Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005378.1 Hibiscus syriacus cultivar Beakdansim tig00012275_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: 184360
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 1 of 2
Found at i:67 original size:2 final size:2
Alignment explanation
Indices: 60--96 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
50 ATCCTAACCC
60 AT AT AT AT AT AT AT A- AT AT AT -T 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 A
97 AAGAATTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1716 original size:20 final size:21
Alignment explanation
Indices: 1678--1718 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1668 CTTCGTTCCC
*
1678 AAATTAGAACCCCAGTTCCTA
1 AAATTAGAACCCCAATTCCTA
*
1699 AAATT-GAACCCTAATTCCTA
1 AAATTAGAACCCCAATTCCTA
1719 TATTATAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.39, C:0.27, G:0.07, T:0.27
Consensus pattern (21 bp):
AAATTAGAACCCCAATTCCTA
Found at i:6410 original size:42 final size:41
Alignment explanation
Indices: 6299--6432 Score: 121
Period size: 42 Copynumber: 3.2 Consensus size: 41
6289 GCGTTTATAT
* *
6299 AAAAACGCCGCTAAAATACTACTCTATTATGGCATTTGTTG
1 AAAAACGCCGCTAAAGTACTACTCTATTACGGCATTTGTTG
* ** * * *
6340 AGAAAATGCTACTATAG-A-TGAACCCTATTACGGAATTTTGTAT-
1 A-AAAACGCCGCTAAAGTACT--ACTCTATTACGGCA-TTTGT-TG
*
6383 AAAAACGCCGCTAAAGTACTACTCTATTGCGGCATTTGTTG
1 AAAAACGCCGCTAAAGTACTACTCTATTACGGCATTTGTTG
6424 AAAAACGCC
1 AAAAACGCC
6433 ATTATATATT
Statistics
Matches: 70, Mismatches: 15, Indels: 16
0.69 0.15 0.16
Matches are distributed among these distances:
40 2 0.03
41 16 0.23
42 43 0.61
43 7 0.10
44 2 0.03
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.29
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGTACTACTCTATTACGGCATTTGTTG
Found at i:8141 original size:2 final size:2
Alignment explanation
Indices: 8134--8191 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
8124 CGGGTGGATG
8134 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8176 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
8192 CGGGTCGGGT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9296 original size:36 final size:36
Alignment explanation
Indices: 9249--9320 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
9239 ACTGTTGATA
9249 ATGCTCAAATTA-AGTTATCCCACTAGTATTAGAAAT
1 ATGCTCAAATTAGA-TTATCCCACTAGTATTAGAAAT
* *
9285 ATGCTCAAATTAGATTATCTCACTAGTATTGGAAAT
1 ATGCTCAAATTAGATTATCCCACTAGTATTAGAAAT
9321 GACGATTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 32 0.97
37 1 0.03
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (36 bp):
ATGCTCAAATTAGATTATCCCACTAGTATTAGAAAT
Found at i:14148 original size:28 final size:30
Alignment explanation
Indices: 14108--14164 Score: 82
Period size: 28 Copynumber: 1.9 Consensus size: 30
14098 AAGAGTTTGG
14108 GAGTTCCAAGTGAG-G-ACATATTGAATGA
1 GAGTTCCAAGTGAGAGTACATATTGAATGA
*
14136 GAGTTCCTAGTGAGAAGTACATATTGAAT
1 GAGTTCCAAGTGAG-AGTACATATTGAAT
14165 TCACCGAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 13 0.52
30 1 0.04
31 11 0.44
ACGTcount: A:0.35, C:0.11, G:0.26, T:0.28
Consensus pattern (30 bp):
GAGTTCCAAGTGAGAGTACATATTGAATGA
Found at i:14810 original size:36 final size:36
Alignment explanation
Indices: 14722--14828 Score: 180
Period size: 35 Copynumber: 3.0 Consensus size: 36
14712 AATGTTGATA
14722 ATGCTCAAATTAGGTTATCCCACTAGTATTAGAAAT
1 ATGCTCAAATTAGGTTATCCCACTAGTATTAGAAAT
* *
14758 ATTCT-AAATTAGGTTATCCCATTAGTATTAGAAAT
1 ATGCTCAAATTAGGTTATCCCACTAGTATTAGAAAT
*
14793 ATGCTCAAATTAGGTTATCCCACTAGTATTGGAAAT
1 ATGCTCAAATTAGGTTATCCCACTAGTATTAGAAAT
14829 GACGATTTTG
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
35 33 0.51
36 32 0.49
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.36
Consensus pattern (36 bp):
ATGCTCAAATTAGGTTATCCCACTAGTATTAGAAAT
Found at i:21137 original size:27 final size:27
Alignment explanation
Indices: 21106--21163 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
21096 CTGAAGAAAA
21106 AAAAGAAGGAACAAGCTGAAAACCACG
1 AAAAGAAGGAACAAGCTGAAAACCACG
*
21133 AAAAGAAGGAACAAGCTGAAAGCCACG
1 AAAAGAAGGAACAAGCTGAAAACCACG
21160 AAAA
1 AAAA
21164 CAAGAGTAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.57, C:0.17, G:0.22, T:0.03
Consensus pattern (27 bp):
AAAAGAAGGAACAAGCTGAAAACCACG
Found at i:21362 original size:23 final size:21
Alignment explanation
Indices: 21327--21370 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
21317 TTAATTATTT
21327 AAAAAATTAAATAAAAATATAA
1 AAAAAATTAAATAAAAA-ATAA
*
21349 AAAAACATTTAATAAAAAATAA
1 AAAAA-ATTAAATAAAAAATAA
21371 TTTTTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAAAATTAAATAAAAAATAA
Found at i:21975 original size:27 final size:27
Alignment explanation
Indices: 21942--22032 Score: 146
Period size: 27 Copynumber: 3.4 Consensus size: 27
21932 TTTAAAGTTT
* *
21942 TCGAGTTCGAGTAGAGCTCAATAATAC
1 TCGAGTTCGAGTCGAGCTCAACAATAC
* *
21969 TCAAGTTCGAGTCGAGCTCAGCAATAC
1 TCGAGTTCGAGTCGAGCTCAACAATAC
21996 TCGAGTTCGAGTCGAGCTCAACAATAC
1 TCGAGTTCGAGTCGAGCTCAACAATAC
22023 TCGAGTTCGA
1 TCGAGTTCGA
22033 CTCATCTTGT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (27 bp):
TCGAGTTCGAGTCGAGCTCAACAATAC
Found at i:23430 original size:19 final size:19
Alignment explanation
Indices: 23408--23445 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
23398 TTATTTTATT
23408 ATTA-TTATTTTATTTAGAA
1 ATTAGTTATTTTA-TTAGAA
23427 ATTAGTTATTTTATTAGAA
1 ATTAGTTATTTTATTAGAA
23446 CTCTTGGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (19 bp):
ATTAGTTATTTTATTAGAA
Found at i:35181 original size:19 final size:19
Alignment explanation
Indices: 35157--35193 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
35147 ACACATATAT
*
35157 TATATTGATTATATATTTA
1 TATATTCATTATATATTTA
*
35176 TATATTCATTATTTATTT
1 TATATTCATTATATATTT
35194 GTTGTACAGG
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:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (19 bp):
TATATTCATTATATATTTA
Found at i:35649 original size:6 final size:6
Alignment explanation
Indices: 35634--35673 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
35624 AAGTTCTGTA
35634 TTTA-T TTTATT TTTATT TTTATT TTTATT TTTATT TTTAT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTAT
35674 AAATAAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.12
6 30 0.88
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTATT
Found at i:38684 original size:2 final size:2
Alignment explanation
Indices: 38677--38704 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
38667 ACCCTTTTTG
38677 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38705 TTGTTTTGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40331 original size:63 final size:64
Alignment explanation
Indices: 40258--40419 Score: 202
Period size: 63 Copynumber: 2.5 Consensus size: 64
40248 CGGTGCACCA
* *
40258 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCAT-G
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAATGCATCGATGCATGG
** * **
40321 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAATGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAATGCATCGATGCATGG
* * *
40386 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
40420 CAATTAATTC
Statistics
Matches: 83, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
63 37 0.45
64 19 0.23
65 27 0.33
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAATGCATCGATGCATGG
Found at i:40395 original size:19 final size:17
Alignment explanation
Indices: 40368--40417 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 17
40358 AAAATATTCA
40368 GAATGCATCGATGCATG
1 GAATGCATCGATGCATG
*
40385 GAGAGTGCATCGGTGCATG
1 GA-A-TGCATCGATGCATG
40404 GAATGCATTCGATG
1 GAATGCA-TCGATG
40418 TTCAATTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 6 0.21
18 7 0.25
19 15 0.54
ACGTcount: A:0.26, C:0.16, G:0.34, T:0.24
Consensus pattern (17 bp):
GAATGCATCGATGCATG
Found at i:40414 original size:65 final size:63
Alignment explanation
Indices: 40261--40468 Score: 199
Period size: 63 Copynumber: 3.2 Consensus size: 63
40251 TGCACCAAGT
** * * ***
40261 GTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTGGTGCATCGATGCAT-GCTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATATTCAGATGCATCGATGCATGGAGA
*
40324 GTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAATGCATCGATGCATGGAGA
1 GTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATATTCAG-ATGCATCGATGCATGGAGA
* * * *
40389 GTGCATCGGTGCATGGAATGCATTCGATG-TT-CAATTAATTCATCGATGCATCGATGCATGGAC
1 GTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAT-ATTCA--GATGCATCGATGCATGGA-
40452 CGA
62 -GA
*
40455 -TGCATCGGTGCATG
1 GTGCATCGATGCATG
40469 CCTTTGAATA
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
62 3 0.02
63 43 0.35
64 34 0.27
65 42 0.34
66 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.29
Consensus pattern (63 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATATTCAGATGCATCGATGCATGGAGA
Found at i:40835 original size:31 final size:31
Alignment explanation
Indices: 40797--40876 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 31
40787 ATTGATTTTG
40797 AAAAACTTACTCCCCCTTACTATAGCACATC
1 AAAAACTTACTCCCCCTTACTATAGCACATC
40828 AAAAACTTACTCCCCCTTACTATAGCACATC
1 AAAAACTTACTCCCCCTTACTATAGCACATC
** * *
40859 TTAAATTTTCTCCCCCTT
1 AAAAACTTACTCCCCCTT
40877 TTTGTTAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.31, C:0.35, G:0.03, T:0.31
Consensus pattern (31 bp):
AAAAACTTACTCCCCCTTACTATAGCACATC
Found at i:47914 original size:19 final size:19
Alignment explanation
Indices: 47890--47940 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
47880 GAAAATATTC
47890 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
47909 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
47928 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
47941 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:52011 original size:194 final size:194
Alignment explanation
Indices: 51654--52012 Score: 468
Period size: 194 Copynumber: 1.9 Consensus size: 194
51644 GTGTTTTTCT
* *
51654 ACAATATTTCTTTCGTCACATATAAGTTGATTTTAATGCATTATTTGTGAAAATATAAATTATCA
1 ACAATATCTCTTTCGTCACATATAAGTTGATTTTAATGCATTATTTGTGAAAATATAAATCATCA
** **
51719 ATAACAAATTCTTATTTAATTTAGTGATGTAACCAACTGTCATAGAATATAAATTATAAAGTGAC
66 ATAACAAATTCTTACATAATTTAGTGACATAACCAACTGTCATAGAATATAAATTATAAAGTGAC
* * *
51784 GTTATGCATAAACATCATTCATAATATTATTAGGTAACATTTATATTATGTCGCTAAAAATGTG
131 GTTATACATAAACATCATCCATAATACTATTAGGTAACATTTATATTATGTCGCTAAAAATGTG
* * ** *
51848 ACAATATCTCTTTCGTCACATATAGGTTGATTTTAATGTATTATTTGTGATGATATAAATCATTA
1 ACAATATCTCTTTCGTCACATATAAGTTGATTTTAATGCATTATTTGTGAAAATATAAATCATCA
** ** * * *
51913 ATAACGAAATT-TTACATAATTTAGTGACATAATTAGTTGTCATTGAATATTAATTATATAGTGA
66 ATAAC-AAATTCTTACATAATTTAGTGACATAACCAACTGTCATAGAATATAAATTATAAAGTGA
* ** **
51977 CGTTATATATAAATGTCATCCATGCTACTATTAGGT
130 CGTTATACATAAACATCATCCATAATACTATTAGGT
52013 GACGATATAC
Statistics
Matches: 138, Mismatches: 26, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
194 133 0.96
195 5 0.04
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Consensus pattern (194 bp):
ACAATATCTCTTTCGTCACATATAAGTTGATTTTAATGCATTATTTGTGAAAATATAAATCATCA
ATAACAAATTCTTACATAATTTAGTGACATAACCAACTGTCATAGAATATAAATTATAAAGTGAC
GTTATACATAAACATCATCCATAATACTATTAGGTAACATTTATATTATGTCGCTAAAAATGTG
Found at i:61397 original size:27 final size:27
Alignment explanation
Indices: 61346--61397 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
61336 TCGTATATGT
* *
61346 TAACAAAACCGGTAAAGCATCTAATAA
1 TAACAAAACCGGTAAAGAATATAATAA
61373 TAACAAAACCGGTAAA-AATAATAAT
1 TAACAAAACCGGTAAAGAAT-ATAAT
61398 TTTCTAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 2 0.09
27 20 0.91
ACGTcount: A:0.56, C:0.15, G:0.10, T:0.19
Consensus pattern (27 bp):
TAACAAAACCGGTAAAGAATATAATAA
Found at i:63285 original size:23 final size:19
Alignment explanation
Indices: 63236--63276 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
63226 TTGTAGCAGT
63236 GAAGGAGAAGAGAGGGAGA
1 GAAGGAGAAGAGAGGGAGA
63255 GAAGGAGAAGAGAGGGAG-
1 GAAGGAGAAGAGAGGGAGA
63273 GAAG
1 GAAG
63277 AACAGGAGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (19 bp):
GAAGGAGAAGAGAGGGAGA
Found at i:67327 original size:19 final size:19
Alignment explanation
Indices: 67289--67327 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
67279 ACCAATAAAA
*
67289 TCGTAACGCGAACTTTAAT
1 TCGTAACGCGAACTTCAAT
* *
67308 TCGTAGCGCGATCTTCAAT
1 TCGTAACGCGAACTTCAAT
67327 T
1 T
67328 TCTCAACTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (19 bp):
TCGTAACGCGAACTTCAAT
Found at i:68035 original size:19 final size:19
Alignment explanation
Indices: 68013--68051 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
68003 TGAGTTTATA
68013 AATTAAAAATCGCGTTGCG
1 AATTAAAAATCGCGTTGCG
* *
68032 AATTAGAATTCGCGTTGCG
1 AATTAAAAATCGCGTTGCG
68051 A
1 A
68052 TTTTGTTGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.28
Consensus pattern (19 bp):
AATTAAAAATCGCGTTGCG
Found at i:78143 original size:23 final size:23
Alignment explanation
Indices: 78082--78193 Score: 142
Period size: 23 Copynumber: 5.0 Consensus size: 23
78072 CATCTCGTAA
78082 TTTGCACCGAAGTGCCACATAA-
1 TTTGCACCGAAGTGCCACATAAG
* * *
78104 TTAT--TCTGAAG-GACCACATAGG
1 TT-TGCACCGAAGTG-CCACATAAG
78126 TTTGCACCGAAGTGCCACATAAG
1 TTTGCACCGAAGTGCCACATAAG
78149 TTTGCACCGAAGTGCCACATAAG
1 TTTGCACCGAAGTGCCACATAAG
*
78172 TTTGCACTGAAGTGCCACATAA
1 TTTGCACCGAAGTGCCACATAA
78194 TTGACCCGAA
Statistics
Matches: 77, Mismatches: 7, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
20 1 0.01
21 13 0.17
22 4 0.05
23 58 0.75
24 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (23 bp):
TTTGCACCGAAGTGCCACATAAG
Found at i:78203 original size:67 final size:66
Alignment explanation
Indices: 78082--78255 Score: 159
Period size: 67 Copynumber: 2.6 Consensus size: 66
78072 CATCTCGTAA
* *
78082 TTTGCACCGAAGTGCCACATAATTATTCTGAAGGACCACATAGGTTTGCACCGAAGTG-CCACAT
1 TTTGCACCGAAGTGCCACATAATTATACTGAAGGACCACATA-GATTGCACCGAAG-GACCACAT
78146 AAG
64 AAG
78149 TTTGCACCGAAGTGCCACATAAGTT-TGCACTGAAGTG-CCACATA-ATTG-ACCCGAAGGACCA
1 TTTGCACCGAAGTGCCACATAA-TTAT--ACTGAAG-GACCACATAGATTGCA-CCGAAGGACCA
78210 CATAA-
61 CATAAG
* * *
78215 -TTGTC-CCGAAG-GACCACATAATTGTCCCGAAGGACCACATA
1 TTTG-CACCGAAGTG-CCACATAATTATACTGAAGGACCACATA
78256 AAACCCTCGA
Statistics
Matches: 93, Mismatches: 4, Indels: 24
0.77 0.03 0.20
Matches are distributed among these distances:
62 1 0.01
63 12 0.13
64 3 0.03
65 18 0.19
66 3 0.03
67 40 0.43
68 2 0.02
69 13 0.14
70 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (66 bp):
TTTGCACCGAAGTGCCACATAATTATACTGAAGGACCACATAGATTGCACCGAAGGACCACATAA
G
Found at i:78210 original size:21 final size:21
Alignment explanation
Indices: 78186--78256 Score: 133
Period size: 21 Copynumber: 3.4 Consensus size: 21
78176 CACTGAAGTG
*
78186 CCACATAATTGACCCGAAGGA
1 CCACATAATTGTCCCGAAGGA
78207 CCACATAATTGTCCCGAAGGA
1 CCACATAATTGTCCCGAAGGA
78228 CCACATAATTGTCCCGAAGGA
1 CCACATAATTGTCCCGAAGGA
78249 CCACATAA
1 CCACATAA
78257 AACCCTCGAC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.37, C:0.30, G:0.17, T:0.17
Consensus pattern (21 bp):
CCACATAATTGTCCCGAAGGA
Found at i:80364 original size:21 final size:21
Alignment explanation
Indices: 80334--80374 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
80324 TTATGAACAG
*
80334 TGCTACAGTGTACCGATGCAT
1 TGCTACAGTGCACCGATGCAT
*
80355 TGCTATAGTGCACCGATGCA
1 TGCTACAGTGCACCGATGCA
80375 CAAAAATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (21 bp):
TGCTACAGTGCACCGATGCAT
Found at i:81142 original size:31 final size:31
Alignment explanation
Indices: 81107--81200 Score: 109
Period size: 31 Copynumber: 3.0 Consensus size: 31
81097 CCCGAAGGAC
* * *
81107 CAGTCCATA-GATTCCAAATAACCTAGGTAAA
1 CAGTCCATATG-TCCCAAAGAACATAGGTAAA
*
81138 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCAAAGAACATAGGTAAA
* * *
81169 TAGTCCATATGTCCCGAAGAACATAAGTAAA
1 CAGTCCATATGTCCCAAAGAACATAGGTAAA
81200 C
1 C
81201 CCTCGACCCT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
31 54 0.98
32 1 0.02
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCAAAGAACATAGGTAAA
Found at i:86070 original size:17 final size:18
Alignment explanation
Indices: 86038--86071 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
86028 AAAATGGTAA
86038 AAATAATAAAGAAAAGAT
1 AAATAATAAAGAAAAGAT
*
86056 AAATAA-AATGAAAAGA
1 AAATAATAAAGAAAAGA
86072 ATATAATCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.15
Consensus pattern (18 bp):
AAATAATAAAGAAAAGAT
Found at i:91794 original size:20 final size:20
Alignment explanation
Indices: 91769--91827 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
91759 AAAAATCCTA
91769 TAGCACTATAAAT-AAATAAT
1 TAGCACTATAAATAAAAT-AT
91789 TAGCACTATAAATAAAATAT
1 TAGCACTATAAATAAAATAT
91809 TAGCACTA-AGAATAAAATA
1 TAGCACTATA-AATAAAATA
91828 AAATGAAGCG
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.03
20 32 0.86
21 4 0.11
ACGTcount: A:0.56, C:0.10, G:0.07, T:0.27
Consensus pattern (20 bp):
TAGCACTATAAATAAAATAT
Found at i:92391 original size:29 final size:29
Alignment explanation
Indices: 92357--92550 Score: 135
Period size: 29 Copynumber: 6.7 Consensus size: 29
92347 TGGTATTTTT
*
92357 GTAAATATTGTTAAAAAAATATTAGTTTC
1 GTAAATATTGTTAAAAAAATGTTAGTTTC
* *
92386 ATAAATATTATTAAAAAAATGTTAGTTTC
1 GTAAATATTGTTAAAAAAATGTTAGTTTC
* * **
92415 GTAAATAATGTTAAGAAGGTGTTAGTTTC
1 GTAAATATTGTTAAAAAAATGTTAGTTTC
** * * *
92444 GTAAATATT-TCGAAAAAATGATATTTTG
1 GTAAATATTGTTAAAAAAATGTTAGTTTC
* * * *
92472 GTAATTATT-TTGAAAAAAATGATATTTTG
1 GTAAATATTGTT-AAAAAAATGTTAGTTTC
* * * * *
92501 GTAATTATT-TCAAAAAAAGTGATATTTTG
1 GTAAATATTGTTAAAAAAA-TGTTAGTTTC
*
92530 GTAATTATT-TTGAAAAAAATG
1 GTAAATATTGTT-AAAAAAATG
92551 ATATTTTGGT
Statistics
Matches: 139, Mismatches: 23, Indels: 6
0.83 0.14 0.04
Matches are distributed among these distances:
28 27 0.19
29 105 0.76
30 7 0.05
ACGTcount: A:0.43, C:0.03, G:0.14, T:0.41
Consensus pattern (29 bp):
GTAAATATTGTTAAAAAAATGTTAGTTTC
Found at i:92486 original size:28 final size:28
Alignment explanation
Indices: 92444--92694 Score: 326
Period size: 29 Copynumber: 8.9 Consensus size: 28
92434 TGTTAGTTTC
* *
92444 GTAAATATTTCGAAAAAATGATATTTTG
1 GTAATTATTTTGAAAAAATGATATTTTG
92472 GTAATTATTTTGAAAAAAATGATATTTTG
1 GTAATTATTTTG-AAAAAATGATATTTTG
**
92501 GTAATTATTTCAAAAAAAGTGATATTTTG
1 GTAATTATTTTGAAAAAA-TGATATTTTG
92530 GTAATTATTTTGAAAAAAATGATATTTTG
1 GTAATTATTTTG-AAAAAATGATATTTTG
* *
92559 GTAATTATTTTGAAAAAGTGATAATTTG
1 GTAATTATTTTGAAAAAATGATATTTTG
* **
92587 GTAATTATTTCGAAAACGTGATATTTTG
1 GTAATTATTTTGAAAAAATGATATTTTG
*
92615 GTAATTATTTTG-AAAAGTGATATTTTG
1 GTAATTATTTTGAAAAAATGATATTTTG
* *
92642 GTAATTATTTTGAAAATAGTGATATTTTC
1 GTAATTATTTTGAAAA-AATGATATTTTG
**
92671 GTAATTATTTAAAAAAAATG-TATT
1 GTAATTATTTTGAAAAAATGATATT
92695 ATTTTCATAA
Statistics
Matches: 201, Mismatches: 17, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.15
28 72 0.36
29 93 0.46
30 6 0.03
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.44
Consensus pattern (28 bp):
GTAATTATTTTGAAAAAATGATATTTTG
Found at i:96190 original size:20 final size:20
Alignment explanation
Indices: 96161--96219 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
96151 AAATATCCTA
96161 TAGCACTATAAAT-AAATAAT
1 TAGCACTATAAATAAAAT-AT
*
96181 TAGCAGTATAAATAAAATAT
1 TAGCACTATAAATAAAATAT
96201 TAGCACTA-AGAATAAAATA
1 TAGCACTATA-AATAAAATA
96220 AAATGAAGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.86
21 4 0.11
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.27
Consensus pattern (20 bp):
TAGCACTATAAATAAAATAT
Found at i:96775 original size:29 final size:29
Alignment explanation
Indices: 96742--96834 Score: 111
Period size: 29 Copynumber: 3.3 Consensus size: 29
96732 TGGTATTTTT
96742 GTAAATATTGTTAAAAAAATGTTAGTTTC
1 GTAAATATTGTTAAAAAAATGTTAGTTTC
* *
96771 GT-AA-ATTATT-AAAAAATATTAGTTTC
1 GTAAATATTGTTAAAAAAATGTTAGTTTC
* * **
96797 GTAAATACTGTTAAGAAGGTGTTAGTTTC
1 GTAAATATTGTTAAAAAAATGTTAGTTTC
96826 GTAAATATT
1 GTAAATATT
96835 TCGAAAAAAT
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
26 17 0.33
27 7 0.13
28 6 0.12
29 22 0.42
ACGTcount: A:0.40, C:0.04, G:0.15, T:0.41
Consensus pattern (29 bp):
GTAAATATTGTTAAAAAAATGTTAGTTTC
Found at i:96880 original size:29 final size:29
Alignment explanation
Indices: 96826--97059 Score: 296
Period size: 28 Copynumber: 8.2 Consensus size: 29
96816 TGTTAGTTTC
* *
96826 GTAAATATTTCGAAAAAA-TTATATTTTG
1 GTAATTATTTCGAAAAAAGTGATATTTTG
96854 GTAATTATTTCGAAAAAAGTGATATTTT-
1 GTAATTATTTCGAAAAAAGTGATATTTTG
* *
96882 TTAATTATTTCGAAAAAAATGATATTTTG
1 GTAATTATTTCGAAAAAAGTGATATTTTG
* **
96911 GTAATTATTTTG-AAAAAGTGATAACTTG
1 GTAATTATTTCGAAAAAAGTGATATTTTG
96939 GTAATTATTTCGAAAAAAGTGATATTTTG
1 GTAATTATTTCGAAAAAAGTGATATTTTG
*
96968 GTAATTATTTTG-AAAAAGTGATATTTTG
1 GTAATTATTTCGAAAAAAGTGATATTTTG
* *
96996 GTAATTATTTTGAAAAAAGTGATATTTTC
1 GTAATTATTTCGAAAAAAGTGATATTTTG
* ** * *
97025 ATAATTATTTAAAAAAAATGTGTTATTTTC
1 GTAATTATTTCGAAAAAA-GTGATATTTTG
97055 GTAAT
1 GTAAT
97060 AGTTGACTGC
Statistics
Matches: 182, Mismatches: 19, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
28 95 0.52
29 73 0.40
30 14 0.08
ACGTcount: A:0.40, C:0.03, G:0.14, T:0.44
Consensus pattern (29 bp):
GTAATTATTTCGAAAAAAGTGATATTTTG
Found at i:97041 original size:57 final size:58
Alignment explanation
Indices: 96826--97059 Score: 287
Period size: 57 Copynumber: 4.1 Consensus size: 58
96816 TGTTAGTTTC
* * **
96826 GTAAATATTTCGAAAAAA-TTATATTTTGGTAATTATTTCGAAAAAAGTGATATTTT-
1 GTAATTATTTCGAAAAAAGTGATATTTTGGTAATTATTTATAAAAAAGTGATATTTTG
* * * **
96882 TTAATTATTTCGAAAAAAATGATATTTTGGTAATTATTT-TGAAAAAGTGATAACTTG
1 GTAATTATTTCGAAAAAAGTGATATTTTGGTAATTATTTATAAAAAAGTGATATTTTG
*
96939 GTAATTATTTCGAAAAAAGTGATATTTTGGTAATTATTT-TGAAAAAGTGATATTTTG
1 GTAATTATTTCGAAAAAAGTGATATTTTGGTAATTATTTATAAAAAAGTGATATTTTG
* ** * * *
96996 GTAATTATTTTGAAAAAAGTGATATTTTCATAATTATTTAAAAAAAATGTGTTATTTTC
1 GTAATTATTTCGAAAAAAGTGATATTTTGGTAATTATTTATAAAAAA-GTGATATTTTG
97055 GTAAT
1 GTAAT
97060 AGTTGACTGC
Statistics
Matches: 156, Mismatches: 18, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
56 29 0.19
57 108 0.69
58 5 0.03
59 14 0.09
ACGTcount: A:0.40, C:0.03, G:0.14, T:0.44
Consensus pattern (58 bp):
GTAATTATTTCGAAAAAAGTGATATTTTGGTAATTATTTATAAAAAAGTGATATTTTG
Found at i:99933 original size:21 final size:21
Alignment explanation
Indices: 99908--99991 Score: 91
Period size: 21 Copynumber: 3.9 Consensus size: 21
99898 GCACCAAAGT
99908 ACCACATAATTATCCCGAATG
1 ACCACATAATTATCCCGAATG
*
99929 ACCACATAGGTT-TGCACCGAAGTG
1 ACCACATA-ATTAT-C-CCGAA-TG
* *
99953 -CCACATAATTGTCCCGAAGG
1 ACCACATAATTATCCCGAATG
99973 ACCACATAATTATCCCGAA
1 ACCACATAATTATCCCGAA
99992 AAACAACATA
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
20 1 0.02
21 31 0.58
22 6 0.11
23 13 0.25
24 2 0.04
ACGTcount: A:0.35, C:0.29, G:0.15, T:0.21
Consensus pattern (21 bp):
ACCACATAATTATCCCGAATG
Found at i:99957 original size:44 final size:44
Alignment explanation
Indices: 99895--99980 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 44
99885 CAGCTTGTAA
*
99895 TTTGCACCAAAGTACCACATAATTATCCCGAATGACCACATAGG
1 TTTGCACCAAAGTACCACATAATTATCCCGAAGGACCACATAGG
* * *
99939 TTTGCACCGAAGTGCCACATAATTGTCCCGAAGGACCACATA
1 TTTGCACCAAAGTACCACATAATTATCCCGAAGGACCACATA
99981 ATTATCCCGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (44 bp):
TTTGCACCAAAGTACCACATAATTATCCCGAAGGACCACATAGG
Found at i:100000 original size:21 final size:21
Alignment explanation
Indices: 99955--100001 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
99945 CCGAAGTGCC
* ** *
99955 ACATAATTGTCCCGAAGGACC
1 ACATAATTATCCCGAAAAACA
99976 ACATAATTATCCCGAAAAACA
1 ACATAATTATCCCGAAAAACA
99997 ACATA
1 ACATA
100002 GAACCCTCGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.45, C:0.26, G:0.11, T:0.19
Consensus pattern (21 bp):
ACATAATTATCCCGAAAAACA
Found at i:100321 original size:13 final size:13
Alignment explanation
Indices: 100303--100328 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
100293 AAGCCTTCCT
100303 CAATTCTAATACG
1 CAATTCTAATACG
100316 CAATTCTAATACG
1 CAATTCTAATACG
100329 AAATCGAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (13 bp):
CAATTCTAATACG
Found at i:103227 original size:2 final size:2
Alignment explanation
Indices: 103220--103246 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
103210 AAAAAGGAAT
103220 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
103247 GAAAATGCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:108028 original size:39 final size:39
Alignment explanation
Indices: 108009--108132 Score: 230
Period size: 39 Copynumber: 3.2 Consensus size: 39
107999 TTAGTTTATG
108009 GTTTAAGGTAAAACAAAATTTTAGTTAATTAGTTAGTCA
1 GTTTAAGGTAAAACAAAATTTTAGTTAATTAGTTAGTCA
108048 GTTTAAGGTAAAACAAAATTTTAGTTAATTAGTTAGTCA
1 GTTTAAGGTAAAACAAAATTTTAGTTAATTAGTTAGTCA
* *
108087 GTTTAAGGTAAAACAAAATTTTAGTTAATTAGTTTGTTA
1 GTTTAAGGTAAAACAAAATTTTAGTTAATTAGTTAGTCA
108126 GTTTAAG
1 GTTTAAG
108133 TTTTATTATT
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 83 1.00
ACGTcount: A:0.40, C:0.04, G:0.16, T:0.40
Consensus pattern (39 bp):
GTTTAAGGTAAAACAAAATTTTAGTTAATTAGTTAGTCA
Found at i:108130 original size:21 final size:22
Alignment explanation
Indices: 108109--108157 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
108099 ACAAAATTTT
108109 AGTTAATTAGT-TTGTTAGTTTA
1 AGTT-ATTAGTATTGTTAGTTTA
*
108131 AGTT-TTATTATTGTTAGTTTA
1 AGTTATTAGTATTGTTAGTTTA
108152 AGTTAT
1 AGTTAT
108158 ATCATATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.27, C:0.00, G:0.16, T:0.57
Consensus pattern (22 bp):
AGTTATTAGTATTGTTAGTTTA
Found at i:108252 original size:28 final size:27
Alignment explanation
Indices: 108213--108265 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
108203 ATATTAAAAA
108213 AATAATTAATTAGTGTGTTAGTTAGTCT
1 AATAATTAATTAGTGTG-TAGTTAGTCT
* *
108241 AATATTTAATTAGTTTGTAGTTAGT
1 AATAATTAATTAGTGTGTAGTTAGT
108266 TAAATAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (27 bp):
AATAATTAATTAGTGTGTAGTTAGTCT
Found at i:108271 original size:27 final size:29
Alignment explanation
Indices: 108212--108276 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 29
108202 TATATTAAAA
108212 AAATAATTAATTAGTGTGTTAGTTAGTCT
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
* *
108241 -AATATTTAATTAGTTTG-TAGTTAGT-T
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
*
108267 AAATAGTTAA
1 AAATAATTAA
108277 GTTATATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 1 0.03
27 16 0.50
28 15 0.47
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (29 bp):
AAATAATTAATTAGTGTGTTAGTTAGTCT
Found at i:108427 original size:18 final size:18
Alignment explanation
Indices: 108404--108458 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
108394 AATAATTATT
108404 TAAATTAGTTTATTGTTA
1 TAAATTAGTTTATTGTTA
108422 TAAATTA--TTA--G-T-
1 TAAATTAGTTTATTGTTA
*
108434 T-AATTAGTTTATTATTA
1 TAAATTAGTTTATTGTTA
108451 TAAATTAG
1 TAAATTAG
108459 GGTAAAACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 5 0.17
12 1 0.03
13 4 0.14
14 1 0.03
16 4 0.14
17 1 0.03
18 13 0.45
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
TAAATTAGTTTATTGTTA
Found at i:108512 original size:21 final size:21
Alignment explanation
Indices: 108486--108525 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
108476 GATAATGAGT
108486 TTGTTAGTTTAAATTATATTA
1 TTGTTAGTTTAAATTATATTA
*
108507 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAATTATAT
108526 CATATAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAATTATATTA
Found at i:108771 original size:30 final size:29
Alignment explanation
Indices: 108704--108777 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 29
108694 TTTAGTTAAT
*
108704 TAGTTTTTTAGTAGTAAATTATAATTAAAAA
1 TAGTTTATTAGT--TAAATTATAATTAAAAA
*
108735 TTGTTTATTAGTTAAAGTTAT-ATTAAAGAA
1 TAGTTTATTAGTTAAA-TTATAATTAAA-AA
108765 TAGTTTATTAGTT
1 TAGTTTATTAGTT
108778 GTTTAAGGGA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
29 10 0.26
30 18 0.47
31 10 0.26
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (29 bp):
TAGTTTATTAGTTAAATTATAATTAAAAA
Found at i:110102 original size:23 final size:23
Alignment explanation
Indices: 110074--110118 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
110064 TTTAATTATT
*
110074 ATTTAAATTAACTATATTATTTG
1 ATTTAAATAAACTATATTATTTG
* *
110097 ATTTAAATAAATTTTATTATTT
1 ATTTAAATAAACTATATTATTT
110119 TTGTAATTTT
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:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
ATTTAAATAAACTATATTATTTG
Found at i:110118 original size:18 final size:20
Alignment explanation
Indices: 110068--110118 Score: 52
Period size: 23 Copynumber: 2.5 Consensus size: 20
110058 GTTATTTTTA
110068 ATTATTATTTAAATTAACTAT
1 ATTATTATTTAAATTAAC-AT
110089 ATTATTTGATTTAAA-TAA-AT
1 ATTA-TT-ATTTAAATTAACAT
*
110109 TTTATTATTT
1 ATTATTATTT
110119 TTGTAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
18 4 0.15
19 2 0.07
20 5 0.19
21 4 0.15
22 5 0.19
23 7 0.26
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (20 bp):
ATTATTATTTAAATTAACAT
Found at i:111071 original size:59 final size:56
Alignment explanation
Indices: 110993--111113 Score: 188
Period size: 59 Copynumber: 2.1 Consensus size: 56
110983 TATTATAATT
* *
110993 TCATTACTAGTAATCATTAGTAAATCATTAGTATCAAATAATTAAATATTAATAATAAA
1 TCATTACTAATAATAATTAGTAAATCATTAGTATCAAATAATTAAATATT--TAA-AAA
*
111052 TCATTATTAATAATAATTAGTAAATCATTAGTATCAAATAATTAAATATTTAAAAA
1 TCATTACTAATAATAATTAGTAAATCATTAGTATCAAATAATTAAATATTTAAAAA
111108 TCATTA
1 TCATTA
111114 ATAAATTCGA
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
56 9 0.15
57 3 0.05
59 47 0.80
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (56 bp):
TCATTACTAATAATAATTAGTAAATCATTAGTATCAAATAATTAAATATTTAAAAA
Found at i:111214 original size:11 final size:11
Alignment explanation
Indices: 111198--111532 Score: 142
Period size: 11 Copynumber: 27.3 Consensus size: 11
111188 ATAAGTGATA
111198 ATTATTAAATC
1 ATTATTAAATC
111209 ATTATTATAAAATC
1 ATTA-T-T-AAATC
*
111223 ATTACTAAATC
1 ATTATTAAATC
111234 ATTATTAAATC
1 ATTATTAAATC
* *
111245 ATTACTATTCAATT
1 A-T--TATTAAATC
*
111259 ATTATTATAATGATT
1 ATTA-T-TAA--ATC
111274 ATTATTAAATC
1 ATTATTAAATC
** *
111285 ATTATTATCGTT
1 ATTATTA-AATC
111297 ATTATTAAATC
1 ATTATTAAATC
*
111308 ATTATTATAATG
1 ATTATTA-AATC
*
111320 ATTATTACTAAATT
1 ATTA-T--TAAATC
*
111334 ATTATTATAATG
1 ATTATTA-AATC
111346 ATTATTATAAAATC
1 ATTA-T-T-AAATC
111360 ATTATTAAATC
1 ATTATTAAATC
111371 ATCAAATATTAAAGTC
1 AT----TATTAAA-TC
111387 ATTATTAAATC
1 ATTATTAAATC
*
111398 ATTATTATAATG
1 ATTATTA-AATC
111410 ATTATTACTAAATC
1 ATTA-T--TAAATC
111424 ATTATTAAATC
1 ATTATTAAATC
111435 ATAATATTAAAATC
1 AT--TATT-AAATC
*
111449 ATTACTAAATC
1 ATTATTAAATC
111460 ATCAAATCATTAAAT-
1 AT----T-ATTAAATC
111475 ATTA--AAATC
1 ATTATTAAATC
*
111484 ATTACTAAATC
1 ATTATTAAATC
111495 ATCAAATCATTAAAT-
1 AT----T-ATTAAATC
111510 ATTA--AAATC
1 ATTATTAAATC
111519 ATTATTAAATC
1 ATTATTAAATC
111530 ATT
1 ATT
111533 TTTATGGTTA
Statistics
Matches: 256, Mismatches: 21, Indels: 94
0.69 0.06 0.25
Matches are distributed among these distances:
8 8 0.03
9 8 0.03
10 2 0.01
11 89 0.35
12 44 0.17
13 17 0.07
14 47 0.18
15 25 0.10
16 16 0.06
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (11 bp):
ATTATTAAATC
Found at i:111259 original size:22 final size:22
Alignment explanation
Indices: 111198--111532 Score: 106
Period size: 26 Copynumber: 15.1 Consensus size: 22
111188 ATAAGTGATA
*
111198 ATTATTAAATCATTATTATAAAATC
1 ATTACTAAATCATTA-T-T-AAATC
111223 ATTACTAAATCATTATTAAATC
1 ATTACTAAATCATTATTAAATC
* *
111245 ATTACTATTCAATTATTATTATAATGATT
1 ATTACTA---AATCATTA-T-TAA--ATC
* ** *
111274 ATTATTAAATCATTATTATCGTT
1 ATTACTAAATCATTATTA-AATC
* *
111297 ATTATTAAATCATTATTATAATGATT
1 ATTACTAAATCATTA-T-TAA--ATC
* *
111323 ATTACTAAATTATTATTATAATG
1 ATTACTAAATCATTATTA-AATC
*
111346 ATTATTATAAAATCATTATTAAATC
1 ATTA--CT-AAATCATTATTAAATC
*
111371 A-T-C-AAAT-ATTA--AAGTC
1 ATTACTAAATCATTATTAAATC
* *
111387 ATTATTAAATCATTATTATAATGATT
1 ATTACTAAATCATTA-T-TAA--ATC
111413 ATTACTAAATCATTATTAAATC
1 ATTACTAAATCATTATTAAATC
* *
111435 ATAATATTAAAATCATTACTAAATC
1 AT--TACT-AAATCATTATTAAATC
111460 A-T-C-AAATC---ATTAAAT-
1 ATTACTAAATCATTATTAAATC
*
111475 ATTA--AAATCATTACTAAATC
1 ATTACTAAATCATTATTAAATC
111495 A-T-C-AAATC---ATTAAAT-
1 ATTACTAAATCATTATTAAATC
111510 ATTA--AAATCATTATTAAATC
1 ATTACTAAATCATTATTAAATC
111530 ATT
1 ATT
111533 TTTATGGTTA
Statistics
Matches: 240, Mismatches: 28, Indels: 89
0.67 0.08 0.25
Matches are distributed among these distances:
15 2 0.01
16 29 0.12
17 1 0.00
18 4 0.02
19 32 0.13
20 8 0.03
22 17 0.07
23 24 0.10
24 15 0.06
25 48 0.20
26 49 0.20
27 3 0.01
29 8 0.03
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (22 bp):
ATTACTAAATCATTATTAAATC
Found at i:111279 original size:26 final size:26
Alignment explanation
Indices: 111185--111436 Score: 229
Period size: 26 Copynumber: 10.0 Consensus size: 26
111175 TTATTCCATA
*
111185 ATTATAAGTGATAATTATTAAATCATT
1 ATTATAA-TGATTATTATTAAATCATT
* * *
111212 ATTATAA-AATCATTACTAAATCATT
1 ATTATAATGATTATTATTAAATCATT
* * * *
111237 ATTA-AATCATTACTATTCAATTATT
1 ATTATAATGATTATTATTAAATCATT
111262 ATTATAATGATTATTATTAAATCATT
1 ATTATAATGATTATTATTAAATCATT
*
111288 ATTAT--CG-TTATTATTAAATCATT
1 ATTATAATGATTATTATTAAATCATT
* *
111311 ATTATAATGATTATTACTAAATTATT
1 ATTATAATGATTATTATTAAATCATT
*
111337 ATTATAATGATTATTATAAAATCATT
1 ATTATAATGATTATTATTAAATCATT
* * *
111363 ATTA-AATCATCAAATATTAAAGTCATT
1 ATTATAATGAT-TATTATTAAA-TCATT
* *
111390 ATTA-AATCATTATTA-T-AATGATT
1 ATTATAATGATTATTATTAAATCATT
*
111413 ATTACTAA--ATCATTATTAAATCAT
1 ATTA-TAATGATTATTATTAAATCAT
111437 AATATTAAAA
Statistics
Matches: 185, Mismatches: 29, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
23 35 0.19
24 6 0.03
25 49 0.26
26 73 0.39
27 22 0.12
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.46
Consensus pattern (26 bp):
ATTATAATGATTATTATTAAATCATT
Found at i:111323 original size:20 final size:21
Alignment explanation
Indices: 111277--111323 Score: 51
Period size: 23 Copynumber: 2.2 Consensus size: 21
111267 AATGATTATT
* *
111277 ATTAAATCATTATTATCGTTATT
1 ATTAAATCATTATTA-C-TAATG
111300 ATTAAATCATTATTA-TAATG
1 ATTAAATCATTATTACTAATG
111320 ATTA
1 ATTA
111324 TTACTAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 7 0.32
23 15 0.68
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.49
Consensus pattern (21 bp):
ATTAAATCATTATTACTAATG
Found at i:111393 original size:90 final size:88
Alignment explanation
Indices: 111296--111487 Score: 284
Period size: 90 Copynumber: 2.2 Consensus size: 88
111286 TTATTATCGT
* * *
111296 TATTATTAAATCATTATTATAATGATTATTACTAAATTATTATTATAATGATTAT-TATAAAATC
1 TATTATTAAATCATTATTATAATGATTATTACTAAATCATTATTA-AATCATAATAT-TAAAATC
*
111360 ATTATTAAATCATCAAAT-ATTAAA
64 ATTACTAAATCATCAAATCATTAAA
111384 GTCATTATTAAATCATTATTATAATGATTATTACTAAATCATTATTAAATCATAATATTAAAATC
1 -T-ATTATTAAATCATTATTATAATGATTATTACTAAATCATTATTAAATCATAATATTAAAATC
111449 ATTACTAAATCATCAAATCATTAAA
64 ATTACTAAATCATCAAATCATTAAA
111474 TATTA--AAATCATTA
1 TATTATTAAATCATTA
111488 CTAAATCATC
Statistics
Matches: 96, Mismatches: 4, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
86 9 0.09
88 4 0.04
89 33 0.34
90 50 0.52
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (88 bp):
TATTATTAAATCATTATTATAATGATTATTACTAAATCATTATTAAATCATAATATTAAAATCAT
TACTAAATCATCAAATCATTAAA
Found at i:111463 original size:14 final size:14
Alignment explanation
Indices: 111198--111463 Score: 74
Period size: 12 Copynumber: 21.1 Consensus size: 14
111188 ATAAGTGATA
*
111198 ATTATTAAATCATT
1 ATTATTAAATCATC
111212 ATTA-TAAA--ATC
1 ATTATTAAATCATC
*
111223 ATTACT-AA--ATC
1 ATTATTAAATCATC
*
111234 ATTATTAAATCATT
1 ATTATTAAATCATC
* *
111248 ACTATTCAAT--T-
1 ATTATTAAATCATC
* *
111259 ATTATTATAATGATT
1 ATTATTA-AATCATC
111274 ATTATT-AA--ATC
1 ATTATTAAATCATC
* *
111285 ATTATT--ATCGTT
1 ATTATTAAATCATC
*
111297 ATTATTAAATCATT
1 ATTATTAAATCATC
* *
111311 ATTA-T-AATGATT
1 ATTATTAAATCATC
*
111323 ATTACTAAAT--T-
1 ATTATTAAATCATC
* *
111334 ATTATTATAATGATT
1 ATTATTA-AATCATC
111349 ATTA-TAAA--ATC
1 ATTATTAAATCATC
111360 ATTATTAAATCATC
1 ATTATTAAATCATC
* *
111374 AAATATTAAA--GTC
1 -ATTATTAAATCATC
*
111387 ATTATTAAATCATT
1 ATTATTAAATCATC
* *
111401 ATTA-T-AATGATT
1 ATTATTAAATCATC
*
111413 ATTACT-AA--ATC
1 ATTATTAAATCATC
111424 ATTATTAAATCAT-
1 ATTATTAAATCATC
*
111437 AATATTAAA--ATC
1 ATTATTAAATCATC
*
111449 ATTACTAAATCATC
1 ATTATTAAATCATC
111463 A
1 A
111464 AATCATTAAA
Statistics
Matches: 196, Mismatches: 25, Indels: 62
0.69 0.09 0.22
Matches are distributed among these distances:
10 1 0.01
11 50 0.26
12 59 0.30
13 24 0.12
14 44 0.22
15 18 0.09
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.45
Consensus pattern (14 bp):
ATTATTAAATCATC
Found at i:111468 original size:19 final size:19
Alignment explanation
Indices: 111444--111506 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
111434 CATAATATTA
111444 AAATCATTACTAAATCATC
1 AAATCATTACTAAATCATC
*
111463 AAATCA-T--TAAAT-ATTA
1 AAATCATTACTAAATCA-TC
111479 AAATCATTACTAAATCATC
1 AAATCATTACTAAATCATC
111498 AAATCATTA
1 AAATCATTA
111507 AATATTAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
15 1 0.03
16 12 0.32
17 1 0.03
18 1 0.03
19 21 0.57
20 1 0.03
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATCATTACTAAATCATC
Found at i:111478 original size:35 final size:35
Alignment explanation
Indices: 111430--111531 Score: 181
Period size: 35 Copynumber: 3.0 Consensus size: 35
111420 AATCATTATT
111430 AAATCA-T-AATATTAAAATCATTACTAAATCATC
1 AAATCATTAAATATTAAAATCATTACTAAATCATC
111463 AAATCATTAAATATTAAAATCATTACTAAATCATC
1 AAATCATTAAATATTAAAATCATTACTAAATCATC
*
111498 AAATCATTAAATATTAAAATCATTATTAAATCAT
1 AAATCATTAAATATTAAAATCATTACTAAATCAT
111532 TTTTATGGTT
Statistics
Matches: 66, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
33 6 0.09
34 1 0.02
35 59 0.89
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (35 bp):
AAATCATTAAATATTAAAATCATTACTAAATCATC
Found at i:111482 original size:16 final size:16
Alignment explanation
Indices: 111426--111522 Score: 69
Period size: 16 Copynumber: 5.9 Consensus size: 16
111416 ACTAAATCAT
111426 TATT-AAATCA-T-AA
1 TATTAAAATCATTAAA
111439 TATTAAAATCATTACTAA
1 TATTAAAATCATTA--AA
*
111457 -ATCATCAAATCATTAAA
1 TAT--TAAAATCATTAAA
111474 TATTAAAATCATTACTAA
1 TATTAAAATCATTA--AA
*
111492 -ATCATCAAATCATTAAA
1 TAT--TAAAATCATTAAA
111509 TATTAAAATCATTA
1 TATTAAAATCATTA
111523 TTAAATCATT
Statistics
Matches: 67, Mismatches: 4, Indels: 23
0.71 0.04 0.24
Matches are distributed among these distances:
13 4 0.06
14 6 0.09
15 1 0.01
16 20 0.30
17 8 0.12
18 8 0.12
19 20 0.30
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (16 bp):
TATTAAAATCATTAAA
Found at i:111517 original size:8 final size:9
Alignment explanation
Indices: 111440--111532 Score: 72
Period size: 8 Copynumber: 10.3 Consensus size: 9
111430 AAATCATAAT
111440 ATTAAAATC
1 ATTAAAATC
111449 ATTACTAAATC
1 ATTA--AAATC
*
111460 A-TCAAATC
1 ATTAAAATC
111468 ATT-AAAT-
1 ATTAAAATC
111475 ATTAAAATC
1 ATTAAAATC
111484 ATTACTAAATC
1 ATTA--AAATC
*
111495 A-TCAAATC
1 ATTAAAATC
111503 ATT-AAAT-
1 ATTAAAATC
111510 ATTAAAATC
1 ATTAAAATC
111519 ATTATTAAATC
1 ATTA--AAATC
111530 ATT
1 ATT
111533 TTTATGGTTA
Statistics
Matches: 70, Mismatches: 2, Indels: 22
0.74 0.02 0.23
Matches are distributed among these distances:
7 6 0.09
8 28 0.40
9 14 0.20
10 2 0.03
11 20 0.29
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.37
Consensus pattern (9 bp):
ATTAAAATC
Found at i:111525 original size:19 final size:19
Alignment explanation
Indices: 111437--111528 Score: 74
Period size: 19 Copynumber: 5.2 Consensus size: 19
111427 ATTAAATCAT
*
111437 AATATTAAAATCATTACTA
1 AATATTAAAATCATTATTA
*
111456 AATCA-TCAAATC---ATTA
1 AAT-ATTAAAATCATTATTA
*
111472 AATATTAAAATCATTACTA
1 AATATTAAAATCATTATTA
*
111491 AATCA-TCAAATC---ATTA
1 AAT-ATTAAAATCATTATTA
111507 AATATTAAAATCATTATTA
1 AATATTAAAATCATTATTA
111526 AAT
1 AAT
111529 CATTTTTATG
Statistics
Matches: 56, Mismatches: 7, Indels: 20
0.67 0.08 0.24
Matches are distributed among these distances:
15 2 0.04
16 24 0.43
19 28 0.50
20 2 0.04
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (19 bp):
AATATTAAAATCATTATTA
Found at i:111803 original size:49 final size:49
Alignment explanation
Indices: 111737--112004 Score: 432
Period size: 49 Copynumber: 5.4 Consensus size: 49
111727 TTATTACTAA
* *
111737 TAATTATTA--AATCATTACTATCAAATCATTAAATATTAACAATAATT
1 TAATTATTACTAATCATTACTACCAAATCATTAAATATTAATAATAATT
*
111784 TAATTATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATT
1 TAATTATTACTAATCATTACTACCAAATCATTAAATATTAATAATAATT
111833 TAATTATTACTAATCATTACTACCAAATCATTAAATATTAATAATAATT
1 TAATTATTACTAATCATTACTACCAAATCATTAAATATTAATAATAATT
*
111882 TCATTATTACTAATCATTACTACCAAATCATTAAATATTAATAATAATT
1 TAATTATTACTAATCATTACTACCAAATCATTAAATATTAATAATAATT
* *
111931 TCATTATTACTAATCATTACTACAAAATCATTAAATATTAATAATAATAATT
1 TAATTATTACTAATCATTACTACCAAATCATTAAATA-T--TAATAATAATT
*
111983 TCATTATTACTAATCATTACTA
1 TAATTATTACTAATCATTACTA
112005 AATAATTATT
Statistics
Matches: 212, Mismatches: 4, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
47 9 0.04
49 169 0.80
50 1 0.00
52 33 0.16
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (49 bp):
TAATTATTACTAATCATTACTACCAAATCATTAAATATTAATAATAATT
Found at i:111909 original size:147 final size:148
Alignment explanation
Indices: 111739--112063 Score: 455
Period size: 147 Copynumber: 2.2 Consensus size: 148
111729 ATTACTAATA
*
111739 ATTATTAAATCATTACTATCAAATCATTAAATATTAACAATAATTTAATTATTACTAATCATTAC
1 ATTATTAAATCATTACTACCAAATCATTAAATATTAACAATAATTTAATTATTACTAATCATTAC
*
111804 TATC-AAATCATTAAATA-T-TAATAATAATTTAATTATTACTAATCATTACTACCA-AATCATT
66 TA-CAAAATCATTAAATATTATAATAATAATTTAATTATTACTAATCATTACTA-AATAATCATT
*
111865 A-AATATT-AATAATAATTTC
129 ATAATATTAAAT-ATAAATTC
* *
111884 ATTATTACTAATCATTACTACCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATT
1 ATTATTA--AATCATTACTACCAAATCATTAAATATTAACAATAATTTAATTATTACTAATCATT
* *
111949 ACTACAAAATCATTAAATATTAATAATAATAATTTCATTATTACTAATCATTACTAAATAATTAT
64 ACTACAAAATCATTAAATATT-ATAATAATAATTTAATTATTACTAATCATTACTAAATAATCAT
*
112014 TATAATTTTAAATATAAATTC
128 TATAATATTAAATATAAATTC
* * *
112035 ATTATTAAATCATGATTAGCAAATCATTA
1 ATTATTAAATCATTACTACCAAATCATTA
112064 CTAAATCAAA
Statistics
Matches: 160, Mismatches: 11, Indels: 14
0.86 0.06 0.08
Matches are distributed among these distances:
145 7 0.04
146 1 0.01
147 70 0.44
148 1 0.01
149 20 0.12
150 39 0.24
151 19 0.12
152 3 0.02
ACGTcount: A:0.46, C:0.11, G:0.01, T:0.42
Consensus pattern (148 bp):
ATTATTAAATCATTACTACCAAATCATTAAATATTAACAATAATTTAATTATTACTAATCATTAC
TACAAAATCATTAAATATTATAATAATAATTTAATTATTACTAATCATTACTAAATAATCATTAT
AATATTAAATATAAATTC
Found at i:115415 original size:19 final size:18
Alignment explanation
Indices: 115384--115441 Score: 70
Period size: 17 Copynumber: 3.3 Consensus size: 18
115374 ATAATATAAA
115384 TTAAACA-AAATATTTTT
1 TTAAACACAAATATTTTT
115401 TTAAACACTAAATA--TTT
1 TTAAACAC-AAATATTTTT
115418 TTAAACAC-AATATTTTTT
1 TTAAACACAAATA-TTTTT
115436 TTAAAC
1 TTAAAC
115442 GGAAATTATC
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
15 4 0.11
17 18 0.50
18 9 0.25
19 5 0.14
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (18 bp):
TTAAACACAAATATTTTT
Found at i:115946 original size:28 final size:30
Alignment explanation
Indices: 115906--115968 Score: 112
Period size: 28 Copynumber: 2.2 Consensus size: 30
115896 ATTTTTTATA
115906 TAATATAATATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
115936 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
115964 TAATA
1 TAATA
115969 ATTTATACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 26 0.79
29 1 0.03
30 6 0.18
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:115975 original size:28 final size:28
Alignment explanation
Indices: 115910--115975 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
115900 TTTATATAAT
115910 ATAATATATAACTTAAACTAACAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
115938 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
115966 ATAATTTATA
1 ATAATATATA
115976 CTAACAAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
27 2 0.06
28 31 0.89
29 2 0.06
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:115978 original size:21 final size:21
Alignment explanation
Indices: 115945--115993 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
115935 CTAATATAAT
115945 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
115966 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
115987 ATTAACT
1 A-TAACT
115994 AAATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:116244 original size:26 final size:26
Alignment explanation
Indices: 116214--116274 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
116204 ATAAAGAAAA
* *
116214 TGAGCGTTGGAGGGCGTCATTAAATT
1 TGAGCGTTGGAGAGCGTAATTAAATT
*
116240 TGAGCATTGGAGAGCGTAATTAAATT
1 TGAGCGTTGGAGAGCGTAATTAAATT
*
116266 TGACCGTTG
1 TGAGCGTTG
116275 AAGCAAATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.26, C:0.11, G:0.31, T:0.31
Consensus pattern (26 bp):
TGAGCGTTGGAGAGCGTAATTAAATT
Found at i:116489 original size:23 final size:23
Alignment explanation
Indices: 116459--116502 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
116449 GCTTAGCTGT
116459 AATCTCCCAGCTATGGATGCAGG
1 AATCTCCCAGCTATGGATGCAGG
116482 AATCTCCCAGCTATGGATGCA
1 AATCTCCCAGCTATGGATGCA
116503 ACGAATGCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (23 bp):
AATCTCCCAGCTATGGATGCAGG
Found at i:116677 original size:32 final size:32
Alignment explanation
Indices: 116634--116698 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
116624 GGCCATGCAC
*
116634 TGCTCCCTGGATAGCTCGCACTCACTCCTTGG
1 TGCTCCATGGATAGCTCGCACTCACTCCTTGG
116666 TGCTCCATGGATAGCTCGCACTCACTCCTTGG
1 TGCTCCATGGATAGCTCGCACTCACTCCTTGG
116698 T
1 T
116699 CGCCCGGAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.14, C:0.35, G:0.22, T:0.29
Consensus pattern (32 bp):
TGCTCCATGGATAGCTCGCACTCACTCCTTGG
Found at i:126648 original size:20 final size:20
Alignment explanation
Indices: 126625--126668 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
126615 TAAATTTTAA
*
126625 TTATTTTAAATAATTAAAAT
1 TTATTTAAAATAATTAAAAT
126645 TTATTTAAAATAATTAAAAT
1 TTATTTAAAATAATTAAAAT
126665 TTAT
1 TTAT
126669 AAAAATATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTATTTAAAATAATTAAAAT
Found at i:126735 original size:35 final size:35
Alignment explanation
Indices: 126660--126735 Score: 82
Period size: 36 Copynumber: 2.1 Consensus size: 35
126650 TAAAATAATT
**
126660 AAAATTTATAAAAATATACTTAAAACTATTTGATTT
1 AAAATTTATAAAAATATACTTAAAAC-ATTTGATCA
* * *
126696 AAAATTTTTAAAATATATATTTAAAA-ATTTTATCA
1 AAAATTTATAAAA-ATATACTTAAAACATTTGATCA
126731 AAAAT
1 AAAAT
126736 AAATTTTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
35 11 0.32
36 12 0.35
37 11 0.32
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (35 bp):
AAAATTTATAAAAATATACTTAAAACATTTGATCA
Found at i:128259 original size:36 final size:36
Alignment explanation
Indices: 128219--128291 Score: 87
Period size: 36 Copynumber: 2.0 Consensus size: 36
128209 AAGGTATAAT
*
128219 TGAGATCGAAAAAA-TTCAAGG-CTCTCAATTAGAAAG
1 TGAGATCAAAAAAACTT-AAGGAC-CTCAATTAGAAAG
* *
128255 TGAGATTAAAAAAACTTAAGGACCTCAATTATAAAG
1 TGAGATCAAAAAAACTTAAGGACCTCAATTAGAAAG
128291 T
1 T
128292 TAAAAAAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 29 0.91
37 3 0.09
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.25
Consensus pattern (36 bp):
TGAGATCAAAAAAACTTAAGGACCTCAATTAGAAAG
Found at i:128501 original size:42 final size:41
Alignment explanation
Indices: 128409--128596 Score: 150
Period size: 41 Copynumber: 4.5 Consensus size: 41
128399 AAATTAAAAG
* * *
128409 CCTCAATTATAAA-GTTAAAAGTGAAATT-ACAAAATTAGGA
1 CCTCAATTATAAAGGTGAAAA-AGAAATTGAAAAAATTAGGA
* * *
128449 CATCAGTTATAAAGGTGAAAAAGAAATTGAAAAAAATAGAGA
1 CCTCAATTATAAAGGTGAAAAAGAAATTGAAAAAATTAG-GA
* * * *
128491 CTTCAATTATAAAGAT-AAAAAGTGAGATTGAATAATATTAGGA
1 CCTCAATTATAAAGGTGAAAAA--GAAATTGAA-AAAATTAGGA
* * * **
128534 CCTCAATTATAAAGGTAAAAAATAAGATTTAAAAAATTAAAA
1 CCTCAATTATAAAGGTGAAAAAGAA-ATTGAAAAAATTAGGA
*
128576 CCT-AATTATAAAGATGAAAAA
1 CCTCAATTATAAAGGTGAAAAA
128597 AATGAGAGTT
Statistics
Matches: 118, Mismatches: 22, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
40 17 0.14
41 35 0.30
42 26 0.22
43 29 0.25
44 11 0.09
ACGTcount: A:0.54, C:0.07, G:0.13, T:0.26
Consensus pattern (41 bp):
CCTCAATTATAAAGGTGAAAAAGAAATTGAAAAAATTAGGA
Found at i:128540 original size:43 final size:42
Alignment explanation
Indices: 128251--128588 Score: 240
Period size: 44 Copynumber: 7.9 Consensus size: 42
128241 TCTCAATTAG
* *
128251 AAAGTGAGATTAAAAAAACTTAAGGACCTCAATTATAAAGTTAAAA
1 AAAGTGAGATTGAAAAAA-TT-AGGACCTCAATTATAAAGGT--AA
* * * *
128297 AAAGTGAGAAT-AAAAAATTAGGGGCATCAATTATGAAGGTAA
1 AAAGTGAGATTGAAAAAATTA-GGACCTCAATTATAAAGGTAA
* * * * *
128339 AAATTGAGATTGGAAAAACTTAGGGGCCTCAGTTGA-AAAGGTAG
1 AAAGTGAGATT-GAAAAAATTA-GGACCTCAATT-ATAAAGGTAA
* * ** *
128383 AAATTGAGATCGAAAAAAATTAAAAGCCTCAATTATAAA-GTTA
1 AAAGTGAGATTG-AAAAAATTAGGA-CCTCAATTATAAAGGTAA
* * * *
128426 AAAGTGAAATT-ACAAAATTAGGACATCAGTTATAAAGGTGAA
1 AAAGTGAGATTGAAAAAATTAGGACCTCAATTATAAAGGT-AA
* * * *
128468 AAA--GAAATTGAAAAAAATAGAGACTTCAATTATAAAGATAA
1 AAAGTGAGATTGAAAAAATTAG-GACCTCAATTATAAAGGTAA
*
128509 AAAGTGAGATTGAATAATATTAGGACCTCAATTATAAAGGTAA
1 AAAGTGAGATTGAA-AAAATTAGGACCTCAATTATAAAGGTAA
* * * **
128552 AAAATAAGATTTAAAAAATTAAAACCT-AATTATAAAG
1 AAAGTGAGATTGAAAAAATTAGGACCTCAATTATAAAG
128589 ATGAAAAAAA
Statistics
Matches: 233, Mismatches: 45, Indels: 33
0.75 0.14 0.11
Matches are distributed among these distances:
40 17 0.07
41 34 0.15
42 40 0.17
43 50 0.21
44 75 0.32
45 7 0.03
46 10 0.04
ACGTcount: A:0.52, C:0.07, G:0.17, T:0.24
Consensus pattern (42 bp):
AAAGTGAGATTGAAAAAATTAGGACCTCAATTATAAAGGTAA
Found at i:128549 original size:85 final size:83
Alignment explanation
Indices: 128389--128596 Score: 226
Period size: 85 Copynumber: 2.5 Consensus size: 83
128379 GTAGAAATTG
* *
128389 AGATCGAAAAAAATTAAAAGCCTCAATTATAAAG-TTAAAAGTGAAATTACAAAATTAGGACATC
1 AGATTGAAAAAAA-TAAAA-CCTCAATTATAAAGATAAAAAGTGAAATTACAAAATTAGGACATC
* *
128453 AGTTATAAAGGTGAAAAAGA
64 AATTATAAAGGTAAAAAAGA
* * * *
128473 A-ATTGAAAAAAATAGAGACTTCAATTATAAAGATAAAAAGTGAGATTGA-ATAATATTAGGACC
1 AGATTGAAAAAAATA-AAACCTCAATTATAAAGATAAAAAGTGAAATT-ACA-AA-ATTAGGACA
*
128536 TCAATTATAAAGGTAAAAAATA
62 TCAATTATAAAGGTAAAAAAGA
* *
128558 AGATTTAAAAAATTAAAACCT-AATTATAAAGATGAAAAA
1 AGATTGAAAAAAATAAAACCTCAATTATAAAGAT-AAAAA
128597 AATGAGAGTT
Statistics
Matches: 104, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
82 15 0.14
83 25 0.24
84 16 0.15
85 37 0.36
86 11 0.11
ACGTcount: A:0.55, C:0.07, G:0.13, T:0.25
Consensus pattern (83 bp):
AGATTGAAAAAAATAAAACCTCAATTATAAAGATAAAAAGTGAAATTACAAAATTAGGACATCAA
TTATAAAGGTAAAAAAGA
Found at i:131243 original size:2 final size:2
Alignment explanation
Indices: 131236--131274 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
131226 CTTCGTTTTC
131236 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
131275 TACAGTGTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:133353 original size:22 final size:22
Alignment explanation
Indices: 133296--133347 Score: 95
Period size: 22 Copynumber: 2.3 Consensus size: 22
133286 CACGAATCTT
133296 CTGCAAACTCGTCCCAATGCAAA
1 CTGC-AACTCGTCCCAATGCAAA
133319 CTGCAACTCGTCCCAATGCAAA
1 CTGCAACTCGTCCCAATGCAAA
133341 CTGCAAC
1 CTGCAAC
133348 GTGTCCAGCC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 25 0.86
23 4 0.14
ACGTcount: A:0.33, C:0.37, G:0.13, T:0.17
Consensus pattern (22 bp):
CTGCAACTCGTCCCAATGCAAA
Found at i:137413 original size:2 final size:2
Alignment explanation
Indices: 137406--137430 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
137396 GTAATTGAGT
137406 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
137431 TGTTATTATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:137736 original size:21 final size:20
Alignment explanation
Indices: 137712--137757 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
137702 CATTCAACTT
*
137712 TAAAAGTTA-CATTTTGATCAA
1 TAAAAATTATCATTTT-ATC-A
137733 TAAAAATTATCATTTTATCA
1 TAAAAATTATCATTTTATCA
137753 TAAAA
1 TAAAA
137758 TGACCATTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 6 0.26
21 11 0.48
22 6 0.26
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (20 bp):
TAAAAATTATCATTTTATCA
Found at i:146274 original size:25 final size:25
Alignment explanation
Indices: 146240--146289 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
146230 TAGTACCAAA
*
146240 AGCCGAATATTTAGGGATTTAGGAC
1 AGCCGAATATTTAGGAATTTAGGAC
146265 AGCCGAATATTTAGGAATTTAGGAC
1 AGCCGAATATTTAGGAATTTAGGAC
146290 TATTTTAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (25 bp):
AGCCGAATATTTAGGAATTTAGGAC
Found at i:146709 original size:24 final size:24
Alignment explanation
Indices: 146668--146724 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
146658 GTAATATGTA
*
146668 AATAA-AATAATAATAATAACGCT
1 AATAATAATAATAATAATAACGAT
146691 AATAATAATAATTAA-AATAACGAT
1 AATAATAATAA-TAATAATAACGAT
146715 AATAATAATA
1 AATAATAATA
146725 TACAAAAAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
23 5 0.16
24 23 0.74
25 3 0.10
ACGTcount: A:0.63, C:0.05, G:0.04, T:0.28
Consensus pattern (24 bp):
AATAATAATAATAATAATAACGAT
Found at i:146724 original size:15 final size:15
Alignment explanation
Indices: 146674--146724 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 15
146664 TGTAAATAAA
146674 ATAATAATAATAACG
1 ATAATAATAATAACG
*
146689 CTAATAATAAT-A--
1 ATAATAATAATAACG
146701 AT--TAA-AATAACG
1 ATAATAATAATAACG
146713 ATAATAATAATA
1 ATAATAATAATA
146725 TACAAAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
9 3 0.11
10 4 0.14
12 3 0.11
14 4 0.14
15 14 0.50
ACGTcount: A:0.61, C:0.06, G:0.04, T:0.29
Consensus pattern (15 bp):
ATAATAATAATAACG
Found at i:147084 original size:43 final size:44
Alignment explanation
Indices: 146886--147214 Score: 155
Period size: 43 Copynumber: 7.6 Consensus size: 44
146876 GGACGCCACT
* * * ** * * *
146886 GCTCATACGTGATGAAGAGTTCGGGTCGTCTAAGG-GTGACATG
1 GCTCCTACGTGATGAAGAGATCTGGTTATCTATGGTATGACACG
* * * * * *
146929 GTTCCTACGTGATGAGGAAATCTGG---TCGAGGGT-TGACACT
1 GCTCCTACGTGATGAAGAGATCTGGTTATCTATGGTATGACACG
* * ** * * *
146969 GCTCATACGTGATGAAGAGTTCTTGGCCATCTTAAGGTGATAACACA
1 GCTCCTACGTGATGAAGAGATC-TGGTTATC-TATGGT-ATGACACG
* * *
147016 GTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGT-TGACACG
1 GCTCCTACGTGATGAAGA-GATCTGGTTATCTATGGTATGACACG
* *
147059 GCTCCTACGTGGTGAAGAGATCTGG---TCT-GGGTAATGACACG
1 GCTCCTACGTGATGAAGAGATCTGGTTATCTATGGT-ATGACACG
* * ** * *
147100 GCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACG
1 GCTCCTACGTGATGAAGAGATCTGGTTATCT-ATGGT-ATGACACG
* * *
147146 GTTCCTACGTGATGAGGACG-GCTGGTTATCTAT--TATTGACACG
1 GCTCCTACGTGATGAAGA-GATCTGGTTATCTATGGTA-TGACACG
*
147189 GCTCCTACGTGATGAGGAGATCTGGT
1 GCTCCTACGTGATGAAGAGATCTGGT
147215 CTGGGGATGA
Statistics
Matches: 217, Mismatches: 49, Indels: 40
0.71 0.16 0.13
Matches are distributed among these distances:
39 3 0.01
40 30 0.14
41 32 0.15
42 3 0.01
43 72 0.33
44 5 0.02
45 10 0.05
46 39 0.18
47 22 0.10
48 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (44 bp):
GCTCCTACGTGATGAAGAGATCTGGTTATCTATGGTATGACACG
Found at i:147126 original size:130 final size:129
Alignment explanation
Indices: 146922--147260 Score: 475
Period size: 130 Copynumber: 2.6 Consensus size: 129
146912 CGTCTAAGGG
* * * * *
146922 TGACATGGTTCCTACGTGATGAGGAAATCTGGTCGAGGGT-TGACACTGCTCATACGTGATGAAG
1 TGACACGGCTCCTACGTGATGAGGAGATCTGGTC-TGGGTATGACACGGCTCATACGTGATGAAG
*
146986 AGTTCTTGGCCATCTTAAGGTGATAACACAGTTCCTACGTGATGAGGACGGCTGGTTATCTATGG
65 AGTTC-TGGCCATCTTAAGGTGATAACACAGTTCCTACGTGATGAGGACGGCTGGTTATCTATGA
147051 T
129 T
* *
147052 TGACACGGCTCCTACGTGGTGAAGAGATCTGGTCTGGGTAATGACACGGCTCATACGTGATGAAG
1 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGT-ATGACACGGCTCATACGTGATGAAG
* * *
147117 AGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATTAT
65 AGTTCTGGCCATCTTAAGGTGATAACACAGTTCCTACGTGATGAGGACGGCTGGTTATCTATGAT
* * * * *
147182 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGATGACACGGTTCCTACATGATGAGGA
1 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGTATGACACGGCTCATACGTGATGAAGA
*
147247 CG-GCTGGCCATCTT
66 -GTTCTGGCCATCTT
147261 TAGGAGTTAT
Statistics
Matches: 186, Mismatches: 20, Indels: 7
0.87 0.09 0.03
Matches are distributed among these distances:
129 36 0.19
130 122 0.66
131 28 0.15
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.27
Consensus pattern (129 bp):
TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGTATGACACGGCTCATACGTGATGAAGA
GTTCTGGCCATCTTAAGGTGATAACACAGTTCCTACGTGATGAGGACGGCTGGTTATCTATGAT
Found at i:147410 original size:63 final size:62
Alignment explanation
Indices: 147342--147459 Score: 168
Period size: 63 Copynumber: 1.9 Consensus size: 62
147332 TTTCAAAAGC
*
147342 AACTGTCTCAAAAGAGACAAAATTTTGTTTCAAA-GGAAATGA-CTCAAAGATTGTTTAAAGGAA
1 AACTGTCTCAAAAGAGACAAAA-TTCGTTT-AAAGGGAAATGATCTCAAAGA-TGTTTAAAGGAA
* *
147405 AACTGTCTTAAATGAGACAAAATTCGTTTAAAGGGAAATGATCTCAAAGATGTTT
1 AACTGTCTCAAAAGAGACAAAATTCGTTTAAAGGGAAATGATCTCAAAGATGTTT
147460 GTTTTGTTTC
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
61 3 0.06
62 19 0.38
63 28 0.56
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.29
Consensus pattern (62 bp):
AACTGTCTCAAAAGAGACAAAATTCGTTTAAAGGGAAATGATCTCAAAGATGTTTAAAGGAA
Found at i:147695 original size:31 final size:30
Alignment explanation
Indices: 147631--147705 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 30
147621 TGAATATTCG
* *
147631 TTTCAAGGGAAACGACTCAAAGATGGTTTTA
1 TTTCAAGAGAAACAACTCAAAGAT-GTTTTA
147662 TTTCAAGAGAAACAAACTCAAAGAT-TTTATA
1 TTTCAAGAGAAAC-AACTCAAAGATGTTT-TA
147693 TTT-ATAGAGAAAC
1 TTTCA-AGAGAAAC
147706 TGCCTCAAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
30 4 0.10
31 25 0.64
32 10 0.26
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (30 bp):
TTTCAAGAGAAACAACTCAAAGATGTTTTA
Found at i:147863 original size:68 final size:67
Alignment explanation
Indices: 147762--147887 Score: 198
Period size: 68 Copynumber: 1.9 Consensus size: 67
147752 GTGGGTGGTT
* * *
147762 TCAAAAGAAGTTGTCTCGAGAGACAAAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTTTT
1 TCAAAAGAAATTGTCTCAAGAGACAAAATTTTGTTTCAAAAGAAACAGACTCAAAGATTTTTTTT
147827 TC
66 TC
* *
147829 TCAAAAGAAATTGTCTTTAAGAGATAAAATTTTGTTTCAAAAGAAACAGACTCAAAGAT
1 TCAAAAGAAATTGTC-TCAAGAGACAAAATTTTGTTTCAAAAGAAACAGACTCAAAGAT
147888 GGATTACATC
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
67 14 0.26
68 39 0.74
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (67 bp):
TCAAAAGAAATTGTCTCAAGAGACAAAATTTTGTTTCAAAAGAAACAGACTCAAAGATTTTTTTT
TC
Found at i:148139 original size:68 final size:68
Alignment explanation
Indices: 148067--148221 Score: 165
Period size: 68 Copynumber: 2.3 Consensus size: 68
148057 AAAGATTTAC
* * * * *
148067 TTCAAGAGAAACTGTCTCAAGAGATACAAAATTCAT-TTT-AAGAGAAACAGATTCAAAGATTTT
1 TTCAAAAGAAACTATCTCAAGAGAGACAAAATT-ATGTTTCAA-AGAAACAAACTCAAAGATTTT
148130 TTTTT
64 TTTTT
* * * *
148135 TTCAAAAGAAATTATCTTAAGAGAGACAACATTTTGTTTCCAAAGAAACAAACTCAAAGA--TTT
1 TTCAAAAGAAACTATCTCAAGAGAGACAAAATTATGTTT-CAAAGAAACAAACTCAAAGATTTTT
148198 TTTT
65 TTTT
*
148202 TTCAAAAGAAACAATCTCAA
1 TTCAAAAGAAACTATCTCAA
148222 AGATTTTTTT
Statistics
Matches: 72, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
67 25 0.35
68 30 0.42
69 15 0.21
70 2 0.03
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.32
Consensus pattern (68 bp):
TTCAAAAGAAACTATCTCAAGAGAGACAAAATTATGTTTCAAAGAAACAAACTCAAAGATTTTTT
TTT
Found at i:148212 original size:30 final size:30
Alignment explanation
Indices: 148166--148231 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
148156 AGAGACAACA
* *
148166 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
1 TTTTTTTTCAAAAGAAACAAACTCAAAGAT
*
148196 TTTTTTTTCAAAAGAAACAATCTCAAAGAT
1 TTTTTTTTCAAAAGAAACAAACTCAAAGAT
148226 TTTTTT
1 TTTTTT
148232 CACAAAATTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (30 bp):
TTTTTTTTCAAAAGAAACAAACTCAAAGAT
Found at i:148238 original size:30 final size:30
Alignment explanation
Indices: 148176--148238 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
148166 TTTTGTTTCC
**
148176 AAAGAAACAAACTCAAAGATTTTTTTTTCA
1 AAAGAAACAAACTCAAAGATTTTTTTCACA
*
148206 AAAGAAACAATCTCAAAGATTTTTTTCACA
1 AAAGAAACAAACTCAAAGATTTTTTTCACA
148236 AAA
1 AAA
148239 TTGTCTCAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.30
Consensus pattern (30 bp):
AAAGAAACAAACTCAAAGATTTTTTTCACA
Found at i:148292 original size:52 final size:53
Alignment explanation
Indices: 148217--148320 Score: 174
Period size: 52 Copynumber: 2.0 Consensus size: 53
148207 AAGAAACAAT
*
148217 CTCAAAGATTTTTTTCACAAAATTGTCTCAAGAGAGACAAAGCTTTGTTTCAGA
1 CTCAAAGA-TTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
*
148271 CTCAAAGA-TTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
1 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
148321 AAATAAATAG
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
52 40 0.83
54 8 0.17
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (53 bp):
CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
Found at i:148500 original size:28 final size:28
Alignment explanation
Indices: 148331--148492 Score: 260
Period size: 28 Copynumber: 5.9 Consensus size: 28
148321 AAATAAATAG
* *
148331 ACTCAAAG--TTTTTTCAAAAAAAAC-A
1 ACTCAAAGATTTTTTTCAAGAGAAACAA
*
148356 ACTCAAAGA-TTTTTTCAAGAGGAACAA
1 ACTCAAAGATTTTTTTCAAGAGAAACAA
148383 ACTCAAAGATTTTTTTCAAGAGAAACAA
1 ACTCAAAGATTTTTTTCAAGAGAAACAA
*
148411 ACTCAAAGATTTTTTTCAAGAGAAACTA
1 ACTCAAAGATTTTTTTCAAGAGAAACAA
148439 ACTCAAAGATTTTTTTCAAGAGAAACAA
1 ACTCAAAGATTTTTTTCAAGAGAAACAA
148467 ACTCAAAGATTTTTTTCAAGAGAAAC
1 ACTCAAAGATTTTTTTCAAGAGAAAC
148493 TGTCTCAAGA
Statistics
Matches: 128, Mismatches: 6, Indels: 3
0.93 0.04 0.02
Matches are distributed among these distances:
25 8 0.06
26 13 0.10
27 10 0.08
28 97 0.76
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (28 bp):
ACTCAAAGATTTTTTTCAAGAGAAACAA
Found at i:148815 original size:36 final size:36
Alignment explanation
Indices: 148731--148834 Score: 124
Period size: 36 Copynumber: 3.0 Consensus size: 36
148721 GAGAAAATGA
* *
148731 TGTCTCAAGCGAGACAAAATTTG-CTTTA-AGATAC
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAC
* ** *
148765 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAC
*
148801 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAA
148835 ACGATCTCAA
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 20 0.34
35 10 0.17
36 28 0.48
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAC
Found at i:148862 original size:36 final size:36
Alignment explanation
Indices: 148732--148850 Score: 120
Period size: 36 Copynumber: 3.4 Consensus size: 36
148722 AGAAAATGAT
* * *
148732 GTCTCAAGCGAGACAAAATTTG-CTTTA-AG-ATAC
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
* **
148765 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 -GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
* *
148802 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
148837 GATCTCAAGTGAGA
1 G-TCTCAAGTGAGA
148851 TCAACTTTGT
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
34 20 0.29
35 11 0.16
36 37 0.54
37 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.29
Consensus pattern (36 bp):
GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
Found at i:149500 original size:4 final size:4
Alignment explanation
Indices: 149491--149546 Score: 66
Period size: 4 Copynumber: 15.0 Consensus size: 4
149481 TTTATGTATC
* *
149491 ATGT ATGT ATG- -TGT ATAT ATGT ATGT ATGT A--T ATAT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
149535 ATGT ATGT ATGT
1 ATGT ATGT ATGT
149547 TTTCTCGATC
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
2 4 0.09
4 41 0.91
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:149514 original size:18 final size:18
Alignment explanation
Indices: 149491--149540 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
149481 TTTATGTATC
*
149491 ATGTATGTATGTGTATAT
1 ATGTATGTATGTATATAT
149509 ATGTATGTATGTATATAT
1 ATGTATGTATGTATATAT
149527 ATGTATGTATGTAT
1 ATGTATGTATGTAT
149541 GTATGTTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (18 bp):
ATGTATGTATGTATATAT
Found at i:151362 original size:20 final size:20
Alignment explanation
Indices: 151339--151379 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
151329 GGATAAATGC
151339 AATGTTTCAAGGTCGCAAAG
1 AATGTTTCAAGGTCGCAAAG
*
151359 AATGTTTCAAGGTCTCAAAG
1 AATGTTTCAAGGTCGCAAAG
151379 A
1 A
151380 TAGGGAGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.27
Consensus pattern (20 bp):
AATGTTTCAAGGTCGCAAAG
Found at i:153875 original size:31 final size:32
Alignment explanation
Indices: 153819--153880 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 32
153809 TGACAAAATG
*
153819 ACACAAACAAAAGAGGAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGGAAAAATAAGTTAGTAT
153851 ACACAAACAAAAGA-GAAAAATAAGTTAGTA
1 ACACAAACAAAAGAGGAAAAATAAGTTAGTA
153881 CATGTAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 15 0.52
32 14 0.48
ACGTcount: A:0.60, C:0.10, G:0.16, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGGAAAAATAAGTTAGTAT
Found at i:153994 original size:50 final size:50
Alignment explanation
Indices: 153933--154058 Score: 236
Period size: 50 Copynumber: 2.5 Consensus size: 50
153923 GAATATAACA
*
153933 CCTACCC-GACATGATATCTACCCAAACATGCTTTCAATTAAATAACAAT
1 CCTACCCGGACATGCTATCTACCCAAACATGCTTTCAATTAAATAACAAT
153982 CCTACCCGGACATGCTATCTACCCAAACATGCTTTCAATTAAATAACAAT
1 CCTACCCGGACATGCTATCTACCCAAACATGCTTTCAATTAAATAACAAT
154032 CCTACCCGGACATGCTATCTACCCAAA
1 CCTACCCGGACATGCTATCTACCCAAA
154059 ATGATCTATT
Statistics
Matches: 75, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
49 7 0.09
50 68 0.91
ACGTcount: A:0.36, C:0.32, G:0.08, T:0.25
Consensus pattern (50 bp):
CCTACCCGGACATGCTATCTACCCAAACATGCTTTCAATTAAATAACAAT
Found at i:157515 original size:25 final size:25
Alignment explanation
Indices: 157481--157530 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
157471 TAGTACCAAA
*
157481 AGCCGAATATTTAGGGATTTAGGAC
1 AGCCGAATATTTAGGAATTTAGGAC
157506 AGCCGAATATTTAGGAATTTAGGAC
1 AGCCGAATATTTAGGAATTTAGGAC
157531 TATTTTAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (25 bp):
AGCCGAATATTTAGGAATTTAGGAC
Found at i:157950 original size:24 final size:24
Alignment explanation
Indices: 157909--157965 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
157899 GTAATATGTA
*
157909 AATAA-AATAATAATAATAACGCT
1 AATAATAATAATAATAATAACGAT
157932 AATAATAATAATTAA-AATAACGAT
1 AATAATAATAA-TAATAATAACGAT
157956 AATAATAATA
1 AATAATAATA
157966 TACAAAAAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
23 5 0.16
24 23 0.74
25 3 0.10
ACGTcount: A:0.63, C:0.05, G:0.04, T:0.28
Consensus pattern (24 bp):
AATAATAATAATAATAATAACGAT
Found at i:157965 original size:15 final size:15
Alignment explanation
Indices: 157915--157965 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 15
157905 TGTAAATAAA
157915 ATAATAATAATAACG
1 ATAATAATAATAACG
*
157930 CTAATAATAAT-A--
1 ATAATAATAATAACG
157942 AT--TAA-AATAACG
1 ATAATAATAATAACG
157954 ATAATAATAATA
1 ATAATAATAATA
157966 TACAAAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
9 3 0.11
10 4 0.14
12 3 0.11
14 4 0.14
15 14 0.50
ACGTcount: A:0.61, C:0.06, G:0.04, T:0.29
Consensus pattern (15 bp):
ATAATAATAATAACG
Found at i:159116 original size:6 final size:6
Alignment explanation
Indices: 159105--159130 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
159095 TCGATTGCTG
159105 CATCTT CATCTT CATCTT CATCTT CA
1 CATCTT CATCTT CATCTT CATCTT CA
159131 ATAGGAGTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.35, G:0.00, T:0.46
Consensus pattern (6 bp):
CATCTT
Found at i:161976 original size:14 final size:14
Alignment explanation
Indices: 161957--161992 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
161947 ACAATCAACC
161957 CTTATTGTCATCAA
1 CTTATTGTCATCAA
161971 CTTATTGTCATCAA
1 CTTATTGTCATCAA
*
161985 CTTGTTGT
1 CTTATTGT
161993 ATCCGAGTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.22, C:0.19, G:0.11, T:0.47
Consensus pattern (14 bp):
CTTATTGTCATCAA
Found at i:162225 original size:17 final size:15
Alignment explanation
Indices: 162189--162218 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
162179 GCTTCAGCAG
162189 ATATCCTTGTAATTA
1 ATATCCTTGTAATTA
162204 ATATCCTTGTAATTA
1 ATATCCTTGTAATTA
162219 TAATATCATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.47
Consensus pattern (15 bp):
ATATCCTTGTAATTA
Found at i:168606 original size:16 final size:16
Alignment explanation
Indices: 168585--168616 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
168575 TTTTCACCTA
168585 AAATCAAATCCGACTT
1 AAATCAAATCCGACTT
168601 AAATCAAATCCGACTT
1 AAATCAAATCCGACTT
168617 TTAAAAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.25, G:0.06, T:0.25
Consensus pattern (16 bp):
AAATCAAATCCGACTT
Found at i:172427 original size:121 final size:112
Alignment explanation
Indices: 172213--172777 Score: 555
Period size: 121 Copynumber: 5.0 Consensus size: 112
172203 GTTAGCGGTC
* *
172213 AGTGGTTAGCAGAGTCCGAACCATAATAATGTGGATCATACTCCAGATCTGGTCACCACAAGGTC
1 AGTGGTTA-CAGAGTCCGAACCATAATAATGTGGATCATACCCCGGATCTGGTCACCACAAGGTC
*
172278 GAATCGAATAATT-CAAACAAATTAATAAAATAAAATACAATAAAAAATAAAAAATT
65 GAATAGAA-AATTACAAACAAATTAATAAAAT---A-A-AAT--AAAA-AAAAAATT
* *
172334 AGTGGTTGACAGAGTCTGAACCATAATAATGTGGATCATGCCCCGGATCTGGTCACCACAAGGTC
1 AGTGGTT-ACAGAGTCCGAACCATAATAATGTGGATCATACCCCGGATCTGGTCACCACAAGGTC
* *
172399 GAATCGAACAATT-CAAACAAATTAATAAAATAAAAT---AAAAAAGTT
65 GAATAGAA-AATTACAAACAAATTAATAAAATAAAATAAAAAAAAAATT
* * * * * * *
172444 AGCGGTTAAGAGAGTCCAAATCATAATAATGTGGATCATACCCTGGATCTGATTACCACAAGGTC
1 AGTGGTT-ACAGAGTCCGAACCATAATAATGTGGATCATACCCCGGATCTGGTCACCACAAGGTC
* * *
172509 GAATAGAATATTAGAAAC-AATTAATAAAATAAAAT----AAAAAGTT
65 GAATAGAAAATTACAAACAAATTAATAAAATAAAATAAAAAAAAAATT
* * * * * *
172552 AATGGTTAGCAGAGTCTGAACCATAATAATGTGGATCATATCCCGAATCTGGTCACCACAAAGTT
1 AGTGGTTA-CAGAGTCCGAACCATAATAATGTGGATCATACCCCGGATCTGGTCACCACAAGGTC
* * *
172617 GAATAGAATATTATAAACAAATTAATAAAGTAAAATAAAATAAAAAAAATT
65 GAATAGAAAATTACAAACAAATTAATAAAATAAAAT--AA-AAAAAAAATT
* * * *
172668 AGTGGTTAACAGAGTCCGAACCATAATAATGTGGATCATATCCCAGATCTAGTTACCACAAGGTC
1 AGTGGTT-ACAGAGTCCGAACCATAATAATGTGGATCATACCCCGGATCTGGTCACCACAAGGTC
* * *
172733 GAATA-AAATATTAGAAAC-AATGAAT-AAAT-AAATAAATAAATAAAT
65 GAATAGAAA-ATTACAAACAAATTAATAAAATAAAATAAA-AAAAAAAT
172778 AAATAATAAT
Statistics
Matches: 382, Mismatches: 48, Indels: 38
0.82 0.10 0.08
Matches are distributed among these distances:
107 1 0.00
108 75 0.20
109 36 0.09
110 74 0.19
111 10 0.03
113 4 0.01
114 3 0.01
115 8 0.02
116 78 0.20
117 2 0.01
118 1 0.00
121 89 0.23
122 1 0.00
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.24
Consensus pattern (112 bp):
AGTGGTTACAGAGTCCGAACCATAATAATGTGGATCATACCCCGGATCTGGTCACCACAAGGTCG
AATAGAAAATTACAAACAAATTAATAAAATAAAATAAAAAAAAAATT
Found at i:172480 original size:110 final size:110
Alignment explanation
Indices: 172321--172768 Score: 523
Period size: 108 Copynumber: 4.1 Consensus size: 110
172311 AATACAATAA
* * *
172321 AAAATAAAAAA-TTAGTGGTTGACAGAGTCTGAACCATAATAATGTGGATCATGCCCCGGATCTG
1 AAAATAAAAAAGTTAGTGGTTAACAGAGTCCGAACCATAATAATGTGGATCATACCCCGGATCTG
* *
172385 GTCACCACAAGGTCGAATCGAACAATT-CAAACAAATTAATAAAAT
66 GTCACCACAAGGTCGAATAGAA-TATTACAAACAAATTAATAAAAT
* * * * *
172430 AAAATAAAAAAGTTAGCGGTTAAGAGAGTCCAAATCATAATAATGTGGATCATACCCTGGATCTG
1 AAAATAAAAAAGTTAGTGGTTAACAGAGTCCGAACCATAATAATGTGGATCATACCCCGGATCTG
* * *
172495 ATTACCACAAGGTCGAATAGAATATTAGAAAC-AATTAATAAAAT
66 GTCACCACAAGGTCGAATAGAATATTACAAACAAATTAATAAAAT
* * * * *
172539 AAAAT-AAAAAGTTAATGGTTAGCAGAGTCTGAACCATAATAATGTGGATCATATCCCGAATCTG
1 AAAATAAAAAAGTTAGTGGTTAACAGAGTCCGAACCATAATAATGTGGATCATACCCCGGATCTG
* * *
172603 GTCACCACAAAGTTGAATAGAATATTATAAACAAATTAATAAAGTAAAAT
66 GTCACCACAAGGTCGAATAGAATATTACAAACAAA-T--T-AA-TAAAAT
* * *
172653 AAAATAAAAAAAATTAGTGGTTAACAGAGTCCGAACCATAATAATGTGGATCATATCCCAGATCT
1 AAAAT-AAAAAAGTTAGTGGTTAACAGAGTCCGAACCATAATAATGTGGATCATACCCCGGATCT
* * * * *
172718 AGTTACCACAAGGTCGAATAAAATATTAGAAAC-AATGAAT-AAAT
65 GGTCACCACAAGGTCGAATAGAATATTACAAACAAATTAATAAAAT
172762 -AAATAAA
1 AAAATAAA
172769 TAAATAAATA
Statistics
Matches: 288, Mismatches: 41, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
107 3 0.01
108 80 0.28
109 37 0.13
110 70 0.24
111 2 0.01
112 1 0.00
113 2 0.01
114 12 0.04
115 2 0.01
116 79 0.27
ACGTcount: A:0.46, C:0.14, G:0.16, T:0.24
Consensus pattern (110 bp):
AAAATAAAAAAGTTAGTGGTTAACAGAGTCCGAACCATAATAATGTGGATCATACCCCGGATCTG
GTCACCACAAGGTCGAATAGAATATTACAAACAAATTAATAAAAT
Found at i:172602 original size:108 final size:109
Alignment explanation
Indices: 172321--172773 Score: 485
Period size: 116 Copynumber: 4.1 Consensus size: 109
172311 AATACAATAA
* ** *
172321 AAAATAAAAAATTAGTGGTT-GACAGAGTCTGAACCATAATAATGTGGATCATGCCCCGGATCTG
1 AAAATAAAAAATTAGTGGTTAG-CAGAGTCCGAACCATAATAATGTGGATCATATCCCGAATCTG
* * * *
172385 GTCACCACAAGGTCGAATCGAACAATT-CAAACAAATTAATAAAAT
65 ATCACCACAAGGTCGAATAGAA-TATTAGAAACAAATTAATAAAAT
* * * *
172430 AAAATAAAAAAGTTAGCGGTTAAG-AGAGTCCAAATCATAATAATGTGGATCATA-CCCTGGATC
1 AAAATAAAAAA-TTAGTGGTT-AGCAGAGTCCGAACCATAATAATGTGGATCATATCCC-GAATC
*
172493 TGATTACCACAAGGTCGAATAGAATATTAGAAAC-AATTAATAAAAT
63 TGATCACCACAAGGTCGAATAGAATATTAGAAACAAATTAATAAAAT
* * * *
172539 AAAATAAAAAGTTAATGGTTAGCAGAGTCTGAACCATAATAATGTGGATCATATCCCGAATCTGG
1 AAAATAAAAAATTAGTGGTTAGCAGAGTCCGAACCATAATAATGTGGATCATATCCCGAATCTGA
* * *
172604 TCACCACAAAGTTGAATAGAATATTATAAACAAATTAATAAAGTAAAAT
66 TCACCACAAGGTCGAATAGAATATTAGAAACAAA-T--T-AA-TAAAAT
*
172653 AAAATAAAAAAAATTAGTGGTTAACAGAGTCCGAACCATAATAATGTGGATCATATCCC-AGATC
1 AAAAT--AAAAAATTAGTGGTTAGCAGAGTCCGAACCATAATAATGTGGATCATATCCCGA-ATC
* * *
172717 T-AGTTACCACAAGGTCGAATAAAATATTAGAAAC-AATGAAT-AAAT
63 TGA-TCACCACAAGGTCGAATAGAATATTAGAAACAAATTAATAAAAT
172762 -AAATAAATAAAT
1 AAAATAAA-AAAT
172774 AAATAAATAA
Statistics
Matches: 293, Mismatches: 33, Indels: 38
0.80 0.09 0.10
Matches are distributed among these distances:
106 3 0.01
107 6 0.02
108 71 0.24
109 48 0.16
110 66 0.23
111 2 0.01
112 2 0.01
113 2 0.01
114 12 0.04
115 3 0.01
116 78 0.27
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.25
Consensus pattern (109 bp):
AAAATAAAAAATTAGTGGTTAGCAGAGTCCGAACCATAATAATGTGGATCATATCCCGAATCTGA
TCACCACAAGGTCGAATAGAATATTAGAAACAAATTAATAAAAT
Found at i:172764 original size:4 final size:4
Alignment explanation
Indices: 172755--172783 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
172745 AGAAACAATG
172755 AATA AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA AATA A
172784 TAATGGTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:172764 original size:218 final size:211
Alignment explanation
Indices: 172314--172769 Score: 560
Period size: 224 Copynumber: 2.1 Consensus size: 211
172304 AAAATAAAAT
* * *
172314 ACAATAAAAAATAAAAAATTAGTGGTTGACAGAGTCTGAACCATAATAATGTGGATCATGCCCCG
1 ACAATAATAAATAAAAAATTAATGGTTGACAGAGTCTGAACCATAATAATGTGGATCATACCCCG
* * * *
172379 GATCTGGTCACCACAAGGTCGAATCGAACAATTCAAACAAATTAATAAAATAAAATAAAAAAGTT
66 AATCTGGTCACCACAAAGTCGAATAGAACAATTCAAACAAATTAATAAAATAAAATAAAAAAATT
* * *
172444 AGCGGTTAAGAGAGTCCAAATCATAATAATGTGGATCATACCCTGGATCTGATTACCACAAGGTC
131 AGCGGTTAACAGAGTCCAAACCATAATAATGTGGATCATACCCTAGATCTGATTACCACAAGGTC
*
172509 GAATAGAATATTAGAA
196 GAATAAAATATTAGAA
172525 ACAATTAATAAAATAAAATAAAAAGTTAATGGTT-AGCAGAGTCTGAACCATAATAATGTGGATC
1 ACAA-TAAT-AAAT---A-AAAAA-TTAATGGTTGA-CAGAGTCTGAACCATAATAATGTGGATC
* * * *
172589 ATATCCCGAATCTGGTCACCACAAAGTTGAATAGAA-TATTATAAACAAATTAATAAAGTAAAAT
58 ATACCCCGAATCTGGTCACCACAAAGTCGAATAGAACAATT-CAAACAAA-T--T-AA-TAAAAT
* *
172653 AAAATAAAAAAAATTAGTGGTTAACAGAGTCCGAACCATAATAATGTGGATCATATCCC-AGATC
117 AAAAT-AAAAAAATTAGCGGTTAACAGAGTCCAAACCATAATAATGTGGATCATA-CCCTAGATC
172717 T-AGTTACCACAAGGTCGAATAAAATATTAGAA
180 TGA-TTACCACAAGGTCGAATAAAATATTAGAA
172749 ACAATGAATAAATAAATAAAT
1 ACAAT-AATAAATAAA-AAAT
172770 AAATAAATAA
Statistics
Matches: 209, Mismatches: 17, Indels: 30
0.82 0.07 0.12
Matches are distributed among these distances:
211 4 0.02
212 3 0.01
213 4 0.02
216 1 0.00
217 9 0.04
218 73 0.35
219 4 0.02
220 4 0.02
221 1 0.00
222 2 0.01
223 17 0.08
224 84 0.40
225 3 0.01
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.24
Consensus pattern (211 bp):
ACAATAATAAATAAAAAATTAATGGTTGACAGAGTCTGAACCATAATAATGTGGATCATACCCCG
AATCTGGTCACCACAAAGTCGAATAGAACAATTCAAACAAATTAATAAAATAAAATAAAAAAATT
AGCGGTTAACAGAGTCCAAACCATAATAATGTGGATCATACCCTAGATCTGATTACCACAAGGTC
GAATAAAATATTAGAA
Found at i:173412 original size:20 final size:20
Alignment explanation
Indices: 173387--173425 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
173377 ACACCCTAAA
173387 CGACGACCTCACTCCCCAAC
1 CGACGACCTCACTCCCCAAC
* *
173407 CGACGACCTTACTTCCCAA
1 CGACGACCTCACTCCCCAA
173426 TCATCACCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.49, G:0.10, T:0.15
Consensus pattern (20 bp):
CGACGACCTCACTCCCCAAC
Found at i:174213 original size:139 final size:139
Alignment explanation
Indices: 173959--174602 Score: 878
Period size: 139 Copynumber: 4.6 Consensus size: 139
173949 ATCTGGAGAC
* * ** *
173959 AATTTGGTGACAACACAGTTCCTACGTGATAAGGAAGTCTGATTGTCTGAGGATGACATTGCTCA
1 AATTTGGAGACAACACAGTTCCTACGTGATGAGGAAGTCTGATTGTCTGAGGATGACGCTGCTCC
* * * * * * * *
174024 TTCGCGTTGAGGAGATCTAGTCGGTGAACGACATTGTTCCTTCATGATGAGAATGTCTAGCTGTC
66 TACGCGTTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACGTCTAGCCGTC
174089 TTTAGGGAT
131 TTTAGGGAT
* * *
174098 AATTTGGAGACGACACAGTTCCTACGTGATGAGGAAGTCTGATTGCCTAAGGATGACGCTGCTCC
1 AATTTGGAGACAACACAGTTCCTACGTGATGAGGAAGTCTGATTGTCTGAGGATGACGCTGCTCC
* * *
174163 TACGCGTTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTTATGAGGTCGTCTAGCCATC
66 TACGCGTTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACGTCTAGCCGTC
*
174228 TCTAGGGAT
131 TTTAGGGAT
* * *
174237 AATTTGGAGACAACACGGTTCCTATGTGATGAGGAAGTTTGATTGTCTGAGGATGACGCTGCTCC
1 AATTTGGAGACAACACAGTTCCTACGTGATGAGGAAGTCTGATTGTCTGAGGATGACGCTGCTCC
* *
174302 TACGCGTTGAGGAGATTTGGTCGGTGGACGACATTGTTCCTATGTGATGAGGACGTCTAGCCGTC
66 TACGCGTTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACGTCTAGCCGTC
174367 TTTAGGGAT
131 TTTAGGGAT
* * * * * * * *
174376 GATTTGGTGACAACACAGTTCTTACATGATAAGGAAGTCTAATTGTATGAGGATGA--CTACTCC
1 AATTTGGAGACAACACAGTTCCTACGTGATGAGGAAGTCTGATTGTCTGAGGATGACGCTGCTCC
* * * * *
174439 TACGCGTTAAGGAGATCTGGTCGGTGGAAGACATTTTTCCTACGTGATGAGGACGTCTAGCTGTA
66 TACGCGTTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACGTCTAGCCGTC
174504 TTTAGGGAT
131 TTTAGGGAT
* * * *
174513 AACTTGGAGACAACACGGTTCTTACGTGATGAGGAAGTCTGGTTGTCTGAGGATGACGCTGCTCC
1 AATTTGGAGACAACACAGTTCCTACGTGATGAGGAAGTCTGATTGTCTGAGGATGACGCTGCTCC
* *
174578 TACGTGTTGAGGAGATCTAGTCGGT
66 TACGCGTTGAGGAGATCTGGTCGGT
174603 TGATGATGAT
Statistics
Matches: 440, Mismatches: 63, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
137 120 0.27
139 320 0.73
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (139 bp):
AATTTGGAGACAACACAGTTCCTACGTGATGAGGAAGTCTGATTGTCTGAGGATGACGCTGCTCC
TACGCGTTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACGTCTAGCCGTC
TTTAGGGAT
Found at i:174987 original size:36 final size:36
Alignment explanation
Indices: 174938--175054 Score: 95
Period size: 36 Copynumber: 3.4 Consensus size: 36
174928 TAAAGGCTTA
*
174938 TGTTTCAAAAGAAAATGTCTCAAAAGATACAAAATT
1 TGTTTCAAGAGAAAATGTCTCAAAAGATACAAAATT
* * *
174974 TGTTTCAAGAGAAACA-ATCTC-AAAGGT-----TTT
1 TGTTTCAAGAGAAA-ATGTCTCAAAAGATACAAAATT
* ** *
175004 ATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATT
1 -TGTTTCAAGAGAAAATGTCTCAAAAGATACAAAATT
175041 TGTTTCAAGAGAAA
1 TGTTTCAAGAGAAA
175055 CAATCTCAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 18
0.68 0.12 0.20
Matches are distributed among these distances:
30 2 0.03
31 18 0.30
32 2 0.03
35 5 0.08
36 31 0.51
37 3 0.05
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGAGAAAATGTCTCAAAAGATACAAAATT
Found at i:175138 original size:65 final size:66
Alignment explanation
Indices: 174915--175326 Score: 600
Period size: 67 Copynumber: 6.3 Consensus size: 66
174905 ATTTATTTTG
* * * * ** *
174915 AGAGAAACAATCTTAAAGGCTTATGTTTCAAAAGAAAATGTCTCAAAAGATACAAAATTTGTTTC
1 AGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTC
174980 A
66 A
174981 AGAGAAACAATCTCAAAGGTTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTT
1 AGAGAAACAATCTCAAAGG-TTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTT
175046 CA
65 CA
175048 AGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGAC-AAATTTGTTTC
1 AGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTC
175112 A
66 A
*
175113 AGAGAAACAATATCAAAGGTTTATGTTTCAA-AGGAAACTGTCTCAAGCGAGACAAAACTTTGTT
1 AGAGAAACAATCTCAAAGGTTTATGTTTCAAGA-GAAACTGTCTCAAGCGAGACAAAA-TTTGTT
175177 TCA
64 TCA
* * * * * * *
175180 AGAGAAACGATCTCAAAGATTTATGTTTCCATAGAAACGGTCTCAAGCGATAC--AA-TTGTTTA
1 AGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTC
175242 A
66 A
175243 AGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTT
1 AGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTG-TTT
*
175308 TA
65 CA
*
175310 AGAAAAACAATCTCAAA
1 AGAGAAACAATCTCAAA
175327 TGCTATCAAT
Statistics
Matches: 314, Mismatches: 23, Indels: 17
0.89 0.06 0.05
Matches are distributed among these distances:
63 54 0.17
64 1 0.00
65 66 0.21
66 58 0.18
67 134 0.43
68 1 0.00
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.28
Consensus pattern (66 bp):
AGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTC
A
Found at i:175184 original size:132 final size:131
Alignment explanation
Indices: 174915--175326 Score: 614
Period size: 132 Copynumber: 3.1 Consensus size: 131
174905 ATTTATTTTG
* * * **
174915 AGAGAAACAATCTTAAAGGCTTATGTTTCAAAAGAAAATGTCTCAAAAGATACAAAATTTGTTTC
1 AGAGAAACAATCTCAAAGGTTTATGTTTCAAAAGAAACTGTCTCAAGCGATAC-AAATTTGTTTC
174980 AAGAGAAACAATCTCAAAGGTTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTT
65 AAGAGAAACAATCTCAAAGG-TTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTT
175045 TCA
129 TCA
* *
175048 AGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAATTTGTTTCA
1 AGAGAAACAATCTCAAAGGTTTATGTTTCAAAAGAAACTGTCTCAAGCGATACAAATTTGTTTCA
*
175113 AGAGAAACAATATCAAAGGTTTATGTTTCAA-AGGAAACTGTCTCAAGCGAGACAAAACTTTGTT
66 AGAGAAACAATCTCAAAGGTTTATGTTTCAAGA-GAAACTGTCTCAAGCGAGACAAAA-TTTGTT
175177 TCA
129 TCA
* * * * * *
175180 AGAGAAACGATCTCAAAGATTTATGTTTCCATAGAAACGGTCTCAAGCGATAC-AA-TTGTTTAA
1 AGAGAAACAATCTCAAAGGTTTATGTTTCAAAAGAAACTGTCTCAAGCGATACAAATTTGTTTCA
175243 AGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTT
66 AGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTG-TTT
*
175308 TA
130 CA
*
175310 AGAAAAACAATCTCAAA
1 AGAGAAACAATCTCAAA
175327 TGCTATCAAT
Statistics
Matches: 256, Mismatches: 19, Indels: 11
0.90 0.07 0.04
Matches are distributed among these distances:
129 4 0.02
130 81 0.32
131 39 0.15
132 86 0.34
133 46 0.18
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.28
Consensus pattern (131 bp):
AGAGAAACAATCTCAAAGGTTTATGTTTCAAAAGAAACTGTCTCAAGCGATACAAATTTGTTTCA
AGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTC
A
Found at i:175287 original size:30 final size:29
Alignment explanation
Indices: 175173--175288 Score: 90
Period size: 30 Copynumber: 3.8 Consensus size: 29
175163 GACAAAACTT
*
175173 TGTTTCAAGAGAAACGATCTCAAAGATTTA
1 TGTTTCAAGAGAAACG-TCTCAAAGGTTTA
* * **
175203 TGTTTCCATAGAAACGGTCTC-AAGCGATACAA
1 TGTTTCAAGAGAAAC-GTCTCAAAG-G-T-TTA
* *
175235 TTGTTTAAAGAGAAACAATCTCAAAGGTTTA
1 -TGTTTCAAGAGAAAC-GTCTCAAAGGTTTA
175266 TGTTTCAAGAGAAACTGTCTCAA
1 TGTTTCAAGAGAAAC-GTCTCAA
175289 GCGAGACAAA
Statistics
Matches: 65, Mismatches: 15, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
29 3 0.05
30 37 0.57
31 3 0.05
32 2 0.03
33 17 0.26
34 3 0.05
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (29 bp):
TGTTTCAAGAGAAACGTCTCAAAGGTTTA
Done.