Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 143 of 292
Found at i:42564930 original size:9 final size:9
Alignment explanation
Indices: 42564918--42564974 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
42564908 TTTGATAAAC
42564918 ATGATATGT
1 ATGATATGT
*
42564927 ATGATATGCAC
1 ATGATATG--T
*
42564938 ATGACATGT
1 ATGATATGT
*
42564947 ATGATATGCAC
1 ATGATATG--T
42564958 ATGATATGT
1 ATGATATGT
42564967 ATGATATG
1 ATGATATG
42564975 CACACGAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:42564941 original size:20 final size:20
Alignment explanation
Indices: 42564916--42564978 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
42564906 ATTTTGATAA
42564916 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
42564936 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
42564956 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
42564976 ACA
1 ACA
42564979 CGAGATGTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:42565089 original size:24 final size:24
Alignment explanation
Indices: 42565033--42565221 Score: 269
Period size: 24 Copynumber: 8.0 Consensus size: 24
42565023 GAGGAAGTGA
*
42565033 AAAATGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
42565056 TAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
42565080 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
42565104 AAAA-GGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
*
42565127 AAAAGGGCTTACGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
*
42565151 -AAAGGGCTTATGCCCCAGTTATA
1 AAAAGGGCTTATGCCCCAGTTATC
* *
42565174 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
42565198 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
42565222 ATGATAAAGC
Statistics
Matches: 151, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
23 65 0.43
24 75 0.50
25 11 0.07
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:42565112 original size:47 final size:47
Alignment explanation
Indices: 42565033--42565202 Score: 268
Period size: 47 Copynumber: 3.6 Consensus size: 47
42565023 GAGGAAGTGA
* * *
42565033 AAAATGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGCTTATGCCCCAGTTATC
42565080 AAAAGGGCTTATGCCCCAGTTATCAAAAGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGCTTATGCCCCAGTTATC
* * *
42565127 AAAAGGGCTTACGCCCCAGTTATCAAAGGGCTTATGCCCCAGTTATA
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGCTTATGCCCCAGTTATC
* *
42565174 AAAAGGGCTTTTGCCCCAGTTATTAAAAG
1 AAAAGGGCTTATGCCCCAGTTATCAAAAG
42565203 AGGCTAGGCC
Statistics
Matches: 113, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 113 1.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGCTTATGCCCCAGTTATC
Found at i:42565446 original size:31 final size:31
Alignment explanation
Indices: 42565411--42565474 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
42565401 CGTTTACCGT
*
42565411 AAAGGCTTCGGCCCAGTAATATGAAATTTGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
42565442 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
42565473 AA
1 AA
42565475 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:42568904 original size:27 final size:27
Alignment explanation
Indices: 42568321--42568903 Score: 717
Period size: 27 Copynumber: 21.6 Consensus size: 27
42568311 AAAGTACTCC
* *
42568321 CGATTTACATAATTGCCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
42568348 C-AGGTTATAGAATTACCGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
*
42568375 CGATTTACAGAATTACCATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
42568402 CGATTTATAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
42568429 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
42568456 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
42568483 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
42568510 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
42568537 C-AGTTTACAGAATTATTGTTTTACCAT
1 CGA-TTTACAGAATTACCGTTTTACCCT
* **
42568564 TGATTTACAGAATTACTATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
42568591 CGATTTATAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
42568618 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
42568645 CGATTTACAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* **
42568672 C-AGTTTACAAAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
* *
42568699 CGATTTATAGAATTACCATTTTACCC-
1 CGATTTACAGAATTACCGTTTTACCCT
* * * *
42568725 CTAATTTACATAATTACCATTTTACCCC
1 C-GATTTACAGAATTACCGTTTTACCCT
* *
42568753 CGATTTACATAATTATCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
42568780 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
42568807 CGATTTACAGAATTACCATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
42568834 CGATTTATAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* * *
42568861 TGATTCACAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
42568888 CGATTTACAAAATTAC
1 CGATTTACAGAATTAC
42568904 TAAAATACCC
Statistics
Matches: 487, Mismatches: 59, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
26 5 0.01
27 477 0.98
28 5 0.01
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (27 bp):
CGATTTACAGAATTACCGTTTTACCCT
Found at i:42570244 original size:9 final size:9
Alignment explanation
Indices: 42570232--42570288 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
42570222 TTTGATAAAC
42570232 ATGATATGT
1 ATGATATGT
*
42570241 ATGATATGCAC
1 ATGATATG--T
*
42570252 ATGACATGT
1 ATGATATGT
*
42570261 ATGATATGCAC
1 ATGATATG--T
42570272 ATGATATGT
1 ATGATATGT
42570281 ATGATATG
1 ATGATATG
42570289 CACACGAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:42570255 original size:20 final size:20
Alignment explanation
Indices: 42570230--42570292 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
42570220 ATTTTGATAA
42570230 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
42570250 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
42570270 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
42570290 ACA
1 ACA
42570293 CGAGATGTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:42570403 original size:24 final size:24
Alignment explanation
Indices: 42570347--42570536 Score: 260
Period size: 24 Copynumber: 8.0 Consensus size: 24
42570337 GAGGAAGTGA
*
42570347 AAAATGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
42570370 TAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
42570394 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
*
42570418 AAAAAGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
* *
42570442 AAAAGGGCTTACGCCGCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
*
42570466 -AAAGGGCTTATGCCCCAGTTATA
1 AAAAGGGCTTATGCCCCAGTTATC
* *
42570489 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
42570513 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
42570537 ATGATAAAGC
Statistics
Matches: 149, Mismatches: 14, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
23 41 0.28
24 97 0.65
25 11 0.07
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:42570471 original size:71 final size:71
Alignment explanation
Indices: 42570346--42570536 Score: 262
Period size: 71 Copynumber: 2.7 Consensus size: 71
42570336 GGAGGAAGTG
* * *
42570346 AAAAATGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCC
1 AAAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTACGCCCCAGTTATCAAAAGGGCTTATGCCCC
42570411 AGTTAT
66 AGTTAT
*
42570417 CAAAAA-GGCTTATGCCCCAGTTATCAAAAGGGCTTACGCCGCAGTTATC-AAAGGGCTTATGCC
1 -AAAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTACGCCCCAGTTATCAAAAGGGCTTATGCC
42570480 CCAGTTAT
64 CCAGTTAT
* *
42570488 AAAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTACGCC-CCAGTTAT
42570537 ATGATAAAGC
Statistics
Matches: 108, Mismatches: 6, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
70 5 0.05
71 66 0.61
72 37 0.34
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (71 bp):
AAAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTACGCCCCAGTTATCAAAAGGGCTTATGCCCC
AGTTAT
Found at i:42570493 original size:47 final size:47
Alignment explanation
Indices: 42570346--42570537 Score: 251
Period size: 47 Copynumber: 4.0 Consensus size: 47
42570336 GGAGGAAGTG
* *
42570346 AAAAATGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
1 AAAAAGGGCTTATGCCCCAGTTATCAAAGGGCTTATGCCCCAGTTAT
* *
42570393 CAAAAGGGCTTATGCCCCAGTTATCAAAAAGGCTTATGCCCCAGTTAT
1 AAAAAGGGCTTATGCCCCAGTTATC-AAAGGGCTTATGCCCCAGTTAT
* * *
42570441 CAAAAGGGCTTACGCCGCAGTTATCAAAGGGCTTATGCCCCAGTTAT
1 AAAAAGGGCTTATGCCCCAGTTATCAAAGGGCTTATGCCCCAGTTAT
* * *
42570488 AAAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAAGGGCTTATGCCCCAGTTA-TCAAAG-GGCTTATGCC-CCAGTTAT
42570537 A
1 A
42570538 TGATAAAGCA
Statistics
Matches: 128, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
47 62 0.48
48 54 0.42
49 12 0.09
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (47 bp):
AAAAAGGGCTTATGCCCCAGTTATCAAAGGGCTTATGCCCCAGTTAT
Found at i:42570768 original size:31 final size:31
Alignment explanation
Indices: 42570730--42570793 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
42570720 CGTTTACCGT
*
42570730 AAAGGCTTCGGCCCAGTAATATGAAATTTGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
42570761 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
42570792 AA
1 AA
42570794 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:42581380 original size:60 final size:60
Alignment explanation
Indices: 42581310--42581451 Score: 230
Period size: 60 Copynumber: 2.4 Consensus size: 60
42581300 GGCTTTGTCG
* *
42581310 ATTACCAGTCCAGGCTAAATCCTTTATATGACAAATAACTCCTTATAGAGTCAAATCTGA
1 ATTACCAGTCCAGGCTAAATCCTTTATATGACAAAGAACTCCATATAGAGTCAAATCTGA
* *
42581370 ATTACCAGTCCATGCTAAATCCTTTATATGACAAAGAACTCCATATAGAGTCAAATCTGG
1 ATTACCAGTCCAGGCTAAATCCTTTATATGACAAAGAACTCCATATAGAGTCAAATCTGA
* *
42581430 ATTACCAATCCAGGATAAATCC
1 ATTACCAGTCCAGGCTAAATCC
42581452 AATCAATTAG
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 75 1.00
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (60 bp):
ATTACCAGTCCAGGCTAAATCCTTTATATGACAAAGAACTCCATATAGAGTCAAATCTGA
Found at i:42584261 original size:138 final size:138
Alignment explanation
Indices: 42583885--42584446 Score: 880
Period size: 138 Copynumber: 4.1 Consensus size: 138
42583875 GAGAACATAG
* *
42583885 ATATAATTAATATATGAATTTGGTTCATACAAAATATTAATTGTATATAGTTTACTGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATT
* * *
42583950 AATATAAACAGTTATATTAATTAATTTTGGTCAAAATATAAAAGATATGAAAATTAATATTCTTT
66 AATATAAACAATTATATTAATTAATTTTAGTCAAAATATAAAAGACATGAAAATTAATATTCTTT
42584015 TGGAAAGA
131 TGGAAAGA
* *
42584023 ATATAATTAATATATGAATTTGTTTCATA-AAAATATTAATTGTATATATTTTA-TCAAATTTAT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACT-GAATTTAT
* * *
42584086 TAATATAAACAATTATATTAATTAATTTCAATCAAAATATAAAAGACATGGAAATTAATATTCTT
65 TAATATAAACAATTATATTAATTAATTTTAGTCAAAATATAAAAGACATGAAAATTAATATTCTT
42584151 TTGGAAAGA
130 TTGGAAAGA
* *
42584160 ATATAATTAATATAAGAATTTGATTCATATAAAATATTAATTGTATATATTTTACTGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATT
*
42584225 AAAATAAACAATTATATTAATTAATTTTAGTCAAAATATAAAAGACATGAAAATTAATATTCTTT
66 AATATAAACAATTATATTAATTAATTTTAGTCAAAATATAAAAGACATGAAAATTAATATTCTTT
42584290 TGGAAAGA
131 TGGAAAGA
* * *
42584298 ATATAATTAATATATGACTTTGATTCATACAAAATATTAATTTTATATATTTTAATGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATT
* * * *
42584363 AATATAAATAATTATATTAATTAATTCCTA-TCAATATATAAAAGACAT-AGAAATTAATACTCT
66 AATATAAACAATTATATTAATTAATT-TTAGTCAAAATATAAAAGACATGA-AAATTAATATTCT
*
42584426 TTTGGAAATA
129 TTTGGAAAGA
42584436 ATATAATTAAT
1 ATATAATTAAT
42584447 TTTTCTAACT
Statistics
Matches: 392, Mismatches: 27, Indels: 10
0.91 0.06 0.02
Matches are distributed among these distances:
136 1 0.00
137 126 0.32
138 262 0.67
139 3 0.01
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (138 bp):
ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATT
AATATAAACAATTATATTAATTAATTTTAGTCAAAATATAAAAGACATGAAAATTAATATTCTTT
TGGAAAGA
Found at i:42585710 original size:13 final size:13
Alignment explanation
Indices: 42585692--42585716 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42585682 ATTTAAAAGA
42585692 TTACATAATCAAT
1 TTACATAATCAAT
42585705 TTACATAATCAA
1 TTACATAATCAA
42585717 ATCCAATCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (13 bp):
TTACATAATCAAT
Found at i:42588050 original size:25 final size:25
Alignment explanation
Indices: 42588022--42588105 Score: 71
Period size: 25 Copynumber: 3.4 Consensus size: 25
42588012 ATAGCTCGTA
42588022 TGAGTATACTGATTTACAGCTCATG
1 TGAGTATACTGATTTACAGCTCATG
* * * ** *
42588047 TGAGCATACCGATTTACAGATTGTA
1 TGAGTATACTGATTTACAGCTCATG
* *
42588072 TGAGTATA-TCGGTTCACAGCTCATG
1 TGAGTATACT-GATTTACAGCTCATG
*
42588097 TGAGAATAC
1 TGAGTATAC
42588106 ATGTACAAGA
Statistics
Matches: 42, Mismatches: 15, Indels: 3
0.70 0.25 0.05
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (25 bp):
TGAGTATACTGATTTACAGCTCATG
Found at i:42589068 original size:46 final size:46
Alignment explanation
Indices: 42589012--42589101 Score: 153
Period size: 46 Copynumber: 2.0 Consensus size: 46
42589002 CATTTTGACC
*
42589012 AAATAGAGTACATGATTAAATATGTTTCCATGTTGTCATTTGAGCA
1 AAATAGAGTACATGATTAAACATGTTTCCATGTTGTCATTTGAGCA
* *
42589058 AAATGGAGTACATGGTTAAACATGTTTCCATGTTGTCATTTGAG
1 AAATAGAGTACATGATTAAACATGTTTCCATGTTGTCATTTGAG
42589102 GTGCCTAATG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.37
Consensus pattern (46 bp):
AAATAGAGTACATGATTAAACATGTTTCCATGTTGTCATTTGAGCA
Found at i:42596960 original size:40 final size:40
Alignment explanation
Indices: 42596915--42597082 Score: 135
Period size: 40 Copynumber: 4.2 Consensus size: 40
42596905 CGGAATATAA
42596915 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
** * *
42596955 CCGGATA-ACATGTCTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATA-ATCACTAGCACAAATGCCTTCGGGTCTTAGC
* ** * * **
42596995 CCGGATGTAGCCACTAGCGCAATTGCCTTCGGGTCTTAAT
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
42597035 CCGGATATAATTTCCAGCATAATTGTCTTCGGGAT-TTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGG-TCTTAGC
42597075 CCGGATAT
1 CCGGATAT
42597083 CATTCAATTT
Statistics
Matches: 99, Mismatches: 25, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
39 2 0.02
40 95 0.96
41 2 0.02
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:42600440 original size:44 final size:43
Alignment explanation
Indices: 42600390--42600540 Score: 148
Period size: 42 Copynumber: 3.5 Consensus size: 43
42600380 CATAGGATTT
*
42600390 CGTGTAAGACCACATCTGGGGCATTGGCATCGACT-TCTGTTTTA
1 CGTGTAAGACCACATCTGGGACATTGGCATCGA-TATCTG-TTTA
** *
42600434 CGTGTAAGACCATGTCTGGGACATCGGCATCG-TATCTGATTT-
1 CGTGTAAGACCACATCTGGGACATTGGCATCGATATCTG-TTTA
* * * *
42600476 CGTGTAAGACC-CTATCTGGGACAGTGGCATCGATGTTTGATTA
1 CGTGTAAGACCAC-ATCTGGGACATTGGCATCGATATCTGTTTA
* *
42600519 CATGTAAGACCACGTCTGGGAC
1 CGTGTAAGACCACATCTGGGAC
42600541 GTTGACATTG
Statistics
Matches: 88, Mismatches: 14, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
42 30 0.34
43 29 0.33
44 29 0.33
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (43 bp):
CGTGTAAGACCACATCTGGGACATTGGCATCGATATCTGTTTA
Found at i:42600537 original size:43 final size:41
Alignment explanation
Indices: 42600385--42600540 Score: 145
Period size: 43 Copynumber: 3.7 Consensus size: 41
42600375 CATGACATAG
* *
42600385 GATTTCGTGTAAGACCACATCTGGGGCATTGGCATCGACTTCT
1 GATTACGTGTAAGACCACATCTGGGACA-TGGCATCGA-TTCT
* **
42600428 GTTTTACGTGTAAGACCATGTCTGGGACATCGGCATCG-TATCT
1 G-ATTACGTGTAAGACCACATCTGGGACAT-GGCATCGAT-TCT
* *
42600471 GATTTCGTGTAAGACC-CTATCTGGGACAGTGGCATCGATGTTT
1 GATTACGTGTAAGACCAC-ATCTGGGACA-TGGCATCGAT-TCT
* *
42600514 GATTACATGTAAGACCACGTCTGGGAC
1 GATTACGTGTAAGACCACATCTGGGAC
42600541 GTTGACATTG
Statistics
Matches: 92, Mismatches: 14, Indels: 14
0.77 0.12 0.12
Matches are distributed among these distances:
42 30 0.33
43 32 0.35
44 30 0.33
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.30
Consensus pattern (41 bp):
GATTACGTGTAAGACCACATCTGGGACATGGCATCGATTCT
Found at i:42602400 original size:27 final size:26
Alignment explanation
Indices: 42602348--42602407 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
42602338 ATATATATAT
*
42602348 ATATCTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
42602374 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
42602401 ATATCTG
1 ATATCTG
42602408 GCAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:42610878 original size:17 final size:17
Alignment explanation
Indices: 42610856--42610892 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
42610846 TATGGCTTGG
42610856 TATGGATGTGATTATGA
1 TATGGATGTGATTATGA
42610873 TATGGATGTGATTATGA
1 TATGGATGTGATTATGA
42610890 TAT
1 TAT
42610893 TTAGCCATGT
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:0.30, C:0.00, G:0.27, T:0.43
Consensus pattern (17 bp):
TATGGATGTGATTATGA
Found at i:42616438 original size:14 final size:15
Alignment explanation
Indices: 42616419--42616448 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
42616409 GTCTATTATA
42616419 TGTG-AAGTATCATG
1 TGTGAAAGTATCATG
42616433 TGTGAAAGTATCATG
1 TGTGAAAGTATCATG
42616448 T
1 T
42616449 CTAAATTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.37
Consensus pattern (15 bp):
TGTGAAAGTATCATG
Found at i:42616688 original size:31 final size:31
Alignment explanation
Indices: 42616631--42616693 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
42616621 TAATATATGC
* *
42616631 ATTTTATATATATAAGAAATATAATTATTAA
1 ATTTTATATATATAAGAAATAGAATTAATAA
* *
42616662 ATTTTTTATA-ATATGAAATAAGAATTAATAA
1 ATTTTATATATATAAGAAAT-AGAATTAATAA
42616693 A
1 A
42616694 ACAAAAAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 8 0.30
31 19 0.70
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (31 bp):
ATTTTATATATATAAGAAATAGAATTAATAA
Found at i:42619137 original size:40 final size:40
Alignment explanation
Indices: 42619078--42619285 Score: 218
Period size: 40 Copynumber: 5.2 Consensus size: 40
42619068 CAATTGAATG
* * * *
42619078 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * * *
42619118 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
42619158 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
42619198 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * **
42619238 CTATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
42619278 ATATCCGG
1 ATATCCGG
42619286 TTGTATTCCG
Statistics
Matches: 142, Mismatches: 26, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 142 1.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
Found at i:42619216 original size:80 final size:80
Alignment explanation
Indices: 42619079--42619285 Score: 247
Period size: 80 Copynumber: 2.6 Consensus size: 80
42619069 AATTGAATGA
* * ** * * *
42619079 TATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATATCCGGGTTAAGACCCGAAGGCAA
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAA
*
42619144 TTGTGCTAGT-G-AC
66 TTGTGCAAGTCGTAC
* * *
42619157 TACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGC
1 T--ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGC
* *
42619222 ATTTGTGCAAGTCGTTC
64 AATTGTGCAAGTCGTAC
* *
42619239 TATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGG
42619286 TTGTATTCCG
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
78 1 0.01
80 105 0.96
81 1 0.01
82 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (80 bp):
TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAA
TTGTGCAAGTCGTAC
Found at i:42623902 original size:28 final size:28
Alignment explanation
Indices: 42623862--42623931 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
42623852 ATAGTAAGTC
*
42623862 CGCACACTTAGTGCT-TAATAATCAAACT
1 CGCACACTTAGTGCTAT-ACAATCAAACT
*
42623890 CGCACACTTAGTGCTATACAATTAAACT
1 CGCACACTTAGTGCTATACAATCAAACT
42623918 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42623932 CAATCTCATT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 38 0.97
29 1 0.03
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATACAATCAAACT
Found at i:42631935 original size:40 final size:38
Alignment explanation
Indices: 42631808--42631946 Score: 170
Period size: 34 Copynumber: 3.8 Consensus size: 38
42631798 ATGATAACCG
*
42631808 GGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-A---
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGT-ACTATATCC
*
42631843 AGCTAAG-CCCGAAGGCATTTGTGC--G-ACTATATCC
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATATCC
42631877 GGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTATATCC
1 GGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATATCC
42631915 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTAC
1 -GGCTAAGTCCCGAAGGCATTTGTGCGAGTAC
42631947 GTAAGTAAGG
Statistics
Matches: 91, Mismatches: 2, Indels: 18
0.82 0.02 0.16
Matches are distributed among these distances:
30 4 0.04
31 1 0.01
32 1 0.01
34 39 0.43
35 6 0.07
36 1 0.01
38 9 0.10
39 11 0.12
40 19 0.21
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATATCC
Found at i:42632050 original size:40 final size:40
Alignment explanation
Indices: 42631967--42632069 Score: 138
Period size: 40 Copynumber: 2.6 Consensus size: 40
42631957 CATTTAGCTA
* *
42631967 TATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTAC
1 TATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTTAC
42632007 TATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAG-TAGC
1 TATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTTA-C
* * *
42632047 TATATCC-GGCTAAATTCCGAAGG
1 TATAACCGGGCTAAGTCCCGAAGG
42632070 TACTTGGTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
39 16 0.28
40 41 0.72
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.23
Consensus pattern (40 bp):
TATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTTAC
Found at i:42637677 original size:28 final size:28
Alignment explanation
Indices: 42637637--42637706 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
42637627 ATAGTAAGTC
*
42637637 CGCACACTTAGTGCT-TAATAATCAAACT
1 CGCACACTTAGTGCTAT-ACAATCAAACT
*
42637665 CGCACACTTAGTGCTATACAATTAAACT
1 CGCACACTTAGTGCTATACAATCAAACT
42637693 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42637707 CAATCTCATT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 38 0.97
29 1 0.03
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATACAATCAAACT
Found at i:42638267 original size:2 final size:2
Alignment explanation
Indices: 42638260--42638291 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
42638250 GGCATACATT
42638260 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42638292 GCCGAATGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42645349 original size:40 final size:39
Alignment explanation
Indices: 42645302--42645379 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 39
42645292 CTAGACAAAC
*
42645302 ATTAATGATG-TCAAAATTAAGACACATAATTAAA-ACACAT
1 ATTAATGATGTTC-AAACTAAG--ACATAATTAAAGACACAT
42645342 ATTAATGATGTTCAAACTAAGACATAATTAAAGACACA
1 ATTAATGATGTTCAAACTAAGACATAATTAAAGACACA
42645380 AACTAAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
38 11 0.31
39 5 0.14
40 17 0.49
41 2 0.06
ACGTcount: A:0.51, C:0.13, G:0.09, T:0.27
Consensus pattern (39 bp):
ATTAATGATGTTCAAACTAAGACATAATTAAAGACACAT
Found at i:42646797 original size:18 final size:18
Alignment explanation
Indices: 42646774--42646808 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
42646764 AAGAGACTTC
42646774 CTACTGCTAAAGCATAAA
1 CTACTGCTAAAGCATAAA
42646792 CTACTGCTAAAGCATAA
1 CTACTGCTAAAGCATAA
42646809 GGAACCTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.23, G:0.11, T:0.23
Consensus pattern (18 bp):
CTACTGCTAAAGCATAAA
Found at i:42651252 original size:28 final size:28
Alignment explanation
Indices: 42651145--42651254 Score: 98
Period size: 28 Copynumber: 3.9 Consensus size: 28
42651135 CATACATGCG
* * *
42651145 TATGGCCCACTAGGCCCAATCTCTTTCA
1 TATGGCCCACTAAGCCCAATCACATTCA
* * *
42651173 TATGGCCCATTAAGCCCATTCACATTTA
1 TATGGCCCACTAAGCCCAATCACATTCA
* * * *
42651201 TGTGG-CCATTAGGCCCAAAGCACATTCA
1 TATGGCCCACTAAGCCC-AATCACATTCA
42651229 TATGG-CCACTAAGCCCAAATCACATT
1 TATGGCCCACTAAGCCC-AATCACATT
42651255 TACACTCATG
Statistics
Matches: 66, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
27 10 0.15
28 56 0.85
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (28 bp):
TATGGCCCACTAAGCCCAATCACATTCA
Found at i:42656215 original size:31 final size:31
Alignment explanation
Indices: 42656177--42656239 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
42656167 AACTTTAAGG
42656177 AATGTTTAGAAAACTTCTAATCATATCAAAA
1 AATGTTTAGAAAACTTCTAATCATATCAAAA
42656208 AATGTTTAGAAAACTTCTAATCATATCAAAA
1 AATGTTTAGAAAACTTCTAATCATATCAAAA
42656239 A
1 A
42656240 TAATTTAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.32
Consensus pattern (31 bp):
AATGTTTAGAAAACTTCTAATCATATCAAAA
Found at i:42656251 original size:30 final size:31
Alignment explanation
Indices: 42656181--42656251 Score: 110
Period size: 31 Copynumber: 2.3 Consensus size: 31
42656171 TTAAGGAATG
*
42656181 TTTAGAAAACTTCTAATCATATCAAAAAATG
1 TTTAGAAAACTTCTAATCATATCAAAAAATA
42656212 TTTAGAAAACTTCTAATCATATC-AAAAATAA
1 TTTAGAAAACTTCTAATCATATCAAAAAAT-A
42656243 TTTA-AAAAC
1 TTTAGAAAAC
42656252 ACTTTGAAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
30 11 0.29
31 27 0.71
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (31 bp):
TTTAGAAAACTTCTAATCATATCAAAAAATA
Found at i:42658868 original size:24 final size:24
Alignment explanation
Indices: 42658836--42659042 Score: 324
Period size: 24 Copynumber: 8.6 Consensus size: 24
42658826 TATCTCAAAT
42658836 GCACTATGTGTGCGATTCACTATG
1 GCACTATGTGTGCGATTCACTATG
42658860 GCACTATGTGTGCGATTCACTATG
1 GCACTATGTGTGCGATTCACTATG
*
42658884 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTCACTATG
42658908 GCACTATGTGTGCGATTCACTATG
1 GCACTATGTGTGCGATTCACTATG
42658932 GCACTATGTGTGCGATTCACTATG
1 GCACTATGTGTGCGATTCACTATG
*
42658956 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTCACTATG
* * *
42658980 GCACTAAGTGTGCGATTTACTATA
1 GCACTATGTGTGCGATTCACTATG
* ** *
42659004 GCACTACGTGTGCGATTTGCTATA
1 GCACTATGTGTGCGATTCACTATG
*
42659028 GCTCTATGTGTGCGA
1 GCACTATGTGTGCGA
42659043 ACATAATAAG
Statistics
Matches: 174, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 174 1.00
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.34
Consensus pattern (24 bp):
GCACTATGTGTGCGATTCACTATG
Found at i:42659055 original size:48 final size:48
Alignment explanation
Indices: 42658860--42659064 Score: 202
Period size: 48 Copynumber: 4.3 Consensus size: 48
42658850 ATTCACTATG
* ** * *
42658860 GCACTATGTGTGCGATTCACTATGGCACTATGTGTGCG-ATTTACTATG
1 GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCGAACATAATA-A
* * *
42658908 GCACTATGTGTGCGATTCACTATGGCACTATGTGTGCGATTCACT-AT-G
1 GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCGA-ACA-TAATAA
* ** *
42658956 GCACTATGTGTGCGATTTACTATGGCACTAAGTGTGCG-ATTTACTATA
1 GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCGAACATAATA-A
* * * *
42659004 GCACTACGTGTGCGATTTGCTATAGCTCTATGTGTGCGAACATAATAA
1 GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCGAACATAATAA
42659052 GCACTATGTGTGC
1 GCACTATGTGTGC
42659065 CACATTCGGT
Statistics
Matches: 130, Mismatches: 20, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
45 1 0.01
46 1 0.01
48 121 0.93
49 5 0.04
50 1 0.01
51 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (48 bp):
GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCGAACATAATAA
Found at i:42673606 original size:12 final size:12
Alignment explanation
Indices: 42673589--42673613 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42673579 TATGTATGTT
42673589 TGAAAATTTTTA
1 TGAAAATTTTTA
42673601 TGAAAATTTTTA
1 TGAAAATTTTTA
42673613 T
1 T
42673614 TATTTGCTGT
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:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TGAAAATTTTTA
Found at i:42673675 original size:3 final size:3
Alignment explanation
Indices: 42673667--42673709 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
42673657 TGTTTATGAA
42673667 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
42673710 GTAATTAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:42676148 original size:26 final size:25
Alignment explanation
Indices: 42676079--42676149 Score: 115
Period size: 25 Copynumber: 2.8 Consensus size: 25
42676069 GAGGAAGTGC
* *
42676079 AAAAGGGCTATGCCCCAATTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
42676104 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
42676129 AAAAGGGCTTTTGCCCCAGTT
1 AAAAGGGC-TTTGCCCCAGTT
42676150 ATTAAAAGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
25 31 0.72
26 12 0.28
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCG
Found at i:42676407 original size:31 final size:31
Alignment explanation
Indices: 42676369--42676452 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 31
42676359 TTGTTACAGT
42676369 AAAGGCTTCGGCCCAGTGATATGAATAATGA
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
*
42676400 AAAGGCTTCGGCCCAGTGATATGAATAATGT
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
*
42676431 AAAGGCTTCAGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
42676453 CTGAGATTGA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
30 5 0.10
31 46 0.90
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGAATAATGA
Found at i:42678524 original size:3 final size:3
Alignment explanation
Indices: 42678516--42678561 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
42678506 TGTTTATGAA
42678516 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
42678562 GTAATTAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:42682590 original size:42 final size:42
Alignment explanation
Indices: 42682527--42682641 Score: 198
Period size: 40 Copynumber: 2.8 Consensus size: 42
42682517 TGGAAAAAAA
42682527 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGCGGGTTAT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGCGGGTTAT
*
42682569 TATGACCGGGTTAAGTCCCGAAGGCATTCGT--GCGGGTTAT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGCGGGTTAT
*
42682609 TATAACCGGGTTAAGTCCCGAAGGCATTTGTGC
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGC
42682642 TGGGTGTTAC
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
40 38 0.56
42 30 0.44
ACGTcount: A:0.22, C:0.21, G:0.30, T:0.27
Consensus pattern (42 bp):
TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGCGGGTTAT
Found at i:42684247 original size:25 final size:25
Alignment explanation
Indices: 42684218--42684265 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
42684208 TTATAATATG
* *
42684218 AAAATGACTATTTTGCCCCTAGGTA
1 AAAATGACCATTTTACCCCTAGGTA
42684243 AAAATGACCATTTTACCCCTAGG
1 AAAATGACCATTTTACCCCTAGG
42684266 GTTTAATTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (25 bp):
AAAATGACCATTTTACCCCTAGGTA
Found at i:42684467 original size:26 final size:25
Alignment explanation
Indices: 42684398--42684468 Score: 124
Period size: 25 Copynumber: 2.8 Consensus size: 25
42684388 GAGGAAGTGC
*
42684398 AAAAGGGCTATGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
42684423 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
42684448 AAAAGGGCTTTTGCCCCAGTT
1 AAAAGGGC-TTTGCCCCAGTT
42684469 ATTAAAAGAG
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
25 32 0.73
26 12 0.27
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCG
Found at i:42684734 original size:31 final size:31
Alignment explanation
Indices: 42684696--42684779 Score: 134
Period size: 31 Copynumber: 2.7 Consensus size: 31
42684686 TTGTTACAGT
42684696 AAAGGCTTCGGCCCAGTGATATGAATAATGA
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
* *
42684727 AAAGGCTTCGGCCCAGTGATATGAATTATGT
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
*
42684758 AAAGGCTTCAGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
42684780 CTGAGATTGA
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
30 5 0.10
31 45 0.90
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGAATAATGA
Found at i:42685656 original size:17 final size:18
Alignment explanation
Indices: 42685620--42685657 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
42685610 ATGATAATTC
*
42685620 TTTTTAATTATTTGTCAT
1 TTTTTAATTATTAGTCAT
*
42685638 TTTTTAATT-TTAGTGAT
1 TTTTTAATTATTAGTCAT
42685655 TTT
1 TTT
42685658 CAATTTAGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.21, C:0.03, G:0.08, T:0.68
Consensus pattern (18 bp):
TTTTTAATTATTAGTCAT
Found at i:42690936 original size:56 final size:56
Alignment explanation
Indices: 42690876--42691137 Score: 400
Period size: 56 Copynumber: 4.7 Consensus size: 56
42690866 AGACAGGTTT
* * * *
42690876 TTACTCGTACACATATATCGGAGTCATATATCGATGCCAACGTATTAAACATGGTC
1 TTACTCGCACACATATATCGGAGTCACATATCGATGCCAACGTATTAAACGTGGAC
* * *
42690932 TTACTCACACACATATATCAGAGTCACATATCGATGCCAACGTATTAAACGTGGTC
1 TTACTCGCACACATATATCGGAGTCACATATCGATGCCAACGTATTAAACGTGGAC
* *
42690988 TTACTCGTACACATATATTGGAGTCACATATCGATGCCAACGTATTAAACGTGGAC
1 TTACTCGCACACATATATCGGAGTCACATATCGATGCCAACGTATTAAACGTGGAC
* *
42691044 TTACTCACACATATATATCGGAGTCACA-ATCGATGCCAACGTATTAAACGTGGAC
1 TTACTCGCACACATATATCGGAGTCACATATCGATGCCAACGTATTAAACGTGGAC
* *
42691099 TTACTCGCACAAATATATTGGAGTCACATATCGATGCCA
1 TTACTCGCACACATATATCGGAGTCACATATCGATGCCA
42691138 CATATACTTC
Statistics
Matches: 188, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
55 52 0.28
56 136 0.72
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (56 bp):
TTACTCGCACACATATATCGGAGTCACATATCGATGCCAACGTATTAAACGTGGAC
Found at i:42697413 original size:31 final size:31
Alignment explanation
Indices: 42697372--42697435 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
42697362 CCTTTTCATA
*
42697372 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
**
42697403 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
42697434 TT
1 TT
42697436 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:42697690 original size:24 final size:24
Alignment explanation
Indices: 42697626--42697739 Score: 205
Period size: 24 Copynumber: 4.8 Consensus size: 24
42697616 CTGCTTTATC
42697626 ACTGGGGCA-AAGCCCTTTTAATA
1 ACTGGGGCATAAGCCCTTTTAATA
42697649 ACTGGGGCA-AAGCCCTTTTAATA
1 ACTGGGGCATAAGCCCTTTTAATA
42697672 ACTGGGGCATAAGCCCTTTTAATA
1 ACTGGGGCATAAGCCCTTTTAATA
*
42697696 ACTGAGGCATAAGCCCTTTTAATA
1 ACTGGGGCATAAGCCCTTTTAATA
42697720 ACTGGGGCATAAGCCCTTTT
1 ACTGGGGCATAAGCCCTTTT
42697740 TGCACTTCCT
Statistics
Matches: 88, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
23 32 0.36
24 56 0.64
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (24 bp):
ACTGGGGCATAAGCCCTTTTAATA
Found at i:42697810 original size:9 final size:9
Alignment explanation
Indices: 42697796--42697875 Score: 70
Period size: 9 Copynumber: 8.2 Consensus size: 9
42697786 ACATCTCGTG
42697796 TGCATATCA
1 TGCATATCA
42697805 TGCATATCA
1 TGCATATCA
42697814 TGTGCATATCA
1 --TGCATATCA
* *
42697825 TACATGTCA
1 TGCATATCA
42697834 TGTGCATATCA
1 --TGCATATCA
*
42697845 TACATATCA
1 TGCATATCA
42697854 TGTGCATATCA
1 --TGCATATCA
*
42697865 TACATATCA
1 TGCATATCA
42697874 TG
1 TG
42697876 TTTATCAAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
9 33 0.58
11 24 0.42
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (9 bp):
TGCATATCA
Found at i:42697819 original size:20 final size:20
Alignment explanation
Indices: 42697794--42697876 Score: 148
Period size: 20 Copynumber: 4.2 Consensus size: 20
42697784 GAACATCTCG
*
42697794 TGTGCATATCATGCATATCA
1 TGTGCATATCATACATATCA
*
42697814 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
42697834 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
42697854 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
42697874 TGT
1 TGT
42697877 TTATCAAAAT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.36
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:42697821 original size:11 final size:11
Alignment explanation
Indices: 42697794--42697865 Score: 75
Period size: 11 Copynumber: 7.1 Consensus size: 11
42697784 GAACATCTCG
42697794 TGTGCATATCA
1 TGTGCATATCA
42697805 --TGCATATCA
1 TGTGCATATCA
42697814 TGTGCATATCA
1 TGTGCATATCA
* *
42697825 --TACATGTCA
1 TGTGCATATCA
42697834 TGTGCATATCA
1 TGTGCATATCA
*
42697845 --TACATATCA
1 TGTGCATATCA
42697854 TGTGCATATCA
1 TGTGCATATCA
42697865 T
1 T
42697866 ACATATCATG
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
9 24 0.49
11 25 0.51
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (11 bp):
TGTGCATATCA
Found at i:42697941 original size:25 final size:25
Alignment explanation
Indices: 42697913--42697960 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
42697903 ATATATAAAC
* * *
42697913 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
42697938 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
42697961 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:42699210 original size:27 final size:27
Alignment explanation
Indices: 42699119--42699202 Score: 125
Period size: 27 Copynumber: 3.1 Consensus size: 27
42699109 GGGCATATTC
*
42699119 GTCATTTTACCATACAGGGG-TATTACG
1 GTCACTTTACCATACAGGGGCT-TTACG
*
42699146 GTCACTTTACCTTACAGGGGCTTTACG
1 GTCACTTTACCATACAGGGGCTTTACG
*
42699173 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCACTTTACCATACAGGGGCTTTACG
42699200 GTC
1 GTC
42699203 TTTTTACCTA
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
27 52 0.98
28 1 0.02
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (27 bp):
GTCACTTTACCATACAGGGGCTTTACG
Found at i:42699219 original size:27 final size:26
Alignment explanation
Indices: 42699119--42699212 Score: 118
Period size: 27 Copynumber: 3.5 Consensus size: 26
42699109 GGGCATATTC
*
42699119 GTCATTTTACCATACAGGGG-TATTACG
1 GTCACTTTACC-TACAGGGGCT-TTACG
42699146 GTCACTTTACCTTACAGGGGCTTTACG
1 GTCACTTTACC-TACAGGGGCTTTACG
42699173 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCACTTTA-CCTACAGGGGCTTTACG
**
42699200 GTCTTTTTACCTA
1 GTCACTTTACCTA
42699213 ATAGGGGTAT
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
26 4 0.07
27 54 0.89
28 3 0.05
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.35
Consensus pattern (26 bp):
GTCACTTTACCTACAGGGGCTTTACG
Found at i:42700657 original size:40 final size:40
Alignment explanation
Indices: 42700597--42700760 Score: 179
Period size: 40 Copynumber: 4.1 Consensus size: 40
42700587 CGGGATTTAA
* ** *
42700597 CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACAACTCGCACAATTGCCTTCGGGTCTTAGC
* *** *
42700637 CCGGATTTGGTAACTTGCACAATTGCCTTCGGGTCTTAGC
1 CCGGATATAACAACTCGCACAATTGCCTTCGGGTCTTAGC
42700677 CCGGATATAACAACTCGCACGAA-TGCCTTCGGGTCTTAGC
1 CCGGATATAACAACTCGCAC-AATTGCCTTCGGGTCTTAGC
* * * *
42700717 CCGGATATAATC-ACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAA-CAACTCGCACAATTGCCTTCGGGTCTTAGC
42700757 CCGG
1 CCGG
42700761 GTATCATTCA
Statistics
Matches: 105, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
39 2 0.02
40 100 0.95
41 3 0.03
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAACAACTCGCACAATTGCCTTCGGGTCTTAGC
Found at i:42700744 original size:80 final size:80
Alignment explanation
Indices: 42700583--42700760 Score: 207
Period size: 80 Copynumber: 2.2 Consensus size: 80
42700573 GAATCACGTA
* * * * **
42700583 CCTTCGGGATTTA-ACCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGATTTGG
1 CCTTCGGGACTTAGCCCGGATATAACAACAAGCACAATTGCCTTCGGGTCTTAACCCGGATATAA
* *
42700647 TAACTTGCACAATTG
66 TAACTAGCACAAATG
* ** *
42700662 CCTTCGGGTCTTAGCCCGGATATAACAACTCGCACGAA-TGCCTTCGGGTCTTAGCCCGGATATA
1 CCTTCGGGACTTAGCCCGGATATAACAACAAGCAC-AATTGCCTTCGGGTCTTAACCCGGATATA
* *
42700726 ATCACTAGCATAAATG
65 ATAACTAGCACAAATG
42700742 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
42700761 GTATCATTCA
Statistics
Matches: 82, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
79 11 0.13
80 69 0.84
81 2 0.02
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (80 bp):
CCTTCGGGACTTAGCCCGGATATAACAACAAGCACAATTGCCTTCGGGTCTTAACCCGGATATAA
TAACTAGCACAAATG
Found at i:42701455 original size:2 final size:2
Alignment explanation
Indices: 42701448--42701483 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
42701438 ATGTGCAAAC
42701448 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
42701484 GCAAGAGCCG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42708701 original size:40 final size:40
Alignment explanation
Indices: 42708641--42708804 Score: 179
Period size: 40 Copynumber: 4.1 Consensus size: 40
42708631 CGGGATTTAA
* ** *
42708641 CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACAACTCGCACAATTGCCTTCGGGTCTTAGC
* *** *
42708681 CCGGATTTGGTAACTTGCACAATTGCCTTCGGGTCTTAGC
1 CCGGATATAACAACTCGCACAATTGCCTTCGGGTCTTAGC
42708721 CCGGATATAACAACTCGCACGAA-TGCCTTCGGGTCTTAGC
1 CCGGATATAACAACTCGCAC-AATTGCCTTCGGGTCTTAGC
* * * *
42708761 CCGGATATAATC-ACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAA-CAACTCGCACAATTGCCTTCGGGTCTTAGC
42708801 CCGG
1 CCGG
42708805 GTATCATTCA
Statistics
Matches: 105, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
39 2 0.02
40 100 0.95
41 3 0.03
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAACAACTCGCACAATTGCCTTCGGGTCTTAGC
Found at i:42708788 original size:80 final size:80
Alignment explanation
Indices: 42708627--42708804 Score: 207
Period size: 80 Copynumber: 2.2 Consensus size: 80
42708617 GAATCACGTA
* * * * **
42708627 CCTTCGGGATTTA-ACCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGATTTGG
1 CCTTCGGGACTTAGCCCGGATATAACAACAAGCACAATTGCCTTCGGGTCTTAACCCGGATATAA
* *
42708691 TAACTTGCACAATTG
66 TAACTAGCACAAATG
* ** *
42708706 CCTTCGGGTCTTAGCCCGGATATAACAACTCGCACGAA-TGCCTTCGGGTCTTAGCCCGGATATA
1 CCTTCGGGACTTAGCCCGGATATAACAACAAGCAC-AATTGCCTTCGGGTCTTAACCCGGATATA
* *
42708770 ATCACTAGCATAAATG
65 ATAACTAGCACAAATG
42708786 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
42708805 GTATCATTCA
Statistics
Matches: 82, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
79 11 0.13
80 69 0.84
81 2 0.02
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (80 bp):
CCTTCGGGACTTAGCCCGGATATAACAACAAGCACAATTGCCTTCGGGTCTTAACCCGGATATAA
TAACTAGCACAAATG
Found at i:42710568 original size:27 final size:27
Alignment explanation
Indices: 42710538--42710645 Score: 94
Period size: 27 Copynumber: 3.9 Consensus size: 27
42710528 GTAAATCTAC
42710538 AAACCAAGGGTATTTCAGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTGT
*
42710565 AAACCAATGGTATTTCTA-TAATTTT-T
1 AAACCAAGGGTATTTC-AGTAATTTTGT
* * *
42710591 AGAAAGTCAAGGGTATTTCTGTAACTTTGT
1 --AAA-CCAAGGGTATTTCAGTAATTTTGT
* * **
42710621 AAATCAGGGGTATTTTGGTAATTTT
1 AAACCAAGGGTATTTCAGTAATTTT
42710646 AAAAATTGAG
Statistics
Matches: 66, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
26 1 0.02
27 40 0.61
28 7 0.11
29 17 0.26
30 1 0.02
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (27 bp):
AAACCAAGGGTATTTCAGTAATTTTGT
Found at i:42710687 original size:54 final size:54
Alignment explanation
Indices: 42710629--42710731 Score: 163
Period size: 54 Copynumber: 1.9 Consensus size: 54
42710619 GTAAATCAGG
*
42710629 GGTATTTTGGTAATTTTAAAAA-TTGAGGGTATTTTGGTAATTTCACAAACCAGT
1 GGTATTTTGGTAATTTTAAAAACTAG-GGGTATTTTGGTAATTTCACAAACCAGT
* *
42710683 GGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAA
1 GGTATTTTGGTAATTTTAAAAACTAGGGGTATTTTGGTAATTTCACAAA
42710732 TTGAGGGTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
54 43 0.96
55 2 0.04
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.42
Consensus pattern (54 bp):
GGTATTTTGGTAATTTTAAAAACTAGGGGTATTTTGGTAATTTCACAAACCAGT
Found at i:42710759 original size:27 final size:27
Alignment explanation
Indices: 42710600--42710848 Score: 148
Period size: 27 Copynumber: 9.2 Consensus size: 27
42710590 TAGAAAGTCA
* *
42710600 AGGGTATTTCT-GTAACTTTGTAAATC-
1 AGGGTATTT-TGGTAATTTTATAAATCG
* *
42710626 AGGGGTATTTTGGTAATTTTAAAAATTG
1 A-GGGTATTTTGGTAATTTTATAAATCG
* * *
42710654 AGGGTATTTTGGTAATTTCACAAA-CC
1 AGGGTATTTTGGTAATTTTATAAATCG
* *
42710680 AGTGGTATTTTGGTAATTTTACAAA-CT
1 AG-GGTATTTTGGTAATTTTATAAATCG
* *
42710707 AGGGGTATTTTGGTAATTTTACAAATTG
1 A-GGGTATTTTGGTAATTTTATAAATCG
*
42710735 AGGGTATTTCT-GTAATTTTGTAAATCG
1 AGGGTATTT-TGGTAATTTTATAAATCG
*** * * *
42710762 AGGGTAAAATAGTAATTCTATAAATCA
1 AGGGTATTTTGGTAATTTTATAAATCG
*** * *
42710789 AGGGTAAAATAGTAATTCTATAAATCG
1 AGGGTATTTTGGTAATTTTATAAATCG
* **** * *
42710816 ACGGTAAAACGATAATTTTGTAAATCG
1 AGGGTATTTTGGTAATTTTATAAATCG
42710843 AGGGTA
1 AGGGTA
42710849 AAACGGTAAT
Statistics
Matches: 186, Mismatches: 29, Indels: 15
0.81 0.13 0.07
Matches are distributed among these distances:
26 5 0.03
27 177 0.95
28 4 0.02
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.37
Consensus pattern (27 bp):
AGGGTATTTTGGTAATTTTATAAATCG
Found at i:42710794 original size:81 final size:81
Alignment explanation
Indices: 42710620--42710875 Score: 205
Period size: 81 Copynumber: 3.2 Consensus size: 81
42710610 TGTAACTTTG
* *** *
42710620 TAAATCAGGGGTATTTTGGTAATTTTAAAAATTGAGGGTATTT-TGGTAATTTCACAAA-CCAGT
1 TAAATCAAGGGTATTTTGGTAATTTTAAAAATTGAGGGTATTTCT-GTAATTTTGTAAATCGAG-
*** *
42710683 GGTATTTTGGTAATTTTA
64 GGTAAAATGGTAATTCTA
* * *
42710701 CAAA-CTAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCTGTAATTTTGTAAATCGAGG
1 TAAATC-AAGGGTATTTTGGTAATTTTAAAAATTGAGGGTATTTCTGTAATTTTGTAAATCGAGG
*
42710765 GTAAAATAGTAATTCTA
65 GTAAAATGGTAATTCTA
*** * * * * * ***
42710782 TAAATCAAGGGTAAAATAGTAATTCTATAAATCGACGGTAAAAC-GATAATTTTGTAAATCGAGG
1 TAAATCAAGGGTATTTTGGTAATTTTAAAAATTGAGGGTATTTCTG-TAATTTTGTAAATCGAGG
* *
42710846 GTAAAACGGTAATTCTG
65 GTAAAATGGTAATTCTA
*
42710863 TAAGTCAAGGGTA
1 TAAATCAAGGGTA
42710876 AAACGGGGTA
Statistics
Matches: 142, Mismatches: 28, Indels: 10
0.79 0.16 0.06
Matches are distributed among these distances:
80 2 0.01
81 135 0.95
82 5 0.04
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.36
Consensus pattern (81 bp):
TAAATCAAGGGTATTTTGGTAATTTTAAAAATTGAGGGTATTTCTGTAATTTTGTAAATCGAGGG
TAAAATGGTAATTCTA
Found at i:42710804 original size:54 final size:54
Alignment explanation
Indices: 42710746--42710995 Score: 200
Period size: 54 Copynumber: 4.5 Consensus size: 54
42710736 GGGTATTTCT
* **
42710746 GTAATTTTGTAAATCGAGGGTAAAATAGTAATTCTATAAATCAAGGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTATAAATCAAGGGTAAAACG
* * * * * *
42710800 GTAATTCTATAAATCGACGGTAAAA-CGATAATTTTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAATAG-TAATTCTATAAATCAAGGGTAAAACG
* * * ** *
42710854 GTAATTCTGTAAGTCAAGGGTAAAACGGGGTAAAATGGTAATTATGA-AAATCGGGGGTAAAATG
1 GTAATTCTGTAAATC----G----A--GGGTAAAATAGTAATTCT-ATAAATCAAGGGTAAAACG
* *
42710918 GTAATT-TGTAAATCAAGGGTAAAACAGTAATTCTATAAATCAAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTATAAATCAAGGGTAAAACG
* *
42710971 GTACTTCTATAAATCGAGGGTAAAA
1 GTAATTCTGTAAATCGAGGGTAAAA
42710996 CGGTAATTAT
Statistics
Matches: 153, Mismatches: 28, Indels: 30
0.73 0.13 0.14
Matches are distributed among these distances:
52 1 0.01
53 35 0.23
54 72 0.47
55 1 0.01
58 1 0.01
62 1 0.01
63 7 0.05
64 34 0.22
65 1 0.01
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (54 bp):
GTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTATAAATCAAGGGTAAAACG
Found at i:42710849 original size:27 final size:27
Alignment explanation
Indices: 42710747--42711018 Score: 167
Period size: 27 Copynumber: 9.8 Consensus size: 27
42710737 GGTATTTCTG
* *
42710747 TAATTTTGTAAATCGAGGGTAAAA-TA
1 TAATTCTGTAAATCGAGGGTAAAACGA
* * *
42710773 GTAATTCTATAAATCAAGGGTAAAA-TA
1 -TAATTCTGTAAATCGAGGGTAAAACGA
* *
42710800 GTAATTCTATAAATCGACGGTAAAACGA
1 -TAATTCTGTAAATCGAGGGTAAAACGA
* *
42710828 TAATTTTGTAAATCGAGGGTAAAACGG
1 TAATTCTGTAAATCGAGGGTAAAACGA
* *
42710855 TAATTCTGTAAGTCAAGGGTAAAACGGGGTA
1 TAATTCTGTAAATCGAGGGTAAAAC---G-A
* * * * * *
42710886 AAATGGTAATTATGAAAATCGGGGGTAAAATGG
1 TAA---T---TCTGTAAATCGAGGGTAAAACGA
*
42710919 TAATT-TGTAAATCAAGGGTAAAAC-A
1 TAATTCTGTAAATCGAGGGTAAAACGA
* * *
42710944 GTAATTCTATAAATCAAGGGTAAAACGG
1 -TAATTCTGTAAATCGAGGGTAAAACGA
* * *
42710972 TACTTCTATAAATCGAGGGTAAAACGG
1 TAATTCTGTAAATCGAGGGTAAAACGA
*
42710999 TAATTATGTAAATCG-GGGTA
1 TAATTCTGTAAATCGAGGGTA
42711019 CTTTGGTAAT
Statistics
Matches: 196, Mismatches: 35, Indels: 29
0.75 0.13 0.11
Matches are distributed among these distances:
26 25 0.13
27 147 0.75
28 1 0.01
30 2 0.01
31 2 0.01
33 2 0.01
34 2 0.01
37 15 0.08
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.28
Consensus pattern (27 bp):
TAATTCTGTAAATCGAGGGTAAAACGA
Found at i:42710905 original size:64 final size:63
Alignment explanation
Indices: 42710818--42710942 Score: 178
Period size: 64 Copynumber: 2.0 Consensus size: 63
42710808 ATAAATCGAC
* * *
42710818 GGTAAAACGATAATTTTGTAAATCGAGGGTAAAACGGTAATTCTGTAAGTCAAGGGTAAAACGG
1 GGTAAAACGATAATTATGAAAATCGAGGGTAAAACGGTAATT-TGTAAATCAAGGGTAAAACGG
* * * *
42710882 GGTAAAATGGTAATTATGAAAATCGGGGGTAAAATGGTAATTTGTAAATCAAGGGTAAAAC
1 GGTAAAACGATAATTATGAAAATCGAGGGTAAAACGGTAATTTGTAAATCAAGGGTAAAAC
42710943 AGTAATTCTA
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
63 18 0.33
64 36 0.67
ACGTcount: A:0.41, C:0.07, G:0.26, T:0.26
Consensus pattern (63 bp):
GGTAAAACGATAATTATGAAAATCGAGGGTAAAACGGTAATTTGTAAATCAAGGGTAAAACGG
Found at i:42710912 original size:37 final size:38
Alignment explanation
Indices: 42710835--42710915 Score: 92
Period size: 37 Copynumber: 2.2 Consensus size: 38
42710825 CGATAATTTT
* * * *
42710835 GTAAATCGAGGGTAAAACGGTAATTCTGTAAGTCAAGG
1 GTAAAACGAGGGTAAAACGGTAATTATGAAAATCAAGG
* **
42710873 GTAAAACG-GGGTAAAATGGTAATTATGAAAATCGGGG
1 GTAAAACGAGGGTAAAACGGTAATTATGAAAATCAAGG
42710910 GTAAAA
1 GTAAAA
42710916 TGGTAATTTG
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
37 29 0.81
38 7 0.19
ACGTcount: A:0.41, C:0.07, G:0.30, T:0.22
Consensus pattern (38 bp):
GTAAAACGAGGGTAAAACGGTAATTATGAAAATCAAGG
Found at i:42710962 original size:90 final size:91
Alignment explanation
Indices: 42710790--42710971 Score: 251
Period size: 90 Copynumber: 2.0 Consensus size: 91
42710780 TATAAATCAA
* * *
42710790 GGGTAAAATAGTAATTCTATAAATCGACGGTAAAACGATAATTTTGTAAATCGAGGGTAAAACGG
1 GGGTAAAATAGTAATTATATAAATCGACGGTAAAACGATAATTTTGTAAATCAAGGGTAAAACAG
* *
42710855 TAATTCTGTAAGTCAAGGGTAAAACG
66 TAATTCTATAAATCAAGGGTAAAACG
* ** * *
42710881 GGGTAAAATGGTAATTATGA-AAATCGGGGGTAAAATGGTAA-TTTGTAAATCAAGGGTAAAACA
1 GGGTAAAATAGTAATTAT-ATAAATCGACGGTAAAACGATAATTTTGTAAATCAAGGGTAAAACA
42710944 GTAATTCTATAAATCAAGGGTAAAACG
65 GTAATTCTATAAATCAAGGGTAAAACG
42710971 G
1 G
42710972 TACTTCTATA
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
90 46 0.57
91 33 0.41
92 1 0.01
ACGTcount: A:0.42, C:0.08, G:0.24, T:0.26
Consensus pattern (91 bp):
GGGTAAAATAGTAATTATATAAATCGACGGTAAAACGATAATTTTGTAAATCAAGGGTAAAACAG
TAATTCTATAAATCAAGGGTAAAACG
Found at i:42711002 original size:54 final size:53
Alignment explanation
Indices: 42710881--42711012 Score: 149
Period size: 53 Copynumber: 2.5 Consensus size: 53
42710871 GGGTAAAACG
* ** * *
42710881 GGGTAAAATGGTAATTATGA-AAATCGGGGGTAAAATGGTAATTTGTAAATCAA
1 GGGTAAAACGGTAATTAT-ATAAATCAAGGGTAAAACGGTAATTTATAAATCAA
* * * *
42710934 GGGTAAAACAGTAATTCTATAAATCAAGGGTAAAACGGTACTTCTATAAATCGA
1 GGGTAAAACGGTAATTATATAAATCAAGGGTAAAACGGTAATT-TATAAATCAA
*
42710988 GGGTAAAACGGTAATTATGTAAATC
1 GGGTAAAACGGTAATTATATAAATC
42711013 GGGGTACTTT
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
52 1 0.02
53 34 0.52
54 30 0.46
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.27
Consensus pattern (53 bp):
GGGTAAAACGGTAATTATATAAATCAAGGGTAAAACGGTAATTTATAAATCAA
Found at i:42713899 original size:31 final size:31
Alignment explanation
Indices: 42713858--42713921 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
42713848 CCTTTTCATA
*
42713858 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
**
42713889 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
42713920 TT
1 TT
42713922 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:42714139 original size:24 final size:24
Alignment explanation
Indices: 42714112--42714226 Score: 180
Period size: 24 Copynumber: 4.8 Consensus size: 24
42714102 CTGCTTTATC
*
42714112 ACTGGGGCA-AATCCCTTTTTAATA
1 ACTGGGGCATAAGCCC-TTTTAATA
42714136 ACTGGGGCA-AAGCCCTTTTAATA
1 ACTGGGGCATAAGCCCTTTTAATA
42714159 ACTGGGGCATAAGCCCTTTTAATA
1 ACTGGGGCATAAGCCCTTTTAATA
*
42714183 ACTAGGGCATAAGCCCTTTTAATA
1 ACTGGGGCATAAGCCCTTTTAATA
*
42714207 ACCGGGGCATAAGCCCTTTT
1 ACTGGGGCATAAGCCCTTTT
42714227 TGCACTTCCT
Statistics
Matches: 86, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
23 17 0.20
24 69 0.80
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (24 bp):
ACTGGGGCATAAGCCCTTTTAATA
Found at i:42714306 original size:20 final size:20
Alignment explanation
Indices: 42714281--42714363 Score: 130
Period size: 20 Copynumber: 4.2 Consensus size: 20
42714271 GAACATCTCG
*
42714281 TGTGCATATCATATATATCA
1 TGTGCATATCATACATATCA
*
42714301 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
*
42714321 TATGCATATCATACATATCA
1 TGTGCATATCATACATATCA
*
42714341 TGTGCGTATCATACATATCA
1 TGTGCATATCATACATATCA
42714361 TGT
1 TGT
42714364 TTATCAAAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:42714317 original size:15 final size:15
Alignment explanation
Indices: 42714289--42714363 Score: 59
Period size: 15 Copynumber: 5.1 Consensus size: 15
42714279 CGTGTGCATA
42714289 TCATAT-ATATCATG
1 TCATATCATATCATG
42714303 TGCATATCATA-CATG
1 T-CATATCATATCATG
42714318 TCATATGCATATCAT-
1 TCATAT-CATATCATG
* * * *
42714333 ACATATCATGTGCGTA
1 TCATATCATAT-CATG
42714349 TCATA-CATATCATG
1 TCATATCATATCATG
42714363 T
1 T
42714364 TTATCAAAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
14 13 0.27
15 25 0.52
16 10 0.21
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (15 bp):
TCATATCATATCATG
Found at i:42714428 original size:25 final size:25
Alignment explanation
Indices: 42714400--42714447 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
42714390 ATATATAAAC
* * *
42714400 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
42714425 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
42714448 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:42715697 original size:27 final size:27
Alignment explanation
Indices: 42715606--42715689 Score: 125
Period size: 27 Copynumber: 3.1 Consensus size: 27
42715596 GGGCATATTC
*
42715606 GTCATTTTACCATACAGGGG-TATTACG
1 GTCACTTTACCATACAGGGGCT-TTACG
*
42715633 GTCACTTTACCTTACAGGGGCTTTACG
1 GTCACTTTACCATACAGGGGCTTTACG
*
42715660 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCACTTTACCATACAGGGGCTTTACG
42715687 GTC
1 GTC
42715690 TTTTTACCTA
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
27 52 0.98
28 1 0.02
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (27 bp):
GTCACTTTACCATACAGGGGCTTTACG
Found at i:42715706 original size:27 final size:26
Alignment explanation
Indices: 42715606--42715699 Score: 118
Period size: 27 Copynumber: 3.5 Consensus size: 26
42715596 GGGCATATTC
*
42715606 GTCATTTTACCATACAGGGG-TATTACG
1 GTCACTTTACC-TACAGGGGCT-TTACG
42715633 GTCACTTTACCTTACAGGGGCTTTACG
1 GTCACTTTACC-TACAGGGGCTTTACG
42715660 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCACTTTA-CCTACAGGGGCTTTACG
**
42715687 GTCTTTTTACCTA
1 GTCACTTTACCTA
42715700 ATAGGGGTAT
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
26 4 0.07
27 54 0.89
28 3 0.05
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.35
Consensus pattern (26 bp):
GTCACTTTACCTACAGGGGCTTTACG
Found at i:42715781 original size:27 final size:27
Alignment explanation
Indices: 42715751--42716007 Score: 128
Period size: 27 Copynumber: 9.4 Consensus size: 27
42715741 GTAAATCTAC
*
42715751 AAACCAAGGGTATTTCAGTAATTTTGT
1 AAACCAAGGGTATTTCGGTAATTTTGT
* **
42715778 AAACCAATGGTATTTCTATAATTTT-T
1 AAACCAAGGGTATTTCGGTAATTTTGT
* * *
42715804 AGAAAGTCAAGGGTATTTCTGTAACTTTGT
1 --AAA-CCAAGGGTATTTCGGTAATTTTGT
* * *
42715834 AAATCAGGGGTATTTTGGTAA-TTT-T
1 AAACCAAGGGTATTTCGGTAATTTTGT
* ***
42715859 AAACATTAAGGGTATTTCGGTAATTTCAC
1 AAAC--CAAGGGTATTTCGGTAATTTTGT
* **
42715888 AAACC-AGTGGTATTTTGGTAATTTTAC
1 AAACCAAG-GGTATTTCGGTAATTTTGT
* * * **
42715915 AAACTAGGGGTATTTTGGTAATTTTAC
1 AAACCAAGGGTATTTCGGTAATTTTGT
*** *
42715942 AAATTGAGGGTATTTCTGTAATTTTGT
1 AAACCAAGGGTATTTCGGTAATTTTGT
* * ** *
42715969 AAATCGAGGGTAAAAT-AGTAATTTTGT
1 AAACCAAGGGT-ATTTCGGTAATTTTGT
*
42715996 AAATCAAGGGTA
1 AAACCAAGGGTA
42716008 AAATAGTAAT
Statistics
Matches: 186, Mismatches: 33, Indels: 23
0.77 0.14 0.10
Matches are distributed among these distances:
25 4 0.02
26 7 0.04
27 141 0.76
28 11 0.06
29 22 0.12
30 1 0.01
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.39
Consensus pattern (27 bp):
AAACCAAGGGTATTTCGGTAATTTTGT
Found at i:42715900 original size:54 final size:54
Alignment explanation
Indices: 42715736--42715944 Score: 172
Period size: 54 Copynumber: 3.8 Consensus size: 54
42715726 TACAAGGGTG
* * * * *** *
42715736 TTTTGGTAAATCTACAAACCAAGGGTATTTCAGTAATTTTGTAAACCAATGGTA
1 TTTTGGTAATTTTACAAACTAAGGGTATTTCGGTAATTTCACAAACCAGTGGTA
* * * * ** * *
42715790 TTTCT-ATAATTTTTAGAAAGTCAAGGGTATTTCTGTAACTTT-GTAAATCAGGGGTA
1 TTT-TGGTAA-TTTTACAAACT-AAGGGTATTTCGGTAA-TTTCACAAACCAGTGGTA
*
42715846 TTTTGGTAATTTTA-AACATTAAGGGTATTTCGGTAATTTCACAAACCAGTGGTA
1 TTTTGGTAATTTTACAA-ACTAAGGGTATTTCGGTAATTTCACAAACCAGTGGTA
* * *
42715900 TTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAA
1 TTTTGGTAATTTTACAAACTAAGGGTATTTCGGTAATTTCACAAA
42715945 TTGAGGGTAT
Statistics
Matches: 126, Mismatches: 21, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
53 3 0.02
54 71 0.56
55 17 0.13
56 32 0.25
57 3 0.02
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (54 bp):
TTTTGGTAATTTTACAAACTAAGGGTATTTCGGTAATTTCACAAACCAGTGGTA
Found at i:42715954 original size:54 final size:53
Alignment explanation
Indices: 42715841--42715966 Score: 148
Period size: 54 Copynumber: 2.3 Consensus size: 53
42715831 TGTAAATCAG
*
42715841 GGGTATTTTGGTAATTTTAAACATTAAGGGTATTTCGGTAATTTCACAAACCA
1 GGGTATTTTGGTAATTTTAAACACTAAGGGTATTTCGGTAATTTCACAAACCA
* * * **
42715894 GTGGTATTTTGGTAATTTTACAA-ACTAGGGGTATTTTGGTAATTTTACAAATTGA
1 G-GGTATTTTGGTAATTTTA-AACACTAAGGGTATTTCGGTAATTTCACAAA-CCA
42715949 GGGTATTTCT-GTAATTTT
1 GGGTATTT-TGGTAATTTT
42715967 GTAAATCGAG
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
53 1 0.02
54 57 0.90
55 5 0.08
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.43
Consensus pattern (53 bp):
GGGTATTTTGGTAATTTTAAACACTAAGGGTATTTCGGTAATTTCACAAACCA
Found at i:42716007 original size:81 final size:81
Alignment explanation
Indices: 42715824--42716007 Score: 194
Period size: 81 Copynumber: 2.3 Consensus size: 81
42715814 GGGTATTTCT
*
42715824 GTAACTTTGTAAATCAGGGGTATTTTGGTAATTTTAAACATTAAGGGTATTTCGGTAATTTCACA
1 GTAATTTTGTAAATCAGGGGTATTTTGGTAATTTTAAACATTAAGGGTATTTCGGTAATTTCACA
*** *
42715889 AACCAGTGGTATTTTG
66 AACCAGTGGTAAAATA
** * * **
42715905 GTAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTACAA-ATTGAGGGTATTTCTGTAATTTTG
1 GTAATTTTGTAAATC-AGGGGTATTTTGGTAATTTTA-AACATTAAGGGTATTTCGGTAATTTCA
* *
42715968 TAAATCGAG-GGTAAAATA
64 CAAA-CCAGTGGTAAAATA
*
42715986 GTAATTTTGTAAATCAAGGGTA
1 GTAATTTTGTAAATCAGGGGTA
42716008 AAATAGTAAT
Statistics
Matches: 83, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
80 1 0.01
81 76 0.92
82 6 0.07
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.39
Consensus pattern (81 bp):
GTAATTTTGTAAATCAGGGGTATTTTGGTAATTTTAAACATTAAGGGTATTTCGGTAATTTCACA
AACCAGTGGTAAAATA
Found at i:42716008 original size:27 final size:27
Alignment explanation
Indices: 42715959--42716234 Score: 167
Period size: 27 Copynumber: 9.8 Consensus size: 27
42715949 GGGTATTTCT
*
42715959 GTAATTTTGTAAATCGAGGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAATA
* *
42715986 GTAATTTTGTAAATCAAGGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAATA
* * ** *
42716013 GTAATTCTATAAATTGACCGTAAAA-C
1 GTAATTCTGTAAATCGAGGGTAAAATA
* ** **
42716039 GATAATTTTGTAAATTAAGGGTAAAACG
1 G-TAATTCTGTAAATCGAGGGTAAAATA
*
42716067 GTAATTCTGTAAGTCGAGGGTAAAACGGGGGTAAAA
1 GTAATTCTGTAAATCGAGGGTAAAA------T---A
* * *
42716103 TGGTAATTATGTAAATCGGGGGTAAAATG
1 --GTAATTCTGTAAATCGAGGGTAAAATA
* * * *
42716132 GTAATTTTGTAAATCAAGGGTATAACA
1 GTAATTCTGTAAATCGAGGGTAAAATA
* * *
42716159 GTAATTCTATAAATCAAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATA
* * **
42716186 GTACTTCTATAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAATA
* *
42716213 GTAATTATGTAAATCGGGGGTA
1 GTAATTCTGTAAATCGAGGGTA
42716235 CTTTGGTAAT
Statistics
Matches: 194, Mismatches: 42, Indels: 26
0.74 0.16 0.10
Matches are distributed among these distances:
26 1 0.01
27 169 0.87
28 1 0.01
32 1 0.01
38 22 0.11
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.30
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAATA
Found at i:42716017 original size:54 final size:54
Alignment explanation
Indices: 42715959--42716227 Score: 225
Period size: 54 Copynumber: 4.8 Consensus size: 54
42715949 GGGTATTTCT
* * * *
42715959 GTAATTTTGTAAATCGAGGGTAAAATAGTAATTTTGTAAATCAAGGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAACAGTAATTATGTAAATCAAGGGTAAAATG
* * ** * * *
42716013 GTAATTCTATAAATTGACCGTAAAAC-GATAATTTTGTAAATTAAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACAG-TAATTATGTAAATCAAGGGTAAAATG
* **
42716067 GTAATTCTGTAAGTCGAGGGTAAAACGGGGGTAAAATGGTAATTATGTAAATCGGGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAAC---------A--GTAATTATGTAAATCAAGGGTAAAATG
* * * * *
42716132 GTAATTTTGTAAATCAAGGGTATAACAGTAATTCTATAAATCAAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACAGTAATTATGTAAATCAAGGGTAAAATG
* * *
42716186 GTACTTCTATAAATCGAGGGTAAAACGGTAATTATGTAAATC
1 GTAATTCTGTAAATCGAGGGTAAAACAGTAATTATGTAAATC
42716228 GGGGGTACTT
Statistics
Matches: 167, Mismatches: 35, Indels: 26
0.73 0.15 0.11
Matches are distributed among these distances:
53 1 0.01
54 121 0.72
56 1 0.01
65 43 0.26
66 1 0.01
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.30
Consensus pattern (54 bp):
GTAATTCTGTAAATCGAGGGTAAAACAGTAATTATGTAAATCAAGGGTAAAATG
Found at i:42716017 original size:81 final size:81
Alignment explanation
Indices: 42715960--42716227 Score: 194
Period size: 81 Copynumber: 3.2 Consensus size: 81
42715950 GGTATTTCTG
* * * *
42715960 TAATTTTGTAAATCGAGGGTAAAATAGTAATTTTGTAAATCAAGGGTAAAATAGTAATTCTATAA
1 TAATTTTGTAAATCAAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAATAGTAATTCTACAA
42716025 ATTGACCGTAAAACGA
66 ATTGACCGTAAAACGA
* * * *
42716041 TAATTTTGTAAATTAAGGGTAAAACGGTAATTCTGTAAGTCGAGGGTAAAACGGGGGTAAAATGG
1 TAATTTTGTAAATCAAGGGTAAAACAGTAATTCTGTAA----A---T-CAA---GGGTAAAATAG
* ** * *** * *
42716106 TAATTATGTAAATCGGGGGTAAAATGG
55 TAATTCTACAAATTGACCGTAAAACGA
* * * * *
42716133 TAATTTTGTAAATCAAGGGTATAACAGTAATTCTATAAATCAAGGGTAAAATGGTACTTCTATAA
1 TAATTTTGTAAATCAAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAATAGTAATTCTACAA
* ** *
42716198 ATCGAGGGTAAAACGG
66 ATTGACCGTAAAACGA
*
42716214 TAATTATGTAAATC
1 TAATTTTGTAAATC
42716228 GGGGGTACTT
Statistics
Matches: 150, Mismatches: 26, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
81 79 0.53
84 2 0.01
85 2 0.01
88 2 0.01
89 2 0.01
92 63 0.42
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (81 bp):
TAATTTTGTAAATCAAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAATAGTAATTCTACAA
ATTGACCGTAAAACGA
Found at i:42716099 original size:38 final size:38
Alignment explanation
Indices: 42716057--42716129 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
42716047 TGTAAATTAA
* *
42716057 GGGTAAAACGGTAATTCTGTAAGTCGAGGGTAAAACGG
1 GGGTAAAACGGTAATTATGTAAATCGAGGGTAAAACGG
* *
42716095 GGGTAAAATGGTAATTATGTAAATCGGGGGTAAAA
1 GGGTAAAACGGTAATTATGTAAATCGAGGGTAAAA
42716130 TGGTAATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.37, C:0.07, G:0.33, T:0.23
Consensus pattern (38 bp):
GGGTAAAACGGTAATTATGTAAATCGAGGGTAAAACGG
Found at i:42716116 original size:65 final size:65
Alignment explanation
Indices: 42716032--42716153 Score: 154
Period size: 65 Copynumber: 1.9 Consensus size: 65
42716022 TAAATTGACC
* * * *
42716032 GTAAAACGATAATTTTGTAAATTAAGGGTAAAACGGTAATTCTGTAAGTCGAGGGTAAAACGGGG
1 GTAAAACGATAATTATGTAAATCAAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAACGGGG
* * ** * *
42716097 GTAAAATGGTAATTATGTAAATCGGGGGTAAAATGGTAATTTTGTAAATCAAGGGTA
1 GTAAAACGATAATTATGTAAATCAAGGGTAAAACGGTAATTCTGTAAATCAAGGGTA
42716154 TAACAGTAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
65 47 1.00
ACGTcount: A:0.39, C:0.06, G:0.27, T:0.29
Consensus pattern (65 bp):
GTAAAACGATAATTATGTAAATCAAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAACGGGG
Found at i:42716118 original size:92 final size:92
Alignment explanation
Indices: 42716003--42716183 Score: 227
Period size: 92 Copynumber: 2.0 Consensus size: 92
42715993 TGTAAATCAA
* * * *
42716003 GGGTAAAATAGTAATTCTATAAATTGACCGTAAAACGATAATTTTGTAAATTAAGGGTAAAACGG
1 GGGTAAAATAGTAATTATATAAATCGACCGTAAAACGATAATTTTGTAAATCAAGGGTAAAACAG
* * *
42716068 TAATTCTGTAAGTCGAGGGTAAAACGG
66 TAATTCTATAAATCAAGGGTAAAACGG
* * *** * * *
42716095 GGGTAAAATGGTAATTATGTAAATCGGGGGTAAAATGGTAATTTTGTAAATCAAGGGTATAACAG
1 GGGTAAAATAGTAATTATATAAATCGACCGTAAAACGATAATTTTGTAAATCAAGGGTAAAACAG
42716160 TAATTCTATAAATCAAGGGTAAAA
66 TAATTCTATAAATCAAGGGTAAAA
42716184 TGGTACTTCT
Statistics
Matches: 74, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
92 74 1.00
ACGTcount: A:0.41, C:0.07, G:0.23, T:0.29
Consensus pattern (92 bp):
GGGTAAAATAGTAATTATATAAATCGACCGTAAAACGATAATTTTGTAAATCAAGGGTAAAACAG
TAATTCTATAAATCAAGGGTAAAACGG
Found at i:42716178 original size:119 final size:119
Alignment explanation
Indices: 42715967--42716213 Score: 289
Period size: 119 Copynumber: 2.1 Consensus size: 119
42715957 CTGTAATTTT
* * * **
42715967 GTAAATCGAGGGTAAAATAGTAATTTTGTAAATCAAGGGTAAAATAGTAATTCTATAAATTGACC
1 GTAAAACGGGGGTAAAATAGTAATTATGTAAATCAAGGGTAAAATAGTAATTCTATAAATCAACC
* * * * *
42716032 GTAAAACGATAATTTTGTAAATTAAGGGTAAAACGGTAATTCTGTAAGTCGAGG
66 GTAAAACGATAATTCTATAAATCAAGGGTAAAACGGTAATTCTATAAATCGAGG
* ** * * * **
42716086 GTAAAACGGGGGTAAAATGGTAATTATGTAAATCGGGGGTAAAATGGTAATTTTGTAAATCAAGG
1 GTAAAACGGGGGTAAAATAGTAATTATGTAAATCAAGGGTAAAATAGTAATTCTATAAATCAACC
* * *
42716151 GTATAAC-AGTAATTCTATAAATCAAGGGTAAAATGGTACTTCTATAAATCGAGG
66 GTAAAACGA-TAATTCTATAAATCAAGGGTAAAACGGTAATTCTATAAATCGAGG
42716205 GTAAAACGG
1 GTAAAACGG
42716214 TAATTATGTA
Statistics
Matches: 106, Mismatches: 21, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
118 1 0.01
119 105 0.99
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (119 bp):
GTAAAACGGGGGTAAAATAGTAATTATGTAAATCAAGGGTAAAATAGTAATTCTATAAATCAACC
GTAAAACGATAATTCTATAAATCAAGGGTAAAACGGTAATTCTATAAATCGAGG
Found at i:42716213 original size:146 final size:146
Alignment explanation
Indices: 42715959--42716234 Score: 381
Period size: 146 Copynumber: 1.9 Consensus size: 146
42715949 GGGTATTTCT
* *
42715959 GTAATTTTGTAAATCGAGGGTAAAATAGTAATTTTGTAAATCAAGGGTAAAATAGTAATTCTATA
1 GTAATTATGTAAATCGAGGGTAAAATAGTAATTTTGTAAATCAAGGGTAAAACAGTAATTCTATA
** * * * * *
42716024 AATTGACCGTAAAACGATAATTTTGTAAATTAAGGGTAAAACGGTAATTCTGTAAGTCGAGGGTA
66 AATCAACCGTAAAACGATAATTCTATAAATCAAGGGTAAAACGGTAATTATGTAAATCGAGGGTA
42716089 AAACGGGGGTAAAATG
131 AAACGGGGGTAAAATG
* * *
42716105 GTAATTATGTAAATCGGGGGTAAAATGGTAATTTTGTAAATCAAGGGTATAACAGTAATTCTATA
1 GTAATTATGTAAATCGAGGGTAAAATAGTAATTTTGTAAATCAAGGGTAAAACAGTAATTCTATA
** * * * * *
42716170 AATCAAGGGTAAAATGGTACTTCTATAAATCGAGGGTAAAACGGTAATTATGTAAATCGGGGGTA
66 AATCAACCGTAAAACGATAATTCTATAAATCAAGGGTAAAACGGTAATTATGTAAATCGAGGGTA
42716235 CTTTGGTAAT
Statistics
Matches: 111, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
146 111 1.00
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.30
Consensus pattern (146 bp):
GTAATTATGTAAATCGAGGGTAAAATAGTAATTTTGTAAATCAAGGGTAAAACAGTAATTCTATA
AATCAACCGTAAAACGATAATTCTATAAATCAAGGGTAAAACGGTAATTATGTAAATCGAGGGTA
AAACGGGGGTAAAATG
Found at i:42716234 original size:54 final size:54
Alignment explanation
Indices: 42716095--42716261 Score: 181
Period size: 54 Copynumber: 3.1 Consensus size: 54
42716085 GGTAAAACGG
* * *
42716095 GGGTAAAATGGTAATTATGTAAATCGGGGGTAAAATGGTAATTTTGTAAATCAA
1 GGGTAAAACGGTAATTATGTAAATCGGGGGTAAAATGGTAATTCTATAAATCAA
* * * * ** * *
42716149 GGGTATAACAGTAATTCTATAAATCAAGGGTAAAATGGTACTTCTATAAATCGA
1 GGGTAAAACGGTAATTATGTAAATCGGGGGTAAAATGGTAATTCTATAAATCAA
*** * * *
42716203 GGGTAAAACGGTAATTATGTAAATCGGGGGTACTTTGGTAATTTTACAAGTCAA
1 GGGTAAAACGGTAATTATGTAAATCGGGGGTAAAATGGTAATTCTATAAATCAA
42716257 GGGTA
1 GGGTA
42716262 TTTCAATAAT
Statistics
Matches: 88, Mismatches: 25, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
54 88 1.00
ACGTcount: A:0.37, C:0.08, G:0.25, T:0.31
Consensus pattern (54 bp):
GGGTAAAACGGTAATTATGTAAATCGGGGGTAAAATGGTAATTCTATAAATCAA
Found at i:42721118 original size:15 final size:15
Alignment explanation
Indices: 42721098--42721128 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
42721088 TTTCATCACT
42721098 TTTCAATATATTAAA
1 TTTCAATATATTAAA
42721113 TTTCAATATATTAAA
1 TTTCAATATATTAAA
42721128 T
1 T
42721129 CATGTCATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTCAATATATTAAA
Found at i:42722233 original size:144 final size:144
Alignment explanation
Indices: 42721816--42722255 Score: 837
Period size: 144 Copynumber: 3.1 Consensus size: 144
42721806 TGAGTTAAAT
*
42721816 TTCGGCCATGCATGTTGTTTTTCCTTGGTGAGTGTTTTGATGTTGTTGTGATGAAAGCATGGAGA
1 TTCGGCCATGCATGTTGTCTTTCCTTGGTGAGTGTTTTGATGTTGTTGTGATGAAAGCATGGAGA
42721881 TGAGTGAGTTCGAATGTTTAACAAAAAGGAAATTTTGTGCCATTGAGTTCTTGTTGTTATGTGTG
66 TGAGTGAGTTCGAATGTTTAACAAAAAGGAAATTTTGTGCCATTGAGTTCTTGTTGTTATGTGTG
42721946 TGTGTGCATGAGTA
131 TGTGTGCATGAGTA
*
42721960 TTCGGCCATGCATGTTGTC-TTCCTTGGTGAGTGTTTTGATGTTGTTGTGATGAAAACATGGAGA
1 TTCGGCCATGCATGTTGTCTTTCCTTGGTGAGTGTTTTGATGTTGTTGTGATGAAAGCATGGAGA
42722024 TGAGTGAGTTCGAATGTTTAACAAAAAGGAAATTTTGTGCCATTGAGTTCTTGTTGTTATGTGTG
66 TGAGTGAGTTCGAATGTTTAACAAAAAGGAAATTTTGTGCCATTGAGTTCTTGTTGTTATGTGTG
42722089 TGTGTGCATGAGTA
131 TGTGTGCATGAGTA
42722103 TTCGGCCATGCATGTTGTCTTTCCTTGGTGAGTGTTTTGATGTTGTTGTGATGAAAGCATGGAGA
1 TTCGGCCATGCATGTTGTCTTTCCTTGGTGAGTGTTTTGATGTTGTTGTGATGAAAGCATGGAGA
* *
42722168 TGAGTGAGTTCAAATGTTTAACAAAAAGGAAATTTTGTGCCATTCAGTTCTTGTTGTTATGTGTG
66 TGAGTGAGTTCGAATGTTTAACAAAAAGGAAATTTTGTGCCATTGAGTTCTTGTTGTTATGTGTG
42722233 TGTGTGCATGAGTA
131 TGTGTGCATGAGTA
42722247 TTCGGCCAT
1 TTCGGCCAT
42722256 ATGGGGTATA
Statistics
Matches: 290, Mismatches: 5, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
143 142 0.49
144 148 0.51
ACGTcount: A:0.22, C:0.10, G:0.28, T:0.40
Consensus pattern (144 bp):
TTCGGCCATGCATGTTGTCTTTCCTTGGTGAGTGTTTTGATGTTGTTGTGATGAAAGCATGGAGA
TGAGTGAGTTCGAATGTTTAACAAAAAGGAAATTTTGTGCCATTGAGTTCTTGTTGTTATGTGTG
TGTGTGCATGAGTA
Found at i:42722777 original size:29 final size:29
Alignment explanation
Indices: 42722744--42722875 Score: 156
Period size: 29 Copynumber: 4.6 Consensus size: 29
42722734 GTGACGAGAT
*
42722744 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
*
42722773 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
* *
42722802 AGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
** * **
42722831 TAACACTATGTGTGCAAGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
* **
42722860 CGGCACTGGGTGTGCG
1 TGGCACTAAGTGTGCG
42722876 AGCTCGAAGG
Statistics
Matches: 89, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 89 1.00
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.24
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAAAATA
Found at i:42729973 original size:143 final size:143
Alignment explanation
Indices: 42729765--42730199 Score: 831
Period size: 143 Copynumber: 3.1 Consensus size: 143
42729755 TGAGTTAAAT
*
42729765 TTCGGCCATGCATGTTGTTTTCCTTGGTGAGTGTTTTGATGTTGTTGTGATGAAAGCATGGAGAT
1 TTCGGCCATGCATGTTGTCTTCCTTGGTGAGTGTTTTGATGTTGTTGTGATGAAAGCATGGAGAT
42729830 GAGTGAGTTCGAATGTTTAACAAAAAGGAAATTTTGTGCCATTGAGTTCTTGTTGTTATGTGTGT
66 GAGTGAGTTCGAATGTTTAACAAAAAGGAAATTTTGTGCCATTGAGTTCTTGTTGTTATGTGTGT
42729895 GTGTGCATGAGTA
131 GTGTGCATGAGTA
42729908 TTCGGCCATGCATGTTGTCTTCCTTGGTGAGTGTTTTGATGTTGTTGTGATGAAAGCATGGAGAT
1 TTCGGCCATGCATGTTGTCTTCCTTGGTGAGTGTTTTGATGTTGTTGTGATGAAAGCATGGAGAT
42729973 GAGTGAGTTCGAATGTTTAACAAAAAGGAAATTTTGTGCCATTGAGTTCTTGTTGTTATGTGTGT
66 GAGTGAGTTCGAATGTTTAACAAAAAGGAAATTTTGTGCCATTGAGTTCTTGTTGTTATGTGTGT
42730038 GTGTGCATGAGTA
131 GTGTGCATGAGTA
*
42730051 TTCGGCCATGCATGTTGTCTTCCTTGGTAAGTGTTTTGATGTTGTTGTGATGAAAGCATGGAGAT
1 TTCGGCCATGCATGTTGTCTTCCTTGGTGAGTGTTTTGATGTTGTTGTGATGAAAGCATGGAGAT
42730116 GAGTGAGTTCGAATGTTTAACAAAAAGGAAA-TTTGTGCCATTGAGTTCTTGTTGTTA--TGTGT
66 GAGTGAGTTCGAATGTTTAACAAAAAGGAAATTTTGTGCCATTGAGTTCTTGTTGTTATGTGTGT
42730178 GTGTGCATGAGTA
131 GTGTGCATGAGTA
42730191 TTCGGCCAT
1 TTCGGCCAT
42730200 ATGGGGTATA
Statistics
Matches: 290, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
140 27 0.09
142 26 0.09
143 237 0.82
ACGTcount: A:0.22, C:0.10, G:0.29, T:0.39
Consensus pattern (143 bp):
TTCGGCCATGCATGTTGTCTTCCTTGGTGAGTGTTTTGATGTTGTTGTGATGAAAGCATGGAGAT
GAGTGAGTTCGAATGTTTAACAAAAAGGAAATTTTGTGCCATTGAGTTCTTGTTGTTATGTGTGT
GTGTGCATGAGTA
Found at i:42730714 original size:29 final size:29
Alignment explanation
Indices: 42730681--42730812 Score: 156
Period size: 29 Copynumber: 4.6 Consensus size: 29
42730671 GTGACGAGAT
*
42730681 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
*
42730710 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
* *
42730739 AGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
** * **
42730768 TAACACTATGTGTGCAAGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
* **
42730797 CGGCACTGGGTGTGCG
1 TGGCACTAAGTGTGCG
42730813 AGCTCGAAGG
Statistics
Matches: 89, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 89 1.00
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.24
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAAAATA
Found at i:42734707 original size:26 final size:26
Alignment explanation
Indices: 42734668--42734741 Score: 121
Period size: 26 Copynumber: 2.8 Consensus size: 26
42734658 TCATCCCTAT
*
42734668 TTTACCCCTGGTAAAATTTTGACGAA
1 TTTACCCCTAGTAAAATTTTGACGAA
* *
42734694 TTTACCCCTAGTAAAATTTTGATGAT
1 TTTACCCCTAGTAAAATTTTGACGAA
42734720 TTTACCCCTAGTAAAATTTTGA
1 TTTACCCCTAGTAAAATTTTGA
42734742 AAAAATATGT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (26 bp):
TTTACCCCTAGTAAAATTTTGACGAA
Found at i:42738653 original size:26 final size:26
Alignment explanation
Indices: 42738624--42738676 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
42738614 TCAAACATGC
42738624 ATTTAAGTCAATTTAAC-CCTAGGGGT
1 ATTTAAGT-AATTTAACTCCTAGGGGT
** *
42738650 ATTTCGGTAATTTATCTCCTAGGGGT
1 ATTTAAGTAATTTAACTCCTAGGGGT
42738676 A
1 A
42738677 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (26 bp):
ATTTAAGTAATTTAACTCCTAGGGGT
Found at i:42743615 original size:46 final size:46
Alignment explanation
Indices: 42743550--42743915 Score: 565
Period size: 46 Copynumber: 8.0 Consensus size: 46
42743540 TTATCTTTGA
* * * * *
42743550 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATAT
***
42743596 CATGTTGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
42743642 CACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
42743688 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* *
42743734 CAGGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* *
42743780 CAGGTTGCCATGGTATCTTTCAACTATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
42743826 TATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TAAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT-AT
42743872 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
42743916 TTCAGAGAGC
Statistics
Matches: 299, Mismatches: 18, Indels: 5
0.93 0.06 0.02
Matches are distributed among these distances:
45 5 0.02
46 293 0.98
47 1 0.00
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.39
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
Found at i:42749198 original size:26 final size:26
Alignment explanation
Indices: 42749169--42749221 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
42749159 TCAAACATGC
42749169 ATTTAAGTCAATTTAAC-CCTAGGGGT
1 ATTTAAGT-AATTTAACTCCTAGGGGT
** *
42749195 ATTTCGGTAATTTATCTCCTAGGGGT
1 ATTTAAGTAATTTAACTCCTAGGGGT
42749221 A
1 A
42749222 AAATTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (26 bp):
ATTTAAGTAATTTAACTCCTAGGGGT
Found at i:42750730 original size:26 final size:26
Alignment explanation
Indices: 42750700--42750753 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
42750690 TGAAATGCCC
42750700 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
42750726 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
42750752 AT
1 AT
42750754 TAATTTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.35, C:0.26, G:0.07, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:42753814 original size:2 final size:2
Alignment explanation
Indices: 42753807--42753836 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
42753797 AACATGTGTC
42753807 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
42753837 TTGTAAGCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42758739 original size:42 final size:42
Alignment explanation
Indices: 42758680--42758763 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
42758670 CCATCATCAA
42758680 GTAAGGTCAAAAGAGCATCCATAGCTCTTAAGACATACAAGG
1 GTAAGGTCAAAAGAGCATCCATAGCTCTTAAGACATACAAGG
42758722 GTAAGGTCAAAAGAGCATCCATAGCTCTTAAGACATACAAGG
1 GTAAGGTCAAAAGAGCATCCATAGCTCTTAAGACATACAAGG
42758764 ATTTTCTACT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.19
Consensus pattern (42 bp):
GTAAGGTCAAAAGAGCATCCATAGCTCTTAAGACATACAAGG
Found at i:42760230 original size:45 final size:44
Alignment explanation
Indices: 42760094--42760308 Score: 270
Period size: 45 Copynumber: 4.9 Consensus size: 44
42760084 ATTTATTCAT
* * * * *
42760094 CGGCATT-TCGCCTACTAGGCTCGAGGCCCCAATAGTGTCTCAC
1 CGGCATTATAGCCTGCTAGGCTCAAGGCCCGAATAGTATCTCAC
42760137 CGGCATTATAGCCTGCTAGGCTCAAGGCCCGAATAGTATCTCAC
1 CGGCATTATAGCCTGCTAGGCTCAAGGCCCGAATAGTATCTCAC
** * * *
42760181 CGGCATTATAGCCTAATAGGCTCAGAGGCCTGAATAATATCTCAT
1 CGGCATTATAGCCTGCTAGGCTCA-AGGCCCGAATAGTATCTCAC
* * *
42760226 CGGCATTATAGTCTGCTAGGGTCAAAGGCCCGAATACTATCTCAC
1 CGGCATTATAGCCTGCTAGGCTC-AAGGCCCGAATAGTATCTCAC
* *
42760271 CAGCATTATAGCCTGCTAGGCTCAAGGCCCAAATAGTA
1 CGGCATTATAGCCTGCTAGGCTCAAGGCCCGAATAGTA
42760309 CTGTATAATA
Statistics
Matches: 147, Mismatches: 22, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
43 7 0.05
44 66 0.45
45 73 0.50
46 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.24
Consensus pattern (44 bp):
CGGCATTATAGCCTGCTAGGCTCAAGGCCCGAATAGTATCTCAC
Found at i:42767803 original size:46 final size:46
Alignment explanation
Indices: 42767750--42767925 Score: 223
Period size: 46 Copynumber: 3.8 Consensus size: 46
42767740 TATTTGGGCA
42767750 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
42767796 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
42767843 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * *
42767889 CCCGAGCTCGCTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42767926 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 66 0.59
47 33 0.30
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:42767905 original size:93 final size:93
Alignment explanation
Indices: 42767746--42767917 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
42767736 GGGATATTTG
* * *
42767746 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGCTGAG
42767811 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
42767839 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGCTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGCTGAG
42767904 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
42767918 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.20, C:0.23, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGCTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:42776805 original size:66 final size:68
Alignment explanation
Indices: 42776729--42776915 Score: 281
Period size: 71 Copynumber: 2.7 Consensus size: 68
42776719 TAGTACCACT
*
42776729 CATGCGACCTAGC-CGATTTGTC-T-CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
1 CATGCGACCTAGCAC-ATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
42776791 CACG
65 CACG
42776795 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
42776860 ATCACG
63 ATCACG
42776866 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGG
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGG
42776916 GATACATCTC
Statistics
Matches: 114, Mismatches: 1, Indels: 7
0.93 0.01 0.06
Matches are distributed among these distances:
66 13 0.11
67 6 0.05
68 1 0.01
69 1 0.01
71 93 0.82
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (68 bp):
CATGCGACCTAGCACATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATC
ACG
Found at i:42776840 original size:71 final size:71
Alignment explanation
Indices: 42776752--42776915 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
42776742 CGATTTGTCT
42776752 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
42776817 CTTTCA
66 CTTTCA
42776823 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
42776888 CTTTCA
66 CTTTCA
42776894 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
42776916 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:42776953 original size:71 final size:70
Alignment explanation
Indices: 42776752--42776949 Score: 276
Period size: 71 Copynumber: 2.8 Consensus size: 70
42776742 CGATTTGTCT
* * *
42776752 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
42776817 CTTTCA
65 CTTTCA
* * *
42776823 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
42776888 CTTTCA
65 CTTTCA
* *
42776894 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACGCATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACGCATGCGACCTAGCTAC
42776950 TACAGGGTGT
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
68 23 0.19
69 1 0.01
70 1 0.01
71 96 0.79
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACGCATGCGACCTAGCTACATTTATC
TTTCA
Found at i:42784372 original size:66 final size:68
Alignment explanation
Indices: 42784296--42784482 Score: 281
Period size: 71 Copynumber: 2.7 Consensus size: 68
42784286 TAGTACCACT
*
42784296 CATGCGACCTAGC-CGATTTGTC-T-CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
1 CATGCGACCTAGCAC-ATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
42784358 CACG
65 CACG
42784362 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
42784427 ATCACG
63 ATCACG
42784433 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGG
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGG
42784483 GATACATCTC
Statistics
Matches: 114, Mismatches: 1, Indels: 7
0.93 0.01 0.06
Matches are distributed among these distances:
66 13 0.11
67 6 0.05
68 1 0.01
69 1 0.01
71 93 0.82
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (68 bp):
CATGCGACCTAGCACATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATC
ACG
Found at i:42784407 original size:71 final size:71
Alignment explanation
Indices: 42784319--42784482 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
42784309 CGATTTGTCT
42784319 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
42784384 CTTTCA
66 CTTTCA
42784390 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
42784455 CTTTCA
66 CTTTCA
42784461 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
42784483 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:42784520 original size:71 final size:70
Alignment explanation
Indices: 42784319--42784516 Score: 276
Period size: 71 Copynumber: 2.8 Consensus size: 70
42784309 CGATTTGTCT
* * *
42784319 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
42784384 CTTTCA
65 CTTTCA
* * *
42784390 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
42784455 CTTTCA
65 CTTTCA
* *
42784461 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACGCATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACGCATGCGACCTAGCTAC
42784517 TACAGGGTGT
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
68 23 0.19
69 1 0.01
70 1 0.01
71 96 0.79
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACGCATGCGACCTAGCTACATTTATC
TTTCA
Found at i:42785556 original size:68 final size:69
Alignment explanation
Indices: 42785447--42785577 Score: 212
Period size: 68 Copynumber: 1.9 Consensus size: 69
42785437 AAAACTAAAC
*
42785447 TAAAAATACCTCAGCGTGCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTGAAAAA
1 TAAAAATACCTCAACGTGCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAA
42785511 AAAT
66 AAAT
**
42785515 TAAAAATACCTCAACGTGTCTTGAGGCTCAACTCAC-TCTCGCAATATGAGTTGATTTTTGAAA
1 TAAAAATACCTCAACGTG-CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAA
42785578 GCAGAATTAA
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
68 35 0.60
69 23 0.40
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (69 bp):
TAAAAATACCTCAACGTGCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAA
AAAT
Found at i:42797578 original size:3 final size:3
Alignment explanation
Indices: 42797572--42797612 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
42797562 TAAAAGTATG
42797572 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
42797613 TCTACAATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:42798112 original size:13 final size:13
Alignment explanation
Indices: 42798074--42798116 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
42798064 ATGTATATAT
42798074 AAAGAAAGAAAAA
1 AAAGAAAGAAAAA
* * *
42798087 AAA-TAACACAAA
1 AAAGAAAGAAAAA
42798099 AAAGAAAGAAAAA
1 AAAGAAAGAAAAA
42798112 AAAGA
1 AAAGA
42798117 TTCGAAAGAA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.81, C:0.05, G:0.12, T:0.02
Consensus pattern (13 bp):
AAAGAAAGAAAAA
Found at i:42798463 original size:28 final size:26
Alignment explanation
Indices: 42798396--42798472 Score: 93
Period size: 26 Copynumber: 2.9 Consensus size: 26
42798386 GGTTTCTTGG
*
42798396 TTTTTTTGGGGGTTTAGG-TTTTTCTT
1 TTTTTTTTGGGG-TTAGGTTTTTTCTT
42798422 TTTTTTTTGGGGTTAGGTTTTTTCTTT
1 TTTTTTTTGGGGTTAGGTTTTTTC-TT
**
42798449 TTTTTATTTTTGGTTAGGTTTTTT
1 TTTTT-TTTGGGGTTAGGTTTTTT
42798473 TTTGGGAGGG
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
25 5 0.11
26 17 0.38
27 7 0.16
28 16 0.36
ACGTcount: A:0.05, C:0.03, G:0.22, T:0.70
Consensus pattern (26 bp):
TTTTTTTTGGGGTTAGGTTTTTTCTT
Found at i:42800062 original size:2 final size:2
Alignment explanation
Indices: 42800055--42800081 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
42800045 CATTTAAATG
42800055 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
42800082 TACTTTACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42804338 original size:15 final size:15
Alignment explanation
Indices: 42804309--42804337 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42804299 TGTTTTGTTG
42804309 GGTTTTAGTGTTTTT
1 GGTTTTAGTGTTTTT
42804324 GGTTTTAG-GTTTTT
1 GGTTTTAGTGTTTTT
42804338 TTTTGGGCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.07, C:0.00, G:0.28, T:0.66
Consensus pattern (15 bp):
GGTTTTAGTGTTTTT
Found at i:42804798 original size:18 final size:18
Alignment explanation
Indices: 42804775--42804809 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42804765 TCAAATCCAA
42804775 CTCTCTCAATTCTCTCAC
1 CTCTCTCAATTCTCTCAC
* *
42804793 CTCTCTTAATTTTCTCA
1 CTCTCTCAATTCTCTCA
42804810 AATTTTGTTT
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:0.17, C:0.37, G:0.00, T:0.46
Consensus pattern (18 bp):
CTCTCTCAATTCTCTCAC
Done.