Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007566.1 Hibiscus syriacus cultivar Beakdansim tig00021514_pilon, whole genome shotgun sequence
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: 93967
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1382 original size:80 final size:80
Alignment explanation
Indices: 1251--1406 Score: 233
Period size: 80 Copynumber: 1.9 Consensus size: 80
1241 TATGAGAGAT
* *
1251 GTCAAGAATATAAGGAAAAATTCTAGCTAAAAGTTCCATCAAATCTGAAGATTACTTTACTATAT
1 GTCAAGAATATAA-GAAAAAATCTAGCTAAAAGCTCCATCAAATCTGAAGA-TACTTTACTATAT
1316 GAAATATATTGAGAAAA
64 GAAATATATTGAGAAAA
* * * *
1333 GTCAAGAATATAA-AAAAAATCTAGCTAAAAGCTCTATCAAATCTTAAGATGCTTTACTTTATGA
1 GTCAAGAATATAAGAAAAAATCTAGCTAAAAGCTCCATCAAATCTGAAGATACTTTACTATATGA
1397 AATATATTGA
66 AATATATTGA
1407 AAAGCATCTA
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
79 23 0.34
80 32 0.47
82 13 0.19
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.31
Consensus pattern (80 bp):
GTCAAGAATATAAGAAAAAATCTAGCTAAAAGCTCCATCAAATCTGAAGATACTTTACTATATGA
AATATATTGAGAAAA
Found at i:7134 original size:3 final size:3
Alignment explanation
Indices: 7122--7176 Score: 58
Period size: 3 Copynumber: 18.0 Consensus size: 3
7112 TTTTTTTTAT
* **
7122 TTA TTG TTA TTA TTA TT- TTA TTTA TTA TTTA TTA TTA TTA AAA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA -TTA TTA TTA TTA TTA TTA
7168 TTA TTA TTA
1 TTA TTA TTA
7177 CAAACAGGTC
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
2 2 0.05
3 35 0.81
4 6 0.14
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:7145 original size:25 final size:22
Alignment explanation
Indices: 7116--7160 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
7106 TACCCATTTT
*
7116 TTTTATTTATT-GTTATTATTA
1 TTTTATTTATTATTTATTATTA
7137 TTTTATTTATTATTTATTATTA
1 TTTTATTTATTATTTATTATTA
7159 TT
1 TT
7161 AAAATTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (22 bp):
TTTTATTTATTATTTATTATTA
Found at i:7161 original size:25 final size:25
Alignment explanation
Indices: 7111--7161 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
7101 TTTTTTACCC
* *
7111 ATTTTTTTTATTTATTGTTATTATT
1 ATTTTATTTATTTATTATTATTATT
7136 ATTTTATTTA-TTATTTATTATTATT
1 ATTTTATTTATTTA-TTATTATTATT
7161 A
1 A
7162 AAATTATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 3 0.13
25 20 0.87
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (25 bp):
ATTTTATTTATTTATTATTATTATT
Found at i:7168 original size:22 final size:21
Alignment explanation
Indices: 7122--7176 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
7112 TTTTTTTTAT
* ** *
7122 TTATTGTTATTATTATTTTAT
1 TTATTATTATTATTATTAAAA
7143 TTATTATTTATTATTATTAAAA
1 TTATTA-TTATTATTATTAAAA
7165 TTATTATTATTA
1 TTATTATTATTA
7177 CAAACAGGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 11 0.38
22 18 0.62
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (21 bp):
TTATTATTATTATTATTAAAA
Found at i:7174 original size:28 final size:28
Alignment explanation
Indices: 7118--7176 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
7108 CCCATTTTTT
* **
7118 TTATTTATTGTTATTATTATTTTATTTA
1 TTATTTATTATTATTAAAATTTTATTTA
7146 TTATTTATTATTATTAAAATTATTA-TTA
1 TTATTTATTATTATTAAAATT-TTATTTA
7174 TTA
1 TTA
7177 CAAACAGGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 24 0.89
29 3 0.11
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (28 bp):
TTATTTATTATTATTAAAATTTTATTTA
Found at i:14501 original size:19 final size:18
Alignment explanation
Indices: 14468--14521 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
14458 CTTTCAAAAT
*
14468 TTTTTTATTA-CTTATTA
1 TTTTTTATTATTTTATTA
14485 TTTTTATATTATTTTATTA
1 TTTTT-TATTATTTTATTA
14504 CTATTTTT-TTATTTTATT
1 -T-TTTTTATTATTTTATT
14522 CAGGTATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
17 5 0.16
18 5 0.16
19 16 0.50
20 2 0.06
21 4 0.12
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTTATTATTTTATTA
Found at i:14508 original size:14 final size:14
Alignment explanation
Indices: 14470--14516 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
14460 TTCAAAATTT
14470 TTTTATTACTTATTA
1 TTTTATTAC-TATTA
14485 -TTT-TTA-TATTA
1 TTTTATTACTATTA
*
14496 TTTTATTACTATTT
1 TTTTATTACTATTA
14510 TTTTATT
1 TTTTATT
14517 TTATTCAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
11 5 0.18
12 3 0.11
13 6 0.21
14 14 0.50
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTATTACTATTA
Found at i:16028 original size:8 final size:7
Alignment explanation
Indices: 16004--16045 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
15994 TTTTCATACA
16004 TGCA-TT
1 TGCATTT
16010 TGCATTT
1 TGCATTT
16017 TGCATCTT
1 TGCAT-TT
16025 TGCATTT
1 TGCATTT
* *
16032 TTCATTG
1 TGCATTT
16039 TGCATTT
1 TGCATTT
16046 ATACTTTTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:16028 original size:15 final size:14
Alignment explanation
Indices: 16004--16045 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
15994 TTTTCATACA
16004 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
16017 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
16032 TTCATTGTGCATTT
1 TGCATTTTGCATTT
16046 ATACTTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:16121 original size:12 final size:12
Alignment explanation
Indices: 16104--16131 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
16094 ACATTCACAT
16104 ATTTACATTTGC
1 ATTTACATTTGC
16116 ATTTACATTTGC
1 ATTTACATTTGC
16128 ATTT
1 ATTT
16132 TTTATGTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.14, G:0.07, T:0.54
Consensus pattern (12 bp):
ATTTACATTTGC
Found at i:18113 original size:11 final size:11
Alignment explanation
Indices: 18094--18149 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
18084 ATCCAGCAAA
*
18094 GAAAGAAGAAG
1 GAAAAAAGAAG
18105 GAAAAAAGAA-
1 GAAAAAAGAAG
18115 -AAAAAAG--G
1 GAAAAAAGAAG
*
18123 AAAAAAAGAAG
1 GAAAAAAGAAG
*
18134 GAAAAAAAAAG
1 GAAAAAAGAAG
18145 GAAAA
1 GAAAA
18150 TTGAATCAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
9 14 0.37
11 24 0.63
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (11 bp):
GAAAAAAGAAG
Found at i:18129 original size:18 final size:18
Alignment explanation
Indices: 18091--18139 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
18081 CTCATCCAGC
*
18091 AAAGAAAGAAGAAGGAAA
1 AAAGAAAGAAAAAGGAAA
18109 AAAGAAA-AAAAAGGAAAA
1 AAAGAAAGAAAAAGG-AAA
*
18127 AAAGAAGGAAAAA
1 AAAGAAAGAAAAA
18140 AAAAGGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 16 0.59
19 5 0.19
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (18 bp):
AAAGAAAGAAAAAGGAAA
Found at i:18134 original size:12 final size:11
Alignment explanation
Indices: 18113--18149 Score: 65
Period size: 11 Copynumber: 3.3 Consensus size: 11
18103 AGGAAAAAAG
18113 AAAAAAAAGGA
1 AAAAAAAAGGA
18124 AAAAAAGAAGGA
1 AAAAAA-AAGGA
18136 AAAAAAAAGGA
1 AAAAAAAAGGA
18147 AAA
1 AAA
18150 TTGAATCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGGA
Found at i:23658 original size:113 final size:112
Alignment explanation
Indices: 23460--23878 Score: 601
Period size: 113 Copynumber: 3.7 Consensus size: 112
23450 ATCCATTACA
* *
23460 ATGGATCAAAATTTCCAGA-AAGAGTTCATAATGAGAAGAACTCATATGAAGAATGAAGAAGAAG
1 ATGGATCAACATTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAG
*
23524 TTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTG
64 TTCATAATGAGAAGAGATTGTTCAACCTTTTGCTCAAATCCATCACTTG
*
23573 ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGT
1 ATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG-AAGAAGAAGT
23638 TCATAATGAGAAGAGATTGTTCAACCTTTTGCTCAAATCCATCACTTG
65 TCATAATGAGAAGAGATTGTTCAACCTTTTGCTCAAATCCATCACTTG
* *
23686 ATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGT
* * ** * *
23751 TCATAATGAGAATA-ATTTGTTCAACCTTTTGTTTGAATTCATCATTTG
65 TCATAATGAGAAGAGA-TTGTTCAACCTTTTGCTCAAATCCATCACTTG
* * * *
23799 ATGGATCAGCATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGGAAGAAGGAGAAA
1 ATGGATCAACATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAA-GAAGAAGAAG-AA
23863 GTTCATAATGAGAAGA
63 GTTCATAATGAGAAGA
23879 ACTTATCTGA
Statistics
Matches: 283, Mismatches: 16, Indels: 13
0.91 0.05 0.04
Matches are distributed among these distances:
112 3 0.01
113 257 0.91
114 23 0.08
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.27
Consensus pattern (112 bp):
ATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTT
CATAATGAGAAGAGATTGTTCAACCTTTTGCTCAAATCCATCACTTG
Found at i:23918 original size:39 final size:41
Alignment explanation
Indices: 23821--23918 Score: 139
Period size: 41 Copynumber: 2.4 Consensus size: 41
23811 TGCCAGGTAG
*
23821 AGTTCATAATGAGAAGAACTCATCTGAAGGAAGAAGGAGAA
1 AGTTCATAATGAGAAGAACTCATCTGAAGGAAGAAGAAGAA
*
23862 AGTTCATAATGAGAAGAACTTATCTGAA-G-AGAAAGAAG-A
1 AGTTCATAATGAGAAGAACTCATCTGAAGGAAG-AAGAAGAA
*
23901 ATTTCATAATGAGAAGAA
1 AGTTCATAATGAGAAGAA
23919 TTTGTTCAAC
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
39 20 0.38
40 6 0.11
41 27 0.51
ACGTcount: A:0.48, C:0.08, G:0.23, T:0.20
Consensus pattern (41 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGGAAGAAGAAGAA
Found at i:24076 original size:124 final size:124
Alignment explanation
Indices: 23857--24176 Score: 481
Period size: 124 Copynumber: 2.6 Consensus size: 124
23847 AAGGAAGAAG
* * * **
23857 GAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGA-AAGAAGAATTTCATAATGAGAAGAATT
1 GAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAGCT
*
23921 TGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGCATCAACTTTTCCA
66 TGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGCATCAACATTTCCA
23980 GAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAGCT
1 GAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAGCT
* * * *
24045 TGTTCGACCTTTTGCATGACTCTATCACAGAAGGAGATATATCATCATCAGCATTTCCA
66 TGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGCATCAACATTTCCA
* *
24104 GA-AGGAGTTCATAATGAGAAGAACTCATCT---G-AAGAAGAAGAAGTTCACAATGAGAAGAGC
1 GAGA-AAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAGC
24164 TTGTTCAACCTTT
65 TTGTTCAACCTTT
24177 GCTAGATTAC
Statistics
Matches: 182, Mismatches: 13, Indels: 7
0.90 0.06 0.03
Matches are distributed among these distances:
120 40 0.22
121 1 0.01
123 36 0.20
124 105 0.58
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.25
Consensus pattern (124 bp):
GAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAGCT
TGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGCATCAACATTTCCA
Found at i:24413 original size:3 final size:3
Alignment explanation
Indices: 24401--24455 Score: 58
Period size: 3 Copynumber: 18.0 Consensus size: 3
24391 ATTTTTTTAT
* **
24401 TTA TTG TTA TTA TTA TT- TTA TTTA TTA TTTA TTA TTA TTA AAA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA -TTA TTA TTA TTA TTA TTA
24447 TTA TTA TTA
1 TTA TTA TTA
24456 CAAACAGGCC
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
2 2 0.05
3 35 0.81
4 6 0.14
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:24419 original size:22 final size:23
Alignment explanation
Indices: 24394--24439 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
24384 TTTACCCATT
24394 TTTTTATTTATT-GTTATTATTA
1 TTTTTATTTATTAGTTATTATTA
*
24416 -TTTTATTTATTATTTATTATTA
1 TTTTTATTTATTAGTTATTATTA
24438 TT
1 TT
24440 AAAATTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 11 0.52
22 9 0.43
23 1 0.05
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (23 bp):
TTTTTATTTATTAGTTATTATTA
Found at i:24425 original size:25 final size:21
Alignment explanation
Indices: 24391--24439 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 21
24381 TTTTTTACCC
24391 ATTTTTTTATTTATTGTTATTATT
1 ATTTTTTTA-TTA-T-TTATTATT
24415 ATTTTATTTATTATTTATTATT
1 ATTTT-TTTATTATTTATTATT
24437 ATT
1 ATT
24440 AAAATTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 11 0.46
23 1 0.04
24 8 0.33
25 4 0.17
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (21 bp):
ATTTTTTTATTATTTATTATT
Found at i:24440 original size:25 final size:24
Alignment explanation
Indices: 24391--24440 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
24381 TTTTTTACCC
*
24391 ATTTTTTTATTTATTGTTATTATT
1 ATTTTTTTATTTATTATTATTATT
24415 ATTTTATTTA-TTATTTATTATTATT
1 ATTTT-TTTATTTA-TTATTATTATT
24440 A
1 A
24441 AAATTATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (24 bp):
ATTTTTTTATTTATTATTATTATT
Found at i:24447 original size:22 final size:21
Alignment explanation
Indices: 24401--24455 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
24391 ATTTTTTTAT
* ** *
24401 TTATTGTTATTATTATTTTAT
1 TTATTATTATTATTATTAAAA
24422 TTATTATTTATTATTATTAAAA
1 TTATTA-TTATTATTATTAAAA
24444 TTATTATTATTA
1 TTATTATTATTA
24456 CAAACAGGCC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 11 0.38
22 18 0.62
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (21 bp):
TTATTATTATTATTATTAAAA
Found at i:24453 original size:28 final size:28
Alignment explanation
Indices: 24397--24455 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
24387 ACCCATTTTT
* **
24397 TTATTTATTGTTATTATTATTTTATTTA
1 TTATTTATTATTATTAAAATTTTATTTA
24425 TTATTTATTATTATTAAAATTATTA-TTA
1 TTATTTATTATTATTAAAATT-TTATTTA
24453 TTA
1 TTA
24456 CAAACAGGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 24 0.89
29 3 0.11
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (28 bp):
TTATTTATTATTATTAAAATTTTATTTA
Found at i:26147 original size:150 final size:150
Alignment explanation
Indices: 25848--26147 Score: 333
Period size: 150 Copynumber: 2.0 Consensus size: 150
25838 ATTATAATAG
* * *
25848 TATTTATTTATTTTTTAATATCAAAGAAAGGGACAGTCTTAAAGCAACTAGATGTCCGATTTCTG
1 TATTTATTTATTTTTTAATATCAAAGAAAGAGACAGTCTTAAAGCAACTAGAAGTCCCATTTCTG
* * * * * ** * *
25913 ATATTTTTAAATAAATAAATATTTTACTTTTATAAAATTGTATATATTAATCTATTTTTTTATTA
66 ATATTTCTAAATAAATAAATATCTTACTTATATAAAATTATATAAATTAATAAATTTTCTTATAA
* * *
25978 TTTTTAGATAAATATTTTAA
131 ATTATAGATAAATAATTTAA
* * *
25998 TATTTATTTATTTTTTTAATATCGAAAGAAAGAG-CTGTCTTAAAGCACCTAGAAG-CCCTTTTC
1 TATTTATTTA-TTTTTTAATATC-AAAGAAAGAGACAGTCTTAAAGCAACTAGAAGTCCCATTTC
*
26061 TGATATTTCTAAATAAATAAATATCTTA-TATATATATATATATATATAAATTAATAAATTTTCT
64 TGATATTTCTAAATAAATAAATATCTTACT-TATATA-AAAT-TATATAAATTAATAAATTTTCT
26125 TA-AAATTATA-AT-AATAAATTTAA
126 TATAAATTATAGATAAAT-AATTTAA
26148 ATTAAATAGG
Statistics
Matches: 125, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
149 4 0.03
150 55 0.44
151 38 0.30
152 28 0.22
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.45
Consensus pattern (150 bp):
TATTTATTTATTTTTTAATATCAAAGAAAGAGACAGTCTTAAAGCAACTAGAAGTCCCATTTCTG
ATATTTCTAAATAAATAAATATCTTACTTATATAAAATTATATAAATTAATAAATTTTCTTATAA
ATTATAGATAAATAATTTAA
Found at i:37834 original size:11 final size:11
Alignment explanation
Indices: 37799--37850 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
37789 AGTGAAAAAG
37799 AAAAATGAAAT
1 AAAAATGAAAT
*
37810 AAAAA-GATGA-
1 AAAAATGA-AAT
37820 AAAAATGAAAT
1 AAAAATGAAAT
*
37831 AAAAATGAAAAG
1 AAAAATG-AAAT
37843 AAAAATGA
1 AAAAATGA
37851 GGGTTTGAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
10 8 0.24
11 16 0.47
12 10 0.29
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (11 bp):
AAAAATGAAAT
Found at i:38206 original size:19 final size:20
Alignment explanation
Indices: 38168--38206 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
38158 CCATCACTTT
**
38168 GTAAATTCAATTTCTTGTTA
1 GTAAATTCAAAGTCTTGTTA
38188 GTAAATTCAAAGT-TTGTTA
1 GTAAATTCAAAGTCTTGTTA
38207 TTTCAAGCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (20 bp):
GTAAATTCAAAGTCTTGTTA
Found at i:38986 original size:105 final size:105
Alignment explanation
Indices: 38797--39091 Score: 401
Period size: 105 Copynumber: 2.8 Consensus size: 105
38787 CCGCAGAAAG
* **
38797 AGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGCCTTAAAGGAGAAAATTCGT
1 AGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCTTAAAGGAGAAGGTTCGT
* * *
38862 GATGAGAAGAACTTTTTCCTTTCAAATCTACCCTAGAAGA
66 AATGAGAAGAACATGTTCCTTTCAAATCTACCCTAGAAGA
* * * * *
38902 ATGTGAACCAACATTTCCAAAAGAGTTCATAGTGAGAAGAACTCATCTTAAATGAGAAGGTTCGT
1 AGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCTTAAAGGAGAAGGTTCGT
* * *
38967 AATGTGAAGAGCATGTTCCTTTCAAATTTACCCTAGAAGA
66 AATGAGAAGAACATGTTCCTTTCAAATCTACCCTAGAAGA
* * *
39007 AGGTGAATCGACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAGAAGTTC
1 AGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCTTAAAGGAGAAG--GTTC
* *
39072 ATAATGAGAAGAACTTGTTC
64 GTAATGAGAAGAACATGTTC
39092 AACTTTAGCT
Statistics
Matches: 162, Mismatches: 26, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
105 142 0.88
107 20 0.12
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.25
Consensus pattern (105 bp):
AGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCTTAAAGGAGAAGGTTCGT
AATGAGAAGAACATGTTCCTTTCAAATCTACCCTAGAAGA
Found at i:39091 original size:20 final size:19
Alignment explanation
Indices: 39031--39092 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
39021 TTCCAGAAGA
39031 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
* *
39050 CG-TCCTAAAGGAGAAGAA--
1 -GTTCAT-AATGAGAAGAACT
39068 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAAC-T
39088 GTTCA
1 GTTCA
39093 ACTTTAGCTC
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
17 11 0.33
18 3 0.09
19 3 0.09
20 16 0.48
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.24
Consensus pattern (19 bp):
GTTCATAATGAGAAGAACT
Found at i:42767 original size:17 final size:17
Alignment explanation
Indices: 42734--42767 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
42724 ATATTTACCT
*
42734 ATATTAGTTATATAAAA
1 ATATTAGTTATACAAAA
*
42751 ATATTAGTTCTACAAAA
1 ATATTAGTTATACAAAA
42768 TTCAAATCTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (17 bp):
ATATTAGTTATACAAAA
Found at i:43418 original size:30 final size:30
Alignment explanation
Indices: 43348--43404 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
43338 GAGAAAATGA
43348 AATTCATTTTACATAAAACAAATTTCAAGT
1 AATTCATTTTACATAAAACAAATTTCAAGT
* *
43378 AATTCATTTTACGTAAAACAATTTTCA
1 AATTCATTTTACATAAAACAAATTTCA
43405 TGTTATTAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.44, C:0.14, G:0.04, T:0.39
Consensus pattern (30 bp):
AATTCATTTTACATAAAACAAATTTCAAGT
Found at i:44050 original size:27 final size:26
Alignment explanation
Indices: 44017--44095 Score: 70
Period size: 27 Copynumber: 3.0 Consensus size: 26
44007 AAAAATGTGT
44017 AAGAATAATTGGGTAACTAAATACAA
1 AAGAATAATTGGGTAACTAAATACAA
* * ***
44043 AAGTAATAGTTTGGTAA-TAAAAATATGC
1 AAG-AATAATTGGGTAACT--AAATACAA
*
44071 GAGAATAATTGGGTAACTAAATACA
1 AAGAATAATTGGGTAACTAAATACA
44096 TAGTTTACCA
Statistics
Matches: 39, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
26 9 0.23
27 22 0.56
28 8 0.21
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.27
Consensus pattern (26 bp):
AAGAATAATTGGGTAACTAAATACAA
Found at i:44050 original size:54 final size:54
Alignment explanation
Indices: 43988--44095 Score: 171
Period size: 54 Copynumber: 2.0 Consensus size: 54
43978 AAATAGAACC
* *
43988 AAAGTAATAGTTTAGTAACAAAAATGTGTAAGAATAATTGGGTAACTAAATACA
1 AAAGTAATAGTTTAGTAACAAAAATATGCAAGAATAATTGGGTAACTAAATACA
* * *
44042 AAAGTAATAGTTTGGTAATAAAAATATGCGAGAATAATTGGGTAACTAAATACA
1 AAAGTAATAGTTTAGTAACAAAAATATGCAAGAATAATTGGGTAACTAAATACA
44096 TAGTTTACCA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.28
Consensus pattern (54 bp):
AAAGTAATAGTTTAGTAACAAAAATATGCAAGAATAATTGGGTAACTAAATACA
Found at i:51229 original size:2 final size:2
Alignment explanation
Indices: 51224--51249 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
51214 ACTCAATTTA
51224 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
51250 GTTCTGAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:52960 original size:13 final size:13
Alignment explanation
Indices: 52942--52968 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
52932 GACCATCGTT
52942 TTTTTTTATTTTA
1 TTTTTTTATTTTA
52955 TTTTTTTATTTTA
1 TTTTTTTATTTTA
52968 T
1 T
52969 ATTAAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTTTATTTTA
Found at i:61263 original size:42 final size:41
Alignment explanation
Indices: 61188--61391 Score: 177
Period size: 42 Copynumber: 4.9 Consensus size: 41
61178 TAAAAAACTA
61188 GGCCTCAAATT-TAAAG-TAAAAGGTGAGATTGAAAAATTAAG
1 GGCCT-AAATTATAAAGTTAAAA-GTGAGATTGAAAAATTAAG
* *
61229 GGCCTAAATTATATAAGTTAAAAGTGGGATTGAAAAAAATT-AT
1 GGCCTAAATTATA-AAGTTAAAAGTGAGATTG--AAAAATTAAG
* * * * *
61272 GGCCTCAATTATAAAGGTAAAAAGTGATATTAAAAAATTAGG
1 GGCCTAAATTATAAA-GTTAAAAGTGAGATTGAAAAATTAAG
* *
61314 GGCCGT-AATTATAAA-TGTAGAAAGAGAGATTGAAAAATCAAG
1 GGCC-TAAATTATAAAGT-TA-AAAGTGAGATTGAAAAATTAAG
* *
61356 AG-CTCAATTATAAAGTTACAAAGTGAGATTGAAAAA
1 GGCCTAAATTATAAAGTTA-AAAGTGAGATTGAAAAA
61392 CTTAGGATCG
Statistics
Matches: 133, Mismatches: 18, Indels: 24
0.76 0.10 0.14
Matches are distributed among these distances:
40 7 0.05
41 43 0.32
42 45 0.34
43 31 0.23
44 7 0.05
ACGTcount: A:0.48, C:0.07, G:0.20, T:0.25
Consensus pattern (41 bp):
GGCCTAAATTATAAAGTTAAAAGTGAGATTGAAAAATTAAG
Found at i:61450 original size:44 final size:43
Alignment explanation
Indices: 61402--61507 Score: 126
Period size: 43 Copynumber: 2.4 Consensus size: 43
61392 CTTAGGATCG
*
61402 TCAATTATAAATG-TAAAAATGTATGATTGA-AAAAATTAAAGACA
1 TCAATTATAAA-GATAAAAA-GTAGGATT-ACAAAAATTAAAGACA
* * * *
61446 TCAATTGTAAAGATAAAAAGTAGGATTACAAGAATTAGAGGCA
1 TCAATTATAAAGATAAAAAGTAGGATTACAAAAATTAAAGACA
61489 TCAATTATAAAGATAAAAA
1 TCAATTATAAAGATAAAAA
61508 AAATTAAGAA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
42 1 0.02
43 37 0.69
44 16 0.30
ACGTcount: A:0.54, C:0.06, G:0.14, T:0.26
Consensus pattern (43 bp):
TCAATTATAAAGATAAAAAGTAGGATTACAAAAATTAAAGACA
Found at i:72345 original size:31 final size:31
Alignment explanation
Indices: 72307--72367 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
72297 GTGAATGAGG
* *
72307 GACTAAAATCGAACGGATCGATAATATTAGA
1 GACTAAAATCGAACGAATCAATAATATTAGA
*
72338 GACTAAAATCGAACGAATCAATAATGTTAG
1 GACTAAAATCGAACGAATCAATAATATTAG
72368 GGATCATTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.46, C:0.13, G:0.18, T:0.23
Consensus pattern (31 bp):
GACTAAAATCGAACGAATCAATAATATTAGA
Found at i:73911 original size:28 final size:27
Alignment explanation
Indices: 73874--73928 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 27
73864 AATTCTTTCC
73874 TTAATTAAGTGAGTTTATTTAACAATA
1 TTAATTAAGTGAGTTTATTTAACAATA
*
73901 TTAATGTAAGTGAGTTTATTTATCAATA
1 TTAAT-TAAGTGAGTTTATTTAACAATA
73929 ATAAAAGTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 5 0.19
28 21 0.81
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.45
Consensus pattern (27 bp):
TTAATTAAGTGAGTTTATTTAACAATA
Found at i:73981 original size:18 final size:17
Alignment explanation
Indices: 73951--73985 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
73941 TAATGGAAAT
73951 TGATTAAACTAAAGTTG
1 TGATTAAACTAAAGTTG
*
73968 TGATCTAAATTAAAGTTG
1 TGAT-TAAACTAAAGTTG
73986 AAATAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.37
Consensus pattern (17 bp):
TGATTAAACTAAAGTTG
Found at i:74821 original size:10 final size:10
Alignment explanation
Indices: 74806--74833 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
74796 ATTAAATAAT
74806 TATTTATATA
1 TATTTATATA
74816 TATTTATATA
1 TATTTATATA
74826 TATTTATA
1 TATTTATA
74834 AAGTTTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
TATTTATATA
Found at i:74882 original size:24 final size:22
Alignment explanation
Indices: 74814--74898 Score: 68
Period size: 23 Copynumber: 3.8 Consensus size: 22
74804 ATTATTTATA
*
74814 TATATTTATATATATTTATAAAG
1 TATATTTATA-ATATTTAAAAAG
*
74837 TTTATATTA-AATTATTCTAAAAAG
1 TATAT-TTATAA-TATT-TAAAAAG
*
74861 TATATTTATAATATTATGAAAA-
1 TATATTTATAATATT-TAAAAAG
*
74883 TAT-TTTAAAATATTTA
1 TATATTTATAATATTTA
74899 TTTAATTTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
20 1 0.02
21 10 0.20
22 4 0.08
23 21 0.41
24 15 0.29
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (22 bp):
TATATTTATAATATTTAAAAAG
Found at i:74922 original size:21 final size:19
Alignment explanation
Indices: 74884--74923 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
74874 TTATGAAAAT
74884 ATTTTAAAATATTTATTTA
1 ATTTTAAAATATTTATTTA
*
74903 ATTTTTAAATCATATTATTTA
1 ATTTTAAAAT-AT-TTATTTA
74924 TTTGAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 2 0.11
21 7 0.39
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTTAAAATATTTATTTA
Found at i:74964 original size:19 final size:19
Alignment explanation
Indices: 74909--74996 Score: 60
Period size: 19 Copynumber: 4.5 Consensus size: 19
74899 TTTAATTTTT
*
74909 AAATCATATTATTTATTTG
1 AAATAATATTATTTATTTG
74928 AAATAATATTAATAATTTATTTG
1 AAATAATA-T--T-ATTTATTTG
*
74951 AAGTAATATTATTT-TTT-
1 AAATAATATTATTTATTTG
74968 AAAT--TATCTATTTAAATTT-
1 AAATAATAT-TATTT--ATTTG
74987 AAATAATATT
1 AAATAATATT
74997 TTACGAAACC
Statistics
Matches: 56, Mismatches: 3, Indels: 19
0.72 0.04 0.24
Matches are distributed among these distances:
15 3 0.05
16 5 0.09
17 3 0.05
18 3 0.05
19 18 0.32
20 3 0.05
21 3 0.05
22 2 0.04
23 16 0.29
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.51
Consensus pattern (19 bp):
AAATAATATTATTTATTTG
Found at i:76044 original size:2 final size:2
Alignment explanation
Indices: 76037--76061 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
76027 ATAAATAATG
76037 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
76062 ATTTAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:76354 original size:14 final size:14
Alignment explanation
Indices: 76321--76363 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
76311 AAATGTTATA
76321 AATTTATTATACAAT
1 AATTT-TTATACAAT
*
76336 AATTTTTATATAAT
1 AATTTTTATACAAT
*
76350 CATTTTTATA-AAT
1 AATTTTTATACAAT
76363 A
1 A
76364 TAGACTAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 3 0.12
14 17 0.68
15 5 0.20
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (14 bp):
AATTTTTATACAAT
Found at i:76414 original size:2 final size:2
Alignment explanation
Indices: 76407--76447 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
76397 ACCATTGATA
76407 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
76448 ATCTGATAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:76634 original size:15 final size:16
Alignment explanation
Indices: 76611--76640 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
76601 TATAAACATA
76611 AAATAATTAAAATTTT
1 AAATAATTAAAATTTT
76627 AAAT-ATTAAAATTT
1 AAATAATTAAAATTT
76641 AGTATATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATAATTAAAATTTT
Found at i:76824 original size:19 final size:19
Alignment explanation
Indices: 76800--76839 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
76790 ACTCATTCAT
*
76800 ATTTATTCTTTTAAATAAA
1 ATTTATTATTTTAAATAAA
*
76819 ATTTATTATTTTAAATCAA
1 ATTTATTATTTTAAATAAA
76838 AT
1 AT
76840 ATTAAATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTATTATTTTAAATAAA
Found at i:77791 original size:21 final size:21
Alignment explanation
Indices: 77765--77808 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
77755 TTTAGGTTTA
77765 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
77786 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
77807 AT
1 AT
77809 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:77816 original size:28 final size:30
Alignment explanation
Indices: 77785--77847 Score: 112
Period size: 28 Copynumber: 2.2 Consensus size: 30
77775 TAGTATAAAT
77785 TATTAGTTTGTTAGTTTAAG-T-TATATTA
1 TATTAGTTTGTTAGTTTAAGTTATATATTA
77813 TATTAGTTTGTTAGTTTAAGTTATATATTA
1 TATTAGTTTGTTAGTTTAAGTTATATATTA
77843 TATTA
1 TATTA
77848 TATAAAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 20 0.61
29 1 0.03
30 12 0.36
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (30 bp):
TATTAGTTTGTTAGTTTAAGTTATATATTA
Found at i:78087 original size:14 final size:15
Alignment explanation
Indices: 78055--78092 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
78045 ATATATTAGA
*
78055 TTGTATAAAATTGTT
1 TTGTATAAAATTATT
78070 TTGTATAAAA-TATT
1 TTGTATAAAATTATT
*
78084 TTGTTTAAA
1 TTGTATAAA
78093 GAAAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (15 bp):
TTGTATAAAATTATT
Found at i:78340 original size:17 final size:17
Alignment explanation
Indices: 78318--78376 Score: 73
Period size: 17 Copynumber: 3.3 Consensus size: 17
78308 TTATTCCCAT
78318 TTTAAAAAAATATTGTG
1 TTTAAAAAAATATTGTG
*
78335 TTTAAAAATATTTATTGTTG
1 TTTAAAAA-A-ATATTG-TG
*
78355 TTTAAAAAAATATTTTG
1 TTTAAAAAAATATTGTG
78372 TTTAA
1 TTTAA
78377 TTTATAATCT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
17 15 0.42
18 5 0.14
19 6 0.17
20 10 0.28
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.49
Consensus pattern (17 bp):
TTTAAAAAAATATTGTG
Found at i:78449 original size:17 final size:17
Alignment explanation
Indices: 78429--78477 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 17
78419 ATTAATAAAA
78429 TTGATATTTAAATTTAT
1 TTGATATTTAAATTTAT
*
78446 TTGATATTTAACAAATTTGT
1 TTGATATTT---AAATTTAT
78466 TTGATATTTAAA
1 TTGATATTTAAA
78478 AAAATAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
17 12 0.43
20 16 0.57
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.53
Consensus pattern (17 bp):
TTGATATTTAAATTTAT
Found at i:78463 original size:20 final size:20
Alignment explanation
Indices: 78438--78476 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
78428 ATTGATATTT
78438 AAATTTATTTGATATTTAAC
1 AAATTTATTTGATATTTAAC
*
78458 AAATTTGTTTGATATTTAA
1 AAATTTATTTGATATTTAA
78477 AAAAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (20 bp):
AAATTTATTTGATATTTAAC
Found at i:82185 original size:55 final size:54
Alignment explanation
Indices: 82092--82231 Score: 185
Period size: 55 Copynumber: 2.6 Consensus size: 54
82082 ATATTCGGAA
* * *
82092 AACGGGTTCGCTCCCTCATTT-TTAGGGAGTATAGAACTCGAACAATTTTCTG-C
1 AACGAGTTCACTCCCTC-TTTCTTAGGGAGTATAGAACTCGAACAATCTTCTGTC
*
82145 GAACGAGTTCACTCCCTCTTTCTTCGGGGAGTATAGAACTCGAACAATCTTCTGTC
1 -AACGAGTTCACTCCCTCTTTCTT-AGGGAGTATAGAACTCGAACAATCTTCTGTC
* *
82201 AACGGGTTCGCTCCCTCTTTCTTAGGGAGTA
1 AACGAGTTCACTCCCTCTTTCTTAGGGAGTA
82232 GGAATTTGAA
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
53 3 0.04
54 24 0.32
55 48 0.63
56 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.31
Consensus pattern (54 bp):
AACGAGTTCACTCCCTCTTTCTTAGGGAGTATAGAACTCGAACAATCTTCTGTC
Found at i:82304 original size:55 final size:55
Alignment explanation
Indices: 82243--82930 Score: 806
Period size: 55 Copynumber: 12.3 Consensus size: 55
82233 GAATTTGAAG
* *
82243 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCTCAGAGAGTATAAGACCCAAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCTCAGAGAGTATAAGACTCGAAC
* * * *
82298 AATCTTCAACAAATCTTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACCCGAAC
1 AATCTTCATC-AATCGTGTCTGCTCCCTATTTCCTCAGAGAGTATAAGACTCGAAC
* *
82354 AATCTTCATCAATCGTGTCTGCTCCCCA-TTCCTTCAGAGAGTATAAGACTTGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCC-TCAGAGAGTATAAGACTCGAAC
*
82409 AATCTTCATCAATCGTGTCTGCTCCCTATTT-CTGCAGAGAGTATAAGACTCCAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCT-CAGAGAGTATAAGACTCGAAC
* *
82464 AATCTTCAACAGTCGTGTCTGCTCCCTATTT-CTGCAGAGAGTATAAGACTCGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCT-CAGAGAGTATAAGACTCGAAC
* * * *
82519 AATTTTCATCAATTGTGTCTGCTCCCCA-TTCCTTCAGAGAGTATAAGACTCGAAT
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCC-TCAGAGAGTATAAGACTCGAAC
*
82574 AATCTTCATCAATCATGTCTGCTCCCTATTT-CTGCAGAGAGTATAAGACTCGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCT-CAGAGAGTATAAGACTCGAAC
* * *
82629 AATTTTCAACAATCGTGTCTGCTCCCCA-TTCCTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCC-TCAGAGAGTATAAGACTCGAAC
*
82684 AATCTTCATCAATCGTGTCTGCTCCCTA-TT--TCAGAGAGTATAAGACTCGAGAG
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCTCAGAGAGTATAAGACTCGA-AC
* * *
82737 AGTATAAGACGAACAATCTTCAACAGTCGTGTCTGCTCCCTATTT-CTGCATAGAGTATAAGACT
1 A--AT--------C-TTCATC-A-A-TCGTGTCTGCTCCCTATTTCCT-CAGAGAGTATAAGACT
82801 CGAAC
51 CGAAC
* * * *
82806 AGTTTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCTCAGAGAGTATAAGACTCGAAC
* * *
82861 AATCTTCA-CAATCGCGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGATC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCTCAGAGAGTATAAGACTCGAAC
82915 AATCTTCAAT-AATCGT
1 AATCTTC-ATCAATCGT
82931 TGGGAAATCT
Statistics
Matches: 551, Mismatches: 51, Indels: 62
0.83 0.08 0.09
Matches are distributed among these distances:
52 20 0.04
53 2 0.00
54 60 0.11
55 359 0.65
56 59 0.11
57 1 0.00
58 3 0.01
63 1 0.00
64 4 0.01
65 1 0.00
66 1 0.00
67 17 0.03
68 2 0.00
69 3 0.01
70 18 0.03
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.31
Consensus pattern (55 bp):
AATCTTCATCAATCGTGTCTGCTCCCTATTTCCTCAGAGAGTATAAGACTCGAAC
Found at i:82543 original size:165 final size:165
Alignment explanation
Indices: 82243--82930 Score: 947
Period size: 165 Copynumber: 4.1 Consensus size: 165
82233 GAATTTGAAG
82243 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCT-CAGAGAGTATAAGAC-CCAAACAATCTTCA
1 AATCTTCATCAATCGTGTCTGCTCCCTATTT-CTGCAGAGAGTATAAGACTCC-AACAATCTTCA
* *
82306 ACAAATCTTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACCCGAACAATCTTCATCAATCGTG
64 AC-AATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTG
*
82371 TCTGCTCCCCATTCCTTCAGAGAGTATAAGACTTGAAC
128 TCTGCTCCCCATTCCTTCAGAGAGTATAAGACTCGAAC
82409 AATCTTCATCAATCGTGTCTGCTCCCTATTTCTGCAGAGAGTATAAGACTCCAACAATCTTCAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCTGCAGAGAGTATAAGACTCCAACAATCTTCAAC
* * * *
82474 AGTCGTGTCTGCTCCCTATTTCTGCAGAGAGTATAAGACTCGAACAATTTTCATCAATTGTGTCT
66 AATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCT
*
82539 GCTCCCCATTCCTTCAGAGAGTATAAGACTCGAAT
131 GCTCCCCATTCCTTCAGAGAGTATAAGACTCGAAC
* * *
82574 AATCTTCATCAATCATGTCTGCTCCCTATTTCTGCAGAGAGTATAAGACTCGAACAATTTTCAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCTGCAGAGAGTATAAGACTCCAACAATCTTCAAC
* *
82639 AATCGTGTCTGCTCCCCATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCT
66 AATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCT
* *
82704 GCTCCCTATTTCAGAGAGTATAAGACTCGAGAGAGTATAAGA--CGAAC
131 GCTCCCCA-TTC-------CT-----TC-AGAGAGTATAAGACTCGAAC
* * * * * *
82751 AATCTTCAACAGTCGTGTCTGCTCCCTATTTCTGCATAGAGTATAAGACTCGAACAGTTTTCAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCTGCAGAGAGTATAAGACTCCAACAATCTTCAAC
*
82816 AATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCA-CAATCGCGTCT
66 AATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCT
* * *
82880 GCTCCCTATTTCTTCAGAGAGTATAAGACTCGATC
131 GCTCCCCATTCCTTCAGAGAGTATAAGACTCGAAC
82915 AATCTTCAAT-AATCGT
1 AATCTTC-ATCAATCGT
82931 TGGGAAATCT
Statistics
Matches: 470, Mismatches: 33, Indels: 40
0.87 0.06 0.07
Matches are distributed among these distances:
162 13 0.03
163 2 0.00
164 16 0.03
165 223 0.47
166 62 0.13
167 2 0.00
168 1 0.00
173 1 0.00
175 2 0.00
176 18 0.04
177 115 0.24
178 2 0.00
179 13 0.03
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.31
Consensus pattern (165 bp):
AATCTTCATCAATCGTGTCTGCTCCCTATTTCTGCAGAGAGTATAAGACTCCAACAATCTTCAAC
AATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCT
GCTCCCCATTCCTTCAGAGAGTATAAGACTCGAAC
Found at i:82773 original size:67 final size:71
Alignment explanation
Indices: 82664--82803 Score: 216
Period size: 67 Copynumber: 2.0 Consensus size: 71
82654 CCATTCCTTC
*
82664 AGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTGCTCCCTA-TT-T-CAGAGAGTATA
1 AGAGAGTATAAGAC-CGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTGCAGAGAGTATA
82726 AGACTCG
65 AGACTCG
* *
82733 AGAGAGTATAAGA-CGAACAATCTTCAACAGTCGTGTCTGCTCCCTATTTCTGCATAGAGTATAA
1 AGAGAGTATAAGACCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTGCAGAGAGTATAA
82797 GACTCG
66 GACTCG
82803 A
1 A
82804 ACAGTTTTCA
Statistics
Matches: 65, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
67 31 0.48
68 2 0.03
69 14 0.22
70 18 0.28
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.27
Consensus pattern (71 bp):
AGAGAGTATAAGACCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTGCAGAGAGTATAA
GACTCG
Found at i:82827 original size:122 final size:125
Alignment explanation
Indices: 82609--82858 Score: 380
Period size: 122 Copynumber: 2.0 Consensus size: 125
82599 CTATTTCTGC
* *
82609 AGAGAGTATAAGACTCGAACAATTTTCAACAATCGTGTCTGCTCCCCATTCCTTCAGAGAGTATA
1 AGAGAGTATAAGAC-CGAACAATCTTCAACAATCGTGTCTGCTCCCCATTCCTGCAGAGAGTATA
*
82674 AGACTCGAACAATCTTCATCAATCGTGTCTGCTCCCTA-T-TTCAGAGAGTATAAGACTCG
65 AGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCTTCAGAGAGTATAAGACTCG
* * * *
82733 AGAGAGTATAAGA-CGAACAATCTTCAACAGTCGTGTCTGCTCCCTATTTCTGCATAGAGTATAA
1 AGAGAGTATAAGACCGAACAATCTTCAACAATCGTGTCTGCTCCCCATTCCTGCAGAGAGTATAA
* *
82797 GACTCGAACAGTTTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCG
66 GACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTA-TTCTTCAGAGAGTATAAGACTCG
82858 A
1 A
82859 ACAATCTTCA
Statistics
Matches: 114, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
122 79 0.69
124 14 0.12
125 21 0.18
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (125 bp):
AGAGAGTATAAGACCGAACAATCTTCAACAATCGTGTCTGCTCCCCATTCCTGCAGAGAGTATAA
GACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCTTCAGAGAGTATAAGACTCG
Found at i:82864 original size:45 final size:46
Alignment explanation
Indices: 82813--82912 Score: 119
Period size: 54 Copynumber: 2.0 Consensus size: 46
82803 AACAGTTTTC
*
82813 AACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACA
1 AACAATCGCGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCG---A
82862 ATCTTCACAATCGCGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGA
1 A-----ACAATCGCGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGA
82913 TCAATCTTCA
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
49 1 0.02
51 1 0.02
54 43 0.96
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (46 bp):
AACAATCGCGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGA
Found at i:82923 original size:109 final size:108
Alignment explanation
Indices: 82733--82930 Score: 299
Period size: 109 Copynumber: 1.8 Consensus size: 108
82723 ATAAGACTCG
* * *
82733 AGAGAGTATAAGACGAACAATCTTCAACAGTCGTGTCTGCTCCCTATTTCTGCATAGAGTATAAG
1 AGAGAGTATAAGACGAACAATCTTCAACAATCGCGTCTGCTCCCTATTTCTGCAGAGAGTATAAG
* *
82798 ACTCGAACAGTTTTCAACAATCGTGTCTGCTCCCTATTTCTTC
66 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTC
*
82841 AGAGAGTATAAGACTCGAACAATCTTC-ACAATCGCGTCTGCTCCCTATTTCTTCAGAGAGTATA
1 AGAGAGTATAAGA--CGAACAATCTTCAACAATCGCGTCTGCTCCCTATTTCTGCAGAGAGTATA
* *
82905 AGACTCGATCAATCTTCAATAATCGT
64 AGACTCGAACAATCTTCAACAATCGT
82931 TGGGAAATCT
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
108 13 0.16
109 55 0.69
110 12 0.15
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (108 bp):
AGAGAGTATAAGACGAACAATCTTCAACAATCGCGTCTGCTCCCTATTTCTGCAGAGAGTATAAG
ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTC
Found at i:83956 original size:7 final size:7
Alignment explanation
Indices: 83946--83974 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
83936 ATTTTTTTCA
83946 TTCATTT
1 TTCATTT
83953 TTCATTT
1 TTCATTT
83960 TTC-TTT
1 TTCATTT
83966 TTCATTT
1 TTCATTT
83973 TT
1 TT
83975 TTTCTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (7 bp):
TTCATTT
Found at i:83958 original size:20 final size:21
Alignment explanation
Indices: 83929--83974 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
83919 AACCCTTCTT
83929 TTTTTCCATTTTT-TTCATTCA
1 TTTTTCCATTTTTCTT-ATTCA
*
83950 TTTTT-CATTTTTCTTTTTCA
1 TTTTTCCATTTTTCTTATTCA
83970 TTTTT
1 TTTTT
83975 TTTCTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTTCCATTTTTCTTATTCA
Found at i:83966 original size:13 final size:13
Alignment explanation
Indices: 83950--83974 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
83940 TTTTCATTCA
83950 TTTTTCATTTTTC
1 TTTTTCATTTTTC
83963 TTTTTCATTTTT
1 TTTTTCATTTTT
83975 TTTCTTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTCATTTTTC
Found at i:83975 original size:21 final size:20
Alignment explanation
Indices: 83928--84007 Score: 65
Period size: 21 Copynumber: 3.8 Consensus size: 20
83918 GAACCCTTCT
*
83928 TTTTTTCCATTTTTTTCATTCA
1 TTTTTT-CATTTTTTT-TTTCA
83950 -TTTTTCATTTTTCTTTTTCA
1 TTTTTTCATTTTT-TTTTTCA
*
83970 TTTTTTTTC-TTTTTTATTTCA
1 --TTTTTTCATTTTTTTTTTCA
*
83991 TTTTTTTATTATTTTTT
1 TTTTTTCATT-TTTTTT
84008 CAAGTAAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
19 6 0.12
20 13 0.27
21 18 0.38
22 5 0.10
23 6 0.12
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTTTCATTTTTTTTTTCA
Found at i:83975 original size:34 final size:33
Alignment explanation
Indices: 83927--84007 Score: 87
Period size: 34 Copynumber: 2.5 Consensus size: 33
83917 TGAACCCTTC
*
83927 TTTTTTTCCA-TTTTTTTCATTCATT-TTTCATT
1 TTTTTTTTCATTTTTTTTC-TTCATTATTTCATT
**
83959 TTTCTTTTTCATTTTTTTTCTTTTTTATTTCATT
1 TTT-TTTTTCATTTTTTTTCTTCATTATTTCATT
*
83993 TTTTTATT-ATTTTTT
1 TTTTTTTTCATTTTTT
84008 CAAGTAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
32 10 0.24
33 14 0.33
34 18 0.43
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (33 bp):
TTTTTTTTCATTTTTTTTCTTCATTATTTCATT
Found at i:83978 original size:16 final size:16
Alignment explanation
Indices: 83957--83988 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
83947 TCATTTTTCA
83957 TTTTTCTTTTTCATTT
1 TTTTTCTTTTTCATTT
*
83973 TTTTTCTTTTTTATTT
1 TTTTTCTTTTTCATTT
83989 CATTTTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTCTTTTTCATTT
Found at i:83997 original size:13 final size:11
Alignment explanation
Indices: 83937--84007 Score: 67
Period size: 11 Copynumber: 6.4 Consensus size: 11
83927 TTTTTTTCCA
83937 TTTTTTTCATT
1 TTTTTTTCATT
**
83948 CATTTTTCATTT
1 TTTTTTTCA-TT
83960 TTCTTTTTCA-T
1 TT-TTTTTCATT
83971 TTTTTTTC-TT
1 TTTTTTTCATT
83981 TTTTATTTCATT
1 TTTT-TTTCATT
83993 TTTTTATT-ATT
1 TTTTT-TTCATT
84004 TTTT
1 TTTT
84008 CAAGTAAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
10 11 0.22
11 22 0.44
12 10 0.20
13 7 0.14
ACGTcount: A:0.11, C:0.10, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTTTCATT
Found at i:84002 original size:16 final size:16
Alignment explanation
Indices: 83952--84004 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
83942 TTCATTCATT
83952 TTTCATTTTTCTTTTTCA
1 TTTCATTTTT-TTTTT-A
*
83970 TTT-TTTTTCTTTTTTA
1 TTTCATTTT-TTTTTTA
*
83986 TTTCATTTTTTTATTA
1 TTTCATTTTTTTTTTA
84002 TTT
1 TTT
84005 TTTCAAGTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 13 0.43
17 13 0.43
18 4 0.13
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTCATTTTTTTTTTA
Done.