Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007957.1 Hibiscus syriacus cultivar Beakdansim tig00110384_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: 8646418
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 43
Found at i:2190513 original size:19 final size:19
Alignment explanation
Indices: 2190477--2190513 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2190467 TGAAAATGAT
*
2190477 TTGATTTTGAAAGCCAAAG
1 TTGATTTTGAAAACCAAAG
*
2190496 TTGATTTTGAAAATCAAA
1 TTGATTTTGAAAACCAAA
2190514 ATGAAATTTT
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:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (19 bp):
TTGATTTTGAAAACCAAAG
Found at i:2193464 original size:23 final size:22
Alignment explanation
Indices: 2193421--2193474 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
2193411 TATATATTAT
* *
2193421 ATATATATATATGGTTTTGAAA
1 ATATATATACATAGTTTTGAAA
*
2193443 ATATATATAGCATAGTTTTGAAT
1 ATATATATA-CATAGTTTTGAAA
2193466 ATATATATA
1 ATATATATA
2193475 TATATATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 9 0.32
23 19 0.68
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.44
Consensus pattern (22 bp):
ATATATATACATAGTTTTGAAA
Found at i:2193469 original size:2 final size:2
Alignment explanation
Indices: 2193464--2193519 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
2193454 ATAGTTTTGA
2193464 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
2193506 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
2193520 GTTATGTATT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2196978 original size:16 final size:15
Alignment explanation
Indices: 2196959--2196997 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
2196949 GAACTAATAT
2196959 TAAAAAAAAGAAGAAA
1 TAAAAAAAAGAA-AAA
*
2196975 TAAAACAAAGAAAAA
1 TAAAAAAAAGAAAAA
*
2196990 CAAAAAAA
1 TAAAAAAA
2196998 CACTCATGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.82, C:0.05, G:0.08, T:0.05
Consensus pattern (15 bp):
TAAAAAAAAGAAAAA
Found at i:2200965 original size:60 final size:59
Alignment explanation
Indices: 2200901--2201028 Score: 150
Period size: 60 Copynumber: 2.2 Consensus size: 59
2200891 TTTGGGTACA
* ** * *
2200901 TTATACAATTATTCTTCGATTATA-AGATATTATTTTATTAAATTCTTAAATTATTAAAAT
1 TTATAAAATTATAATTCGACTATAGA-ATATTATTTTATTAAATT-TTAAATTATTAAAAG
* * **
2200961 TTATAAAATTATAATTGGACTATAGAATATTATTTTATTAAGTTTTCGATTATTAAAAG
1 TTATAAAATTATAATTCGACTATAGAATATTATTTTATTAAATTTTAAATTATTAAAAG
2201020 TTATAAAAT
1 TTATAAAAT
2201029 AATTGTTCAA
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
59 21 0.36
60 36 0.62
61 1 0.02
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.48
Consensus pattern (59 bp):
TTATAAAATTATAATTCGACTATAGAATATTATTTTATTAAATTTTAAATTATTAAAAG
Found at i:2208642 original size:36 final size:36
Alignment explanation
Indices: 2208553--2208694 Score: 223
Period size: 36 Copynumber: 3.9 Consensus size: 36
2208543 TTCTCAAGTT
2208553 AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGC-
1 AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGCA
*
2208588 AATCAAGCATTCACAAAAGAGTAGTGAAGCAATGCA
1 AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGCA
* *
2208624 AATCAAGCCTTCATAAAAGATTAGTGAAGCAATGCA
1 AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGCA
2208660 AATCAAGCCTTCACGAAAAAAGAGTAGTGAAGCAA
1 AATCAAGCCTTCAC---AAAAGAGTAGTGAAGCAA
2208695 GATCATATCA
Statistics
Matches: 97, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
35 34 0.35
36 46 0.47
39 17 0.18
ACGTcount: A:0.46, C:0.18, G:0.19, T:0.18
Consensus pattern (36 bp):
AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGCA
Found at i:2208888 original size:20 final size:20
Alignment explanation
Indices: 2208863--2208902 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2208853 CCGAGTGATG
*
2208863 TTTATACGCTTATTATTATA
1 TTTATACGATTATTATTATA
**
2208883 TTTATATTATTATTATTATA
1 TTTATACGATTATTATTATA
2208903 GATGTAATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.60
Consensus pattern (20 bp):
TTTATACGATTATTATTATA
Found at i:2210218 original size:39 final size:39
Alignment explanation
Indices: 2210175--2210313 Score: 116
Period size: 39 Copynumber: 3.3 Consensus size: 39
2210165 TTATCTTAAT
2210175 TAATATTAATGTTTTTATATTTTAAACCATTAATTATTA
1 TAATATTAATGTTTTTATATTTTAAACCATTAATTATTA
** * * * *
2210214 TAATATTAATCATATTACTAGTATTTATATCTTATATCATGATTAGTAATT
1 TAATATTAATGTTTTTA-TA-T-TTTA-AAC-CAT-T-A--ATTA-T--TA
2210265 TAATATTAATGTTTTTATATTTTAAACCATTAATTATTA
1 TAATATTAATGTTTTTATATTTTAAACCATTAATTATTA
2210304 TAATATTAAT
1 TAATATTAAT
2210314 CATATTACAG
Statistics
Matches: 76, Mismatches: 12, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
39 25 0.33
40 2 0.03
41 2 0.03
42 8 0.11
43 2 0.03
44 3 0.04
45 2 0.03
46 3 0.04
47 2 0.03
48 8 0.11
49 2 0.03
50 2 0.03
51 15 0.20
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.52
Consensus pattern (39 bp):
TAATATTAATGTTTTTATATTTTAAACCATTAATTATTA
Found at i:2210270 original size:90 final size:90
Alignment explanation
Indices: 2210174--2210362 Score: 353
Period size: 90 Copynumber: 2.1 Consensus size: 90
2210164 ATTATCTTAA
2210174 TTAATATTAATGTTTTTATATTTTAAACCATTAATTATTATAATATTAATCATATTACTA-GTAT
1 TTAATATTAATGTTTTTATATTTTAAACCATTAATTATTATAATATTAATCATATTAC-AGGTAT
2210238 TTATATCTTATATCATGATTAGTAAT
65 TTATATCTTATATCATGATTAGTAAT
2210264 TTAATATTAATGTTTTTATATTTTAAACCATTAATTATTATAATATTAATCATATTACAGGTATT
1 TTAATATTAATGTTTTTATATTTTAAACCATTAATTATTATAATATTAATCATATTACAGGTATT
2210329 TATATCTTATATCATGATTAGTAAT
66 TATATCTTATATCATGATTAGTAAT
2210354 TTACATATT
1 TTA-ATATT
2210363 TTATAACTTT
Statistics
Matches: 97, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
89 1 0.01
90 91 0.94
91 5 0.05
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.51
Consensus pattern (90 bp):
TTAATATTAATGTTTTTATATTTTAAACCATTAATTATTATAATATTAATCATATTACAGGTATT
TATATCTTATATCATGATTAGTAAT
Found at i:2213272 original size:19 final size:20
Alignment explanation
Indices: 2213236--2213283 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
2213226 AAATAAAAAT
2213236 TTTGAAAAAGAAATTTTTGA
1 TTTGAAAAAGAAATTTTTGA
2213256 TTTGAAAAAGAAATTTTTGA
1 TTTGAAAAAGAAATTTTTGA
2213276 TTTGAAAA
1 TTTGAAAA
2213284 TTAAGCTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.40
Consensus pattern (20 bp):
TTTGAAAAAGAAATTTTTGA
Found at i:2217681 original size:22 final size:22
Alignment explanation
Indices: 2217648--2217706 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
2217638 AAGATTCAAG
*
2217648 AAAAAAATAAAAGATATAATAT
1 AAAAAAAGAAAAGATATAATAT
* *
2217670 ATAAAAAGAAAATATATAATAT
1 AAAAAAAGAAAAGATATAATAT
2217692 AAAAAAAGAAGAAGA
1 AAAAAAAGAA-AAGA
2217707 GAACTAATAG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
22 28 0.90
23 3 0.10
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (22 bp):
AAAAAAAGAAAAGATATAATAT
Found at i:2218105 original size:24 final size:23
Alignment explanation
Indices: 2218078--2218122 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
2218068 AAACTACATT
*
2218078 TTTAATATTTAAATTATTATTTGA
1 TTTAATATGTAAATT-TTATTTGA
2218102 TTTAATATGTAAATTTTATTT
1 TTTAATATGTAAATTTTATTT
2218123 TTCAAAATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (23 bp):
TTTAATATGTAAATTTTATTTGA
Found at i:2218924 original size:19 final size:20
Alignment explanation
Indices: 2218890--2218927 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2218880 AATTTTGAAG
*
2218890 TTCTTCTATATTTTATATTT
1 TTCTTCTATATCTTATATTT
2218910 TTCTT-TATATCTTATATT
1 TTCTTCTATATCTTATATT
2218928 GATGATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.21, C:0.11, G:0.00, T:0.68
Consensus pattern (20 bp):
TTCTTCTATATCTTATATTT
Found at i:2218947 original size:20 final size:20
Alignment explanation
Indices: 2218924--2218983 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 20
2218914 TTATATCTTA
2218924 TATTGATGATTTATTTTTAT
1 TATTGATGATTTATTTTTAT
**
2218944 TATT-A--A-AAATTTTTAT
1 TATTGATGATTTATTTTTAT
*
2218960 AATTGATGATTTATTTTTAT
1 TATTGATGATTTATTTTTAT
2218980 TATT
1 TATT
2218984 AAATTTTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
16 11 0.37
17 2 0.07
19 2 0.07
20 15 0.50
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.62
Consensus pattern (20 bp):
TATTGATGATTTATTTTTAT
Found at i:2218966 original size:36 final size:36
Alignment explanation
Indices: 2218921--2218999 Score: 133
Period size: 36 Copynumber: 2.2 Consensus size: 36
2218911 TCTTTATATC
2218921 TTAT-ATTGATGATTTATTTTTATTATTAAAAATTT
1 TTATAATTGATGATTTATTTTTATTATTAAAAATTT
**
2218956 TTATAATTGATGATTTATTTTTATTATTAAATTTTT
1 TTATAATTGATGATTTATTTTTATTATTAAAAATTT
2218992 TTATAATT
1 TTATAATT
2219000 TTTCTTTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 4 0.10
36 37 0.90
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (36 bp):
TTATAATTGATGATTTATTTTTATTATTAAAAATTT
Found at i:2227156 original size:17 final size:17
Alignment explanation
Indices: 2227134--2227166 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2227124 CTAAGCCTTT
*
2227134 ATTATTGCATGTACATC
1 ATTATTGCATGCACATC
2227151 ATTATTGCATGCACAT
1 ATTATTGCATGCACAT
2227167 ACTCTAGAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (17 bp):
ATTATTGCATGCACATC
Found at i:2236639 original size:204 final size:201
Alignment explanation
Indices: 2236084--2236771 Score: 825
Period size: 201 Copynumber: 3.4 Consensus size: 201
2236074 TTAACCCTAT
2236084 TTACAATGTCTCATATGTGCTGATATTAC-CATCAACTGAAAGATAAGTTGCAATACTATG-CTT
1 TTACAATGTCTCATATGTGCTGATATTACAC-TCAACTGAAAGATAAGTTGCAATACTATGAC-T
* * * *
2236147 CTAAGCTTA-AAACTACAAAAA-AAATCCAATTAACTTCCCATAAATACACCACTAACATGCCTA
64 CTAAGCTTATAAACTACAAAAATAAAT-CAATTAACTTCCCAGAAATACCCCTCGAACATGCCTA
* * * * * *
2236210 TCAAGCCATTTTAGGTTATTCTTCATGTACAACACCAAGCTTTCGAACCATTTTTAACGCAATTT
128 TCAAGCCATTTTAGCTTGTTTTTCATGCACAAAACCAAGCTTTCGAACCATTTTCAACGCAATTT
*
2236275 TTATCCCGC
193 TTACCCCGC
* * * *
2236284 TTAAAATGTTTCATATGTGTTGATATTACACTCAACTGAAAGATAAGTTGCAGTACTACT-ACTC
1 TTACAATGTCTCATATGTGCTGATATTACACTCAACTGAAAGATAAGTTGCAATACTA-TGACTC
* * * *** ** *
2236348 TAAGCTTAAAAATTACAAAACTTTTTCAATTAACTTCTTAGAAATACCCCTCGAATATGCCTATC
65 TAAGCTTATAAACTACAAAAATAAATCAATTAACTTCCCAGAAATACCCCTCGAACATGCCTATC
* * *
2236413 AAGCCAATTTAGCTTGTTTTTCATGCACAAAACAAAGCTTTCTAACCATTTTCAACGCAATTTTT
130 AAGCCATTTTAGCTTGTTTTTCATGCACAAAACCAAGCTTTCGAACCATTTTCAACGCAATTTTT
*
2236478 ACCCCTC
195 ACCCCGC
* * * *
2236485 TTACAATGTTTCGTATGTGTTGATATTAC-CTTCAAATTGAAAGATAAGTTGCAATACTATAGAC
1 TTACAATGTCTCATATGTGCTGATATTACAC-TC-AACTGAAAGATAAGTTGCAATACTAT-GAC
* *
2236549 -CTAACCTTATAAACTACAAAAAATAAATCTGATTAACTTCCC-GAAAATACCCCTCGAACATGC
63 TCTAAGCTTATAAACTAC-AAAAATAAATC-AATTAACTTCCCAG-AAATACCCCTCGAACATGC
* * *
2236612 CTATCAAGCCATTTTAGCTTGTTTTTCATACACAAAACCAAGCTTTCGAACCATTTTCAATGCGA
125 CTATCAAGCCATTTTAGCTTGTTTTTCATGCACAAAACCAAGCTTTCGAACCATTTTCAACGCAA
**
2236677 TTTTTACTTCGC
190 TTTTTACCCCGC
** * *
2236689 TTACAATGTCTCATATGTGCTGATATTACACTCAGTTGAAAGATAAGTTGCAATACCATGCCTCT
1 TTACAATGTCTCATATGTGCTGATATTACACTCAACTGAAAGATAAGTTGCAATACTATGACTCT
* *
2236754 AATCTTATAAATTACAAA
66 AAGCTTATAAACTACAAA
2236772 TATTTTCCAA
Statistics
Matches: 415, Mismatches: 59, Indels: 26
0.83 0.12 0.05
Matches are distributed among these distances:
200 63 0.15
201 136 0.33
202 43 0.10
203 49 0.12
204 123 0.30
205 1 0.00
ACGTcount: A:0.35, C:0.22, G:0.10, T:0.33
Consensus pattern (201 bp):
TTACAATGTCTCATATGTGCTGATATTACACTCAACTGAAAGATAAGTTGCAATACTATGACTCT
AAGCTTATAAACTACAAAAATAAATCAATTAACTTCCCAGAAATACCCCTCGAACATGCCTATCA
AGCCATTTTAGCTTGTTTTTCATGCACAAAACCAAGCTTTCGAACCATTTTCAACGCAATTTTTA
CCCCGC
Found at i:2238018 original size:18 final size:18
Alignment explanation
Indices: 2237995--2238029 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2237985 TTTAAGGGAC
*
2237995 AATTTAATAAAAAAATAT
1 AATTTAAGAAAAAAATAT
*
2238013 AATTTAAGAAATAAATA
1 AATTTAAGAAAAAAATA
2238030 AATAAACACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (18 bp):
AATTTAAGAAAAAAATAT
Found at i:2239336 original size:10 final size:10
Alignment explanation
Indices: 2239321--2239349 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
2239311 CTAAAAATGC
2239321 TCTCTCTCTA
1 TCTCTCTCTA
2239331 TCTCTCTCTA
1 TCTCTCTCTA
2239341 TCTCTCTCT
1 TCTCTCTCT
2239350 TATTTAGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.07, C:0.41, G:0.00, T:0.52
Consensus pattern (10 bp):
TCTCTCTCTA
Found at i:2242236 original size:18 final size:18
Alignment explanation
Indices: 2242210--2242255 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
2242200 CTACAAGTGC
*
2242210 TTTAGGTCCCCTTTGTCA
1 TTTATGTCCCCTTTGTCA
*
2242228 TTTATGTCCCCTTTTTCA
1 TTTATGTCCCCTTTGTCA
2242246 TTTATGTCCC
1 TTTATGTCCC
2242256 TTACGAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.11, C:0.28, G:0.11, T:0.50
Consensus pattern (18 bp):
TTTATGTCCCCTTTGTCA
Found at i:2248788 original size:96 final size:97
Alignment explanation
Indices: 2248628--2248824 Score: 297
Period size: 96 Copynumber: 2.0 Consensus size: 97
2248618 ATCATTGATT
* * *
2248628 TACTGGTTTTATGAATTATGGTTAACTGAAATATGTTATTTGGTTTCCTGTTTTCACTGGAAAAT
1 TACTGGTTTTATGAACTATGGTTAACTGAAATATGTTATCTGGTTTCCTATTTTCACTGGAAAAT
* *
2248693 ATGATTGTTCCTGATTTATGGATCATGGAATC
66 ATGATTATTCCTGATTTATGGATCATGGAATA
* * * *
2248725 TACTGG-TTTATGAACTATGGTTACCTGAAATGTGTTATCTGGTTTCCTATTTTTACTGTAAAAT
1 TACTGGTTTTATGAACTATGGTTAACTGAAATATGTTATCTGGTTTCCTATTTTCACTGGAAAAT
*
2248789 ATGATTATTCCTGATTTATGGATCTTGGAATA
66 ATGATTATTCCTGATTTATGGATCATGGAATA
2248821 TACT
1 TACT
2248825 AGTTACTACT
Statistics
Matches: 90, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
96 84 0.93
97 6 0.07
ACGTcount: A:0.26, C:0.11, G:0.18, T:0.45
Consensus pattern (97 bp):
TACTGGTTTTATGAACTATGGTTAACTGAAATATGTTATCTGGTTTCCTATTTTCACTGGAAAAT
ATGATTATTCCTGATTTATGGATCATGGAATA
Found at i:2251295 original size:20 final size:20
Alignment explanation
Indices: 2251270--2251307 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2251260 TTTCACCCTA
2251270 GTTCATCCAATATCGATATT
1 GTTCATCCAATATCGATATT
* *
2251290 GTTCATCTAGTATCGATA
1 GTTCATCCAATATCGATA
2251308 CTCGAACTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.39
Consensus pattern (20 bp):
GTTCATCCAATATCGATATT
Found at i:2251815 original size:14 final size:11
Alignment explanation
Indices: 2251771--2251806 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
2251761 ATGGTATTTG
*
2251771 GAGAAGAAATGT
1 GAGAAGAAA-AT
2251783 GAGAAGAAAAT
1 GAGAAGAAAAT
2251794 GAGAAGAAAAT
1 GAGAAGAAAAT
2251805 GA
1 GA
2251807 AGAGCAGAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.58, C:0.00, G:0.31, T:0.11
Consensus pattern (11 bp):
GAGAAGAAAAT
Found at i:2254436 original size:3 final size:3
Alignment explanation
Indices: 2254376--2254425 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
2254366 CGGTAACTAT
2254376 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2254424 TT
1 TT
2254426 CTCATATTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2255310 original size:2 final size:2
Alignment explanation
Indices: 2255303--2255379 Score: 92
Period size: 2 Copynumber: 40.5 Consensus size: 2
2255293 ATATTCAAAT
*
2255303 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2255344 TA -A TA TA -A T- TA -A TGA TA AA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA T
2255380 TATGTATTAT
Statistics
Matches: 66, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
1 5 0.08
2 59 0.89
3 2 0.03
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2265830 original size:24 final size:24
Alignment explanation
Indices: 2265803--2265850 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2265793 GGCTCGATTT
2265803 TCTTCCAACAATCAGACCTTTTAA
1 TCTTCCAACAATCAGACCTTTTAA
2265827 TCTTCCAACAATCAGACCTTTTAA
1 TCTTCCAACAATCAGACCTTTTAA
2265851 ATTCCAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.33
Consensus pattern (24 bp):
TCTTCCAACAATCAGACCTTTTAA
Found at i:2266219 original size:24 final size:26
Alignment explanation
Indices: 2266192--2266250 Score: 68
Period size: 29 Copynumber: 2.2 Consensus size: 26
2266182 TCCTACATGG
*
2266192 TTAATTT-A-CTTCACTGTAATTTGT
1 TTAATTTCATCTTCAATGTAATTTGT
2266216 TTAATTGCTTCATCTTCAATGTAATTTGT
1 TTAA-T--TTCATCTTCAATGTAATTTGT
2266245 TTAATT
1 TTAATT
2266251 GTTTATATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
24 4 0.14
25 1 0.03
26 1 0.03
27 2 0.07
28 2 0.07
29 19 0.66
ACGTcount: A:0.25, C:0.12, G:0.08, T:0.54
Consensus pattern (26 bp):
TTAATTTCATCTTCAATGTAATTTGT
Found at i:2266361 original size:28 final size:29
Alignment explanation
Indices: 2266320--2266374 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
2266310 TCCGCTTCAC
*
2266320 TGTTAAGGTGATCTGCTT-ATTGTTATTT
1 TGTTAAGGTAATCTGCTTAATTGTTATTT
*
2266348 TGTTAAGGTAATCTGTTTAATTGTTAT
1 TGTTAAGGTAATCTGCTTAATTGTTAT
2266375 CTATAATATG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.22, C:0.05, G:0.20, T:0.53
Consensus pattern (29 bp):
TGTTAAGGTAATCTGCTTAATTGTTATTT
Found at i:2266413 original size:22 final size:20
Alignment explanation
Indices: 2266347--2266408 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 20
2266337 TATTGTTATT
2266347 TTGTTAAGGTAATCTGTTTAA
1 TTGTT-AGGTAATCTGTTTAA
** *
2266368 TTGTTATCTATAATATGTTTAA
1 TTGTTA--GGTAATCTGTTTAA
2266390 TTGTTAGGTAATCTGTTTA
1 TTGTTAGGTAATCTGTTTA
2266409 GAATTTAGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
20 11 0.33
21 5 0.15
22 17 0.52
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (20 bp):
TTGTTAGGTAATCTGTTTAA
Found at i:2268386 original size:23 final size:23
Alignment explanation
Indices: 2268339--2268386 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
2268329 ACTAACATAT
* **
2268339 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAACGCTTATATAATAAAA
2268362 TAGGTAACGCTTATATAATAAAA
1 TAGGTAACGCTTATATAATAAAA
2268385 TA
1 TA
2268387 TGTATTTAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (23 bp):
TAGGTAACGCTTATATAATAAAA
Found at i:2272950 original size:201 final size:198
Alignment explanation
Indices: 2272458--2274270 Score: 1052
Period size: 200 Copynumber: 9.1 Consensus size: 198
2272448 GCGTAATTTT
* * * * * * * *
2272458 AAAAAGTGTCAACACTAATTTAAAAAGTGTCGACACATTATGTTGACCTATTTTCT-ATTTACAC
1 AAAAAGTATCGACAC-AAATTATAAAGTGTCGATACATTATGTAGACCTATTTTCTCA-TAAAAC
* * *
2272522 CGGTAAATTTCAACCGGTTACATTGTAAATTGACCTATTACATTATAATT-TCCGGTCTTGATGT
64 CGGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTAT-CGGTCTCGATGT
* * * * * * *
2272586 ATTTGGGGTCGATACTTTTTATAAATGTATCGAAACTTTATGCGTGGACATCGGTTGGCATTCAT
128 ATTTGGGATCGACAC-TTTTATAAATGTATCGACACTTTATGCGTGCACATAGTTTGGAATTCAT
2272651 TATGGAC
192 TATGGAC
* * * *
2272658 ATAAAGTATCGACACAAATGTACAAAGTATCGATACATTATGTAGACCTATTTGCTCATAAAACC
1 AAAAAGTATCGACACAAAT-TATAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACC
*
2272723 GGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTTTCGGTCTCGATGTAT
65 GGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTATCGGTCTCGATGTAT
* * *
2272788 TTGGGGTCGATACTTTTAATAAATGTATCGACACTTTAAGCGTGCACATAGTTTGTGAATTCATT
130 TTGGGATCGACACTTTT-ATAAATGTATCGACACTTTATGCGTGCACATAGTTTG-GAATTCATT
* *
2272853 ATAGAT
193 ATGGAC
* * *
2272859 AAAAAGTATCGACACAAATAAATAAAGTGTCGATACATTATTTAGACTTATTTTCTCATAAAACC
1 AAAAAGTATCGACACAAAT-TATAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACC
* *
2272924 GGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTATAGGTTTCGATGTAT
65 GGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTATCGGTCTCGATGTAT
* ** * * *
2272989 TTGGGATCGACACATGTTATAAATGTATCGACACTTT-TTTGTGCACTTGGTTTGGAAAATACAT
130 TTGGGATCGACAC-TTTTATAAATGTATCGACACTTTATGCGTGCACATAGTTTGG--AATTCAT
*
2273053 TCTGGAC
192 TATGGAC
** * ** * * * *
2273060 AAAAAGTATCGACACTTATTGTATTTGTGTCGATACTTTATGTATACATGTTTTCTCAT-AAACC
1 AAAAAGTATCGACACAAATTATA-AAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACC
* * * * * ** * * * *
2273124 AGTATATTTAGACCGCTTACATTGTTATTTTACCTATTACATTATAATTATGGGTTTCGATGTTT
65 GGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTATCGGTCTCGATGTAT
*** * * ** * *
2273189 TTGGGATCGACACTTGTTATAAATGTATCGACACTTT-TTTATGCACTTGGTTTTTAAAATACAC
130 TTGGGATCGACACTT-TTATAAATGTATCGACACTTTATGCGTGCACATAG--TTTGGAATTCAT
*
2273253 TCTGGAC
192 TATGGAC
* *** ** ** * *
2273260 AAAAAGTATCAACACTTGTTGGAT-TTGTGTCGATA-ATTTATGTATTCATGTTTTCTCAT-AAA
1 AAAAAGTATCGACACAAATT--ATAAAGTGTCGATACA-TTATGTAGACCTATTTTCTCATAAAA
** * * * * ** * * * * *
2273322 TTGGTATATTTAGACCAGTTACATTGTTATTTTACGTATTATATTATAATTATGGGTTTCGATGT
63 CCGGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTATCGGTCTCGATGT
* * * * * ** *
2273387 -TTTGGGATCGACACTTGTTATAAATGTATCGACACTTTGT-TGTGCGCTTGGTTTTAAAATACA
128 ATTTGGGATCGACACTT-TTATAAATGTATCGACACTTTATGCGTGCACATAG-TTTGGAATTCA
* *
2273450 CTCTGGAC
191 TTATGGAC
*** * ** * * *
2273458 AAAAAGTATCGACACTTGTGGAT-TTGTGTCGATACTTTATGTATACCTGTTTTCTCAT-AAACC
1 AAAAAGTATCGACACAAAT-TATAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACC
* * * * * ** * * * *
2273521 AGTATATTTAGACCGCTTACATTGTTATTTTACCTATTACATTATAATTATGGGTTTCGATGTTT
65 GGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTATCGGTCTCGATGTAT
* * * * * ** * *
2273586 TTGGGATCGACAATTATTATAAATGTATCGACACTTTGT-TGTGCACTTGGTTTTTAAAATACAC
130 TTGGGATCGACACTT-TTATAAATGTATCGACACTTTATGCGTGCACATAG--TTTGGAATTCAT
*
2273650 TCTGGAC
192 TATGGAC
*** ** * * * *
2273657 AAAAAGTATCGACACTTGTTGGAT-TTGTGTCAATA-ATTTATGTATACATGTTTTCTCAT-AAA
1 AAAAAGTATCGACACAAATT--ATAAAGTGTCGATACA-TTATGTAGACCTATTTTCTCATAAAA
* * * * * ** * * * * *
2273719 TCGGTATATTTAGACCAGTTACATTGTTATTTTACGTATTATATTATAATTATGGGTTTCGATGT
63 CCGGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTATCGGTCTCGATGT
* * * * * * ** *
2273784 TTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTGT-TGTGCGCTTGGTTTTTAAATACA
128 ATTTGGGATCGACACTT-TTATAAATGTATCGACACTTTATGCGTGCACATAG-TTTGGAATTCA
* *
2273848 CTCTGGAC
191 TTATGGAC
*** ** * * * *
2273856 AAAAAGTATCGACACTTGTTGGAT-TTGTGTCGATACTTTATGTATATCTGTTTTCTCA-AAAAC
1 AAAAAGTATCGACACAAATT--ATAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAAC
* * ** * ** * *
2273919 TGGTATATTTAGGCCGGTTACATTGTTATTTTACCTATTACATTAT-ATCTAT-GTGTTTCGATG
64 CGGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAAT-TATCG-GTCTCGATG
* * * * * * * * *
2273982 TTTTTAGTATCGAAACTTGTTATAAATGTATCGACACTTTGT-CGTGCACTTGGTTTAGAAAATA
127 TATTTGGGATCGACACTT-TTATAAATGTATCGACACTTTATGCGTGCACATAGTTT-G-GAATT
*
2274046 CATTTTGGAC
189 CATTATGGAC
* *** ** * * * * *
2274056 AAAAACTATCGACACTTGTTGGAT-TTGTGTCAATACTTTATGTATACATGTTTTCTCA-AAAAC
1 AAAAAGTATCGACACAAATT--ATAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAAC
* * ** * ** * *
2274119 TGGTATATTTAGGCCGGTTACATTGTTATTTTACCTATTACATTAT-ATCTAT-GTGTTTCGATG
64 CGGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAAT-TATCG-GTCTCGATG
* * * * * * *
2274182 TTTTTAGTATCGACACTTATTATAAATGTATCGACACCTTT-TTCGTGCACTTGGTTTGGAAATA
127 TATTTGGGATCGACACTT-TTATAAATGTATCGACA-CTTTATGCGTGCACATAGTTTGG-AATT
2274246 CATTATGGAC
189 CATTATGGAC
* *
2274256 AACATGTATCGACAC
1 AAAAAGTATCGACAC
2274271 GAATGAATAA
Statistics
Matches: 1438, Mismatches: 143, Indels: 64
0.87 0.09 0.04
Matches are distributed among these distances:
197 94 0.07
198 92 0.06
199 271 0.19
200 738 0.51
201 236 0.16
202 7 0.00
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.40
Consensus pattern (198 bp):
AAAAAGTATCGACACAAATTATAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCG
GTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTATCGGTCTCGATGTATT
TGGGATCGACACTTTTATAAATGTATCGACACTTTATGCGTGCACATAGTTTGGAATTCATTATG
GAC
Found at i:2273209 original size:200 final size:200
Alignment explanation
Indices: 2272687--2274270 Score: 2008
Period size: 200 Copynumber: 7.9 Consensus size: 200
2272677 GTACAAAGTA
* * * * * * * * **
2272687 TCGATACATTATGTAGACCTATTTGCTCATAAAACCGGTAAATTTAAACCGGTTACATTGTAAAG
1 TCGATACTTTATGTATACATGTTTTCTCAT-AAACCGGTATATTTAGACCGGTTACATTGTTATT
* * * * * * *
2272752 TGACCTATTACATTATAATTTTCGGTCTCGATGTATTTGGGGTCGATACTT-TTAATAAATGTAT
65 TTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTT-ATAAATGTAT
* * * * * * * ***
2272816 CGACACTTTAAG-CGTGCACATAGTTTGTG--AATTCATTATAGATAAAAAGTATCGACAC-AAA
129 CGACACTTT--GTTGTGCACTTGGTTTG-GAAAATACATTCTGGACAAAAAGTATCGACACTTGT
** **
2272877 TAAATAAAGTG
191 TGGAT-TTGTG
* * * * * * * * **
2272888 TCGATACATTATTTAGACTTATTTTCTCATAAAACCGGTAAATTTAAACCGGTTACATTGTAAAG
1 TCGATACTTTATGTATACATGTTTTCTCAT-AAACCGGTATATTTAGACCGGTTACATTGTTATT
* * * *
2272953 TGACCTATTACATTATAATTATAGGTTTCGATGTATTTGGGATCGACACATGTTATAAATGTATC
65 TTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATC
* * *
2273018 GACACTTTTTTGTGCACTTGGTTTGGAAAATACATTCTGGACAAAAAGTATCGACACTTATTGTA
130 GACACTTTGTTGTGCACTTGGTTTGGAAAATACATTCTGGACAAAAAGTATCGACACTTGTTGGA
2273083 TTTGTG
195 TTTGTG
* *
2273089 TCGATACTTTATGTATACATGTTTTCTCATAAACCAGTATATTTAGACCGCTTACATTGTTATTT
1 TCGATACTTTATGTATACATGTTTTCTCATAAACCGGTATATTTAGACCGGTTACATTGTTATTT
2273154 TACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCG
66 TACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCG
* * ** * *
2273219 ACACTTTTTTATGCACTTGGTTTTTAAAATACACTCTGGACAAAAAGTATCAACACTTGTTGGAT
131 ACACTTTGTTGTGCACTTGGTTTGGAAAATACATTCTGGACAAAAAGTATCGACACTTGTTGGAT
2273284 TTGTG
196 TTGTG
* * ** *
2273289 TCGATAATTTATGTATTCATGTTTTCTCATAAATTGGTATATTTAGACCAGTTACATTGTTATTT
1 TCGATACTTTATGTATACATGTTTTCTCATAAACCGGTATATTTAGACCGGTTACATTGTTATTT
* *
2273354 TACGTATTATATTATAATTATGGGTTTCGATG-TTTTGGGATCGACACTTGTTATAAATGTATCG
66 TACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCG
* * *
2273418 ACACTTTGTTGTGCGCTTGGTTT-TAAAATACACTCTGGACAAAAAGTATCGACACTTG-TGGAT
131 ACACTTTGTTGTGCACTTGGTTTGGAAAATACATTCTGGACAAAAAGTATCGACACTTGTTGGAT
2273481 TTGTG
196 TTGTG
* * *
2273486 TCGATACTTTATGTATACCTGTTTTCTCATAAACCAGTATATTTAGACCGCTTACATTGTTATTT
1 TCGATACTTTATGTATACATGTTTTCTCATAAACCGGTATATTTAGACCGGTTACATTGTTATTT
* *
2273551 TACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACAATTATTATAAATGTATCG
66 TACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCG
** *
2273616 ACACTTTGTTGTGCACTTGGTTTTTAAAATACACTCTGGACAAAAAGTATCGACACTTGTTGGAT
131 ACACTTTGTTGTGCACTTGGTTTGGAAAATACATTCTGGACAAAAAGTATCGACACTTGTTGGAT
2273681 TTGTG
196 TTGTG
* * * *
2273686 TCAATAATTTATGTATACATGTTTTCTCATAAATCGGTATATTTAGACCAGTTACATTGTTATTT
1 TCGATACTTTATGTATACATGTTTTCTCATAAACCGGTATATTTAGACCGGTTACATTGTTATTT
* *
2273751 TACGTATTATATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCG
66 TACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCG
* ** *
2273816 ACACTTTGTTGTGCGCTTGGTTT-TTAAATACACTCTGGACAAAAAGTATCGACACTTGTTGGAT
131 ACACTTTGTTGTGCACTTGGTTTGGAAAATACATTCTGGACAAAAAGTATCGACACTTGTTGGAT
2273880 TTGTG
196 TTGTG
* * *
2273885 TCGATACTTTATGTATATC-TGTTTTCTCAAAAACTGGTATATTTAGGCCGGTTACATTGTTATT
1 TCGATACTTTATGTATA-CATGTTTTCTCATAAACCGGTATATTTAGACCGGTTACATTGTTATT
* * * *
2273949 TTACCTATTACATTAT-ATCTATGTGTTTCGATGTTTTTAGTATCGAAACTTGTTATAAATGTAT
65 TTACCTATTACATTATAAT-TATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTAT
* * * *
2274013 CGACACTTTGTCGTGCACTTGGTTTAGAAAATACATTTTGGACAAAAACTATCGACACTTGTTGG
129 CGACACTTTGTTGTGCACTTGGTTTGGAAAATACATTCTGGACAAAAAGTATCGACACTTGTTGG
2274078 ATTTGTG
194 ATTTGTG
* * * *
2274085 TCAATACTTTATGTATACATGTTTTCTCAAAAACTGGTATATTTAGGCCGGTTACATTGTTATTT
1 TCGATACTTTATGTATACATGTTTTCTCATAAACCGGTATATTTAGACCGGTTACATTGTTATTT
* * * *
2274150 TACCTATTACATTAT-ATCTATGTGTTTCGATGTTTTTAGTATCGACACTTATTATAAATGTATC
66 TACCTATTACATTATAAT-TATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATC
* * *
2274214 GACACCTTT-TTCGTGCACTTGGTTTGG-AAATACATTATGGACAACATGTATCGACAC
130 GACA-CTTTGTT-GTGCACTTGGTTTGGAAAATACATTCTGGACAAAAAGTATCGACAC
2274271 GAATGAATAA
Statistics
Matches: 1255, Mismatches: 114, Indels: 29
0.90 0.08 0.02
Matches are distributed among these distances:
197 97 0.08
198 88 0.07
199 267 0.21
200 600 0.48
201 197 0.16
202 6 0.00
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (200 bp):
TCGATACTTTATGTATACATGTTTTCTCATAAACCGGTATATTTAGACCGGTTACATTGTTATTT
TACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCG
ACACTTTGTTGTGCACTTGGTTTGGAAAATACATTCTGGACAAAAAGTATCGACACTTGTTGGAT
TTGTG
Found at i:2273554 original size:397 final size:398
Alignment explanation
Indices: 2272958--2274270 Score: 2049
Period size: 399 Copynumber: 3.3 Consensus size: 398
2272948 TAAAGTGACC
* * *
2272958 TATTACATTATAATTATAGGTTTCGATGTATTTGGGATCGACACATGTTATAAATGTATCGACAC
1 TATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACAC
* * * *
2273023 TTTTTTGTGCACTTGGTTTGGAAAATACATTCTGGACAAAAAGTATCGACACTTATTGTATTTGT
66 TTTGTTGTGCACTTGGTTT-GAAAATACACTCTGGACAAAAAGTATCGACACTT-GTGGATTTGT
*
2273088 GTCGATACTTTATGTATACATGTTTTCTCATAAACCAGTATATTTAGACCGCTTACATTGTTATT
129 GTCGATACTTTATGTATACCTGTTTTCTCATAAACCAGTATATTTAGACCGCTTACATTGTTATT
2273153 TTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATC
194 TTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATC
* * *
2273218 GACACTTTTTTATGCACTTGGTTTTTAAAATACACTCTGGACAAAAAGTATCAACACTTGTTGGA
259 GACACTTTGTTGTGCACTTGGTTTTTAAAATACACTCTGGACAAAAAGTATCGACACTTGTTGGA
* *
2273283 TTTGTGTCGATAATTTATGTATTCATGTTTTCTCATAAATTGGTATATTTAGACCAGTTACATTG
324 TTTGTGTCAATAATTTATGTATACATGTTTTCTCATAAATTGGTATATTTAGACCAGTTACATTG
2273348 TTATTTTACG
389 TTATTTTACG
*
2273358 TATTATATTATAATTATGGGTTTCGATG-TTTTGGGATCGACACTTGTTATAAATGTATCGACAC
1 TATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACAC
* *
2273422 TTTGTTGTGCGCTTGGTTTTAAAATACACTCTGGACAAAAAGTATCGACACTTGTGGATTTGTGT
66 TTTGTTGTGCACTTGGTTTGAAAATACACTCTGGACAAAAAGTATCGACACTTGTGGATTTGTGT
2273487 CGATACTTTATGTATACCTGTTTTCTCATAAACCAGTATATTTAGACCGCTTACATTGTTATTTT
131 CGATACTTTATGTATACCTGTTTTCTCATAAACCAGTATATTTAGACCGCTTACATTGTTATTTT
* *
2273552 ACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACAATTATTATAAATGTATCGA
196 ACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGA
2273617 CACTTTGTTGTGCACTTGGTTTTTAAAATACACTCTGGACAAAAAGTATCGACACTTGTTGGATT
261 CACTTTGTTGTGCACTTGGTTTTTAAAATACACTCTGGACAAAAAGTATCGACACTTGTTGGATT
*
2273682 TGTGTCAATAATTTATGTATACATGTTTTCTCATAAATCGGTATATTTAGACCAGTTACATTGTT
326 TGTGTCAATAATTTATGTATACATGTTTTCTCATAAATTGGTATATTTAGACCAGTTACATTGTT
2273747 ATTTTACG
391 ATTTTACG
*
2273755 TATTATATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACAC
1 TATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACAC
* **
2273820 TTTGTTGTGCGCTTGGTTTTTAAATACACTCTGGACAAAAAGTATCGACACTTGTTGGATTTGTG
66 TTTGTTGTGCACTTGGTTTGAAAATACACTCTGGACAAAAAGTATCGACACTTG-TGGATTTGTG
* * ** * *
2273885 TCGATACTTTATGTATATCTGTTTTCTCAAAAACTGGTATATTTAGGCCGGTTACATTGTTATTT
130 TCGATACTTTATGTATACCTGTTTTCTCATAAACCAGTATATTTAGACCGCTTACATTGTTATTT
* * * *
2273950 TACCTATTACATTAT-ATCTATGTGTTTCGATGTTTTTAGTATCGAAACTTGTTATAAATGTATC
195 TACCTATTACATTATAAT-TATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATC
* ** * * *
2274014 GACACTTTGTCGTGCACTTGGTTTAGAAAATACATTTTGGACAAAAACTATCGACACTTGTTGGA
259 GACACTTTGTTGTGCACTTGGTTTTTAAAATACACTCTGGACAAAAAGTATCGACACTTGTTGGA
* * * * *
2274079 TTTGTGTCAATACTTTATGTATACATGTTTTCTCAAAAACTGGTATATTTAGGCCGGTTACATTG
324 TTTGTGTCAATAATTTATGTATACATGTTTTCTCATAAATTGGTATATTTAGACCAGTTACATTG
*
2274144 TTATTTTACC
389 TTATTTTACG
* * * *
2274154 TATTACATTAT-ATCTATGTGTTTCGATGTTTTTAGTATCGACACTTATTATAAATGTATCGACA
1 TATTACATTATAAT-TATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACA
* * * * *
2274218 CCTTT-TTCGTGCACTTGGTTTGGAAATACATTATGGACAACATGTATCGACAC
65 -CTTTGTT-GTGCACTTGGTTTGAAAATACACTCTGGACAAAAAGTATCGACAC
2274271 GAATGAATAA
Statistics
Matches: 850, Mismatches: 57, Indels: 12
0.92 0.06 0.01
Matches are distributed among these distances:
397 297 0.35
398 125 0.15
399 360 0.42
400 68 0.08
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.42
Consensus pattern (398 bp):
TATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACAC
TTTGTTGTGCACTTGGTTTGAAAATACACTCTGGACAAAAAGTATCGACACTTGTGGATTTGTGT
CGATACTTTATGTATACCTGTTTTCTCATAAACCAGTATATTTAGACCGCTTACATTGTTATTTT
ACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGA
CACTTTGTTGTGCACTTGGTTTTTAAAATACACTCTGGACAAAAAGTATCGACACTTGTTGGATT
TGTGTCAATAATTTATGTATACATGTTTTCTCATAAATTGGTATATTTAGACCAGTTACATTGTT
ATTTTACG
Found at i:2273616 original size:597 final size:599
Alignment explanation
Indices: 2272885--2274270 Score: 2079
Period size: 597 Copynumber: 2.3 Consensus size: 599
2272875 AATAAATAAA
* * * * * * * *
2272885 GTGTCGATACATTATTTAGACTTATTTTCTCATAAAACCGGTAAATTTAAACCGGTTACATTGTA
1 GTGTCGATACTTTATGTATACATGTTTTCTCAT-AAACCGGTATATTTAGACCGGTTACATTGTT
** * * * *
2272950 AAGTGACCTATTACATTATAATTATAGGTTTCGATGTATTTGGGATCGACACA-TGTTATAAATG
65 ATTTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACA-ATTATTATAAATG
2273014 TATCGACACTTTTTTGTGCACTTGGTTTGGAAAATACATTCTGGACAAAAAGTATCGACACTTAT
129 TATCGACACTTTTTTGTGCACTTGGTTTGGAAAATACATTCTGGACAAAAAGTATCGACACTTAT
* * *
2273079 TGTATTTGTGTCGATACTTTATGTATACATGTTTTCTCATAAACCAGTATATTTAGACC-GCTTA
194 TGGATTTGTGTCAATAATTTATGTATACATGTTTTCTCATAAACCAGTATATTTAGACCAG-TTA
2273143 CATTGTTATTTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTA
258 CATTGTTATTTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTA
*
2273208 TAAATGTATCGACACTTTTTTATGCACTTGGTTTTTAAAATACACTCTGGACAAAAAGTATCAAC
323 TAAATGTATCGACACTTTGTTATGCACTTGGTTTTT-AAATACACTCTGGACAAAAAGTATCAAC
* *
2273273 ACTTGTTGGATTTGTGTCGATAATTTATGTAT-TCATGTTTTCTCATAAATTGGTATATTTAGAC
387 ACTTGTTGGATTTGTGTCGATAATTTATGTATATC-TGTTTTCTCAAAAACTGGTATATTTAGAC
* * * *
2273337 CAGTTACATTGTTATTTTACGTATTATATTATAAT-TATGGGTTTCGATG-TTTTGGGATCGACA
451 CAGTTACATTGTTATTTTACCTATTACATTAT-ATCTATGGGTTTCGATGTTTTTAGGATCGAAA
* * * *
2273400 CTTGTTATAAATGTATCGACACTTTGTTGTGCGCTTGGTTT-TAAAATACACTCTGGACAAAAAG
515 CTTGTTATAAATGTATCGACACTTTGTCGTGCACTTGGTTTAGAAAATACACTCTGGACAAAAAC
2273464 TATCGACACTTG-TGGATTT
580 TATCGACACTTGTTGGATTT
* * *
2273483 GTGTCGATACTTTATGTATACCTGTTTTCTCATAAACCAGTATATTTAGACCGCTTACATTGTTA
1 GTGTCGATACTTTATGTATACATGTTTTCTCATAAACCGGTATATTTAGACCGGTTACATTGTTA
2273548 TTTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACAATTATTATAAATGTA
66 TTTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACAATTATTATAAATGTA
* ** * *
2273613 TCGACACTTTGTTGTGCACTTGGTTTTTAAAATACACTCTGGACAAAAAGTATCGACACTTGTTG
131 TCGACACTTTTTTGTGCACTTGGTTTGGAAAATACATTCTGGACAAAAAGTATCGACACTTATTG
* *
2273678 GATTTGTGTCAATAATTTATGTATACATGTTTTCTCATAAATCGGTATATTTAGACCAGTTACAT
196 GATTTGTGTCAATAATTTATGTATACATGTTTTCTCATAAACCAGTATATTTAGACCAGTTACAT
* *
2273743 TGTTATTTTACGTATTATATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAA
261 TGTTATTTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAA
* * *
2273808 ATGTATCGACACTTTGTTGTGCGCTTGGTTTTTAAATACACTCTGGACAAAAAGTATCGACACTT
326 ATGTATCGACACTTTGTTATGCACTTGGTTTTTAAATACACTCTGGACAAAAAGTATCAACACTT
* * *
2273873 GTTGGATTTGTGTCGATACTTTATGTATATCTGTTTTCTCAAAAACTGGTATATTTAGGCCGGTT
391 GTTGGATTTGTGTCGATAATTTATGTATATCTGTTTTCTCAAAAACTGGTATATTTAGACCAGTT
* *
2273938 ACATTGTTATTTTACCTATTACATTATATCTATGTGTTTCGATGTTTTTAGTATCGAAACTTGTT
456 ACATTGTTATTTTACCTATTACATTATATCTATGGGTTTCGATGTTTTTAGGATCGAAACTTGTT
* *
2274003 ATAAATGTATCGACACTTTGTCGTGCACTTGGTTTAGAAAATACATTTTGGACAAAAACTATCGA
521 ATAAATGTATCGACACTTTGTCGTGCACTTGGTTTAGAAAATACACTCTGGACAAAAACTATCGA
2274068 CACTTGTTGGATTT
586 CACTTGTTGGATTT
* * * *
2274082 GTGTCAATACTTTATGTATACATGTTTTCTCAAAAACTGGTATATTTAGGCCGGTTACATTGTTA
1 GTGTCGATACTTTATGTATACATGTTTTCTCATAAACCGGTATATTTAGACCGGTTACATTGTTA
* * * *
2274147 TTTTACCTATTACATTAT-ATCTATGTGTTTCGATGTTTTTAGTATCGACACTTATTATAAATGT
66 TTTTACCTATTACATTATAAT-TATGGGTTTCGATGTTTTTGGGATCGACAATTATTATAAATGT
* * * *
2274211 ATCGACACCTTTTTCGTGCACTTGGTTTGG-AAATACATTATGGACAACATGTATCGACAC
130 ATCGACA-CTTTTTTGTGCACTTGGTTTGGAAAATACATTCTGGACAAAAAGTATCGACAC
2274271 GAATGAATAA
Statistics
Matches: 711, Mismatches: 68, Indels: 17
0.89 0.09 0.02
Matches are distributed among these distances:
595 2 0.00
596 127 0.18
597 347 0.49
598 62 0.09
599 155 0.22
600 18 0.03
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (599 bp):
GTGTCGATACTTTATGTATACATGTTTTCTCATAAACCGGTATATTTAGACCGGTTACATTGTTA
TTTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACAATTATTATAAATGTA
TCGACACTTTTTTGTGCACTTGGTTTGGAAAATACATTCTGGACAAAAAGTATCGACACTTATTG
GATTTGTGTCAATAATTTATGTATACATGTTTTCTCATAAACCAGTATATTTAGACCAGTTACAT
TGTTATTTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAA
ATGTATCGACACTTTGTTATGCACTTGGTTTTTAAATACACTCTGGACAAAAAGTATCAACACTT
GTTGGATTTGTGTCGATAATTTATGTATATCTGTTTTCTCAAAAACTGGTATATTTAGACCAGTT
ACATTGTTATTTTACCTATTACATTATATCTATGGGTTTCGATGTTTTTAGGATCGAAACTTGTT
ATAAATGTATCGACACTTTGTCGTGCACTTGGTTTAGAAAATACACTCTGGACAAAAACTATCGA
CACTTGTTGGATTT
Found at i:2274506 original size:24 final size:24
Alignment explanation
Indices: 2274455--2274506 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
2274445 ATTTACATTT
* *
2274455 AAATTCAAACTCAAATTGAAATTT
1 AAATTCAAACTCAAATTGAAAATG
*
2274479 AAATTCAAACTCTAATT-ATAAATG
1 AAATTCAAACTCAAATTGA-AAATG
2274503 AAAT
1 AAAT
2274507 GAAAATGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.52, C:0.12, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATTCAAACTCAAATTGAAAATG
Found at i:2275861 original size:12 final size:12
Alignment explanation
Indices: 2275844--2275881 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
2275834 ACTTGTTTGG
*
2275844 ATCATCATCATC
1 ATCATCATCTTC
2275856 ATCATCATCTTC
1 ATCATCATCTTC
*
2275868 ATCGTCATCTTC
1 ATCATCATCTTC
2275880 AT
1 AT
2275882 TGACATCTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.26, C:0.32, G:0.03, T:0.39
Consensus pattern (12 bp):
ATCATCATCTTC
Found at i:2277069 original size:15 final size:15
Alignment explanation
Indices: 2277045--2277088 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
2277035 AGGAGGTTGT
2277045 GGTTGAGAAGAGCTG
1 GGTTGAGAAGAGCTG
*
2277060 GGTTGGGAAGAAG-TG
1 GGTTGAGAAG-AGCTG
2277075 GGTTGAGAAGAGCT
1 GGTTGAGAAGAGCT
2277089 TTGAGAAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 2 0.08
15 21 0.84
16 2 0.08
ACGTcount: A:0.27, C:0.05, G:0.48, T:0.20
Consensus pattern (15 bp):
GGTTGAGAAGAGCTG
Found at i:2277848 original size:199 final size:199
Alignment explanation
Indices: 2277440--2278325 Score: 1170
Period size: 199 Copynumber: 4.4 Consensus size: 199
2277430 AATTAAACCA
* *** * * * * * * *
2277440 GTATATTTATACCGGTTACATTACAAAATAACATATTACACTAAAATTTTGGGTTTCGATGTTCT
1 GTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTT
* * *
2277505 TAGGATCGATACTTGTTATAAATGTATCGACACTTTTTC-CTGCACTTGGTTTTTA-AAATACAC
66 TGGGATCGATACTTGTTATAAATGTATCGACAC-TTTTCAATGCACTTGG--TTTAGAAATACAT
* * * * *
2277568 TCTGGACAAAAAGTATCGACACTTGTTAGATTTCTGTCGATACTTTATGTATACCTGTTTTCTCA
128 TCTGGACCAAAAGTATCGACACTTGTTATATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCA
2277633 TAAA-CCG
193 -AAATCCG
* * *
2277640 TTATATTTAGACTGGTTAAATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTT
1 GTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTT
* *
2277705 TGGGATCGACACTTGTTATAAATGTATCGACACTTTTCAATGCACTTGCTTTAGAAATACATTCT
66 TGGGATCGATACTTGTTATAAATGTATCGACACTTTTCAATGCACTTGGTTTAGAAATACATTCT
* *
2277770 GGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACATGTTTTCTCAAAA
131 GGACCAAAAGTATCGACACTTGTTATATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAA
2277835 TCCG
196 TCCG
* * *
2277839 GTATATTTAGACCGGTTACTTTGTTAATTTATCTATTACATTATAATTATGGGTTTTGATGTTTT
1 GTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTT
** *
2277904 TGGGATCGATACTTGTTATAAATGTATCGACACTTTTCCGTGCACTTGGTTTAGAAATATATTCT
66 TGGGATCGATACTTGTTATAAATGTATCGACACTTTTCAATGCACTTGGTTTAGAAATACATTCT
* * *
2277969 AGACCAAAAGTATCGACACTTGTTATA-TTGTCTCGATACTTTTTGTACACTTGTTTTCTCAAAA
131 GGACCAAAAGTATCGACACTTGTTATATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAA
* *
2278033 ACTG
196 TCCG
* *
2278037 GTATATTTAGACCAGTTACATTGCTAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTT
1 GTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTT
* * *
2278102 TGGGATCGATACTTATTATAAATGTATCGACAAATGTATCGACACTTTTTGTGCACTTGGTTTAG
66 TGGGATCGATACTTGTTATAAATGTATCGAC-ACT-TTTC-A-A-------TGCACTTGGTTTAG
*
2278167 AAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTG
120 AAATACATTCTGGACCAAAAGTATCGACACTTGTTATATTTGTGTCGATACTTTTTGTACACCTG
2278232 TTTTCTCAAAAAT-CG
185 TTTTCTC-AAAATCCG
* * *
2278247 GTATATTTAGACCGGTTACATTGTTAATTTACATATTACATTATAAGTATGGGTTTCGATATTTT
1 GTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTT
*
2278312 TGGGATCGACACTT
66 TGGGATCGATACTT
2278326 TTTAGTGCAC
Statistics
Matches: 604, Mismatches: 66, Indels: 22
0.87 0.10 0.03
Matches are distributed among these distances:
198 134 0.22
199 219 0.36
200 93 0.15
209 49 0.08
210 105 0.17
211 4 0.01
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (199 bp):
GTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTT
TGGGATCGATACTTGTTATAAATGTATCGACACTTTTCAATGCACTTGGTTTAGAAATACATTCT
GGACCAAAAGTATCGACACTTGTTATATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAA
TCCG
Found at i:2278138 original size:12 final size:12
Alignment explanation
Indices: 2278121--2278145 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2278111 TACTTATTAT
2278121 AAATGTATCGAC
1 AAATGTATCGAC
2278133 AAATGTATCGAC
1 AAATGTATCGAC
2278145 A
1 A
2278146 CTTTTTGTGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (12 bp):
AAATGTATCGAC
Found at i:2278286 original size:210 final size:210
Alignment explanation
Indices: 2277923--2278325 Score: 666
Period size: 210 Copynumber: 1.9 Consensus size: 210
2277913 TACTTGTTAT
*
2277923 AAATGTATCGACACTTTTCCGTGCACTTGGTTTAGAAATATATTCTAGACCAAAAGTATCGACAC
1 AAATGTATCGACACTTTTCCGTGCACTTGGTTTAGAAATACATTCTAGACCAAAAGTATCGACAC
*
2277988 TTGTTATATTGTCTCGATACTTTTTGTACACTTGTTTTCTCAAAAACTGGTATATTTAGACCAGT
66 TTGTTATATTGTCTCGATACTTTTTGTACACCTGTTTTCTCAAAAACTGGTATATTTAGACCAGT
* * * *
2278053 TACATTGCTAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGATACTTAT
131 TACATTGCTAATTTACATATTACATTATAAGTATGGGTTTCGATATTTTTGGGATCGACACTTAT
2278118 TATAAATGTATCGAC
196 TATAAATGTATCGAC
* *
2278133 AAATGTATCGACACTTTT-TGTGCACTTGGTTTAGAAATACATTCTGGACCAAAAGTATCGACAC
1 AAATGTATCGACACTTTTCCGTGCACTTGGTTTAGAAATACATTCTAGACCAAAAGTATCGACAC
* * *
2278197 TTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAA-TCGGTATATTTAGACCG
66 TTGTTATA-TTGTCTCGATACTTTTTGTACACCTGTTTTCTCAAAAACT-GGTATATTTAGACCA
*
2278261 GTTACATTGTTAATTTACATATTACATTATAAGTATGGGTTTCGATATTTTTGGGATCGACACTT
129 GTTACATTGCTAATTTACATATTACATTATAAGTATGGGTTTCGATATTTTTGGGATCGACACTT
2278326 TTTAGTGCAC
Statistics
Matches: 179, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
209 51 0.28
210 128 0.72
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (210 bp):
AAATGTATCGACACTTTTCCGTGCACTTGGTTTAGAAATACATTCTAGACCAAAAGTATCGACAC
TTGTTATATTGTCTCGATACTTTTTGTACACCTGTTTTCTCAAAAACTGGTATATTTAGACCAGT
TACATTGCTAATTTACATATTACATTATAAGTATGGGTTTCGATATTTTTGGGATCGACACTTAT
TATAAATGTATCGAC
Found at i:2278360 original size:177 final size:177
Alignment explanation
Indices: 2278139--2278900 Score: 790
Period size: 199 Copynumber: 4.1 Consensus size: 177
2278129 CGACAAATGT
*
2278139 ATCGACACTTTTTGTGCACTTGGTTTAGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTT
1 ATCGACACTTTTTGTGCACTTGGTTTAGAAATACATTCTGGACCAAAAGTATCAACACTTGTTTT
* * * *
2278204 ATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAATCGGTATATTTAGACCGGTTACATT
66 ATTTGTGTCAATACTTTTTGTACACCTGTTTTCTCAAAAACCGATATATTTAGACCGATTACATT
*
2278269 GTTAATTTACATATTACATTATAAGTATGGGTTTCGATATTTTTGGG
131 GTTAATTTACATATTACATTATAAGTATGGGTTTCAATATTTTTGGG
*
2278316 ATCGACACTTTTTAGTGCACTTGGTTTTGAAATA-ATTCTGGACCAAAAGTATCAACACTTGTTT
1 ATCGACACTTTTT-GTGCACTTGGTTTAGAAATACATTCTGGACCAAAAGTATCAACACTTGTTT
2278380 TATTTGTGTCAATACTTTTTGTACACCTGTTTTCTCAAAAACCGATATATTTAGACCGATTACAT
65 TATTTGTGTCAATACTTTTTGTACACCTGTTTTCTCAAAAACCGATATATTTAGACCGATTACAT
* *
2278445 TGTTAATTTACATATTACATTATAATTATGGGTTTCAATGTTTTTGGG
130 TGTTAATTTACATATTACATTATAAGTATGGGTTTCAATATTTTTGGG
* *
2278493 ATCGACACTTGTTATAAATGTATTGACACTTTTTAGTGCACTTGGTTTTGAAATATATTCTGGAC
1 ATCGACAC-T-TT-T---TG---TG---C-----A-----CTTGGTTTAGAAATACATTCTGGAC
* * * *
2278558 CAAAAGTATCGACACTTGTTTTATTTGTGTCGATATTTTTTGTACAACTGTTTTCTCAAAAACCG
44 CAAAAGTATCAACACTTGTTTTATTTGTGTCAATACTTTTTGTACACCTGTTTTCTCAAAAACCG
* * * * * * *
2278623 GTATATTTAGTCCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTT
109 ATATATTTAGACCGATTACATTGTTAATTTACATATTACATTATAAGTATGGGTTTCAATATTTT
2278688 TGGG
174 TGGG
*
2278692 ATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGCACTTGATTTTGAAAATACATTCTGGA
1 ATCGACAC-T-TT-T---TG--T-G-CAC----T--TG-----G-TTTAG-AAATACATTCTGGA
* * *
2278757 CCAAAAGTATCGACACTTGTTTTATTTGTGTCGATATTTTTTGTACACCTGTTTTCTCAAAAACC
43 CCAAAAGTATCAACACTTGTTTTATTTGTGTCAATACTTTTTGTACACCTGTTTTCTCAAAAACC
* * * * * * *
2278822 GGTATAATTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGAT-GTT
108 GATATATTTAGACCGATTACATTGTTAATTTACATATTACATTATAAGTATGGGTTTCAATATTT
2278886 TTGGG
173 TTGGG
*
2278891 ATCGATACTT
1 ATCGACACTT
2278901 GTTATAAATG
Statistics
Matches: 521, Mismatches: 26, Indels: 56
0.86 0.04 0.09
Matches are distributed among these distances:
177 156 0.30
178 20 0.04
179 2 0.00
180 1 0.00
182 1 0.00
183 1 0.00
185 2 0.00
187 1 0.00
188 1 0.00
191 1 0.00
192 1 0.00
193 3 0.01
197 3 0.01
198 18 0.03
199 174 0.33
200 136 0.26
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (177 bp):
ATCGACACTTTTTGTGCACTTGGTTTAGAAATACATTCTGGACCAAAAGTATCAACACTTGTTTT
ATTTGTGTCAATACTTTTTGTACACCTGTTTTCTCAAAAACCGATATATTTAGACCGATTACATT
GTTAATTTACATATTACATTATAAGTATGGGTTTCAATATTTTTGGG
Found at i:2278562 original size:585 final size:586
Alignment explanation
Indices: 2277434--2278919 Score: 2007
Period size: 585 Copynumber: 2.5 Consensus size: 586
2277424 TTTTCAAATT
* * * * * * * * * * *
2277434 AAACCAGTATATTTATACCGGTTACATTACAAAATAACATATTACACTAAAATTTTGGGTTTCGA
1 AAACCGGTATATTTAGACCAGTTACATTGCTAATTTACCTATTACATTATAATTATGGGTTTCGA
* * * * * **
2277499 TGTTCTTAGGATCGATACTTGTTATAAATGTATCGACACTTTTTCCTGCACTTGGTTTTTA-AAA
66 TGTTTTTGGGATCGACAATTGTTACAAATGTATCGACACTTTTTAGTGCACTTGG--TTTAGAAA
* * ** * * *
2277563 TACACTCTGGACAAAAAGTATCGACACTTGTTAGATTTCTGTCGATACTTTATGTATACCTGTTT
129 TACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTT
* * * *
2277628 TCTCATAAACCGTTATATTTAGACTGGTTAAATTGTTAATTTACCTATTACATTATAATTATGGG
194 TCTCAAAAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGG
2277693 TTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTCAATGCACTTGCTTTA
259 TTTCGAT-TTTTTGGGATCGACACTTGTTAT-AATG-ATCGACAC--TT--ATG--C--GCTTTA
* *
2277758 GAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACAT
313 GAAATACATTCTGGACCAAAAGTATCAACACTTGTTTTATTTGTGTCAATACTTTTTGTACACAT
* * * *
2277823 GTTTTCTCAAAATCCGGTATATTTAGACCGGTTACTTTGTTAATTTATCTATTACATTATAATTA
378 GTTTTCTCAAAAACCGATATATTTAGACCGATTACATTGTTAATTTATCTATTACATTATAATTA
** * *
2277888 TGGGTTTTGATGTTTTTGGGATCGATACTTGTTATAAATGTATCGACACTTTTCCGTGCACTTGG
443 TGGGTTTCAATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTCAGTGCACTTGG
2277953 TTTAGAAATATATTCTAGACCAAAAGTATCGACACTTGTTATA-TTGTCTCGATACTTTTTGTAC
508 TTTAGAAATATATTCTAGACCAAAAGTATCGACACTTGTTATATTTGTCTCGATACTTTTTGTAC
2278017 -ACTTGTTTTCTCAA
573 AAC-TGTTTTCTCAA
*
2278031 AAACTGGTATATTTAGACCAGTTACATTGCTAATTTACCTATTACATTATAATTATGGGTTTCGA
1 AAACCGGTATATTTAGACCAGTTACATTGCTAATTTACCTATTACATTATAATTATGGGTTTCGA
2278096 TGTTTTTGGGATCGATACTTATTATAAATGTATCGACAAATGTATCGACACTTTTT-GTGCACTT
66 TGTTTTTGGGATCG--AC--A--AT---TGT-T--ACAAATGTATCGACACTTTTTAGTGCACTT
2278160 GGTTTAGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGT
119 GGTTTAGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGT
* *
2278225 ACACCTGTTTTCTCAAAAATCGGTATATTTAGACCGGTTACATTGTTAATTTACATATTACATTA
184 ACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTA
* *
2278290 TAAGTATGGGTTTCGATATTTTTGGGATCGACACTT-TT-T-A-G-T-G-CAC-T-TG-G-TTTT
249 TAATTATGGGTTTCGAT-TTTTTGGGATCGACACTTGTTATAATGATCGACACTTATGCGCTTTA
*
2278344 GAAATA-ATTCTGGACCAAAAGTATCAACACTTGTTTTATTTGTGTCAATACTTTTTGTACACCT
313 GAAATACATTCTGGACCAAAAGTATCAACACTTGTTTTATTTGTGTCAATACTTTTTGTACACAT
2278408 GTTTTCTCAAAAACCGATATATTTAGACCGATTACATTGTTAATTTA-CATATTACATTATAATT
378 GTTTTCTCAAAAACCGATATATTTAGACCGATTACATTGTTAATTTATC-TATTACATTATAATT
* *
2278472 ATGGGTTTCAATGTTTTTGGGATCGACACTTGTTATAAATGTATTGACACTTTTTAGTGCACTTG
442 ATGGGTTTCAATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTCAGTGCACTTG
* * * * *
2278537 GTTTTGAAATATATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATATTTTTTGTA
507 GTTTAGAAATATATTCTAGACCAAAAGTATCGACACTTGTTATATTTGTCTCGATACTTTTTGTA
2278602 CAACTGTTTTCTCAA
572 CAACTGTTTTCTCAA
* * *
2278617 AAACCGGTATATTTAGTCCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
1 AAACCGGTATATTTAGACCAGTTACATTGCTAATTTACCTATTACATTATAATTATGGGTTTCGA
* * * *
2278682 TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGCACTTGATTTTGAAAAT
66 TGTTTTTGGGATCGACAATTGTTACAAATGTATCGACACTTTTTAGTGCACTTGGTTTAG-AAAT
*
2278747 ACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATATTTTTTGTACACCTGTTTT
130 ACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTT
*
2278812 CTCAAAAACCGGTATAATTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGT
195 CTCAAAAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGT
* *
2278877 TTCGATGTTTTGGGATCGATACTTGTTATAAATGTATCGACAC
260 TTCGATTTTTTGGGATCGACACTTGTTAT-AATG-ATCGACAC
2278920 ATAAGTTTAC
Statistics
Matches: 795, Mismatches: 67, Indels: 67
0.86 0.07 0.07
Matches are distributed among these distances:
574 20 0.03
575 29 0.04
576 138 0.17
577 4 0.01
579 1 0.00
580 2 0.00
582 2 0.00
583 1 0.00
584 6 0.01
585 213 0.27
586 114 0.14
587 3 0.00
592 2 0.00
595 1 0.00
597 65 0.08
598 3 0.00
599 2 0.00
600 1 0.00
601 1 0.00
602 1 0.00
603 2 0.00
605 1 0.00
606 9 0.01
607 145 0.18
608 9 0.01
609 20 0.03
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (586 bp):
AAACCGGTATATTTAGACCAGTTACATTGCTAATTTACCTATTACATTATAATTATGGGTTTCGA
TGTTTTTGGGATCGACAATTGTTACAAATGTATCGACACTTTTTAGTGCACTTGGTTTAGAAATA
CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTC
TCAAAAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTT
TCGATTTTTTGGGATCGACACTTGTTATAATGATCGACACTTATGCGCTTTAGAAATACATTCTG
GACCAAAAGTATCAACACTTGTTTTATTTGTGTCAATACTTTTTGTACACATGTTTTCTCAAAAA
CCGATATATTTAGACCGATTACATTGTTAATTTATCTATTACATTATAATTATGGGTTTCAATGT
TTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTCAGTGCACTTGGTTTAGAAATATAT
TCTAGACCAAAAGTATCGACACTTGTTATATTTGTCTCGATACTTTTTGTACAACTGTTTTCTCA
A
Found at i:2279326 original size:19 final size:19
Alignment explanation
Indices: 2279298--2279335 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2279288 CATATACAAT
2279298 AAATCGTATACAAAATTAA
1 AAATCGTATACAAAATTAA
*
2279317 AAATCTTATACAAAATTAA
1 AAATCGTATACAAAATTAA
2279336 CCCTACATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.58, C:0.11, G:0.03, T:0.29
Consensus pattern (19 bp):
AAATCGTATACAAAATTAA
Found at i:2281530 original size:22 final size:21
Alignment explanation
Indices: 2281502--2281556 Score: 58
Period size: 24 Copynumber: 2.5 Consensus size: 21
2281492 AACCTGCATT
*
2281502 TATAATAAAAGTTATCATTTTA
1 TATAATAAAA-ATATCATTTTA
2281524 TATAATAACTATAATATCATTTTA
1 TATAATAA--A-AATATCATTTTA
2281548 TATAA-AAAA
1 TATAATAAAA
2281557 CAAAAACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
20 1 0.03
21 1 0.03
22 8 0.28
23 2 0.07
24 16 0.55
25 1 0.03
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (21 bp):
TATAATAAAAATATCATTTTA
Found at i:2282840 original size:19 final size:19
Alignment explanation
Indices: 2282818--2282879 Score: 115
Period size: 19 Copynumber: 3.3 Consensus size: 19
2282808 TACAACCTCA
*
2282818 AATATCATTTTGTACCTAT
1 AATATCATTTTTTACCTAT
2282837 AATATCATTTTTTACCTAT
1 AATATCATTTTTTACCTAT
2282856 AATATCATTTTTTACCTAT
1 AATATCATTTTTTACCTAT
2282875 AATAT
1 AATAT
2282880 TAAATAAAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.34, C:0.15, G:0.02, T:0.50
Consensus pattern (19 bp):
AATATCATTTTTTACCTAT
Found at i:2283627 original size:182 final size:182
Alignment explanation
Indices: 2283310--2284333 Score: 1416
Period size: 182 Copynumber: 5.6 Consensus size: 182
2283300 TACGCGTACT
* ** *
2283310 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGATTTTGTCATTTTGAGACCG
1 TATTAAAGTATCGACACTTTCAACATATCTGGTAGCTTTTTACCGGTTTTGTCATTTTGAGACCG
* * *
2283375 GTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTAAAAGTATCGACATT
2283440 TTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
131 TTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* * * *
2283492 TATTAAATTATCGACACTTTCAACATATCTGGTATCTTTTTACCGGTTTTGTCATTTTTTAGATC
1 TATTAAAGTATCGACACTTTCAACATATCTGGTAGCTTTTTACCGGTTTTGTCA-TTTTGAGACC
* * * *
2283557 TGTTTTGTCATATTTTTACCT-TTATATTATTATGGATCGATATATTTTTTAAAAGTATCAACAT
65 GGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTAAAAGTATCGACAT
* * *
2283621 TTTATAGGCGTTATAACTTATTCTCTTTTAAATTCCAAAAGTGTCTATACTTA
130 TTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
**
2283674 TATTAAAGTATCGACACTTTCAACATAT-TCGGTAGCGCTTTACCGGTTTTGTCATTTTGAGACC
1 TATTAAAGTATCGACACTTTCAACATATCT-GGTAGCTTTTTACCGGTTTTGTCATTTTGAGACC
** * *
2283738 GGTTTTGTCATATTTTTAGTTGTTATATTGTTATGGATCGATACA-TTTTCATAAAGTGTCGACA
65 GGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTA-AAAGTATCGACA
*
2283802 CTTTT-TAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCAATACTTA
129 -TTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* * * * * * * **
2283856 TATTAAATTATCGTCATTTTCAACATATCCGATATCTTTTTACCGGTTTTGTCATTTTTAGACAT
1 TATTAAAGTATCGACACTTTCAACATATCTGGTAGCTTTTTACCGGTTTTGTCATTTTGAGACCG
* * *
2283921 GTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTAAAAGTATCGACATT
* *
2283986 TTATAGGCACTATAACTTCTTCTCTTTTAAATTTCAAAAGTGTCGATACTTA
131 TTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* * * *
2284038 TATTAAAGTATCGACACTTTCAATATATCTGGTAG-TTATTTACCTGTTTTGTCATTTTAAGACT
1 TATTAAAGTATCGACACTTTCAACATATCTGGTAGCTT-TTTACCGGTTTTGTCATTTTGAGACC
* ** * *
2284102 GGTTTTGTCATATTTTTAACTGTTATATTGTTATGGATTTATACA-TTTTCATAAAGTGTCGACA
65 GGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTA-AAAGTATCGACA
*
2284166 CTTTT-TAGGCGCTATAACTTCTTTTCTTTTAAATT-CAGAAAGTGTCGATACTTA
129 -TTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCA-AAAGTGTCGATACTTA
* * *
2284220 TATTAAATTATCGACACTTTCAACATATCTGGTAGCATTTTACCGGTTTTGTCATTTCGAGACCG
1 TATTAAAGTATCGACACTTTCAACATATCTGGTAGCTTTTTACCGGTTTTGTCATTTTGAGACCG
* * * *
2284285 GTTTTGTCATATTTTTACCTGTAATATTGCTATGGAGCAATACATTTTT
66 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
2284334 CATTTGTATC
Statistics
Matches: 738, Mismatches: 90, Indels: 27
0.86 0.11 0.03
Matches are distributed among these distances:
181 43 0.06
182 652 0.88
183 43 0.06
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (182 bp):
TATTAAAGTATCGACACTTTCAACATATCTGGTAGCTTTTTACCGGTTTTGTCATTTTGAGACCG
GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTAAAAGTATCGACATT
TTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
Found at i:2283943 original size:20 final size:19
Alignment explanation
Indices: 2283892--2283943 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
2283882 ATCCGATATC
* *
2283892 TTTTTACCGGTTTTGTCAT
1 TTTTTACCTGTTTTATCAT
* *
2283911 TTTTAGACATGTTTTATCAT
1 TTTT-TACCTGTTTTATCAT
2283931 ATTTTTACCTGTT
1 -TTTTTACCTGTT
2283944 ATATTGTTAT
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
19 4 0.16
20 17 0.68
21 4 0.16
ACGTcount: A:0.17, C:0.13, G:0.12, T:0.58
Consensus pattern (19 bp):
TTTTTACCTGTTTTATCAT
Found at i:2283979 original size:364 final size:363
Alignment explanation
Indices: 2283310--2284333 Score: 1568
Period size: 364 Copynumber: 2.8 Consensus size: 363
2283300 TACGCGTACT
* *
2283310 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGATTTTGTCATTTTGAGACCG
1 TATTAAAGTATCGACACTTTCAACATATTCGGTAGCGCTTTACCGGTTTTGTCATTTTGAGACCG
* * ** *
2283375 GTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACT
66 GTTTTGTCATATTTTTAACTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACT
*
2283440 TTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAATTATCG
131 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAATTATCG
2283505 ACACTTTCAACATATCTGGTATCTTTTTACCGGTTTTGTCATTTTTTAGATCTGTTTTGTCATAT
196 ACACTTTCAACATATCTGGTATCTTTTTACCGGTTTTGTCA-TTTTTAGA-CTGTTTTGTCATAT
* * * **
2283570 TTTTACCT-TTATATTATTATGGATCGATATATTTTTTAAAAGTATCAACATTTTATAGGCGTTA
259 TTTTACCTGTTATATTGTTATGGATCGATACATTTTTTAAAAGTATCAACACTTTATAGGCACTA
*
2283634 TAACTTATTCTCTTTTAAATTCCAAAAGTGTCTATACTTA
324 TAACTTATTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
2283674 TATTAAAGTATCGACACTTTCAACATATTCGGTAGCGCTTTACCGGTTTTGTCATTTTGAGACCG
1 TATTAAAGTATCGACACTTTCAACATATTCGGTAGCGCTTTACCGGTTTTGTCATTTTGAGACCG
**
2283739 GTTTTGTCATATTTTTAGTTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACT
66 GTTTTGTCATATTTTTAACTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACT
*
2283804 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCAATACTTATATTAAATTATCG
131 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAATTATCG
* * * * *
2283869 TCATTTTCAACATATCCGATATCTTTTTACCGGTTTTGTCATTTTTAGACATGTTTTATCATATT
196 ACACTTTCAACATATCTGGTATCTTTTTACCGGTTTTGTCATTTTTAGAC-TGTTTTGTCATATT
* *
2283934 TTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACTTTATAGGCACTAT
260 TTTACCTGTTATATTGTTATGGATCGATACATTTTTTAAAAGTATCAACACTTTATAGGCACTAT
* *
2283999 AACTTCTTCTCTTTTAAATTTCAAAAGTGTCGATACTTA
325 AACTTATTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* *** * * *
2284038 TATTAAAGTATCGACACTTTCAATATA-TCTGGTAGTTATTTACCTGTTTTGTCATTTTAAGACT
1 TATTAAAGTATCGACACTTTCAACATATTC-GGTAGCGCTTTACCGGTTTTGTCATTTTGAGACC
**
2284102 GGTTTTGTCATATTTTTAACTGTTATATTGTTATGGATTTATACATTTTCATAAAGTGTCGACAC
65 GGTTTTGTCATATTTTTAACTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACAC
*
2284167 TTTTTAGGCGCTATAACTTCTTTTCTTTTAAATT-CAGAAAGTGTCGATACTTATATTAAATTAT
130 TTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCCA-AAAGTGTCGATACTTATATTAAATTAT
* * ** *
2284231 CGACACTTTCAACATATCTGGTAGCATTTTACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATA
194 CGACACTTTCAACATATCTGGTATCTTTTTACCGGTTTTGTCATTTTTAGA-CTGTTTTGTCATA
* * * *
2284296 TTTTTACCTGTAATATTGCTATGGAGCAATACATTTTT
258 TTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
2284334 CATTTGTATC
Statistics
Matches: 603, Mismatches: 52, Indels: 10
0.91 0.08 0.02
Matches are distributed among these distances:
362 1 0.00
363 32 0.05
364 569 0.94
365 1 0.00
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (363 bp):
TATTAAAGTATCGACACTTTCAACATATTCGGTAGCGCTTTACCGGTTTTGTCATTTTGAGACCG
GTTTTGTCATATTTTTAACTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACT
TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAATTATCG
ACACTTTCAACATATCTGGTATCTTTTTACCGGTTTTGTCATTTTTAGACTGTTTTGTCATATTT
TTACCTGTTATATTGTTATGGATCGATACATTTTTTAAAAGTATCAACACTTTATAGGCACTATA
ACTTATTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
Found at i:2285199 original size:19 final size:19
Alignment explanation
Indices: 2285155--2285199 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
2285145 AATTTAAAAA
*
2285155 TTAAAAATTTCATATATTT
1 TTAAAAATTTCATATACTT
* *
2285174 TTGAAAAATTTTATTTACTT
1 TT-AAAAATTTCATATACTT
2285194 TTAAAA
1 TTAAAA
2285200 TTAATTGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.51
Consensus pattern (19 bp):
TTAAAAATTTCATATACTT
Found at i:2285455 original size:33 final size:33
Alignment explanation
Indices: 2285418--2285480 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
2285408 TTTACCTTCT
*
2285418 TTTTTTAATTATAATTTTATTCACTTTTAATTC
1 TTTTTTAATTATAATTTTATTCAATTTTAATTC
* * * *
2285451 TTTTTTTATTGTATTTTTATTGAATTTTAA
1 TTTTTTAATTATAATTTTATTCAATTTTAA
2285481 ATATATAAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.67
Consensus pattern (33 bp):
TTTTTTAATTATAATTTTATTCAATTTTAATTC
Found at i:2286318 original size:20 final size:19
Alignment explanation
Indices: 2286271--2286307 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2286261 TTAACGTTAT
*
2286271 AAAAAAATCAATGATTTTC
1 AAAAAAATCAATCATTTTC
2286290 AAAAAAATCAATCATTTT
1 AAAAAAATCAATCATTTT
2286308 TCGGAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.11, G:0.03, T:0.32
Consensus pattern (19 bp):
AAAAAAATCAATCATTTTC
Found at i:2286823 original size:27 final size:28
Alignment explanation
Indices: 2286782--2286845 Score: 112
Period size: 27 Copynumber: 2.3 Consensus size: 28
2286772 CTGGATATTG
2286782 ACCCATATAATTTTTTTTAGGATAAATA
1 ACCCATATAATTTTTTTTAGGATAAATA
2286810 ACCCATATAA-TTTTTTTAGGATAAATA
1 ACCCATATAATTTTTTTTAGGATAAATA
*
2286837 ACACATATA
1 ACCCATATA
2286846 GTTCTTTGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 25 0.71
28 10 0.29
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.39
Consensus pattern (28 bp):
ACCCATATAATTTTTTTTAGGATAAATA
Found at i:2291387 original size:32 final size:31
Alignment explanation
Indices: 2291351--2291427 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
2291341 CGGGGCCGTG
*
2291351 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
2291383 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
2291414 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
2291428 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:2291410 original size:63 final size:63
Alignment explanation
Indices: 2291304--2291427 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
2291294 CCCTAAGGGA
* * ** *
2291304 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
2291367 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
2291428 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:2292308 original size:7 final size:7
Alignment explanation
Indices: 2292296--2292333 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
2292286 GTCAAAGAAA
2292296 GTCAACG
1 GTCAACG
2292303 GTCAACG
1 GTCAACG
2292310 GTCAACG
1 GTCAACG
2292317 GTCAACG
1 GTCAACG
*
2292324 GTCAATG
1 GTCAACG
2292331 GTC
1 GTC
2292334 GGGTCGGATC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.18
Consensus pattern (7 bp):
GTCAACG
Found at i:2292340 original size:5 final size:5
Alignment explanation
Indices: 2292330--2292404 Score: 60
Period size: 5 Copynumber: 13.8 Consensus size: 5
2292320 AACGGTCAAT
* * *
2292330 GGTCG GGTCG GATCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAT GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
*
2292379 GGTCG GGTCAAC GGTCG GGTCG GGTC
1 GGTCG GGTC--G GGTCG GGTCG GGTC
2292405 AGACCGGTCA
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
5 44 0.79
7 12 0.21
ACGTcount: A:0.09, C:0.21, G:0.49, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:2292357 original size:17 final size:17
Alignment explanation
Indices: 2292357--2292405 Score: 89
Period size: 17 Copynumber: 2.9 Consensus size: 17
2292347 TCAACGGTCG
*
2292357 GGTCGGGTCGGGTCAAT
1 GGTCGGGTCGGGTCAAC
2292374 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
2292391 GGTCGGGTCGGGTCA
1 GGTCGGGTCGGGTCA
2292406 GACCGGTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.10, C:0.20, G:0.49, T:0.20
Consensus pattern (17 bp):
GGTCGGGTCGGGTCAAC
Found at i:2292385 original size:22 final size:22
Alignment explanation
Indices: 2292323--2292387 Score: 112
Period size: 22 Copynumber: 3.0 Consensus size: 22
2292313 AACGGTCAAC
*
2292323 GGTCAATGGTCGGGTCGGATCG
1 GGTCAATGGTCGGGTCGGGTCG
*
2292345 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAATGGTCGGGTCGGGTCG
2292367 GGTCAATGGTCGGGTCGGGTC
1 GGTCAATGGTCGGGTCGGGTC
2292388 AACGGTCGGG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.11, C:0.20, G:0.48, T:0.22
Consensus pattern (22 bp):
GGTCAATGGTCGGGTCGGGTCG
Found at i:2292459 original size:29 final size:31
Alignment explanation
Indices: 2292426--2292500 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
2292416 ACCAAGTCAG
2292426 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
2292455 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
2292485 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
2292501 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:2292497 original size:9 final size:9
Alignment explanation
Indices: 2292426--2292500 Score: 69
Period size: 9 Copynumber: 7.8 Consensus size: 9
2292416 ACCAAGTCAG
*
2292426 ACCGGTCAA
1 ACCGGTTAA
*
2292435 ACCGGTTCGA
1 ACCGGTT-AA
2292445 ACCGGTTGAA
1 ACCGGTT-AA
*
2292455 ACCGGTCAA
1 ACCGGTTAA
*
2292464 ACCGGTCAGA
1 ACCGGTTA-A
2292474 ACCGGTTGAAA
1 ACCGGTT--AA
2292485 ACCGGTTAA
1 ACCGGTTAA
2292494 ACCGGTT
1 ACCGGTT
2292501 TCCAGCAGCC
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
9 25 0.45
10 22 0.39
11 8 0.14
12 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (9 bp):
ACCGGTTAA
Found at i:2294210 original size:84 final size:83
Alignment explanation
Indices: 2294122--2294340 Score: 226
Period size: 83 Copynumber: 2.6 Consensus size: 83
2294112 ACTATAGATG
* * * *
2294122 AACCCTATTAAGGCTTTTATATTAAAACACCGCTAAAGTACT-CTTTATTGCGGCATTTTTTTTG
1 AACCCTATTAAGGCTTTTATATAAAAACACCGCTAAAGTACTACTATATCGCGGC--TTTTGTTG
*
2294186 GAAAAACGCCACTATAAACA
64 AAAAAACGCCACTATAAACA
* * * * * *
2294206 AACCCTATT-ACGATATTTATATAAAAACGCCACTAAAATACTACTATATCGTGGCTTTTGTTGA
1 AACCCTATTAAGGCT-TTTATATAAAAACACCGCTAAAGTACTACTATATCGCGGCTTTTGTTGA
* *
2294270 AAAAATGCCACTATAAACT
65 AAAAACGCCACTATAAACA
* * * * * *
2294289 AACTCTATTACGGCGTTTGTATAAAAATACCGCTAAAGTACTACTCTATCGC
1 AACCCTATTAAGGCTTTTATATAAAAACACCGCTAAAGTACTACTATATCGC
2294341 AGAGTTTGTT
Statistics
Matches: 107, Mismatches: 25, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
83 65 0.61
84 33 0.31
85 9 0.08
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.32
Consensus pattern (83 bp):
AACCCTATTAAGGCTTTTATATAAAAACACCGCTAAAGTACTACTATATCGCGGCTTTTGTTGAA
AAAACGCCACTATAAACA
Found at i:2294349 original size:83 final size:82
Alignment explanation
Indices: 2294089--2294350 Score: 213
Period size: 83 Copynumber: 3.1 Consensus size: 82
2294079 CATGTGTTTA
* * * * * *
2294089 GCAGCGTTTGCTTGAAAAATGTCACTATAGA-TGAACCCTATTAAGGCTTTTATATTAAAACACC
1 GCAGAGTTTG-TTGAAAAATGCCACTATAAACT-AACCCTATTACGGCATTTATATAAAAACACC
* *
2294153 GCTAAAGTACT-CTTTATT
64 GCTAAAGTACTACTATATC
* * * * * ** *
2294171 GCGGCATTTTTTTTGGAAAAACGCCACTATAAACAAACCCTATTACGATATTTATATAAAAACGC
1 GCAG-A-GTTTGTT-GAAAAATGCCACTATAAACTAACCCTATTACGGCATTTATATAAAAACAC
* *
2294236 CACTAAAATACTACTATATC
63 CGCTAAAGTACTACTATATC
** ** * * * *
2294256 GTGGCTTTTGTTGAAAAAATGCCACTATAAACTAACTCTATTACGGCGTTTGTATAAAAATACCG
1 GCAGAGTTTGTTG-AAAAATGCCACTATAAACTAACCCTATTACGGCATTTATATAAAAACACCG
*
2294321 CTAAAGTACTACTCTATC
65 CTAAAGTACTACTATATC
2294339 GCAGAGTTTGTT
1 GCAGAGTTTGTT
2294351 TAAGAAACGC
Statistics
Matches: 137, Mismatches: 37, Indels: 11
0.74 0.20 0.06
Matches are distributed among these distances:
82 4 0.03
83 73 0.53
84 52 0.38
85 8 0.06
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (82 bp):
GCAGAGTTTGTTGAAAAATGCCACTATAAACTAACCCTATTACGGCATTTATATAAAAACACCGC
TAAAGTACTACTATATC
Found at i:2294818 original size:72 final size:72
Alignment explanation
Indices: 2294728--2294871 Score: 288
Period size: 72 Copynumber: 2.0 Consensus size: 72
2294718 CCTTAATGAG
2294728 TTTTGTCACAGTTACTTATGATTTTTGTGACTATGTTTTTTTTACTCAAAAAGATTAATAACAGT
1 TTTTGTCACAGTTACTTATGATTTTTGTGACTATGTTTTTTTTACTCAAAAAGATTAATAACAGT
2294793 GACGGAA
66 GACGGAA
2294800 TTTTGTCACAGTTACTTATGATTTTTGTGACTATGTTTTTTTTACTCAAAAAGATTAATAACAGT
1 TTTTGTCACAGTTACTTATGATTTTTGTGACTATGTTTTTTTTACTCAAAAAGATTAATAACAGT
2294865 GACGGAA
66 GACGGAA
2294872 CTTTAGACAC
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.43
Consensus pattern (72 bp):
TTTTGTCACAGTTACTTATGATTTTTGTGACTATGTTTTTTTTACTCAAAAAGATTAATAACAGT
GACGGAA
Found at i:2297098 original size:21 final size:22
Alignment explanation
Indices: 2297047--2297099 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
2297037 ATGGTATCGA
*
2297047 TATCGATACCTTAATAGAGAAG
1 TATCGATACTTTAATAGAGAAG
**
2297069 TATTTATACTTTACATA-AG-AG
1 TATCGATACTTTA-ATAGAGAAG
2297090 TATCGATACT
1 TATCGATACT
2297100 ATAAGGCATT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 10 0.40
22 12 0.48
23 3 0.12
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (22 bp):
TATCGATACTTTAATAGAGAAG
Found at i:2300330 original size:19 final size:20
Alignment explanation
Indices: 2300306--2300353 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
2300296 AAATATTTTC
*
2300306 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
2300325 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
2300345 TTTTGAAAA
1 TTTTGAAAA
2300354 ATGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:2301776 original size:21 final size:21
Alignment explanation
Indices: 2301747--2301810 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
2301737 AATCAGATTG
2301747 CCCAAGGGGTACAGATTCCCC
1 CCCAAGGGGTACAGATTCCCC
* *
2301768 CCCAGGGGGAACAGATTCCCC
1 CCCAAGGGGTACAGATTCCCC
* *
2301789 CCCATGGGGTACCGATTCCCC
1 CCCAAGGGGTACAGATTCCCC
2301810 C
1 C
2301811 TGTCTAACGG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.20, C:0.41, G:0.25, T:0.14
Consensus pattern (21 bp):
CCCAAGGGGTACAGATTCCCC
Found at i:2304159 original size:23 final size:22
Alignment explanation
Indices: 2304117--2304177 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 22
2304107 TTAGTACAGA
* *
2304117 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCCTTGAAG
*
2304139 GGGAACTGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-TTGAAG
2304162 GGGAACCGATTCCCCC
1 GGGAACCGATTCCCCC
2304178 CTGGGGTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 13 0.38
23 21 0.62
ACGTcount: A:0.23, C:0.31, G:0.26, T:0.20
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTTGAAG
Found at i:2305745 original size:18 final size:18
Alignment explanation
Indices: 2305724--2305763 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
2305714 GAACAGCACA
2305724 AGGAACAAGCACGAG-CAG
1 AGGAACAAGCAC-AGCCAG
2305742 AGGAACAAGCACAGCCAG
1 AGGAACAAGCACAGCCAG
2305760 AGGA
1 AGGA
2305764 TCAAATGCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.45, C:0.23, G:0.33, T:0.00
Consensus pattern (18 bp):
AGGAACAAGCACAGCCAG
Found at i:2312433 original size:17 final size:18
Alignment explanation
Indices: 2312408--2312442 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2312398 ATTTAACAAA
2312408 AATTAAAAATA-TTAATT
1 AATTAAAAATACTTAATT
*
2312425 AATTTAAAATACTTAATT
1 AATTAAAAATACTTAATT
2312443 TAAAATTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
AATTAAAAATACTTAATT
Found at i:2312466 original size:21 final size:19
Alignment explanation
Indices: 2312445--2312534 Score: 73
Period size: 19 Copynumber: 4.7 Consensus size: 19
2312435 ACTTAATTTA
2312445 AAATTATATATATAATCATT
1 AAATTATA-ATATAATCATT
**
2312465 AAATTATAATATAAAAATTT
1 AAATTATAATATAATCA-TT
*
2312485 GAAA--ATACT-TAAT--TT
1 -AAATTATAATATAATCATT
2312500 AAAATTATATATATAATCATT
1 -AAATTATA-ATATAATCATT
2312521 AAATTATAATATAA
1 AAATTATAATATAA
2312535 AAAGGAAAAG
Statistics
Matches: 56, Mismatches: 6, Indels: 17
0.71 0.08 0.22
Matches are distributed among these distances:
15 5 0.09
17 3 0.05
18 4 0.07
19 21 0.38
20 18 0.32
21 5 0.09
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (19 bp):
AAATTATAATATAATCATT
Found at i:2312491 original size:56 final size:55
Alignment explanation
Indices: 2312425--2312537 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 55
2312415 AATATTAATT
2312425 AATTTAAAATACTTAATTTAAAATTATATATATAATCATTAAATTATAATATAAA
1 AATTTAAAATACTTAATTTAAAATTATATATATAATCATTAAATTATAATATAAA
2312480 AATTTGAAAATACTTAATTTAAAATTATATATATAATCATTAAATTATAATATAAA
1 AATTT-AAAATACTTAATTTAAAATTATATATATAATCATTAAATTATAATATAAA
2312536 AA
1 AA
2312538 GGAAAAGGAA
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 5 0.09
56 52 0.91
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.41
Consensus pattern (55 bp):
AATTTAAAATACTTAATTTAAAATTATATATATAATCATTAAATTATAATATAAA
Found at i:2313905 original size:28 final size:30
Alignment explanation
Indices: 2313837--2313919 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 30
2313827 AACTAAATTT
* *
2313837 TTTTA-GTCAAAATAAATACTTAAAGTTAA
1 TTTTATGTCAAAATAGATACCTAAAGTTAA
* *
2313866 TTTTTTGGTCAAAATAGATACCTAATG-T-A
1 TTTTAT-GTCAAAATAGATACCTAAAGTTAA
*
2313895 TTTTATGTCAAAATAGGTACCTAAA
1 TTTTATGTCAAAATAGATACCTAAA
2313920 CTATTCAAAC
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
28 17 0.38
29 10 0.22
30 1 0.02
31 17 0.38
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.39
Consensus pattern (30 bp):
TTTTATGTCAAAATAGATACCTAAAGTTAA
Found at i:2314072 original size:32 final size:32
Alignment explanation
Indices: 2314036--2314097 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
2314026 GACCAAAAAT
** *
2314036 ACTTTAAGTTTTTATTTTAACAAAACAATATA
1 ACTTTAAGTACTTATTTTAACAAAAAAATATA
* *
2314068 ACTTTAGGTACTTATTTTGACAAAAAAATA
1 ACTTTAAGTACTTATTTTAACAAAAAAATA
2314098 CTTTAGATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (32 bp):
ACTTTAAGTACTTATTTTAACAAAAAAATATA
Found at i:2315271 original size:29 final size:29
Alignment explanation
Indices: 2315229--2315287 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
2315219 ATTTTCACCT
2315229 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
*
2315258 AACTAATTTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
2315287 A
1 A
2315288 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.25
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:2319953 original size:29 final size:29
Alignment explanation
Indices: 2319911--2319969 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
2319901 ATTTTCACCT
2319911 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
2319940 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
2319969 A
1 A
2319970 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:2322855 original size:23 final size:23
Alignment explanation
Indices: 2322829--2322880 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
2322819 AATAACATAT
* **
2322829 TAGGTAACGCTTATATAATGTAA
1 TAGGTAACACTTATATAATAAAA
*
2322852 TAGGTAGCACTTATATAATAAAA
1 TAGGTAACACTTATATAATAAAA
2322875 TAGGTA
1 TAGGTA
2322881 TTTAACCGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (23 bp):
TAGGTAACACTTATATAATAAAA
Found at i:2322933 original size:23 final size:23
Alignment explanation
Indices: 2322907--2322954 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
2322897 AACAAGTACA
2322907 ATAA-CAAATTAGGTAGCGCTTAT
1 ATAATCAAA-TAGGTAGCGCTTAT
**
2322930 ATAATGTAATAGGTAGCGCTTAT
1 ATAATCAAATAGGTAGCGCTTAT
2322953 AT
1 AT
2322955 TGACCTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAATCAAATAGGTAGCGCTTAT
Found at i:2322939 original size:87 final size:87
Alignment explanation
Indices: 2322793--2322954 Score: 270
Period size: 87 Copynumber: 1.9 Consensus size: 87
2322783 ATATTATATC
* *
2322793 ATTTAACCGAAAATATTATCAAGCACAATAACATATTAGGTAACGCTTATATAATGTAATAGGTA
1 ATTTAACCGAAAATATTAACAAGCACAATAACAAATTAGGTAACGCTTATATAATGTAATAGGTA
2322858 GCACTTATATAATAAAATAGGT
66 GCACTTATATAATAAAATAGGT
* * *
2322880 ATTTAACCGGAAATATTAACAAGTACAATAACAAATTAGGTAGCGCTTATATAATGTAATAGGTA
1 ATTTAACCGAAAATATTAACAAGCACAATAACAAATTAGGTAACGCTTATATAATGTAATAGGTA
*
2322945 GCGCTTATAT
66 GCACTTATAT
2322955 TGACCTATTT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 69 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (87 bp):
ATTTAACCGAAAATATTAACAAGCACAATAACAAATTAGGTAACGCTTATATAATGTAATAGGTA
GCACTTATATAATAAAATAGGT
Found at i:2323306 original size:198 final size:198
Alignment explanation
Indices: 2322976--2323471 Score: 556
Period size: 198 Copynumber: 2.5 Consensus size: 198
2322966 GTCATAAAAT
* * * * * *
2322976 CGGTAAATTTGAACCGGTTACATTATAAATTGACCTATTACATTAT-GTATATCGGTTTCGATGT
1 CGGTATATTTTAACCGGTTACATTGTAAATTTACCTATTACATTATAAT-TATCGGTTTCGATGA
* * * *
2323040 TTTCGGGATCGATACAATTTT-AAATATATCGACACTTTATGCGTGCAACTCGTTTGTGCTTTAT
65 TTTCGGGATCGATAC-TTTTTAAAATGTATCGACACTTTATGCGTGCAACTCGTTTGTCCTTCAT
* *
2323104 TTTGGAAAAAAGTATCGACACATATT-TAAAGAGTGTCGATACATAATGTAGACCTATT-TGCTA
129 TTTGGAAAAAAGTATCGACACAAATTAAAAAG-GTGTCGATACATAATGTAGACCTATTCT-CTA
*
2323167 ATTA-AC
192 ATGAGAC
* * *
2323173 CGGTATATTTTAACCGGTTACATTGTAAATTTACCTGTTACATAATAATTATCGATTTCGATG-T
1 CGGTATATTTTAACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGAT
* *
2323237 TTCGAGGATCGATACTTTTTACAAATGTATCGACACTTTATGTGTGCATCTCGTTTG-CCATTCA
66 TTCG-GGATCGATACTTTTTA-AAATGTATCGACACTTTATGCGTGCAACTCGTTTGTCC-TTCA
* * * * * *
2323301 TTTTGGAAAAATGTTTCGACACAAATTAAAAAGGTGTCGATACTTTATGTTGACCTATTCTCTCA
128 TTTTGGAAAAAAGTATCGACACAAATTAAAAAGGTGTCGATACATAATGTAGACCTATTCTCTAA
*
2323366 TGAGCC
193 TGAGAC
* * * * * * **
2323372 CGGTATATTTTTACCGATTACATTGGAAATTTACATATTACATTATAATTATAGGTCTCTTTGAT
1 CGGTATATTTTAACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGAT
* *
2323437 TTTGGGATCGATACTTGTTATAAATGTATCGACAC
66 TTCGGGATCGATACTTTTTA-AAATGTATCGACAC
2323472 AAAATCTAAT
Statistics
Matches: 252, Mismatches: 38, Indels: 16
0.82 0.12 0.05
Matches are distributed among these distances:
196 9 0.04
197 64 0.25
198 88 0.35
199 87 0.35
200 4 0.02
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (198 bp):
CGGTATATTTTAACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGAT
TTCGGGATCGATACTTTTTAAAATGTATCGACACTTTATGCGTGCAACTCGTTTGTCCTTCATTT
TGGAAAAAAGTATCGACACAAATTAAAAAGGTGTCGATACATAATGTAGACCTATTCTCTAATGA
GAC
Found at i:2326231 original size:20 final size:20
Alignment explanation
Indices: 2326185--2326231 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2326175 ACCGGTAGCG
2326185 CTTTACCGGTTTTGTCATTT
1 CTTTACCGGTTTTGTCATTT
**
2326205 CGATACCGGTTTTGTCATATT
1 CTTTACCGGTTTTGTCAT-TT
2326226 -TTTACC
1 CTTTACC
2326232 TATTTTATTG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.15, C:0.21, G:0.15, T:0.49
Consensus pattern (20 bp):
CTTTACCGGTTTTGTCATTT
Found at i:2326836 original size:362 final size:362
Alignment explanation
Indices: 2326159--2327109 Score: 1441
Period size: 362 Copynumber: 2.6 Consensus size: 362
2326149 ATTAAAGTAC
* * * *
2326159 CGACACTTTCAACATAACCGGTAGCGCTTTACCGGTTTTGTCATTTCGATACCGGTTTTGTCATA
1 CGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTCGAGACCGGTTTTGTCATA
* * * * * *
2326224 TTTTTACCTATTTTATTGTTATGGATCGATATATTT-TCATAAAGTATCGACACTTTTTAGACGC
66 TTATTACCTGTTATATTGATAT-GATCGATACATTTGT-ATAAAGTATCGACACTTTTTAGGCGC
* * *
2326288 TATAATTTCTTCTCTTTTAAATTACGAAAGTATCGATACTTATATTAATTTATCGACACTTTCAA
129 TATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTATCGACACTTTCAA
* * *
2326353 TATATCTGATAGCTTTTTACCGATTTTATCATTTCGAACCTGTTTTGTCATATTATTACATGTTA
194 TATATCTGGTAGCTTTTTACCGGTTTTATCATTTCGAACCTGTTTTGTCATATTATTACATATTA
2326418 TATTGCTATGGATCGATACATTTGTATAAAATATCGACACTTTTTAGGCGCTATAACTTCTTCTC
259 TATTGCTATGGATCGATACATTTGTATAAAATATCGACACTTTTTAGGCGCTATAACTTCTTCTC
2326483 TTTTAAATATA-AAAAGTGTCGATAATTATATTAATTTAT
324 TTTTAAAT-TACAAAAGTGTCGATAATTATATTAATTTAT
*** *
2326522 CGACACTTTCAATATATCCGGTAGTTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
1 CGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTCGAGACCGGTTTTGTCATA
*
2326587 TTATTA-CTGTTATATTGATATGTATCGATACATTTGTATAAAGT-TCGACACTTTTTAGGCGTT
66 TTATTACCTGTTATATTGATATG-ATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCT
*
2326650 ATAACTTATTCTCTTTTAAA-TATCAAAAGTGTCGATACTTATATTAATTTATCGACACTTTCAA
130 ATAACTTCTTCTCTTTTAAATTA-CAAAAGTGTCGATACTTATATTAATTTATCGACACTTTCAA
* * *
2326714 TATATCTGGTAGCTTTTTACCGGTTTTATCATTTTGAGATCTGTTTTGTCATATTATTACCTATT
194 TATATCTGGTAGCTTTTTACCGGTTTTATCATTTCGA-ACCTGTTTTGTCATATTATTACATATT
* *
2326779 ATATTGCTATGGATTGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCTATAACTTCTTCT
258 ATATTGCTATGGATCGATACATTTGTATAAAATATCGACACTTTTTAGGCGCTATAACTTCTTCT
*
2326844 CTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
323 CTTTTAAATTACAAAAGTGTCGATAATTATATTAATTTAT
* *
2326884 CGACACTTTCAATATATCCGGTAGCGGTTTACCGGTTTTATCATAAT-G-GCACCGGTTTTGTCA
1 CGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTATCAT-TTCGAG-ACCGGTTTTGTCA
* *
2326947 TATTATTACCTGTTATATTGCTATAGATCGATACATTTGTATAAAGTATCGACACTTTATAGGCG
64 TATTATTACCTGTTATATTGATAT-GATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCG
*
2327012 CTATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATATTTATATTAATTTATCGACACTTTCA
128 CTATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTATCGACACTTTCA
* *
2327077 ATATATCCGGTAG-TGGTTTACCGGTTTTATCAT
193 ATATATCTGGTAGCT-TTTTACCGGTTTTATCAT
2327110 ATTTTTACCT
Statistics
Matches: 536, Mismatches: 40, Indels: 23
0.89 0.07 0.04
Matches are distributed among these distances:
360 2 0.00
361 112 0.21
362 215 0.40
363 100 0.19
364 105 0.20
365 2 0.00
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (362 bp):
CGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTCGAGACCGGTTTTGTCATA
TTATTACCTGTTATATTGATATGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCTA
TAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTATCGACACTTTCAATA
TATCTGGTAGCTTTTTACCGGTTTTATCATTTCGAACCTGTTTTGTCATATTATTACATATTATA
TTGCTATGGATCGATACATTTGTATAAAATATCGACACTTTTTAGGCGCTATAACTTCTTCTCTT
TTAAATTACAAAAGTGTCGATAATTATATTAATTTAT
Found at i:2326889 original size:182 final size:182
Alignment explanation
Indices: 2326159--2327109 Score: 1425
Period size: 182 Copynumber: 5.2 Consensus size: 182
2326149 ATTAAAGTAC
* * ** * * *
2326159 CGACACTTTCAACATAACCGGTAGCGCTTTACCGGTTTTGTCATTTCGATACCGGTTTTGTCATA
1 CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
* * * * * *
2326224 TTTTTACCTATTTTATTGTTATGGATCGATATATTT-TCATAAAGTATCGACACTTTTTAGACGC
66 TTATTACCTGTTATATTGCTATGGATCGATACATTTGT-ATAAAGTATCGACACTTTTTAGGCGC
* * *
2326288 TATAATTTCTTCTCTTTTAAATTACGAAAGTATCGATACTTATATTAATTTAT
130 TATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
* * *
2326341 CGACACTTTCAATATATCTGATAGCTTTTTACCGATTTTATCATTTCGA-ACCTGTTTTGTCATA
1 CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
* *
2326405 TTATTACATGTTATATTGCTATGGATCGATACATTTGTATAAAATATCGACACTTTTTAGGCGCT
66 TTATTACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCT
*
2326470 ATAACTTCTTCTCTTTTAAATATA-AAAAGTGTCGATAATTATATTAATTTAT
131 ATAACTTCTTCTCTTTTAAAT-TACAAAAGTGTCGATACTTATATTAATTTAT
*
2326522 CGACACTTTCAATATATCCGGTAGTTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
1 CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
* * *
2326587 TTATTA-CTGTTATATTGATATGTATCGATACATTTGTATAAAGT-TCGACACTTTTTAGGCGTT
66 TTATTACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCT
*
2326650 ATAACTTATTCTCTTTTAAA-TATCAAAAGTGTCGATACTTATATTAATTTAT
131 ATAACTTCTTCTCTTTTAAATTA-CAAAAGTGTCGATACTTATATTAATTTAT
* * *
2326702 CGACACTTTCAATATATCTGGTAGCTTTTTACCGGTTTTATCATTTTGAGATCTGTTTTGTCATA
1 CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
* *
2326767 TTATTACCTATTATATTGCTATGGATTGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCT
66 TTATTACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCT
2326832 ATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
131 ATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
** * *
2326884 CGACACTTTCAATATATCCGGTAGCGGTTTACCGGTTTTATCATAAT-G-GCACCGGTTTTGTCA
1 CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCAT-TTCGAG-ACCTGTTTTGTCA
* *
2326947 TATTATTACCTGTTATATTGCTATAGATCGATACATTTGTATAAAGTATCGACACTTTATAGGCG
64 TATTATTACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCG
*
2327012 CTATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATATTTATATTAATTTAT
129 CTATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
*
2327066 CGACACTTTCAATATATCCGGTAG-TGGTTTACCGGTTTTATCAT
1 CGACACTTTCAATATATCCGGTAGCT-TTTTACCGGTTTTATCAT
2327110 ATTTTTACCT
Statistics
Matches: 704, Mismatches: 54, Indels: 22
0.90 0.07 0.03
Matches are distributed among these distances:
178 2 0.00
180 131 0.19
181 228 0.32
182 340 0.48
183 3 0.00
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (182 bp):
CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
TTATTACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCT
ATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
Found at i:2328158 original size:13 final size:14
Alignment explanation
Indices: 2328112--2328158 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 14
2328102 TTTATATTAG
2328112 TTATAATCATTATA
1 TTATAATCATTATA
*
2328126 TTATAAAGC-TTA-A
1 TTAT-AATCATTATA
2328139 TTATAATCATTATA
1 TTATAATCATTATA
2328153 TT-TAAT
1 TTATAAT
2328159 TTAATTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
12 3 0.11
13 12 0.43
14 10 0.36
15 3 0.11
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (14 bp):
TTATAATCATTATA
Found at i:2328320 original size:2 final size:2
Alignment explanation
Indices: 2328313--2328347 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2328303 ATGGTATAAT
2328313 TA TA TA TA 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 TA TA TA TA T
2328348 TCACGTGAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2328799 original size:2 final size:2
Alignment explanation
Indices: 2328792--2328817 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2328782 ATGTTTAATG
2328792 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
2328818 GTGTGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2328870 original size:12 final size:12
Alignment explanation
Indices: 2328853--2328907 Score: 65
Period size: 12 Copynumber: 4.3 Consensus size: 12
2328843 TACATCATAC
2328853 ATATATACTTAT
1 ATATATACTTAT
*
2328865 ATATATAGTTAT
1 ATATATACTTAT
*
2328877 GTATATACTTAT
1 ATATATACTTAT
2328889 ATATAATATGCTTAT
1 ATAT-ATA--CTTAT
2328904 ATAT
1 ATAT
2328908 TATATGCTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
12 24 0.67
13 3 0.08
15 9 0.25
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.49
Consensus pattern (12 bp):
ATATATACTTAT
Found at i:2328902 original size:15 final size:15
Alignment explanation
Indices: 2328879--2328920 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
2328869 ATAGTTATGT
*
2328879 ATATACTTATATATA
1 ATATGCTTATATATA
*
2328894 ATATGCTTATATATT
1 ATATGCTTATATATA
2328909 ATATGCTT-TATA
1 ATATGCTTATATA
2328921 CTTTTATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 4 0.16
15 21 0.84
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (15 bp):
ATATGCTTATATATA
Found at i:2329054 original size:9 final size:9
Alignment explanation
Indices: 2329042--2329139 Score: 52
Period size: 9 Copynumber: 11.4 Consensus size: 9
2329032 ATATATGCAC
2329042 TATATAGTT
1 TATATAGTT
2329051 TATATA-TT
1 TATATAGTT
*
2329059 T-TACAGTT
1 TATATAGTT
* *
2329067 CATATA--C
1 TATATAGTT
2329074 TATATAGTT
1 TATATAGTT
2329083 TATA-A-TT
1 TATATAGTT
*
2329090 TATATACTAT
1 TATATAGT-T
*
2329100 ATATACATATTT
1 -TAT--ATAGTT
2329112 TATATAG-T
1 TATATAGTT
2329120 T-TATAGTT
1 TATATAGTT
2329128 TATATA-TT
1 TATATAGTT
2329136 TATA
1 TATA
2329140 CTGTATAATT
Statistics
Matches: 69, Mismatches: 8, Indels: 25
0.68 0.08 0.25
Matches are distributed among these distances:
7 19 0.28
8 17 0.25
9 21 0.30
10 1 0.01
11 6 0.09
12 1 0.01
13 4 0.06
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (9 bp):
TATATAGTT
Found at i:2329084 original size:23 final size:23
Alignment explanation
Indices: 2329051--2329102 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
2329041 CTATATAGTT
* *
2329051 TATATATTTTACAGTTCATATAC
1 TATATAGTTTACAATTCATATAC
* *
2329074 TATATAGTTTATAATTTATATAC
1 TATATAGTTTACAATTCATATAC
2329097 TATATA
1 TATATA
2329103 TACATATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (23 bp):
TATATAGTTTACAATTCATATAC
Found at i:2329238 original size:2 final size:2
Alignment explanation
Indices: 2328997--2329221 Score: 85
Period size: 2 Copynumber: 110.0 Consensus size: 2
2328987 TATAAAAGTA
2328997 AT AT AT A- 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
** * * *
2329038 GC ACT AT AT AGT TT AT AT AT -T TT AC AGT -T CAT AT ACT AT AT AGT
1 AT A-T AT AT A-T AT AT AT AT AT AT AT A-T AT -AT AT A-T AT AT A-T
* * * * *
2329082 TT AT A- AT TT AT AT ACT AT AT AT AC AT AT -T TT AT AT AGT TT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT
* * * * *
2329124 AGT TT AT AT AT TT AT ACT GT AT A- AT TT AT AT ACT -T AT ACT TT
1 A-T AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT A-T AT
*
2329166 AT ACT AT -T ACT AT AT AT AT AT AT AT AT AC ACT -T AT AT AT ACT
1 AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT AT A-T
2329208 -T AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT
2329222 TTTAAGTATA
Statistics
Matches: 166, Mismatches: 30, Indels: 54
0.66 0.12 0.22
Matches are distributed among these distances:
1 11 0.07
2 137 0.83
3 18 0.11
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2329272 original size:4 final size:4
Alignment explanation
Indices: 2329250--2329510 Score: 400
Period size: 4 Copynumber: 65.2 Consensus size: 4
2329240 TTATATAGGT
* * * * *
2329250 ATAC GTAC ATAC GTAC ATAC ATAC GTATAT ATAC ATAC GTAC ATAC GTAC
1 ATAC ATAC ATAC ATAC ATAC ATAC --ATAC ATAC ATAC ATAC ATAC ATAC
* *
2329300 ATAC GTAC ATAC AT-- ATAC ATAC GTAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
2329346 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
2329394 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
2329442 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC GTAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* *
2329490 GTAC ATAC ATAC ATAC GTAC A
1 ATAC ATAC ATAC ATAC ATAC A
2329511 ATAATTGTTT
Statistics
Matches: 233, Mismatches: 20, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
2 2 0.01
4 228 0.98
6 3 0.01
ACGTcount: A:0.46, C:0.24, G:0.04, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:2331557 original size:12 final size:11
Alignment explanation
Indices: 2331491--2331558 Score: 52
Period size: 11 Copynumber: 6.3 Consensus size: 11
2331481 AAAATTACAT
2331491 TATTAAAAATA
1 TATTAAAAATA
2331502 TATTAAAAATA
1 TATTAAAAATA
* * ***
2331513 CACTATTGATA
1 TATTAAAAATA
2331524 -ATTATAAAAT-
1 TATTA-AAAATA
2331534 T-TTAAAAATA
1 TATTAAAAATA
2331544 TATTAAAAATTA
1 TATTAAAAA-TA
2331556 TAT
1 TAT
2331559 AATACAACTA
Statistics
Matches: 43, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
9 5 0.12
10 7 0.16
11 26 0.60
12 5 0.12
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:2331877 original size:25 final size:26
Alignment explanation
Indices: 2331849--2331903 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 26
2331839 TTAATAAAAA
2331849 AATAT-TTATCTAATGATAA-ATATTT
1 AATATATT-TCTAATGATAATATATTT
*
2331874 AATATATTTCTAATGATAATATTTTT
1 AATATATTTCTAATGATAATATATTT
2331900 AATA
1 AATA
2331904 ACTAATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 16 0.59
26 11 0.41
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49
Consensus pattern (26 bp):
AATATATTTCTAATGATAATATATTT
Found at i:2331969 original size:24 final size:22
Alignment explanation
Indices: 2331941--2331987 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
2331931 TTGAGGTTTT
*
2331941 GGGTTTAAATATTATAAATATCAA
1 GGGTTTAAACATT-T-AATATCAA
*
2331965 GGGTTTGAACATTTAATATCAA
1 GGGTTTAAACATTTAATATCAA
2331987 G
1 G
2331988 ATACTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 9 0.43
23 1 0.05
24 11 0.52
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.36
Consensus pattern (22 bp):
GGGTTTAAACATTTAATATCAA
Found at i:2332698 original size:19 final size:19
Alignment explanation
Indices: 2332674--2332721 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
2332664 GCCATATATG
2332674 CAGCAGTCCATATACAGAT
1 CAGCAGTCCATATACAGAT
2332693 CAGCAGTCCATATACAGAT
1 CAGCAGTCCATATACAGAT
*
2332712 CAGTAGTCCA
1 CAGCAGTCCA
2332722 AACAACAGCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (19 bp):
CAGCAGTCCATATACAGAT
Found at i:2334537 original size:32 final size:31
Alignment explanation
Indices: 2334496--2334556 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 31
2334486 AACATACTCA
*
2334496 TTTCATCTCTTACACAACACACTCCTTTCAT
1 TTTCATCTCTTACACAACAAACTCCTTTCAT
2334527 TTTCAATCTCTTACACAACAAACTCCTTTC
1 TTTC-ATCTCTTACACAACAAACTCCTTTC
2334557 TTCTAACCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 4 0.14
32 24 0.86
ACGTcount: A:0.28, C:0.34, G:0.00, T:0.38
Consensus pattern (31 bp):
TTTCATCTCTTACACAACAAACTCCTTTCAT
Found at i:2336830 original size:160 final size:156
Alignment explanation
Indices: 2336386--2336849 Score: 443
Period size: 156 Copynumber: 3.0 Consensus size: 156
2336376 AATGAATGTT
* * * * *
2336386 TACTTTCAATTCCGCTTTTTGATAAC-AA-TTTTT--TTTTCAATTTAGTCCTTCAATTTTTCAT
1 TACTATCAATTCCTCTTTTT-ATAACAAATTTTTTAATTTTTAA-TT-GTCATTCAATTTTTTAT
** ****
2336447 AATCT-TCTTATTTCTTCAATTCGTCATTTATTTTAAG-TC-CCTTTTTACCAAATTTGTGTCAC
63 AATCTCT-TTATTTCTTCAATTCGTCATTTATTTTAAGTTCGTTTTTTTACCAAATTTAAACCAC
* *
2336509 TTGCTCCTAAATCATAGTAGAATACATGAG
127 ATGCTCCTAAATCATAGTAGAATACAGGAG
* * *
2336539 TGCTATCAATTCCTCTTTTTATAACAAATTTTTTAGTTTTTAATTGTCCTTCAATTTTTTATAAT
1 TACTATCAATTCCTCTTTTTATAACAAATTTTTTAATTTTTAATTGTCATTCAATTTTTTATAAT
* *
2336604 CTCTTTATTTCTTCAATTCGTCATTTATTTTAAGTTCGTTTTTTTACCAAATTTGAGCCACATGC
66 CTCTTTATTTCTTCAATTCGTCATTTATTTTAAGTTCGTTTTTTTACCAAATTTAAACCACATGC
*
2336669 TCCTAAATCATAGTAGAATACAGGTG
131 TCCTAAATCATAGTAGAATACAGGAG
* * *
2336695 TACTTTCAATTCTTCTTTCTTATAACAATTCTTTTTAATTTTTAAATTTAGTCATTC-A-TTTTT
1 TACTATCAATTCCTCTTT-TTATAACAAAT-TTTTTAATTTTT-AA-TT-GTCATTCAATTTTTT
* *
2336758 ATTAATAT-TCTTA-TTCATTCAATTTGTCATTTATTTT-AGATAT-GTTGTTTTTA-CAAATTT
61 A-TAATCTCT-TTATTTC-TTCAATTCGTCATTTATTTTAAG-T-TCGTT-TTTTTACCAAATTT
* * * *
2336818 AAACCACATGCTCATATATCATAATATAATAC
120 AAACCACATGCTCCTAAATCATAGTAGAATAC
2336850 CTATGTAACT
Statistics
Matches: 267, Mismatches: 26, Indels: 29
0.83 0.08 0.09
Matches are distributed among these distances:
152 5 0.02
153 19 0.07
154 56 0.21
155 5 0.02
156 67 0.25
157 10 0.04
158 11 0.04
159 14 0.05
160 67 0.25
161 13 0.05
ACGTcount: A:0.28, C:0.16, G:0.07, T:0.49
Consensus pattern (156 bp):
TACTATCAATTCCTCTTTTTATAACAAATTTTTTAATTTTTAATTGTCATTCAATTTTTTATAAT
CTCTTTATTTCTTCAATTCGTCATTTATTTTAAGTTCGTTTTTTTACCAAATTTAAACCACATGC
TCCTAAATCATAGTAGAATACAGGAG
Found at i:2337589 original size:15 final size:15
Alignment explanation
Indices: 2337569--2337631 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 15
2337559 ATTTTGATCA
*
2337569 TTTTAATAATTTTAT
1 TTTTAAAAATTTTAT
2337584 TTTTAAAAATTTTA-
1 TTTTAAAAATTTTAT
**
2337598 --AAAATAAATTATTAT
1 TTTTAA-AAATT-TTAT
*
2337613 ATTTAAAAATTTTAT
1 TTTTAAAAATTTTAT
2337628 TTTT
1 TTTT
2337632 GGAAAAAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
12 2 0.05
13 5 0.14
14 3 0.08
15 20 0.54
16 5 0.14
17 2 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTTAAAAATTTTAT
Found at i:2337719 original size:29 final size:30
Alignment explanation
Indices: 2337681--2337737 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
2337671 ACCTAACAGT
* *
2337681 AAATAATTACCTATC-AAGCACCGTTTCTCC
1 AAATAATTACCAATCTAA-CACCCTTTCTCC
2337711 AAAT-ATTACCAATCTAACACCCTTTCT
1 AAATAATTACCAATCTAACACCCTTTCT
2337738 GACAGGTGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.35, C:0.30, G:0.04, T:0.32
Consensus pattern (30 bp):
AAATAATTACCAATCTAACACCCTTTCTCC
Found at i:2338532 original size:156 final size:161
Alignment explanation
Indices: 2338254--2338573 Score: 578
Period size: 156 Copynumber: 2.0 Consensus size: 161
2338244 ATTTTTTAAT
2338254 TTTTTTAGTATTATTTTATATTTTAATTCGTATACTATTTAATTAATTAAGAGAATGATCGTAAA
1 TTTTTTAGTATTATTTTATATTTTAATTCGTATACTATTTAATTAATTAAGAGAATGATCGTAAA
2338319 TTAGAAACAATTAATTATTTTTGCATATATAAGACTCTCTATCTTTCAAACTCTCAAACTCTCAA
66 TTAGAAACAATTAATTATTTTTGCATATATAAGACTCTCTATCTTTCAAACTCTCAAACTCTCAA
2338384 AATGAGCCAT-TTTCAGC-TGTTTTCTATGA
131 AATGAGCCATATTTCAGCTTGTTTTCTATGA
2338413 TTTTTTAGTATTA-TTT-TATTTT-ATTCGTATACTATTTAATTAATTAAGAGAATGATCGTAAA
1 TTTTTTAGTATTATTTTATATTTTAATTCGTATACTATTTAATTAATTAAGAGAATGATCGTAAA
*
2338475 TTAGAAACAATTATTTATTTTTGCATATATAAGACTCTCTATCTTTCAAACTCTCAAACTCTCAA
66 TTAGAAACAATTAATTATTTTTGCATATATAAGACTCTCTATCTTTCAAACTCTCAAACTCTCAA
2338540 AATGAGCCATATTTCAGCTATTGTTTTCTATGA
131 AATGAGCCATATTTCAGC--TTGTTTTCTATGA
2338573 T
1 T
2338574 GGAGAAATTC
Statistics
Matches: 156, Mismatches: 1, Indels: 7
0.95 0.01 0.04
Matches are distributed among these distances:
156 114 0.73
157 13 0.08
158 3 0.02
159 13 0.08
160 13 0.08
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.45
Consensus pattern (161 bp):
TTTTTTAGTATTATTTTATATTTTAATTCGTATACTATTTAATTAATTAAGAGAATGATCGTAAA
TTAGAAACAATTAATTATTTTTGCATATATAAGACTCTCTATCTTTCAAACTCTCAAACTCTCAA
AATGAGCCATATTTCAGCTTGTTTTCTATGA
Found at i:2349918 original size:2 final size:2
Alignment explanation
Indices: 2349911--2349977 Score: 120
Period size: 2 Copynumber: 34.5 Consensus size: 2
2349901 ATTGAAATTA
2349911 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2349952 AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2349978 ACGACAATTA
Statistics
Matches: 63, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 61 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2352591 original size:16 final size:17
Alignment explanation
Indices: 2352561--2352592 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2352551 ATATTTATTT
2352561 ATATAAAATATAATATA
1 ATATAAAATATAATATA
2352578 ATATAAAA-ATAATAT
1 ATATAAAATATAATAT
2352593 TACGATCTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATATAAAATATAATATA
Found at i:2378100 original size:2 final size:2
Alignment explanation
Indices: 2378093--2378134 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2378083 TCTCATTTTC
2378093 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
2378135 TTAAAAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2382279 original size:29 final size:28
Alignment explanation
Indices: 2382219--2382304 Score: 84
Period size: 29 Copynumber: 3.0 Consensus size: 28
2382209 TTTAAGTACC
* * *
2382219 TATTTTGACATAAAATACTTCATG-TATT
1 TATTTTGACAAAAAATACTTTA-GATACT
2382247 TATTTTGACAAAAAATAACTTTAGATACT
1 TATTTTGACAAAAAAT-ACTTTAGATACT
* * *
2382276 TATTTTAATTAAAAAATACTTTAGGTACT
1 TATTTTGA-CAAAAAATACTTTAGATACT
2382305 CAAAGAAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
28 16 0.33
29 26 0.53
30 7 0.14
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (28 bp):
TATTTTGACAAAAAATACTTTAGATACT
Found at i:2382552 original size:17 final size:17
Alignment explanation
Indices: 2382530--2382566 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
2382520 AATAACACTT
2382530 ACTCTTTGAATTTAATA
1 ACTCTTTGAATTTAATA
2382547 ACTCTTTGAATTTAATA
1 ACTCTTTGAATTTAATA
2382564 ACT
1 ACT
2382567 TTTACCTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.35, C:0.14, G:0.05, T:0.46
Consensus pattern (17 bp):
ACTCTTTGAATTTAATA
Found at i:2385470 original size:36 final size:36
Alignment explanation
Indices: 2385430--2385568 Score: 235
Period size: 36 Copynumber: 3.9 Consensus size: 36
2385420 ACGGTACTGG
*
2385430 ACATTGATACACGAATGTACCAAAGCTAATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
*
2385466 ACATTGATACACGAATGTACCAAAGCCGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
*
2385502 ACATTGATACACAAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
2385538 ACATTGATACACGAATGTATCC-AAGCTGATA
1 ACATTGATACACGAATGTA-CCAAAGCTGATA
2385569 ATGGATAAAT
Statistics
Matches: 97, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
36 95 0.98
37 2 0.02
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.24
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATATGATA
Found at i:2393031 original size:36 final size:36
Alignment explanation
Indices: 2392989--2393163 Score: 287
Period size: 36 Copynumber: 4.9 Consensus size: 36
2392979 AAGATGCTGG
2392989 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
2393025 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
*
2393061 ACATTGATACACGAATGTACCAAAGCTAATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
* * *
2393097 TCATTGATACACGAATGTACCAAAGGTGATATAATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
* * *
2393133 ACATTGATACATGAATGTATCAACGCTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
2393164 ATGGATAAAT
Statistics
Matches: 129, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 129 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATATGATA
Found at i:2398434 original size:60 final size:60
Alignment explanation
Indices: 2398369--2398531 Score: 172
Period size: 60 Copynumber: 2.7 Consensus size: 60
2398359 TATTTCAAAA
2398369 TAGTCCCTAAACTTTTAAACATTTCAATTTCATCCCTAAATTATGACGA-TCATTCTAAAT
1 TAGTCCCTAAACTTTTAAACATTTCAATTTCATCCCTAAATTATGA-GATTCATTCTAAAT
* * * * * * * *
2398429 TAGT-CCTCAAACTTTTGAATATTTCATTTTCATCCCCAAACTATGATATTTATTTTAAAT
1 TAGTCCCT-AAACTTTTAAACATTTCAATTTCATCCCTAAATTATGAGATTCATTCTAAAT
* * *
2398489 TAGTCCTTAAACCTTTTAAGCATTTCAATTTTAT--CTAAATTAT
1 TAGTCCCTAAA-CTTTTAAACATTTCAATTTCATCCCTAAATTAT
2398532 ACATATATAT
Statistics
Matches: 83, Mismatches: 16, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
59 11 0.13
60 53 0.64
61 19 0.23
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.43
Consensus pattern (60 bp):
TAGTCCCTAAACTTTTAAACATTTCAATTTCATCCCTAAATTATGAGATTCATTCTAAAT
Found at i:2398771 original size:60 final size:58
Alignment explanation
Indices: 2398647--2398791 Score: 200
Period size: 60 Copynumber: 2.5 Consensus size: 58
2398637 TGGAAGATTC
* ** * * * *
2398647 AAAAGTTTAGGGACTAAAATAGAATGATATTCATATTTGGGATGAAATTGGATTGTTT
1 AAAAGTTTAAGGACTAATTTAGAATGAGAGTCATATTTGGGATAAAATTGAATTGTTT
2398705 AAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTTGGGATAAAATTGAATTGTTT
1 AAAAGTTTAAGGACTAATTTAGAATGAGAGTCATA--TTTGGGATAAAATTGAATTGTTT
*
2398765 AAAAGTTTAAGGACTAATTTAAAATGA
1 AAAAGTTTAAGGACTAATTTAGAATGA
2398792 AGGTTATATT
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
58 30 0.39
60 47 0.61
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (58 bp):
AAAAGTTTAAGGACTAATTTAGAATGAGAGTCATATTTGGGATAAAATTGAATTGTTT
Found at i:2403334 original size:22 final size:18
Alignment explanation
Indices: 2403316--2403363 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
2403306 TCCTTTTATC
*
2403316 ATTTTTATTATTATTTTTT
1 ATTTTTTTTATT-TTTTTT
2403335 ATTTTTTTTA-TTTTTTT
1 ATTTTTTTTATTTTTTTT
2403352 A-TTTTTTTATTT
1 ATTTTTTTTATTT
2403364 ATACGATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 8 0.30
17 9 0.33
18 1 0.04
19 9 0.33
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (18 bp):
ATTTTTTTTATTTTTTTT
Found at i:2403341 original size:9 final size:9
Alignment explanation
Indices: 2403316--2403363 Score: 64
Period size: 8 Copynumber: 5.4 Consensus size: 9
2403306 TCCTTTTATC
*
2403316 ATTTTTATT
1 ATTTTTTTT
2403325 ATTATTTTTT
1 ATT-TTTTTT
2403335 ATTTTTTTT
1 ATTTTTTTT
2403344 A-TTTTTTT
1 ATTTTTTTT
2403352 A-TTTTTTT
1 ATTTTTTTT
2403360 ATTT
1 ATTT
2403364 ATACGATATT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
8 16 0.44
9 12 0.33
10 8 0.22
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:2403342 original size:8 final size:8
Alignment explanation
Indices: 2403329--2403445 Score: 72
Period size: 8 Copynumber: 13.8 Consensus size: 8
2403319 TTTATTATTA
2403329 TTTTTTATT
1 TTTTTTA-T
2403338 TTTTTTAT
1 TTTTTTAT
2403346 TTTTTTAT
1 TTTTTTAT
2403354 TTTTTTAT
1 TTTTTTAT
**
2403362 TTATACGATAT
1 TT-T--TTTAT
* *
2403373 TATATATAT
1 T-TTTTTAT
*
2403382 TATTTTAT
1 TTTTTTAT
*
2403390 TTTTTAAT
1 TTTTTTAT
**
2403398 CCTTTTAT
1 TTTTTTAT
2403406 TATTTTTAT
1 T-TTTTTAT
*
2403415 TTGTTTAT
1 TTTTTTAT
*
2403423 TTTATTAT
1 TTTTTTAT
*
2403431 TATTTTAT
1 TTTTTTAT
2403439 TTCTTTT
1 TT-TTTT
2403446 TTCTACTACT
Statistics
Matches: 82, Mismatches: 20, Indels: 12
0.72 0.18 0.11
Matches are distributed among these distances:
8 53 0.65
9 24 0.29
11 4 0.05
12 1 0.01
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.74
Consensus pattern (8 bp):
TTTTTTAT
Found at i:2406903 original size:95 final size:94
Alignment explanation
Indices: 2406719--2406979 Score: 314
Period size: 95 Copynumber: 2.7 Consensus size: 94
2406709 AGATTATAAT
* * * *
2406719 ATTATATATATACAATAAAGCTTGA-TCTGTCCCTCTAAAGCAATT-GTTAAAGGCCCGTCTTTA
1 ATTATA-ATATATAATAAAGCTTGAGT-TGTCCCTCTAGAGCAATTGGTTAAAGCCCCGACTTTA
*
2406782 TGGATAAGATTCAGCTAGCCTGATAAAGGTG
64 TGGATAAGATTCAACTAGCCTGATAAAGGTG
*
2406813 ATTATAATGTATAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCC-AGCTTTA
1 ATTATAATATATAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAA-GCCCCGA-CTTTA
*
2406877 TGGATAATATTCAACTAGCCTGATAAAGGTG
64 TGGATAAGATTCAACTAGCCTGATAAAGGTG
* * * *
2406908 ATTATAATATCT-ATACAATGATATTAAGCTGTCCCTCTAGAGCAATTGGTTAAATGCCCCGACT
1 ATTATAATATATAATA-AA-G--CTTGAGTTGTCCCTCTAGAGCAATTGGTTAAA-GCCCCGACT
2406972 TTATGGAT
61 TTATGGAT
2406980 TTAGCTAGCC
Statistics
Matches: 145, Mismatches: 13, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
93 33 0.23
94 16 0.11
95 50 0.34
96 1 0.01
98 44 0.30
99 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Consensus pattern (94 bp):
ATTATAATATATAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAAGCCCCGACTTTATG
GATAAGATTCAACTAGCCTGATAAAGGTG
Found at i:2408347 original size:36 final size:36
Alignment explanation
Indices: 2408292--2408406 Score: 178
Period size: 36 Copynumber: 3.2 Consensus size: 36
2408282 AATTTACTCA
*
2408292 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
2408329 AAACAAATTTTGTCTCTCTTGAGACCGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
**
2408365 AAA-AAAAATTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
2408400 AAACAAA
1 AAACAAA
2408407 ATCTTTGAAT
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
35 32 0.44
36 33 0.46
37 7 0.10
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.36
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
Found at i:2408384 original size:35 final size:35
Alignment explanation
Indices: 2408302--2408408 Score: 160
Period size: 35 Copynumber: 3.0 Consensus size: 35
2408292 AAACAAAGTT
* **
2408302 TTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAA-AAAAA
*
2408338 TTGTCTCTCTTGAGACCGTTTCCCTTGAAAAAAAA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAAAAAA
*
2408373 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAAAAAA
2408408 T
1 T
2408409 CTTTGAATAT
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
35 37 0.57
36 28 0.43
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.37
Consensus pattern (35 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAAAAAAA
Found at i:2408442 original size:65 final size:65
Alignment explanation
Indices: 2408292--2408728 Score: 385
Period size: 65 Copynumber: 6.6 Consensus size: 65
2408282 AATTTACTCA
* **
2408292 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGA-CCG
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA------ATCT-TTGA-ATATG
*
2408356 TTTCCCTTG
57 TTTTCCTTG
** *
2408365 AAA-AAAAATTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGTTTTCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATCTTTGAATATGTTTTCCTTG
* * * * *
2408429 AAACAAATTTTGTCTCCCTTGAGACAGTTTCT-TTCAAAACAAAGT-TTTG----T-CTCT-CTT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT-GAAACAAAATCTTTGAATATGTTTTCCTT
2408486 G
65 G
*
2408487 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGTTTTCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATCTTTGAATATGTTTTCCTTG
* * * ** * *
2408552 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTCTCTCTTGAGACA-GTTTCC
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AA-AATCT-TTGA-ATATGTTTTC
2408616 CTTG
62 CTTG
* ** *
2408620 AAACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAACTCCAATATTTGAATATG-TTTCTC
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AAAATCTTTGAATATGTTTTC-C
2408684 TTG
63 TTG
* * *
2408687 AAACAAAATTTTGCCTCCCTGGAGACAGTTTCTCTTGAAACA
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
2408729 CAAAAAACCT
Statistics
Matches: 300, Mismatches: 45, Indels: 45
0.77 0.12 0.12
Matches are distributed among these distances:
58 42 0.14
59 8 0.03
60 1 0.00
63 2 0.01
64 24 0.08
65 75 0.25
66 7 0.02
67 45 0.15
68 25 0.08
69 32 0.11
71 33 0.11
72 3 0.01
73 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (65 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATCTTTGAATATGTTTTCCTTG
Found at i:2408450 original size:21 final size:21
Alignment explanation
Indices: 2408424--2408508 Score: 58
Period size: 21 Copynumber: 4.3 Consensus size: 21
2408414 AATATGTTTT
2408424 CCTTGAAACAAATTTTGTCTC
1 CCTTGAAACAAATTTTGTCTC
* *
2408445 CCTTGAGAC--A-GTT-TCT-
1 CCTTGAAACAAATTTTGTCTC
*
2408461 --TTCAAAACAAAGTTTTGTCTC
1 CCTTGAA-ACAAA-TTTTGTCTC
*
2408482 TCTTGAAACAAATTTTGTCTC
1 CCTTGAAACAAATTTTGTCTC
*
2408503 TCTTGA
1 CCTTGA
2408509 GACAGTTTCC
Statistics
Matches: 49, Mismatches: 6, Indels: 18
0.67 0.08 0.25
Matches are distributed among these distances:
14 3 0.06
15 2 0.04
17 4 0.08
18 2 0.04
19 3 0.06
20 3 0.06
21 23 0.47
22 5 0.10
23 4 0.08
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (21 bp):
CCTTGAAACAAATTTTGTCTC
Found at i:2408490 original size:22 final size:21
Alignment explanation
Indices: 2408465--2408508 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 21
2408455 GTTTCTTTCA
2408465 AAACAAAGTTTTGTCTCTCTTG
1 AAACAAA-TTTTGTCTCTCTTG
2408487 AAACAAATTTTGTCTCTCTTG
1 AAACAAATTTTGTCTCTCTTG
2408508 A
1 A
2408509 GACAGTTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.41
Consensus pattern (21 bp):
AAACAAATTTTGTCTCTCTTG
Found at i:2408645 original size:37 final size:36
Alignment explanation
Indices: 2408542--2408660 Score: 129
Period size: 32 Copynumber: 3.4 Consensus size: 36
2408532 CTTTGAATAT
* *
2408542 GTTTTCCTTGAAACAAATTTTGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
** * *
2408578 GTTTCTTTTGGAACTAA----GTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
2408610 GTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACA
* *
2408647 ATTTCTCTTGAAAC
1 GTTTCCCTTGAAAC
2408661 TCCAATATTT
Statistics
Matches: 66, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
32 27 0.41
36 12 0.18
37 27 0.41
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.39
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:2408712 original size:67 final size:67
Alignment explanation
Indices: 2408480--2408764 Score: 278
Period size: 67 Copynumber: 4.2 Consensus size: 67
2408470 AAGTTTTGTC
* * * *
2408480 TCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAAATCTTTGAATATG
1 TCTCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACTCAAATATTTGAATATG
2408543 TT
66 TT
* * * *
2408545 T-TCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTTTTGGAACT-AAGTCTCTCTTGAG
1 TCT-CTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACTCAA--ATAT-TTGA-
*
2408607 ACA-GTT
61 ATATGTT
* * * * *
2408613 TCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAACTCCAATATTTGAATATG
1 TCTCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACTCAAATATTTGAATATG
2408678 TT
66 TT
* * * *
2408680 TCTCTTGAAACAAAATTTTGCCTCCCTGGAGACAGTTTCTCTTGAAACACAAAAAACCTTTGAA-
1 TCTCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACTC-AAATA--TTTGAAT
2408744 ATTGTT
63 A-TGTT
2408750 TCTCTTGAAACAAAA
1 TCTCTTGAAACAAAA
2408765 AAACCTTTGA
Statistics
Matches: 181, Mismatches: 25, Indels: 23
0.79 0.11 0.10
Matches are distributed among these distances:
64 1 0.01
65 43 0.24
66 2 0.01
67 53 0.29
68 21 0.12
69 35 0.19
70 26 0.14
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (67 bp):
TCTCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACTCAAATATTTGAATATG
TT
Done.