTACATTCAGTTAAAATAATGCA
Found at i:1811165 original size:18 final size:18
Alignment explanation
Indices: 1811141--1811186 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
1811131 TTTGAGCTAT
*
1811141 ATATATTTTAATATTTTC
1 ATATATTTTAATATATTC
*
1811159 GTATATTTTAATATATTC
1 ATATATTTTAATATATTC
1811177 ATATTATTTT
1 ATA-TATTTT
1811187 TTATATTGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (18 bp):
ATATATTTTAATATATTC
Done.