Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 86 of 143
Found at i:27175037 original size:18 final size:18
Alignment explanation
Indices: 27175019--27175063 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
27175009 TGTAATTAAT
27175019 TTAAATTT-TTTAATGAA
1 TTAAATTTATTTAATGAA
*
27175036 TTAAATTTATTTAATTAA
1 TTAAATTTATTTAATGAA
*
27175054 -AAAATTTATT
1 TTAAATTTATT
27175064 CCCATCCCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 17 0.68
18 8 0.32
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
TTAAATTTATTTAATGAA
Found at i:27177923 original size:131 final size:132
Alignment explanation
Indices: 27177713--27177958 Score: 341
Period size: 131 Copynumber: 1.9 Consensus size: 132
27177703 AAAATATATA
* * ** * *
27177713 GAAGAGATGAACAAGGGAAGGCGGCGTCTATCGCTTAAGAGAGCCAGATATTTAAAGAGCAAGGA
1 GAAGAGATGAACAAGAGAAGGCGGCGACTAAAGCTTAAGAGAGCCAGATAATTAAAGAGCAAGAA
* *
27177778 ATGAGAAGGAATAGGGTTTAATTTTAGGTATAATGACAAATTTAACCTTTCCCATCTTTTATCAA
66 ATGAGAAGGAATAGGATTTAATTTTAGGTATAATAACAAATTTAACCTTTCCCATCTTTTATCAA
27177843 TT
131 TT
* * * *
27177845 GAAGAGATGAACAAGAGAAGGCGGCGAC-AAAGGTTAAGATAGCCAGATAATTATAGAGGAAGAA
1 GAAGAGATGAACAAGAGAAGGCGGCGACTAAAGCTTAAGAGAGCCAGATAATTAAAGAGCAAGAA
* * * *
27177909 ATGAGAAGGTATAGGATTTAGTTTTAGGTATAATAACTAATTTAATCTTT
66 ATGAGAAGGAATAGGATTTAATTTTAGGTATAATAACAAATTTAACCTTT
27177959 AATTTTTACA
Statistics
Matches: 98, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
131 72 0.73
132 26 0.27
ACGTcount: A:0.39, C:0.10, G:0.24, T:0.26
Consensus pattern (132 bp):
GAAGAGATGAACAAGAGAAGGCGGCGACTAAAGCTTAAGAGAGCCAGATAATTAAAGAGCAAGAA
ATGAGAAGGAATAGGATTTAATTTTAGGTATAATAACAAATTTAACCTTTCCCATCTTTTATCAA
TT
Found at i:27178548 original size:15 final size:17
Alignment explanation
Indices: 27178527--27178567 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
27178517 TAATATTTTA
27178527 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATGAT
*
27178543 -AAATTATTAAAATGAT
1 AAAATTATAAAAATGAT
27178559 AAAATTATA
1 AAAATTATA
27178568 TTTTTTTACG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATGAT
Found at i:27181673 original size:4 final size:4
Alignment explanation
Indices: 27181664--27181725 Score: 63
Period size: 4 Copynumber: 15.2 Consensus size: 4
27181654 AAATAAACGG
* * *
27181664 GAAA GAAA GAAA GAAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA G-AA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA GAAA
*
27181713 GAAG GAAA GAAA G
1 GAAA GAAA GAAA G
27181726 GTAATGTGTT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
3 3 0.06
4 38 0.78
5 8 0.16
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:27181686 original size:17 final size:17
Alignment explanation
Indices: 27181664--27181725 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
27181654 AAATAAACGG
27181664 GAAAGAAAGAAAGAAAA
1 GAAAGAAAGAAAGAAAA
* *
27181681 GAAAGAAAGGAAG-AAG
1 GAAAGAAAGAAAGAAAA
*
27181697 GAGAGGAAAGAAAGAAGAA
1 GA-AAGAAAGAAAGAA-AA
27181716 GGAAAGAAAG
1 -GAAAGAAAG
27181726 GTAATGTGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
16 4 0.11
17 21 0.60
18 1 0.03
19 7 0.20
20 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (17 bp):
GAAAGAAAGAAAGAAAA
Found at i:27181695 original size:25 final size:23
Alignment explanation
Indices: 27181666--27181725 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 23
27181656 ATAAACGGGA
27181666 AAGAAAGAAAGAAAAGAAAGAAAGG
1 AAGAAAGAAAGAAAAGAAAG-AA-G
* * *
27181691 AAGAAGGAGAGGAAAGAAAGAAG
1 AAGAAAGAAAGAAAAGAAAGAAG
27181714 AAGGAAAGAAAG
1 AA-GAAAGAAAG
27181726 GTAATGTGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 3 0.10
24 9 0.31
25 17 0.59
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (23 bp):
AAGAAAGAAAGAAAAGAAAGAAG
Found at i:27184764 original size:14 final size:13
Alignment explanation
Indices: 27184736--27184801 Score: 53
Period size: 14 Copynumber: 4.8 Consensus size: 13
27184726 TGTATAGGAC
27184736 TAGGGTTTGAAGTT
1 TAGGGTTT-AAGTT
27184750 TAGGGTTTAAGGTT
1 TAGGGTTTAA-GTT
* *
27184764 TATAGTTTTAAGTGT
1 TA-GGGTTTAAGT-T
*
27184779 T-GGGTTTAGGGTT
1 TAGGGTTTA-AGTT
27184792 TAGGGTTTAA
1 TAGGGTTTAA
27184802 TGTTATGAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
13 9 0.22
14 24 0.59
15 8 0.20
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.45
Consensus pattern (13 bp):
TAGGGTTTAAGTT
Found at i:27184799 original size:28 final size:28
Alignment explanation
Indices: 27184736--27184799 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
27184726 TGTATAGGAC
27184736 TAGGGTTTGAAGTTTAGGGTTTAAGGTT
1 TAGGGTTTGAAGTTTAGGGTTTAAGGTT
** * *
27184764 TATAGTTTTAAGTGTT-GGGTTTAGGGTT
1 TAGGGTTTGAAGT-TTAGGGTTTAAGGTT
27184792 TAGGGTTT
1 TAGGGTTT
27184800 AATGTTATGA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
28 27 0.93
29 2 0.07
ACGTcount: A:0.19, C:0.00, G:0.34, T:0.47
Consensus pattern (28 bp):
TAGGGTTTGAAGTTTAGGGTTTAAGGTT
Found at i:27185046 original size:21 final size:21
Alignment explanation
Indices: 27185020--27185064 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
27185010 TTAGGGTCCA
27185020 ATTACCCCGGAGGAGTAAAGT
1 ATTACCCCGGAGGAGTAAAGT
**
27185041 ATTACCTGGGAGGAGTAAAGT
1 ATTACCCCGGAGGAGTAAAGT
27185062 ATT
1 ATT
27185065 GCGATGGCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.24
Consensus pattern (21 bp):
ATTACCCCGGAGGAGTAAAGT
Found at i:27185178 original size:6 final size:6
Alignment explanation
Indices: 27185167--27185197 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
27185157 TTATCCAATG
*
27185167 CCTCTT CCTCTT CCCCTT CCTCTT CCTCTT C
1 CCTCTT CCTCTT CCTCTT CCTCTT CCTCTT C
27185198 TTGTTGCTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (6 bp):
CCTCTT
Found at i:27187851 original size:12 final size:13
Alignment explanation
Indices: 27187781--27187852 Score: 51
Period size: 12 Copynumber: 5.6 Consensus size: 13
27187771 AAATTAAACA
*
27187781 AAATAAAAAAATT
1 AAATTAAAAAATT
* *
27187794 AAAATAATCAAATT
1 AAATTAA-AAAATT
* *
27187808 -AACTAATAAATT
1 AAATTAAAAAATT
*
27187820 AAATT-TAAAATT
1 AAATTAAAAAATT
27187832 AAACTTAAAAAATT
1 AAA-TTAAAAAATT
27187846 -AATTAAA
1 AAATTAAA
27187853 CTTACCTTTC
Statistics
Matches: 46, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
12 18 0.39
13 17 0.37
14 11 0.24
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATTAAAAAATT
Found at i:27188046 original size:23 final size:23
Alignment explanation
Indices: 27187998--27188040 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
27187988 ACACATTACT
*
27187998 TTTTTCTCTTTCTCCTCTTCCCC
1 TTTTTCTCCTTCTCCTCTTCCCC
*
27188021 TTTTTCTCCTTC-CTTCTTCC
1 TTTTTCTCCTTCTCCTCTTCC
27188041 TTCTTTCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTTTCTCCTTCTCCTCTTCCCC
Found at i:27188058 original size:12 final size:11
Alignment explanation
Indices: 27188041--27188085 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
27188031 TCCTTCTTCC
27188041 TTCTTTCTTTCT
1 TTCTTT-TTTCT
27188053 TTCTTTTTTTCT
1 TTC-TTTTTTCT
*
27188065 CTCTTTTTTCT
1 TTCTTTTTTCT
*
27188076 TTTTTTTTTC
1 TTCTTTTTTC
27188086 CTTCAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
11 16 0.55
12 10 0.34
13 3 0.10
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTCTTTTTTCT
Found at i:27189449 original size:13 final size:13
Alignment explanation
Indices: 27189439--27189463 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27189429 CATTAAATCT
27189439 ATTAAAAAAATAG
1 ATTAAAAAAATAG
27189452 ATTAAAAAAATA
1 ATTAAAAAAATA
27189464 AAAATTGATA
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:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (13 bp):
ATTAAAAAAATAG
Found at i:27189475 original size:18 final size:19
Alignment explanation
Indices: 27189444--27189479 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
27189434 AATCTATTAA
27189444 AAAAATAGATTAAAAAAAT
1 AAAAATAGATTAAAAAAAT
*
27189463 AAAAATTGA-TAAAAAAA
1 AAAAATAGATTAAAAAAA
27189480 AAACTCAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (19 bp):
AAAAATAGATTAAAAAAAT
Found at i:27189480 original size:19 final size:19
Alignment explanation
Indices: 27189444--27189480 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
27189434 AATCTATTAA
*
27189444 AAAAATAGATTAAAAAAAT
1 AAAAATAGATAAAAAAAAT
*
27189463 AAAAATTGATAAAAAAAA
1 AAAAATAGATAAAAAAAA
27189481 AACTCAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (19 bp):
AAAAATAGATAAAAAAAAT
Found at i:27190307 original size:23 final size:22
Alignment explanation
Indices: 27190269--27190318 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 22
27190259 TTTTTTGTAT
*
27190269 TATATATAATTAAAAAAGAAAG
1 TATATATAATTAAAAAAGAAAA
27190291 TATATATATATTAAAAAAGAAAA
1 TATATATA-ATTAAAAAAGAAAA
27190314 TATAT
1 TATAT
27190319 TTTTTATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 8 0.31
23 18 0.69
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (22 bp):
TATATATAATTAAAAAAGAAAA
Found at i:27190626 original size:29 final size:28
Alignment explanation
Indices: 27190594--27190653 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 28
27190584 TTTTCACATT
* *
27190594 TTTTAATAATTTTTATTATTAATAAAATA
1 TTTTAATAATATTTACTATTAA-AAAATA
*
27190623 TTTTAATAATATTTACTATTAACAAATA
1 TTTTAATAATATTTACTATTAAAAAATA
27190651 TTT
1 TTT
27190654 GAATTAATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 8 0.29
29 20 0.71
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (28 bp):
TTTTAATAATATTTACTATTAAAAAATA
Found at i:27191353 original size:21 final size:21
Alignment explanation
Indices: 27191324--27191364 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
27191314 TTAATGATGA
27191324 TTAAGTTAAGTTAATTAAGGG
1 TTAAGTTAAGTTAATTAAGGG
*
27191345 TTAATTTAAGTTAATTAAGG
1 TTAAGTTAAGTTAATTAAGG
27191365 TTTATTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.20, T:0.41
Consensus pattern (21 bp):
TTAAGTTAAGTTAATTAAGGG
Found at i:27193183 original size:37 final size:37
Alignment explanation
Indices: 27193118--27193331 Score: 221
Period size: 37 Copynumber: 5.8 Consensus size: 37
27193108 TCTAATCATT
* * * *
27193118 GGCACAAAAGCCCGTTAGGCATATAGCCCGAGTACACC
1 GGCAC-AAAGCCTGCTAGGCACATAGCCCGAATACACC
* *** * *
27193156 GGTACTCGGCCTACTAGGCACATAGCCCGAATTCACC
1 GGCACAAAGCCTGCTAGGCACATAGCCCGAATACACC
* * *
27193193 GGCACAAAGCTTGCTAGGCAAATAGCCCGATTACACC
1 GGCACAAAGCCTGCTAGGCACATAGCCCGAATACACC
**
27193230 GGCACAAAGCCTGCTAGGCACATAGCCTAAATACACC
1 GGCACAAAGCCTGCTAGGCACATAGCCCGAATACACC
* * * * *
27193267 GACACGAAGCTTGCTAGGTACATAGCCCGAATACATC
1 GGCACAAAGCCTGCTAGGCACATAGCCCGAATACACC
* *
27193304 GACACGAAGCCTGCTAGGCACATAGCCC
1 GGCACAAAGCCTGCTAGGCACATAGCCC
27193332 AATTTACTTA
Statistics
Matches: 143, Mismatches: 33, Indels: 1
0.81 0.19 0.01
Matches are distributed among these distances:
37 139 0.97
38 4 0.03
ACGTcount: A:0.31, C:0.32, G:0.22, T:0.15
Consensus pattern (37 bp):
GGCACAAAGCCTGCTAGGCACATAGCCCGAATACACC
Found at i:27198107 original size:35 final size:35
Alignment explanation
Indices: 27198063--27198140 Score: 120
Period size: 35 Copynumber: 2.2 Consensus size: 35
27198053 ACAAACAACG
* * *
27198063 TTTCTCGGCTTAAGGCATTAAAAACAAAATTAGCC
1 TTTCCCGGCTTAAAGCATTAAAAACAAAATTAACC
27198098 TTTCCCGGCTTAAAGCATTAAAAACAAAATTAACC
1 TTTCCCGGCTTAAAGCATTAAAAACAAAATTAACC
*
27198133 TTTTCCGG
1 TTTCCCGG
27198141 ATGATAATCA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (35 bp):
TTTCCCGGCTTAAAGCATTAAAAACAAAATTAACC
Found at i:27202793 original size:24 final size:24
Alignment explanation
Indices: 27202761--27202841 Score: 126
Period size: 24 Copynumber: 3.4 Consensus size: 24
27202751 ACTCTGTATA
*
27202761 GGCTTGTAAGAGCTAACCATTTTG
1 GGCTCGTAAGAGCTAACCATTTTG
*
27202785 GGCTCGTAAGTGCTAACCATTTTG
1 GGCTCGTAAGAGCTAACCATTTTG
*
27202809 GGCTCGTAAGAGCTAACCATTCTG
1 GGCTCGTAAGAGCTAACCATTTTG
*
27202833 GGGTCGTAA
1 GGCTCGTAA
27202842 TGAGTTAATG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (24 bp):
GGCTCGTAAGAGCTAACCATTTTG
Found at i:27208939 original size:18 final size:18
Alignment explanation
Indices: 27208916--27208952 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
27208906 TTTGTGATCA
*
27208916 AAATTGAAAGTGAAAGTG
1 AAATTGAAACTGAAAGTG
*
27208934 AAATTGGAACTGAAAGTG
1 AAATTGAAACTGAAAGTG
27208952 A
1 A
27208953 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.03, G:0.27, T:0.22
Consensus pattern (18 bp):
AAATTGAAACTGAAAGTG
Found at i:27210294 original size:24 final size:24
Alignment explanation
Indices: 27210262--27210316 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
27210252 ACTCTGTCTG
27210262 GGCTCGTAAGAGCTAACCATTCTA
1 GGCTCGTAAGAGCTAACCATTCTA
*
27210286 GGCTCGTAAGAGCTTACCATTCTA
1 GGCTCGTAAGAGCTAACCATTCTA
27210310 GGCTCGT
1 GGCTCGT
27210317 GTGGGCTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (24 bp):
GGCTCGTAAGAGCTAACCATTCTA
Found at i:27212642 original size:41 final size:41
Alignment explanation
Indices: 27212579--27212846 Score: 295
Period size: 41 Copynumber: 6.4 Consensus size: 41
27212569 CCGAAGCATA
* * *
27212579 AGTCTTCCTTTCAAACATAATCTCATGCTTATTCCGAGACATG
1 AGTCTTCCTTT--AACATATTCTCATTCTCATTCCGAGACATG
* * *
27212622 AGTCTTTCTTTAACATAATCTCATTCTCA-TCCTCAGACATG
1 AGTCTTCCTTTAACATATTCTCATTCTCATTCC-GAGACATG
* *
27212663 AGTCTTCCTTTAACATATTCTTATTCTCATCCCGAGACATG
1 AGTCTTCCTTTAACATATTCTCATTCTCATTCCGAGACATG
* *
27212704 AGTCTTCCTTTAACATATTCTTATTCTCATCCCGAGACATG
1 AGTCTTCCTTTAACATATTCTCATTCTCATTCCGAGACATG
* * *
27212745 AGTCTTCCTTTAACATATTCTCATGCTCATTCCGAGTCACG
1 AGTCTTCCTTTAACATATTCTCATTCTCATTCCGAGACATG
* * ** **
27212786 AGTCTTCCATTTATAGAAATTCTCATGATCAACCCGAGACATG
1 AGTCTTCC-TTTA-ACATATTCTCATTCTCATTCCGAGACATG
27212829 AGTCTTCCATTTATACAT
1 AGTCTTCC-TTTA-ACAT
27212847 CAAGTGTCTC
Statistics
Matches: 198, Mismatches: 23, Indels: 8
0.86 0.10 0.03
Matches are distributed among these distances:
40 3 0.02
41 141 0.71
42 6 0.03
43 48 0.24
ACGTcount: A:0.26, C:0.26, G:0.10, T:0.37
Consensus pattern (41 bp):
AGTCTTCCTTTAACATATTCTCATTCTCATTCCGAGACATG
Found at i:27218466 original size:37 final size:37
Alignment explanation
Indices: 27218372--27218584 Score: 221
Period size: 37 Copynumber: 5.7 Consensus size: 37
27218362 GTTCTCTAAT
* *
27218372 CACCGGCACAAAGGCCTGCTAGGCATATAGCCCGAGTA
1 CACCGGCACAAA-GCCTGCTAGGCACATAGCCCGAATA
* ** ** * *
27218410 CGCCAACACATGGCCTGCTAGGCACACAGCCCGAATT
1 CACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATA
* * ** *
27218447 CACCAGCACAAAGCTTGCTAGGCACATAGCTTGATTA
1 CACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATA
* * * *
27218484 CACCGGCATAAAGCTTGCTAGGCACATAACTCGAATA
1 CACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATA
*
27218521 CACCGGCCCAAAGCCTGCTAGGCACATAGCCCGAATA
1 CACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATA
*
27218558 CACCGGCACGAAG-CTAGCTAGGCACAT
1 CACCGGCACAAAGCCT-GCTAGGCACAT
27218585 GGCCTGATTT
Statistics
Matches: 143, Mismatches: 31, Indels: 3
0.81 0.18 0.02
Matches are distributed among these distances:
36 2 0.01
37 134 0.94
38 7 0.05
ACGTcount: A:0.31, C:0.32, G:0.22, T:0.15
Consensus pattern (37 bp):
CACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATA
Found at i:27222333 original size:3 final size:3
Alignment explanation
Indices: 27222325--27222350 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
27222315 TCTCCATTCT
27222325 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
27222351 GCCAAACTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:27242496 original size:18 final size:18
Alignment explanation
Indices: 27242473--27242507 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
27242463 TTTCCTATTG
*
27242473 TAATTAATTTAAATTTTT
1 TAATTAATTAAAATTTTT
27242491 TAATTAATTAAAATTTT
1 TAATTAATTAAAATTTT
27242508 ATTCTCATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TAATTAATTAAAATTTTT
Found at i:27245332 original size:142 final size:142
Alignment explanation
Indices: 27245076--27245360 Score: 570
Period size: 142 Copynumber: 2.0 Consensus size: 142
27245066 AATTATAAAG
27245076 TTTTGAGAGGTAAAATATAATTTATCACTGTTTTTATAAAAGTTAAATCCCAATTTTACCATTCT
1 TTTTGAGAGGTAAAATATAATTTATCACTGTTTTTATAAAAGTTAAATCCCAATTTTACCATTCT
27245141 TGAATTTACATGCAATTTTTATCATATATTAATTTATAATTATACAAATTTAAAAGGTTTTAAAA
66 TGAATTTACATGCAATTTTTATCATATATTAATTTATAATTATACAAATTTAAAAGGTTTTAAAA
27245206 GGAAATTTATCA
131 GGAAATTTATCA
27245218 TTTTGAGAGGTAAAATATAATTTATCACTGTTTTTATAAAAGTTAAATCCCAATTTTACCATTCT
1 TTTTGAGAGGTAAAATATAATTTATCACTGTTTTTATAAAAGTTAAATCCCAATTTTACCATTCT
27245283 TGAATTTACATGCAATTTTTATCATATATTAATTTATAATTATACAAATTTAAAAGGTTTTAAAA
66 TGAATTTACATGCAATTTTTATCATATATTAATTTATAATTATACAAATTTAAAAGGTTTTAAAA
27245348 GGAAATTTATCA
131 GGAAATTTATCA
27245360 T
1 T
27245361 ATATCTTTTT
Statistics
Matches: 143, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
142 143 1.00
ACGTcount: A:0.39, C:0.09, G:0.08, T:0.43
Consensus pattern (142 bp):
TTTTGAGAGGTAAAATATAATTTATCACTGTTTTTATAAAAGTTAAATCCCAATTTTACCATTCT
TGAATTTACATGCAATTTTTATCATATATTAATTTATAATTATACAAATTTAAAAGGTTTTAAAA
GGAAATTTATCA
Found at i:27246933 original size:14 final size:15
Alignment explanation
Indices: 27246905--27246934 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
27246895 AAAAAAATTG
27246905 TAAAATTATTTTAAA
1 TAAAATTATTTTAAA
27246920 TAAAATTA-TTTAAA
1 TAAAATTATTTTAAA
27246934 T
1 T
27246935 TATTTAAAAA
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAAAATTATTTTAAA
Found at i:27249286 original size:7 final size:7
Alignment explanation
Indices: 27249274--27249299 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
27249264 GGAGTTCTCG
27249274 GAATTAT
1 GAATTAT
27249281 GAATTAT
1 GAATTAT
27249288 GAATTAT
1 GAATTAT
27249295 GAATT
1 GAATT
27249300 CACTACAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (7 bp):
GAATTAT
Found at i:27249483 original size:39 final size:40
Alignment explanation
Indices: 27249411--27249560 Score: 108
Period size: 41 Copynumber: 3.7 Consensus size: 40
27249401 AAAGGTAAAG
* * *
27249411 AGCAATAGCGGCGTTTATGGGAAAACGCAGCAAAAGCTAA
1 AGCAATAACGGCATTTATGGGAAAACGCAGCAAAAGATAA
* * *
27249451 AGCAATAACGGCATTT-TTGGAGAACGCCGCAAAAGATAAA
1 AGCAATAACGGCATTTATGGGAAAACGCAGCAAAAGAT-AA
* * * * * *
27249491 GAGCTATAGCGAC-GTTATGAGAAAACGTC-GCAAAAGGTAA
1 -AGCAATAACGGCATTTATGGGAAAACG-CAGCAAAAGATAA
* *
27249531 AGAATATTAACGGCGTTTATGGGAAAACGC
1 AGCA-A-TAACGGCATTTATGGGAAAACGC
27249561 CGCTAATGCT
Statistics
Matches: 83, Mismatches: 20, Indels: 13
0.72 0.17 0.11
Matches are distributed among these distances:
39 19 0.23
40 21 0.25
41 30 0.36
42 13 0.16
ACGTcount: A:0.40, C:0.16, G:0.26, T:0.18
Consensus pattern (40 bp):
AGCAATAACGGCATTTATGGGAAAACGCAGCAAAAGATAA
Found at i:27250911 original size:7 final size:7
Alignment explanation
Indices: 27250901--27250925 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
27250891 ATAAAAAATT
27250901 ATTTTAA
1 ATTTTAA
27250908 ATTTTAA
1 ATTTTAA
27250915 ATTTTAA
1 ATTTTAA
27250922 ATTT
1 ATTT
27250926 ATCAATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
ATTTTAA
Found at i:27255346 original size:43 final size:43
Alignment explanation
Indices: 27255289--27255515 Score: 274
Period size: 43 Copynumber: 5.3 Consensus size: 43
27255279 TGTCCAAATG
* * * *
27255289 ATAGCGGCATTTGTGGGAAAAGCACTGCTAAAGGCCATGTTCT
1 ATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* * * * ** * *
27255332 ATAACGACGTTTGTGGTAAAAACGCTACTAAAGACCAAGCTCT
1 ATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* * *
27255375 ATAGTGGCGTTTGTGGGAAAAGCGCCGCTAAAAATCATGTTCT
1 ATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* * *
27255418 GTAGCGACGTTTGTGGGGAAAGCGCCGCTAAAGACCATGTTCT
1 ATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* *
27255461 ATAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGATCATGTTCT
1 ATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
27255504 ATAGCGGCGTTT
1 ATAGCGGCGTTT
27255516 TCCCACATAA
Statistics
Matches: 152, Mismatches: 32, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 152 1.00
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (43 bp):
ATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
Found at i:27257480 original size:23 final size:25
Alignment explanation
Indices: 27257454--27257499 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
27257444 CCAATTAGAG
27257454 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
27257477 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
27257500 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:27258210 original size:18 final size:18
Alignment explanation
Indices: 27258187--27258226 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
27258177 GATACTAAGT
27258187 GAATAAATTCTTAATTCA
1 GAATAAATTCTTAATTCA
*
27258205 GAATAAATTTTTAATTCA
1 GAATAAATTCTTAATTCA
27258223 GAAT
1 GAAT
27258227 GATAATGGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (18 bp):
GAATAAATTCTTAATTCA
Found at i:27258262 original size:22 final size:22
Alignment explanation
Indices: 27258237--27258280 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
27258227 GATAATGGCA
27258237 GATGAAATTTAGGTGGATTCTT
1 GATGAAATTTAGGTGGATTCTT
27258259 GATGAAATTTAGGTGGATTCTT
1 GATGAAATTTAGGTGGATTCTT
27258281 TCTTGGGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.05, G:0.27, T:0.41
Consensus pattern (22 bp):
GATGAAATTTAGGTGGATTCTT
Found at i:27262317 original size:49 final size:48
Alignment explanation
Indices: 27262149--27262407 Score: 139
Period size: 49 Copynumber: 5.5 Consensus size: 48
27262139 ATTGTCAAGC
* * * * *
27262149 TATAAGATTCGCCGTTGCGACTTCAATCTTTCTCTTCACATCTCTAAGG
1 TATAAGGTTCGCCATTGCGGCTTCAATCTTTCCCATCA-ATCTCTAAGG
* * * *
27262198 CATAAGG---G-CATTTG-TGCTTCAACCTTTCCC-TCCATATCTCTAGGG
1 TATAAGGTTCGCCA-TTGCGGCTTCAATCTTTCCCAT-CA-ATCTCTAAGG
* * * * **
27262243 TATAAGATTCGTCTTTACAACTTCAATCTTTCCCATCAAATCTCTAAGG
1 TATAAGGTTCGCCATTGCGGCTTCAATCTTTCCCATC-AATCTCTAAGG
* * *
27262292 TATAAGGTTCGCCATTGCGGTTTCAA-CCTT-CC--C---CTCTAGGG
1 TATAAGGTTCGCCATTGCGGCTTCAATCTTTCCCATCAATCTCTAAGG
* * * * * *
27262333 CATAAGATTCGTCATTGTGGCTTCAATCTTTCCGATCACATCTTTAAGG
1 TATAAGGTTCGCCATTGCGGCTTCAATCTTTCCCATCA-ATCTCTAAGG
* *
27262382 TATAAGGTTCACTATTGCGGCTTCAA
1 TATAAGGTTCGCCATTGCGGCTTCAA
27262408 CCCTTCCTTC
Statistics
Matches: 152, Mismatches: 41, Indels: 34
0.67 0.18 0.15
Matches are distributed among these distances:
41 28 0.18
42 3 0.02
43 1 0.01
44 1 0.01
45 31 0.20
46 4 0.03
47 2 0.01
48 6 0.04
49 74 0.49
50 2 0.01
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (48 bp):
TATAAGGTTCGCCATTGCGGCTTCAATCTTTCCCATCAATCTCTAAGG
Found at i:27262361 original size:90 final size:89
Alignment explanation
Indices: 27262235--27262509 Score: 309
Period size: 90 Copynumber: 3.1 Consensus size: 89
27262225 CCCTCCATAT
* **** * *
27262235 CTCTAGGGTATAAGATTCGTCTTTACAACTTCAATCTTTCCCATCAAATCTCTAAGGTATAAGGT
1 CTCTAGGGTATAAGATTCGTCATTGTGGCTTCAATCTTTCCCATCACATCTTTAAGGTATAAGGT
*
27262300 TCGCCATTGCGGTTTCAACCTTCCC
66 TCACCATTGCGGTTTCAACCTT-CC
* *
27262325 CTCTAGGGCATAAGATTCGTCATTGTGGCTTCAATCTTTCCGATCACATCTTTAAGGTATAAGGT
1 CTCTAGGGTATAAGATTCGTCATTGTGGCTTCAATCTTTCCCATCACATCTTTAAGGTATAAGGT
* *
27262390 TCACTATTGCGGCTTCAACCCTTCC
66 TCACCATTGCGGTTTCAA-CCTTCC
* * * * * ** *
27262415 TTCCAGAGTACAAGATACACCGTTGTGGCTTCAATCTTTCCCATCACATCTTTAAGGTATAAGGT
1 CTCTAGGGTATAAGATTCGTCATTGTGGCTTCAATCTTTCCCATCACATCTTTAAGGTATAAGGT
* *
27262480 TCACCGTTACGGCTTT-AACCTTTCC
66 TCACCATTGCGG-TTTCAACC-TTCC
27262505 CTCTA
1 CTCTA
27262510 CATCTTTAGG
Statistics
Matches: 154, Mismatches: 28, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
89 2 0.01
90 146 0.95
91 6 0.04
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.34
Consensus pattern (89 bp):
CTCTAGGGTATAAGATTCGTCATTGTGGCTTCAATCTTTCCCATCACATCTTTAAGGTATAAGGT
TCACCATTGCGGTTTCAACCTTCC
Found at i:27262504 original size:49 final size:47
Alignment explanation
Indices: 27262426--27262563 Score: 141
Period size: 49 Copynumber: 2.9 Consensus size: 47
27262416 TCCAGAGTAC
* **
27262426 AAGATACACCGTTGTGGCTTCAATCTTTCCCATCACATCTTTAAGGTA
1 AAGATTCACCGTTACGGCTTCAATCTTTCCC-TCACATCTTTAAGGTA
* * * *
27262474 TAAGGTTCACCGTTACGGCTTTAACCTTTCCCTCTACATCTTTAGGGTA
1 -AAGATTCACCGTTACGGCTTCAATCTTTCCCTC-ACATCTTTAAGGTA
* ***
27262523 CAGATTCGTTGTTACGGCTTCAATCTTTCCCTTCACATCTT
1 AAGATTCACCGTTACGGCTTCAATCTTTCCC-TCACATCTT
27262564 ATTCAACATT
Statistics
Matches: 73, Mismatches: 14, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
48 33 0.45
49 40 0.55
ACGTcount: A:0.22, C:0.27, G:0.14, T:0.37
Consensus pattern (47 bp):
AAGATTCACCGTTACGGCTTCAATCTTTCCCTCACATCTTTAAGGTA
Found at i:27265800 original size:41 final size:41
Alignment explanation
Indices: 27265743--27265933 Score: 283
Period size: 41 Copynumber: 4.6 Consensus size: 41
27265733 AATCACTTGA
27265743 TATATTAAAGGAAGACTCGTGACTCGAAATGAGCATGAGAT
1 TATATTAAAGGAAGACTCGTGACTCGAAATGAGCATGAGAT
27265784 TATATTAAAGGAAGACTCGTGACTCGAAATGAGCATGAGAT
1 TATATTAAAGGAAGACTCGTGACTCGAAATGAGCATGAGAT
* * * ***
27265825 TATATTAAAGGAAGACTCATGTCTTGGGGTGAGCATGAGAT
1 TATATTAAAGGAAGACTCGTGACTCGAAATGAGCATGAGAT
**
27265866 TATATTAAAGGAAGACTCGTGACTCGGGATGAGCATGAGAT
1 TATATTAAAGGAAGACTCGTGACTCGAAATGAGCATGAGAT
**
27265907 TATATTTAAAGGAAGACTTATGACTCG
1 TATA-TTAAAGGAAGACTCGTGACTCG
27265934 GTGAGCATAA
Statistics
Matches: 137, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
41 117 0.85
42 20 0.15
ACGTcount: A:0.36, C:0.12, G:0.26, T:0.27
Consensus pattern (41 bp):
TATATTAAAGGAAGACTCGTGACTCGAAATGAGCATGAGAT
Found at i:27277120 original size:18 final size:20
Alignment explanation
Indices: 27277082--27277120 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
27277072 ATCTTATTTG
*
27277082 TTAAAAGTTTGAAAATTCGA
1 TTAAAAGTTTGAAAATGCGA
27277102 TTAAAAG-TT-AAAATGCGA
1 TTAAAAGTTTGAAAATGCGA
27277120 T
1 T
27277121 CCATAAATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 2 0.11
20 7 0.39
ACGTcount: A:0.46, C:0.05, G:0.15, T:0.33
Consensus pattern (20 bp):
TTAAAAGTTTGAAAATGCGA
Found at i:27285511 original size:22 final size:20
Alignment explanation
Indices: 27285455--27285511 Score: 51
Period size: 22 Copynumber: 2.6 Consensus size: 20
27285445 AAATAAAATA
27285455 TTTTATATTTAAATATTATTC
1 TTTTATA-TTAAATATTATTC
** *
27285476 TTTTGATAGAAAATATTATTTT
1 TTTT-ATATTAAATATTA-TTC
27285498 TTTTAATATTAAAT
1 TTTT-ATATTAAAT
27285512 TAATGGGGAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 12 0.43
22 16 0.57
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.58
Consensus pattern (20 bp):
TTTTATATTAAATATTATTC
Found at i:27285605 original size:26 final size:26
Alignment explanation
Indices: 27285567--27285625 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
27285557 TTTTAAATAT
* *
27285567 TATTTTCATTATAATAATAGATATTA
1 TATTTTAACTATAATAATAGATATTA
* *
27285593 TATTTTAACTATATTTATAGATATTA
1 TATTTTAACTATAATAATAGATATTA
*
27285619 AATTTTA
1 TATTTTA
27285626 TTATTTTATG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (26 bp):
TATTTTAACTATAATAATAGATATTA
Found at i:27286696 original size:2 final size:2
Alignment explanation
Indices: 27286689--27286727 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
27286679 GTAATTATTT
27286689 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
27286728 TGTTTAATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:27287512 original size:6 final size:6
Alignment explanation
Indices: 27287501--27287525 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
27287491 TGAGGAGGAA
27287501 GAAGAG GAAGAG GAAGAG GAAGAG G
1 GAAGAG GAAGAG GAAGAG GAAGAG G
27287526 TGAGGGAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (6 bp):
GAAGAG
Found at i:27287536 original size:156 final size:156
Alignment explanation
Indices: 27287354--27287673 Score: 525
Period size: 156 Copynumber: 2.1 Consensus size: 156
27287344 TTACAATGAG
* * *
27287354 GAGGAAGAGGACGAGGTGAGAGAGGTTGTTAGGTTGAAAAGAGGACGGATATCTTCGGTAAGGGA
1 GAGGAAGAGGAAGAGGTGAGAGAGGTTGTTAGGTTGAAAAGAGAACGGATATCTTCAGTAAGGGA
* * * *
27287419 GAGGAAGATTGTGGATAAAAATTCTGTGAAA-TGGGAAAGCGTGTCTGTTGAAGAAGATGAAGAC
66 GAGGAAGATTGCGGATAAAAAATCTGT-AAAGCGGGAAAGCGTGTCTATTGAAGAAGATGAAGAC
* *
27287483 GAGGATTATGAGGAGGAAGAAGAGGAA
130 AAGGATTATGAGGAGGAAGAAGAAGAA
*
27287510 GAGGAAGAGGAAGAGGTGAGGGAGGTTGTTAGGTTGAAAAGAGAACGGATATCTTCAGTAAGGGA
1 GAGGAAGAGGAAGAGGTGAGAGAGGTTGTTAGGTTGAAAAGAGAACGGATATCTTCAGTAAGGGA
27287575 GAGGAAGATTGCGGATAAAAAATCTGTAAAGCGGGAAAGCGTGTCTATTGAAGAAGATGAAGACA
66 GAGGAAGATTGCGGATAAAAAATCTGTAAAGCGGGAAAGCGTGTCTATTGAAGAAGATGAAGACA
27287640 AGGATTATGAGGAGGAAGAAGAAGAA
131 AGGATTATGAGGAGGAAGAAGAAGAA
*
27287666 AAGGAAGA
1 GAGGAAGA
27287674 TGACGATGAG
Statistics
Matches: 152, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
155 3 0.02
156 149 0.98
ACGTcount: A:0.39, C:0.05, G:0.38, T:0.18
Consensus pattern (156 bp):
GAGGAAGAGGAAGAGGTGAGAGAGGTTGTTAGGTTGAAAAGAGAACGGATATCTTCAGTAAGGGA
GAGGAAGATTGCGGATAAAAAATCTGTAAAGCGGGAAAGCGTGTCTATTGAAGAAGATGAAGACA
AGGATTATGAGGAGGAAGAAGAAGAA
Found at i:27287719 original size:36 final size:36
Alignment explanation
Indices: 27287678--27287794 Score: 180
Period size: 36 Copynumber: 3.2 Consensus size: 36
27287668 GGAAGATGAC
* * * *
27287678 GATGAGGAGTTCACTCCAGATGTAGAAGATTGTTTG
1 GATGAGGAATTCACTCCGGATGAAGAGGATTGTTTG
27287714 GATGAGGAATTCACTCCGGATGAAGAGGATTGTTTG
1 GATGAGGAATTCACTCCGGATGAAGAGGATTGTTTG
* *
27287750 GATGAAGAATTCACTCCGGATGAAGAGGATTGTTTA
1 GATGAGGAATTCACTCCGGATGAAGAGGATTGTTTG
27287786 GATGAGGAA
1 GATGAGGAA
27287795 GAGGAATTGA
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 74 1.00
ACGTcount: A:0.31, C:0.10, G:0.32, T:0.27
Consensus pattern (36 bp):
GATGAGGAATTCACTCCGGATGAAGAGGATTGTTTG
Found at i:27287770 original size:18 final size:18
Alignment explanation
Indices: 27287713--27287775 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 18
27287703 AAGATTGTTT
*
27287713 GGATGAGGAATTCACTCC
1 GGATGAAGAATTCACTCC
* **
27287731 GGATGAAGAGGATT--GTTT
1 GGATGAAGA--ATTCACTCC
27287749 GGATGAAGAATTCACTCC
1 GGATGAAGAATTCACTCC
27287767 GGATGAAGA
1 GGATGAAGA
27287776 GGATTGTTTA
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
16 3 0.09
18 28 0.82
20 3 0.09
ACGTcount: A:0.32, C:0.13, G:0.32, T:0.24
Consensus pattern (18 bp):
GGATGAAGAATTCACTCC
Found at i:27292749 original size:24 final size:24
Alignment explanation
Indices: 27292722--27292767 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
27292712 GCATATCTTA
27292722 AATTA-ATCTACTTTTATTTTTAAC
1 AATTATAT-TACTTTTATTTTTAAC
* *
27292746 AATTATATTAGTTTTTTTTTTA
1 AATTATATTACTTTTATTTTTA
27292768 CTTAATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 17 0.89
25 2 0.11
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (24 bp):
AATTATATTACTTTTATTTTTAAC
Found at i:27294435 original size:31 final size:29
Alignment explanation
Indices: 27294400--27294464 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
27294390 GATTTGAGAA
* *
27294400 AATTGAATTAAAATTAAAGTTTTATGTATAT
1 AATTGAA-CAAAATTAAA-ATTTATGTATAT
*
27294431 AATTGAACAAAATTAAAATTTGTGTATAT
1 AATTGAACAAAATTAAAATTTATGTATAT
*
27294460 GATTG
1 AATTG
27294465 TACATTAGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 14 0.47
30 9 0.30
31 7 0.23
ACGTcount: A:0.45, C:0.02, G:0.12, T:0.42
Consensus pattern (29 bp):
AATTGAACAAAATTAAAATTTATGTATAT
Found at i:27297760 original size:3 final size:3
Alignment explanation
Indices: 27297752--27297780 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
27297742 TTGATAGTTT
27297752 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
27297781 GGTCTTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:27298051 original size:21 final size:21
Alignment explanation
Indices: 27298005--27298043 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
27297995 TTCATTAATC
*
27298005 AATTTTTAATTACATAAAAAT
1 AATTTTTAATTAAATAAAAAT
27298026 AATTTTTAA-TAAATAAAA
1 AATTTTTAATTAAATAAAA
27298044 TTATATTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (21 bp):
AATTTTTAATTAAATAAAAAT
Found at i:27299052 original size:31 final size:31
Alignment explanation
Indices: 27299007--27299069 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
27298997 GAACCGATTG
27299007 ATCCGCAAACTGATATAGGCCGGTTGAACCA
1 ATCCGCAAACTGATATAGGCCGGTTGAACCA
* * *
27299038 ATCCGCTAATTGATATAGGTCGGTTGAACCA
1 ATCCGCAAACTGATATAGGCCGGTTGAACCA
27299069 A
1 A
27299070 GTTAAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (31 bp):
ATCCGCAAACTGATATAGGCCGGTTGAACCA
Found at i:27300111 original size:32 final size:30
Alignment explanation
Indices: 27300054--27300121 Score: 100
Period size: 32 Copynumber: 2.2 Consensus size: 30
27300044 TTTGGTATTA
*
27300054 AAACTTGACACTTTTTTTAATTTGGTACCT
1 AAACTTGACACTTTTTTTAAATTGGTACCT
*
27300084 AAACTTGACACTTTTTTTTAAAATTGGTACTT
1 AAACTTGACAC-TTTTTTT-AAATTGGTACCT
27300116 AAACTT
1 AAACTT
27300122 TTTGGGCTCC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 11 0.32
31 7 0.21
32 16 0.47
ACGTcount: A:0.31, C:0.15, G:0.09, T:0.46
Consensus pattern (30 bp):
AAACTTGACACTTTTTTTAAATTGGTACCT
Found at i:27300184 original size:60 final size:59
Alignment explanation
Indices: 27300072--27300183 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 59
27300062 CACTTTTTTT
*
27300072 AATTTGGTACCTAAACTTGACACTTTTTTTTAAAATTGGTACTTAAACTTTTTGGGCTCC
1 AATTTGGTACCTAAACTT-ACACTTTTTTTTAAAATTGGTACCTAAACTTTTTGGGCTCC
* * *
27300132 AATTTGGTACCTAAACTT-TACTTTTTTTCCT-AATTTGGTACCTAATCTTTTT
1 AATTTGGTACCTAAACTTACACTTTTTTT--TAAAATTGGTACCTAAACTTTTT
27300184 TTTAATATTA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
58 9 0.20
59 18 0.39
60 19 0.41
ACGTcount: A:0.25, C:0.17, G:0.11, T:0.47
Consensus pattern (59 bp):
AATTTGGTACCTAAACTTACACTTTTTTTTAAAATTGGTACCTAAACTTTTTGGGCTCC
Found at i:27300511 original size:59 final size:59
Alignment explanation
Indices: 27300343--27300515 Score: 195
Period size: 59 Copynumber: 2.9 Consensus size: 59
27300333 AATTGAATCT
* * * * *
27300343 AAAAAAAGTTTAGGTGCCAAATTAGGGAAAAAAATG-CTAAGTTCAGGTACCAAATTGGGTT
1 AAAAAAAGTTTAGGTACCAAATTA-GG-AAAAAGTGTC-AAGTTCAGATACCAAATTGAGTA
* * ** *
27300404 CAAAAAAGTTTAGGTACTAAATTAAAAAAAAGTGTCAAGTTCAAATACCAAATTGAGTA
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTCAGATACCAAATTGAGTA
* **
27300463 AAAAAAAGTTTATGTACCAAATTAGGAAAAAGTGTCAAGTTTTGATACCAAAT
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTCAGATACCAAAT
27300516 ATTATATTAA
Statistics
Matches: 93, Mismatches: 18, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
59 71 0.76
60 1 0.01
61 21 0.23
ACGTcount: A:0.47, C:0.10, G:0.17, T:0.26
Consensus pattern (59 bp):
AAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTCAGATACCAAATTGAGTA
Found at i:27306923 original size:23 final size:23
Alignment explanation
Indices: 27306897--27306941 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
27306887 GAAATATATT
* *
27306897 TATTTTTATTTTGGTATCTAAAA
1 TATTTTTAATTTGATATCTAAAA
*
27306920 TATTTTTAATTTGATATTTAAA
1 TATTTTTAATTTGATATCTAAA
27306942 GAATCAATCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (23 bp):
TATTTTTAATTTGATATCTAAAA
Found at i:27313049 original size:3 final size:3
Alignment explanation
Indices: 27313041--27313082 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
27313031 TTCATATATT
27313041 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
27313083 ACACGACCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:27313579 original size:18 final size:19
Alignment explanation
Indices: 27313548--27313583 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
27313538 AATTTTCCTA
27313548 AAATGGACTAAATTGTGTT
1 AAATGGACTAAATTGTGTT
*
27313567 AAAT-GACTCAATTGTGT
1 AAATGGACTAAATTGTGT
27313584 GATATAATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.36
Consensus pattern (19 bp):
AAATGGACTAAATTGTGTT
Found at i:27316365 original size:6 final size:6
Alignment explanation
Indices: 27316346--27316390 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
27316336 ACAATTCATA
*
27316346 TCACTT TCAATT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
27316391 ATTTTGATCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.20, C:0.31, G:0.00, T:0.49
Consensus pattern (6 bp):
TCACTT
Found at i:27318693 original size:32 final size:32
Alignment explanation
Indices: 27318657--27318724 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
27318647 TTTTTAAAGG
* *
27318657 TTGATTAAT-GCAAATCCTTAAAGAAATTAGAA
1 TTGATTAATAG-AAACCCCTAAAGAAATTAGAA
* *
27318689 TTGATTAATAGAAACCCCTGAAGAAATTAGGA
1 TTGATTAATAGAAACCCCTAAAGAAATTAGAA
27318721 TTGA
1 TTGA
27318725 ATAGAAAGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 30 0.97
33 1 0.03
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.29
Consensus pattern (32 bp):
TTGATTAATAGAAACCCCTAAAGAAATTAGAA
Found at i:27319832 original size:19 final size:19
Alignment explanation
Indices: 27319808--27319852 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
27319798 GTAGCGTAGG
27319808 ACCCGACCATACTACTTGA
1 ACCCGACCATACTACTTGA
27319827 ACCCGACCATACTACTTGA
1 ACCCGACCATACTACTTGA
27319846 ACCCGAC
1 ACCCGAC
27319853 TAATTGAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.31, C:0.40, G:0.11, T:0.18
Consensus pattern (19 bp):
ACCCGACCATACTACTTGA
Found at i:27329148 original size:38 final size:38
Alignment explanation
Indices: 27329106--27329181 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
27329096 AGTTGGATGC
*
27329106 ATATTTGAGTGTCGACAACAAATAGCAATAAGATTTTG
1 ATATTTGAGTATCGACAACAAATAGCAATAAGATTTTG
* *
27329144 ATATTTGAGTATCGACAACAAATAGCAGTGAGATTTTG
1 ATATTTGAGTATCGACAACAAATAGCAATAAGATTTTG
27329182 TCGAAATATC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.32
Consensus pattern (38 bp):
ATATTTGAGTATCGACAACAAATAGCAATAAGATTTTG
Found at i:27329468 original size:25 final size:24
Alignment explanation
Indices: 27329424--27329500 Score: 82
Period size: 25 Copynumber: 3.1 Consensus size: 24
27329414 CTACTCTACT
*
27329424 AAATAAAAATAATAATAACAAATC
1 AAATAAAAATAATAATAACAAAAC
* *
27329448 AAATAAAAATTATATTAAACAAAAC
1 AAATAAAAATAATAAT-AACAAAAC
** *
27329473 AAATAACTTATAATAATTACAAAAC
1 AAATAA-AAATAATAATAACAAAAC
27329498 AAA
1 AAA
27329501 ATATAACTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
24 14 0.33
25 23 0.53
26 6 0.14
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.23
Consensus pattern (24 bp):
AAATAAAAATAATAATAACAAAAC
Found at i:27329687 original size:17 final size:17
Alignment explanation
Indices: 27329667--27329725 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 17
27329657 TAAATAGCTT
27329667 TAAAAATAAATTTAAAA
1 TAAAAATAAATTTAAAA
* *
27329684 TAAAAAT-AA-TCACACA
1 TAAAAATAAATTTA-AAA
27329700 -AAAAA-AAATTTAAAA
1 TAAAAATAAATTTAAAA
27329715 T-AAAATAAATT
1 TAAAAATAAATT
27329726 AACCTTCTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 11
0.69 0.08 0.23
Matches are distributed among these distances:
15 15 0.45
16 11 0.33
17 7 0.21
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.25
Consensus pattern (17 bp):
TAAAAATAAATTTAAAA
Found at i:27329876 original size:198 final size:198
Alignment explanation
Indices: 27329538--27330104 Score: 1010
Period size: 198 Copynumber: 2.9 Consensus size: 198
27329528 TTTACATTTA
27329538 CCTTTCTTTTAGATTTTTTTCTCCTTTAATCAACCTACTAAACAAATAAAATTATAATAATAAAT
1 CCTTTCTTTTAGATTTTTTTCTCCTTTAATCAACCTACTAAACAAATAAAATTATAATAATAAAT
27329603 CAATCATATTAAACATTAAAATTAAAAACTAAATAATTACTACTACAAATAAATTAAATAGCTTT
66 CAATCATATTAAACATTAAAATTAAAAACTAAATAATTACTACTACAAATAAATTAAATAGCTTT
27329668 AAAAATAAATTTAAAATAAAAATAATCACACAAAAAAAAATTTAAAATAAAATAAATTAACCTTC
131 AAAAATAAATTTAAAATAAAAATAATCACACAAAAAAAAATTTAAAATAAAATAAATTAACCTTC
27329733 TTC
196 TTC
27329736 CCTTTCTTTTAGATTTTTTTCTCCTTTAATCAACCTACTAAACAAATAAAATTATAATAATAAAT
1 CCTTTCTTTTAGATTTTTTTCTCCTTTAATCAACCTACTAAACAAATAAAATTATAATAATAAAT
27329801 CAATCATATTAAACATTAAAATTAAAAACTAAATAATTACTACTACAAATAAATTAAATAGCTTT
66 CAATCATATTAAACATTAAAATTAAAAACTAAATAATTACTACTACAAATAAATTAAATAGCTTT
27329866 AAAAATAAATTTAAAATAAAAATAATCACACAAAAAAAAATTTAAAATAAAATAAATTAACCTTC
131 AAAAATAAATTTAAAATAAAAATAATCACACAAAAAAAAATTTAAAATAAAATAAATTAACCTTC
27329931 TTC
196 TTC
* * * *
27329934 CCTTTCTTTTA-AATTTTTTCTCCTTTAATCTAACATACTAAACAAATGAAATTATAATAACAAA
1 CCTTTCTTTTAGATTTTTTTCTCCTTTAATC-AACCTACTAAACAAATAAAATTATAATAATAAA
* * * * * *
27329998 TCCATCAAATTAAACATTAAAATTAAAAATTAAATAATTACTACTACTAACAAATTAAATAACTT
65 TCAATCATATTAAACATTAAAATTAAAAACTAAATAATTACTACTACAAATAAATTAAATAGCTT
* *
27330063 TAAAAATAAATTTAAAATTAAAATAATCACACAAAATAAAAT
130 TAAAAATAAATTTAAAATAAAAATAATCACACAAAAAAAAAT
27330105 AAATTAACCT
Statistics
Matches: 356, Mismatches: 12, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
197 18 0.05
198 338 0.95
ACGTcount: A:0.52, C:0.13, G:0.01, T:0.34
Consensus pattern (198 bp):
CCTTTCTTTTAGATTTTTTTCTCCTTTAATCAACCTACTAAACAAATAAAATTATAATAATAAAT
CAATCATATTAAACATTAAAATTAAAAACTAAATAATTACTACTACAAATAAATTAAATAGCTTT
AAAAATAAATTTAAAATAAAAATAATCACACAAAAAAAAATTTAAAATAAAATAAATTAACCTTC
TTC
Found at i:27329885 original size:17 final size:17
Alignment explanation
Indices: 27329865--27329923 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 17
27329855 TAAATAGCTT
27329865 TAAAAATAAATTTAAAA
1 TAAAAATAAATTTAAAA
* *
27329882 TAAAAAT-AA-TCACACA
1 TAAAAATAAATTTA-AAA
27329898 -AAAAA-AAATTTAAAA
1 TAAAAATAAATTTAAAA
27329913 T-AAAATAAATT
1 TAAAAATAAATT
27329924 AACCTTCTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 11
0.69 0.08 0.23
Matches are distributed among these distances:
15 15 0.45
16 11 0.33
17 7 0.21
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.25
Consensus pattern (17 bp):
TAAAAATAAATTTAAAA
Found at i:27330135 original size:4 final size:4
Alignment explanation
Indices: 27330121--27330158 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
27330111 ACCTTCTTCC
*
27330121 CTTT C-TT CTTT CTTT CTTT CTTT CTTT CTTT CCTT CTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTT
27330159 CTCCCTTCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 3 0.10
4 28 0.90
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (4 bp):
CTTT
Found at i:27332333 original size:55 final size:55
Alignment explanation
Indices: 27332264--27332449 Score: 203
Period size: 55 Copynumber: 3.3 Consensus size: 55
27332254 CCGACACCTT
*
27332264 TTTATCAGAT-AAAAAAAAATTTAGGGTGTTTGCCAAGCCATGATCGACACCCCC
1 TTTATCAGATAAAAAAAAAATTTTGGGTGTTTGCCAAGCCATGATCGACACCCCC
* * * * * *
27332318 TTTATCAGATAAAAAAATATTTTTGGGTATTTACCAAGCCATGGTGGACACCCCC
1 TTTATCAGATAAAAAAAAAATTTTGGGTGTTTGCCAAGCCATGATCGACACCCCC
* * * ** *
27332373 TTTTTCATATACAAAAAAATATATTTTTTGGGTGTTTGTCAAGTTATGACCGACACCCCC
1 TTTATCAGATA-AAAAAAA-A-A--TTTTGGGTGTTTGCCAAGCCATGATCGACACCCCC
27332433 TTTATCAGATAAAAAAA
1 TTTATCAGATAAAAAAA
27332450 TATTTGTAAT
Statistics
Matches: 105, Mismatches: 21, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
54 10 0.10
55 46 0.44
56 6 0.06
57 1 0.01
59 6 0.06
60 36 0.34
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.32
Consensus pattern (55 bp):
TTTATCAGATAAAAAAAAAATTTTGGGTGTTTGCCAAGCCATGATCGACACCCCC
Found at i:27335294 original size:25 final size:27
Alignment explanation
Indices: 27335257--27335310 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 27
27335247 TGGTACCTAA
*
27335257 ACTTAACACTTTTT-A-CTAATTTGGT
1 ACTTAACACTTTTTAACCAAATTTGGT
27335282 ACTTAA-ACTTTTTTAACCAAATTTGGT
1 ACTTAACAC-TTTTTAACCAAATTTGGT
27335309 AC
1 AC
27335311 CTGAACTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 2 0.08
25 11 0.44
26 1 0.04
27 11 0.44
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.44
Consensus pattern (27 bp):
ACTTAACACTTTTTAACCAAATTTGGT
Found at i:27335309 original size:58 final size:60
Alignment explanation
Indices: 27335244--27335355 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 60
27335234 TCAATATAAT
*
27335244 ATTTGGTACCTAAACTTAACA-CTTTTTAC-TAATTTGGTACTTAAACTTTTTTAACCAA
1 ATTTGGTACCTAAACTTAACATCTTTTTACTTAATTTGGTACCTAAACTTTTTTAACCAA
* * * * *
27335302 ATTTGGTACCTGAACTTGACATTTTTTTTCTTAATTTGGTACCTAAGCTTTTTT
1 ATTTGGTACCTAAACTTAACATCTTTTTACTTAATTTGGTACCTAAACTTTTTT
27335356 TTTTTAAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
58 19 0.41
59 6 0.13
60 21 0.46
ACGTcount: A:0.27, C:0.16, G:0.10, T:0.47
Consensus pattern (60 bp):
ATTTGGTACCTAAACTTAACATCTTTTTACTTAATTTGGTACCTAAACTTTTTTAACCAA
Found at i:27335637 original size:31 final size:31
Alignment explanation
Indices: 27335581--27335660 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 31
27335571 GGACCCCAAA
* *
27335581 AAGTTTAAGTA-TCAACTTAGAAAAAAGTGTC
1 AAGTTTAAGTACT-AAATTAGAAAAAAGTATC
* * *
27335612 ATGTTTAAGTACTAAATTAGGAAAAATTATC
1 AAGTTTAAGTACTAAATTAGAAAAAAGTATC
* *
27335643 AAGTTTTAGTACCAAATT
1 AAGTTTAAGTACTAAATT
27335661 GGACACAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 39 0.98
32 1 0.03
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.34
Consensus pattern (31 bp):
AAGTTTAAGTACTAAATTAGAAAAAAGTATC
Found at i:27338147 original size:62 final size:62
Alignment explanation
Indices: 27338050--27338176 Score: 254
Period size: 62 Copynumber: 2.0 Consensus size: 62
27338040 AGCAGGAATT
27338050 AGTATTGAAGGAGATGGGTACTTGAAAAAACCACAGAATTTTAGATTTAGATCAAGCAAACA
1 AGTATTGAAGGAGATGGGTACTTGAAAAAACCACAGAATTTTAGATTTAGATCAAGCAAACA
27338112 AGTATTGAAGGAGATGGGTACTTGAAAAAACCACAGAATTTTAGATTTAGATCAAGCAAACA
1 AGTATTGAAGGAGATGGGTACTTGAAAAAACCACAGAATTTTAGATTTAGATCAAGCAAACA
27338174 AGT
1 AGT
27338177 TAGAAATAGA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 65 1.00
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.24
Consensus pattern (62 bp):
AGTATTGAAGGAGATGGGTACTTGAAAAAACCACAGAATTTTAGATTTAGATCAAGCAAACA
Found at i:27344198 original size:165 final size:160
Alignment explanation
Indices: 27344024--27344349 Score: 553
Period size: 165 Copynumber: 2.0 Consensus size: 160
27344014 AAACAAAACA
27344024 AGACATGTATTCTACTAAATAATTGTTTTCCTGACAAAGATTCAATACCGCCAAGAATATTCCTA
1 AGACATGTATTCTACTAAATAATTGTTTTCCTGACAAAGATTCAATACCGCCAAGAATATTCCTA
* *
27344089 GTTAAATATACCCAAGTTTTGTTTTTCTCACTAAATCTCAAAACCTCAATTCTTCCTCTTTTCTT
66 GTT-AA-ATACCCAAGTTTTGCTTTTCTCACTAAATCTCAAAACCTCAATTC-T--TCTTTTCTC
*
27344154 TGCACTACTTTTGCTTTGCAAATATATATACATAT
126 TGCACTACTTTTGCTTTGCAAATATAAATACATAT
27344189 AGACATGTATTCTACTAAATAATTGTTTTCCTGACAAAGATTCAATACCGCCAAGAATATTCCTA
1 AGACATGTATTCTACTAAATAATTGTTTTCCTGACAAAGATTCAATACCGCCAAGAATATTCCTA
*
27344254 GTTAAATACCCAAGTTTTGCTTTTCTCACTAAATCTCAAAACTTCAATTCTTCTTTTCTCTGCAC
66 GTTAAATACCCAAGTTTTGCTTTTCTCACTAAATCTCAAAACCTCAATTCTTCTTTTCTCTGCAC
* *
27344319 TACTTTTGCTTTGCATATATAAATATATAT
131 TACTTTTGCTTTGCAAATATAAATACATAT
27344349 A
1 A
27344350 TTCTTGGCGA
Statistics
Matches: 155, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
160 41 0.26
162 1 0.01
163 43 0.28
164 2 0.01
165 68 0.44
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.39
Consensus pattern (160 bp):
AGACATGTATTCTACTAAATAATTGTTTTCCTGACAAAGATTCAATACCGCCAAGAATATTCCTA
GTTAAATACCCAAGTTTTGCTTTTCTCACTAAATCTCAAAACCTCAATTCTTCTTTTCTCTGCAC
TACTTTTGCTTTGCAAATATAAATACATAT
Found at i:27344924 original size:14 final size:13
Alignment explanation
Indices: 27344890--27344920 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
27344880 AAACATAGAA
27344890 ACAAAGAACAGAG
1 ACAAAGAACAGAG
*
27344903 GCAAAGAACAGAG
1 ACAAAGAACAGAG
27344916 ACAAA
1 ACAAA
27344921 AGAATAGTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.61, C:0.16, G:0.23, T:0.00
Consensus pattern (13 bp):
ACAAAGAACAGAG
Found at i:27346005 original size:25 final size:25
Alignment explanation
Indices: 27345969--27346019 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
27345959 CTTCATTCTA
*
27345969 TATTTTACTATTCTT-TTATATATTT
1 TATTTTACTATTATTATTAT-TATTT
*
27345994 TATTTTATTATTATTATTATTATTT
1 TATTTTACTATTATTATTATTATTT
27346019 T
1 T
27346020 CCAGTATGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (25 bp):
TATTTTACTATTATTATTATTATTT
Found at i:27346313 original size:35 final size:35
Alignment explanation
Indices: 27346274--27346384 Score: 86
Period size: 35 Copynumber: 3.1 Consensus size: 35
27346264 TATTATTCTA
27346274 AAATTAATCATTATTTTAATTTTTCCCTTTATTTC
1 AAATTAATCATTATTTTAATTTTTCCCTTTATTTC
** *** * *
27346309 AAATTTGTTCA-TACCCATATATATTTT---ATTATTCTA
1 AAA-TTAATCATTA-TTTTA-AT-TTTTCCCTTTATT-TC
27346345 AAATTAATCATTATTTTAATTTTTCCCTTTATTTC
1 AAATTAATCATTATTTTAATTTTTCCCTTTATTTC
27346380 AAATT
1 AAATT
27346385 TGTTCATACC
Statistics
Matches: 53, Mismatches: 14, Indels: 18
0.62 0.16 0.21
Matches are distributed among these distances:
33 4 0.08
34 2 0.04
35 23 0.43
36 18 0.34
37 2 0.04
38 4 0.08
ACGTcount: A:0.32, C:0.14, G:0.01, T:0.54
Consensus pattern (35 bp):
AAATTAATCATTATTTTAATTTTTCCCTTTATTTC
Found at i:27346341 original size:71 final size:71
Alignment explanation
Indices: 27346263--27346412 Score: 300
Period size: 71 Copynumber: 2.1 Consensus size: 71
27346253 ATTAGTGTGG
27346263 TTATTATTCTAAAATTAATCATTATTTTAATTTTTCCCTTTATTTCAAATTTGTTCATACCCATA
1 TTATTATTCTAAAATTAATCATTATTTTAATTTTTCCCTTTATTTCAAATTTGTTCATACCCATA
27346328 TATATT
66 TATATT
27346334 TTATTATTCTAAAATTAATCATTATTTTAATTTTTCCCTTTATTTCAAATTTGTTCATACCCATA
1 TTATTATTCTAAAATTAATCATTATTTTAATTTTTCCCTTTATTTCAAATTTGTTCATACCCATA
27346399 TATATT
66 TATATT
27346405 TTATTATT
1 TTATTATT
27346413 TGTTTTTTAA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 79 1.00
ACGTcount: A:0.31, C:0.13, G:0.01, T:0.55
Consensus pattern (71 bp):
TTATTATTCTAAAATTAATCATTATTTTAATTTTTCCCTTTATTTCAAATTTGTTCATACCCATA
TATATT
Found at i:27346377 original size:36 final size:36
Alignment explanation
Indices: 27346266--27346377 Score: 90
Period size: 36 Copynumber: 3.1 Consensus size: 36
27346256 AGTGTGGTTA
27346266 TTATTCTAAAATTAATCATTATTTTAATTTTTCCCT
1 TTATTCTAAAATTAATCATTATTTTAATTTTTCCCT
* ** *** *
27346302 TTATT-TCAAATTTGTTCA-TACCCATATATATTTT---A
1 TTATTCT-AAAATTAATCATTA-TTTTA-AT-TTTTCCCT
27346337 TTATTCTAAAATTAATCATTATTTTAATTTTTCCCT
1 TTATTCTAAAATTAATCATTATTTTAATTTTTCCCT
27346373 TTATT
1 TTATT
27346378 TCAAATTTGT
Statistics
Matches: 53, Mismatches: 14, Indels: 18
0.62 0.16 0.21
Matches are distributed among these distances:
33 4 0.08
34 2 0.04
35 18 0.34
36 23 0.43
37 2 0.04
38 4 0.08
ACGTcount: A:0.30, C:0.13, G:0.01, T:0.55
Consensus pattern (36 bp):
TTATTCTAAAATTAATCATTATTTTAATTTTTCCCT
Found at i:27346412 original size:35 final size:35
Alignment explanation
Indices: 27346302--27346413 Score: 88
Period size: 35 Copynumber: 3.2 Consensus size: 35
27346292 ATTTTTCCCT
27346302 TTATTTCAAATTTGTTCATACCCATATATATTTTA
1 TTATTTCAAATTTGTTCATACCCATATATATTTTA
* ** *** *
27346337 TTA-TTCTAAAATTAATCATTA-TTTTA-AT-TTTTCCCT
1 TTATTTC-AAATTTGTTCA-TACCCATATATATTTT---A
27346373 TTATTTCAAATTTGTTCATACCCATATATATTTTA
1 TTATTTCAAATTTGTTCATACCCATATATATTTTA
27346408 TTATTT
1 TTATTT
27346414 GTTTTTTAAA
Statistics
Matches: 54, Mismatches: 14, Indels: 18
0.63 0.16 0.21
Matches are distributed among these distances:
33 4 0.07
34 5 0.09
35 21 0.39
36 15 0.28
37 5 0.09
38 4 0.07
ACGTcount: A:0.30, C:0.13, G:0.02, T:0.54
Consensus pattern (35 bp):
TTATTTCAAATTTGTTCATACCCATATATATTTTA
Found at i:27350788 original size:3 final size:3
Alignment explanation
Indices: 27350780--27350816 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
27350770 ACACTATTAA
27350780 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
27350817 TGAAAAGGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:27350897 original size:62 final size:66
Alignment explanation
Indices: 27350795--27350924 Score: 171
Period size: 62 Copynumber: 2.0 Consensus size: 66
27350785 GAAGAAGAAG
* ***
27350795 AAGAAGAAGAAGAAGAAAAGAATGAAAAGGTCAAGATGAAAACTTGCAAAGGGCATCTTTAAAAA
1 AAGAAGAAGAAGAAGAAAAGAAGGAAAAGGTCAAGATGAAAACCCACAAAGGGCATC-TTAAAAA
27350860 AA
65 AA
*
27350862 AAGAA-AAGAA-AAG-AAA-AAGGAAAA-GTCAAGATGAAAACCCACAAAGGGTATCTTAAAAAA
1 AAGAAGAAGAAGAAGAAAAGAAGGAAAAGGTCAAGATGAAAACCCACAAAGGGCATCTTAAAAAA
27350922 A
66 A
27350923 AA
1 AA
27350925 CTCCTTCTCT
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
61 11 0.19
62 24 0.41
63 7 0.12
64 3 0.05
65 3 0.05
66 5 0.09
67 5 0.09
ACGTcount: A:0.60, C:0.08, G:0.20, T:0.12
Consensus pattern (66 bp):
AAGAAGAAGAAGAAGAAAAGAAGGAAAAGGTCAAGATGAAAACCCACAAAGGGCATCTTAAAAAA
A
Found at i:27352809 original size:49 final size:48
Alignment explanation
Indices: 27352753--27353082 Score: 187
Period size: 49 Copynumber: 6.8 Consensus size: 48
27352743 GAAGATATAG
* *
27352753 AGGGAAAGGTTTAAGTCGTAACGGCGAACCTTATACCTTAGAAGCATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTATACC-TAGAAGCATGA
* * * * *
27352802 AGGGAAAGATTTAAGCCGTAACGACGAATC-TAGTACC-ACGAA-AAT-A
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTA-TACCTA-GAAGCATGA
* * * *
27352848 TAGGGAAAGGTTTAAGTCGCAACAGCGAACCTTGTACCTCAGAAACATGA
1 -AGGGAAAGATTTAAGTCGCAACGGCGAACCTTATACCT-AGAAGCATGA
* * * * * *
27352898 AGGGAAAGATTTAAG-CAGCAATGGTGAATC-TAGTACC-ACGAGGATATGG
1 AGGGAAAGATTTAAGTC-GCAACGGCGAACCTTA-TACCTA-GAAG-CATGA
* * * * *
27352947 AGGGAAAGGTTTAAGTCGCAATGGTGAACCTTGTACCTCAGAAGCATAA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTATACCT-AGAAGCATGA
* * * * *
27352996 AGGGAAAGATTTAAGCCGCAACGACGGATCC--AGTACC-ATGAAGATATGG
1 AGGGAAAGATTTAAGTCGCAACGGC-GAACCTTA-TACCTA-GAAG-CATGA
* *
27353045 AGGGAAA-AGTTTAAGTCGCAATGGCGAACCTTGTACCT
1 AGGGAAAGA-TTTAAGTCGCAACGGCGAACCTTATACCT
27353083 CAAAAACGTA
Statistics
Matches: 212, Mismatches: 45, Indels: 47
0.70 0.15 0.15
Matches are distributed among these distances:
46 1 0.00
47 33 0.16
48 22 0.10
49 145 0.68
50 10 0.05
51 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.20
Consensus pattern (48 bp):
AGGGAAAGATTTAAGTCGCAACGGCGAACCTTATACCTAGAAGCATGA
Found at i:27352987 original size:98 final size:98
Alignment explanation
Indices: 27352737--27353089 Score: 485
Period size: 98 Copynumber: 3.6 Consensus size: 98
27352727 TAGGTTTCAT
* * * * *
27352737 TACCACGAAGATATAGAGGGAAAGGTTTAAGTCGTAACGGCGAACCTTATACCTTAGAAGCATGA
1 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGA
*
27352802 AGGGAAAGATTTAAGCCGTAACGACGAATCTAG
66 AGGGAAAGATTTAAGCCGCAACGACGAATCTAG
* *
27352835 TACCACGAAAATAT--AGGGAAAGGTTTAAGTCGCAACAGCGAACCTTGTACCTCAGAAACATGA
1 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGA
* * **
27352898 AGGGAAAGATTTAAGCAGCAATGGTGAATCTAG
66 AGGGAAAGATTTAAGCCGCAACGACGAATCTAG
* * * * *
27352931 TACCACGAGGATATGGAGGGAAAGGTTTAAGTCGCAATGGTGAACCTTGTACCTCAGAAGCATAA
1 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGA
* *
27352996 AGGGAAAGATTTAAGCCGCAACGACGGATCCAG
66 AGGGAAAGATTTAAGCCGCAACGACGAATCTAG
* * * *
27353029 TACCATGAAGATATGGAGGGAAAAGTTTAAGTCGCAATGGCGAACCTTGTACCTCAAAAAC
1 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAAC
27353090 GTAAAAGAAA
Statistics
Matches: 223, Mismatches: 30, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
96 84 0.38
98 139 0.62
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.20
Consensus pattern (98 bp):
TACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGA
AGGGAAAGATTTAAGCCGCAACGACGAATCTAG
Found at i:27354127 original size:52 final size:52
Alignment explanation
Indices: 27354044--27354386 Score: 542
Period size: 52 Copynumber: 6.6 Consensus size: 52
27354034 TAAATGAAAA
* *
27354044 AGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCATTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
27354096 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * *
27354148 AGGTCCGATGATTATGTGTCAACGTGAGTATATAAATCATTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
27354200 AGGTCCGATGACTATGTGTCATTGTGAGTATATGAATCCTTTACAGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
27354252 AGGTCCGATAACTATTTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * *
27354304 AGGTCCGATGATTATGTGTCATCTTGAGTATATGAATCCTATACGGATTAAG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
27354356 AGGTCCGATGACTATATATCATCGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
27354387 TAAATGAAAT
Statistics
Matches: 265, Mismatches: 26, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 265 1.00
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:27360481 original size:52 final size:52
Alignment explanation
Indices: 27360403--27360641 Score: 372
Period size: 52 Copynumber: 4.6 Consensus size: 52
27360393 TAAATGAAAA
* * *
27360403 AGGTCCGATAACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATG
1 AGGTCCGATGACTATATGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
27360455 AGGTCCGTTGACTATATGTCATCGTGAGTATATGAATCCTTTATGGATTATG
1 AGGTCCGATGACTATATGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * *
27360507 AGGTCCGATGATTATGTATCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATATGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
27360559 AGGGCCGATGACTATATGTCATCGTGAGTATATGAAT-CTTATACGGATTAAG
1 AGGTCCGATGACTATATGTCATCGTGAGTATATGAATCCTT-TACGGATTATG
27360611 AGGTCCGATGACTATATGTCATCGTGAGTAT
1 AGGTCCGATGACTATATGTCATCGTGAGTAT
27360642 TAAATGAAAT
Statistics
Matches: 170, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
51 3 0.02
52 167 0.98
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (52 bp):
AGGTCCGATGACTATATGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:27361405 original size:21 final size:21
Alignment explanation
Indices: 27361376--27361451 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
27361366 GGAGTTTTTA
27361376 GTATCGGTAGAAGTAAT-ACTT
1 GTATCGGTAGAAG-AATCACTT
* *
27361397 GTTTCGGTAGAAGAGTCACTT
1 GTATCGGTAGAAGAATCACTT
****
27361418 GTATCGGTAGACCTGTCACTT
1 GTATCGGTAGAAGAATCACTT
*
27361439 GTATTGGTAGAAG
1 GTATCGGTAGAAG
27361452 TCTGTACTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 2 0.04
21 43 0.96
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.33
Consensus pattern (21 bp):
GTATCGGTAGAAGAATCACTT
Found at i:27365858 original size:16 final size:18
Alignment explanation
Indices: 27365831--27365863 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
27365821 TAGAATTAGG
27365831 TTGAGAAAATTG-TTTAA
1 TTGAGAAAATTGATTTAA
27365848 TTGAG-AAATTGATTTA
1 TTGAGAAAATTGATTTA
27365864 TTTAGATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (18 bp):
TTGAGAAAATTGATTTAA
Found at i:27375122 original size:24 final size:24
Alignment explanation
Indices: 27375108--27375173 Score: 105
Period size: 24 Copynumber: 2.8 Consensus size: 24
27375098 TTGTCATTCG
27375108 CTATACGTTTATGCTCGTCAACCA
1 CTATACGTTTATGCTCGTCAACCA
* *
27375132 CTATAAGTTTATGCTCGTCAGCCA
1 CTATACGTTTATGCTCGTCAACCA
*
27375156 CTATACTTTTATGCTCGT
1 CTATACGTTTATGCTCGT
27375174 ATACTTAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.38
Consensus pattern (24 bp):
CTATACGTTTATGCTCGTCAACCA
Found at i:27382771 original size:19 final size:19
Alignment explanation
Indices: 27382688--27382771 Score: 59
Period size: 18 Copynumber: 4.5 Consensus size: 19
27382678 TTATAAAAAA
* *
27382688 TTCAAAATAATTTTTAAAAT
1 TTCAAAA-AATTTATAAATT
* *
27382708 TTCTAAATATTTATAACA--
1 TTCAAAAAATTTATAA-ATT
* *
27382726 TTCAACAAA-TTATATATT
1 TTCAAAAAATTTATAAATT
*
27382744 TT-TAAAAATTTATAAATT
1 TTCAAAAAATTTATAAATT
27382762 TTCAAAAAAT
1 TTCAAAAAAT
27382772 ATATTCTAAA
Statistics
Matches: 48, Mismatches: 11, Indels: 11
0.69 0.16 0.16
Matches are distributed among these distances:
16 1 0.02
17 9 0.19
18 18 0.38
19 13 0.27
20 7 0.15
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (19 bp):
TTCAAAAAATTTATAAATT
Found at i:27392638 original size:25 final size:25
Alignment explanation
Indices: 27392593--27392640 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
27392583 GAAGGAGCGT
* *
27392593 CAGAGAAGAGGTGACGGAGGGTCCG
1 CAGAGAAGAGGCGACGAAGGGTCCG
*
27392618 CAGAGAAGAGGCGGCGAAGGGTC
1 CAGAGAAGAGGCGACGAAGGGTC
27392641 TATAGAGGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.29, C:0.17, G:0.48, T:0.06
Consensus pattern (25 bp):
CAGAGAAGAGGCGACGAAGGGTCCG
Found at i:27400453 original size:29 final size:29
Alignment explanation
Indices: 27400404--27400472 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
27400394 ATGATAGGGG
*
27400404 AATGGTTTGATATGCAGACTAAGATAGGAA
1 AATGG-TTGATATGCAAACTAAGATAGGAA
* *
27400434 AATGGTTGATATGCAAACTAAGGTGGGAA
1 AATGGTTGATATGCAAACTAAGATAGGAA
27400463 AATGGGTTGA
1 AAT-GGTTGA
27400473 AAGGATAAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 24 0.69
30 11 0.31
ACGTcount: A:0.38, C:0.06, G:0.30, T:0.26
Consensus pattern (29 bp):
AATGGTTGATATGCAAACTAAGATAGGAA
Found at i:27400581 original size:19 final size:17
Alignment explanation
Indices: 27400541--27400607 Score: 59
Period size: 19 Copynumber: 3.8 Consensus size: 17
27400531 TTTTTTGTAA
27400541 TTTTCTATATTT-TTAGACT
1 TTTTCTAT-TTTCTTA-A-T
27400560 TTTT-TATTTTCTATATAT
1 TTTTCTATTTTCT-TA-AT
27400578 TTTTCTATTTTCTTAAT
1 TTTTCTATTTTCTTAAT
*
27400595 TTTT-AATTTTCTT
1 TTTTCTATTTTCTT
27400608 TTTACAAGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
16 8 0.19
17 9 0.21
18 11 0.26
19 15 0.35
ACGTcount: A:0.19, C:0.09, G:0.01, T:0.70
Consensus pattern (17 bp):
TTTTCTATTTTCTTAAT
Found at i:27401754 original size:15 final size:15
Alignment explanation
Indices: 27401736--27401775 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
27401726 TAAAAAGTAA
27401736 AAAAATTAAATCTAT
1 AAAAATTAAATCTAT
**
27401751 AAAAA-TAAAAGTAT
1 AAAAATTAAATCTAT
27401765 AAAAATTAAAT
1 AAAAATTAAAT
27401776 TTAAAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.28
Consensus pattern (15 bp):
AAAAATTAAATCTAT
Found at i:27402669 original size:67 final size:69
Alignment explanation
Indices: 27402579--27402712 Score: 173
Period size: 70 Copynumber: 2.0 Consensus size: 69
27402569 ATTATATAAA
* * ** * *
27402579 TAATATAATGGTTTTGCCTTTTAA-TTT-AATGGGTAAACATTTATCAAAATGATGTAGTTCTGC
1 TAATATAATGATTTTGACTTTTAACTTTAAAAAGGTAAACATTTAACAAAATGACGTAGTTCTGC
27402642 TATT
66 TATT
* *
27402646 TAATTTAATGATTTTGACTTTTAACTTTAGAAAAGGTAAACATTTAACAAAATGACGTAGTTTTG
1 TAATATAATGATTTTGACTTTTAACTTTA-AAAAGGTAAACATTTAACAAAATGACGTAGTTCTG
27402711 CT
65 CT
27402713 TTTTCTTATT
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
67 21 0.38
68 3 0.05
70 32 0.57
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (69 bp):
TAATATAATGATTTTGACTTTTAACTTTAAAAAGGTAAACATTTAACAAAATGACGTAGTTCTGC
TATT
Found at i:27409343 original size:16 final size:14
Alignment explanation
Indices: 27409319--27409391 Score: 56
Period size: 16 Copynumber: 4.7 Consensus size: 14
27409309 ATTTAATGAT
27409319 AAATAAATAAATAAA
1 AAAT-AATAAATAAA
27409334 CAAGATAATAAATATAA
1 -AA-ATAATAAATA-AA
*
27409351 ATATAAATTAAATAAA
1 AAAT-AA-TAAATAAA
*
27409367 AAATAATAAAAAAGA
1 AAATAATAAATAA-A
*
27409382 AAATGATAAA
1 AAATAATAAA
27409392 ATGGCATGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
14 6 0.12
15 14 0.29
16 18 0.38
17 10 0.21
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.22
Consensus pattern (14 bp):
AAATAATAAATAAA
Found at i:27409476 original size:27 final size:28
Alignment explanation
Indices: 27409415--27409478 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 28
27409405 AAATAACAAC
*
27409415 AATATAAATAAACAAAAAAAAATTAAAT
1 AATAAAAATAAACAAAAAAAAATTAAAT
** * *
27409443 GCT-AAAATAAACAAACAAATA-TAAAT
1 AATAAAAATAAACAAAAAAAAATTAAAT
27409469 AATAAAAATA
1 AATAAAAATA
27409479 CTTGAGATTA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
26 6 0.21
27 21 0.75
28 1 0.04
ACGTcount: A:0.72, C:0.06, G:0.02, T:0.20
Consensus pattern (28 bp):
AATAAAAATAAACAAAAAAAAATTAAAT
Found at i:27410479 original size:50 final size:49
Alignment explanation
Indices: 27410417--27410520 Score: 118
Period size: 50 Copynumber: 2.1 Consensus size: 49
27410407 TTTTTTTCAA
* * * *
27410417 AAGGTGTAAGATTCGCCGTTACGGCTTCAATCTGTTTCCTATTTGGTTTT
1 AAGGTGTAAGATTCGCCGTCACGACTTCAATCT-ATCCCTATTTGGTTTT
* * * * *
27410467 AAGGTGTTAGATTTGTCGTCATGACTTTAATCTATCCCTATTTGGTTTT
1 AAGGTGTAAGATTCGCCGTCACGACTTCAATCTATCCCTATTTGGTTTT
27410516 AAGGT
1 AAGGT
27410521 ATTAAGTTAC
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
49 19 0.42
50 26 0.58
ACGTcount: A:0.20, C:0.15, G:0.21, T:0.43
Consensus pattern (49 bp):
AAGGTGTAAGATTCGCCGTCACGACTTCAATCTATCCCTATTTGGTTTT
Found at i:27410608 original size:49 final size:49
Alignment explanation
Indices: 27410539--27411250 Score: 256
Period size: 49 Copynumber: 14.5 Consensus size: 49
27410529 ACCGTCGTGG
* * *
27410539 CTTCAA-CTTATCCCTATTCAATTTTAAAGTGTAAGATCTGTCGTTGTGA
1 CTTCAACCTT-TCCCTCTTCAATTTTAAGGTGTAAGGTCTGTCGTTGTGA
* * * * *
27410588 CTTCAATCTTTCCCTCTTCAATTTTAGGGTGTTAGGTCTGTCATTGCGA
1 CTTCAACCTTTCCCTCTTCAATTTTAAGGTGTAAGGTCTGTCGTTGTGA
* * *
27410637 CTTCAACCTATCCCTCTTCAGTTTTAAGGTGTAAGGTCCGTCGTTGCTG-
1 CTTCAACCTTTCCCTCTTCAATTTTAAGGTGTAAGGTCTGTCGTTG-TGA
*** * * * * ** *
27410686 CTTCAACCTTTCCCTCTTTGGTTTTAGGGTGTTAGAT-TCGTCATTAAGG
1 CTTCAACCTTTCCCTCTTCAATTTTAAGGTGTAAGGTCT-GTCGTTGTGA
* * * * ** * * * * *
27410735 CTTTAA-TTTATCCTTTTTTGATTTTAGGGTGTTAGGTCCGTCATTATGA
1 CTTCAACCTT-TCCCTCTTCAATTTTAAGGTGTAAGGTCTGTCGTTGTGA
* * * * * **
27410784 CTTTAACCTATCCCTCTTTAATTTTAAGGTGTAAGATCTCTCGTTGCAA
1 CTTCAACCTTTCCCTCTTCAATTTTAAGGTGTAAGGTCTGTCGTTGTGA
* * ** ** * *** * *
27410833 CTTCAATCTTTCCCTTTTCGGTTTTTGGGTGTTAGGTCCACCGTTGCGG
1 CTTCAACCTTTCCCTCTTCAATTTTAAGGTGTAAGGTCTGTCGTTGTGA
* * * * * ** *
27410882 CTTCAACCTATCCCTTTTCAGTTTTAAGGTGTAAGGT-TCGCCATTACGG
1 CTTCAACCTTTCCCTCTTCAATTTTAAGGTGTAAGGTCT-GTCGTTGTGA
* * * * * *** *
27410931 CTTTAACCTTTCCCTTTTCGATTTTAAGGTGTTAGATCCACCATTGTGA
1 CTTCAACCTTTCCCTCTTCAATTTTAAGGTGTAAGGTCTGTCGTTGTGA
* * * * * * * * *** * **
27410980 CTTTAATCTATCCCTATTCGATTTTAGGGTGTTAGATCCACCATTACGA
1 CTTCAACCTTTCCCTCTTCAATTTTAAGGTGTAAGGTCTGTCGTTGTGA
* * * * * * **
27411029 TTTCAATCTATCCCTCTTCAATTTTAAAGTTTTAA-GTCCGTCGTTACGA
1 CTTCAACCTTTCCCTCTTCAATTTT-AAGGTGTAAGGTCTGTCGTTGTGA
* * *** **
27411078 CTTCAACCTATCCCTCTTCAATTTTAAGGTGTAAGATCCACCGTT-ACA
1 CTTCAACCTTTCCCTCTTCAATTTTAAGGTGTAAGGTCTGTCGTTGTGA
* ** * * * * *
27411126 GCTTCAATCTTTCCCTCTTTGATTTTAGGGTCTTAGGT-TCGCCATTGCT-A
1 -CTTCAACCTTTCCCTCTTCAATTTTAAGGTGTAAGGTCT-GTCGTTG-TGA
* * * * * *
27411176 CTTCAACCTATCCCTCTTCAGTTTTACGGTATAAGGTC-GACCGTTGTGG
1 CTTCAACCTTTCCCTCTTCAATTTTAAGGTGTAAGGTCTG-TCGTTGTGA
*
27411225 CTTCAACCTTTCCCTCTTCAGTTTTA
1 CTTCAACCTTTCCCTCTTCAATTTTA
27411251 GGATGTTATG
Statistics
Matches: 510, Mismatches: 135, Indels: 36
0.75 0.20 0.05
Matches are distributed among these distances:
48 13 0.03
49 486 0.95
50 11 0.02
ACGTcount: A:0.20, C:0.23, G:0.16, T:0.41
Consensus pattern (49 bp):
CTTCAACCTTTCCCTCTTCAATTTTAAGGTGTAAGGTCTGTCGTTGTGA
Found at i:27410711 original size:147 final size:147
Alignment explanation
Indices: 27410586--27411201 Score: 590
Period size: 147 Copynumber: 4.2 Consensus size: 147
27410576 CTGTCGTTGT
* * * *
27410586 GACTTCAATCTTTCCCTCTTCAATTTTAGGGTGTTAGGTCTGTCATTGCGACTTCAACCTATCCC
1 GACTTCAATCTATCCCTCTTCAATTTTAAGGTGTTAGGTCCGTCATTACGACTTCAACCTATCCC
* * ** * * *
27410651 TCTTCAGTTTTAAGGTGTAAGGTCCGTCGTTGCTGCTTCAACCTTTCCCTCTTTGGTTTTAGGGT
66 TCTTCAATTTTAAGGTGTAAGATCCACCGTTGCAGCTTCAATCTTTCCCTCTTTGATTTTAGGGT
* ** *
27410716 GTTAGATTCGTCATTAA
131 GTTAGATCCACCATTAC
* * * * * ** * * *
27410733 GGCTTTAATTTATCCTTTTTTGATTTTAGGGTGTTAGGTCCGTCATTATGACTTTAACCTATCCC
1 GACTTCAATCTATCCCTCTTCAATTTTAAGGTGTTAGGTCCGTCATTACGACTTCAACCTATCCC
* * * * *
27410798 TCTTTAATTTTAAGGTGTAAGATCTC-TCGTTGCAACTTCAATCTTTCCCT-TTTCGGTTTTTGG
66 TCTTCAATTTTAAGGTGTAAGATC-CACCGTTGCAGCTTCAATCTTTCCCTCTTT-GATTTTAGG
* * *
27410861 GTGTTAGGTCCACCGTTGC
129 GTGTTAGATCCACCATTAC
* * * * * * * * * *
27410880 GGCTTCAACCTATCCCTTTTCAGTTTTAAGGTGTAAGGTTCGCCATTACGGCTTTAACCTTTCCC
1 GACTTCAATCTATCCCTCTTCAATTTTAAGGTGTTAGGTCCGTCATTACGACTTCAACCTATCCC
* * * * * * * * *
27410945 TTTTCGATTTTAAGGTGTTAGATCCACCATTG-TGACTTTAATCTATCCCTATTCGATTTTAGGG
66 TCTTCAATTTTAAGGTGTAAGATCCACCGTTGCAG-CTTCAATCTTTCCCTCTTTGATTTTAGGG
27411009 TGTTAGATCCACCATTAC
130 TGTTAGATCCACCATTAC
* * * * *
27411027 GATTTCAATCTATCCCTCTTCAATTTTAAAGTTTTAAGTCCGTCGTTACGACTTCAACCTATCCC
1 GACTTCAATCTATCCCTCTTCAATTTTAAGGTGTTAGGTCCGTCATTACGACTTCAACCTATCCC
*
27411092 TCTTCAATTTTAAGGTGTAAGATCCACCGTTACAGCTTCAATCTTTCCCTCTTTGATTTTAGGGT
66 TCTTCAATTTTAAGGTGTAAGATCCACCGTTGCAGCTTCAATCTTTCCCTCTTTGATTTTAGGGT
* * * * *
27411157 CTTAGGTTCGCCATTGC
131 GTTAGATCCACCATTAC
* * *
27411174 TACTTCAACCTATCCCTCTTCAGTTTTA
1 GACTTCAATCTATCCCTCTTCAATTTTA
27411202 CGGTATAAGG
Statistics
Matches: 373, Mismatches: 90, Indels: 12
0.79 0.19 0.03
Matches are distributed among these distances:
146 4 0.01
147 365 0.98
148 4 0.01
ACGTcount: A:0.19, C:0.23, G:0.16, T:0.41
Consensus pattern (147 bp):
GACTTCAATCTATCCCTCTTCAATTTTAAGGTGTTAGGTCCGTCATTACGACTTCAACCTATCCC
TCTTCAATTTTAAGGTGTAAGATCCACCGTTGCAGCTTCAATCTTTCCCTCTTTGATTTTAGGGT
GTTAGATCCACCATTAC
Found at i:27411116 original size:98 final size:98
Alignment explanation
Indices: 27410539--27411294 Score: 436
Period size: 98 Copynumber: 7.7 Consensus size: 98
27410529 ACCGTCGTGG
* * * * * * *
27410539 CTTCAA-CTTATCCCTATTCAATTTTAAAGTG-TAAGATCTGTCGTTGTGACTTCAATCTTTCCC
1 CTTCAATC-TATCCCTCTTCGATTTTAAGGTGTTAAG-TCCGTCGTTGCGACTTCAACCTATCCC
* * * * * *
27410602 TCTTCAATTTTAGGGTGTTAGGTCTGTCATTGCGA
64 TCTTCAATTTTAAGGTGTAAGATCCGCCATTACGA
* *
27410637 CTTCAACCTATCCCTCTTC-AGTTTTAAGGTG-TAAGGTCCGTCGTTGCTG-CTTCAACCTTTCC
1 CTTCAATCTATCCCTCTTCGA-TTTTAAGGTGTTAA-GTCCGTCGTTGC-GACTTCAACCTATCC
*** * * * * * *
27410699 CTCTTTGGTTTTAGGGTGTTAGATTCGTCATTAAGG
63 CTCTTCAATTTTAAGGTGTAAGATCCGCCATTACGA
* * * * * * * * ** *
27410735 CTTTAATTTATCCTTTTTTGATTTTAGGGTGTTAGGTCCGTCATTATGACTTTAACCTATCCCTC
1 CTTCAATCTATCCCTCTTCGATTTTAAGGTGTTAAGTCCGTCGTTGCGACTTCAACCTATCCCTC
* * * * *
27410800 TTTAATTTTAAGGTGTAAGATCTC-TCGTTGCAA
66 TTCAATTTTAAGGTGTAAGATC-CGCCATTACGA
* * * ** * ** * *
27410833 CTTCAATCTTTCCCTTTTCGGTTTTTGGGTGTTAGGTCCACCGTTGCGGCTTCAACCTATCCCTT
1 CTTCAATCTATCCCTCTTCGATTTTAAGGTGTTAAGTCCGTCGTTGCGACTTCAACCTATCCCTC
* * * *
27410898 TTCAGTTTTAAGGTGTAAGGTTCGCCATTACGG
66 TTCAATTTTAAGGTGTAAGATCCGCCATTACGA
* * * * ** * * * *
27410931 CTTTAACCTTTCCCTTTTCGATTTTAAGGTGTT-AGATCCACCATTGTGACTTTAATCTATCCCT
1 CTTCAATCTATCCCTCTTCGATTTTAAGGTGTTAAG-TCCGTCGTTGCGACTTCAACCTATCCCT
* * * * *
27410995 ATTCGATTTTAGGGTGTTAGATCCACCATTACGA
65 CTTCAATTTTAAGGTGTAAGATCCGCCATTACGA
* * * * *
27411029 TTTCAATCTATCCCTCTTCAATTTTAAAGTTTTAAGTCCGTCGTTACGACTTCAACCTATCCCTC
1 CTTCAATCTATCCCTCTTCGATTTTAAGGTGTTAAGTCCGTCGTTGCGACTTCAACCTATCCCTC
* *
27411094 TTCAATTTTAAGGTGTAAGATCCACCGTTAC-A
66 TTCAATTTTAAGGTGTAAGATCCGCCATTACGA
* * * * * * * * *
27411126 GCTTCAATCTTTCCCTCTTTGATTTTAGGGTCTTAGGTTCGCCATTGCTACTTCAACCTATCCCT
1 -CTTCAATCTATCCCTCTTCGATTTTAAGGTGTTAAGTCCGTCGTTGCGACTTCAACCTATCCCT
* * * * * ** *
27411191 CTTCAGTTTTACGGTATAAGGT-CGACCGTTGTGG
65 CTTCAATTTTAAGGTGTAAGATCCG-CCATTACGA
* * * * * * *
27411225 CTTCAACCTTTCCCTCTTC-AGTTTT-AGGATGTTATGTTCGCCGTTGCGGCTTCAACCTATCCT
1 CTTCAATCTATCCCTCTTCGA-TTTTAAGG-TGTTAAGTCCGTCGTTGCGACTTCAACCTATCCC
27411288 TCTTCAA
64 TCTTCAA
27411295 ACTCTATGAT
Statistics
Matches: 510, Mismatches: 132, Indels: 32
0.76 0.20 0.05
Matches are distributed among these distances:
97 9 0.02
98 492 0.96
99 9 0.02
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.41
Consensus pattern (98 bp):
CTTCAATCTATCCCTCTTCGATTTTAAGGTGTTAAGTCCGTCGTTGCGACTTCAACCTATCCCTC
TTCAATTTTAAGGTGTAAGATCCGCCATTACGA
Found at i:27411269 original size:49 final size:47
Alignment explanation
Indices: 27411030--27411293 Score: 163
Period size: 49 Copynumber: 5.4 Consensus size: 47
27411020 CCATTACGAT
* * * * * ** *
27411030 TTCAATCTATCCCTCTTCAATTTTAAAGTTTTAAGTCCGTCGTTACGAC
1 TTCAACCTATCCCTCTTCAGTTTT--AGGTTTAAGTTCGCCGTTGTGGC
* * * * ***
27411079 TTCAACCTATCCCTCTTCAATTTTAAGGTGTAAGATCCACCGTTACAGC
1 TTCAACCTATCCCTCTTCAGTTTT-AGGTTTAAG-TTCGCCGTTGTGGC
* * * * * *
27411128 TTCAATCTTTCCCTCTT-TGATTTTAGGGTCTTAGGTTCGCCATTGCT-AC
1 TTCAACCTATCCCTCTTCAG-TTTTA-GGT-TTAAGTTCGCCGTTG-TGGC
* *
27411177 TTCAACCTATCCCTCTTCAGTTTTACGGTATAAGGTCGACCGTTGTGGC
1 TTCAACCTATCCCTCTTCAGTTTTA-GGTTTAAGTTCG-CCGTTGTGGC
* * *
27411226 TTCAACCTTTCCCTCTTCAGTTTTAGGATGTTATGTTCGCCGTTGCGGC
1 TTCAACCTATCCCTCTTCAGTTTTAGG-T-TTAAGTTCGCCGTTGTGGC
*
27411275 TTCAACCTATCCTTCTTCA
1 TTCAACCTATCCCTCTTCA
27411294 AACTCTATGA
Statistics
Matches: 170, Mismatches: 35, Indels: 20
0.76 0.16 0.09
Matches are distributed among these distances:
48 18 0.11
49 142 0.84
50 10 0.06
ACGTcount: A:0.19, C:0.27, G:0.15, T:0.39
Consensus pattern (47 bp):
TTCAACCTATCCCTCTTCAGTTTTAGGTTTAAGTTCGCCGTTGTGGC
Found at i:27419089 original size:26 final size:26
Alignment explanation
Indices: 27419033--27419094 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 26
27419023 ATACAAAACA
* *
27419033 AAAATAAAATGCAAAGCAACATATAT
1 AAAATAAAATGCAAAGCAACACAAAT
* *
27419059 AAAATAAAATGCAAAGGATCACAAAT
1 AAAATAAAATGCAAAGCAACACAAAT
* *
27419085 TAAATTAAAT
1 AAAATAAAAT
27419095 CGAATTTTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.61, C:0.10, G:0.08, T:0.21
Consensus pattern (26 bp):
AAAATAAAATGCAAAGCAACACAAAT
Found at i:27420234 original size:4 final size:4
Alignment explanation
Indices: 27420225--27420270 Score: 53
Period size: 4 Copynumber: 12.2 Consensus size: 4
27420215 AAAATTAATG
* *
27420225 ATAA ATAA ATAA ATAA ATAA ATAC A-AA TTAA ATAA A-AA AT-A ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
27420270 A
1 A
27420271 AGAGATAACA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
3 7 0.20
4 28 0.80
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:27420242 original size:12 final size:11
Alignment explanation
Indices: 27420227--27420271 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
27420217 AATTAATGAT
27420227 AAATAAATAAA
1 AAATAAATAAA
*
27420238 TAAATAAATACA
1 -AAATAAATAAA
*
27420250 AATTAAATAAA
1 AAATAAATAAA
27420261 AAAT-AATAAA
1 AAATAAATAAA
27420271 A
1 A
27420272 GAGATAACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
10 7 0.24
11 12 0.41
12 10 0.34
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (11 bp):
AAATAAATAAA
Found at i:27420425 original size:12 final size:12
Alignment explanation
Indices: 27420410--27420439 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
27420400 TTTTTGAATG
27420410 CTCTCAGAAAAT
1 CTCTCAGAAAAT
*
27420422 CTCTCCGAAAAT
1 CTCTCAGAAAAT
27420434 CTCTCA
1 CTCTCA
27420440 ATCTTATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.33, C:0.33, G:0.07, T:0.27
Consensus pattern (12 bp):
CTCTCAGAAAAT
Found at i:27424461 original size:29 final size:30
Alignment explanation
Indices: 27424406--27424475 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 30
27424396 ATTTCAAAAT
* *
27424406 TATACATGAACTTTAATTTAATGTGCAATTG
1 TATACATGAACTTTAATTT-AGGTGCAATTA
27424437 TATACATGAACTTTAATTT-GGTGCAATTA
1 TATACATGAACTTTAATTTAGGTGCAATTA
*
27424466 TATATATGAA
1 TATACATGAA
27424476 ACTCTATTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 17 0.47
31 19 0.53
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (30 bp):
TATACATGAACTTTAATTTAGGTGCAATTA
Found at i:27424484 original size:29 final size:29
Alignment explanation
Indices: 27424406--27424485 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 29
27424396 ATTTCAAAAT
* * *
27424406 TATACATGAACTTTAATTTAATGTGCAATTG
1 TATACATGAACTCTAATTT--GGTGCAATTA
*
27424437 TATACATGAACTTTAATTTGGTGCAATTA
1 TATACATGAACTCTAATTTGGTGCAATTA
*
27424466 TATATATGAAACTCT-ATTTG
1 TATACATG-AACTCTAATTTG
27424486 TGGTTCAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
29 20 0.45
30 5 0.11
31 19 0.43
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.42
Consensus pattern (29 bp):
TATACATGAACTCTAATTTGGTGCAATTA
Found at i:27424700 original size:29 final size:30
Alignment explanation
Indices: 27424659--27424717 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
27424649 GAATTGAATC
27424659 AAATCAAAATTTCATATATAAAATTGCACA
1 AAATCAAAATTTCATATATAAAATTGCACA
* * *
27424689 AAATC-AAATTTCATGTTTACAATTGCACA
1 AAATCAAAATTTCATATATAAAATTGCACA
27424718 TTAAACCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.47, C:0.15, G:0.05, T:0.32
Consensus pattern (30 bp):
AAATCAAAATTTCATATATAAAATTGCACA
Found at i:27429608 original size:196 final size:196
Alignment explanation
Indices: 27429267--27429913 Score: 918
Period size: 196 Copynumber: 3.3 Consensus size: 196
27429257 GAAATCGACG
* * * * * *
27429267 CGATGGTTGGGGTACTGCATATGTTGCGAGTCCTCGATAGCTCGTGTGAGTAGCATTGTGAGTCG
1 CGATGGCTGGGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAACATCGTGAGTCG
* * * *
27429332 GGAAAATGAGAAATGAATCCAAGAATGGATTACAAGCCCTACAATGGCTAAGATTTATGCATAAG
66 GGAAAATGAGAAATGAATCCAAAAATGGATTACAAGCCCTACGATGGTTGAGATTTATGCATAAG
*
27429397 TGCATATTCTCGACAGCTCGTGTGAGCAGCATCGTTAGGGAACAATTATATGCACAGATACCGTA
131 TGCATATTCTCGACAGCTCATGTGAGCAGCATCGTTAGGGAACAATTATATGCACAGATACCGTA
27429462 T
196 T
* * *
27429463 CGATGGCTGGGGTACCGCACATGATACGAGTCCTCGACAGCTCGTGTGAGCAACATCGTGAGTCG
1 CGATGGCTGGGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAACATCGTGAGTCG
*
27429528 GGAAAATGAGAAATGAATCCAAAAATGGATTACAAGCCCTACGATGGTTGGGATTTATGCATAAG
66 GGAAAATGAGAAATGAATCCAAAAATGGATTACAAGCCCTACGATGGTTGAGATTTATGCATAAG
* * *
27429593 TGCATATTCTCGACAGCTCATGTGAGCATCATTGTTAGGGAACAATTATATGCACAAATACCGTA
131 TGCATATTCTCGACAGCTCATGTGAGCAGCATCGTTAGGGAACAATTATATGCACAGATACCGTA
27429658 T
196 T
* ** * *
27429659 CGATGGCTGAGGTACAACATATGTTGCGAGTCCTCAACAGCTCGTGTGAGCAACATCGTGAGTCA
1 CGATGGCTGGGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAACATCGTGAGTCG
* * * * *
27429724 GGAAAATGAAAAATGAATCTAATAATGGATTACATGCCCTATGATGGTTGAGATTTATGCATAAG
66 GGAAAATGAGAAATGAATCCAAAAATGGATTACAAGCCCTACGATGGTTGAGATTTATGCATAAG
* * * * * *
27429789 TGAATATTCTCAATAGCTCATGTGAGCAGCATCGTTAGGGAGCAGTTATATGCATAGATACCGTA
131 TGCATATTCTCGACAGCTCATGTGAGCAGCATCGTTAGGGAACAATTATATGCACAGATACCGTA
27429854 T
196 T
* * * * * *
27429855 CGATGACTAGGGTACCGCATATGTTGTGAGTCC-CTGTCAGCTCGTGTGAACAGCATCGT
1 CGATGGCTGGGGTACCGCATATGTTGCGAGTCCTC-GACAGCTCGTGTGAGCAACATCGT
27429914 ATACTAGTAA
Statistics
Matches: 399, Mismatches: 51, Indels: 2
0.88 0.11 0.00
Matches are distributed among these distances:
195 1 0.00
196 398 1.00
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (196 bp):
CGATGGCTGGGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAACATCGTGAGTCG
GGAAAATGAGAAATGAATCCAAAAATGGATTACAAGCCCTACGATGGTTGAGATTTATGCATAAG
TGCATATTCTCGACAGCTCATGTGAGCAGCATCGTTAGGGAACAATTATATGCACAGATACCGTA
T
Found at i:27431657 original size:15 final size:15
Alignment explanation
Indices: 27431633--27431662 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
27431623 AGTTAGTATC
*
27431633 TTGTTTTGTGGAAGG
1 TTGTTGTGTGGAAGG
27431648 TTGTTGTGTGGAAGG
1 TTGTTGTGTGGAAGG
27431663 GCCAAATCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.00, G:0.43, T:0.43
Consensus pattern (15 bp):
TTGTTGTGTGGAAGG
Found at i:27438645 original size:15 final size:15
Alignment explanation
Indices: 27438621--27438650 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
27438611 AGTTAGTATC
*
27438621 TTGTTTTGTGGAAGG
1 TTGTTGTGTGGAAGG
27438636 TTGTTGTGTGGAAGG
1 TTGTTGTGTGGAAGG
27438651 GCGAAATCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.00, G:0.43, T:0.43
Consensus pattern (15 bp):
TTGTTGTGTGGAAGG
Found at i:27438922 original size:21 final size:21
Alignment explanation
Indices: 27438896--27438984 Score: 85
Period size: 21 Copynumber: 4.2 Consensus size: 21
27438886 ATTAGTCGAC
*
27438896 CCGTTGATAGTTGATCATTGG
1 CCGTTGATAGTTGATCATTGA
*
27438917 CCGTTGACAGTTGATCATTGA
1 CCGTTGATAGTTGATCATTGA
* *
27438938 TCGTTGATCGTTGA-CAGTTGA
1 CCGTTGATAGTTGATCA-TTGA
*
27438959 TCGTTGATCA-TTGA-CAGTTGA
1 CCGTTGAT-AGTTGATCA-TTGA
27438980 CCGTT
1 CCGTT
27438985 AACTTTGATC
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
20 2 0.03
21 57 0.97
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.37
Consensus pattern (21 bp):
CCGTTGATAGTTGATCATTGA
Found at i:27438930 original size:28 final size:28
Alignment explanation
Indices: 27438898--27438980 Score: 105
Period size: 28 Copynumber: 3.0 Consensus size: 28
27438888 TAGTCGACCC
*
27438898 GTTGATAGTTGATCATTGGCCGTTGACA
1 GTTGATAGTTGATCATTGACCGTTGACA
* *
27438926 GTTGATCA-TTGATCGTTGATCGTTGACA
1 GTTGAT-AGTTGATCATTGACCGTTGACA
* *
27438954 GTTGATCGTTGATCATTGACAGTTGAC
1 GTTGATAGTTGATCATTGACCGTTGAC
27438981 CGTTAACTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
28 45 0.98
29 1 0.02
ACGTcount: A:0.22, C:0.14, G:0.27, T:0.37
Consensus pattern (28 bp):
GTTGATAGTTGATCATTGACCGTTGACA
Found at i:27438999 original size:7 final size:7
Alignment explanation
Indices: 27438897--27438999 Score: 70
Period size: 7 Copynumber: 14.9 Consensus size: 7
27438887 TTAGTCGACC
27438897 CGTTGAT
1 CGTTGAT
*
27438904 AGTTGAT
1 CGTTGAT
* **
27438911 CATTGGC
1 CGTTGAT
27438918 CGTTGA-
1 CGTTGAT
27438924 CAGTTGAT
1 C-GTTGAT
*
27438932 CATTGAT
1 CGTTGAT
27438939 CGTTGAT
1 CGTTGAT
27438946 CGTTGA-
1 CGTTGAT
27438952 CAGTTGAT
1 C-GTTGAT
27438960 CGTTGAT
1 CGTTGAT
*
27438967 CATTGA-
1 CGTTGAT
*
27438973 CAGTTGAC
1 C-GTTGAT
*
27438981 CGTT-AA
1 CGTTGAT
*
27438987 CTTTGAT
1 CGTTGAT
27438994 CGTTGA
1 CGTTGA
27439000 CTTTTTTTTA
Statistics
Matches: 74, Mismatches: 15, Indels: 14
0.72 0.15 0.14
Matches are distributed among these distances:
6 7 0.09
7 64 0.86
8 3 0.04
ACGTcount: A:0.21, C:0.16, G:0.25, T:0.38
Consensus pattern (7 bp):
CGTTGAT
Found at i:27440063 original size:19 final size:19
Alignment explanation
Indices: 27440026--27440064 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
27440016 TATAGACTTA
*
27440026 TTTAATTTTATTTTATTAT
1 TTTAATTTTAGTTTATTAT
27440045 TTTAATTTTAGGTTT-TTAT
1 TTTAATTTTA-GTTTATTAT
27440064 T
1 T
27440065 ATACTTTGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (19 bp):
TTTAATTTTAGTTTATTAT
Found at i:27445562 original size:42 final size:42
Alignment explanation
Indices: 27445375--27445563 Score: 243
Period size: 42 Copynumber: 4.5 Consensus size: 42
27445365 ACTTGGCGTA
* * *
27445375 TAAATGGAAGACTCATGTCTCGGGATGAGCATGAGGTTATGTT
1 TAAA-GGAAGACTCATGACTCGAGATGAGCATGAGATTATGTT
* * *
27445418 TAAAAGGAAGACTCGTGACTCGAAAAGAGCATGAGATTATGTT
1 T-AAAGGAAGACTCATGACTCGAGATGAGCATGAGATTATGTT
** * *
27445461 TAAAGGAAGACTTGTGATTTGAGATGAGCATGAGATTATGTT
1 TAAAGGAAGACTCATGACTCGAGATGAGCATGAGATTATGTT
* *
27445503 TAAAGGAAGACTCATGACTCGGGATGAGTATGAGATTATGTT
1 TAAAGGAAGACTCATGACTCGAGATGAGCATGAGATTATGTT
*
27445545 TAAAGGAAGACTTATGACT
1 TAAAGGAAGACTCATGACT
27445564 TGGTTGGAGT
Statistics
Matches: 127, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
42 90 0.71
43 34 0.27
44 3 0.02
ACGTcount: A:0.34, C:0.10, G:0.28, T:0.29
Consensus pattern (42 bp):
TAAAGGAAGACTCATGACTCGAGATGAGCATGAGATTATGTT
Found at i:27446207 original size:21 final size:21
Alignment explanation
Indices: 27446174--27446227 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
27446164 AGAGTTTTTA
*
27446174 GTATCGATAGAAGAAAGACTT
1 GTATCGGTAGAAGAAAGACTT
* ** *
27446195 GTTTCGGTAGAAGTTATACTT
1 GTATCGGTAGAAGAAAGACTT
27446216 GTATCGGTAGAA
1 GTATCGGTAGAA
27446228 CCATTAGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.33, C:0.09, G:0.26, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAAGAAAGACTT
Found at i:27447313 original size:29 final size:29
Alignment explanation
Indices: 27447281--27447433 Score: 111
Period size: 29 Copynumber: 5.2 Consensus size: 29
27447271 TAAAAACGAG
27447281 ATTTTGGAAAGTTCGAGGGTAAAATGGTA
1 ATTTTGGAAAGTTCGAGGGTAAAATGGTA
*
27447310 ATTTTTGGCAAAATT--AGGGTCAAAAATGG-A
1 A-TTTTGG-AAAGTTCGAGGGT--AAAATGGTA
* * *
27447340 ATTTTGGAAAGCTCGAGTGTAAAGTGGTA
1 ATTTTGGAAAGTTCGAGGGTAAAATGGTA
* * * *
27447369 CTTTTGGTGAAA--TCGAAGTTAAAAAT-GAA
1 ATTTT-G-GAAAGTTCGAGGGT-AAAATGGTA
* *
27447398 ATTTTAGAAAGTTCGGGGGTAAAATGGTA
1 ATTTTGGAAAGTTCGAGGGTAAAATGGTA
27447427 ATTTTGG
1 ATTTTGG
27447434 TGAAATCGGG
Statistics
Matches: 93, Mismatches: 18, Indels: 26
0.68 0.13 0.19
Matches are distributed among these distances:
27 4 0.04
28 15 0.16
29 41 0.44
30 17 0.18
31 16 0.17
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.32
Consensus pattern (29 bp):
ATTTTGGAAAGTTCGAGGGTAAAATGGTA
Done.