Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007967.1 Hibiscus syriacus cultivar Beakdansim tig00110402_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2476418
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 11
Found at i:1823414 original size:33 final size:33
Alignment explanation
Indices: 1823289--1823414 Score: 93
Period size: 33 Copynumber: 3.8 Consensus size: 33
1823279 ATTCTTTTTA
* *
1823289 TTTCATTTTTT-ATTTATTTACTTTATATATA-TT
1 TTTCATTTTTTCATTT-TTTA-TTAATATTTATTT
* * ** *
1823322 TTTCATTTTCTC-CTAATT-TTAATATTTTTTT
1 TTTCATTTTTTCATTTTTTATTAATATTTATTT
*
1823353 ATTTC-TTTTTACATTGTTTTA-TATATATTTATTT
1 -TTTCATTTTTTCATT-TTTTATTA-ATATTTATTT
1823387 TTTCATTTTTTCATTTTTTATTAATATT
1 TTTCATTTTTTCATTTTTTATTAATATT
1823415 ATTATATTAA
Statistics
Matches: 70, Mismatches: 14, Indels: 18
0.69 0.14 0.18
Matches are distributed among these distances:
30 7 0.10
31 7 0.10
32 7 0.10
33 29 0.41
34 20 0.29
ACGTcount: A:0.22, C:0.08, G:0.01, T:0.69
Consensus pattern (33 bp):
TTTCATTTTTTCATTTTTTATTAATATTTATTT
Found at i:1825760 original size:14 final size:15
Alignment explanation
Indices: 1825743--1825771 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1825733 ATATTTTCAC
1825743 AATTTTT-TTTTTTG
1 AATTTTTGTTTTTTG
1825757 AATTTTTGTTTTTTG
1 AATTTTTGTTTTTTG
1825772 GATAATTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.14, C:0.00, G:0.10, T:0.76
Consensus pattern (15 bp):
AATTTTTGTTTTTTG
Found at i:1830973 original size:25 final size:25
Alignment explanation
Indices: 1830944--1830992 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1830934 TAGGATGGAC
* *
1830944 ATAAGACTC-TTTTTCTCTCTCTTTG
1 ATAAGACCCATTTTTATCT-TCTTTG
1830969 ATAAGACCCATTTTTATCTTCTTT
1 ATAAGACCCATTTTTATCTTCTTT
1830993 AGCGATTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.20, C:0.22, G:0.06, T:0.51
Consensus pattern (25 bp):
ATAAGACCCATTTTTATCTTCTTTG
Found at i:1844419 original size:15 final size:17
Alignment explanation
Indices: 1844388--1844419 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1844378 GTTTACGAGC
1844388 TAAAATATATAACTTTT
1 TAAAATATATAACTTTT
1844405 TAAAAT-TAT-ACTTTT
1 TAAAATATATAACTTTT
1844420 GGTCCCTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 3 0.20
17 6 0.40
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
TAAAATATATAACTTTT
Found at i:1844729 original size:14 final size:14
Alignment explanation
Indices: 1844710--1844739 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1844700 CTTAATAAAA
*
1844710 CTTCTTCTATTTAT
1 CTTCTTCTATTAAT
1844724 CTTCTTCTATTAAT
1 CTTCTTCTATTAAT
1844738 CT
1 CT
1844740 GATTCCATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.23, G:0.00, T:0.60
Consensus pattern (14 bp):
CTTCTTCTATTAAT
Found at i:1845812 original size:21 final size:21
Alignment explanation
Indices: 1845775--1845814 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1845765 AATTAGTTAA
*
1845775 AAAATTAAAGATGAATTATTT
1 AAAATTAAAGATAAATTATTT
1845796 AAAA-TAAAGAGTAAATTAT
1 AAAATTAAAGA-TAAATTAT
1845815 ATCAGTGACC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (21 bp):
AAAATTAAAGATAAATTATTT
Found at i:1846577 original size:16 final size:16
Alignment explanation
Indices: 1846558--1846592 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1846548 TAATTTTTTG
1846558 AAAAAGGTTTTGTTAT
1 AAAAAGGTTTTGTTAT
**
1846574 AAAAATTTTTTGTTAT
1 AAAAAGGTTTTGTTAT
1846590 AAA
1 AAA
1846593 TATAGAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (16 bp):
AAAAAGGTTTTGTTAT
Found at i:1848804 original size:16 final size:16
Alignment explanation
Indices: 1848758--1848804 Score: 85
Period size: 16 Copynumber: 2.9 Consensus size: 16
1848748 TTCTAATTTT
*
1848758 TTTTTGAGTTCAAGCC
1 TTTTTGAGTTCAAGTC
1848774 TTTTTGAGTTCAAGTC
1 TTTTTGAGTTCAAGTC
1848790 TTTTTGAGTTCAAGT
1 TTTTTGAGTTCAAGT
1848805 TTTAATATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.49
Consensus pattern (16 bp):
TTTTTGAGTTCAAGTC
Found at i:1849296 original size:17 final size:17
Alignment explanation
Indices: 1849274--1849307 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1849264 AAAAAAATTA
*
1849274 AATTTTTTTTATATTTT
1 AATTTTTTATATATTTT
1849291 AATTTTTTATATATTTT
1 AATTTTTTATATATTTT
1849308 TTATTGATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
AATTTTTTATATATTTT
Found at i:1858623 original size:3 final size:3
Alignment explanation
Indices: 1858610--1858642 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1858600 CATTTTCAAC
1858610 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1858643 TAAAACAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1863438 original size:33 final size:32
Alignment explanation
Indices: 1863369--1863438 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
1863359 AATATGAACT
* * *
1863369 TTAAAAAATTTTAGAGGGGTTAAATTAATTTT
1 TTAAAAAAATTTAGAAGGGTTAAATTAATTTC
*
1863401 TTAAAAAAATTTA-AAGGTTTAAATTATAATTTC
1 TTAAAAAAATTTAGAAGGGTTAAA-T-TAATTTC
1863434 TTAAA
1 TTAAA
1863439 TTTGGGGGGC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 8 0.25
32 13 0.41
33 11 0.34
ACGTcount: A:0.46, C:0.01, G:0.10, T:0.43
Consensus pattern (32 bp):
TTAAAAAAATTTAGAAGGGTTAAATTAATTTC
Found at i:1863533 original size:3 final size:3
Alignment explanation
Indices: 1863525--1863606 Score: 114
Period size: 3 Copynumber: 27.0 Consensus size: 3
1863515 GTCCGGATCT
*
1863525 TTA TTA TTA TTA TAA TTA -TA TTA TTTA TTA TTA TTA TTAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TT-A TTA TTA
1863571 TTA TTA TTA TTA TTA TTA TT- TTGA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
1863607 CTTTTTTTTG
Statistics
Matches: 72, Mismatches: 2, Indels: 10
0.86 0.02 0.12
Matches are distributed among these distances:
2 4 0.06
3 60 0.83
4 8 0.11
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1865036 original size:30 final size:30
Alignment explanation
Indices: 1864951--1865037 Score: 104
Period size: 29 Copynumber: 2.9 Consensus size: 30
1864941 TGTTAATACC
* * *
1864951 ATTTTAGTCCTTTAACTTTCTATTTTATCT
1 ATTTTAGTTCTTTAAGTTTCTATTTTTTCT
** *
1864981 ATTTTA-TTCCCTAAGTTTCTGTTTTTTCT
1 ATTTTAGTTCTTTAAGTTTCTATTTTTTCT
*
1865010 ATTTTAGTTATTTAAGTTTCTATTTTTT
1 ATTTTAGTTCTTTAAGTTTCTATTTTTT
1865038 TTGTTATTTA
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
29 23 0.50
30 23 0.50
ACGTcount: A:0.18, C:0.13, G:0.06, T:0.63
Consensus pattern (30 bp):
ATTTTAGTTCTTTAAGTTTCTATTTTTTCT
Found at i:1868308 original size:20 final size:20
Alignment explanation
Indices: 1868283--1868324 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1868273 GACATTTCCT
1868283 TTCTTTAAGACCTTGAAACA
1 TTCTTTAAGACCTTGAAACA
1868303 TTCTTTAAGACCTTGAAACA
1 TTCTTTAAGACCTTGAAACA
1868323 TT
1 TT
1868325 GCATTTATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (20 bp):
TTCTTTAAGACCTTGAAACA
Found at i:1870154 original size:12 final size:11
Alignment explanation
Indices: 1870137--1870178 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 11
1870127 TCGAGAAAAG
1870137 CATACATCAATA
1 CATACAT-AATA
1870149 CATACATATATA
1 CATACATA-ATA
1870161 CATACATAAATA
1 CATACAT-AATA
1870173 CATACA
1 CATACA
1870179 CTTTGCATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 1 0.04
12 26 0.93
13 1 0.04
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.26
Consensus pattern (11 bp):
CATACATAATA
Found at i:1870155 original size:4 final size:4
Alignment explanation
Indices: 1870137--1870178 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
1870127 TCGAGAAAAG
* *
1870137 CATA CAT- CAATA CATA CATA TATA CATA CATA AATA CATA CA
1 CATA CATA C-ATA CATA CATA CATA CATA CATA CATA CATA CA
1870179 CTTTGCATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
3 1 0.03
4 30 0.94
5 1 0.03
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:1870563 original size:36 final size:35
Alignment explanation
Indices: 1870509--1870650 Score: 176
Period size: 36 Copynumber: 4.0 Consensus size: 35
1870499 TGAGAATTTT
1870509 AAAACAAATGTTTGTCTCGCTTGAGACAATTTATCTC
1 AAAACAAAT-TTTGTCTCGCTTGAGACAATTT-TCTC
* *
1870546 AAAACAAATTTTGTCTCGCTTGAGACAGTTTTCTA
1 AAAACAAATTTTGTCTCGCTTGAGACAATTTTCTC
* * *
1870581 AAAACAAATTTTGTCTCGTTTGAGATAATTTCTTTC
1 AAAACAAATTTTGTCTCGCTTGAGACAATTT-TCTC
* * * *
1870617 AAAATAAATTTCGTCTCACTTGAGACATTTTTCT
1 AAAACAAATTTTGTCTCGCTTGAGACAATTTTCT
1870651 TTTGAGATAC
Statistics
Matches: 90, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
35 33 0.37
36 48 0.53
37 9 0.10
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (35 bp):
AAAACAAATTTTGTCTCGCTTGAGACAATTTTCTC
Found at i:1870594 original size:71 final size:72
Alignment explanation
Indices: 1870509--1870650 Score: 205
Period size: 71 Copynumber: 2.0 Consensus size: 72
1870499 TGAGAATTTT
* *
1870509 AAAACAAATGTTTGTCTCGCTTGAGACAATTTATCTCAAAACAAATTTTGTCTCGCTTGAGACAG
1 AAAACAAATGTTTGTCTCGCTTGAGACAATTTATCTCAAAACAAATTTCGTCTCACTTGAGACAG
1870574 TTTTCTA
66 TTTTCTA
* * * * * *
1870581 AAAACAAAT-TTTGTCTCGTTTGAGATAATTTCTTTCAAAATAAATTTCGTCTCACTTGAGACAT
1 AAAACAAATGTTTGTCTCGCTTGAGACAATTTATCTCAAAACAAATTTCGTCTCACTTGAGACAG
1870645 TTTTCT
66 TTTTCT
1870651 TTTGAGATAC
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
71 53 0.85
72 9 0.15
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (72 bp):
AAAACAAATGTTTGTCTCGCTTGAGACAATTTATCTCAAAACAAATTTCGTCTCACTTGAGACAG
TTTTCTA
Found at i:1870946 original size:105 final size:103
Alignment explanation
Indices: 1870629--1870949 Score: 358
Period size: 105 Copynumber: 3.1 Consensus size: 103
1870619 AATAAATTTC
* * * *
1870629 GTCTCACTTGAGACATTTTTCTTTTGAG-ATACAAAATTCGAGTTTGTTTCACATTAAACAAAGT
1 GTCTCGCTTGAGACATTTTTCCTTTGAGAATACAAATTTCGAATTTGTTTCACATTAAACAAAGT
* * *
1870693 TGATCTCATTTGAGATTGCTTTCTAAAAAA-AAACTTC
66 TGATCTCACTTGAGATTGTTTTCTAAAAAACAAACTTT
* * *
1870730 GTCTCGCTTGAGACA-TTTT-CTATGA-AATAAAAATTT-AAATTTGTTGT-AC-TTGAAACAAA
1 GTCTCGCTTGAGACATTTTTCCTTTGAGAATACAAATTTCGAATTTGTT-TCACATT-AAACAAA
* **
1870789 -TTAATCTCACTTGAGATTGTTATTTCTTTCAAAAC-AA-TTT
64 GTTGATCTCACTTGAGATTG-T-TTTC-TAAAAAACAAACTTT
*
1870829 CGTCTCGTTTGAGACATTTTTCCTTTGAGAATACAAATTTCGAATTTGTTTCACATTAAACAAAG
1 -GTCTCGCTTGAGACATTTTTCCTTTGAGAATACAAATTTCGAATTTGTTTCACATTAAACAAAG
*
1870894 TTGATCTCACTTGAGATCGTTTTCTAAAAAAAACAAACTTT
65 TTGATCTCACTTGAGATTGTTTTCT--AAAAAACAAACTTT
1870935 GTCTCGCTTGAGACA
1 GTCTCGCTTGAGACA
1870950 ATTTCTCTAA
Statistics
Matches: 179, Mismatches: 22, Indels: 34
0.76 0.09 0.14
Matches are distributed among these distances:
97 19 0.11
98 16 0.09
99 19 0.11
100 25 0.14
101 18 0.10
102 6 0.03
103 15 0.08
104 23 0.13
105 35 0.20
106 3 0.02
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.39
Consensus pattern (103 bp):
GTCTCGCTTGAGACATTTTTCCTTTGAGAATACAAATTTCGAATTTGTTTCACATTAAACAAAGT
TGATCTCACTTGAGATTGTTTTCTAAAAAACAAACTTT
Found at i:1870972 original size:36 final size:36
Alignment explanation
Indices: 1870922--1871024 Score: 143
Period size: 36 Copynumber: 2.9 Consensus size: 36
1870912 GTTTTCTAAA
* *
1870922 AAAAACAAACTTTGTCTCGCTTGAGACAATTTCTCT
1 AAAAACAAATTTTGTCTCACTTGAGACAATTTCTCT
* * * *
1870958 AAAAACAATTTTTGTCTCATTTAAAACAATTTCTCT
1 AAAAACAAATTTTGTCTCACTTGAGACAATTTCTCT
*
1870994 AAAAACAAATGTTGTCTCACTTGAGACAATT
1 AAAAACAAATTTTGTCTCACTTGAGACAATT
1871025 CTACAAATTA
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (36 bp):
AAAAACAAATTTTGTCTCACTTGAGACAATTTCTCT
Found at i:1871203 original size:30 final size:29
Alignment explanation
Indices: 1871129--1871212 Score: 69
Period size: 30 Copynumber: 2.8 Consensus size: 29
1871119 TGAAAAAAAT
* * * * *
1871129 CTTTGAGTCCTTTCTTTTCAAACACCTAT
1 CTTTGAGTCATTTCTATTAAAACACCCAC
* * *
1871158 CTTTGAGTTAATTTCTCTTGAAACACCCAC
1 CTTTGAG-TCATTTCTATTAAAACACCCAC
*
1871188 CTTTGAGATCGTTTCTATTAAAACA
1 CTTTGAG-TCATTTCTATTAAAACA
1871213 ATATTATTTC
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
29 7 0.16
30 36 0.84
ACGTcount: A:0.26, C:0.24, G:0.10, T:0.40
Consensus pattern (29 bp):
CTTTGAGTCATTTCTATTAAAACACCCAC
Found at i:1871652 original size:65 final size:63
Alignment explanation
Indices: 1871526--1871652 Score: 155
Period size: 65 Copynumber: 2.0 Consensus size: 63
1871516 TGTCTCTCTC
* * ** *
1871526 GAGACAATTTCTTTTGAAAAATCATTGAATATGTTTCTTTGGAAATAAAATTTTTTCTCTTTT
1 GAGACAATTTCTTTTGAAAAATCATTGAATATGTTTCTTTGGAAACAAAATATACTATCTTTT
* * * *
1871589 GAGACAGTTTCTTTTAAGAAAAATCGTTGAGTCTGTTTCTTTGGAAACAAAATATACTATCTTT
1 GAGACAATTTCTTTT--GAAAAATCATTGAATATGTTTCTTTGGAAACAAAATATACTATCTTT
1871653 GAGTTTGTTT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
63 14 0.26
65 39 0.74
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.43
Consensus pattern (63 bp):
GAGACAATTTCTTTTGAAAAATCATTGAATATGTTTCTTTGGAAACAAAATATACTATCTTTT
Found at i:1871692 original size:38 final size:37
Alignment explanation
Indices: 1871608--1871713 Score: 126
Period size: 36 Copynumber: 2.8 Consensus size: 37
1871598 TCTTTTAAGA
* *
1871608 AAAATCGTTGAGTCTGTTTCTTTGGAAACAAAATATAC
1 AAAATCTTTGAGTCTGTTTCTTT-GAAACAAAACATAC
* * *
1871646 --TATCTTTGAGTTTGTTTCTCTTGAAAGAAAACATAC
1 AAAATCTTTGAGTCTGTTTCT-TTGAAACAAAACATAC
1871682 AAAATCTTTGAGTCTGTTTCTTTTGAAACAAA
1 AAAATCTTTGAGTCTGTTTC-TTTGAAACAAA
1871714 TCTTTGAGTC
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
36 28 0.50
37 2 0.04
38 25 0.45
39 1 0.02
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (37 bp):
AAAATCTTTGAGTCTGTTTCTTTGAAACAAAACATAC
Found at i:1871721 original size:28 final size:28
Alignment explanation
Indices: 1871683--1871738 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
1871673 AAAACATACA
* **
1871683 AAATCTTTGAGTCTGTTTCTTTTGAAAC
1 AAATCTTTGAGTCGGTTTCCCTTGAAAC
1871711 AAATCTTTGAGTCGGTTTCCCTTGAAAC
1 AAATCTTTGAGTCGGTTTCCCTTGAAAC
1871739 CATAATCACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (28 bp):
AAATCTTTGAGTCGGTTTCCCTTGAAAC
Found at i:1871987 original size:134 final size:131
Alignment explanation
Indices: 1871767--1872103 Score: 376
Period size: 134 Copynumber: 2.5 Consensus size: 131
1871757 CCAGCCATCC
* * * * **
1871767 TCATCACGTAGGAACCGTGTCATCCCCTTACCAGATCTCCTCATCATGTAGGAACCGTGTCAACC
1 TCATCACGTATGAGCCGTGTCATCCCC-GACCAGATCTCCTCATCACGTAGGAGTCGTGTC-ACC
* * *
1871832 ATAGATAACCAATCATCCTCATCACGTATAAACCGAGTTATCACAACC-CCTAAACATGGCCAGA
64 CTAGATAACCAATCATCCTCATCACGTAGAAACCGAGTTATCAC--CCTCCTAAACATGACCAGA
1871896 ACTCT
127 ACTCT
* *
1871901 TCATCACGTATGAGCCGTGTCATCCCTCGACCAGATCTCCTCATCGCATAGGAGTCGTGTCATCC
1 TCATCACGTATGAGCCGTGTCATCCC-CGACCAGATCTCCTCATCACGTAGGAGTCGTGTCA-CC
* * * * *
1871966 CTAGATAACC-AGCTGTCCTCATCGCGTAGGAACCGAGTTATCACCCTTCCTAAAGATGACCAGA
64 CTAGATAACCAATC-ATCCTCATCACGTAGAAACCGAGTTATCACCC-TCCTAAACATGACCAGA
1872030 ACTCT
127 ACTCT
* * * *
1872035 TCATCACGTATGAGCAGTATCATCCCCCGACTAGA--TCCTCATCACGTAGGAGTTGTGTCACCC
1 TCATCACGTATGAGCCGTGTCAT-CCCCGACCAGATCTCCTCATCACGTAGGAGTCGTGTCACCC
1872098 TTAGAT
65 -TAGAT
1872104 GATCAGACCT
Statistics
Matches: 174, Mismatches: 22, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
131 3 0.02
132 29 0.17
133 3 0.02
134 135 0.78
135 4 0.02
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (131 bp):
TCATCACGTATGAGCCGTGTCATCCCCGACCAGATCTCCTCATCACGTAGGAGTCGTGTCACCCT
AGATAACCAATCATCCTCATCACGTAGAAACCGAGTTATCACCCTCCTAAACATGACCAGAACTC
T
Found at i:1872297 original size:3 final size:3
Alignment explanation
Indices: 1872283--1872364 Score: 105
Period size: 3 Copynumber: 27.0 Consensus size: 3
1872273 CGGGTCTTTT
*
1872283 TTA TTA TGA TTA TTA -TA TTA TTTA TTA TTA TTA TTA TTAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TT-A TTA TTA
*
1872329 TTA TTA TTA TTA TTA TTA TT- TTGA TTA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
1872365 CTTTTTTTTG
Statistics
Matches: 70, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
2 4 0.06
3 58 0.83
4 8 0.11
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1879629 original size:24 final size:23
Alignment explanation
Indices: 1879602--1879682 Score: 56
Period size: 24 Copynumber: 3.4 Consensus size: 23
1879592 ATTTGAATTA
*
1879602 TGTTATGATACATGA-CATGGATTT
1 TGTTATGATAC-TGATC-TGGATTC
* *
1879626 TGTTCTGATTTCTGATCTGGATTC
1 TGTTATGA-TACTGATCTGGATTC
* * *
1879650 TGTTATGATATATGTTCTGAATTC
1 TGTTATGATA-CTGATCTGGATTC
*
1879674 TGTTTTGAT
1 TGTTATGAT
1879683 TTTTGATATC
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
23 1 0.02
24 41 0.91
25 3 0.07
ACGTcount: A:0.21, C:0.10, G:0.20, T:0.49
Consensus pattern (23 bp):
TGTTATGATACTGATCTGGATTC
Found at i:1881052 original size:16 final size:16
Alignment explanation
Indices: 1881031--1881063 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1881021 TAATAAATAA
1881031 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1881047 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
1881063 A
1 A
1881064 ATTTTTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.21, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1881150 original size:16 final size:16
Alignment explanation
Indices: 1881129--1881175 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
1881119 TTTAATAAAT
*
1881129 AAACGAAAATAAACGA
1 AAACGAACATAAACGA
*
1881145 AAACGAACATTAACGA
1 AAACGAACATAAACGA
*
1881161 ACACGAACATAAACG
1 AAACGAACATAAACG
1881176 TTGGAGACCC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.60, C:0.19, G:0.13, T:0.09
Consensus pattern (16 bp):
AAACGAACATAAACGA
Found at i:1882281 original size:10 final size:10
Alignment explanation
Indices: 1882266--1882323 Score: 53
Period size: 10 Copynumber: 5.4 Consensus size: 10
1882256 ATAAATGAAT
1882266 GAACATAAAC
1 GAACATAAAC
*
1882276 GAACATAACCGAAT
1 GAACAT-A---AAC
1882290 GAACATAAAC
1 GAACATAAAC
*
1882300 GAACATAACC
1 GAACATAAAC
*
1882310 GAACATAACC
1 GAACATAAAC
1882320 GAAC
1 GAAC
1882324 GAATATAACT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
10 31 0.76
11 1 0.02
13 1 0.02
14 8 0.20
ACGTcount: A:0.53, C:0.24, G:0.12, T:0.10
Consensus pattern (10 bp):
GAACATAAAC
Found at i:1882289 original size:24 final size:24
Alignment explanation
Indices: 1882253--1882312 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
1882243 GATTGGGTTA
**
1882253 AACATAAATGAATGAACATAAACG
1 AACATAACCGAATGAACATAAACG
1882277 AACATAACCGAATGAACATAAACG
1 AACATAACCGAATGAACATAAACG
1882301 AACATAACCGAA
1 AACATAACCGAA
1882313 CATAACCGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.57, C:0.18, G:0.12, T:0.13
Consensus pattern (24 bp):
AACATAACCGAATGAACATAAACG
Found at i:1882293 original size:14 final size:14
Alignment explanation
Indices: 1882253--1882302 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 14
1882243 GATTGGGTTA
*
1882253 AACATAAATGAATG
1 AACATAAACGAATG
1882267 AACATAAAC----G
1 AACATAAACGAATG
*
1882277 AACATAACCGAATG
1 AACATAAACGAATG
1882291 AACATAAACGAA
1 AACATAAACGAA
1882303 CATAACCGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
10 9 0.31
14 20 0.69
ACGTcount: A:0.58, C:0.16, G:0.12, T:0.14
Consensus pattern (14 bp):
AACATAAACGAATG
Found at i:1882307 original size:34 final size:34
Alignment explanation
Indices: 1882266--1882331 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
1882256 ATAAATGAAT
*
1882266 GAACATAAACGAACATAACCGAATGAACATAAAC
1 GAACATAAACGAACATAACCGAACGAACATAAAC
* *
1882300 GAACATAACCGAACATAACCGAACGAATATAA
1 GAACATAAACGAACATAACCGAACGAACATAA
1882332 CTGAACGTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.55, C:0.21, G:0.12, T:0.12
Consensus pattern (34 bp):
GAACATAAACGAACATAACCGAACGAACATAAAC
Found at i:1882993 original size:19 final size:19
Alignment explanation
Indices: 1882965--1883003 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1882955 TGGTAAAATA
*
1882965 TTATCTAAAATATTATTTT
1 TTATCGAAAATATTATTTT
*
1882984 TTATCGAAAATGTTATTTT
1 TTATCGAAAATATTATTTT
1883003 T
1 T
1883004 CGTTAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.56
Consensus pattern (19 bp):
TTATCGAAAATATTATTTT
Found at i:1883701 original size:16 final size:16
Alignment explanation
Indices: 1883668--1883708 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
1883658 GTTTACTTCA
1883668 GAATGATT-AAATGAT
1 GAATGATTCAAATGAT
1883683 GAATGATTCAAAT-ACT
1 GAATGATTCAAATGA-T
1883699 GAATGATTCA
1 GAATGATTCA
1883709 GAGGCTCTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.38
16 15 0.62
ACGTcount: A:0.44, C:0.07, G:0.17, T:0.32
Consensus pattern (16 bp):
GAATGATTCAAATGAT
Found at i:1883829 original size:15 final size:15
Alignment explanation
Indices: 1883809--1883842 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1883799 GCACTGTTTT
1883809 ACTGAATCAATCAGC
1 ACTGAATCAATCAGC
*
1883824 ACTGAATCATTCAGC
1 ACTGAATCAATCAGC
1883839 ACTG
1 ACTG
1883843 TTTTGCTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (15 bp):
ACTGAATCAATCAGC
Found at i:1883838 original size:38 final size:38
Alignment explanation
Indices: 1883787--1883875 Score: 160
Period size: 38 Copynumber: 2.3 Consensus size: 38
1883777 TATTTATGTG
1883787 CTGAATCATTCAGCACTGTTTTACTGAATCAATCAGCA
1 CTGAATCATTCAGCACTGTTTTACTGAATCAATCAGCA
* *
1883825 CTGAATCATTCAGCACTGTTTTGCTGAATCAGTCAGCA
1 CTGAATCATTCAGCACTGTTTTACTGAATCAATCAGCA
1883863 CTGAATCATTCAG
1 CTGAATCATTCAG
1883876 AGGTGCGAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (38 bp):
CTGAATCATTCAGCACTGTTTTACTGAATCAATCAGCA
Found at i:1887645 original size:51 final size:51
Alignment explanation
Indices: 1887580--1887687 Score: 207
Period size: 51 Copynumber: 2.1 Consensus size: 51
1887570 GTGTTTAACC
*
1887580 TAAGGATAGGTCATTTTTAGTCCAAGTAAATTTTGGGGATGGAATCTCTTT
1 TAAGAATAGGTCATTTTTAGTCCAAGTAAATTTTGGGGATGGAATCTCTTT
1887631 TAAGAATAGGTCATTTTTAGTCCAAGTAAATTTTGGGGATGGAATCTCTTT
1 TAAGAATAGGTCATTTTTAGTCCAAGTAAATTTTGGGGATGGAATCTCTTT
1887682 TAAGAA
1 TAAGAA
1887688 GGGGAATGTT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (51 bp):
TAAGAATAGGTCATTTTTAGTCCAAGTAAATTTTGGGGATGGAATCTCTTT
Found at i:1887958 original size:14 final size:16
Alignment explanation
Indices: 1887939--1887984 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
1887929 TTTTCTTCAT
1887939 TTATTT-CT-TCCTTC
1 TTATTTCCTCTCCTTC
1887953 TTATTTTCCTCTCCTTC
1 TTA-TTTCCTCTCCTTC
1887970 TTATTTTCCTCTCCT
1 TTA-TTTCCTCTCCT
1887985 ACTTCCTCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
14 3 0.10
15 3 0.10
16 2 0.07
17 21 0.72
ACGTcount: A:0.07, C:0.33, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATTTCCTCTCCTTC
Found at i:1887969 original size:17 final size:17
Alignment explanation
Indices: 1887947--1887984 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1887937 ATTTATTTCT
1887947 TCCTTCTTATTTTCCTC
1 TCCTTCTTATTTTCCTC
1887964 TCCTTCTTATTTTCCTC
1 TCCTTCTTATTTTCCTC
1887981 TCCT
1 TCCT
1887985 ACTTCCTCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.05, C:0.37, G:0.00, T:0.58
Consensus pattern (17 bp):
TCCTTCTTATTTTCCTC
Found at i:1889284 original size:32 final size:32
Alignment explanation
Indices: 1889196--1889284 Score: 151
Period size: 32 Copynumber: 2.8 Consensus size: 32
1889186 CTAATAACTT
*
1889196 GAGTCAGTGTTGCATTCAGATAATACACAACA
1 GAGTCAGTGTTGCATTCAGATAATGCACAACA
*
1889228 GAGTCAATGTTGCATTCAGATAATGCACAACA
1 GAGTCAGTGTTGCATTCAGATAATGCACAACA
*
1889260 GAGTCAGTGTCGCATTCAGATAATG
1 GAGTCAGTGTTGCATTCAGATAATG
1889285 TGTAGCAGTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (32 bp):
GAGTCAGTGTTGCATTCAGATAATGCACAACA
Found at i:1892837 original size:46 final size:46
Alignment explanation
Indices: 1892786--1893108 Score: 547
Period size: 46 Copynumber: 7.0 Consensus size: 46
1892776 TTTAATCATG
* *
1892786 GCATCCATTCATGCATTTTAATCATGGCATCCTTTCATGCTTTAAT
1 GCATCCGTTCATGCATTTTAATCATGGCATCCTTTCATGCCTTAAT
1892832 GCATCCGTTCATGCATTTTAATCATGGCATCCTTTCATGCCTTAAT
1 GCATCCGTTCATGCATTTTAATCATGGCATCCTTTCATGCCTTAAT
*
1892878 GCATCCATTCATGCATTTTAATCATGGCATCCTTTCATGCCTTAAT
1 GCATCCGTTCATGCATTTTAATCATGGCATCCTTTCATGCCTTAAT
*
1892924 GCATCCGTTCATGCATTTTAATCATGGCATTCTTTCATGCCTTAAT
1 GCATCCGTTCATGCATTTTAATCATGGCATCCTTTCATGCCTTAAT
*
1892970 GCATCCGTTCATGCGTTTTAATCATGGCATCCTTTCATGCCTTAAT
1 GCATCCGTTCATGCATTTTAATCATGGCATCCTTTCATGCCTTAAT
* * *
1893016 GCATCCGTTCATGCGTTTTAATCATGACATCTTTTCATGCCTTAAT
1 GCATCCGTTCATGCATTTTAATCATGGCATCCTTTCATGCCTTAAT
* * *
1893062 GCATCTGTTCATACATTTTAATCATGGTATCCTTTCATGCCTTAAT
1 GCATCCGTTCATGCATTTTAATCATGGCATCCTTTCATGCCTTAAT
1893108 G
1 G
1893109 ATTTTTAATC
Statistics
Matches: 262, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 262 1.00
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.41
Consensus pattern (46 bp):
GCATCCGTTCATGCATTTTAATCATGGCATCCTTTCATGCCTTAAT
Found at i:1892947 original size:138 final size:138
Alignment explanation
Indices: 1892786--1893298 Score: 654
Period size: 138 Copynumber: 3.8 Consensus size: 138
1892776 TTTAATCATG
* *
1892786 GCATCCATTCATGCATTTTAATCATGGCATCCTTTCATGCTTTAATGCATCCGTTCATGCATTTT
1 GCATCCGTTCATGCATTTTAATCATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTT
1892851 AATCATGGCATCCTTTCATGCCTTAATGCATCCATTCATGCATTTTAATCATGGCATCCTTTCAT
66 AATCATGGCATCCTTTCATGCCTTAATGCATCCATTCATGCATTTTAATCATGGCATCCTTTCAT
1892916 GCCTTAAT
131 GCCTTAAT
* *
1892924 GCATCCGTTCATGCATTTTAATCATGGCATTCTTTCATGCCTTAATGCATCCGTTCATGCGTTTT
1 GCATCCGTTCATGCATTTTAATCATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTT
* * * *
1892989 AATCATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCGTTTTAATCATGACATCTTTTCAT
66 AATCATGGCATCCTTTCATGCCTTAATGCATCCATTCATGCATTTTAATCATGGCATCCTTTCAT
1893054 GCCTTAAT
131 GCCTTAAT
* * *
1893062 GCATCTGTTCATACATTTTAATCATGGTATCCTTTCATGCCTT-A---AT--G---AT---TTTT
1 GCATCCGTTCATGCATTTTAATCATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTT
* ** *
1893115 AATCATGGCATCCTTTCATGCCTTAATGCATCCATTAATAATATATTTTAATTATGGCATCCTTT
66 AATCATGGCATCCTTTCATGCCTTAATGCATCCA-T--TCATGCATTTTAATCATGGCATCCTTT
*
1893180 TATGCCTT-A-
128 CATGCCTTAAT
* *
1893189 --A----TTCATGCATTTTAATCATGACATCCTTTCATGCCTTAATACATCCGTTCATGCATTTT
1 GCATCCGTTCATGCATTTTAATCATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTT
* * * *
1893248 AATCATGGCATACATTCATGCCTTAATGTATCAATTCATGCA-TTTAATCAT
66 AATCATGGCATCCTTTCATGCCTTAATGCATCCATTCATGCATTTTAATCAT
1893299 TTTGTTCATT
Statistics
Matches: 328, Mismatches: 32, Indels: 39
0.82 0.08 0.10
Matches are distributed among these distances:
121 33 0.10
122 1 0.00
125 3 0.01
126 37 0.11
127 2 0.01
128 1 0.00
129 37 0.11
130 6 0.02
132 2 0.01
133 34 0.10
134 2 0.01
137 1 0.00
138 169 0.52
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.41
Consensus pattern (138 bp):
GCATCCGTTCATGCATTTTAATCATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTT
AATCATGGCATCCTTTCATGCCTTAATGCATCCATTCATGCATTTTAATCATGGCATCCTTTCAT
GCCTTAAT
Found at i:1893120 original size:34 final size:34
Alignment explanation
Indices: 1893077--1893142 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
1893067 TGTTCATACA
*
1893077 TTTTAATCATGGTATCCTTTCATGCCTTAATGAT
1 TTTTAATCATGGCATCCTTTCATGCCTTAATGAT
1893111 TTTTAATCATGGCATCCTTTCATGCCTTAATG
1 TTTTAATCATGGCATCCTTTCATGCCTTAATG
1893143 CATCCATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.23, C:0.20, G:0.12, T:0.45
Consensus pattern (34 bp):
TTTTAATCATGGCATCCTTTCATGCCTTAATGAT
Found at i:1893153 original size:46 final size:45
Alignment explanation
Indices: 1893101--1893298 Score: 162
Period size: 46 Copynumber: 4.4 Consensus size: 45
1893091 TCCTTTCATG
1893101 CCTTAATG-ATTTTTAATCATGGCATCCTTTCATGCCTTAATGCAT
1 CCTTAATGCA-TTTTAATCATGGCATCCTTTCATGCCTTAATGCAT
** * *
1893146 CCATTAATAATATATTTTAATTATGGCATCCTTTTATGCCTTAAT---T
1 CC--T--TAATGCATTTTAATCATGGCATCCTTTCATGCCTTAATGCAT
* *
1893192 -C---ATGCATTTTAATCATGACATCCTTTCATGCCTTAATACAT
1 CCTTAATGCATTTTAATCATGGCATCCTTTCATGCCTTAATGCAT
* * * *
1893233 CCGTTCATGCATTTTAATCATGGCATACATTCATGCCTTAATGTAT
1 CC-TTAATGCATTTTAATCATGGCATCCTTTCATGCCTTAATGCAT
* *
1893279 CAATTCATGCA-TTTAATCAT
1 C-CTTAATGCATTTTAATCAT
1893299 TTTGTTCATT
Statistics
Matches: 125, Mismatches: 14, Indels: 28
0.75 0.08 0.17
Matches are distributed among these distances:
38 31 0.25
41 1 0.01
42 1 0.01
45 12 0.10
46 45 0.36
47 1 0.01
49 33 0.26
50 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.42
Consensus pattern (45 bp):
CCTTAATGCATTTTAATCATGGCATCCTTTCATGCCTTAATGCAT
Found at i:1893219 original size:26 final size:26
Alignment explanation
Indices: 1893189--1893268 Score: 73
Period size: 26 Copynumber: 3.3 Consensus size: 26
1893179 TTATGCCTTA
1893189 ATTCATGCATTTTAATCATGACATCC
1 ATTCATGCATTTTAATCATGACATCC
* *
1893215 TTTCATGC--CTT-A--AT-ACATCC
1 ATTCATGCATTTTAATCATGACATCC
* * *
1893235 GTTCATGCATTTTAATCATGGCATAC
1 ATTCATGCATTTTAATCATGACATCC
1893261 ATTCATGC
1 ATTCATGC
1893269 CTTAATGTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
20 13 0.32
21 2 0.05
22 2 0.05
23 2 0.05
24 2 0.05
25 2 0.05
26 18 0.44
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.39
Consensus pattern (26 bp):
ATTCATGCATTTTAATCATGACATCC
Found at i:1893835 original size:20 final size:20
Alignment explanation
Indices: 1893810--1893861 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1893800 ATTTTGAAAT
1893810 GGTATCGATACCTTCCCT-TC
1 GGTATCGATACC-TCCCTCTC
*
1893830 GGTATCGATA-CTCCCTCCTT
1 GGTATCGATACCTCCCT-CTC
1893850 GGTATCGATACC
1 GGTATCGATACC
1893862 GATTGAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 5 0.18
19 1 0.04
20 21 0.75
21 1 0.04
ACGTcount: A:0.17, C:0.33, G:0.17, T:0.33
Consensus pattern (20 bp):
GGTATCGATACCTCCCTCTC
Found at i:1911413 original size:19 final size:18
Alignment explanation
Indices: 1911353--1911440 Score: 55
Period size: 17 Copynumber: 5.1 Consensus size: 18
1911343 TTTATGTTAG
1911353 TATTTTT-TTAAATAGTTA
1 TATTTTTATTAAATA-TTA
1911371 T-TATTTT-TT--ATATTAA
1 TAT-TTTTATTAAATATT-A
*
1911387 TATATTTATGTAAATATTA
1 TATTTTTAT-TAAATATTA
*
1911406 TATTTTTATTAAA-ATAA
1 TATTTTTATTAAATATTA
* *
1911423 TATTTATA-TAATTATTA
1 TATTTTTATTAAATATTA
1911440 T
1 T
1911441 TTATTTAGAA
Statistics
Matches: 56, Mismatches: 6, Indels: 17
0.71 0.08 0.22
Matches are distributed among these distances:
15 2 0.04
16 11 0.20
17 17 0.30
18 12 0.21
19 9 0.16
20 5 0.09
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
TATTTTTATTAAATATTA
Found at i:1911446 original size:36 final size:33
Alignment explanation
Indices: 1911359--1911447 Score: 85
Period size: 34 Copynumber: 2.7 Consensus size: 33
1911349 TTAGTATTTT
* *
1911359 TTTAAATAGTTATTATTT-TTTATATTAATATA
1 TTTATATAATTATTATTTATTTATATTAATATA
* * *
1911391 TTTATGTAAATATTATATT-TTTAT-TAAAATAATA
1 TTTATATAATTATTAT-TTATTTATAT-TAAT-ATA
1911425 TTTATATAATTATTATTTATTTA
1 TTTATATAATTATTATTTATTTA
1911448 GAATTATTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
32 13 0.28
33 12 0.26
34 21 0.46
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.58
Consensus pattern (33 bp):
TTTATATAATTATTATTTATTTATATTAATATA
Found at i:1913205 original size:21 final size:21
Alignment explanation
Indices: 1913175--1913222 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1913165 GCAGGGGTAC
* *
1913175 ATGCCTAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
1913196 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
1913217 ATGCCA
1 ATGCCA
1913223 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.38, G:0.12, T:0.25
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:1913252 original size:21 final size:20
Alignment explanation
Indices: 1913226--1913319 Score: 109
Period size: 21 Copynumber: 4.5 Consensus size: 20
1913216 TATGCCATCT
1913226 CCGCAGGGTTACATTCTGAGC
1 CCGCAGGGTTACATTCT-AGC
*
1913247 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATT-CTAGC
*
1913268 CCGTAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATT-CTAGC
*
1913289 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACAT-TCTAGC
1913310 CCGCAGGGTT
1 CCGCAGGGTT
1913320 TTATACCATA
Statistics
Matches: 64, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
20 2 0.03
21 60 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.32, G:0.28, T:0.22
Consensus pattern (20 bp):
CCGCAGGGTTACATTCTAGC
Found at i:1913277 original size:42 final size:42
Alignment explanation
Indices: 1913226--1913319 Score: 129
Period size: 42 Copynumber: 2.2 Consensus size: 42
1913216 TATGCCATCT
*
1913226 CCGCAGGGTTACATT-CTGAGCCCG-CAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCT-AGCCCGCCA-GGTTACATGCCGAGC
* *
1913268 CCGTAGGGTTACATTCCTAGCCCGCCAGGTTACATGCCTAGC
1 CCGCAGGGTTACATTCCTAGCCCGCCAGGTTACATGCCGAGC
1913310 CCGCAGGGTT
1 CCGCAGGGTT
1913320 TTATACCATA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
42 42 0.91
43 4 0.09
ACGTcount: A:0.18, C:0.32, G:0.28, T:0.22
Consensus pattern (42 bp):
CCGCAGGGTTACATTCCTAGCCCGCCAGGTTACATGCCGAGC
Found at i:1913901 original size:33 final size:34
Alignment explanation
Indices: 1913842--1913938 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
1913832 AAATGTTTTT
*
1913842 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
1913876 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
1913909 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
1913939 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:1913945 original size:34 final size:33
Alignment explanation
Indices: 1913840--1913945 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
1913830 ATAAATGTTT
*
1913840 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
1913874 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
1913906 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
1913941 TTAAA
1 TTAAA
1913946 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:1914563 original size:128 final size:128
Alignment explanation
Indices: 1914335--1915215 Score: 1545
Period size: 128 Copynumber: 6.9 Consensus size: 128
1914325 TTACCTGATT
*
1914335 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
** *** *
1914400 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
66 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
1914463 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *** *
1914528 TGATGAAATAATGGAAGGCGCCCCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
66 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
1914591 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1914656 TGATGAAATAATGGAAGGCGCGCCCCC-GGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
1914718 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGATATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
1914783 TGATGAAATAATGGAAGGCGCGCCCCCAGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
1914846 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
1914911 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGTGCCTTCATGTGAATAGTGAAATAATAGG
66 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
1914974 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
1915039 TGATGAAATAATAGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
1915102 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
1915167 TGACGAAATAATGGAAGGCGC-CCCCCGGGAACGTGCCTTCATGTGAATA
66 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATA
1915216 ATACTCCAAT
Statistics
Matches: 731, Mismatches: 20, Indels: 5
0.97 0.03 0.01
Matches are distributed among these distances:
126 1 0.00
127 147 0.20
128 583 0.80
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:1915045 original size:383 final size:384
Alignment explanation
Indices: 1914335--1915215 Score: 1554
Period size: 383 Copynumber: 2.3 Consensus size: 384
1914325 TTACCTGATT
*
1914335 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* ***
1914400 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGGT
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGAGAAATAATAGGT
1914464 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
130 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
**
1914529 GATGAAATAATGGAAGGCGCCCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGGTAC
195 GATGAAATAATGGAAGGCGCCCCCCCGGGAACGCGCCTTCATGTCCAATGAGAAATAATAGGTAC
*
1914594 TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
260 TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTATGA
*
1914659 TGAAATAATGGAAGGCGCGCCCCC-GGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
325 TGAAATAATAGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
1914718 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGATATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * *
1914783 TGATGAAATAATGGAAGGCGCGCCCCCAGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGAGAAATAATAGGTA
1914848 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
131 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
* * * *
1914913 ATGAAATAATGGAAGGCGCGCCCCCGGGAACGTGCCTTCATGT-GAATAGTGAAATAATAGGTAC
196 ATGAAATAATGGAAGGCGCCCCCCCGGGAACGCGCCTTCATGTCCAAT-GAGAAATAATAGGTAC
1914977 TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTATGA
260 TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTATGA
1915042 TGAAATAATAGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
325 TGAAATAATAGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
1915102 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
1915167 TGACGAAATAATGGAAGGCGC-CCCCCGGGAACGTGCCTTCATGTGAATA
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATA
1915216 ATACTCCAAT
Statistics
Matches: 474, Mismatches: 21, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
382 2 0.00
383 353 0.74
384 119 0.25
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (384 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGAGAAATAATAGGTA
CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
ATGAAATAATGGAAGGCGCCCCCCCGGGAACGCGCCTTCATGTCCAATGAGAAATAATAGGTACT
GATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTATGAT
GAAATAATAGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:1915301 original size:8 final size:8
Alignment explanation
Indices: 1915288--1915328 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1915278 TCACAATCTT
1915288 TCAAATTC
1 TCAAATTC
1915296 TCAAATTC
1 TCAAATTC
* *
1915304 CCAAACTC
1 TCAAATTC
1915312 T-AAATTC
1 TCAAATTC
1915319 TCAAATTC
1 TCAAATTC
1915327 TC
1 TC
1915329 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:1919193 original size:6 final size:6
Alignment explanation
Indices: 1919182--1919223 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
1919172 TAGCCTTAAT
1919182 GGCTTA GGCTTA GGCTTA GGCTTA GGCTTA GGCTTA GGCTTA
1 GGCTTA GGCTTA GGCTTA GGCTTA GGCTTA GGCTTA GGCTTA
1919224 TCTATTGAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.17, C:0.17, G:0.33, T:0.33
Consensus pattern (6 bp):
GGCTTA
Found at i:1924705 original size:54 final size:54
Alignment explanation
Indices: 1924619--1924734 Score: 160
Period size: 54 Copynumber: 2.1 Consensus size: 54
1924609 TACCTCTAAG
* * * * * *
1924619 GGGGTATCAGTACCTATAGGGTATTCTGTTTTTCTCGGAGCTAAAATTTGCATA
1 GGGGTATCAGTACCCATAGGGCATTCTATTTTTCTCGAAGCCAAAATTAGCATA
* *
1924673 GGGGTATCAGTACCCATTGGGCATTCTATTTTTCTCGAAGCCAATATTAGCATA
1 GGGGTATCAGTACCCATAGGGCATTCTATTTTTCTCGAAGCCAAAATTAGCATA
1924727 GGGGTATC
1 GGGGTATC
1924735 GGCACACCCT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (54 bp):
GGGGTATCAGTACCCATAGGGCATTCTATTTTTCTCGAAGCCAAAATTAGCATA
Found at i:1926525 original size:14 final size:14
Alignment explanation
Indices: 1926498--1926532 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1926488 ATTGGGCAAA
*
1926498 TTTG-AAAACTATG
1 TTTGAAAAACAATG
1926511 TTTGAAAAACAATG
1 TTTGAAAAACAATG
1926525 TTTGAAAA
1 TTTGAAAA
1926533 TTAATATGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.34
Consensus pattern (14 bp):
TTTGAAAAACAATG
Found at i:1927081 original size:21 final size:21
Alignment explanation
Indices: 1927009--1927089 Score: 67
Period size: 21 Copynumber: 3.7 Consensus size: 21
1926999 TACCCTTATA
* *
1927009 GGGGTATCGATACATATTCAAAGG
1 GGGGTATCGATACCTA-GC-AA-G
*
1927033 GGGGTATCGATACACGTTG-AA-
1 GGGGTATCGATAC-C-TAGCAAG
*
1927054 GGAGTATCGATACCTAGCAAG
1 GGGGTATCGATACCTAGCAAG
1927075 GGGGTATCGATACCT
1 GGGGTATCGATACCT
1927090 GGTGCACAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
19 2 0.04
20 3 0.06
21 26 0.55
23 2 0.04
24 13 0.28
26 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.31, T:0.23
Consensus pattern (21 bp):
GGGGTATCGATACCTAGCAAG
Found at i:1932900 original size:74 final size:73
Alignment explanation
Indices: 1932822--1933058 Score: 339
Period size: 74 Copynumber: 3.2 Consensus size: 73
1932812 GTTAAATGAC
* *
1932822 TAGGGGTATCGTTACCTCTAATGGGGTATCGGTACCCATAGGGCATTCTGTTTTTCTCGGTGCCA
1 TAGGGGTATCGGTACC-CTAATGGGGTATCGGTACCCATAGGGCATTCTGTTTTTCTCGGAGCCA
1932887 AAATTTGCA
65 AAATTTGCA
1932896 TAGGGGTATCGGTACCACTAATGGGGTATCGGTACCCATAGGGCATTCTGTTTTTCTCGGAGCCA
1 TAGGGGTATCGGTACC-CTAATGGGGTATCGGTACCCATAGGGCATTCTGTTTTTCTCGGAGCCA
1932961 AAATTTGCA
65 AAATTTGCA
* * * * * * *
1932970 TAGGGTTATCGGTACCCTATTAGGGGTATTGCTACCCATTGGGCATTTTGTTTTTCTCGAAGCCA
1 TAGGGGTATCGGTACCCTAAT-GGGGTATCGGTACCCATAGGGCATTCTGTTTTTCTCGGAGCCA
* * *
1933035 ATATTGGTA
65 AAATTTGCA
1933044 TAGGGGTATCGGTAC
1 TAGGGGTATCGGTAC
1933059 ACCCTATGAA
Statistics
Matches: 148, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
73 4 0.03
74 144 0.97
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (73 bp):
TAGGGGTATCGGTACCCTAATGGGGTATCGGTACCCATAGGGCATTCTGTTTTTCTCGGAGCCAA
AATTTGCA
Found at i:1934282 original size:3 final size:3
Alignment explanation
Indices: 1934268--1934327 Score: 68
Period size: 3 Copynumber: 19.3 Consensus size: 3
1934258 ATCTTGTTAA
*
1934268 TAT TAA TAT TAT TAT TAT TAT TAAT TAT TATT TAGT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TA-T TA-T TAT TAT TAT TAT
*
1934316 TAG T-T TAT TAT T
1 TAT TAT TAT TAT T
1934328 TTTTTTTATA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
2 1 0.02
3 39 0.80
4 9 0.18
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1934314 original size:27 final size:28
Alignment explanation
Indices: 1934276--1934328 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
1934266 AATATTAATA
1934276 TTATTATTATTATTA-ATTATTATTTAG
1 TTATTATTATTATTAGATTATTATTTAG
*
1934303 TTATTATTATTATTAGTTTATTATTT
1 TTATTATTATTATTAGATTATTATTT
1934329 TTTTTTATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (28 bp):
TTATTATTATTATTAGATTATTATTTAG
Found at i:1948050 original size:55 final size:55
Alignment explanation
Indices: 1947397--1948038 Score: 760
Period size: 55 Copynumber: 11.7 Consensus size: 55
1947387 TGATACAGTC
* * * * * * *
1947397 ATTCAAAAACTCATTGTGAATTACGT-AGGTTGCACACATAGTGCCAATACAGTA
1 ATTCATAAACTCATTATGAATTTCTTGGGGTTGCACACATAGTGCCAATACGGAA
* * * * **
1947451 ATTCACAAACTCATTATG-AGTT-ATGTGGGTTGCACACATAGTGCCATTACATAA
1 ATTCATAAACTCATTATGAATTTCTTG-GGGTTGCACACATAGTGCCAATACGGAA
* * * *
1947505 ATTCATAAACTCAATATGAATTTCTTAGGGTTACACACATAGT-CTCAATACGAAA
1 ATTCATAAACTCATTATGAATTTCTTGGGGTTGCACACATAGTGC-CAATACGGAA
* * *
1947560 ATTCATAAACTCAATATGAATTTCTTGGCGTTGCACACATAGT-CTCAATACGAAA
1 ATTCATAAACTCATTATGAATTTCTTGGGGTTGCACACATAGTGC-CAATACGGAA
* * *
1947615 ATTCATAAACTCATTATGAATTT-TGTGGGGTTGCACAAATAGTGTCGATACGGAA
1 ATTCATAAACTCATTATGAATTTCT-TGGGGTTGCACACATAGTGCCAATACGGAA
* *
1947670 ATTCATAAACTCATTATGAATTTCATGGGGTTGCACACATAGTGCCAATATGGAA
1 ATTCATAAACTCATTATGAATTTCTTGGGGTTGCACACATAGTGCCAATACGGAA
* **
1947725 ATTCATAAACTCATTATGAATTTCTTAGGGTTATACACATAGTGCCAATACGGAA
1 ATTCATAAACTCATTATGAATTTCTTGGGGTTGCACACATAGTGCCAATACGGAA
* ** *
1947780 ATTCATAAACTCATTATGAATTTCTTAGGGTTATACACATAGTGTCAATACGGAA
1 ATTCATAAACTCATTATGAATTTCTTGGGGTTGCACACATAGTGCCAATACGGAA
* * * *
1947835 ATTCATAAACTCATTATGAATTTCTTGTGGTTGCACACATAGTACCAATAAGAAA
1 ATTCATAAACTCATTATGAATTTCTTGGGGTTGCACACATAGTGCCAATACGGAA
* * * * * *
1947890 ATTCATACACTCATTATTAATTTCATGGGGTTGCACATATAGTG-C-GTATGGAA
1 ATTCATAAACTCATTATGAATTTCTTGGGGTTGCACACATAGTGCCAATACGGAA
* * *
1947943 ATTCATAAACCCATTATGAATTTCTTGGGGCTGCATACATAGTGCCAATACGGAA
1 ATTCATAAACTCATTATGAATTTCTTGGGGTTGCACACATAGTGCCAATACGGAA
* * *
1947998 TTTTATAAACTCATTATGAATTTCGTGGGGTTGCACACATA
1 ATTCATAAACTCATTATGAATTTCTTGGGGTTGCACACATA
1948039 TTGAAAATAC
Statistics
Matches: 508, Mismatches: 70, Indels: 19
0.85 0.12 0.03
Matches are distributed among these distances:
52 1 0.00
53 44 0.09
54 60 0.12
55 402 0.79
56 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (55 bp):
ATTCATAAACTCATTATGAATTTCTTGGGGTTGCACACATAGTGCCAATACGGAA
Found at i:1953398 original size:55 final size:55
Alignment explanation
Indices: 1953241--1953779 Score: 614
Period size: 55 Copynumber: 9.9 Consensus size: 55
1953231 TGATACGATC
* * * *
1953241 ATTCAAAAACTCATTATGAATTACGTA-GGTTGCACACATAGTGCCAATACGGTA
1 ATTCATAAACTCATTATGAATTTCTTAGGGTTGCACACATAGTGCCAATACGGAA
* * * * * *
1953295 ATTCAAAAACACATTACGAATTACGT-GGGTTGCACACATAGTGCCAATACAGAA
1 ATTCATAAACTCATTATGAATTTCTTAGGGTTGCACACATAGTGCCAATACGGAA
* * **
1953349 ATTTATAAACTCGTTATGAATTTCTTAGGGTTGCACACAATA-TGCCAATACAAAA
1 ATTCATAAACTCATTATGAATTTCTTAGGGTTGCACAC-ATAGTGCCAATACGGAA
* *
1953404 ATTCATAAACTCAATATGAATTT-TGTAGGGTTGCACACATAGTGCCAATATGGAA
1 ATTCATAAACTCATTATGAATTTCT-TAGGGTTGCACACATAGTGCCAATACGGAA
* * ** *
1953459 ATTCATAAACTCAATATGAATTT-TGTGGGGTTTTACACATAGTGCCATTACGGAA
1 ATTCATAAACTCATTATGAATTTCT-TAGGGTTGCACACATAGTGCCAATACGGAA
* * *
1953514 ATTCATAAACTCATTATGAATTTCTTAGGATTACACACATAGTGCCAATACGAAA
1 ATTCATAAACTCATTATGAATTTCTTAGGGTTGCACACATAGTGCCAATACGGAA
* * *
1953569 ATTCATAAACTCTTTATGAATTTCTT-GTGGTTGAACACATAGTGTCAATACGGAA
1 ATTCATAAACTCATTATGAATTTCTTAG-GGTTGCACACATAGTGCCAATACGGAA
* * * * *
1953624 ATTCAT--ACTCATTATGAATTTCATCGGGTTGCATACATAATGCCAATACGAAA
1 ATTCATAAACTCATTATGAATTTCTTAGGGTTGCACACATAGTGCCAATACGGAA
* * **
1953677 ATTCATAAACTCATTATGAATTTCTTGGGGTT-C-CACACAGTGCCAATTTGGAA
1 ATTCATAAACTCATTATGAATTTCTTAGGGTTGCACACATAGTGCCAATACGGAA
* *
1953730 ATTCATAAACTCATTATGAATTT-TGTGGGGTTGCACACATAGTGTCAATA
1 ATTCATAAACTCATTATGAATTTCT-TAGGGTTGCACACATAGTGCCAATA
1953780 TGGTAATTGC
Statistics
Matches: 418, Mismatches: 54, Indels: 25
0.84 0.11 0.05
Matches are distributed among these distances:
52 1 0.00
53 88 0.21
54 76 0.18
55 249 0.60
56 4 0.01
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32
Consensus pattern (55 bp):
ATTCATAAACTCATTATGAATTTCTTAGGGTTGCACACATAGTGCCAATACGGAA
Found at i:1957929 original size:6 final size:6
Alignment explanation
Indices: 1957918--1957958 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
1957908 AGTCCTTTTA
*
1957918 TTGCAT TTGCAT TTGCAT ATGCAT TT---T TTGCAT TTGCAT TT
1 TTGCAT TTGCAT TTGCAT TTGCAT TTGCAT TTGCAT TTGCAT TT
1957959 ACCTTTACAC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
3 3 0.10
6 27 0.90
ACGTcount: A:0.17, C:0.15, G:0.15, T:0.54
Consensus pattern (6 bp):
TTGCAT
Found at i:1957949 original size:15 final size:15
Alignment explanation
Indices: 1957929--1957958 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1957919 TGCATTTGCA
1957929 TTTGCATATGCATTT
1 TTTGCATATGCATTT
*
1957944 TTTGCATTTGCATTT
1 TTTGCATATGCATTT
1957959 ACCTTTACAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.13, G:0.13, T:0.57
Consensus pattern (15 bp):
TTTGCATATGCATTT
Found at i:1963759 original size:52 final size:52
Alignment explanation
Indices: 1963693--1963887 Score: 200
Period size: 52 Copynumber: 3.7 Consensus size: 52
1963683 ACTTTAAAAA
*
1963693 AGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATATTTTTAAATGAGTTTTT
1 AGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATATTTTTAAATGAGTTTTT
* *
1963745 AGAAACTAAGCCTAATTTTCT-GGGGTTTCTTGATGATTATTTCCAAA-CAATTTTT
1 AGAAACTAAGCCTAATTTT-TAGGGGTTTCTTGAT-ATT-TTT--AAATGAGTTTTT
* * * *
1963800 AAAAGAAGCTAAGCCTAA-TTTTAGGGGCTTT-TTAATGTTTTCAAATGAGTTTTT
1 ---AGAAACTAAGCCTAATTTTTAGGGG-TTTCTTGATATTTTTAAATGAGTTTTT
* *
1963854 AGAAACTAAGCCTTATTTTCAGGGGTTTCTTGAT
1 AGAAACTAAGCCTAATTTTTAGGGGTTTCTTGAT
1963888 GATTATTTCC
Statistics
Matches: 117, Mismatches: 13, Indels: 26
0.75 0.08 0.17
Matches are distributed among these distances:
51 16 0.14
52 43 0.37
53 7 0.06
54 9 0.08
55 8 0.07
56 6 0.05
57 11 0.09
58 17 0.15
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.42
Consensus pattern (52 bp):
AGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATATTTTTAAATGAGTTTTT
Found at i:1963854 original size:109 final size:110
Alignment explanation
Indices: 1963690--1963944 Score: 354
Period size: 109 Copynumber: 2.3 Consensus size: 110
1963680 TGAACTTTAA
* *
1963690 AAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATATTTTTAAATGAGTTTTTAGAAACTAAG
1 AAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTAATATTTTCAAATGAGTTTTTAGAAACTAAG
*
1963755 CCTAATTTTCTGGGGTTTCTTGATGATTATTTCCAAACAATTTTT
66 CCTAATTTTCAGGGGTTTCTTGATGATTATTTCCAAACAATTTTT
*
1963800 AAAAGAAGCTAAGCCTAA-TTTTAGGGGCTTT-TTAATGTTTTCAAATGAGTTTTTAGAAACTAA
1 AAAAGAAGCTAAGCCTAATTTTTAGGGG-TTTCTTAATATTTTCAAATGAGTTTTTAGAAACTAA
* * ***
1963863 GCCTTATTTTCAGGGGTTTCTTGATGATTATTTCCACAAAAAAAAACTT
65 GCCTAATTTTCAGGGGTTTCTTGATGATTATTT-C-C-AAACAATTTTT
* *
1963912 -AAAGAAGCTGAGTCTAATTTTTAGGGGTTTCTT
1 AAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTT
1963945 GATGATAACT
Statistics
Matches: 128, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
109 69 0.54
110 22 0.17
111 19 0.15
112 18 0.14
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.40
Consensus pattern (110 bp):
AAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTAATATTTTCAAATGAGTTTTTAGAAACTAAG
CCTAATTTTCAGGGGTTTCTTGATGATTATTTCCAAACAATTTTT
Found at i:1964075 original size:42 final size:41
Alignment explanation
Indices: 1964019--1964130 Score: 109
Period size: 41 Copynumber: 2.7 Consensus size: 41
1964009 CAGTATTCCG
*
1964019 GGCCATC-AGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCA
1 GGCCATCTA-TAAGTCTTTCGAGCATGATG-ATAAATCCTTCA
* * * * * *
1964061 GGTCATCTATAAGTCTTTAGAGTAAGATGATAAGTCTTTCA
1 GGCCATCTATAAGTCTTTCGAGCATGATGATAAATCCTTCA
* * *
1964102 GGCCATCTATAAGACCTTCGGGCATGATG
1 GGCCATCTATAAGTCTTTCGAGCATGATG
1964131 TTTTCAACAT
Statistics
Matches: 55, Mismatches: 14, Indels: 3
0.76 0.19 0.04
Matches are distributed among these distances:
41 31 0.56
42 23 0.42
43 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (41 bp):
GGCCATCTATAAGTCTTTCGAGCATGATGATAAATCCTTCA
Found at i:1964238 original size:59 final size:59
Alignment explanation
Indices: 1964136--1964263 Score: 202
Period size: 59 Copynumber: 2.2 Consensus size: 59
1964126 TGATGTTTTC
* * *
1964136 AACATTTCCTTTGCTCAATTCACAACACTCCGAATTAGTAACGCCCCACCAGAGGGGTT
1 AACATTTCCTTTGCTCAATTCACAACACTCAGAATCAGCAACGCCCCACCAGAGGGGTT
* * *
1964195 AACATTTTCTTTGCTCAATTCACAACACTTAGAATCAGCAACGCCCCACCATAGGGGTT
1 AACATTTCCTTTGCTCAATTCACAACACTCAGAATCAGCAACGCCCCACCAGAGGGGTT
1964254 AACATTTCCT
1 AACATTTCCT
1964264 AGTGCTCGAT
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.30, C:0.30, G:0.13, T:0.27
Consensus pattern (59 bp):
AACATTTCCTTTGCTCAATTCACAACACTCAGAATCAGCAACGCCCCACCAGAGGGGTT
Found at i:1968485 original size:125 final size:126
Alignment explanation
Indices: 1968296--1968540 Score: 307
Period size: 125 Copynumber: 2.0 Consensus size: 126
1968286 AATCGAGTTT
* * ** * *
1968296 GATTCAAATCTTCCCTAAAGAACTGTGGAGGGAATCAACATTTCCAGATCTGATCTTCCATGAAG
1 GATTCAAATCTTCCCTAAAAAACAGTGGAACGAATCAACATTTCCAGATCTAATCTACCATGAAG
* * * *
1968361 AGTAGC-GAAACATATCCTCTTTTTTCAGATTTGATCTTCCCTGAGGAGCAATGGATGCCTC
66 AGCAGCAG-AACAGATCCTCATTTTCCAGATTTGATCTTCCCTGAGGAGCAATGGATGCCTC
* * *
1968422 GATTC-AATCTTCCC-AGAAAAACAGTGGAACGAATCAACTTTTCCAGATTTAATCTACCTTGAA
1 GATTCAAATCTTCCCTA-AAAAACAGTGGAACGAATCAACATTTCCAGATCTAATCTACCATGAA
* * *
1968485 GAGCAGCAGAGCAGATCCTCATTTTCCATATTTGATCTTCCCTGAGGAGCAGTGGA
65 GAGCAGCAGAACAGATCCTCATTTTCCAGATTTGATCTTCCCTGAGGAGCAATGGA
1968541 ACAAGTATGC
Statistics
Matches: 101, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
124 1 0.01
125 94 0.93
126 6 0.06
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (126 bp):
GATTCAAATCTTCCCTAAAAAACAGTGGAACGAATCAACATTTCCAGATCTAATCTACCATGAAG
AGCAGCAGAACAGATCCTCATTTTCCAGATTTGATCTTCCCTGAGGAGCAATGGATGCCTC
Found at i:1968749 original size:3 final size:3
Alignment explanation
Indices: 1968741--1968800 Score: 70
Period size: 3 Copynumber: 19.7 Consensus size: 3
1968731 ATCGCTAATT
1968741 TTA TTA TTAA TTA TTA TTTA GTTA TTA TTA TTA TTA TTA TTA TT- TTA
1 TTA TTA TT-A TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
1968788 TTT TTA TT- TTA TT
1 TTA TTA TTA TTA TT
1968801 TGTAGTCTAA
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
2 4 0.08
3 37 0.74
4 9 0.18
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:1968770 original size:17 final size:16
Alignment explanation
Indices: 1968740--1968800 Score: 76
Period size: 17 Copynumber: 3.9 Consensus size: 16
1968730 AATCGCTAAT
1968740 TTTATTATTAATTATTA
1 TTTATTATT-ATTATTA
1968757 TTTAGTTATTATTATTA
1 TTTA-TTATTATTATTA
1968774 -TTATTATTATT-TTA
1 TTTATTATTATTATTA
1968788 TTT-TTATT-TTATT
1 TTTATTATTATTATT
1968801 TGTAGTCTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
13 2 0.05
14 10 0.24
15 10 0.24
16 3 0.07
17 11 0.27
18 5 0.12
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (16 bp):
TTTATTATTATTATTA
Found at i:1968788 original size:11 final size:11
Alignment explanation
Indices: 1968738--1968800 Score: 67
Period size: 11 Copynumber: 5.7 Consensus size: 11
1968728 AAAATCGCTA
1968738 ATTTTATTATT
1 ATTTTATTATT
*
1968749 A-ATTATTATT
1 ATTTTATTATT
*
1968759 -TAGTTATTATT
1 AT-TTTATTATT
1968770 ATTATTATTATT
1 ATT-TTATTATT
*
1968782 ATTTTATTTTT
1 ATTTTATTATT
1968793 ATTTTATT
1 ATTTTATT
1968801 TGTAGTCTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
10 8 0.18
11 24 0.55
12 12 0.27
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.70
Consensus pattern (11 bp):
ATTTTATTATT
Found at i:1972994 original size:2 final size:2
Alignment explanation
Indices: 1972983--1973032 Score: 72
Period size: 2 Copynumber: 27.0 Consensus size: 2
1972973 ATAAGCCAAC
1972983 TA TA -A TA TA TA T- TA TA TA TA TA TA TA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1973022 TA TA TA T- TA TA
1 TA TA TA TA TA TA
1973033 GTGTAAAATT
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
1 4 0.09
2 40 0.91
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1973007 original size:15 final size:15
Alignment explanation
Indices: 1972987--1973032 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
1972977 GCCAACTATA
1972987 ATATATAT-TATA-T
1 ATATATATATATATT
*
1973000 ATATATATATATATA
1 ATATATATATATATT
1973015 ATATATATATATATT
1 ATATATATATATATT
1973030 ATA
1 ATA
1973033 GTGTAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 8 0.28
14 4 0.14
15 17 0.59
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATATATATATATT
Found at i:1973011 original size:19 final size:19
Alignment explanation
Indices: 1972983--1973032 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
1972973 ATAAGCCAAC
*
1972983 TATA-ATATATATTATATA
1 TATATATATATATAATATA
1973001 TATATATATATATAATATA
1 TATATATATATATAATATA
1973020 TATATATAT-TATA
1 TATATATATATATA
1973033 GTGTAAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 8 0.27
19 22 0.73
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TATATATATATATAATATA
Found at i:1973241 original size:2 final size:2
Alignment explanation
Indices: 1973234--1973261 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1973224 ATCCTAACTC
1973234 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
1973262 GTGTGTGTGT
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:1974173 original size:25 final size:26
Alignment explanation
Indices: 1974126--1974182 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
1974116 CAAACTTGAC
*
1974126 CCGACCTGAAAATTATATATCCTCCA
1 CCGACCCGAAAATTATATATCCTCCA
1974152 CCGACCCGAAAA-TATATATCCTCCA
1 CCGACCCGAAAATTATATATCCTCCA
1974177 CTCGAC
1 C-CGAC
1974183 TCTGACCCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 14 0.48
26 15 0.52
ACGTcount: A:0.33, C:0.35, G:0.09, T:0.23
Consensus pattern (26 bp):
CCGACCCGAAAATTATATATCCTCCA
Found at i:1977601 original size:109 final size:109
Alignment explanation
Indices: 1977482--1977686 Score: 315
Period size: 109 Copynumber: 1.9 Consensus size: 109
1977472 GTAAGAGGAC
1977482 TAAAAAGAAAATATA-CCAATAAATATATAACATGCATG-AAAAGGGGTAAATAACAAGTTTGGT
1 TAAAAAGAAAATA-ACCCAATAAATATATAACATGCATGAAAAAGGGG-AAATAACAAGTTTGGT
*
1977545 CCTCACAGGTGACCAAAGTGAAAAAATGCGCTAAACTTAGAGGGAT
64 CCTCACAGGTGACCAAAGTGAAAAAACGCGCTAAACTTAGAGGGAT
* * * *
1977591 TAAACAGAAAATAACCCAATAAATATATAACATGTATGAAAAAGGGGAAATAACGATTTTGGTCC
1 TAAAAAGAAAATAACCCAATAAATATATAACATGCATGAAAAAGGGGAAATAACAAGTTTGGTCC
* *
1977656 TCTCAGGTGACCAAAGTGCAAAAACGCGCTA
66 TCACAGGTGACCAAAGTGAAAAAACGCGCTA
1977687 TACCTAAGAG
Statistics
Matches: 87, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
108 1 0.01
109 78 0.90
110 8 0.09
ACGTcount: A:0.46, C:0.15, G:0.19, T:0.21
Consensus pattern (109 bp):
TAAAAAGAAAATAACCCAATAAATATATAACATGCATGAAAAAGGGGAAATAACAAGTTTGGTCC
TCACAGGTGACCAAAGTGAAAAAACGCGCTAAACTTAGAGGGAT
Found at i:1977717 original size:109 final size:108
Alignment explanation
Indices: 1977468--1977718 Score: 301
Period size: 109 Copynumber: 2.3 Consensus size: 108
1977458 AAAACATGCT
* * * *
1977468 TAAAGTAAGAGGACTAAAAAGAAAATATA-CCAATAAATATATAACATGCATGAAAAGGGGTAAA
1 TAAACTAAGAGGACT-TAAAGAGAATTTACCCAATAAATATATAACATGCATGAAAAGGGGTAAA
*
1977532 TAACAAGTTTGGTCCTCACAGGTGACCAAAGTGAAAAAATGCGC
65 TAACAAGTTTGGTCCTCACAGGTGACCAAAGTGAAAAAACGCGC
* * * * *
1977576 TAAACTTAGAGGGA-TTAAACAGAAAATAACCCAATAAATATATAACATGTATGAAAAAGGGG-A
1 TAAACTAAGA-GGACTTAAAGAG-AATTTACCCAATAAATATATAACATGCATG-AAAAGGGGTA
* * * *
1977639 AATAACGATTTTGGTCCTCTCAGGTGACCAAAGTGCAAAAACGCGC
63 AATAACAAGTTTGGTCCTCACAGGTGACCAAAGTGAAAAAACGCGC
*
1977685 TATACCTAAGAGGACTTAAAGAGAATTTACCCAA
1 TA-AACTAAGAGGACTTAAAGAGAATTTACCCAA
1977719 AGCTTTATGT
Statistics
Matches: 118, Mismatches: 19, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
107 4 0.03
108 12 0.10
109 81 0.69
110 21 0.18
ACGTcount: A:0.46, C:0.15, G:0.19, T:0.21
Consensus pattern (108 bp):
TAAACTAAGAGGACTTAAAGAGAATTTACCCAATAAATATATAACATGCATGAAAAGGGGTAAAT
AACAAGTTTGGTCCTCACAGGTGACCAAAGTGAAAAAACGCGC
Found at i:1979787 original size:24 final size:24
Alignment explanation
Indices: 1979755--1979808 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1979745 CACCACTGCT
*
1979755 CATATAATTTTCACCGAAGTGCCA
1 CATAGAATTTTCACCGAAGTGCCA
*
1979779 CATAGAATTTTCACTGAAGTGCCA
1 CATAGAATTTTCACCGAAGTGCCA
1979803 CATAGA
1 CATAGA
1979809 TATGTCCCGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (24 bp):
CATAGAATTTTCACCGAAGTGCCA
Found at i:1979842 original size:24 final size:24
Alignment explanation
Indices: 1979811--1979881 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
1979801 CACATAGATA
*
1979811 TGTCCCGAAGGACCGCGTAGAATT
1 TGTCCCGAAGGACCACGTAGAATT
1979835 TGTCCCGAAGGACCACGTAGAAATT
1 TGTCCCGAAGGACCACGTAG-AATT
* * *
1979860 TGTCTCGAAGCACCTCGTAGAA
1 TGTCCCGAAGGACCACGTAGAA
1979882 CCCTCGACTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 21 0.50
25 21 0.50
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.21
Consensus pattern (24 bp):
TGTCCCGAAGGACCACGTAGAATT
Found at i:1979868 original size:25 final size:25
Alignment explanation
Indices: 1979811--1979881 Score: 99
Period size: 25 Copynumber: 2.9 Consensus size: 25
1979801 CACATAGATA
*
1979811 TGTCCCGAAGGACCGCGTAG-AATT
1 TGTCCCGAAGGACCACGTAGAAATT
1979835 TGTCCCGAAGGACCACGTAGAAATT
1 TGTCCCGAAGGACCACGTAGAAATT
* * *
1979860 TGTCTCGAAGCACCTCGTAGAA
1 TGTCCCGAAGGACCACGTAGAA
1979882 CCCTCGACTT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
24 19 0.45
25 23 0.55
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.21
Consensus pattern (25 bp):
TGTCCCGAAGGACCACGTAGAAATT
Found at i:1980030 original size:15 final size:15
Alignment explanation
Indices: 1980012--1980074 Score: 81
Period size: 15 Copynumber: 4.1 Consensus size: 15
1980002 CACATAGGGA
1980012 ATTTTCACGTAGAAC
1 ATTTTCACGTAGAAC
* *
1980027 ATTTTTCACTTAGCAC
1 A-TTTTCACGTAGAAC
*
1980043 ATTTTCACATAGAAC
1 ATTTTCACGTAGAAC
*
1980058 ATTTTCATGTAGAAC
1 ATTTTCACGTAGAAC
1980073 AT
1 AT
1980075 ACTCACATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
15 28 0.68
16 13 0.32
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (15 bp):
ATTTTCACGTAGAAC
Found at i:1980081 original size:30 final size:30
Alignment explanation
Indices: 1980016--1980092 Score: 75
Period size: 30 Copynumber: 2.5 Consensus size: 30
1980006 TAGGGAATTT
* * **
1980016 TCACGTAGAACATTTTTCACTTAGCACATTT
1 TCACATAGAACA-TTTTCACTTAGAACATAC
1980047 TCACATAGAACATTTTCA-TGTAGAACATAC
1 TCACATAGAACATTTTCACT-TAGAACATAC
*
1980077 TCACATATAAACATTT
1 TCACATA-GAACATTT
1980093 CCGCATACCA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
29 1 0.03
30 20 0.51
31 18 0.46
ACGTcount: A:0.36, C:0.21, G:0.08, T:0.35
Consensus pattern (30 bp):
TCACATAGAACATTTTCACTTAGAACATAC
Found at i:1986761 original size:24 final size:24
Alignment explanation
Indices: 1986729--1986782 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1986719 CACCACTGCT
*
1986729 CATATAATTTGCACCGAAGTGCCA
1 CATAGAATTTGCACCGAAGTGCCA
*
1986753 CGTAGAATTTGCACCGAAGTGCCA
1 CATAGAATTTGCACCGAAGTGCCA
1986777 CATAGA
1 CATAGA
1986783 TATGTCCCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.22
Consensus pattern (24 bp):
CATAGAATTTGCACCGAAGTGCCA
Found at i:1987008 original size:15 final size:15
Alignment explanation
Indices: 1986990--1987047 Score: 71
Period size: 15 Copynumber: 3.8 Consensus size: 15
1986980 TTTACTTAGG
1986990 ACATTTTCACATAAA
1 ACATTTTCACATAAA
* *
1987005 ACATTTTCATATAGA
1 ACATTTTCACATAAA
* *
1987020 ACATATTAACATATAA
1 ACATTTTCACATA-AA
1987036 ACATTTTCACAT
1 ACATTTTCACAT
1987048 GCCGATAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
15 23 0.68
16 11 0.32
ACGTcount: A:0.45, C:0.17, G:0.02, T:0.36
Consensus pattern (15 bp):
ACATTTTCACATAAA
Found at i:1989451 original size:117 final size:118
Alignment explanation
Indices: 1989273--1989505 Score: 342
Period size: 117 Copynumber: 2.0 Consensus size: 118
1989263 TGAGCTAAGT
* * *
1989273 TTGAACAAGTTCTTCTCATTATAAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCATCTCATTATAAACTTCCTCTCCCTCATCGAATGAGTTCTTCTCATTATGAAC
* * * * *
1989338 TC-TCTACCGAAAATATTGATCCACCTCCTTCTGTGATGGAATCGAACAAATG
66 CCTTCCACCGAAAATATTGATCCACCTCATTATGTGATAGAATCGAACAAATG
* **
1989390 TTGAACAAGTTCATCTCATTATGAACTTCCTCTCCCTTGTCGAATGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCATCTCATTATAAACTTCCTCTCCCTCATCGAATGAGTTCTTCTCATTATGAAC
**
1989455 CCTTCCATTGAAAATATTGATCCACCTCATTATGTGATAGAATCGAACAAA
66 CCTTCCACCGAAAATATTGATCCACCTCATTATGTGATAGAATCGAACAAA
1989506 GTGATGAGGC
Statistics
Matches: 102, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
117 60 0.59
118 42 0.41
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (118 bp):
TTGAACAAGTTCATCTCATTATAAACTTCCTCTCCCTCATCGAATGAGTTCTTCTCATTATGAAC
CCTTCCACCGAAAATATTGATCCACCTCATTATGTGATAGAATCGAACAAATG
Found at i:1989654 original size:321 final size:323
Alignment explanation
Indices: 1989067--1989716 Score: 947
Period size: 321 Copynumber: 2.0 Consensus size: 323
1989057 TTAAGCTAAG
* *
1989067 GTTGAACAAGTTCTTCTCATTATAAACTTCTTCTCCCTCTCCGAACGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCATCTCATTATAAACTTCCTCTCCCTCTCCGAACGAGTTCTTCTCATTATGAA
* * * * * * *
1989132 CTCTTCCCTGGAAATGTCGATCCACCTCCTTCTGTGATGTAATCAAACCAAGGTTGATGATGCTG
66 CCCTTCCCTGAAAATATCGATCCACCTCATTATGTGATGTAATCAAACCAAAGTTGATGAGGCTG
*
1989197 ATCCAACTCCATATGTGATGGATGAGCCAAGTATTGGTGTTGTTTCAACTCCTTATATGATGGAA
131 ATCCAACTCCATATGTGATGGATGAGCCAAGTATTGGTGTTGTTCCAACTCCTTATATGATGGAA
* *
1989262 ATGAGCTAAGTTTGAACAAGTTCTTCTCATTATAAACTTCTTCTCCCTCATCGGATGAGTTCTTC
196 AAGAGCTAAGCTTGAACAAGTTCTTCTCATTATAAACTTCTTCTCCCTCATCGGATGAGTTCTTC
* *
1989327 TCATTATGAACTCTCTACC-GA-AAATATTGATCCACCTCCTTCTGTGATGGAATCGAACAAA-T
261 TCATTATGAACTC-C-ACCAGAGAAATATTAATCCACATCCTTCTGTGATGGAATCGAACAAAGT
* * *
1989389 GTTGAACAAGTTCATCTCATTATGAACTTCCTCTCCCT-TGTCGAATGAGTTCTTCTCATTATGA
1 GTTGAACAAGTTCATCTCATTATAAACTTCCTCTCCCTCT-CCGAACGAGTTCTTCTCATTATGA
* * *
1989453 ACCCTTCCATTGAAAATATTGATCCACCTCATTATGTGATAG-AATCGAA-CAAAG-TGATGAGG
65 ACCCTTCC-CTGAAAATATCGATCCACCTCATTATGTGAT-GTAATCAAACCAAAGTTGATGAGG
*
1989515 CTGATCCAACTCCATATGTGATGGATGAGCCAAGTATTGGTGTTGTTCCAACTTCTTATGA-GAT
128 CTGATCCAACTCCATATGTGATGGATGAGCCAAGTATTGGTGTTGTTCCAACTCCTTAT-ATGAT
*
1989579 GGAAAAGAGCTAAGCTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTT
192 GGAAAAGAGCTAAGCTTGAACAAGTTCTTCTCATTATAAACTTCTTCTCCCTCATCGGATGAGTT
* * * *
1989644 CTTGTCATTATGAACTCCCCCATTAGAAATGTTAATCCACATCCTTCTGTGATGGAATCGAACAA
257 CTTCTCATTATGAACTCCACCA-GAGAAATATTAATCCACATCCTTCTGTGATGGAATCGAACAA
1989709 AGT
321 AGT
1989712 GTTGA
1 GTTGA
1989717 TATTGATCCA
Statistics
Matches: 294, Mismatches: 26, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
319 2 0.01
320 1 0.00
321 147 0.50
322 106 0.36
323 37 0.13
324 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (323 bp):
GTTGAACAAGTTCATCTCATTATAAACTTCCTCTCCCTCTCCGAACGAGTTCTTCTCATTATGAA
CCCTTCCCTGAAAATATCGATCCACCTCATTATGTGATGTAATCAAACCAAAGTTGATGAGGCTG
ATCCAACTCCATATGTGATGGATGAGCCAAGTATTGGTGTTGTTCCAACTCCTTATATGATGGAA
AAGAGCTAAGCTTGAACAAGTTCTTCTCATTATAAACTTCTTCTCCCTCATCGGATGAGTTCTTC
TCATTATGAACTCCACCAGAGAAATATTAATCCACATCCTTCTGTGATGGAATCGAACAAAGT
Found at i:1991517 original size:54 final size:54
Alignment explanation
Indices: 1991459--1991564 Score: 151
Period size: 54 Copynumber: 2.0 Consensus size: 54
1991449 AGTCTTAACC
*
1991459 TCTTT-AAAATATCATTTGAAAACATCAAGAAACCCATGAAAATCAAGCTTAGCT
1 TCTTTAAAAAT-TCATTAGAAAACATCAAGAAACCCATGAAAATCAAGCTTAGCT
* * * *
1991513 TCTTTAAAAATTCATTAGAAAACTTTAAGAAACCCCTGAAAATCAGGCTTAG
1 TCTTTAAAAATTCATTAGAAAACATCAAGAAACCCATGAAAATCAAGCTTAG
1991565 TTTAAAAGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
54 41 0.89
55 5 0.11
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.28
Consensus pattern (54 bp):
TCTTTAAAAATTCATTAGAAAACATCAAGAAACCCATGAAAATCAAGCTTAGCT
Found at i:1993706 original size:27 final size:27
Alignment explanation
Indices: 1993670--1993727 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
1993660 TTTTTTTCCC
* * * *
1993670 TTTTGTTTTCTTTTCTCTCTCTTTTTT
1 TTTTGCTTTCTTTTATCTCTATTATTT
1993697 TTTTGCTTTCTTTTATCTCTATTATTT
1 TTTTGCTTTCTTTTATCTCTATTATTT
1993724 TTTT
1 TTTT
1993728 ATCTCTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.05, C:0.16, G:0.03, T:0.76
Consensus pattern (27 bp):
TTTTGCTTTCTTTTATCTCTATTATTT
Found at i:1993744 original size:17 final size:18
Alignment explanation
Indices: 1993703--1993744 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
1993693 TTTTTTTTGC
1993703 TTTCTTTTATCTCTATTA
1 TTTCTTTTATCTCTATTA
*
1993721 TTT-TTTTATCTCT-TTT
1 TTTCTTTTATCTCTATTA
1993737 TTTCTTTT
1 TTTCTTTT
1993745 TGTTATATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 5 0.23
17 14 0.64
18 3 0.14
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTCTTTTATCTCTATTA
Found at i:1993750 original size:21 final size:19
Alignment explanation
Indices: 1993721--1993765 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
1993711 ATCTCTATTA
* *
1993721 TTTTTTTATCTCTTTTTTT
1 TTTTTTTATATCTTTTCTT
1993740 CTTTTTGTTATATCTTTTCTT
1 -TTTTT-TTATATCTTTTCTT
1993761 TTTTT
1 TTTTT
1993766 CTCTTTGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.07, C:0.11, G:0.02, T:0.80
Consensus pattern (19 bp):
TTTTTTTATATCTTTTCTT
Found at i:1997684 original size:110 final size:110
Alignment explanation
Indices: 1997476--1997684 Score: 289
Period size: 110 Copynumber: 1.9 Consensus size: 110
1997466 AGCGAATATA
* *
1997476 CCAATAAATATATAACATGCATGAAAAAGGGGTAAATAACAAGTTTGGTCCTCATAGGTGACCAA
1 CCAATAAATATATAACATGCATCAAAAAGGGGTAAATAACAAGTTTGGTCCTCATAAGTGACCAA
* *
1997541 AGTGCAAAAACGTGCTAAATATAGAGGGATTAAACATAAAATAAC
66 AGTGCAAAAACGCGCTAAACATAGAGGGATTAAACATAAAATAAC
** * *
1997586 CCAATAAATATATAACATGTGTCAAAAAGGAGG-AAATAACAATTTTGGTCCTC-TCAAGTGACT
1 CCAATAAATATATAACATGCATCAAAAAGG-GGTAAATAACAAGTTTGGTCCTCAT-AAGTGACC
*
1997649 AAAGTGCAAAAACGCGCTAAACCTAG-GGGACTTAAA
64 AAAGTGCAAAAACGCGCTAAACATAGAGGGA-TTAAA
1997685 GAGAATTTAC
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
109 5 0.06
110 80 0.92
111 2 0.02
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.22
Consensus pattern (110 bp):
CCAATAAATATATAACATGCATCAAAAAGGGGTAAATAACAAGTTTGGTCCTCATAAGTGACCAA
AGTGCAAAAACGCGCTAAACATAGAGGGATTAAACATAAAATAAC
Found at i:1998367 original size:16 final size:18
Alignment explanation
Indices: 1998347--1998380 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1998337 TCGATTTTTC
*
1998347 TTTTTTT-TTTTTTTGTG
1 TTTTTTTCTTTATTTGTG
1998364 TTTTTTTCTTTATTTGT
1 TTTTTTTCTTTATTTGT
1998381 CGTTGTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.03, C:0.03, G:0.09, T:0.85
Consensus pattern (18 bp):
TTTTTTTCTTTATTTGTG
Found at i:1998731 original size:3 final size:3
Alignment explanation
Indices: 1998723--1998783 Score: 77
Period size: 3 Copynumber: 19.7 Consensus size: 3
1998713 GTAATAAATA
* * *
1998723 AAT AAT AAT AAT AGT AAT ATT TAT AAT AAT AAT AAT AAAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
1998769 AAT ATAT AAT AAT AA
1 AAT A-AT AAT AAT AA
1998784 ATATATATAT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
3 44 0.88
4 6 0.12
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:1998765 original size:13 final size:13
Alignment explanation
Indices: 1998714--1998783 Score: 81
Period size: 13 Copynumber: 5.5 Consensus size: 13
1998704 AATGGGTTTG
1998714 TAATAAATAAATAA
1 TAAT-AATAAATAA
*
1998728 TAATAAT-AGTAA
1 TAATAATAAATAA
* *
1998740 TATTTAT-AATAA
1 TAATAATAAATAA
1998752 TAATAATAAATAA
1 TAATAATAAATAA
*
1998765 TAATAATATATAA
1 TAATAATAAATAA
1998778 TAATAA
1 TAATAA
1998784 ATATATATAT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
12 18 0.38
13 26 0.54
14 4 0.08
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (13 bp):
TAATAATAAATAA
Found at i:1998789 original size:16 final size:16
Alignment explanation
Indices: 1998714--1998792 Score: 76
Period size: 16 Copynumber: 4.9 Consensus size: 16
1998704 AATGGGTTTG
*
1998714 TAATAAATAAATAATAA
1 TAATAAATATAT-ATAA
*
1998731 TAATAGTAATATTTATAA
1 TAATA--AATATATATAA
1998749 TAAT-AATA-ATA-AA
1 TAATAAATATATATAA
1998762 TAAT-AATAATATATAA
1 TAATAAAT-ATATATAA
1998778 TAATAAATATATATA
1 TAATAAATATATATA
1998793 TGAGAGTTGA
Statistics
Matches: 53, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
13 9 0.17
14 3 0.06
15 7 0.13
16 13 0.25
17 8 0.15
18 8 0.15
19 5 0.09
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (16 bp):
TAATAAATATATATAA
Found at i:2001695 original size:21 final size:21
Alignment explanation
Indices: 2001669--2001717 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
2001659 CTATTAAAAG
*
2001669 TTTTAATTATTTA-TATTTATT
1 TTTTAATTAATTATTATTTA-T
2001690 TTTTAA-TAATTATTATTTAT
1 TTTTAATTAATTATTATTTAT
*
2001710 ATTTAATT
1 TTTTAATT
2001718 TTAAATGTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTAATTAATTATTATTTAT
Found at i:2015083 original size:5 final size:5
Alignment explanation
Indices: 2015066--2015105 Score: 64
Period size: 5 Copynumber: 8.2 Consensus size: 5
2015056 TTTCATCGCT
*
2015066 TTTTA TTTT- TTTTA TTTTA TTTTA TTGTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
2015106 CTTGGTGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:2020147 original size:36 final size:37
Alignment explanation
Indices: 2020107--2020191 Score: 109
Period size: 36 Copynumber: 2.3 Consensus size: 37
2020097 AGTTTTCTTA
*
2020107 AAAACAAATTTTGTCTCGCTTGAGACAATTTCTATC-
1 AAAACAAATTTTGTCTCACTTGAGACAATTTCTATCG
* * * *
2020143 AAAACAATTTTTTTCTCACTTGAGACAGTTTCTCTCG
1 AAAACAAATTTTGTCTCACTTGAGACAATTTCTATCG
2020180 AAATACAAATTT
1 AAA-ACAAATTT
2020192 CAAAGTTGTT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
36 31 0.76
37 3 0.07
38 7 0.17
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (37 bp):
AAAACAAATTTTGTCTCACTTGAGACAATTTCTATCG
Found at i:2020711 original size:131 final size:131
Alignment explanation
Indices: 2020474--2020813 Score: 378
Period size: 131 Copynumber: 2.6 Consensus size: 131
2020464 CTTGAAACAA
* * * * *
2020474 ATCCCTAAAGATGGCCTACCGTTCTCATCACGTAGGAACCATGTCATCCATCGACTAGATCTCCT
1 ATCCCTAAAGATGGCATACCGTCCTCATCACGTAGGAACCATGTCATCCATAGACCAGACCTCCT
* * * ***
2020539 CATCACGTAGGTGCCATGTCAACCTTAGATAACCTGTCGTCCTCATCATGTAGGAACCATGTTAT
66 CATCACGTAAGAGCCATGTCAACCCTAGATAACCAACCGTCCTCATCATGTAGGAACCATGTTAT
2020604 C
131 C
* * * *
2020605 ATCCCTAAAGATGGCATATCGTCCTCATCACGTAGGAACCTTGTCATCCCTAGACCATACCTCCT
1 ATCCCTAAAGATGGCATACCGTCCTCATCACGTAGGAACCATGTCATCCATAGACCAGACCTCCT
* * *
2020670 CATCACGTAAGAGTCGTGTCAACCCTAGATAACCAACCGTCCTCATCGTGTAGGAACCATGTTAT
66 CATCACGTAAGAGCCATGTCAACCCTAGATAACCAACCGTCCTCATCATGTAGGAACCATGTTAT
2020735 C
131 C
* * ** * ** *
2020736 AACCTTCCTAAAGATGGC-TAGCCATCCTCATCGTGTAGG-AGCAGTGTCATCCACCGACCAGAT
1 -A--TCCCTAAAGATGGCATA-CCGTCCTCATCACGTAGGAACCA-TGTCATCCATAGACCAGAC
*
2020799 CTCCCCATCACGTAA
61 CTCCTCATCACGTAA
2020814 CAATTGTGTC
Statistics
Matches: 173, Mismatches: 31, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
131 113 0.65
132 1 0.01
133 4 0.02
134 55 0.32
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (131 bp):
ATCCCTAAAGATGGCATACCGTCCTCATCACGTAGGAACCATGTCATCCATAGACCAGACCTCCT
CATCACGTAAGAGCCATGTCAACCCTAGATAACCAACCGTCCTCATCATGTAGGAACCATGTTAT
C
Found at i:2020850 original size:134 final size:131
Alignment explanation
Indices: 2020474--2020851 Score: 316
Period size: 131 Copynumber: 2.9 Consensus size: 131
2020464 CTTGAAACAA
* * * * * * *
2020474 ATCCCTAAAGATGGCCTACCGTTCTCATCACGTAGGAACCA-TGTCATCCATCGACTAGATCTCC
1 ATCCCTAAAGATGGCATACCATCCTCATCACGTAGGAA-CAGTGTCATCCCTAGACCAGACCTCC
* ***** * * ***
2020538 TCATCACGTAGGTGCCATGTCAACCTTAGATAACCTGTCGTCCTCATCATGTAGGAACCATGTTA
65 CCATCACGTAACAATCGTGTCAACCCTAGATAACCAAACGTCCTCATCATGTAGGAACCATGTTA
2020603 TC
130 TC
* * ** * *
2020605 ATCCCTAAAGATGGCATATCGTCCTCATCACGTAGGAACCTTGTCATCCCTAGACCATACCTCCT
1 ATCCCTAAAGATGGCATACCATCCTCATCACGTAGGAACAGTGTCATCCCTAGACCAGACCTCCC
* * * *
2020670 CATCACGTAAGAGTCGTGTCAACCCTAGATAACCAACCGTCCTCATCGTGTAGGAACCATGTTAT
66 CATCACGTAACAATCGTGTCAACCCTAGATAACCAAACGTCCTCATCATGTAGGAACCATGTTAT
2020735 C
131 C
* ** * * *
2020736 AACCTTCCTAAAGATGGC-TAGCCATCCTCATCGTGTAGGAGCAGTGTCATCCAC-CGACCAGAT
1 -A--TCCCTAAAGATGGCATA-CCATCCTCATCACGTAGGAACAGTGTCATCC-CTAGACCAGAC
* * *
2020799 CTCCCCATCACGTAACAATTGTGTC-ACCCTTAGATGACCAGAAC-TCTTCATCA
61 CTCCCCATCACGTAACAATCGTGTCAACCC-TAGATAACCA-AACGTCCTCATCA
2020852 CGTTTGAGTT
Statistics
Matches: 202, Mismatches: 37, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
130 1 0.00
131 111 0.55
132 1 0.00
133 6 0.03
134 80 0.40
135 3 0.01
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.26
Consensus pattern (131 bp):
ATCCCTAAAGATGGCATACCATCCTCATCACGTAGGAACAGTGTCATCCCTAGACCAGACCTCCC
CATCACGTAACAATCGTGTCAACCCTAGATAACCAAACGTCCTCATCATGTAGGAACCATGTTAT
C
Found at i:2021029 original size:3 final size:3
Alignment explanation
Indices: 2021023--2021062 Score: 55
Period size: 3 Copynumber: 13.0 Consensus size: 3
2021013 ATTTTTTTTA
2021023 ATT ATT ATT -TAT ATT ATT ATT ATT ATT ATT ATT AATT ATT
1 ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT -ATT ATT
2021063 TTACATGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 1 0.03
3 29 0.85
4 4 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2021040 original size:12 final size:12
Alignment explanation
Indices: 2021019--2021055 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2021009 TCAAATTTTT
2021019 TTTA-ATTATTA
1 TTTATATTATTA
2021030 TTTATATTATTA
1 TTTATATTATTA
2021042 -TTATTATTATTA
1 TTTA-TATTATTA
2021054 TT
1 TT
2021056 AATTATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 7 0.30
12 15 0.65
13 1 0.04
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTATATTATTA
Found at i:2023427 original size:39 final size:38
Alignment explanation
Indices: 2023277--2023425 Score: 183
Period size: 39 Copynumber: 3.8 Consensus size: 38
2023267 TACAGTACAT
** *
2023277 CCCAAAGACGCATTGTACTCCATACGTCTCTTCTCCTAC
1 CCCAAAGACGCATTACACTCCATACATCTC-TCTCCTAC
*
2023316 CCCAAAGACGCATTACACTCCATACATATCTCCTCCTAC
1 CCCAAAGACGCATTACACTCCATACATCTCT-CTCCTAC
*
2023355 CCCAAAGACGCATTACACTCCATGCATCTCTC-CCTATCC
1 CCCAAAGACGCATTACACTCCATACATCTCTCTCCTA--C
* * *
2023394 CCCGAAGACGCATTGCACTCCATGCATCTCTC
1 CCCAAAGACGCATTACACTCCATACATCTCTC
2023426 CCCTGCATGC
Statistics
Matches: 99, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 93 0.94
ACGTcount: A:0.26, C:0.41, G:0.09, T:0.24
Consensus pattern (38 bp):
CCCAAAGACGCATTACACTCCATACATCTCTCTCCTAC
Found at i:2023700 original size:5 final size:4
Alignment explanation
Indices: 2023655--2023705 Score: 50
Period size: 4 Copynumber: 12.5 Consensus size: 4
2023645 AATATAAAAG
* * *
2023655 AGAA AGAA AGAA AGAA ATAA ATAA ATAA AGAA AGAA GAGAA TAG-A AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA -AGAA -AGAA AGAA
2023704 AG
1 AG
2023706 TTAAAGTTGG
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
3 2 0.05
4 34 0.81
5 6 0.14
ACGTcount: A:0.71, C:0.00, G:0.22, T:0.08
Consensus pattern (4 bp):
AGAA
Found at i:2023991 original size:15 final size:15
Alignment explanation
Indices: 2023971--2024000 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2023961 GTTTTTCACG
2023971 ATTGTCCATTATAAT
1 ATTGTCCATTATAAT
2023986 ATTGTCCATTATAAT
1 ATTGTCCATTATAAT
2024001 GAACATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.47
Consensus pattern (15 bp):
ATTGTCCATTATAAT
Found at i:2029453 original size:18 final size:19
Alignment explanation
Indices: 2029416--2029460 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
2029406 TACCATTTAC
2029416 TAATAATATTTTTCTCAAA
1 TAATAATATTTTTCTCAAA
2029435 TAATAATATTTTAT-T-AAA
1 TAATAATATTTT-TCTCAAA
2029453 TAATAATA
1 TAATAATA
2029461 ACCCCATTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.44
19 13 0.52
20 1 0.04
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (19 bp):
TAATAATATTTTTCTCAAA
Found at i:2029721 original size:16 final size:15
Alignment explanation
Indices: 2029674--2029722 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
2029664 ACTTGATTAT
*
2029674 TTTCTTTTCTTCCTC
1 TTTCTTTTCTTCTTC
* *
2029689 TTTTCTTTTTTTTTTC
1 -TTTCTTTTCTTCTTC
2029705 TTTCTTCTTCTTCTTC
1 TTTCTT-TTCTTCTTC
2029721 TT
1 TT
2029723 CCTTCTCCTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 6 0.22
16 21 0.78
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTCTTTTCTTCTTC
Found at i:2029855 original size:12 final size:12
Alignment explanation
Indices: 2029823--2029861 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
2029813 CCAACCCATG
*
2029823 ATTGCAGC-ATC
1 ATTGCAGCTATT
*
2029834 ATTGCTGCTATT
1 ATTGCAGCTATT
2029846 ATTGCAGCTATT
1 ATTGCAGCTATT
2029858 ATTG
1 ATTG
2029862 TTGCATGCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 7 0.29
12 17 0.71
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (12 bp):
ATTGCAGCTATT
Found at i:2030128 original size:21 final size:21
Alignment explanation
Indices: 2030084--2030151 Score: 82
Period size: 21 Copynumber: 3.1 Consensus size: 21
2030074 AAAATATATT
*
2030084 AAAAATATTAAAAGTATTTCAAAA
1 AAAAAT-TTAAAA-T-TTTAAAAA
2030108 AAAAATTTAAAATTTTAAAAA
1 AAAAATTTAAAATTTTAAAAA
* *
2030129 AATAATATAAAATTTTAAAAA
1 AAAAATTTAAAATTTTAAAAA
2030150 AA
1 AA
2030152 CATTCAAGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
21 28 0.68
22 1 0.02
23 6 0.15
24 6 0.15
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (21 bp):
AAAAATTTAAAATTTTAAAAA
Found at i:2032971 original size:16 final size:16
Alignment explanation
Indices: 2032940--2032981 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
2032930 TAAAATGAAT
* *
2032940 ATAAATAATATCAAAAG
1 ATAAAT-ATATAAAAAA
2032957 ATAAATATATAAAAAA
1 ATAAATATATAAAAAA
2032973 ATAAATATA
1 ATAAATATA
2032982 AAATAATATG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 17 0.74
17 6 0.26
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (16 bp):
ATAAATATATAAAAAA
Found at i:2033698 original size:11 final size:10
Alignment explanation
Indices: 2033669--2033702 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
2033659 AAAATATAAA
2033669 ATATAATTTT
1 ATATAATTTT
*
2033679 TTATAATTTT
1 ATATAATTTT
2033689 ATATTAATTTT
1 ATA-TAATTTT
2033700 ATA
1 ATA
2033703 GTTTATGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
ATATAATTTT
Found at i:2038969 original size:7 final size:7
Alignment explanation
Indices: 2038957--2038982 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2038947 AAATTATTAA
2038957 AATTTAT
1 AATTTAT
2038964 AATTTAT
1 AATTTAT
2038971 AATTTAT
1 AATTTAT
2038978 AATTT
1 AATTT
2038983 TCGAGAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
AATTTAT
Found at i:2039756 original size:20 final size:20
Alignment explanation
Indices: 2039720--2039775 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
2039710 TGAACCTGAT
* *
2039720 CCGTTGATCATTTACTTTAA
1 CCGTTGATCGTTGACTTTAA
*
2039740 CCGTTGATCGTTGACTTTGA
1 CCGTTGATCGTTGACTTTAA
*
2039760 CCATTGA-CTGTTGACT
1 CCGTTGATC-GTTGACT
2039776 ATTGGCTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.20, C:0.21, G:0.18, T:0.41
Consensus pattern (20 bp):
CCGTTGATCGTTGACTTTAA
Found at i:2039846 original size:21 final size:22
Alignment explanation
Indices: 2039825--2039868 Score: 70
Period size: 24 Copynumber: 1.9 Consensus size: 22
2039815 CCCACCTATA
2039825 TGTTTTTCAATGTCTTGAATATGT
1 TGTTTTTCAATGTCTTGAATA--T
2039849 TGTTTTTCAATGTCTTGAAT
1 TGTTTTTCAATGTCTTGAAT
2039869 CTGATTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.20, C:0.09, G:0.16, T:0.55
Consensus pattern (22 bp):
TGTTTTTCAATGTCTTGAATAT
Done.