Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 30 of 187
Found at i:9677900 original size:21 final size:20
Alignment explanation
Indices: 9677874--9677919 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
9677864 ATATATGCAT
*
9677874 TTTTTTATGTATTAA-ACACA
1 TTTTTTATATA-TAATACACA
9677894 TATTTTTATATATAATACACA
1 T-TTTTTATATATAATACACA
9677915 TTTTT
1 TTTTT
9677920 AAAATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.54
Consensus pattern (20 bp):
TTTTTTATATATAATACACA
Found at i:9679534 original size:12 final size:12
Alignment explanation
Indices: 9679519--9679552 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
9679509 TTCTTTTTCT
9679519 TTTTTGTTTTGA
1 TTTTTGTTTTGA
9679531 -TTTTGATTTTGA
1 TTTTTG-TTTTGA
9679543 TTTTTGTTTT
1 TTTTTGTTTT
9679553 TTTTACCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 5 0.25
12 10 0.50
13 5 0.25
ACGTcount: A:0.09, C:0.00, G:0.15, T:0.76
Consensus pattern (12 bp):
TTTTTGTTTTGA
Found at i:9680199 original size:23 final size:23
Alignment explanation
Indices: 9680171--9680217 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
9680161 AATTTTTAAA
*
9680171 TTTTAAAAAAATATAAAAATTAT
1 TTTTAAAAAAATAAAAAAATTAT
9680194 TTTTAAAAAAATAAAAAAATTAT
1 TTTTAAAAAAATAAAAAAATTAT
9680217 T
1 T
9680218 AAATTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
TTTTAAAAAAATAAAAAAATTAT
Found at i:9680226 original size:32 final size:32
Alignment explanation
Indices: 9680174--9680264 Score: 134
Period size: 32 Copynumber: 2.9 Consensus size: 32
9680164 TTTTAAATTT
*
9680174 TAAAAAAA-TATAAAAATTATTTTTAAAAAAA
1 TAAAAAAATTATTAAAATTATTTTTAAAAAAA
*
9680205 TAAAAAAATTATTAAATTTATTTTT-AAAAAA
1 TAAAAAAATTATTAAAATTATTTTTAAAAAAA
9680236 TAAAAAAATTTATTAAAATTA-TTTTAAAA
1 TAAAAAAA-TTATTAAAATTATTTTTAAAA
9680265 CATAAAGAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
31 26 0.48
32 28 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (32 bp):
TAAAAAAATTATTAAAATTATTTTTAAAAAAA
Found at i:9680284 original size:32 final size:31
Alignment explanation
Indices: 9680186--9680287 Score: 125
Period size: 32 Copynumber: 3.2 Consensus size: 31
9680176 AAAAAATATA
*
9680186 AAAATTATTTTTAAAAAAATAAAAAAATTATT
1 AAAATTATTTTT-AAAAAATAAAAAATTTATT
*
9680218 AAATTTATTTTTAAAAAATAAAAAAATTTATT
1 AAAATTATTTTTAAAAAAT-AAAAAATTTATT
* *
9680250 AAAATTA-TTTTAAAACATAAAGAATATTTTTT
1 AAAATTATTTTTAAAAAATAAA-AA-ATTTATT
9680282 AAAATT
1 AAAATT
9680288 TAAAATTTTA
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
30 3 0.05
31 19 0.31
32 40 0.65
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (31 bp):
AAAATTATTTTTAAAAAATAAAAAATTTATT
Found at i:9683001 original size:34 final size:35
Alignment explanation
Indices: 9682963--9683028 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
9682953 GGATGTTTAA
*
9682963 TTTTTCAATT-AAGGAATCTTATTGACTTGTTTCT
1 TTTTTCAATTGAAGAAATCTTATTGACTTGTTTCT
**
9682997 TTTTTCCTTTGAAGAAATCTTATTGACTTGTT
1 TTTTTCAATTGAAGAAATCTTATTGACTTGTT
9683029 ATTTACACGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 8 0.29
35 20 0.71
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.53
Consensus pattern (35 bp):
TTTTTCAATTGAAGAAATCTTATTGACTTGTTTCT
Found at i:9685127 original size:2 final size:2
Alignment explanation
Indices: 9685120--9685163 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
9685110 TTTCCCTTCA
9685120 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9685162 AT
1 AT
9685164 CCTTCTATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9691141 original size:237 final size:237
Alignment explanation
Indices: 9690726--9691194 Score: 767
Period size: 237 Copynumber: 2.0 Consensus size: 237
9690716 TTGATCCGAC
* * * **
9690726 CCATTATGTAACACCCATCGTCTAATCCGGTCGCTGGACCTAAGCTATAGGATACTGCAACAGTC
1 CCATTATGTAACACCCATCGCCCAATCCGGTCGCCGGACCTAAGCTATAGGATACAACAACAGTC
** * *
9690791 CAACTTGCACTTTTACTACAACACTCATGTTGACGCAGCTCGTGTATTGACATAATTCGCACGTC
66 CAACTTGCACCATTACTACAACACTCATGTTGACGCAGCTCGCGTATTGACATAATTCGCACATC
* *
9690856 AATACAACTCACAGATTTTTACAACACACATACTATTACTTTACAAACCAGCTCGCATTTAGATA
131 AATACAACTCACAGATTTTTACAACACACATACTATTACTTTACAAACCAGCTCGCACTTAAATA
* *
9690921 CTTTACAGAGAGTTTGCATATACACACCCTACAAAGTTCAAT
196 CTTTACAGAGAGTTCGCACATACACACCCTACAAAGTTCAAT
* * * *
9690963 CCATTATGTAACACCCCTCGCCCGATCTGGTCGCCGGACCTAAGCTATAGGATACAACAACAGTT
1 CCATTATGTAACACCCATCGCCCAATCCGGTCGCCGGACCTAAGCTATAGGATACAACAACAGTC
* *
9691028 CAACTTGCACCATTACTATAACACTCATGTTGACGTAGCTCGCGTATTGACATAATTCGCACATC
66 CAACTTGCACCATTACTACAACACTCATGTTGACGCAGCTCGCGTATTGACATAATTCGCACATC
9691093 AATACAACTCACAGATTTTTACAACACACATACTATTACTTTACAAACCAGCTCGCACTTAAATA
131 AATACAACTCACAGATTTTTACAACACACATACTATTACTTTACAAACCAGCTCGCACTTAAATA
9691158 CTTTACAGAGAGTTCGCACATACACACCCTACAAAGT
196 CTTTACAGAGAGTTCGCACATACACACCCTACAAAGT
9691195 CAGTTCACAC
Statistics
Matches: 213, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
237 213 1.00
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.27
Consensus pattern (237 bp):
CCATTATGTAACACCCATCGCCCAATCCGGTCGCCGGACCTAAGCTATAGGATACAACAACAGTC
CAACTTGCACCATTACTACAACACTCATGTTGACGCAGCTCGCGTATTGACATAATTCGCACATC
AATACAACTCACAGATTTTTACAACACACATACTATTACTTTACAAACCAGCTCGCACTTAAATA
CTTTACAGAGAGTTCGCACATACACACCCTACAAAGTTCAAT
Found at i:9691402 original size:17 final size:17
Alignment explanation
Indices: 9691380--9691447 Score: 68
Period size: 17 Copynumber: 4.0 Consensus size: 17
9691370 ACATAGTTCG
9691380 CATATAAACACAACTTA
1 CATATAAACACAACTTA
* *
9691397 CATATAAACATAGCTCT-
1 CATATAAACACAACT-TA
* *
9691414 CATATAAACA-TAGTTA
1 CATATAAACACAACTTA
9691430 GCATATAAACACAACTTA
1 -CATATAAACACAACTTA
9691448 TGGATTGTCA
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
15 1 0.03
16 1 0.03
17 33 0.82
18 5 0.12
ACGTcount: A:0.49, C:0.21, G:0.04, T:0.26
Consensus pattern (17 bp):
CATATAAACACAACTTA
Found at i:9691418 original size:34 final size:34
Alignment explanation
Indices: 9691370--9691440 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
9691360 CCACAAATTG
*
9691370 ACATAGTTCGCATATAAACACAACTTA-CATATAA
1 ACATAGCTCGCATATAAACA-AACTTAGCATATAA
* * *
9691404 ACATAGCTCTCATATAAACATAGTTAGCATATAA
1 ACATAGCTCGCATATAAACAAACTTAGCATATAA
9691438 ACA
1 ACA
9691441 CAACTTATGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 4 0.12
34 28 0.88
ACGTcount: A:0.46, C:0.20, G:0.07, T:0.27
Consensus pattern (34 bp):
ACATAGCTCGCATATAAACAAACTTAGCATATAA
Found at i:9692699 original size:28 final size:28
Alignment explanation
Indices: 9692649--9692718 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
9692639 AACACACCAA
* * *
9692649 GGTCTCTATAGATACAATCAGTAACAAT
1 GGTCTCCATAGAGAAAATCAGTAACAAT
* *
9692677 GGTCTCCATAGAGAAAATTAGTAACAGT
1 GGTCTCCATAGAGAAAATCAGTAACAAT
9692705 GGTCT-CAGTAGAGA
1 GGTCTCCA-TAGAGA
9692719 CAAAGCTCGA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
27 2 0.06
28 34 0.94
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (28 bp):
GGTCTCCATAGAGAAAATCAGTAACAAT
Found at i:9697554 original size:2 final size:2
Alignment explanation
Indices: 9697547--9697603 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
9697537 ACCTTTCATA
9697547 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9697589 AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT
9697604 TAACTAAGAG
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9706443 original size:17 final size:17
Alignment explanation
Indices: 9706421--9706453 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
9706411 TCTCATATTT
9706421 TGATACCCATATCTTTC
1 TGATACCCATATCTTTC
9706438 TGATACCCATATCTTT
1 TGATACCCATATCTTT
9706454 GACTTTCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.27, G:0.06, T:0.42
Consensus pattern (17 bp):
TGATACCCATATCTTTC
Found at i:9709971 original size:17 final size:17
Alignment explanation
Indices: 9709945--9709977 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
9709935 TCTCAGATTT
9709945 TGATACCCATATCTTTC
1 TGATACCCATATCTTTC
*
9709962 TGATATCCATATCTTT
1 TGATACCCATATCTTT
9709978 GACTTTCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.45
Consensus pattern (17 bp):
TGATACCCATATCTTTC
Found at i:9710924 original size:3 final size:3
Alignment explanation
Indices: 9710916--9710952 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
9710906 TAGTCCTAGA
9710916 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
9710953 TAAAAAAAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:9714824 original size:49 final size:49
Alignment explanation
Indices: 9714716--9714839 Score: 151
Period size: 49 Copynumber: 2.5 Consensus size: 49
9714706 CATTATATGT
* * * *
9714716 TTTGCA-TTTAATTAAGTCATGCATAAAAGCATCTCATATATTAATTAAG
1 TTTGCATTTTAATTAAGTCATGCAT-TAAGAAACTCATATATTAAATAAG
** * * *
9714765 TTTGTGTTTTAATTATGTCATGCATTATGAAACTCATATGTTAAATAAG
1 TTTGCATTTTAATTAAGTCATGCATTAAGAAACTCATATATTAAATAAG
9714814 TTTGCATTTTAATTAAGTCATGCATT
1 TTTGCATTTTAATTAAGTCATGCATT
9714840 TATGCATCTT
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
49 45 0.73
50 17 0.27
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (49 bp):
TTTGCATTTTAATTAAGTCATGCATTAAGAAACTCATATATTAAATAAG
Found at i:9715265 original size:37 final size:36
Alignment explanation
Indices: 9715222--9715316 Score: 109
Period size: 37 Copynumber: 2.6 Consensus size: 36
9715212 CATCAAGTAT
* * * *
9715222 AGAGACATGACTATTCAAATACATATGGACCAAGTGA
1 AGAGACATGACT-TTCAAATACACACGAAACAAGTGA
* *
9715259 AGAGACATGACTTTTCAACTATACACGAAACAAGTGA
1 AGAGACATGAC-TTTCAAATACACACGAAACAAGTGA
9715296 AGAGACATGACCTTTCAAATA
1 AGAGACATGA-CTTTCAAATA
9715317 TCTTCCATTA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
37 47 0.96
38 2 0.04
ACGTcount: A:0.43, C:0.18, G:0.17, T:0.22
Consensus pattern (36 bp):
AGAGACATGACTTTCAAATACACACGAAACAAGTGA
Found at i:9724387 original size:21 final size:22
Alignment explanation
Indices: 9724352--9724392 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
9724342 TTATGTTTGT
9724352 TAAACATCACTTAATTAGTTAG
1 TAAACATCACTTAATTAGTTAG
*
9724374 TAAAC-TCAGTTAATTAGTT
1 TAAACATCACTTAATTAGTT
9724393 TATTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (22 bp):
TAAACATCACTTAATTAGTTAG
Found at i:9738183 original size:14 final size:14
Alignment explanation
Indices: 9738164--9738191 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
9738154 ATTCCAATGG
9738164 CTAGTTACAACCAA
1 CTAGTTACAACCAA
9738178 CTAGTTACAACCAA
1 CTAGTTACAACCAA
9738192 TCTATCAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.29, G:0.07, T:0.21
Consensus pattern (14 bp):
CTAGTTACAACCAA
Found at i:9744848 original size:24 final size:24
Alignment explanation
Indices: 9744785--9744842 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
9744775 GAACTAAGCA
9744785 AGAAGCTCATAAGAGCTGTATTCG
1 AGAAGCTCATAAGAGCTGTATTCG
9744809 AGAAGCTCATAAGAGCTGTATTCG
1 AGAAGCTCATAAGAGCTGTATTCG
9744833 AGAAGCTCAT
1 AGAAGCTCAT
9744843 GTGAGCCTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.24
Consensus pattern (24 bp):
AGAAGCTCATAAGAGCTGTATTCG
Found at i:9744977 original size:26 final size:26
Alignment explanation
Indices: 9744919--9744996 Score: 92
Period size: 26 Copynumber: 3.2 Consensus size: 26
9744909 AAGTTCAAGC
**
9744919 GAGCCA-T-ATCAGGAAGCTC-CGGA
1 GAGCCATTAATCAGGAAGCTCACAAA
9744942 GAGCCATTAATCAGGAAGCTCACAAA
1 GAGCCATTAATCAGGAAGCTCACAAA
* *
9744968 GAGCCTTTAATCGGGAAGCTCA-AAA
1 GAGCCATTAATCAGGAAGCTCACAAA
9744993 GAGC
1 GAGC
9744997 TAAGGTGTGC
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
23 6 0.12
24 1 0.02
25 19 0.40
26 22 0.46
ACGTcount: A:0.36, C:0.23, G:0.26, T:0.15
Consensus pattern (26 bp):
GAGCCATTAATCAGGAAGCTCACAAA
Found at i:9749028 original size:18 final size:18
Alignment explanation
Indices: 9749005--9749039 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
9748995 TGAACTTATA
9749005 TGAATGATGTGTTGATTT
1 TGAATGATGTGTTGATTT
9749023 TGAATGATGTGTTGATT
1 TGAATGATGTGTTGATT
9749040 GAATTGGTAG
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:0.23, C:0.00, G:0.29, T:0.49
Consensus pattern (18 bp):
TGAATGATGTGTTGATTT
Found at i:9749043 original size:16 final size:17
Alignment explanation
Indices: 9749005--9749043 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
9748995 TGAACTTATA
9749005 TGAATGATGTGTTGATTT
1 TGAATGATGTGTTGA-TT
9749023 TGAATGATGTGTTGA-T
1 TGAATGATGTGTTGATT
9749039 TGAAT
1 TGAAT
9749044 TGGTAGAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 6 0.29
18 15 0.71
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.46
Consensus pattern (17 bp):
TGAATGATGTGTTGATT
Found at i:9749775 original size:41 final size:41
Alignment explanation
Indices: 9749718--9749800 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
9749708 GGTTTTGAAG
9749718 AATATATATTTGAAGTAACAACCGTTTGAATAAAAGTAATC
1 AATATATATTTGAAGTAACAACCGTTTGAATAAAAGTAATC
*
9749759 AATATATATTTGAAGTAACAACCGTTTGAATAAAATTAATC
1 AATATATATTTGAAGTAACAACCGTTTGAATAAAAGTAATC
9749800 A
1 A
9749801 TTATGAATAC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.47, C:0.10, G:0.11, T:0.33
Consensus pattern (41 bp):
AATATATATTTGAAGTAACAACCGTTTGAATAAAAGTAATC
Found at i:9752068 original size:10 final size:10
Alignment explanation
Indices: 9752055--9752124 Score: 70
Period size: 10 Copynumber: 7.0 Consensus size: 10
9752045 ACAAAATCAT
*
9752055 TTAAAATTTA
1 TTAAAAATTA
9752065 TTAAAAATTA
1 TTAAAAATTA
*
9752075 TAAAAAATTA
1 TTAAAAATTA
*
9752085 TT-GAAATTA
1 TTAAAAATTA
*
9752094 TAAAAAATTA
1 TTAAAAATTA
* *
9752104 ATATAAATTA
1 TTAAAAATTA
9752114 TTTAAAAATTA
1 -TTAAAAATTA
9752125 AATTTTAATT
Statistics
Matches: 47, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
9 7 0.15
10 32 0.68
11 8 0.17
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:9752080 original size:20 final size:20
Alignment explanation
Indices: 9752057--9752124 Score: 75
Period size: 19 Copynumber: 3.4 Consensus size: 20
9752047 AAAATCATTT
*
9752057 AAAATTTATTAAAAATTATA
1 AAAAATTATTAAAAATTATA
*
9752077 AAAAATTATT-GAAATTATA
1 AAAAATTATTAAAAATTATA
* * *
9752096 AAAAATTAATATAAATTATTT
1 AAAAATTATTAAAAATTA-TA
9752117 AAAAATTA
1 AAAAATTA
9752125 AATTTTAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
19 17 0.41
20 15 0.37
21 9 0.22
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (20 bp):
AAAAATTATTAAAAATTATA
Found at i:9754205 original size:22 final size:19
Alignment explanation
Indices: 9754155--9754213 Score: 55
Period size: 22 Copynumber: 2.9 Consensus size: 19
9754145 TTTTTTTTCC
9754155 CTTTTTCCTCTTTTTTGTT
1 CTTTTTCCTCTTTTTTGTT
* * *
9754174 CTTATCCCTCTTCTCTTATTTT
1 CTTTTTCCTCTT-T-TT-TGTT
*
9754196 CTTTTTCCTCTTTATTGT
1 CTTTTTCCTCTTTTTTGT
9754214 CGCTTAGAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
19 12 0.40
20 2 0.07
21 3 0.10
22 13 0.43
ACGTcount: A:0.05, C:0.25, G:0.03, T:0.66
Consensus pattern (19 bp):
CTTTTTCCTCTTTTTTGTT
Found at i:9754737 original size:12 final size:12
Alignment explanation
Indices: 9754720--9754749 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
9754710 AACCACACGA
*
9754720 CCGTGTGTCAGG
1 CCGTGTGGCAGG
9754732 CCGTGTGGCAGG
1 CCGTGTGGCAGG
9754744 CCGTGT
1 CCGTGT
9754750 AACTCACTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.27, G:0.43, T:0.23
Consensus pattern (12 bp):
CCGTGTGGCAGG
Found at i:9754949 original size:30 final size:31
Alignment explanation
Indices: 9754913--9754987 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 31
9754903 CAGGAAAGCG
** *
9754913 ACACGGGCGTGTGTT-AGGTCGTGTGGAACC
1 ACACGGGCGTGTGTTCAGACCGTGTGAAACC
*
9754943 ACACGGGC-TAGTTATTCAGACCGTGTGAAACC
1 ACACGGGCGT-G-TGTTCAGACCGTGTGAAACC
9754975 ACACGGGCGTGTG
1 ACACGGGCGTGTG
9754988 GACCAATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
29 1 0.03
30 9 0.25
31 4 0.11
32 21 0.58
33 1 0.03
ACGTcount: A:0.21, C:0.23, G:0.35, T:0.21
Consensus pattern (31 bp):
ACACGGGCGTGTGTTCAGACCGTGTGAAACC
Found at i:9755106 original size:19 final size:19
Alignment explanation
Indices: 9755060--9755100 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
9755050 TATGGGGTCC
* *
9755060 GTATGAATTGAATTAAACT
1 GTATGAACTAAATTAAACT
9755079 GTATGAACTAAATTAAACT
1 GTATGAACTAAATTAAACT
9755098 GTA
1 GTA
9755101 GAAACTGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.34
Consensus pattern (19 bp):
GTATGAACTAAATTAAACT
Found at i:9756690 original size:23 final size:21
Alignment explanation
Indices: 9756642--9756691 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 21
9756632 TCAAAAAAAT
*
9756642 TTTAATATAAAAAAATTATAA
1 TTTAATATAAAAAAATTACAA
* *
9756663 ATTAATATATAATAAAATTACAC
1 TTTAATATA-AA-AAAATTACAA
9756686 TTTAAT
1 TTTAAT
9756692 CTTTTAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 8 0.35
22 2 0.09
23 13 0.57
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (21 bp):
TTTAATATAAAAAAATTACAA
Found at i:9757548 original size:2 final size:2
Alignment explanation
Indices: 9757541--9757575 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
9757531 CTCATCTTTT
9757541 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
9757576 TATATATGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:9762845 original size:63 final size:64
Alignment explanation
Indices: 9762740--9762884 Score: 220
Period size: 63 Copynumber: 2.3 Consensus size: 64
9762730 AAAGTCAAAC
*
9762740 ATATATGTGATCTAAAATATGCTATCAAAGTCAAGCACATATGTGATCCATATCAC-AATCACCA
1 ATATATGTGATC-AAAATATGCTATCAAAATCAAGCACATATGTGATCCATATCACAAATCACCA
* * * *
9762804 ATATATGTGATCAAAATATGCTATCAAAATCAAGCATATATGTGGTCTATATCACAAATCACTA
1 ATATATGTGATCAAAATATGCTATCAAAATCAAGCACATATGTGATCCATATCACAAATCACCA
*
9762868 ATATATGCGATCAAAAT
1 ATATATGTGATCAAAAT
9762885 CAAGCATATA
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
63 39 0.53
64 35 0.47
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (64 bp):
ATATATGTGATCAAAATATGCTATCAAAATCAAGCACATATGTGATCCATATCACAAATCACCA
Found at i:9763379 original size:178 final size:169
Alignment explanation
Indices: 9763037--9763386 Score: 492
Period size: 178 Copynumber: 2.0 Consensus size: 169
9763027 ATCCTAGATA
* *
9763037 ATTATTAGACATGAACTCTTGGTCCATCTTGTTGCCTATCTTTATTCCATTATCAAGGCTTTGTC
1 ATTATTAGACATGAACTCTTGGTCCATCTTGTCGCCTATCTTTATTCCATTATCAAGGCCTTGTC
*
9763102 CTCATGTCTTAAAGAAAGAGGAAAGAGAAATTTTGGAAGGTCTGACATCACCTTATATATTCTTA
66 CTCATATCTTAAAGAAAGAGGAAAGAGAAATTTTGGAAGGTCTGACATCACCTTATATATTCTTA
*
9763167 TGAGAATCAACATATAATTCTATCATTGTATTGATTTAT
131 TGAGAATCAACATATAATTCTATCATTATATTGATTTAT
9763206 ATTATTAGACATGAACTGC-TGGTCCATCTCT-TCGCCTATCTTTATTCCATTATCAAGGCCTTG
1 ATTATTAGACATGAACT-CTTGGTCCATCT-TGTCGCCTATCTTTATTCCATTATCAAGGCCTTG
* * *
9763269 TCCTCATATCTTACCTCCAGTGAGGAAAGAGGAGAA-AGAAATTTTTGAAGGTAC-GGCATTACC
64 TCCTCATATCTTA-----A---A-GAAAGAGGA-AAGAGAAATTTTGGAAGGT-CTGACATCACC
9763332 TTATATATTCTTATGAGAATCAACATATAATTCTATCATTATATTGATTTAT
118 TTATATATTCTTATGAGAATCAACATATAATTCTATCATTATATTGATTTAT
9763384 ATT
1 ATT
9763387 TTTACAATTT
Statistics
Matches: 161, Mismatches: 7, Indels: 17
0.87 0.04 0.09
Matches are distributed among these distances:
169 69 0.43
170 2 0.01
174 1 0.01
177 1 0.01
178 85 0.53
179 3 0.02
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.38
Consensus pattern (169 bp):
ATTATTAGACATGAACTCTTGGTCCATCTTGTCGCCTATCTTTATTCCATTATCAAGGCCTTGTC
CTCATATCTTAAAGAAAGAGGAAAGAGAAATTTTGGAAGGTCTGACATCACCTTATATATTCTTA
TGAGAATCAACATATAATTCTATCATTATATTGATTTAT
Found at i:9768668 original size:4 final size:4
Alignment explanation
Indices: 9768659--9768701 Score: 77
Period size: 4 Copynumber: 10.8 Consensus size: 4
9768649 TTAGCTTTCA
*
9768659 ATGT ATGT ATGT ATGT ATGA ATGT ATGT ATGT ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
9768702 AGACTCTGTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.47
Consensus pattern (4 bp):
ATGT
Found at i:9770771 original size:2 final size:2
Alignment explanation
Indices: 9770764--9770802 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
9770754 NNNNNNNNNN
9770764 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9770803 ACAATTTGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9776507 original size:35 final size:35
Alignment explanation
Indices: 9776424--9776513 Score: 83
Period size: 35 Copynumber: 2.5 Consensus size: 35
9776414 ATATGGCTGA
* * * *
9776424 GTTAGGGGTTTAGAGATTATGGTGTAATGGTTGGG
1 GTTAGGGGTTAAGAGTTTAGGGTGTAAAGGTTGGG
* * *
9776459 GTCTAAGGTTTAAGTGTTTAGGGT-TAAAGGTTAGGG
1 GT-TAGGGGTTAAGAGTTTAGGGTGTAAAGGTT-GGG
*
9776495 GTTAGGGGTTAAGGGTTTA
1 GTTAGGGGTTAAGAGTTTA
9776514 TAGTTAATGT
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
35 23 0.53
36 20 0.47
ACGTcount: A:0.22, C:0.01, G:0.40, T:0.37
Consensus pattern (35 bp):
GTTAGGGGTTAAGAGTTTAGGGTGTAAAGGTTGGG
Found at i:9776727 original size:14 final size:14
Alignment explanation
Indices: 9776691--9776740 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
9776681 TCTAGGTCAA
* *
9776691 TTTAGGATTAAGGG
1 TTTAGGGTTAAAGG
* * *
9776705 TTAAGGGTTTAATG
1 TTTAGGGTTAAAGG
9776719 TTTAGGGTTAAAGG
1 TTTAGGGTTAAAGG
9776733 TTTAGGGT
1 TTTAGGGT
9776741 ACTCTAAATT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.26, C:0.00, G:0.34, T:0.40
Consensus pattern (14 bp):
TTTAGGGTTAAAGG
Found at i:9777516 original size:251 final size:251
Alignment explanation
Indices: 9777107--9777602 Score: 723
Period size: 251 Copynumber: 2.0 Consensus size: 251
9777097 TTGGCTAAAG
* * *
9777107 GAATTTGAATTTTAGTGGCGTTTTTCGTAAAAATGCCACTGAAGGTATGCTATAGTGGCGTTTTA
1 GAATTTGAATTTTAGTGGCGTTTTTCGTAAAAACGCCACAGAAGGTATACTATAGTGGCGTTTTA
* *
9777172 TATTGAAACGCCGCAAATCCATAAATGTTTGTCTATACGAAAACGGCGTCGTTTTCTTAAATGAT
66 TATAGAAACGCCGCAAATCCATAAATGTTTGTCTATACAAAAACGGCGTCGTTTTCTTAAATGAT
* * * * *
9777237 TTGAACTCCTTACTGGCGTTTTTATTTAAAACGCCGCAAACTGTGATCTTTAGCGGCGTTTGGTA
131 TTGAACTCCTTACTGGCATTTGTATTTAAAACGCCGC-AACTGTAAGCTTTAGCGGCGTTTAGTA
*
9777302 TGGAAACGCCACAAATGTGCATTACAAAATGTTCAGAACGTCACCGTTTCGTTACAT
195 TGAAAACGCCACAAATGTGCATTACAAAATGTTCAGAACGTCACCGTTTCGTTACAT
9777359 GAATTTGAATTTTAGTGGCGTTTCTAT-G-AAAAACGCCACAGAAGGTATAC-AGTAGTGGCGTT
1 GAATTTGAATTTTAGTGGCGTTT-T-TCGTAAAAACGCCACAGAAGGTATACTA-TAGTGGCGTT
* * *
9777421 TT-TATAGAAACGCCGCAAATCCATATATGTTTTTGTGA-ACAAAAACGGCGTCGTTTTCTTAAA
63 TTATATAGAAACGCCGCAAATCCATAAATGTTTGTCT-ATACAAAAACGGCGTCGTTTTCTTAAA
* * * *
9777484 TGATTTGAACTCGTTAGTGGCATTTGTATTTAAAACGCCGCAATTGTAAGCTTTAGTGGCGTTTA
127 TGATTTGAACTCCTTACTGGCATTTGTATTTAAAACGCCGCAACTGTAAGCTTTAGCGGCGTTTA
* * *
9777549 GTATGAAAACGCCACAAATGTGTATTTCAAAATGTTCAGAACGTCGCCGTTTCG
192 GTATGAAAACGCCACAAATGTGCATTACAAAATGTTCAGAACGTCACCGTTTCG
9777603 GTTGAGGAAC
Statistics
Matches: 219, Mismatches: 21, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
250 69 0.32
251 92 0.42
252 55 0.25
253 2 0.01
254 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (251 bp):
GAATTTGAATTTTAGTGGCGTTTTTCGTAAAAACGCCACAGAAGGTATACTATAGTGGCGTTTTA
TATAGAAACGCCGCAAATCCATAAATGTTTGTCTATACAAAAACGGCGTCGTTTTCTTAAATGAT
TTGAACTCCTTACTGGCATTTGTATTTAAAACGCCGCAACTGTAAGCTTTAGCGGCGTTTAGTAT
GAAAACGCCACAAATGTGCATTACAAAATGTTCAGAACGTCACCGTTTCGTTACAT
Found at i:9777547 original size:126 final size:123
Alignment explanation
Indices: 9777159--9777547 Score: 295
Period size: 124 Copynumber: 3.1 Consensus size: 123
9777149 AGGTATGCTA
* * * *
9777159 TAGTGGCGTTTTATATTGAAACGCCGCAAATCCATAAATGTTTGTCTATACGAAAACGGCGTCGT
1 TAGTGGCGTTTT-TATAGAAACGCCGCAAATCCATATATGTTTATGTA-AC-AAAACGGCGTCGT
* * *
9777224 TTTCTTAAATGATTTGAACTCCTTACTGGCGTTTTTATTTAAAACGCCGCAAACTGTGATCTT
63 TTTCTTAAATGATTTGAACTCCTTAGTGGCGTTTCTATTTAAAACGCCGCAAA-TGT-AACTT
* * * * * **** * * * **
9777287 TAGCGGCGTTTGGTATGGAAACGCCACAAATGTGCAT-TA-CAAAATGT-TCAGAACGTCACCG-
1 TAGTGGCGTTT-TTATAGAAACGCCGCAAA--TCCATATATGTTTATGTAACAAAACGGCGTCGT
* * ** * * **
9777348 TTTCGTTACATGAATTTGAA-T-TTTAGTGGCGTTTCTATGAAAAACGCCACAGAAGGTATACAG
63 TTTC-TTAAATG-ATTTGAACTCCTTAGTGGCGTTTCTATTTAAAACGCCGCA-AATGTA-ACTT
*
9777411 TAGTGGCGTTTTTATAGAAACGCCGCAAATCCATATATGTTTTTGTGAACAAAAACGGCGTCGTT
1 TAGTGGCGTTTTTATAGAAACGCCGCAAATCCATATATGTTTATGT-AAC-AAAACGGCGTCGTT
* * * *
9777476 TTCTTAAATGATTTGAACTCGTTAGTGGCATTTGTATTTAAAACGCCGCAATTGTAAGCTT
64 TTCTTAAATGATTTGAACTCCTTAGTGGCGTTTCTATTTAAAACGCCGCAAATGTAA-CTT
9777537 TAGTGGCGTTT
1 TAGTGGCGTTT
9777548 AGTATGAAAA
Statistics
Matches: 191, Mismatches: 54, Indels: 34
0.68 0.19 0.12
Matches are distributed among these distances:
121 4 0.02
122 2 0.01
123 19 0.10
124 41 0.21
125 26 0.14
126 39 0.20
127 28 0.15
128 27 0.14
129 1 0.01
130 4 0.02
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.34
Consensus pattern (123 bp):
TAGTGGCGTTTTTATAGAAACGCCGCAAATCCATATATGTTTATGTAACAAAACGGCGTCGTTTT
CTTAAATGATTTGAACTCCTTAGTGGCGTTTCTATTTAAAACGCCGCAAATGTAACTT
Found at i:9780565 original size:25 final size:25
Alignment explanation
Indices: 9780515--9780587 Score: 71
Period size: 26 Copynumber: 3.0 Consensus size: 25
9780505 AGAAAATATG
* **
9780515 AAATAT-A-AAAAAATGTGTATTTA
1 AAATATAATAAAAAATGTATATGAA
9780538 AAATA-AATAAAGAATATGTATATGAA
1 AAATATAATAAA-AA-ATGTATATGAA
*
9780564 AAATATAGTAAAAAATGTATATGA
1 AAATATAATAAAAAATGTATATGA
9780588 GTATATATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
23 6 0.15
24 3 0.07
25 12 0.29
26 15 0.37
27 5 0.12
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (25 bp):
AAATATAATAAAAAATGTATATGAA
Found at i:9782308 original size:82 final size:81
Alignment explanation
Indices: 9782227--9783322 Score: 1529
Period size: 82 Copynumber: 13.4 Consensus size: 81
9782217 TATGGTTTTG
* * * * *
9782227 TCTGCTCTACTACTGTTTAGGGAGATAAGA-CT-TGATATGATCTGCTCCACTACTGCTTAGGGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTG-TCTGCTCCGCTACTGCTTAGGGA
* * **
9782290 GATAAGATCAGTGGTTTTG-
65 GATAAGA-C--TTGATGCGA
* * * *
9782309 TCTACTCCGCTACTGCTTAGGGAGATAAGATCTGTGGCTTTGTCTGATCCGCTACTGCTTAGGAA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGG-TTTGTCTGCTCCGCTACTGCTTAGGGA
9782374 GATAAGACTTGATGCGA
65 GATAAGACTTGATGCGA
* *
9782391 TCTACTCCACTACTGCTTAGGGAGATAAGATCTGTGGTGTTGTCCGCTCCGCTACTGCTTAGGGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGT-TTGTCTGCTCCGCTACTGCTTAGGGA
*
9782456 GATAAGACTTGATGTGA
65 GATAAGACTTGATGCGA
* * *
9782473 TCTGCTCAACTACTGCTTAGGGAGATAAAATCTGTGGTTTTGTCTGCTCCGCTACTTCTTAGGGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGG-TTTGTCTGCTCCGCTACTGCTTAGGGA
*
9782538 GATAAGACTTGATGTGA
65 GATAAGACTTGATGCGA
*
9782555 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTGTTGTCTGCTCCACTACTGCTTAGGGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGT-TTGTCTGCTCCGCTACTGCTTAGGGA
*
9782620 GATAAGGCTTGATGCGA
65 GATAAGACTTGATGCGA
* * * *
9782637 TCTGCTGCACTACTGCTTAGTGAGATAAGATCTGTGGCTTTGTCTGATCCGCTACTACTTAGGGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGG-TTTGTCTGCTCCGCTACTGCTTAGGGA
9782702 GATAAGACTTGATGCGA
65 GATAAGACTTGATGCGA
* *
9782719 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTGTTGTCCGCTCCGCTACTGCTTAAGGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGT-TTGTCTGCTCCGCTACTGCTTAGGGA
9782784 GATAAGACTTGATGCGA
65 GATAAGACTTGATGCGA
* * * *
9782801 TCTACTCCACTACTGTTTAGGGAGATAAGATCTGTAGTTTTGTCCGCTCCGCTACTGCTTAGGGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT-GGTTTGTCTGCTCCGCTACTGCTTAGGGA
9782866 GATAAGACTTGATGCGA
65 GATAAGACTTGATGCGA
*
9782883 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTGTCTGCTCCGCTACTGTTTAGGGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGG-TTTGTCTGCTCCGCTACTGCTTAGGGA
* *
9782948 GATAAGACTTGATGTGG
65 GATAAGACTTGATGCGA
9782965 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTGTTGTCTGCTCCGCTACTGCTTAGGGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGT-TTGTCTGCTCCGCTACTGCTTAGGGA
*
9783030 GATAAGACTTGATGGGA
65 GATAAGACTTGATGCGA
* * *
9783047 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTGTTGTCCGCTCCGTTATTGCTTAGGGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGT-TTGTCTGCTCCGCTACTGCTTAGGGA
9783112 GATAAGACTTGATGCGA
65 GATAAGACTTGATGCGA
* * *
9783129 TCTGCTCCACTACTGTTTAGGGAGATAAGATCTGTGGTTTTGTCCGCTCTGCTACTGCTTAGGGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGG-TTTGTCTGCTCCGCTACTGCTTAGGGA
*
9783194 GATAAGGCTTGATGCGA
65 GATAAGACTTGATGCGA
* ** * *
9783211 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGATGCGATCTGCTCCACTACTGTTTAGGGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTG-TCTGCTCCGCTACTGCTTAGGGA
* *
9783274 GATAAGATCTGTGGTTCTG-
65 GATAAGA-CT-TGATGC-GA
9783293 TCTGCTCCACTACTGCTTAGGGAGATAAGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA
9783323 CTATTGGCTT
Statistics
Matches: 922, Mismatches: 75, Indels: 34
0.89 0.07 0.03
Matches are distributed among these distances:
79 2 0.00
80 27 0.03
81 13 0.01
82 839 0.91
83 9 0.01
84 29 0.03
85 3 0.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (81 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTGTCTGCTCCGCTACTGCTTAGGGAG
ATAAGACTTGATGCGA
Found at i:9783348 original size:82 final size:87
Alignment explanation
Indices: 9783208--9783410 Score: 217
Period size: 82 Copynumber: 2.4 Consensus size: 87
9783198 AGGCTTGATG
* *
9783208 CGATCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGT-T-T-A
1 CGATCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCAATCTACTCCACTACTGTATCTCA
* **
9783270 GGGAGATAAGATCTGT--GGTT
66 GGGAGATAAAATCTGTCATCTT
* * *
9783290 CTG-TCTGCTCCACTACTGCTTAGGGAGATAAGACTATTGGCTTCAATGTACT-C-C-ACTGTAA
1 C-GATCTGCTCCACTACTGCTTAGGGAGATAAGAC--TT-GATGCAATCTACTCCACTACTGT-A
*
9783351 TCTCAGGGAGGTAAAATCTGTCATCTT
61 TCTCAGGGAGATAAAATCTGTCATCTT
9783378 CGATCTGCTCCACTACTGCTTAGGGAGATAAGA
1 CGATCTGCTCCACTACTGCTTAGGGAGATAAGA
9783411 TCTGTAATCT
Statistics
Matches: 101, Mismatches: 9, Indels: 16
0.80 0.07 0.13
Matches are distributed among these distances:
82 37 0.37
83 2 0.02
84 4 0.04
85 9 0.09
86 15 0.15
87 1 0.01
88 33 0.33
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (87 bp):
CGATCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCAATCTACTCCACTACTGTATCTCA
GGGAGATAAAATCTGTCATCTT
Found at i:9783489 original size:132 final size:132
Alignment explanation
Indices: 9783248--9783641 Score: 578
Period size: 132 Copynumber: 3.0 Consensus size: 132
9783238 AGACTTGATG
* ** ** ** * * **
9783248 CGATCTGCTCCACTACTGTTTAGGGAGATAAGATCTGT--GGTTCTGTCTGCTCCACTACTGCTT
1 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCTCTGCTGCCC
*** *
9783311 AGGGAGATA-AGACTATTGGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCTGTCAT
66 AGGGAGATAGA-ACTACCAGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCTGCCAT
9783375 CTT
130 CTT
9783378 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCTCTGCTGCCC
1 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCTCTGCTGCCC
* *
9783443 AGGGAGATAGAACTGCCAGCTTCAATGTACTCCAATGTAATCTCAGGGAGGTAAAATCTGCCATC
66 AGGGAGATAGAACTACCAGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCTGCCATC
9783508 TT
131 TT
*
9783510 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTTAATCTATTCCTCTGCTGCCC
1 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCTCTGCTGCCC
* *
9783575 AGGGAGATAGAATTACCGGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCTGCCATC
66 AGGGAGATAGAACTACCAGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCTGCCATC
9783640 TT
131 TT
9783642 TGACCTGCCT
Statistics
Matches: 239, Mismatches: 22, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
130 37 0.15
132 201 0.84
133 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (132 bp):
CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCTCTGCTGCCC
AGGGAGATAGAACTACCAGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCTGCCATC
TT
Found at i:9783579 original size:44 final size:44
Alignment explanation
Indices: 9783354--9783583 Score: 151
Period size: 44 Copynumber: 5.2 Consensus size: 44
9783344 ACTGTAATCT
* * * * * *
9783354 CAGGGAGGTAAAATCTGTC-ATCTTCGATCTGCTCCACTACTGCT
1 CAGGGAGATAAGATCTG-CAATCTTCAATCTACTCCACTGCTGCC
* * * *
9783398 TAGGGAGATAAGATCTGTAATCTTCAATCTATTCCTCTGCTGCC
1 CAGGGAGATAAGATCTGCAATCTTCAATCTACTCCACTGCTGCC
* * * * * * *
9783442 CAGGGAGAT-AGAACTGCCAGCTTCAATGTACTCCAATG-TAATCT
1 CAGGGAGATAAGATCTGCAATCTTCAATCTACTCCACTGCT--GCC
* * * * * * *
9783486 CAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCT
1 CAGGGAGATAAGATCTGCAATCTTCAATCTACTCCACTGCTGCC
* * * * *
9783530 TAGGGAGATAAGATCTGTAATCTTTAATCTATTCCTCTGCTGCC
1 CAGGGAGATAAGATCTGCAATCTTCAATCTACTCCACTGCTGCC
9783574 CAGGGAGATA
1 CAGGGAGATA
9783584 GAATTACCGG
Statistics
Matches: 137, Mismatches: 44, Indels: 10
0.72 0.23 0.05
Matches are distributed among these distances:
42 1 0.01
43 21 0.15
44 93 0.68
45 21 0.15
46 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (44 bp):
CAGGGAGATAAGATCTGCAATCTTCAATCTACTCCACTGCTGCC
Found at i:9783800 original size:88 final size:88
Alignment explanation
Indices: 9783646--9784599 Score: 1376
Period size: 88 Copynumber: 10.9 Consensus size: 88
9783636 CATCTTTGAC
* * * * *
9783646 CTGCCTCGCTGTTGATGCAGGAGGGCAATATCTGTTGTCTTCAACCAGCTCTGCTACACCCGAGA
1 CTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGA
*
9783711 GAGACAAGGTTTGTGTCTTCGAT
66 GAGGCAAGGTTTGTGTCTTCGAT
* * * * *
9783734 CTGCTTCGCTGTTAATGCAGGAAGGCAAAATTTGTTGTCTTTAACCAGCTCCGCTACAACCAAGA
1 CTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGA
**
9783799 GAGGCAAGGTTTGTGTCTTTAAT
66 GAGGCAAGGTTTGTGTCTTCGAT
* * ** *
9783822 CTTCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTTAACCAGCTCCACTGCAACCGATG
1 CTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGA-G
* **
9783887 -GAGGCAAGGTTT-TGTTTTTTAT
65 AGAGGCAAGGTTTGTGTCTTCGAT
* *
9783909 CTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCAACTAGCTCTGCCACAACCGAGA
1 CTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGA
9783974 GAGGCAAGGTTTGTGTCTTCGAT
66 GAGGCAAGGTTTGTGTCTTCGAT
* * *
9783997 CTGCTTCGCTATCAATGTAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGA
1 CTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGA
* * **
9784062 GAGGTAAGGTTT-TGTTTTTTAT
66 GAGGCAAGGTTTGTGTCTTCGAT
* * * *
9784084 TTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTTTTCGACCAGCTCTGCTACAACCAAGA
1 CTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGA
9784149 GAGGCAAGGTTTGTGTCTTCGAT
66 GAGGCAAGGTTTGTGTCTTCGAT
* * *
9784172 CTGCTTCGCTATCAATGTAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGA
1 CTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGA
* * *
9784237 GAGGTAAGGTTT-TGTTTTTGAT
66 GAGGCAAGGTTTGTGTCTTCGAT
*
9784259 CTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCGACCAGCTCTGCTACAACCGAGA
1 CTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGA
9784324 GAGGCAAGGTTTGTGTCTTCGAT
66 GAGGCAAGGTTTGTGTCTTCGAT
* * * * * *
9784347 CTACTTCGCTATCAGTGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTACAACTGAGA
1 CTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGA
*
9784412 GAGGCAAGGTTTGTGTCTTCGAC
66 GAGGCAAGGTTTGTGTCTTCGAT
* *
9784435 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTACAACCGAGA
1 CTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGA
*
9784500 GAGGCAAGGTTTGTGTCTTCGAC
66 GAGGCAAGGTTTGTGTCTTCGAT
* * **
9784523 CTGCTTCGCTGTCAATGCAGGAAAGCAAGATCTGTTGTCTTCAACCAGCTCCACTACAACCGAGA
1 CTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGA
9784588 GAGGCAAGGTTT
66 GAGGCAAGGTTT
9784600 TTTGTTTCTT
Statistics
Matches: 780, Mismatches: 81, Indels: 10
0.90 0.09 0.01
Matches are distributed among these distances:
86 1 0.00
87 232 0.30
88 546 0.70
89 1 0.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (88 bp):
CTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGA
GAGGCAAGGTTTGTGTCTTCGAT
Found at i:9783848 original size:44 final size:44
Alignment explanation
Indices: 9783715--9783937 Score: 161
Period size: 44 Copynumber: 5.1 Consensus size: 44
9783705 CCGAGAGAGA
**
9783715 CAAGGTTTGTGTCTTCGATCTGCTTCGCTGTTAATGCAGGAAGG
1 CAAGGTTTGTGTCTTTAATCTGCTTCGCTGTTAATGCAGGAAGG
** * * * ** * *
9783759 CAAAATTTGTTGTCTTTAACCAGCTCCGCT-ACAA-CCAAGAGAGG
1 CAAGGTTTG-TGTCTTTAATCTGCTTCGCTGTTAATGCAGGA-AGG
*
9783803 CAAGGTTTGTGTCTTTAATCTTCTTCGCTGTTAATGCAGGAAGG
1 CAAGGTTTGTGTCTTTAATCTGCTTCGCTGTTAATGCAGGAAGG
* * * * * * * *
9783847 CAAGATCTGTTGTCTTTAACCAGCTCCACTG-CAA-CCGATGG-AGG
1 CAAGGTTTG-TGTCTTTAATCTGCTTCGCTGTTAATGC-A-GGAAGG
* *
9783891 CAAGGTTT-TGTTTTTTATCTGCTTCGCTGTTAATGCAGGAAGG
1 CAAGGTTTGTGTCTTTAATCTGCTTCGCTGTTAATGCAGGAAGG
9783934 CAAG
1 CAAG
9783938 ATCTGTTGTC
Statistics
Matches: 129, Mismatches: 40, Indels: 21
0.68 0.21 0.11
Matches are distributed among these distances:
42 17 0.13
43 31 0.24
44 44 0.34
45 37 0.29
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.32
Consensus pattern (44 bp):
CAAGGTTTGTGTCTTTAATCTGCTTCGCTGTTAATGCAGGAAGG
Found at i:9783977 original size:175 final size:175
Alignment explanation
Indices: 9783660--9784600 Score: 1425
Period size: 175 Copynumber: 5.4 Consensus size: 175
9783650 CTCGCTGTTG
* * * * *
9783660 ATGCAGGAGGGCAATATCTGTTGTCTTCAACCAGCTCTGCTACACCCGAGAGAGACAAGGTTTGT
1 ATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTACAACCGAGAGAGGCAAGGTTT-T
* * * * * *
9783725 GTCTTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAAATTTGTTGTCTTTAACCAGCTCCGCTA
65 GTTTTTGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTA
* ** * * *
9783790 CAACCAAGAGAGGCAAGGTTTGTGTCTTTAATCTTCTTCGCTGTTA
130 CAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTATCA
* * *
9783836 ATGCAGGAAGGCAAGATCTGTTGTCTTTAACCAGCTCCACTGCAACCGATG-GAGGCAAGGTTTT
1 ATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTACAACCGA-GAGAGGCAAGGTTTT
* * *
9783900 GTTTTTTATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCAACTAGCTCTGCCA
65 GTTTTTGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTA
9783965 CAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTATCA
130 CAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTATCA
* * *
9784011 ATGTAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAGAGGTAAGGTTTTG
1 ATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTACAACCGAGAGAGGCAAGGTTTTG
* * * *
9784076 TTTTTTATTTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTTTTCGACCAGCTCTGCTAC
66 TTTTTGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTAC
*
9784141 AACCAAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTATCA
131 AACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTATCA
* * *
9784186 ATGTAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAGAGGTAAGGTTTTG
1 ATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTACAACCGAGAGAGGCAAGGTTTTG
*
9784251 TTTTTGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCGACCAGCTCTGCTAC
66 TTTTTGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTAC
*
9784316 AACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTACTTCGCTATCA
131 AACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTATCA
* *
9784361 GTGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTACAACTGAGAGAGGCAAGGTTTGT
1 ATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTACAACCGAGAGAGGCAAGGTTT-T
* * * * *
9784426 GTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTA
65 GTTTTTGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTA
* *
9784491 CAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCA
130 CAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTATCA
* *
9784537 ATGCAGGAAAGCAAGATCTGTTGTCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTT
1 ATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTACAACCGAGAGAGGCAAGGTTTT
9784601 TTGTTTCTTT
Statistics
Matches: 704, Mismatches: 58, Indels: 7
0.92 0.08 0.01
Matches are distributed among these distances:
174 1 0.00
175 487 0.69
176 215 0.31
177 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (175 bp):
ATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTACAACCGAGAGAGGCAAGGTTTTG
TTTTTGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTAC
AACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTATCA
Found at i:9784176 original size:263 final size:263
Alignment explanation
Indices: 9783646--9784599 Score: 1369
Period size: 263 Copynumber: 3.6 Consensus size: 263
9783636 CATCTTTGAC
* ** * * *
9783646 CTGCCTCGCTGTTGATGCAGGAGGGCAATATCTGTTGTCTTCAACCAGCTCTGCTACACCCGAGA
1 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGA
* * * * *
9783711 GAGACAAGGTTTGTGTCTTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAAATTTGTTGTCTTT
66 GAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTC
*
9783776 AACCAGCTCCGCTACAACCAAGAGAGGCAAGGTTTGTGTCTTTAATCTTCTTCGCTGTTAATGCA
131 AACCAGCTCCGCTACAACCGAGAGAGGCAAGGTTTGTGTCTTTAAT-TTCTTCGCTGTTAATGCA
* * * *
9783841 GGAAGGCAAGATCTGTTGTCTTT-AACCAGCTCCACTGCAACCGATG-GAGGCAAGGTTT-TGTT
195 GGAAGGCAAGATCTGTTGT-TTTCAACCAGCTCCGCTACAACC-AAGAGAGGCAAGGTTTGTGTC
**
9783903 TTTTAT
258 TTCGAT
* * *
9783909 CTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCAACTAGCTCTGCCACAACCGAGA
1 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGA
* *
9783974 GAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTATCAATGTAGGAAGGCAAGATCTGTTGTCTTC
66 GAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTC
* * * *
9784039 AACCAGCTCTGCTACAACCGAGAGAGGTAAGGTTT-TGTTTTTTATTTGCTTCGCTGTTAATGCA
131 AACCAGCTCCGCTACAACCGAGAGAGGCAAGGTTTGTGTCTTTAATTT-CTTCGCTGTTAATGCA
* *
9784103 GGAAGGCAAGATCTGTTGTTTTCGACCAGCTCTGCTACAACCAAGAGAGGCAAGGTTTGTGTCTT
195 GGAAGGCAAGATCTGTTGTTTTCAACCAGCTCCGCTACAACCAAGAGAGGCAAGGTTTGTGTCTT
9784168 CGAT
260 CGAT
* *
9784172 CTGCTTCGCTATCAATGTAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGA
1 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGA
* * * *
9784237 GAGGTAAGGTTT-TGTTTTTGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTC
66 GAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTC
* * ** * * * *
9784301 GACCAGCTCTGCTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTACTTCGCTATCAGTGCA
131 AACCAGCTCCGCTACAACCGAGAGAGGCAAGGTTTGTGTCTTTAAT-TTCTTCGCTGTTAATGCA
* **
9784366 GGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTACAACTGAGAGAGGCAAGGTTTGTGTCTT
195 GGAAGGCAAGATCTGTTGTTTTCAACCAGCTCCGCTACAACCAAGAGAGGCAAGGTTTGTGTCTT
*
9784431 CGAC
260 CGAT
*
9784435 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTACAACCGAGA
1 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGA
* *
9784500 GAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAAGCAAGATCTGTTGTCTTC
66 GAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTC
*
9784565 AACCAGCTCCACTACAACCGAGAGAGGCAAGGTTT
131 AACCAGCTCCGCTACAACCGAGAGAGGCAAGGTTT
9784600 TTTGTTTCTT
Statistics
Matches: 619, Mismatches: 65, Indels: 13
0.89 0.09 0.02
Matches are distributed among these distances:
261 7 0.01
262 150 0.24
263 382 0.62
264 80 0.13
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (263 bp):
CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGA
GAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTC
AACCAGCTCCGCTACAACCGAGAGAGGCAAGGTTTGTGTCTTTAATTTCTTCGCTGTTAATGCAG
GAAGGCAAGATCTGTTGTTTTCAACCAGCTCCGCTACAACCAAGAGAGGCAAGGTTTGTGTCTTC
GAT
Found at i:9785230 original size:108 final size:108
Alignment explanation
Indices: 9785041--9785236 Score: 313
Period size: 108 Copynumber: 1.8 Consensus size: 108
9785031 GAAAAATGCT
9785041 TGAAAAAGATTATCAAAATGGACAAAATGAAATTTTGTTGAGAGCAAAGCTCTAAACAAACAAAT
1 TGAAAAAGATTATCAAAATGGACAAAATGAAATTTTGTTGAGAGCAAAGCTCTAAACAAACAAAT
9785106 CAATCAAGACAACAAATTTTGCTGAGATACGAGATGTATAAGA
66 CAATCAAGACAACAAATTTTGCTGAGATACGAGATGTATAAGA
* * **
9785149 TGAAAAAGATTATCACAATGGATAAAATGGAAA-TTTGTTGAGAGCAAAGCTCTAAATGAACAAA
1 TGAAAAAGATTATCAAAATGGACAAAAT-GAAATTTTGTTGAGAGCAAAGCTCTAAACAAACAAA
* * *
9785213 TTAATCAAGATAGCAAATTTTGCT
65 TCAATCAAGACAACAAATTTTGCT
9785237 AGAATACAAA
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
108 76 0.95
109 4 0.05
ACGTcount: A:0.47, C:0.11, G:0.17, T:0.25
Consensus pattern (108 bp):
TGAAAAAGATTATCAAAATGGACAAAATGAAATTTTGTTGAGAGCAAAGCTCTAAACAAACAAAT
CAATCAAGACAACAAATTTTGCTGAGATACGAGATGTATAAGA
Found at i:9785300 original size:45 final size:43
Alignment explanation
Indices: 9785202--9785302 Score: 112
Period size: 45 Copynumber: 2.3 Consensus size: 43
9785192 GCAAAGCTCT
* * *
9785202 AAATGAACAAATTAATCAAGATAGCAAATTTTGCTAGAATACA
1 AAATGAATAAATTAATCAAGATAGCAAATTTTGCAAAAATACA
* **
9785245 AAATGAGAATAAATTAATCAAGATGGCGTATTTTGTCAAAAATACAA
1 AAAT--GAATAAATTAATCAAGATAGCAAATTTTG-CAAAAATAC-A
9785292 AAATGAATAAA
1 AAATGAATAAA
9785303 ATGGAAATAG
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
43 4 0.08
45 32 0.67
46 7 0.15
47 5 0.10
ACGTcount: A:0.52, C:0.09, G:0.13, T:0.26
Consensus pattern (43 bp):
AAATGAATAAATTAATCAAGATAGCAAATTTTGCAAAAATACA
Found at i:9785624 original size:17 final size:17
Alignment explanation
Indices: 9785584--9785623 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
9785574 TTTTTCATTC
*
9785584 TTCTTTTCTTTTCTTTT
1 TTCTTTTCGTTTCTTTT
9785601 TTCTTTTCGTTTCTTTT
1 TTCTTTTCGTTTCTTTT
9785618 TT-TTTT
1 TTCTTTT
9785624 TTGAGTGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (17 bp):
TTCTTTTCGTTTCTTTT
Found at i:9786068 original size:9 final size:9
Alignment explanation
Indices: 9786048--9786122 Score: 64
Period size: 9 Copynumber: 8.1 Consensus size: 9
9786038 CCCGGTAGAG
9786048 GTTTTTTCTT
1 GTTTTTT-TT
9786058 GTTTTTTTT
1 GTTTTTTTT
9786067 GTTTTGTTTT
1 GTTTT-TTTT
*
9786077 -TTTTTGCTCT
1 GTTTTT--TTT
* *
9786087 CTTTTTCTT
1 GTTTTTTTT
*
9786096 G-CTTTTTT
1 GTTTTTTTT
9786104 GTTTTTTTT
1 GTTTTTTTT
9786113 GTTTTTTTT
1 GTTTTTTTT
9786122 G
1 G
9786123 CCTCCACTGA
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
8 7 0.13
9 28 0.53
10 13 0.25
11 5 0.09
ACGTcount: A:0.00, C:0.08, G:0.12, T:0.80
Consensus pattern (9 bp):
GTTTTTTTT
Found at i:9789756 original size:26 final size:24
Alignment explanation
Indices: 9789699--9789758 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
9789689 CATGTAGAAA
* *
9789699 ATATGAAATATAAAAAAAATGTGT
1 ATATGAAAAATAAAAAAAATATGT
*
9789723 AT-T-TAAAATAAATAAAGAATATGT
1 ATATGAAAAATAAA-AAA-AATATGT
9789747 ATATGAAAAATA
1 ATATGAAAAATA
9789759 TAGTAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
22 7 0.25
23 4 0.14
24 10 0.36
25 1 0.04
26 6 0.21
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (24 bp):
ATATGAAAAATAAAAAAAATATGT
Found at i:9789885 original size:2 final size:2
Alignment explanation
Indices: 9789878--9789912 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
9789868 AGATATACAG
9789878 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9789913 ACTTAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9791298 original size:9 final size:9
Alignment explanation
Indices: 9791284--9791322 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
9791274 AATTTTTAAA
9791284 TTACATAAC
1 TTACATAAC
*
9791293 TTACATAAA
1 TTACATAAC
*
9791302 TTATATAAC
1 TTACATAAC
9791311 TTACATAAC
1 TTACATAAC
9791320 TTA
1 TTA
9791323 TAAATATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (9 bp):
TTACATAAC
Found at i:9791323 original size:18 final size:18
Alignment explanation
Indices: 9791280--9791324 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
9791270 AAACAATTTT
*
9791280 TAAATTACATAACTTACA
1 TAAATTATATAACTTACA
9791298 TAAATTATATAACTTACA
1 TAAATTATATAACTTACA
*
9791316 TAACTTATA
1 TAAATTATA
9791325 AATATTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAATTATATAACTTACA
Found at i:9791366 original size:17 final size:18
Alignment explanation
Indices: 9791346--9791379 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
9791336 ACATTTTTAA
9791346 TATATATTTTT-AAAATC
1 TATATATTTTTCAAAATC
*
9791363 TATATTTTTTTCAAAAT
1 TATATATTTTTCAAAAT
9791380 TTATCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATATTTTTCAAAATC
Found at i:9791513 original size:9 final size:9
Alignment explanation
Indices: 9791494--9791553 Score: 75
Period size: 9 Copynumber: 6.7 Consensus size: 9
9791484 CTTATATATA
*
9791494 AACTTGCAT
1 AACTTACAT
*
9791503 AACTTATAT
1 AACTTACAT
*
9791512 AAATTACAT
1 AACTTACAT
9791521 AACTTACAT
1 AACTTACAT
* *
9791530 AAATTATAT
1 AACTTACAT
9791539 AACTTACAT
1 AACTTACAT
9791548 AACTTA
1 AACTTA
9791554 TAAATATTTA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 42 1.00
ACGTcount: A:0.47, C:0.15, G:0.02, T:0.37
Consensus pattern (9 bp):
AACTTACAT
Found at i:9791530 original size:27 final size:27
Alignment explanation
Indices: 9791494--9791553 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
9791484 CTTATATATA
* *
9791494 AACTTGCATAACTTATATAAATTACAT
1 AACTTACATAAATTATATAAATTACAT
*
9791521 AACTTACATAAATTATATAACTTACAT
1 AACTTACATAAATTATATAAATTACAT
9791548 AACTTA
1 AACTTA
9791554 TAAATATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.47, C:0.15, G:0.02, T:0.37
Consensus pattern (27 bp):
AACTTACATAAATTATATAAATTACAT
Found at i:9791554 original size:18 final size:18
Alignment explanation
Indices: 9791501--9791555 Score: 83
Period size: 18 Copynumber: 3.1 Consensus size: 18
9791491 ATAAACTTGC
* *
9791501 ATAACTTATATAAATTAC
1 ATAACTTACATAAATTAT
9791519 ATAACTTACATAAATTAT
1 ATAACTTACATAAATTAT
*
9791537 ATAACTTACATAACTTAT
1 ATAACTTACATAAATTAT
9791555 A
1 A
9791556 AATATTTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAACTTACATAAATTAT
Found at i:9791597 original size:17 final size:18
Alignment explanation
Indices: 9791577--9791610 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
9791567 ACATTTTTAA
9791577 TATATATTTTT-AAAATC
1 TATATATTTTTCAAAATC
*
9791594 TATATTTTTTTCAAAAT
1 TATATATTTTTCAAAAT
9791611 TTATCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATATTTTTCAAAATC
Found at i:9791683 original size:231 final size:231
Alignment explanation
Indices: 9791280--9791780 Score: 975
Period size: 231 Copynumber: 2.2 Consensus size: 231
9791270 AAACAATTTT
9791280 TAAATTACATAACTTACATAAATTATATAACTTACATAACTTATAAATATTTATATACATTTTTA
1 TAAATTACATAACTTACATAAATTATATAACTTACATAACTTATAAATATTTATATACATTTTTA
9791345 ATATATATTTTTAAAATCTATATTTTTTTCAAAATTTATCAATCATAGCATAACTTACATAACTC
66 ATATATATTTTTAAAATCTATATTTTTTTCAAAATTTATCAATCATAGCATAACTTACATAACTC
* *
9791410 AAATTTATCAATCATATCATAACTTATATATAAACTTACATAATACATAACTTAAATAACATACG
131 AAATTTATCAATCATATCATAACTTAAATATAAACTTACATAATACATAACTTAAATAACATACA
9791475 ATACATAAACTTATATATAAACTTGCATAACTTATA
196 ATACATAAACTTATATATAAACTTGCATAACTTATA
9791511 TAAATTACATAACTTACATAAATTATATAACTTACATAACTTATAAATATTTATATACATTTTTA
1 TAAATTACATAACTTACATAAATTATATAACTTACATAACTTATAAATATTTATATACATTTTTA
*
9791576 ATATATATTTTTAAAATCTATATTTTTTTCAAAATTTATCAATCATAGCATAATTTACATAACTC
66 ATATATATTTTTAAAATCTATATTTTTTTCAAAATTTATCAATCATAGCATAACTTACATAACTC
9791641 AAATTTATCAATCATATCATAACTTAAATATAAACTTACATAATACATAACTTAAATAACATACA
131 AAATTTATCAATCATATCATAACTTAAATATAAACTTACATAATACATAACTTAAATAACATACA
9791706 ATACATAAACTTATATATAAACTTGCATAACTTATA
196 ATACATAAACTTATATATAAACTTGCATAACTTATA
9791742 TAAATTACATAACTTACATAAATTATATAACTTACATAA
1 TAAATTACATAACTTACATAAATTATATAACTTACATAA
9791781 ATTAAATAAC
Statistics
Matches: 267, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
231 267 1.00
ACGTcount: A:0.46, C:0.13, G:0.01, T:0.40
Consensus pattern (231 bp):
TAAATTACATAACTTACATAAATTATATAACTTACATAACTTATAAATATTTATATACATTTTTA
ATATATATTTTTAAAATCTATATTTTTTTCAAAATTTATCAATCATAGCATAACTTACATAACTC
AAATTTATCAATCATATCATAACTTAAATATAAACTTACATAATACATAACTTAAATAACATACA
ATACATAAACTTATATATAAACTTGCATAACTTATA
Found at i:9791744 original size:9 final size:9
Alignment explanation
Indices: 9791725--9791905 Score: 240
Period size: 9 Copynumber: 20.3 Consensus size: 9
9791715 CTTATATATA
*
9791725 AACTTGCAT
1 AACTTACAT
*
9791734 AACTTATAT
1 AACTTACAT
*
9791743 AAATTACAT
1 AACTTACAT
9791752 AACTTACAT
1 AACTTACAT
* *
9791761 AAATTATAT
1 AACTTACAT
9791770 AACTTACAT
1 AACTTACAT
* *
9791779 AAATTAAAT
1 AACTTACAT
9791788 AACTTACAT
1 AACTTACAT
*
9791797 AACTTAAAT
1 AACTTACAT
9791806 AACTTACAT
1 AACTTACAT
9791815 AACTTACAT
1 AACTTACAT
*
9791824 ATCTTACAT
1 AACTTACAT
9791833 AACTTACAT
1 AACTTACAT
* *
9791842 AAATTAAAT
1 AACTTACAT
9791851 AACTTACAT
1 AACTTACAT
9791860 AACTTACAT
1 AACTTACAT
*
9791869 AAATTACAT
1 AACTTACAT
9791878 AACTTACAT
1 AACTTACAT
9791887 AACTTACAT
1 AACTTACAT
9791896 AA--TACAT
1 AACTTACAT
9791903 AAC
1 AAC
9791906 CTTCCTTACT
Statistics
Matches: 148, Mismatches: 23, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
7 7 0.05
9 141 0.95
ACGTcount: A:0.49, C:0.17, G:0.01, T:0.34
Consensus pattern (9 bp):
AACTTACAT
Found at i:9797586 original size:21 final size:21
Alignment explanation
Indices: 9797561--9797626 Score: 89
Period size: 21 Copynumber: 3.1 Consensus size: 21
9797551 CAACTTAAAA
*
9797561 CAGAGGCAGCAGCGAGGGAAG
1 CAGAGGCAGCAGCGAGAGAAG
*
9797582 CAGAGGCTA-CTGCGAGAGAAG
1 CAGAGGC-AGCAGCGAGAGAAG
*
9797603 CAGAGGCCGCAGCGAGAGAAG
1 CAGAGGCAGCAGCGAGAGAAG
9797624 CAG
1 CAG
9797627 CGAGAGAAGC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
21 38 0.97
22 1 0.03
ACGTcount: A:0.33, C:0.21, G:0.42, T:0.03
Consensus pattern (21 bp):
CAGAGGCAGCAGCGAGAGAAG
Found at i:9797628 original size:12 final size:12
Alignment explanation
Indices: 9797611--9797638 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
9797601 AGCAGAGGCC
9797611 GCAGCGAGAGAA
1 GCAGCGAGAGAA
9797623 GCAGCGAGAGAA
1 GCAGCGAGAGAA
9797635 GCAG
1 GCAG
9797639 AGGTTCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.18, G:0.43, T:0.00
Consensus pattern (12 bp):
GCAGCGAGAGAA
Found at i:9798211 original size:43 final size:42
Alignment explanation
Indices: 9798117--9798259 Score: 171
Period size: 43 Copynumber: 3.3 Consensus size: 42
9798107 TTTGTAGATG
* * * *
9798117 AAGCGCCGCTAAAGAACATTACTTTTAGCGGC-ATTTTTTACC
1 AAGCGCCGCTAAAGAACATGAC-TTTAGCGGCGTTTTTTTTCT
*
9798159 AAGCGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTTTTCT
1 AAGCGCCGCTAAAGAACATGA-CTTTAGCGGCGTTTTTTTTCT
*
9798202 AAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTTATGT
1 AAGCGCCGCTAAAGAACATGA-CTTTAGCGGCGTTTTTTT-TCT
* *
9798246 AAGCACCGCAAAAG
1 AAGCGCCGCTAAAG
9798260 TTAGCGACGT
Statistics
Matches: 88, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
42 28 0.32
43 46 0.52
44 14 0.16
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (42 bp):
AAGCGCCGCTAAAGAACATGACTTTAGCGGCGTTTTTTTTCT
Found at i:9802549 original size:25 final size:24
Alignment explanation
Indices: 9802494--9802551 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 24
9802484 ATCAAATACA
*
9802494 CTAAAAACATTAAAATAAATATTT
1 CTAAAAAAATTAAAATAAATATTT
* * *
9802518 CTCAAAAAATTAAAAATAATTGTTT
1 CTAAAAAAATT-AAAATAAATATTT
*
9802543 TTAAAAAAA
1 CTAAAAAAA
9802552 CTCTTTGTAC
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
24 9 0.33
25 18 0.67
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (24 bp):
CTAAAAAAATTAAAATAAATATTT
Found at i:9805301 original size:11 final size:11
Alignment explanation
Indices: 9805287--9805329 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
9805277 AGTTAAAAAT
9805287 TATTTTATTAA
1 TATTTTATTAA
9805298 TATTTTACTTAGA
1 TATTTTA-TTA-A
9805311 TA-TTTATTAA
1 TATTTTATTAA
9805321 TATTTTATT
1 TATTTTATT
9805330 TAGAAAATGG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 3 0.10
11 16 0.55
12 7 0.24
13 3 0.10
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:9805316 original size:23 final size:23
Alignment explanation
Indices: 9805290--9805333 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
9805280 TAAAAATTAT
9805290 TTTATTAATATTTTACTTAGATA
1 TTTATTAATATTTTACTTAGATA
*
9805313 TTTATTAATATTTTATTTAGA
1 TTTATTAATATTTTACTTAGA
9805334 AAATGGTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (23 bp):
TTTATTAATATTTTACTTAGATA
Found at i:9807132 original size:12 final size:12
Alignment explanation
Indices: 9807117--9807141 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9807107 TTCGTTTAAG
9807117 TTTTTTTCTTTC
1 TTTTTTTCTTTC
9807129 TTTTTTTCTTTC
1 TTTTTTTCTTTC
9807141 T
1 T
9807142 CTGCTCTTTT
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTTCTTTC
Found at i:9807984 original size:3 final size:3
Alignment explanation
Indices: 9807978--9808044 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
9807968 TTATGACGTT
9807978 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
9808026 TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA T
9808045 AACAACTTTA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:9808190 original size:21 final size:25
Alignment explanation
Indices: 9808166--9808213 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 25
9808156 TAGCGTTTTC
9808166 TTGTTA-TG-TGTTATT-TT-ATTA
1 TTGTTATTGTTGTTATTATTCATTA
9808187 TTGTTATTGTTGTTATTATTCATTA
1 TTGTTATTGTTGTTATTATTCATTA
9808212 TT
1 TT
9808214 TGTCTTATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 6 0.26
22 2 0.09
23 7 0.30
24 2 0.09
25 6 0.26
ACGTcount: A:0.19, C:0.02, G:0.12, T:0.67
Consensus pattern (25 bp):
TTGTTATTGTTGTTATTATTCATTA
Found at i:9808341 original size:15 final size:15
Alignment explanation
Indices: 9808321--9808355 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
9808311 GTTGTAATCG
9808321 TTCATTAGC-TTAATT
1 TTCATTA-CATTAATT
9808336 TTCATTACATTAATT
1 TTCATTACATTAATT
9808351 TTCAT
1 TTCAT
9808356 CCAAATTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 1 0.05
15 18 0.95
ACGTcount: A:0.29, C:0.14, G:0.03, T:0.54
Consensus pattern (15 bp):
TTCATTACATTAATT
Found at i:9809336 original size:18 final size:19
Alignment explanation
Indices: 9809296--9809338 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
9809286 ATTTGTAAAA
9809296 CTTTAATATTTGTGTTAAT
1 CTTTAATATTTGTGTTAAT
9809315 -TTTATATATTT-TGTT-AT
1 CTTTA-ATATTTGTGTTAAT
9809332 CTTTAAT
1 CTTTAAT
9809339 TGAATATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 4 0.18
18 12 0.55
19 6 0.27
ACGTcount: A:0.26, C:0.05, G:0.07, T:0.63
Consensus pattern (19 bp):
CTTTAATATTTGTGTTAAT
Found at i:9817693 original size:20 final size:20
Alignment explanation
Indices: 9817670--9817707 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
9817660 AACATAAACA
*
9817670 TGTATAAACAAGCACGAACT
1 TGTATAAACAAACACGAACT
*
9817690 TGTATAAATAAACACGAA
1 TGTATAAACAAACACGAA
9817708 AATAAAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.16, G:0.13, T:0.21
Consensus pattern (20 bp):
TGTATAAACAAACACGAACT
Found at i:9822361 original size:13 final size:13
Alignment explanation
Indices: 9822343--9822369 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
9822333 GGTTTTACAG
9822343 ACTAAGTTCTCAA
1 ACTAAGTTCTCAA
9822356 ACTAAGTTCTCAA
1 ACTAAGTTCTCAA
9822369 A
1 A
9822370 GGGAGAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (13 bp):
ACTAAGTTCTCAA
Found at i:9824947 original size:31 final size:31
Alignment explanation
Indices: 9824912--9824971 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
9824902 TATATTTTTG
9824912 TTAATACACATGGCT-TAATATGATTGGTTTC
1 TTAATACACATGG-TGTAATATGATTGGTTTC
* * *
9824943 TTAATATACGTGGTGTAATATGGTTGGTT
1 TTAATACACATGGTGTAATATGATTGGTT
9824972 GAAAATGATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 1 0.04
31 24 0.96
ACGTcount: A:0.27, C:0.08, G:0.22, T:0.43
Consensus pattern (31 bp):
TTAATACACATGGTGTAATATGATTGGTTTC
Found at i:9825304 original size:11 final size:11
Alignment explanation
Indices: 9825288--9825322 Score: 70
Period size: 11 Copynumber: 3.2 Consensus size: 11
9825278 TACAATCGTG
9825288 TCAAAAATTAC
1 TCAAAAATTAC
9825299 TCAAAAATTAC
1 TCAAAAATTAC
9825310 TCAAAAATTAC
1 TCAAAAATTAC
9825321 TC
1 TC
9825323 TCACGACATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (11 bp):
TCAAAAATTAC
Found at i:9832953 original size:21 final size:23
Alignment explanation
Indices: 9832928--9832979 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
9832918 GGATTTTTTT
9832928 AAAAATAAAAGAAC-A-GATTCA
1 AAAAATAAAAGAACAAGGATTCA
*
9832949 AAAAA-AGAAGAACAAGGATTCA
1 AAAAATAAAAGAACAAGGATTCA
*
9832971 AAAATTAAA
1 AAAAATAAA
9832980 GGTGCCTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 7 0.28
21 6 0.24
22 10 0.40
23 2 0.08
ACGTcount: A:0.67, C:0.08, G:0.12, T:0.13
Consensus pattern (23 bp):
AAAAATAAAAGAACAAGGATTCA
Found at i:9833925 original size:3 final size:3
Alignment explanation
Indices: 9833919--9833963 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
9833909 CTTTTTTTAG
* *
9833919 ATT ATT ATT ATT ATT ACT ATT ATT ATT ATT ATT GTT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
9833964 TTGTTTTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:9839798 original size:2 final size:2
Alignment explanation
Indices: 9839791--9839818 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9839781 TGATTTTCGG
9839791 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
9839819 TAATTTATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9848883 original size:31 final size:31
Alignment explanation
Indices: 9848821--9848883 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
9848811 CATCCTAGTA
* * *
9848821 ACTTAAATAAAACTTTTTGAATAGTTTAGTG
1 ACTTAAATAAAACTTTTTAAATAATTCAGTG
9848852 ACTTAAATAAAAAC-TTTTAAATAATTCAGTG
1 ACTTAAAT-AAAACTTTTTAAATAATTCAGTG
9848883 A
1 A
9848884 TCATTTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 23 0.82
32 5 0.18
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (31 bp):
ACTTAAATAAAACTTTTTAAATAATTCAGTG
Found at i:9850688 original size:16 final size:16
Alignment explanation
Indices: 9850651--9850690 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
9850641 TTAATAAAAT
* *
9850651 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
9850667 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
9850683 TAAAATTA
1 TAAAATTA
9850691 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:9850760 original size:66 final size:68
Alignment explanation
Indices: 9850679--9850821 Score: 236
Period size: 68 Copynumber: 2.1 Consensus size: 68
9850669 AAATTAATTG
* *
9850679 TTAGTAAAATTATCAAATTATTAA-T-TGTTAATTGTATTAATTGTTATAATAAAATCTAACATT
1 TTAGTAAAATTATCAAATTATTAACTGTATTAATTGTATTAATTGTTATAACAAAATCTAACATT
9850742 TGA
66 TGA
* *
9850745 TTAGTAAATTTATCAAATTATTAACTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAAATTATCAAATTATTAACTGTATTAATTGTATTAATTGTTATAACAAAATCTAACATT
9850810 TGA
66 TGA
9850813 TTAGTAAAA
1 TTAGTAAAA
9850822 CAAACTTGAT
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
66 23 0.33
67 1 0.01
68 46 0.66
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (68 bp):
TTAGTAAAATTATCAAATTATTAACTGTATTAATTGTATTAATTGTTATAACAAAATCTAACATT
TGA
Found at i:9850927 original size:22 final size:24
Alignment explanation
Indices: 9850887--9850930 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
9850877 AAATAAACTT
9850887 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
9850911 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
9850931 AATATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:9852665 original size:2 final size:2
Alignment explanation
Indices: 9852660--9852721 Score: 63
Period size: 2 Copynumber: 31.0 Consensus size: 2
9852650 AAAGAACAAA
* * ** *
9852660 AT AT AT AT AT A- AT AT AT AT AA AT AA ACT AT GG AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
9852702 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
9852722 GTGTGTGTGA
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
1 1 0.02
2 47 0.96
3 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (2 bp):
AT
Found at i:9852773 original size:16 final size:17
Alignment explanation
Indices: 9852752--9852795 Score: 72
Period size: 16 Copynumber: 2.6 Consensus size: 17
9852742 GTATATAAAG
9852752 GTATATATAAAATG-AA
1 GTATATATAAAATGTAA
*
9852768 GTATATAAAAAATGTAA
1 GTATATATAAAATGTAA
9852785 GTATATATAAA
1 GTATATATAAA
9852796 CTATAAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 13 0.52
17 12 0.48
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (17 bp):
GTATATATAAAATGTAA
Found at i:9856409 original size:33 final size:31
Alignment explanation
Indices: 9856349--9856409 Score: 77
Period size: 33 Copynumber: 1.9 Consensus size: 31
9856339 AGTTAGTCCT
* *
9856349 TAAATTTAATAATTGTTCTCATATTGGGGCC
1 TAAATTTAATAATTATTCTCACATTGGGGCC
*
9856380 TAAACTTTAGATAATTATTCTCACGTTGGG
1 TAAA-TTTA-ATAATTATTCTCACATTGGG
9856410 CTTGGCAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 4 0.16
32 4 0.16
33 17 0.68
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.41
Consensus pattern (31 bp):
TAAATTTAATAATTATTCTCACATTGGGGCC
Found at i:9858785 original size:24 final size:24
Alignment explanation
Indices: 9858741--9858791 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
9858731 GAGCAAACCG
9858741 ATTTTTAATTAAAAATTTTAAT-TT
1 ATTTTTAATTAAAAA-TTTAATATT
9858765 ATTTTTAATATTAAAAA-TTAATATT
1 ATTTTT-A-ATTAAAAATTTAATATT
9858790 AT
1 AT
9858792 CAAATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
24 11 0.46
25 5 0.21
26 8 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
ATTTTTAATTAAAAATTTAATATT
Found at i:9866472 original size:26 final size:26
Alignment explanation
Indices: 9866435--9866484 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
9866425 TGGATGACTC
*
9866435 TCTACCTAGCATCGCCCGACTGGTTT
1 TCTACCTAGCATCACCCGACTGGTTT
*
9866461 TCTACCTTGCATCACCCGACTGGT
1 TCTACCTAGCATCACCCGACTGGT
9866485 AGCACCTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.16, C:0.36, G:0.18, T:0.30
Consensus pattern (26 bp):
TCTACCTAGCATCACCCGACTGGTTT
Found at i:9869296 original size:26 final size:26
Alignment explanation
Indices: 9869267--9869324 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
9869257 ATATACATAA
*
9869267 TATTTGGGGTAAAAGTATAATAAAAG
1 TATTTGGAGTAAAAGTATAATAAAAG
* *
9869293 TATTTGTATTAAAAGTATAATAAAAG
1 TATTTGGAGTAAAAGTATAATAAAAG
*
9869319 GATTTG
1 TATTTG
9869325 TATTAAAGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.45, C:0.00, G:0.19, T:0.36
Consensus pattern (26 bp):
TATTTGGAGTAAAAGTATAATAAAAG
Found at i:9869325 original size:26 final size:26
Alignment explanation
Indices: 9869276--9869331 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
9869266 ATATTTGGGG
*
9869276 TAAAAGTATAATAAAAGTATTTGTAT
1 TAAAAGTATAATAAAAGGATTTGTAT
9869302 TAAAAGTATAATAAAAGGATTTGTAT
1 TAAAAGTATAATAAAAGGATTTGTAT
9869328 TAAA
1 TAAA
9869332 GGTCAGATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (26 bp):
TAAAAGTATAATAAAAGGATTTGTAT
Found at i:9876403 original size:16 final size:16
Alignment explanation
Indices: 9876382--9876418 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
9876372 TTGGTTCGCT
9876382 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
9876398 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
9876414 GTAAT
1 GTAAT
9876419 AGGTAATTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.35, T:0.22
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:9876487 original size:44 final size:46
Alignment explanation
Indices: 9876398--9876488 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
9876388 GAATAGAGGC
*
9876398 GTAATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGGTAATTCTTATGTTTGGTTGAAT
9876444 GTAATGGAATAGAGGCGTAAT-GGT-ATTCTTATGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGGTAATTCTTATGTTTGGTTGAAT
9876488 G
1 G
9876489 GAATAGAGGT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 20 0.45
45 3 0.07
46 21 0.48
ACGTcount: A:0.27, C:0.04, G:0.30, T:0.38
Consensus pattern (46 bp):
GTAATGGAATAGAGGCGTAATAGGTAATTCTTATGTTTGGTTGAAT
Found at i:9876489 original size:39 final size:44
Alignment explanation
Indices: 9876398--9876505 Score: 145
Period size: 46 Copynumber: 2.5 Consensus size: 44
9876388 GAATAGAGGC
*
9876398 GTAATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGGTAATTCTTATGTTTGGTT--AT
9876444 GTAATGGAATAGAGGCGTAAT-GGT-ATTCTTATGTTTGG-T-T
1 GTAATGGAATAGAGGCGTAATAGGTAATTCTTATGTTTGGTTAT
*
9876484 G-AATGGAATAGAGGTGTAATAG
1 GTAATGGAATAGAGGCGTAATAG
9876506 CATAAGGAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 8
0.86 0.03 0.12
Matches are distributed among these distances:
39 18 0.31
40 3 0.05
43 1 0.02
44 13 0.22
45 3 0.05
46 21 0.36
ACGTcount: A:0.30, C:0.04, G:0.31, T:0.36
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATAGGTAATTCTTATGTTTGGTTAT
Found at i:9876667 original size:15 final size:15
Alignment explanation
Indices: 9876647--9876685 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 15
9876637 CATAATTGTT
9876647 ATAAAATATAATTTA
1 ATAAAATATAATTTA
9876662 ATAAAATATATAATTTA
1 AT-AAA-ATATAATTTA
9876679 ATAAAAT
1 ATAAAAT
9876686 TGTTAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.18
16 6 0.27
17 12 0.55
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAAAATATAATTTA
Found at i:9876692 original size:17 final size:17
Alignment explanation
Indices: 9876652--9876685 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
9876642 TTGTTATAAA
9876652 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
9876669 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
9876686 TGTTAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:9876757 original size:20 final size:21
Alignment explanation
Indices: 9876718--9876757 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
9876708 AATTTACTAA
*
9876718 TAAAATCATAATATATAATAC
1 TAAAATCATAATATAAAATAC
*
9876739 TAAAAT-ATAATTTAAAATA
1 TAAAATCATAATATAAAATA
9876758 ATTATTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAAATCATAATATAAAATAC
Found at i:9876799 original size:54 final size:54
Alignment explanation
Indices: 9876609--9876804 Score: 144
Period size: 54 Copynumber: 3.4 Consensus size: 54
9876599 TATTAATATA
* * * * * *
9876609 AATAATAAATAATTTAATCATATTTTAACATAATTGTTATAAAATATAATTTAAT
1 AATAATAAATAATTAAAT-AAAATTTAAAATAATTATTATTAAATATAATTTAAT
* * * **
9876664 AA-AATATATAATTTAATAAAATTGTTAATAA-ATATTCTTATATAAATTTACTAATAAAAT
1 AATAATAAATAATTAAATAAAA-T-TTAA-AATA-ATTATTAT-TAAA--TA-TAATTTAAT
* * *
9876724 CATAATATATAATACTAAAATATAATTTAAAATAATTATTATTAAATATAATTTAAT
1 AATAATAAATAAT--T-AAATAAAATTTAAAATAATTATTATTAAATATAATTTAAT
9876781 AATAATAAATAATTAAATAAAATT
1 AATAATAAATAATTAAATAAAATT
9876805 CTTATTCTTA
Statistics
Matches: 111, Mismatches: 17, Indels: 27
0.72 0.11 0.17
Matches are distributed among these distances:
53 2 0.02
54 24 0.22
55 8 0.07
56 8 0.07
57 21 0.19
58 2 0.02
59 2 0.02
60 12 0.11
61 19 0.17
62 5 0.05
63 2 0.02
64 6 0.05
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (54 bp):
AATAATAAATAATTAAATAAAATTTAAAATAATTATTATTAAATATAATTTAAT
Found at i:9876883 original size:32 final size:32
Alignment explanation
Indices: 9876847--9876910 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
9876837 TATATAATAC
*
9876847 TATAAAATATAATTTAAATAATTATTATTAAA
1 TATAAAATATAATATAAATAATTATTATTAAA
** ** *
9876879 TATAATTTATAATATACTTTATTATTATTAAA
1 TATAAAATATAATATAAATAATTATTATTAAA
9876911 CTGCAATACA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (32 bp):
TATAAAATATAATATAAATAATTATTATTAAA
Found at i:9878353 original size:49 final size:50
Alignment explanation
Indices: 9878250--9878354 Score: 140
Period size: 50 Copynumber: 2.1 Consensus size: 50
9878240 AGAAAAAAAC
* ** * *
9878250 AAATTAAAATTAAGTTTAATATCATGAATCAAAAAGGTGAACACTTTATA
1 AAATTAAAATTAAGTTCAATATCATGAATCAAAAAACTCAACACTGTATA
* *
9878300 AAATTAAAATTGAGTTCAATATCATGAAT-AAAAAACTCAACACTGTATT
1 AAATTAAAATTAAGTTCAATATCATGAATCAAAAAACTCAACACTGTATA
9878349 AAATTA
1 AAATTA
9878355 TAACACATGA
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
49 21 0.44
50 27 0.56
ACGTcount: A:0.50, C:0.10, G:0.09, T:0.31
Consensus pattern (50 bp):
AAATTAAAATTAAGTTCAATATCATGAATCAAAAAACTCAACACTGTATA
Found at i:9879358 original size:12 final size:12
Alignment explanation
Indices: 9879337--9879370 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
9879327 CCACATTTTA
9879337 AGCAAAAGAACG
1 AGCAAAAGAACG
*
9879349 AGCCAAAGAACG
1 AGCAAAAGAACG
9879361 AGCAAAAGAA
1 AGCAAAAGAA
9879371 AATAAATAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.59, C:0.18, G:0.24, T:0.00
Consensus pattern (12 bp):
AGCAAAAGAACG
Found at i:9882987 original size:15 final size:15
Alignment explanation
Indices: 9882967--9882995 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
9882957 ATTTGATTAA
9882967 AAAAATACCAAAAAT
1 AAAAATACCAAAAAT
9882982 AAAAATACCAAAAA
1 AAAAATACCAAAAA
9882996 ATTTAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.76, C:0.14, G:0.00, T:0.10
Consensus pattern (15 bp):
AAAAATACCAAAAAT
Found at i:9892059 original size:24 final size:23
Alignment explanation
Indices: 9892019--9892064 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
9892009 AAATATTTCT
*
9892019 AAAATAATCAGAATTTAATTGGA
1 AAAATAAGCAGAATTTAATTGGA
*
9892042 AAAATATAGCAGATTTTAATTGG
1 AAAATA-AGCAGAATTTAATTGG
9892065 GAGAAGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.48, C:0.04, G:0.15, T:0.33
Consensus pattern (23 bp):
AAAATAAGCAGAATTTAATTGGA
Found at i:9903492 original size:19 final size:19
Alignment explanation
Indices: 9903468--9903513 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
9903458 ATTAAGTCCT
*
9903468 TTATTTATTTACTTATTTA
1 TTATTTACTTACTTATTTA
* *
9903487 TTATTTCCTTACTTTTTTA
1 TTATTTACTTACTTATTTA
9903506 TATATTTA
1 T-TATTTA
9903514 AAATCGTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATTTACTTACTTATTTA
Found at i:9903597 original size:3 final size:3
Alignment explanation
Indices: 9903589--9903684 Score: 115
Period size: 3 Copynumber: 32.0 Consensus size: 3
9903579 TTGTGCCCTT
* * * *
9903589 TTA TTA TTA TTG GTA TTG TTA TTTA TTA TTA TT- TTA TTA TCA TCTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA T-TA
*
9903635 -TA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
9903682 TTA
1 TTA
9903685 CATATACTTA
Statistics
Matches: 80, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
2 4 0.05
3 72 0.90
4 4 0.05
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:9903995 original size:42 final size:42
Alignment explanation
Indices: 9903936--9904040 Score: 210
Period size: 42 Copynumber: 2.5 Consensus size: 42
9903926 TTTCCGAGAA
9903936 ATCGCGTCCACGTCAGCGCGATGTCAGGGTACGTGTCAGGAC
1 ATCGCGTCCACGTCAGCGCGATGTCAGGGTACGTGTCAGGAC
9903978 ATCGCGTCCACGTCAGCGCGATGTCAGGGTACGTGTCAGGAC
1 ATCGCGTCCACGTCAGCGCGATGTCAGGGTACGTGTCAGGAC
9904020 ATCGCGTCCACGTCAGCGCGA
1 ATCGCGTCCACGTCAGCGCGA
9904041 CCTGCTGAAG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.19, C:0.30, G:0.32, T:0.18
Consensus pattern (42 bp):
ATCGCGTCCACGTCAGCGCGATGTCAGGGTACGTGTCAGGAC
Found at i:9907553 original size:10 final size:10
Alignment explanation
Indices: 9907538--9907562 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
9907528 GAAATCTAAC
9907538 ATTATGTAAA
1 ATTATGTAAA
9907548 ATTATGTAAA
1 ATTATGTAAA
9907558 ATTAT
1 ATTAT
9907563 TAAGCCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (10 bp):
ATTATGTAAA
Found at i:9907654 original size:55 final size:55
Alignment explanation
Indices: 9907546--9907727 Score: 312
Period size: 55 Copynumber: 3.3 Consensus size: 55
9907536 ACATTATGTA
* *
9907546 AAATTATGTAAAATTATTAAG-CCAAAATTCTTTTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTATTAAGTCCAAAA--ATTGTGTTAATGGTTAGTAAAATTATC
9907602 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
*
9907657 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTGGTAAAATTATC
1 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
9907712 AAATTATGTAAAATTA
1 AAATTATGTAAAATTA
9907728 GGTTAGGGTT
Statistics
Matches: 122, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
55 95 0.78
56 21 0.17
57 6 0.05
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.39
Consensus pattern (55 bp):
AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
Found at i:9907764 original size:29 final size:29
Alignment explanation
Indices: 9907722--9907845 Score: 230
Period size: 29 Copynumber: 4.3 Consensus size: 29
9907712 AAATTATGTA
9907722 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
9907751 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
* *
9907780 AAATTAGGTTAGGGTTAAGGTGTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
9907809 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
9907838 AAATTAGG
1 AAATTAGG
9907846 GTTTTTATTA
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 91 1.00
ACGTcount: A:0.30, C:0.00, G:0.27, T:0.43
Consensus pattern (29 bp):
AAATTAGGTTAGGGTTAGGGTTTTTAATT
Found at i:9907958 original size:71 final size:71
Alignment explanation
Indices: 9907851--9908035 Score: 309
Period size: 71 Copynumber: 2.6 Consensus size: 71
9907841 TTAGGGTTTT
*
9907851 TATTACATCAAATAGAACTTCTATTTTATTATATCAAATAATATCAAAATAACTCGAAAAAAT-T
1 TATTACATCAAATA-AACTTCTATTTTATTACATCAAATAATATCAAAATAACTCG-AAAAATGT
9907915 TCTATGCC
64 TCTATGCC
* *
9907923 TATTATATCAAATAAACTTCTATTTTATTACATCAAATAATATTAAAATAACTCGAAAAATGTTC
1 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAATGTTC
*
9907988 TATGCG
66 TATGCC
9907994 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATA
1 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATA
9908036 AATTTAAATA
Statistics
Matches: 107, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
70 6 0.06
71 88 0.82
72 13 0.12
ACGTcount: A:0.44, C:0.14, G:0.04, T:0.38
Consensus pattern (71 bp):
TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAATGTTC
TATGCC
Found at i:9908014 original size:26 final size:25
Alignment explanation
Indices: 9907985--9908033 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
9907975 TCGAAAAATG
9907985 TTCTATGCGTATTACATCAAATAAAC
1 TTCTAT-CGTATTACATCAAATAAAC
**
9908011 TTCTATTTTATTACATCAAATAA
1 TTCTATCGTATTACATCAAATAA
9908034 TAAATTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.39, C:0.16, G:0.04, T:0.41
Consensus pattern (25 bp):
TTCTATCGTATTACATCAAATAAAC
Found at i:9910227 original size:10 final size:10
Alignment explanation
Indices: 9910208--9910258 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
9910198 GCCATTGATG
9910208 AAAATATAAA
1 AAAATATAAA
*
9910218 AAAATTTAAA
1 AAAATATAAA
* * *
9910228 ATTATTTTAAA
1 A-AAATATAAA
9910239 AAAATAT-AA
1 AAAATATAAA
9910248 AAAATATAAA
1 AAAATATAAA
9910258 A
1 A
9910259 TTATTTTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
9 9 0.27
10 16 0.48
11 8 0.24
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AAAATATAAA
Found at i:9910252 original size:30 final size:31
Alignment explanation
Indices: 9910208--9910271 Score: 112
Period size: 30 Copynumber: 2.1 Consensus size: 31
9910198 GCCATTGATG
*
9910208 AAAATATAAAAAAATTTAAAATTATTTTAAA
1 AAAATATAAAAAAATATAAAATTATTTTAAA
9910239 AAAATAT-AAAAAATATAAAATTATTTTAAA
1 AAAATATAAAAAAATATAAAATTATTTTAAA
9910269 AAA
1 AAA
9910272 TGAAATTGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 25 0.78
31 7 0.22
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (31 bp):
AAAATATAAAAAAATATAAAATTATTTTAAA
Found at i:9910388 original size:51 final size:51
Alignment explanation
Indices: 9910273--9910388 Score: 196
Period size: 51 Copynumber: 2.3 Consensus size: 51
9910263 TTTAAAAAAT
* *
9910273 GAAATTGAGGGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGATATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
* *
9910324 GAAATTGAGAGGATGTTGAAATTAAATATGGGTTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGATATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
9910375 GAAATTGAGAGGAT
1 GAAATTGAGAGGAT
9910389 TAGAGAGGAA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.40, C:0.00, G:0.31, T:0.29
Consensus pattern (51 bp):
GAAATTGAGAGGATATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
Found at i:9910782 original size:17 final size:17
Alignment explanation
Indices: 9910762--9910795 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
9910752 TATTATTACA
9910762 ATGATAAGATTATTATT
1 ATGATAAGATTATTATT
* *
9910779 ATGATTATATTATTATT
1 ATGATAAGATTATTATT
9910796 GTAGTATTCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (17 bp):
ATGATAAGATTATTATT
Found at i:9910898 original size:25 final size:25
Alignment explanation
Indices: 9910870--9910918 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
9910860 ACTTTAACCT
9910870 TTTATAATCAT-TTTATTTTATTTTA
1 TTTATAA-CATATTTATTTTATTTTA
* *
9910895 TTTATTACTTATTTATTTTATTTT
1 TTTATAACATATTTATTTTATTTT
9910919 TTCAGATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 19 0.90
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (25 bp):
TTTATAACATATTTATTTTATTTTA
Found at i:9910969 original size:3 final size:3
Alignment explanation
Indices: 9910961--9910990 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
9910951 ATTATTCCTC
9910961 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
9910991 CACTAGCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:9911551 original size:11 final size:11
Alignment explanation
Indices: 9911535--9911567 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
9911525 AATCCTTCCT
9911535 CGTGCGTAACC
1 CGTGCGTAACC
9911546 CGTGCGTAACC
1 CGTGCGTAACC
9911557 CGTGCGTAACC
1 CGTGCGTAACC
9911568 GACTCCCGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.18, C:0.36, G:0.27, T:0.18
Consensus pattern (11 bp):
CGTGCGTAACC
Done.