Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008165.1 Hibiscus syriacus cultivar Beakdansim tig00110745_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: 2894944
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 11
Found at i:1903740 original size:26 final size:26
Alignment explanation
Indices: 1903691--1903761 Score: 90
Period size: 26 Copynumber: 2.7 Consensus size: 26
1903681 AACTTGGTAA
* * *
1903691 TACATATTCTTCATGAATACTGTTAT
1 TACATATTGTTCATGCATAATGTTAT
1903717 TACATATTGTT-ACTGCATAATGTTAT
1 TACATATTGTTCA-TGCATAATGTTAT
*
1903743 TGCATATTGTTCATGCATA
1 TACATATTGTTCATGCATA
1903762 CAGTTGTTGG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
25 1 0.03
26 37 0.95
27 1 0.03
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (26 bp):
TACATATTGTTCATGCATAATGTTAT
Found at i:1903761 original size:13 final size:13
Alignment explanation
Indices: 1903719--1903753 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1903709 ACTGTTATTA
1903719 CATATTGTTACTG
1 CATATTGTTACTG
* *
1903732 CATAATGTTATTG
1 CATATTGTTACTG
1903745 CATATTGTT
1 CATATTGTT
1903754 CATGCATACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.14, T:0.49
Consensus pattern (13 bp):
CATATTGTTACTG
Found at i:1904876 original size:28 final size:28
Alignment explanation
Indices: 1904843--1904923 Score: 101
Period size: 29 Copynumber: 2.9 Consensus size: 28
1904833 TTTGATCAGC
1904843 TGATATTGTTAGGTTTTGTGGTGATAGT
1 TGATATTGTTAGGTTTTGTGGTGATAGT
****
1904871 TGATATTGTTAGGACACGTAAGG-GATAGT
1 TGATATTGTTAGGTTTTGT--GGTGATAGT
1904900 TGATATTGTTAGGTTTTGTGGTGA
1 TGATATTGTTAGGTTTTGTGGTGA
1904924 CAATTCACAA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
27 2 0.05
28 17 0.40
29 21 0.50
30 2 0.05
ACGTcount: A:0.22, C:0.02, G:0.32, T:0.43
Consensus pattern (28 bp):
TGATATTGTTAGGTTTTGTGGTGATAGT
Found at i:1905774 original size:26 final size:24
Alignment explanation
Indices: 1905748--1905796 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
1905738 TTTCTTATGT
*
1905748 TTTAATTGAGGTGGCGTCCTGCATG
1 TTTAA-TGACGTGGCGTCCTGCATG
*
1905773 -TTGATGACGTGGCGTCCTGCATG
1 TTTAATGACGTGGCGTCCTGCATG
1905796 T
1 T
1905797 CAAACTTGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.14, C:0.18, G:0.33, T:0.35
Consensus pattern (24 bp):
TTTAATGACGTGGCGTCCTGCATG
Found at i:1906665 original size:15 final size:15
Alignment explanation
Indices: 1906647--1906702 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
1906637 TAACCGGTTT
1906647 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
1906662 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
1906679 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
1906694 CGATTTTAA
1 CGGTTTTAA
1906703 TATTCCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:1906675 original size:17 final size:17
Alignment explanation
Indices: 1906650--1906700 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
1906640 CCGGTTTCGG
1906650 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
1906667 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
1906682 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
1906699 TT
1 TT
1906701 AATATTCCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:1907053 original size:13 final size:13
Alignment explanation
Indices: 1907032--1907086 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
1907022 AAGTTCGATA
*
1907032 AATTCAAATACTT
1 AATTGAAATACTT
1907045 AATTGAAATACTT
1 AATTGAAATACTT
* *
1907058 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
1907072 AATTGAAATACTT
1 AATTGAAATACTT
1907085 AA
1 AA
1907087 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:1907130 original size:32 final size:32
Alignment explanation
Indices: 1907072--1907169 Score: 153
Period size: 32 Copynumber: 3.0 Consensus size: 32
1907062 AACTCAACAT
* *
1907072 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAA-ACTTCCAAGTTCGATA
1907105 AATTCAAATACTTAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAACTTCCAAGTTCGATA
1907137 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTT-AAAACTTCCAAGTTCGATA
1907169 A
1 A
1907170 TTGAAACAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
32 40 0.65
33 22 0.35
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (32 bp):
AATTCAAATACTTAAAACTTCCAAGTTCGATA
Found at i:1907188 original size:21 final size:21
Alignment explanation
Indices: 1907164--1907203 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1907154 ACTTCAAGTT
1907164 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
1907185 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
1907204 ATCGACTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:1909428 original size:14 final size:13
Alignment explanation
Indices: 1909398--1909435 Score: 60
Period size: 12 Copynumber: 2.9 Consensus size: 13
1909388 TTTCGGATAA
1909398 AAACCGGTTTTTT
1 AAACCGGTTTTTT
1909411 -AACCGGTTTTTT
1 AAACCGGTTTTTT
1909423 CAAACCGGTTTTT
1 -AAACCGGTTTTT
1909436 ATCCGGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.52
14 11 0.48
ACGTcount: A:0.21, C:0.18, G:0.16, T:0.45
Consensus pattern (13 bp):
AAACCGGTTTTTT
Found at i:1909750 original size:29 final size:29
Alignment explanation
Indices: 1909719--1909774 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1909709 TCTGTTTTTC
1909719 CCCCCT-AAATTATA-TATGTTCAAGTTCA
1 CCCCCTGAAATTATATTA-GTTCAAGTTCA
*
1909747 CCCCCTGAAATTTTATTAGTTCAAGTTC
1 CCCCCTGAAATTATATTAGTTCAAGTTC
1909775 GTTCCACCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 6 0.24
29 17 0.68
30 2 0.08
ACGTcount: A:0.29, C:0.25, G:0.09, T:0.38
Consensus pattern (29 bp):
CCCCCTGAAATTATATTAGTTCAAGTTCA
Found at i:1910503 original size:23 final size:24
Alignment explanation
Indices: 1910457--1910504 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
1910447 AATATAGAAG
** *
1910457 AACTATTAAATATTATCTATAAAA
1 AACTATTAAATATTAAATAAAAAA
1910481 AACTATTAAA-ATTAAATAAAAAA
1 AACTATTAAATATTAAATAAAAAA
1910504 A
1 A
1910505 GGTTCCCTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (24 bp):
AACTATTAAATATTAAATAAAAAA
Found at i:1911180 original size:2 final size:2
Alignment explanation
Indices: 1911173--1911198 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1911163 TAGCTTCACA
1911173 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
1911199 TACTTAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1915168 original size:2 final size:2
Alignment explanation
Indices: 1915161--1915192 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1915151 AACTAATTAA
1915161 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
1915193 TCATAACCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1915292 original size:30 final size:30
Alignment explanation
Indices: 1915258--1915519 Score: 117
Period size: 30 Copynumber: 9.2 Consensus size: 30
1915248 TTTGATAATA
*
1915258 TTTTA-AATTTAAGATAAAAATATAATATAT
1 TTTTATAA-TTAAGATAAAAATAAAATATAT
1915288 TTTTATAATTAAGATAAAAATAAAATATA-
1 TTTTATAATTAAGATAAAAATAAAATATAT
* * *
1915317 -TTT-T--GT-AG-TTAAAATAAAAAATAT
1 TTTTATAATTAAGATAAAAATAAAATATAT
* * * * *
1915341 TTTTA-AGTTAATATAAGAATAAAAGATGT
1 TTTTATAATTAAGATAAAAATAAAATATAT
* * * * *
1915370 TCTTTA-AGTTAAAATAAGAATTAATTATA-
1 T-TTTATAATTAAGATAAAAATAAAATATAT
* * *
1915399 TTTAATAATTTAAGGTAAGAATAAAATATA-
1 TTTTATAA-TTAAGATAAAAATAAAATATAT
* * *
1915429 TTTAATAATTTAAGTTAAGAAT---ATA-AT
1 TTTTATAA-TTAAGATAAAAATAAAATATAT
* * * *
1915456 TTATGTAA-TAAGTTAAGAATAAAATATAT
1 TTTTATAATTAAGATAAAAATAAAATATAT
* * * *
1915485 TTTAAAAATTAATATAAAAATAAAATATTT
1 TTTTATAATTAAGATAAAAATAAAATATAT
1915515 TTTTA
1 TTTTA
1915520 ATGTTAATAT
Statistics
Matches: 181, Mismatches: 34, Indels: 34
0.73 0.14 0.14
Matches are distributed among these distances:
23 13 0.07
24 2 0.01
25 16 0.09
26 1 0.01
27 10 0.06
28 10 0.06
29 21 0.12
30 106 0.59
31 2 0.01
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (30 bp):
TTTTATAATTAAGATAAAAATAAAATATAT
Found at i:1915330 original size:23 final size:23
Alignment explanation
Indices: 1915304--1915361 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
1915294 AATTAAGATA
1915304 AAAATAAAATATATTTTGT-AGTT
1 AAAATAAAATATATTTT-TAAGTT
*
1915327 AAAATAAAAAATATTTTTAAGTT
1 AAAATAAAATATATTTTTAAGTT
*
1915350 AATATAAGAATA
1 AAAATAA-AATA
1915362 AAAGATGTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 1 0.03
23 26 0.87
24 3 0.10
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (23 bp):
AAAATAAAATATATTTTTAAGTT
Found at i:1919391 original size:4 final size:4
Alignment explanation
Indices: 1919382--1919448 Score: 62
Period size: 4 Copynumber: 16.0 Consensus size: 4
1919372 ATCTAGAGGC
* * **
1919382 ATTT ATTT ATTT ATTC AATT ATTT ATTT ATTTT ATTT GGTT ATTT ATGTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT A-TTT ATTT ATTT ATTT AT-TT
*
1919432 ATTTT AATT ATTT ATTT
1 A-TTT ATTT ATTT ATTT
1919449 GAAGAGGTAT
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
4 39 0.78
5 10 0.20
6 1 0.02
ACGTcount: A:0.25, C:0.01, G:0.04, T:0.69
Consensus pattern (4 bp):
ATTT
Found at i:1922875 original size:12 final size:12
Alignment explanation
Indices: 1922860--1922884 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1922850 TGAGGAATAA
1922860 GAGGAGGATTTG
1 GAGGAGGATTTG
1922872 GAGGAGGATTTG
1 GAGGAGGATTTG
1922884 G
1 G
1922885 TTGACGACTA
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:0.24, C:0.00, G:0.52, T:0.24
Consensus pattern (12 bp):
GAGGAGGATTTG
Found at i:1923592 original size:21 final size:22
Alignment explanation
Indices: 1923566--1923646 Score: 78
Period size: 21 Copynumber: 3.8 Consensus size: 22
1923556 CAGAACCCCA
*
1923566 GGGGGGTATCGATTCCCCT-AT
1 GGGGGGAATCGATTCCCCTCAT
* * *
1923587 GGGGGGAATCGGTTCCTCTTCAA
1 GGGGGGAATCGATTCC-CCTCAT
* *
1923610 AGGGGGAATCGGTT-CCCTCAT
1 GGGGGGAATCGATTCCCCTCAT
1923631 GGGGGG-ATCGATTCCC
1 GGGGGGAATCGATTCCC
1923647 TCTGCACCAA
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
20 6 0.12
21 25 0.52
22 3 0.06
23 14 0.29
ACGTcount: A:0.16, C:0.23, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGGGGAATCGATTCCCCTCAT
Found at i:1930951 original size:15 final size:15
Alignment explanation
Indices: 1930928--1930978 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
1930918 CTGCATATGT
*
1930928 TGATAGCGATGGTGA
1 TGATGGCGATGGTGA
1930943 TGATGGCGATGGTGA
1 TGATGGCGATGGTGA
* *
1930958 TGATGGTGATGATGA
1 TGATGGCGATGGTGA
1930973 TGATGG
1 TGATGG
1930979 TGTTGCTGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.24, C:0.04, G:0.43, T:0.29
Consensus pattern (15 bp):
TGATGGCGATGGTGA
Found at i:1938829 original size:61 final size:64
Alignment explanation
Indices: 1938740--1938863 Score: 148
Period size: 61 Copynumber: 2.0 Consensus size: 64
1938730 ACTAATCCAG
* * *
1938740 ATATGACACATAAGGTCGTTCCCACCACCTACAC-TAG-GT-TTACACTCTAGTGTTAATCTGA
1 ATATGACACATAAGGTCGTTCACACCACCTACACTTAGTGTCTTACACACTAGTGCTAATCTGA
* * *
1938801 ATATGACACATAAGGTTG-TGACATCCACCTGCACTTAGTGTCCTTACACACTAGTGCTAATCT
1 ATATGACACATAAGGTCGTTCACA-CCACCTACACTTAGTGT-CTTACACACTAGTGCTAATCT
1938864 AAACTTGTAG
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
60 3 0.06
61 26 0.50
62 3 0.06
63 2 0.04
65 18 0.35
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (64 bp):
ATATGACACATAAGGTCGTTCACACCACCTACACTTAGTGTCTTACACACTAGTGCTAATCTGA
Found at i:1942297 original size:18 final size:18
Alignment explanation
Indices: 1942276--1942335 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
1942266 GTTAAATTTT
1942276 GTTTAAATTATTAATTAA
1 GTTTAAATTATTAATTAA
* *
1942294 GTTTAAAGTGTTAAATT--
1 GTTTAAATTATT-AATTAA
* *
1942311 GTTTAAGTTACTAATTAA
1 GTTTAAATTATTAATTAA
1942329 GTTTAAA
1 GTTTAAA
1942336 ATGATAATTT
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
16 4 0.12
17 8 0.25
18 16 0.50
19 4 0.12
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.47
Consensus pattern (18 bp):
GTTTAAATTATTAATTAA
Found at i:1942326 original size:35 final size:36
Alignment explanation
Indices: 1942265--1942335 Score: 108
Period size: 35 Copynumber: 2.0 Consensus size: 36
1942255 TCGAATATAA
*
1942265 TGTTAAATTTTGTTTAAATTATTAATTAAGTTTAAAG
1 TGTTAAA-TTTGTTTAAATTACTAATTAAGTTTAAAG
*
1942302 TGTTAAA-TTGTTTAAGTTACTAATTAAGTTTAAA
1 TGTTAAATTTGTTTAAATTACTAATTAAGTTTAAA
1942336 ATGATAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 25 0.78
37 7 0.22
ACGTcount: A:0.38, C:0.01, G:0.11, T:0.49
Consensus pattern (36 bp):
TGTTAAATTTGTTTAAATTACTAATTAAGTTTAAAG
Found at i:1943103 original size:18 final size:18
Alignment explanation
Indices: 1943080--1943115 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1943070 TCAAATTTTG
*
1943080 CTACCACGTCAGAAATCT
1 CTACCACGACAGAAATCT
1943098 CTACCACGACAGAAATCT
1 CTACCACGACAGAAATCT
1943116 TTACAACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.33, G:0.11, T:0.19
Consensus pattern (18 bp):
CTACCACGACAGAAATCT
Found at i:1944519 original size:32 final size:31
Alignment explanation
Indices: 1944483--1944543 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
1944473 ACCTTAGGGA
**
1944483 GTACTGTGGGGCCTTAGAGCTTACCCAAGGTG
1 GTACTGTGGGG-CTTAGAAATTACCCAAGGTG
* *
1944515 GTACTTTGGGGCTTTGAAATTACCCAAGG
1 GTACTGTGGGGCTTAGAAATTACCCAAGG
1944544 GAGTACCTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 15 0.60
32 10 0.40
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.28
Consensus pattern (31 bp):
GTACTGTGGGGCTTAGAAATTACCCAAGGTG
Found at i:1944630 original size:32 final size:31
Alignment explanation
Indices: 1944557--1944671 Score: 95
Period size: 32 Copynumber: 3.6 Consensus size: 31
1944547 TACCTTGGGG
** * * * *
1944557 GCCTAAGAGCCTACTTAAGAGAGTATCCTAGG
1 GCCTAAGAGCCTACCCAAGAAAGTA-CATTGA
* ***
1944589 GCCTTAGAGCCTACCCAAGGGGGTACATTCGA
1 GCCTAAGAGCCTACCCAAGAAAGTACATT-GA
* *
1944621 GCCTAAGAGCCTACCCAAGAAAGTACCTTGG
1 GCCTAAGAGCCTACCCAAGAAAGTACATTGA
1944652 GACCTAAGAGCCTACCCAAG
1 G-CCTAAGAGCCTACCCAAG
1944672 TGTCACCATA
Statistics
Matches: 67, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
31 4 0.06
32 63 0.94
ACGTcount: A:0.30, C:0.28, G:0.24, T:0.17
Consensus pattern (31 bp):
GCCTAAGAGCCTACCCAAGAAAGTACATTGA
Found at i:1945761 original size:27 final size:28
Alignment explanation
Indices: 1945718--1945771 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
1945708 AGACTATTTT
*
1945718 AATATTTTCAAACAATT-GTATTCATAC
1 AATACTTTCAAACAATTGGTATTCATAC
*
1945745 AATACTTTCAATA-AATTGGTCTTCATA
1 AATACTTTCAA-ACAATTGGTATTCATA
1945772 TATTTATTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.39, C:0.15, G:0.06, T:0.41
Consensus pattern (28 bp):
AATACTTTCAAACAATTGGTATTCATAC
Found at i:1949287 original size:20 final size:20
Alignment explanation
Indices: 1949262--1949336 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
1949252 TTTTCCTAAT
1949262 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
1949282 TCGCAAACGCGAATTTGGAAAA
1 TCGC-AATGCGAA-TACGTAAA
1949304 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1949324 TCGCAATGCGAAT
1 TCGCAATGCGAAT
1949337 CTGACTATCG
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 22 0.49
21 14 0.31
22 9 0.20
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1949295 original size:21 final size:21
Alignment explanation
Indices: 1949269--1949329 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
1949259 AATTCGCAAT
1949269 GCGAATACGTAAATCGCAAAC
1 GCGAATACGTAAATCGCAAAC
** * *
1949290 GCGAATTTGGAAAATCGC-AAT
1 GCGAA-TACGTAAATCGCAAAC
1949311 GCGAATACGTAAATCGCAA
1 GCGAATACGTAAATCGCAA
1949330 TGCGAATCTG
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 9 0.29
21 13 0.42
22 9 0.29
ACGTcount: A:0.41, C:0.20, G:0.21, T:0.18
Consensus pattern (21 bp):
GCGAATACGTAAATCGCAAAC
Found at i:1949346 original size:20 final size:20
Alignment explanation
Indices: 1949323--1949370 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1949313 GAATACGTAA
*
1949323 ATCGCAATGCGAATCTGACT
1 ATCGCAATGAGAATCTGACT
* *
1949343 ATCGCAACGAGATTCTGACT
1 ATCGCAATGAGAATCTGACT
1949363 ATCGCAAT
1 ATCGCAAT
1949371 ACTGAATTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAATGAGAATCTGACT
Found at i:1950233 original size:24 final size:24
Alignment explanation
Indices: 1950206--1950256 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
1950196 TTCGAAATTC
1950206 GATCTTGGTCAATACACGGACTTT
1 GATCTTGGTCAATACACGGACTTT
* *
1950230 GATCTTGGTCAATACTCGGATTTT
1 GATCTTGGTCAATACACGGACTTT
1950254 GAT
1 GAT
1950257 GTTTTTTCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.37
Consensus pattern (24 bp):
GATCTTGGTCAATACACGGACTTT
Found at i:1952679 original size:20 final size:19
Alignment explanation
Indices: 1952654--1952736 Score: 89
Period size: 20 Copynumber: 4.2 Consensus size: 19
1952644 CAACGCGGAA
1952654 ATCGCAACGTGAATATGACT
1 ATCGCAACG-GAATATGACT
1952674 ATCGCAACACGGAA-ATGACT
1 ATCGC-A-ACGGAATATGACT
1952694 ATCGCAACGCGGAAT-TGACT
1 ATCGCAA--CGGAATATGACT
*
1952714 ATCGCAACGCGAAAATGACT
1 ATCGCAACG-GAATATGACT
1952734 ATC
1 ATC
1952737 AACAGTTAAT
Statistics
Matches: 55, Mismatches: 1, Indels: 14
0.79 0.01 0.20
Matches are distributed among these distances:
18 3 0.05
19 4 0.07
20 41 0.75
21 4 0.07
22 3 0.05
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.19
Consensus pattern (19 bp):
ATCGCAACGGAATATGACT
Found at i:1952713 original size:40 final size:40
Alignment explanation
Indices: 1952654--1952736 Score: 123
Period size: 40 Copynumber: 2.1 Consensus size: 40
1952644 CAACGCGGAA
* *
1952654 ATCGCAACGTGAATATGACTATCGCAACACGGAAATGACT
1 ATCGCAACGGGAATATGACTATCGCAACACGAAAATGACT
*
1952694 ATCGCAACGCGGAAT-TGACTATCGCAACGCGAAAATGACT
1 ATCGCAACG-GGAATATGACTATCGCAACACGAAAATGACT
1952734 ATC
1 ATC
1952737 AACAGTTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
40 35 0.90
41 4 0.10
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.19
Consensus pattern (40 bp):
ATCGCAACGGGAATATGACTATCGCAACACGAAAATGACT
Found at i:1955007 original size:20 final size:20
Alignment explanation
Indices: 1954984--1955123 Score: 123
Period size: 20 Copynumber: 7.3 Consensus size: 20
1954974 GAAACTTAAA
*
1954984 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
*
1955004 ATCGCAAT--G-AGA-GA--
1 ATCGCAATGCGAAAATGACT
* **
1955018 ATCACAATGCG-AAATGAAA
1 ATCGCAATGCGAAAATGACT
*
1955037 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
1955057 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
* ** *
1955077 ATCGCAATACGAATTTGACA
1 ATCGCAATGCGAAAATGACT
**
1955097 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
1955117 ATCGCAA
1 ATCGCAA
1955124 CGAGAGAATC
Statistics
Matches: 99, Mismatches: 15, Indels: 12
0.79 0.12 0.10
Matches are distributed among these distances:
14 7 0.07
16 5 0.05
17 4 0.04
18 1 0.01
19 9 0.09
20 73 0.74
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:1955195 original size:20 final size:20
Alignment explanation
Indices: 1955170--1955216 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1955160 GATTCTCTCG
1955170 TTGCGATAGTCAAATTCACA
1 TTGCGATAGTCAAATTCACA
** *
1955190 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCAAATTCACA
1955210 TTGCGAT
1 TTGCGAT
1955217 TTTATTGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCACA
Found at i:1955240 original size:87 final size:87
Alignment explanation
Indices: 1955142--1955303 Score: 279
Period size: 87 Copynumber: 1.9 Consensus size: 87
1955132 TCGCAATACA
1955142 ATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCACATTGCGATAGTCATTTTC
1 ATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCACATTGCGATAGTCATTTTC
1955207 GCATTGCGATTTTATTGTTGCG
66 GCATTGCGATTTTATTGTTGCG
** * *
1955229 ATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTC
1 ATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCACATTGCGATAGTCATTTTC
*
1955294 GTATTGCGAT
66 GCATTGCGAT
1955304 AGTAAACTAT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 70 1.00
ACGTcount: A:0.18, C:0.20, G:0.19, T:0.43
Consensus pattern (87 bp):
ATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCACATTGCGATAGTCATTTTC
GCATTGCGATTTTATTGTTGCG
Found at i:1955245 original size:33 final size:34
Alignment explanation
Indices: 1955190--1955283 Score: 127
Period size: 33 Copynumber: 2.8 Consensus size: 34
1955180 CAAATTCACA
* *
1955190 TTGCGATAGTCATTTTCGCATTGCGATTTTATTG
1 TTGCGATAGTCATTTTCGCATTGCGATTCTATCG
** *
1955224 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCG
1 TTGCGATAGTCATTTTCGCATTGCGATTCTATCG
*
1955257 TTGCGATAGTCATTTTCGCGTTGCGAT
1 TTGCGATAGTCATTTTCGCATTGCGAT
1955284 AGTCATTTTC
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.55
34 23 0.45
ACGTcount: A:0.15, C:0.19, G:0.21, T:0.45
Consensus pattern (34 bp):
TTGCGATAGTCATTTTCGCATTGCGATTCTATCG
Found at i:1955280 original size:20 final size:20
Alignment explanation
Indices: 1955255--1955306 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1955245 GCGATTCTCT
1955255 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
1955275 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
**
1955295 TATTGCGATAGT
1 CGTTGCGATAGT
1955307 AAACTATTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.17, C:0.17, G:0.25, T:0.40
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1957201 original size:20 final size:20
Alignment explanation
Indices: 1957178--1957232 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
1957168 CTGAAACTTT
1957178 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
1957198 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
** *
1957218 CTATCGCAACGCGAA
1 AAATCGCAACACGAA
1957233 TTAGACTATC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.11
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:1957650 original size:22 final size:22
Alignment explanation
Indices: 1957612--1957668 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
1957602 ATGATTTCGC
* *
1957612 CGGAGATGGAGATTGATATCAT
1 CGGAGATGGGGACTGATATCAT
* * *
1957634 CGGTGATGGGGACTGATTTCGT
1 CGGAGATGGGGACTGATATCAT
1957656 CGGAGATGGGGAC
1 CGGAGATGGGGAC
1957669 GGATGTCGCC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (22 bp):
CGGAGATGGGGACTGATATCAT
Found at i:1957889 original size:20 final size:20
Alignment explanation
Indices: 1957848--1957959 Score: 118
Period size: 20 Copynumber: 5.5 Consensus size: 20
1957838 GCTATGTAAA
* *
1957848 TCGCATTGCGATAGT-CAGAT
1 TCGCATTGCGAT-TTACATAT
*
1957868 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACATAT
*
1957888 TCGCATTGCGATTTACATAA
1 TCGCATTGCGATTTACATAT
* *
1957908 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGA-TTTACATAT
* *
1957929 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACATAT
*
1957949 TCGTATTGCGA
1 TCGCATTGCGA
1957960 ATTAGGAAAA
Statistics
Matches: 76, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
19 1 0.01
20 59 0.78
21 16 0.21
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:1957941 original size:41 final size:40
Alignment explanation
Indices: 1957868--1957959 Score: 112
Period size: 41 Copynumber: 2.3 Consensus size: 40
1957858 ATAGTCAGAT
**
1957868 TCGCATTGCGATTTACGTATTCGCATTGCGATTTACATAA
1 TCGCATTGCGATTTACAAATTCGCATTGCGATTTACATAA
* * * *
1957908 TCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACGTAT
1 TCGCATTGCGA-TTTACAAATTCGCATTGCGATTTACATAA
*
1957949 TCGTATTGCGA
1 TCGCATTGCGA
1957960 ATTAGGAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 11 0.25
41 33 0.75
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.38
Consensus pattern (40 bp):
TCGCATTGCGATTTACAAATTCGCATTGCGATTTACATAA
Found at i:1957941 original size:61 final size:60
Alignment explanation
Indices: 1957846--1957959 Score: 174
Period size: 61 Copynumber: 1.9 Consensus size: 60
1957836 GCGCTATGTA
*
1957846 AATCGCATTGCGATAGTCAGATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACAT
1 AATCGCATTGCGATAGTCAAATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACAT
** * *
1957906 AATCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACGTATTCGTATTGCGA
1 AATCGCATTGCGATAGT-CAAATTCGCATTGCGATTTACGTATTCGCATTGCGA
1957960 ATTAGGAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
60 15 0.31
61 33 0.69
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (60 bp):
AATCGCATTGCGATAGTCAAATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACAT
Found at i:1957982 original size:21 final size:21
Alignment explanation
Indices: 1957956--1958001 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1957946 TATTCGTATT
1957956 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
1957977 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
1957998 GCGA
1 GCGA
1958002 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:1959136 original size:67 final size:67
Alignment explanation
Indices: 1959028--1959162 Score: 270
Period size: 67 Copynumber: 2.0 Consensus size: 67
1959018 TATGAAGGGC
1959028 ACTGTAACCTTGAATCCAACCTTGTTTCTGCATTGGTTGAGAGGTGGAGACCAGAGGCACACATT
1 ACTGTAACCTTGAATCCAACCTTGTTTCTGCATTGGTTGAGAGGTGGAGACCAGAGGCACACATT
1959093 CT
66 CT
1959095 ACTGTAACCTTGAATCCAACCTTGTTTCTGCATTGGTTGAGAGGTGGAGACCAGAGGCACACATT
1 ACTGTAACCTTGAATCCAACCTTGTTTCTGCATTGGTTGAGAGGTGGAGACCAGAGGCACACATT
1959160 CT
66 CT
1959162 A
1 A
1959163 TATTATGTGT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (67 bp):
ACTGTAACCTTGAATCCAACCTTGTTTCTGCATTGGTTGAGAGGTGGAGACCAGAGGCACACATT
CT
Found at i:1965371 original size:29 final size:29
Alignment explanation
Indices: 1965308--1965379 Score: 69
Period size: 29 Copynumber: 2.6 Consensus size: 29
1965298 TATAATATTG
** * *
1965308 TTAT-ATTATAATTTTTTGTTCTTTATGA
1 TTATAATTATAATTTTTTAATATTTATAA
1965336 -TATTAATTATAATTTTTTAATATTTATAA
1 TTA-TAATTATAATTTTTTAATATTTATAA
*
1965365 TTATAA-TATTATTTT
1 TTATAATTATAATTTT
1965380 ATAAACTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
27 2 0.06
28 9 0.25
29 23 0.64
30 2 0.06
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.62
Consensus pattern (29 bp):
TTATAATTATAATTTTTTAATATTTATAA
Found at i:1965374 original size:35 final size:35
Alignment explanation
Indices: 1965330--1965407 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 35
1965320 TTTTTGTTCT
* **
1965330 TTATGATATTA-ATTATAATTTTTTAATATTTATAA
1 TTATAATATTATATTATAAACTTTTAATATTTA-AA
* *
1965365 TTATAATATTATTTTATAAACTTTTAATCTTTAAA
1 TTATAATATTATATTATAAACTTTTAATATTTAAA
*
1965400 CTATAATA
1 TTATAATA
1965408 CTATTCATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
35 19 0.53
36 17 0.47
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (35 bp):
TTATAATATTATATTATAAACTTTTAATATTTAAA
Found at i:1966417 original size:5 final size:5
Alignment explanation
Indices: 1966407--1966454 Score: 53
Period size: 5 Copynumber: 9.6 Consensus size: 5
1966397 ATATTTATTG
* * *
1966407 AAAAT AAAAT AAAAT AAAAT AAAGAT ATAAT ATAA- AAAAG AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAA-AT AAAAT AAAAT AAAAT AAAAT AAA
1966455 GAATACAGAC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
4 3 0.08
5 31 0.82
6 4 0.11
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:1971746 original size:26 final size:26
Alignment explanation
Indices: 1971710--1971763 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
1971700 ACTAAGTGCA
* *
1971710 TATGGTGGGCACGACCTTATGTGTAT
1 TATGGTAGGCACGACCATATGTGTAT
1971736 TATGGTAGGCACGACCATATGTGTAT
1 TATGGTAGGCACGACCATATGTGTAT
1971762 TA
1 TA
1971764 GCACTTCGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (26 bp):
TATGGTAGGCACGACCATATGTGTAT
Found at i:1972908 original size:3 final size:3
Alignment explanation
Indices: 1972802--1972899 Score: 169
Period size: 3 Copynumber: 32.7 Consensus size: 3
1972792 TGATGTTTAA
* * *
1972802 AAT AAT AAT AGT AAT AGT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1972850 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1972898 AA
1 AA
1972900 GCTAATAATG
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 89 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1988713 original size:26 final size:26
Alignment explanation
Indices: 1988672--1988722 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
1988662 ACTAAGTGCA
*
1988672 TATGGTGGGCACGACCTTATGTGTAT
1 TATGGTGGGAACGACCTTATGTGTAT
* *
1988698 TATGGTGGGAATGACCTTATTTGTA
1 TATGGTGGGAACGACCTTATGTGTA
1988723 GTATCAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.22, C:0.12, G:0.29, T:0.37
Consensus pattern (26 bp):
TATGGTGGGAACGACCTTATGTGTAT
Found at i:1999228 original size:42 final size:41
Alignment explanation
Indices: 1999170--1999249 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 41
1999160 GATCAATCCC
*
1999170 TTCACCAAAGGATCGATCCCTCGA-GAAAAAGGACTGATTAA
1 TTCACCAAAGGATCGATCACTCGATG-AAAAGGACTGATTAA
*
1999211 TTCACCAAAAGGATCGATCACTCGATGAAAAGGATTGAT
1 TTCACC-AAAGGATCGATCACTCGATGAAAAGGACTGAT
1999250 CCCTTCCCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
41 6 0.17
42 28 0.80
43 1 0.03
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (41 bp):
TTCACCAAAGGATCGATCACTCGATGAAAAGGACTGATTAA
Found at i:1999959 original size:37 final size:37
Alignment explanation
Indices: 1999909--1999983 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
1999899 GCAACTCAAA
*
1999909 TGGATTTGAGAAATCTTTATTGTGGATGCTAAGGTAG
1 TGGATTTGAGAAATCCTTATTGTGGATGCTAAGGTAG
*
1999946 TGGATTTGAGAAATCCTTATTGTGGATGTTAAGGTAG
1 TGGATTTGAGAAATCCTTATTGTGGATGCTAAGGTAG
1999983 T
1 T
1999984 AGATGTATAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.27, C:0.05, G:0.29, T:0.39
Consensus pattern (37 bp):
TGGATTTGAGAAATCCTTATTGTGGATGCTAAGGTAG
Found at i:2012848 original size:26 final size:26
Alignment explanation
Indices: 2012819--2012871 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
2012809 AGACATTGAA
*
2012819 TAAGCTAATTCTTATATGTTTAATTT
1 TAAGCTAATTCTTATATGCTTAATTT
*
2012845 TAAGCTAATTCTTATATGCTTCATTT
1 TAAGCTAATTCTTATATGCTTAATTT
2012871 T
1 T
2012872 CTTTTGTCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.28, C:0.11, G:0.08, T:0.53
Consensus pattern (26 bp):
TAAGCTAATTCTTATATGCTTAATTT
Found at i:2037486 original size:20 final size:20
Alignment explanation
Indices: 2037444--2037487 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2037434 AGATTTTTTA
* *
2037444 TGAATAGTGAACAATACCCG
1 TGAATAGTGAACAATAACAG
*
2037464 TGAATAGTGAACAGTAACAG
1 TGAATAGTGAACAATAACAG
2037484 TGAA
1 TGAA
2037488 CAATACCCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.23, T:0.20
Consensus pattern (20 bp):
TGAATAGTGAACAATAACAG
Found at i:2037581 original size:12 final size:12
Alignment explanation
Indices: 2037564--2037588 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2037554 TTATTGTTCA
2037564 TGCTACAATAAC
1 TGCTACAATAAC
2037576 TGCTACAATAAC
1 TGCTACAATAAC
2037588 T
1 T
2037589 TTCGAAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.28
Consensus pattern (12 bp):
TGCTACAATAAC
Found at i:2038158 original size:59 final size:59
Alignment explanation
Indices: 2038065--2038253 Score: 243
Period size: 59 Copynumber: 3.2 Consensus size: 59
2038055 CCGTAGTGCT
*
2038065 ATCCCGAGTATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTACA
1 ATCCCGAATATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTACA
* * *
2038124 GTCCCGAATATGATACGTAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTACA
1 ATCCCGAATATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTACA
* * * * ** * * **
2038183 ATCCTGAATATGACACATAAGGTTGTGCCCACCATATACACTAGGTATTCTTTAGTGTA
1 ATCCCGAATATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTACA
*
2038242 TTCCCGAATATG
1 ATCCCGAATATG
2038254 CAGCCTGTTT
Statistics
Matches: 111, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
59 111 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.30
Consensus pattern (59 bp):
ATCCCGAATATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTACA
Found at i:2040232 original size:77 final size:81
Alignment explanation
Indices: 2040094--2040245 Score: 197
Period size: 77 Copynumber: 1.9 Consensus size: 81
2040084 AGTAAGTAAG
2040094 CATTAAAGGAATGTAATTTAGATTACAACTCTTTTAATTGATATATATAATTCAGAATAATTAAA
1 CATTAAAGGAATGTAATTTAGATTACAACTCTTTTAATTGATATATATAATTCAGAATAATTAAA
2040159 TAAGATTTTAAATAAA
66 TAAGATTTTAAATAAA
* * * * * *
2040175 CATTAAA-GATTGTAGTTTAGATTATAAGTC-TTTAA-TG-TATATTTAATT-TGAATTAATTAA
1 CATTAAAGGAATGTAATTTAGATTACAACTCTTTTAATTGATATATATAATTCAGAA-TAATTAA
*
2040235 ATAATATTTTA
65 ATAAGATTTTA
2040246 TTTATTAATT
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
76 3 0.05
77 27 0.43
78 2 0.03
79 5 0.08
80 19 0.30
81 7 0.11
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (81 bp):
CATTAAAGGAATGTAATTTAGATTACAACTCTTTTAATTGATATATATAATTCAGAATAATTAAA
TAAGATTTTAAATAAA
Found at i:2046365 original size:78 final size:76
Alignment explanation
Indices: 2046271--2046413 Score: 175
Period size: 74 Copynumber: 1.9 Consensus size: 76
2046261 AGTAAGTAAG
2046271 CATTAAAAGAATGTAATTTAGATTACAACTCTTTTAATTGATATATATAATTCAGAA-TAATT-A
1 CATTAAAAGAATGTAA-TTAGATTACAACTC-TTTAA-TG-TATATATAATT-AGAATTAATTAA
2046334 ATAATTTTTAAATAAA
61 ATAATTTTTAAATAAA
* * * * *
2046350 CATT-AAAGATTGTAATTAGATTATAAGTCTTTAATGTATATTTAATTTGAATTAATTAAATAAT
1 CATTAAAAGAATGTAATTAGATTACAACTCTTTAATGTATATATAATTAGAATTAATTAAATAAT
2046414 ATTATTATTA
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
73 3 0.05
74 15 0.26
75 8 0.14
76 5 0.09
77 12 0.21
78 10 0.18
79 4 0.07
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.43
Consensus pattern (76 bp):
CATTAAAAGAATGTAATTAGATTACAACTCTTTAATGTATATATAATTAGAATTAATTAAATAAT
TTTTAAATAAA
Found at i:2053728 original size:19 final size:19
Alignment explanation
Indices: 2053690--2053729 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2053680 CGAATAAGTG
* * *
2053690 AATCGAATATTATATTTTA
1 AATCGAATATGAAATCTTA
2053709 AATCGAATATGAAATCTTA
1 AATCGAATATGAAATCTTA
2053728 AA
1 AA
2053730 ATTACTTAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.38
Consensus pattern (19 bp):
AATCGAATATGAAATCTTA
Found at i:2056941 original size:80 final size:81
Alignment explanation
Indices: 2056655--2056950 Score: 441
Period size: 81 Copynumber: 3.7 Consensus size: 81
2056645 ATGGATCCAT
* * * * *
2056655 AAAGGTGTAAATCATGCTAGTTATAAGAAAGGTTAAATACCTTTGCGTAAAAGATTAATTGCCTA
1 AAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATTGCCTA
*
2056720 GCTGTGCATTTGACAG
66 GTTGTGCATTTGACAG
* * * *
2056736 AAAGGTGTCAATCATGCTAGTTAGATGAAAGGTTAAATACCTTTAAATAAAAGATTAATTGCCCA
1 AAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATTGCCTA
*
2056801 GTTGTGCATTTTACAG
66 GTTGTGCATTTGACAG
* *
2056817 AAAGGTGTCAATCTTGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATTACCTA
1 AAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATTGCCTA
2056882 GTTGTGCATTTGACA-
66 GTTGTGCATTTGACAG
* * *
2056897 AAATGTGTCAATCATGCCAGTTAGATGAAAGTTTAAATCCCTTTGAGTAAAAGA
1 AAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGA
2056951 CTAAATGCTT
Statistics
Matches: 195, Mismatches: 20, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
80 50 0.26
81 145 0.74
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.31
Consensus pattern (81 bp):
AAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATTGCCTA
GTTGTGCATTTGACAG
Found at i:2063121 original size:94 final size:95
Alignment explanation
Indices: 2062951--2063129 Score: 247
Period size: 94 Copynumber: 1.9 Consensus size: 95
2062941 GATACCAAAA
* *
2062951 AGGAAAGTATCGATACCATGGATTCCAGAATACCGAAATGGTATCGATACTGAAAGGGAGTATCT
1 AGGAAAGTATCGATACCATGGATTCCAGAATACAGAAATGGTATCGATACTGAAAAGGAGTATCT
* *
2063016 GTACTATAATATAGAAGTATTGGTACTAGG
66 GTACCACAATATAGAAGTATTGGTACTAGG
** * *
2063046 AGGAAAGTATCGATACCATGGA-TCCAGAATGTAGAAA-GTGTATCGATACTGAAAATGAGTCTC
1 AGGAAAGTATCGATACCATGGATTCCAGAATACAGAAATG-GTATCGATACTGAAAAGGAGTATC
2063109 -GATACCACAATATAGAAGTAT
65 TG-TACCACAATATAGAAGTAT
2063130 CGATACCATG
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
93 2 0.03
94 50 0.68
95 22 0.30
ACGTcount: A:0.39, C:0.13, G:0.23, T:0.25
Consensus pattern (95 bp):
AGGAAAGTATCGATACCATGGATTCCAGAATACAGAAATGGTATCGATACTGAAAAGGAGTATCT
GTACCACAATATAGAAGTATTGGTACTAGG
Found at i:2063154 original size:94 final size:94
Alignment explanation
Indices: 2062936--2063155 Score: 205
Period size: 94 Copynumber: 2.3 Consensus size: 94
2062926 TACTGATAGG
** * *
2062936 GTATCGATACCAAAAAGGAAAGTATCGATACCATGGATTCCAGAATACCGAAATGGTATCGATAC
1 GTATCGATACC-AGGAGG-AAGTACCGATACCATGGATTCCAGAATACAGAAATGGTATCGATAC
* * *
2063001 TGAAAGGGAGTATCTGTACTATAATATAGAA
64 TGAAAAGGAGTATCTGTACCACAATATAGAA
* * * * **
2063032 GTATTGGTACTAGGAGGAAAGTATCGATACCATGGA-TCCAGAATGTAGAAA-GTGTATCGATAC
1 GTATCGATACCAGGAGG-AAGTACCGATACCATGGATTCCAGAATACAGAAATG-GTATCGATAC
* *
2063095 TGAAAATGAGTCTC-GATACCACAATATAGAA
64 TGAAAAGGAGTATCTG-TACCACAATATAGAA
*
2063126 GTATCGATACCATGGTAGG-GGTACCGATAC
1 GTATCGATACCA-GG-AGGAAGTACCGATAC
2063156 TATTGAGACA
Statistics
Matches: 102, Mismatches: 18, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
93 2 0.02
94 64 0.63
95 25 0.25
96 11 0.11
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.24
Consensus pattern (94 bp):
GTATCGATACCAGGAGGAAGTACCGATACCATGGATTCCAGAATACAGAAATGGTATCGATACTG
AAAAGGAGTATCTGTACCACAATATAGAA
Found at i:2063963 original size:81 final size:81
Alignment explanation
Indices: 2063530--2063941 Score: 576
Period size: 81 Copynumber: 5.1 Consensus size: 81
2063520 TATTTTAAAA
* * * *
2063530 TAAAAGATTAATTGTCTA-CTTGAGCATTTGACAGAAAGATGAT-AATCATGTCAGTTAGATGAA
1 TAAAAGATTAATTGCCTAGC-TGTGCATTTGACAGAAAGGTG-TCAATCATGCCAGTTAGATGAA
* * *
2063593 AGGTTAAATACATTCGAT
64 AGGTTAAATACCTTTGAG
* * * * *
2063611 TACAAGATTAATTCCCTAACTGTGCATTTGACATAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
2063676 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* **
2063692 TAAAAGATTAATTGCCTAGCTGTGCATTTGATAGAAAGGTGTCAATTGTGCCAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
2063757 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * *
2063773 TAAAAGATTAATTGTCTACCTGTGCATTTGACAGAAAGGTGTCAATCGTGACAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
2063838 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * *
2063854 TAAAAGATTAATTGCCTAGCTGTGCATTTGAAAAAAAGGTGTCAATCATGCCAGTTAAATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
* *
2063919 GTTAATTCCCTTTGAG
66 GTTAAATACCTTTGAG
2063935 TAAAAGA
1 TAAAAGA
2063942 CTAAATGCTT
Statistics
Matches: 298, Mismatches: 31, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
80 1 0.00
81 296 0.99
82 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.31
Consensus pattern (81 bp):
TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:2070553 original size:14 final size:13
Alignment explanation
Indices: 2070536--2070568 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 13
2070526 AATATTATTA
2070536 TATTATAATTATAT
1 TATTATAATTA-AT
2070550 TATTATAATTAAT
1 TATTATAATTAAT
2070563 TATTAT
1 TATTAT
2070569 CATTTTACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TATTATAATTAAT
Found at i:2071893 original size:47 final size:46
Alignment explanation
Indices: 2071790--2071894 Score: 104
Period size: 47 Copynumber: 2.2 Consensus size: 46
2071780 TTTTATTTAT
* **
2071790 TTATGTTTTAGTCCTTAATATATTAATACATATATTTTAGGTAAAA
1 TTATGATTTAGTCCTTAATATATTAATACATATATTTTAGCCAAAA
* ** * *
2071836 TTATATATTTAGTCCTTAA-ATATTAATTATTTATATTTATATCCCAAA
1 TTAT-GATTTAGTCCTTAATATATTAA-TACATATATTT-TAGCCAAAA
2071884 TTATGATTTAG
1 TTATGATTTAG
2071895 GTTAAATTAT
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
46 11 0.23
47 27 0.57
48 9 0.19
ACGTcount: A:0.36, C:0.08, G:0.07, T:0.50
Consensus pattern (46 bp):
TTATGATTTAGTCCTTAATATATTAATACATATATTTTAGCCAAAA
Found at i:2076603 original size:20 final size:20
Alignment explanation
Indices: 2076580--2076664 Score: 67
Period size: 20 Copynumber: 4.5 Consensus size: 20
2076570 AATCGCAAAC
2076580 CGAATTTGACTTTCGCGTTG
1 CGAATTTGACTTTCGCGTTG
* **
2076600 CGAATTTGACTAT--CGTAA
1 CGAATTTGACTTTCGCGTTG
*
2076618 CG--CTT-A-TTTCGCGTTG
1 CGAATTTGACTTTCGCGTTG
*
2076634 CAAATTT-ACCTTTCGCGTTG
1 CGAATTTGA-CTTTCGCGTTG
2076654 CGAATTTGACT
1 CGAATTTGACT
2076665 ATCACGTTGT
Statistics
Matches: 48, Mismatches: 10, Indels: 14
0.67 0.14 0.19
Matches are distributed among these distances:
14 2 0.04
15 1 0.02
16 6 0.12
18 8 0.17
20 30 0.62
21 1 0.02
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (20 bp):
CGAATTTGACTTTCGCGTTG
Found at i:2077460 original size:38 final size:39
Alignment explanation
Indices: 2077418--2077503 Score: 111
Period size: 38 Copynumber: 2.2 Consensus size: 39
2077408 TCTGATGCTC
* * *
2077418 ATCAAAATCCAAAGCCCATTTGGTGCTAAGTAAAAGG-A
1 ATCAAAATCCAAAGCCCATATGGTGCCAAGCAAAAGGAA
* * *
2077456 ATCAAAATCCAAATCTCATATGGTGCCAAGCGAAAGGAA
1 ATCAAAATCCAAAGCCCATATGGTGCCAAGCAAAAGGAA
2077495 ATCAAAATC
1 ATCAAAATC
2077504 TACAACTTGA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
38 31 0.76
39 10 0.24
ACGTcount: A:0.44, C:0.20, G:0.16, T:0.20
Consensus pattern (39 bp):
ATCAAAATCCAAAGCCCATATGGTGCCAAGCAAAAGGAA
Found at i:2077738 original size:20 final size:20
Alignment explanation
Indices: 2077715--2077766 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
2077705 GAAAAATCGT
2077715 GTTGCGAATTTGACTTTCGC
1 GTTGCGAATTTGACTTTCGC
*
2077735 GTTGCAAATTTGACTTTCGC
1 GTTGCGAATTTGACTTTCGC
*
2077755 ATTGCGAATTTG
1 GTTGCGAATTTG
2077767 TACCTTCAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.19, C:0.17, G:0.23, T:0.40
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTCGC
Found at i:2077909 original size:14 final size:14
Alignment explanation
Indices: 2077892--2077928 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
2077882 ATCAAATTAA
2077892 ACAAATCAACTTTT
1 ACAAATCAACTTTT
2077906 ACAAATCAACTTTT
1 ACAAATCAACTTTT
2077920 ACAAATCAA
1 ACAAATCAA
2077929 TTAATCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2077961 original size:75 final size:77
Alignment explanation
Indices: 2077826--2077978 Score: 197
Period size: 80 Copynumber: 2.0 Consensus size: 77
2077816 TTTTAAAACA
* *
2077826 ACAAATCAAGTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATCTACACATCAAATTA
1 ACAAATCAACTTTTACAAATCAATTAAACAA-CAAAAAAATAATTATTATCTA-ACATC-AATTA
2077891 AACAAATCAACTTTT
63 AACAAATCAACTTTT
* * *
2077906 ACAAATCAACTTTTACAAATCAATTAATCAA-AAAATAAAT-CTTATT-TCT-TCATCAATTAAA
1 ACAAATCAACTTTTACAAATCAATTAAACAACAAAA-AAATAATTATTATCTAACATCAATTAAA
2077967 CAAATCAACTTT
65 CAAATCAACTTT
2077979 CAATGTAAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
74 19 0.28
75 4 0.06
77 3 0.04
78 8 0.12
79 4 0.06
80 29 0.43
ACGTcount: A:0.50, C:0.18, G:0.01, T:0.31
Consensus pattern (77 bp):
ACAAATCAACTTTTACAAATCAATTAAACAACAAAAAAATAATTATTATCTAACATCAATTAAAC
AAATCAACTTTT
Found at i:2079351 original size:21 final size:21
Alignment explanation
Indices: 2079327--2079418 Score: 85
Period size: 21 Copynumber: 4.4 Consensus size: 21
2079317 GTGAATTGGG
* *
2079327 CTCTTGAACGGTGGGTGGGAC
1 CTCTTGAACGGTGGGAGGGGC
* ***
2079348 CTCTTGAACGATAACAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
*
2079369 CTCTTGAACTGTGGGAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
* * * *
2079390 CTCTTGAACGATAGAAGGTGC
1 CTCTTGAACGGTGGGAGGGGC
2079411 CTCTTGAA
1 CTCTTGAA
2079419 TGATGATAGG
Statistics
Matches: 55, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.22, C:0.21, G:0.34, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Found at i:2079393 original size:42 final size:42
Alignment explanation
Indices: 2079327--2079418 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 42
2079317 GTGAATTGGG
*
2079327 CTCTTGAACGGTGGGTGGGACCTCTTGAACGATA-ACAGGGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATAGA-AGGGGC
* * *
2079369 CTCTTGAACTGTGGGAGGGGCCTCTTGAACGATAGAAGGTGC
1 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATAGAAGGGGC
2079411 CTCTTGAA
1 CTCTTGAA
2079419 TGATGATAGG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 44 0.98
43 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.34, T:0.24
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCTCTTGAACGATAGAAGGGGC
Found at i:2081621 original size:19 final size:19
Alignment explanation
Indices: 2081576--2081622 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
2081566 TTCTGAAACT
*
2081576 TAAATTCGCAACGCGAAAA
1 TAAAATCGCAACGCGAAAA
* *
2081595 TGAAAATCGCAACGCGGAAC
1 T-AAAATCGCAACGCGAAAA
2081615 TAAAATCG
1 TAAAATCG
2081623 TGTTGCGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.45, C:0.21, G:0.19, T:0.15
Consensus pattern (19 bp):
TAAAATCGCAACGCGAAAA
Found at i:2081794 original size:2 final size:2
Alignment explanation
Indices: 2081787--2081824 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2081777 GAAATGGTTA
2081787 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
2081825 TGAAATTACC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2091832 original size:44 final size:44
Alignment explanation
Indices: 2091627--2091919 Score: 183
Period size: 44 Copynumber: 6.7 Consensus size: 44
2091617 AGAAATGATT
** * * * * *
2091627 AAATTAGGGGGATAAATTATAAAAGT-AAAAGGCGAAATTTAAA
1 AAATTAGGGGTCTCAATTATAAAAGTAAAAAAGTGAGATTGAAA
* * * * *
2091670 AAATTA-GAGTCTCAATTATAAATGTAGAAAA-TGAGAATAAAA
1 AAATTAGGGGTCTCAATTATAAAAGTAAAAAAGTGAGATTGAAA
** * * * * *
2091712 ATAATTAAAGATCTCAATTAT-AAAGTTAGAAA-TAGAAATTAAAA
1 A-AATTAGGGGTCTCAATTATAAAAGTAAAAAAGT-GAGATTGAAA
** ** * *
2091756 AAATTAGGGACCTCGCTCA-ATAAGGTAAAAAAGT-ATGATTGAAA
1 AAATTAGGGGTCTCAATTATA-AAAGTAAAAAAGTGA-GATTGAAA
* * *
2091800 AAAGTTAGGGGCCTCAATTATTAATGT-AAAAAGTGAGATTGAAA
1 AAA-TTAGGGGTCTCAATTATAAAAGTAAAAAAGTGAGATTGAAA
* *
2091844 AAATTAGGAGTCTCAATTATAAAAGTAAAAAAGTGAGATTACAAA
1 AAATTAGGGGTCTCAATTATAAAAGTAAAAAAGTGAGATT-GAAA
2091889 AAATTAGGGGTCTC-ATTAT-AAAGATAAAAAA
1 AAATTAGGGGTCTCAATTATAAAAG-TAAAAAA
2091920 ATAGAATTGA
Statistics
Matches: 193, Mismatches: 43, Indels: 27
0.73 0.16 0.10
Matches are distributed among these distances:
42 22 0.11
43 58 0.30
44 79 0.41
45 34 0.18
ACGTcount: A:0.51, C:0.06, G:0.17, T:0.26
Consensus pattern (44 bp):
AAATTAGGGGTCTCAATTATAAAAGTAAAAAAGTGAGATTGAAA
Found at i:2091929 original size:88 final size:86
Alignment explanation
Indices: 2091662--2091931 Score: 221
Period size: 88 Copynumber: 3.1 Consensus size: 86
2091652 TAAAAGGCGA
* * * * ** *
2091662 AATTTAAAAAATTA-GAGTCTCAATTATAAATGTAGAAAA-TGAGAATAAAAATAATTAAAGATC
1 AATTGAAAAAATTAGGAGTCTCAATTATAAAAGTAAAAAAGTGAGATTAAAAA-AATTAGGGGTC
* *
2091725 TCAATTATAAAGTTAGAAATAG
65 TCAATTATAAAGTAAAAAATAG
* * ** * * *
2091747 AAATTAAAAAAATTAGG-GACCTCGCTCA-ATAAGGTAAAAAAGT-ATGATTGAAAAAAGTTAGG
1 -AATTGAAAAAATTAGGAG-TCTCAATTATA-AAAGTAAAAAAGTGA-GATT-AAAAAAATTAGG
* * *
2091809 GGCCTCAATTATTAATGTAAAAAGT-G
61 GGTCTCAATTA-TAAAGTAAAAAATAG
2091835 AGATTGAAAAAATTAGGAGTCTCAATTATAAAAGTAAAAAAGTGAGATTACAAAAAATTAGGGGT
1 A-ATTGAAAAAATTAGGAGTCTCAATTATAAAAGTAAAAAAGTGAGATTA-AAAAAATTAGGGGT
2091900 CTC-ATTATAAAGATAAAAAAATAG
64 CTCAATTATAAAG-T-AAAAAATAG
2091924 AATTGAAA
1 AATTGAAA
2091932 CCTTAAGGGC
Statistics
Matches: 142, Mismatches: 27, Indels: 28
0.72 0.14 0.14
Matches are distributed among these distances:
86 19 0.13
87 23 0.16
88 81 0.57
89 19 0.13
ACGTcount: A:0.51, C:0.06, G:0.16, T:0.26
Consensus pattern (86 bp):
AATTGAAAAAATTAGGAGTCTCAATTATAAAAGTAAAAAAGTGAGATTAAAAAAATTAGGGGTCT
CAATTATAAAGTAAAAAATAG
Found at i:2092097 original size:18 final size:17
Alignment explanation
Indices: 2092074--2092116 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
2092064 GGAATTTTCT
2092074 GATAAATTTAAAAAAAAA
1 GATAAATTT-AAAAAAAA
** *
2092092 GATAAAAATAAAAATAA
1 GATAAATTTAAAAAAAA
2092109 GATAAATT
1 GATAAATT
2092117 AAGTTTACGG
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (17 bp):
GATAAATTTAAAAAAAA
Found at i:2094716 original size:24 final size:24
Alignment explanation
Indices: 2094689--2094785 Score: 122
Period size: 24 Copynumber: 4.0 Consensus size: 24
2094679 ATAAACGGAG
*
2094689 ATATCAAAAATCAAAACAGAATTC
1 ATATCAAAAATCAGAACAGAATTC
* * *
2094713 ATATCATATATCAGAACAGAATCC
1 ATATCAAAAATCAGAACAGAATTC
*
2094737 ATATCAAAAATCAGAACAAAATTC
1 ATATCAAAAATCAGAACAGAATTC
* * *
2094761 AGATCAGAAATCAGAACATAATTC
1 ATATCAAAAATCAGAACAGAATTC
2094785 A
1 A
2094786 AATTGGAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.54, C:0.18, G:0.07, T:0.22
Consensus pattern (24 bp):
ATATCAAAAATCAGAACAGAATTC
Found at i:2094794 original size:24 final size:24
Alignment explanation
Indices: 2094691--2094797 Score: 88
Period size: 24 Copynumber: 4.5 Consensus size: 24
2094681 AAACGGAGAT
* * * *
2094691 ATCAAAAATCAAAACAGAATTCAT
1 ATCAGAAATCAGAACAAAATTCAA
* * * * *
2094715 ATCATATATCAGAACAGAATCCAT
1 ATCAGAAATCAGAACAAAATTCAA
* *
2094739 ATCAAAAATCAGAACAAAATTCAG
1 ATCAGAAATCAGAACAAAATTCAA
*
2094763 ATCAGAAATCAGAACATAATTCAA
1 ATCAGAAATCAGAACAAAATTCAA
**
2094787 ATTGGAAATCA
1 ATCAGAAATCA
2094798 AATAAAACAT
Statistics
Matches: 69, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 69 1.00
ACGTcount: A:0.53, C:0.17, G:0.08, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAGAACAAAATTCAA
Found at i:2096562 original size:70 final size:70
Alignment explanation
Indices: 2096449--2096588 Score: 271
Period size: 70 Copynumber: 2.0 Consensus size: 70
2096439 AACCCTCTTG
2096449 GGGTTAAAAATCAGTTATCTATATTTTCTAAGCAAAACTAGCAATTTACATACACATCAATAGTT
1 GGGTTAAAAATCAGTTATCTATATTTTCTAAGCAAAACTAGCAATTTACATACACATCAATAGTT
2096514 TCATC
66 TCATC
*
2096519 GGGTTAAAAATCAGTTATCTATATTTTCTAAGCAAAACTAGCAATTTGCATACACATCAATAGTT
1 GGGTTAAAAATCAGTTATCTATATTTTCTAAGCAAAACTAGCAATTTACATACACATCAATAGTT
2096584 TCATC
66 TCATC
2096589 AGCTCAATAT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (70 bp):
GGGTTAAAAATCAGTTATCTATATTTTCTAAGCAAAACTAGCAATTTACATACACATCAATAGTT
TCATC
Found at i:2105919 original size:23 final size:23
Alignment explanation
Indices: 2105889--2105967 Score: 74
Period size: 21 Copynumber: 3.6 Consensus size: 23
2105879 GCATGGCCTT
2105889 GTGCATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTCAAGGA
* * * *
2105912 GTGCATCGGTGTACCTTC-ATG-
1 GTGCATCGATGCACATTCAAGGA
* *
2105933 GTGTATCGATGTACATTCAAGGA
1 GTGCATCGATGCACATTCAAGGA
*
2105956 -TGCATTGATGCA
1 GTGCATCGATGCA
2105968 TTGTTAGGTG
Statistics
Matches: 43, Mismatches: 11, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
21 15 0.35
22 13 0.30
23 15 0.35
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAGGA
Found at i:2111890 original size:65 final size:63
Alignment explanation
Indices: 2111815--2111983 Score: 191
Period size: 65 Copynumber: 2.6 Consensus size: 63
2111805 TTCAAAATAG
*
2111815 CCTGAGTGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTTAATGTTTTC-A-TTAT
1 CCTGAGTGCATCGATGCATGG-TTGTGCATCGATGCATCAAATGCATTCAATG--TTCAATTTAT
2111878 AT
63 -T
* * *
2111880 CCTGAGTGCATCGATGCATGGTATGTGCATAGATGCATAAAATGCATTCGATGTTCAATTTATT
1 CCTGAGTGCATCGATGCATGGT-TGTGCATCGATGCATCAAATGCATTCAATGTTCAATTTATT
* *
2111944 CATTG-GTGCATCGATGCATGGATTGGTGCATCGGTGCATC
1 C-CTGAGTGCATCGATGCATGG-TT-GTGCATCGATGCATC
2111984 CGTGCATCCC
Statistics
Matches: 90, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
63 3 0.03
64 21 0.23
65 66 0.73
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (63 bp):
CCTGAGTGCATCGATGCATGGTTGTGCATCGATGCATCAAATGCATTCAATGTTCAATTTATT
Found at i:2111970 original size:20 final size:20
Alignment explanation
Indices: 2111945--2111982 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2111935 CAATTTATTC
2111945 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
2111965 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
2111983 CCGTGCATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:2113407 original size:35 final size:35
Alignment explanation
Indices: 2113362--2113430 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
2113352 CGTCACGTAC
* *
2113362 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTGTA
1 AGTAAAGCCCTGAGCACAAAGCCGAGGAGACTGTA
2113397 AGTAAAGCCCTGAGCACAAAGCCGAGGAGACTGT
1 AGTAAAGCCCTGAGCACAAAGCCGAGGAGACTGT
2113431 CAAAAAATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.33, C:0.25, G:0.30, T:0.12
Consensus pattern (35 bp):
AGTAAAGCCCTGAGCACAAAGCCGAGGAGACTGTA
Found at i:2114164 original size:45 final size:45
Alignment explanation
Indices: 2114100--2114199 Score: 119
Period size: 45 Copynumber: 2.2 Consensus size: 45
2114090 CTTTTTGATA
* ** * * **
2114100 TTTTTAAAAACTTCAGGTCATCTGTAAGCCCTTCAGTGCATTATG
1 TTTTCAAAAACTTCAGGTCATCCATAAGACCTGCAGTGCAGGATG
* *
2114145 TTTTCAAAATCTTCGGGTCATCCATAAGACCTGCAGTGCAGGATG
1 TTTTCAAAAACTTCAGGTCATCCATAAGACCTGCAGTGCAGGATG
2114190 TTTTCAAAAA
1 TTTTCAAAAA
2114200 GCCTTCGGGA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (45 bp):
TTTTCAAAAACTTCAGGTCATCCATAAGACCTGCAGTGCAGGATG
Found at i:2114270 original size:45 final size:45
Alignment explanation
Indices: 2114216--2114364 Score: 226
Period size: 45 Copynumber: 3.3 Consensus size: 45
2114206 GGGAGCTTTT
** *
2114216 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATATTTTCAAAACCTTCGGGTCATCCATAAGACCTTCAGTGCA
* * *
2114261 TGATGTTTTCAAAACCTTCGGGCCATCCATAAGACCTTCAATGCA
1 TGATATTTTCAAAACCTTCGGGTCATCCATAAGACCTTCAGTGCA
*
2114306 TGATATTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCA
1 TGATATTTTCAAAACCTTCGGGTCATCCATAAGACCTTCAGTGCA
*
2114351 TGATGTTTTCAAAA
1 TGATATTTTCAAAA
2114365 AGCCTTCGAG
Statistics
Matches: 93, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 93 1.00
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (45 bp):
TGATATTTTCAAAACCTTCGGGTCATCCATAAGACCTTCAGTGCA
Found at i:2114271 original size:121 final size:121
Alignment explanation
Indices: 2114057--2114327 Score: 438
Period size: 121 Copynumber: 2.3 Consensus size: 121
2114047 GTACGCCCTT
*
2114057 CAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTTAAAAACTTCAGGTCATC
1 CAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAAACTTCAGGTCATC
* * *
2114122 TGTAAGCCCTTCAGTGCATTATGTTTTCAAAATCTTCGGGTCATCCATAAGACCTG
66 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGCCATCCATAAGACCTG
* * *
2114178 CAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATC
1 CAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAAACTTCAGGTCATC
*
2114243 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGCCATCCATAAGACCTT
66 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGCCATCCATAAGACCTG
* *
2114299 CAATGCATGATATTTTC-AAAA-CCTTCGGG
1 CAGTGCATGATGTTTTCAAAAAGCCTTCGGG
2114328 TCATCCATAA
Statistics
Matches: 139, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
119 8 0.06
120 4 0.03
121 127 0.91
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (121 bp):
CAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAAACTTCAGGTCATC
TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGCCATCCATAAGACCTG
Found at i:2114391 original size:121 final size:121
Alignment explanation
Indices: 2114261--2114485 Score: 315
Period size: 121 Copynumber: 1.9 Consensus size: 121
2114251 CTTCAGTGCA
* **
2114261 TGATGTTTTCAAAACCTTCGGGCCATCCATAAGACCTTCAATGCATGATATTTTCAAAACCTTCG
1 TGATATTTTCAAAACCTTCAAGCCATCCATAAGACCTTCAATGCATGATATTTTCAAAACCTTCG
* *
2114326 GGTCATCCATAAGACCTGCAGTGCATGATGTTTTCAAAAAGCCTTCGAGAGCTTTT
66 GATCATCCATAAGACCTGCAGTGCATAATGTTTTCAAAAAGCCTTCGAGAGCTTTT
** ** * *
2114382 TGATATTTTCAAAACCTTCAATTCATCTGTAAGCCCTTCAGTGCATGATATTTTCAAAACCTTCG
1 TGATATTTTCAAAACCTTCAAGCCATCCATAAGACCTTCAATGCATGATATTTTCAAAACCTTCG
** * *
2114447 GATCATCTGTAAGCCCTTCAGTGCATAATGTTTTCAAAA
66 GATCATCCATAAGACCTGCAGTGCATAATGTTTTCAAAA
2114486 CCTTCGGGTC
Statistics
Matches: 89, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
121 89 1.00
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (121 bp):
TGATATTTTCAAAACCTTCAAGCCATCCATAAGACCTTCAATGCATGATATTTTCAAAACCTTCG
GATCATCCATAAGACCTGCAGTGCATAATGTTTTCAAAAAGCCTTCGAGAGCTTTT
Found at i:2114419 original size:166 final size:166
Alignment explanation
Indices: 2114124--2114530 Score: 625
Period size: 166 Copynumber: 2.5 Consensus size: 166
2114114 AGGTCATCTG
* * *
2114124 TAAGCCCTTCAGTGCATTATGTTTTCAAAATCTTCGGGTCATCCATAAGACCTGCAGTGCAGGAT
1 TAAGCCCTTCAGTGCATAATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCATGAT
* **
2114189 GTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTT
66 GTTTTCAAAAAGCCTTCGAGAGCTTTTTGATATTTTCAAAACCTTCAAGTCATCTGTAAGCCCTT
* *
2114254 CAGTGCATGATGTTTTCAAAACCTTCGGGCCATCCA
131 CAGTGCATGATATTTTCAAAACCTTCGGACCATCCA
* * * *
2114290 TAAGACCTTCAATGCATGATATTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCATGAT
1 TAAGCCCTTCAGTGCATAATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCATGAT
*
2114355 GTTTTCAAAAAGCCTTCGAGAGCTTTTTGATATTTTCAAAACCTTCAATTCATCTGTAAGCCCTT
66 GTTTTCAAAAAGCCTTCGAGAGCTTTTTGATATTTTCAAAACCTTCAAGTCATCTGTAAGCCCTT
* **
2114420 CAGTGCATGATATTTTCAAAACCTTCGGATCATCTG
131 CAGTGCATGATATTTTCAAAACCTTCGGACCATCCA
** * *
2114456 TAAGCCCTTCAGTGCATAATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
1 TAAGCCCTTCAGTGCATAATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCATGAT
*
2114521 ATTTTCAAAA
66 GTTTTCAAAA
2114531 CCTTCGGGTC
Statistics
Matches: 217, Mismatches: 24, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
166 217 1.00
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (166 bp):
TAAGCCCTTCAGTGCATAATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCATGAT
GTTTTCAAAAAGCCTTCGAGAGCTTTTTGATATTTTCAAAACCTTCAAGTCATCTGTAAGCCCTT
CAGTGCATGATATTTTCAAAACCTTCGGACCATCCA
Found at i:2114431 original size:45 final size:45
Alignment explanation
Indices: 2114382--2114570 Score: 290
Period size: 45 Copynumber: 4.2 Consensus size: 45
2114372 GAGAGCTTTT
* *
2114382 TGATATTTTCAAAACCTTCAATTCATCTGTAAGCCCTTCAGTGCA
1 TGATATTTTCAAAACCTTCGAGTCATCTGTAAGCCCTTCAGTGCA
2114427 TGATATTTTCAAAACCTTCG-GATCATCTGTAAGCCCTTCAGTGCA
1 TGATATTTTCAAAACCTTCGAG-TCATCTGTAAGCCCTTCAGTGCA
* * *
2114472 TAATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATATTTTCAAAACCTTCGAGTCATCTGTAAGCCCTTCAGTGCA
* *
2114517 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTACA
1 TGATATTTTCAAAACCTTCGAGTCATCTGTAAGCCCTTCAGTGCA
*
2114562 TGATGTTTT
1 TGATATTTT
2114571 TAAGACCTCT
Statistics
Matches: 134, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
45 133 0.99
46 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.35
Consensus pattern (45 bp):
TGATATTTTCAAAACCTTCGAGTCATCTGTAAGCCCTTCAGTGCA
Found at i:2114775 original size:15 final size:15
Alignment explanation
Indices: 2114727--2114775 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
2114717 TTCGTTTTAT
* *
2114727 TATTATTATTAAAAA
1 TATTATTATTATATA
2114742 TATTATTATTAT-TA
1 TATTATTATTATATA
2114756 TTATTATTATTATATA
1 -TATTATTATTATATA
2114772 TATT
1 TATT
2114776 GCTTTATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 1 0.03
15 27 0.90
16 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TATTATTATTATATA
Found at i:2114787 original size:3 final size:3
Alignment explanation
Indices: 2114723--2114768 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
2114713 TCATTTCGTT
** *
2114723 TTA TTA TTA TTA TTA AAA ATA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2114769 ATATATTGCT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:2115009 original size:16 final size:16
Alignment explanation
Indices: 2114988--2115030 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
2114978 CCAGTAAAGA
*
2114988 AACCCTAGGGTATCAT
1 AACCCTAGGGCATCAT
2115004 AACCCTAGGGCATCAT
1 AACCCTAGGGCATCAT
2115020 AACCCTAGGGC
1 AACCCTAGGGC
2115031 CACGAGGCTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (16 bp):
AACCCTAGGGCATCAT
Found at i:2116755 original size:155 final size:153
Alignment explanation
Indices: 2116510--2116790 Score: 320
Period size: 155 Copynumber: 1.8 Consensus size: 153
2116500 ATTTATTTTA
2116510 ATTTTTTAGGAAAAATTATTACATTTTTCAATATTTTATTTTTAATATCAAAGAAAATGGCAGTC
1 ATTTTTTAGGAAAAATTATTA-ATTTTTCAATATTTTATTTTTAATATCAAAGAAAATGGCAGTC
* * *
2116575 TTAAAGCAACTAGATGTCCTATTCTGGTATATTAAAAAT-AATAAATATCCTACTTATAAAACCA
65 GTAAAGCAACTAGAAGTCCTATTCTGATAT-TTAAAAATAAATAAATATCCTACTTATAAAACCA
2116639 AAAATACATATTGTTTATTTAAATT
129 AAAATACATATTGTTTATTTAAATT
* * *
2116664 ATTTTCTTAGTAAAAATTATT-ATTTTT-ATTATTTATTAATTTTATAATAT-TAAG-AAATGGA
1 ATTTT-TTAGGAAAAATTATTAATTTTTCAATA-TT-TT-ATTTT-TAATATCAAAGAAAATGG-
* * * * ** * * *
2116725 CTGTCGTAAAGCACCTAGAAGTCTTTTTCTGATATTTCTAAGTAAATAAATATCTTATTTATAAA
60 CAGTCGTAAAGCAACTAGAAGTCCTATTCTGATATTTAAAAATAAATAAATATCCTACTTATAAA
2116790 A
125 A
2116791 ATAGAAATAT
Statistics
Matches: 105, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
152 3 0.03
153 8 0.08
154 18 0.17
155 70 0.67
156 6 0.06
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (153 bp):
ATTTTTTAGGAAAAATTATTAATTTTTCAATATTTTATTTTTAATATCAAAGAAAATGGCAGTCG
TAAAGCAACTAGAAGTCCTATTCTGATATTTAAAAATAAATAAATATCCTACTTATAAAACCAAA
AATACATATTGTTTATTTAAATT
Found at i:2125165 original size:26 final size:25
Alignment explanation
Indices: 2125136--2125195 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 25
2125126 ATCTTTTGAT
*
2125136 ATTCGATTCGAATTTTTTTTAAAAAA
1 ATTCGAGTCGAA-TTTTTTTAAAAAA
* *
2125162 ATTCGGGTCGGATTTTTTTAAAAAA
1 ATTCGAGTCGAATTTTTTTAAAAAA
2125187 ATTTCGAGT
1 A-TTCGAGT
2125196 TCAGGTCGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 14 0.48
26 15 0.52
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.43
Consensus pattern (25 bp):
ATTCGAGTCGAATTTTTTTAAAAAA
Found at i:2125233 original size:33 final size:33
Alignment explanation
Indices: 2125196--2125279 Score: 87
Period size: 38 Copynumber: 2.4 Consensus size: 33
2125186 AATTTCGAGT
* *
2125196 TCAGGTCGGGTTTTTTTAAGTTTGATATTCGGG
1 TCAGGTAGGGTTTTTTTAAGTGTGATATTCGGG
*
2125229 TCAGGTTGGGTTGGGGTTTTTTAAGTGTGATATTCGGG
1 TCAGGTAGGG-T----TTTTTTAAGTGTGATATTCGGG
*
2125267 TCGGGTAGGGTTT
1 TCAGGTAGGGTTT
2125280 AAGGTGAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
33 11 0.26
34 1 0.02
37 1 0.02
38 29 0.69
ACGTcount: A:0.13, C:0.07, G:0.37, T:0.43
Consensus pattern (33 bp):
TCAGGTAGGGTTTTTTTAAGTGTGATATTCGGG
Found at i:2125840 original size:16 final size:18
Alignment explanation
Indices: 2125819--2125866 Score: 73
Period size: 16 Copynumber: 2.8 Consensus size: 18
2125809 TTTTCAGATT
2125819 CAGATTCCAATTCC-T-A
1 CAGATTCCAATTCCTTCA
2125835 CAGATTCCAATTCCTTCA
1 CAGATTCCAATTCCTTCA
*
2125853 CAGATTTCAATTCC
1 CAGATTCCAATTCC
2125867 CTTAGAAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 14 0.48
17 1 0.03
18 14 0.48
ACGTcount: A:0.29, C:0.31, G:0.06, T:0.33
Consensus pattern (18 bp):
CAGATTCCAATTCCTTCA
Found at i:2129441 original size:132 final size:132
Alignment explanation
Indices: 2129243--2129616 Score: 452
Period size: 132 Copynumber: 2.8 Consensus size: 132
2129233 AAATCCTTTT
* * *
2129243 TTTTCCAGATTTGATC-TCCTCTAAAGAGCAGT-GAGCAAATCTACCCCGATTCAATCTTCCCCA
1 TTTTCTAGATTTGATCTTCC-CTAAAGAGCAGTGGAGCAAATCTACCTCGATTCAATCTTCCCTA
* * * *
2129306 AAGAATAGTGGAGTGAATTAAAATTTTTCAGATATGATATTCATTGAAGACCAACATAGCATATC
65 AAGAGTAGTGGAGTGAATTAAAATTTTTCAGATCTGATCTTCATTGAAGACCAACAGAGCATATC
2129371 CAC
130 CAC
*
2129374 TTTTCTAGATTTGATCTTCCCTAAAGAGCAGTGGAGCAAATCTACCTCAATTCAATCTTCCCTAA
1 TTTTCTAGATTTGATCTTCCCTAAAGAGCAGTGGAGCAAATCTACCTCGATTCAATCTTCCCTAA
* * ** ** * **
2129439 AGAGCAATGGAGTGAA-TAATTTTTTTCCAGATCTGATCTTCCCTGAAGAGCAATGGAGCATATC
66 AGAGTAGTGGAGTGAATTAAAATTTTT-CAGATCTGATCTTCATTGAAGACCAACAGAGCATATC
*
2129503 CAT
130 CAC
* * * * *
2129506 TTTTCTAGATTTGATCTTCCTTGAAGAGCAATGGAGCAGATCTAACTCGATTCAATCTTCCCTGA
1 TTTTCTAGATTTGATCTTCCCTAAAGAGCAGTGGAGCAAATCTACCTCGATTCAATCTTCCCT-A
* *
2129571 AA-AGTAGTGGAGTGAATCAAAAATTTTT-AGATCTAATCTTCATTGA
65 AAGAGTAGTGGAGTGAAT-TAAAATTTTTCAGATCTGATCTTCATTGA
2129617 GTAGATCCCC
Statistics
Matches: 205, Mismatches: 32, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
131 35 0.17
132 160 0.78
133 3 0.01
134 7 0.03
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (132 bp):
TTTTCTAGATTTGATCTTCCCTAAAGAGCAGTGGAGCAAATCTACCTCGATTCAATCTTCCCTAA
AGAGTAGTGGAGTGAATTAAAATTTTTCAGATCTGATCTTCATTGAAGACCAACAGAGCATATCC
AC
Found at i:2129524 original size:45 final size:44
Alignment explanation
Indices: 2129363--2129543 Score: 154
Period size: 45 Copynumber: 4.1 Consensus size: 44
2129353 AGACCAACAT
* *
2129363 AGCATATCCACTTTTCTAGATTTGATCTTCCCTAAAGAGCAGTGG
1 AGCATAT-CATTTTTCTAGATTTGATCTTCCCTAAAGAGCAATGG
* *** **
2129408 AGCAAATC-TACCTC-A-ATTCAATCTTCCCTAAAGAGCAATGG
1 AGCATATCATTTTTCTAGATTTGATCTTCCCTAAAGAGCAATGG
* * * * *
2129449 AGTGAATAAT-TTTTTTCCAGATCTGATCTTCCCTGAAGAGCAATGG
1 A--GCAT-ATCATTTTTCTAGATTTGATCTTCCCTAAAGAGCAATGG
* *
2129495 AGCATATCCATTTTTCTAGATTTGATCTTCCTTGAAGAGCAATGG
1 AGCATAT-CATTTTTCTAGATTTGATCTTCCCTAAAGAGCAATGG
2129540 AGCA
1 AGCA
2129544 GATCTAACTC
Statistics
Matches: 106, Mismatches: 22, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
41 24 0.23
42 1 0.01
43 6 0.06
44 9 0.08
45 43 0.41
46 23 0.22
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (44 bp):
AGCATATCATTTTTCTAGATTTGATCTTCCCTAAAGAGCAATGG
Found at i:2130617 original size:21 final size:21
Alignment explanation
Indices: 2130566--2130618 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
2130556 ATTATTACTA
2130566 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
2130587 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
2130608 TCGCAATGCGA
1 TCGCAATGCGA
2130619 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:2130651 original size:21 final size:21
Alignment explanation
Indices: 2130608--2130721 Score: 83
Period size: 21 Copynumber: 5.5 Consensus size: 21
2130598 TTTTCCCAAT
* *
2130608 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTAGAAAA
*
2130628 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTAGAAAA
* **
2130649 TCGCAATGCG-ATACT-GACTA
1 TCGCAATGCGAAT-TTAGAAAA
* * *
2130669 TCGCAACGCG-ATAATACAAAA
1 TCGCAATGCGAAT-TTAGAAAA
* *
2130690 TCACAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTAGAAAA
2130711 TCGCAATGCGA
1 TCGCAATGCGA
2130722 TATTGACTAT
Statistics
Matches: 73, Mismatches: 17, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
20 30 0.41
21 41 0.56
22 2 0.03
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTTAGAAAA
Found at i:2130659 original size:62 final size:60
Alignment explanation
Indices: 2130608--2130746 Score: 172
Period size: 62 Copynumber: 2.3 Consensus size: 60
2130598 TTTTCCCAAT
* * * *
2130608 TCGCAATGCGAATAAGT-AAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACTA
1 TCGCAACGCG-ATAA-TAAAATCACAATGCGAATTTGGAAAATCGCAATGCGATACTCACAA
* * *
2130669 TCGCAACGCGATAATACAAAATCACAATGCGAATTTGGAAAATCGCAATGCGATATTGACTA
1 TCGCAACGCGATAAT--AAAATCACAATGCGAATTTGGAAAATCGCAATGCGATACTCACAA
2130731 TCGCAACGCGATAATA
1 TCGCAACGCGATAATA
2130747 CAAAATCGCA
Statistics
Matches: 72, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
59 1 0.01
60 5 0.07
61 9 0.12
62 57 0.79
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.22
Consensus pattern (60 bp):
TCGCAACGCGATAATAAAATCACAATGCGAATTTGGAAAATCGCAATGCGATACTCACAA
Found at i:2130735 original size:20 final size:20
Alignment explanation
Indices: 2130710--2130864 Score: 93
Period size: 20 Copynumber: 7.7 Consensus size: 20
2130700 AATTTGGAAA
*
2130710 ATCGCAATGCGATATTGACT
1 ATCGCAACGCGATATTGACT
* *
2130730 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATATTGAC--T
*
2130751 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATATTGACT
* * ** *
2130771 TTCGCAATGTTATAGTGACT
1 ATCGCAACGCGATATTGACT
*
2130791 TTCGCAACGCGAT-TCTGACT
1 ATCGCAACGCGATAT-TGACT
* *
2130811 TTCGCAACGCAAT-TCTGACT
1 ATCGCAACGCGATAT-TGACT
* * *
2130831 CTCGCAACGAGAT-TCTAACT
1 ATCGCAACGCGATAT-TGACT
*
2130851 ATCGCAACGAGATA
1 ATCGCAACGCGATA
2130865 ATACAGAATC
Statistics
Matches: 110, Mismatches: 20, Indels: 9
0.79 0.14 0.06
Matches are distributed among these distances:
19 2 0.02
20 91 0.83
21 15 0.14
22 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATATTGACT
Found at i:2130747 original size:62 final size:62
Alignment explanation
Indices: 2130625--2130762 Score: 249
Period size: 62 Copynumber: 2.2 Consensus size: 62
2130615 GCGAATAAGT
2130625 AAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACTATCGCAACGCGATAATACA
1 AAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACTATCGCAACGCGATAATACA
* *
2130687 AAATCACAATGCGAATTTGGAAAATCGCAATGCGATATTGACTATCGCAACGCGATAATACA
1 AAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACTATCGCAACGCGATAATACA
*
2130749 AAATCGCAACGCGA
1 AAATCGCAATGCGA
2130763 TACTGACTTT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 72 1.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.20
Consensus pattern (62 bp):
AAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACTATCGCAACGCGATAATACA
Found at i:2130756 original size:21 final size:21
Alignment explanation
Indices: 2130668--2130764 Score: 83
Period size: 21 Copynumber: 4.7 Consensus size: 21
2130658 GATACTGACT
2130668 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
* * * **
2130689 ATCACAATGCGA-ATTTGGAAA
1 ATCGCAACGCGATA-ATACAAA
* * *
2130710 ATCGCAATGCGATATTGAC--T
1 ATCGCAACGCGATAAT-ACAAA
2130730 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
2130751 ATCGCAACGCGATA
1 ATCGCAACGCGATA
2130765 CTGACTTTCG
Statistics
Matches: 59, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
19 2 0.03
20 15 0.25
21 41 0.69
22 1 0.02
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGATAATACAAA
Found at i:2130830 original size:40 final size:40
Alignment explanation
Indices: 2130752--2130859 Score: 126
Period size: 40 Copynumber: 2.7 Consensus size: 40
2130742 TAATACAAAA
* * ** * *
2130752 TCGCAACGCGATACTGACTTTCGCAATGTTATAGTGACTT
1 TCGCAACGCGATTCTGACTTTCGCAACGCAATACTGACTC
*
2130792 TCGCAACGCGATTCTGACTTTCGCAACGCAATTCTGACTC
1 TCGCAACGCGATTCTGACTTTCGCAACGCAATACTGACTC
* * *
2130832 TCGCAACGAGATTCTAACTATCGCAACG
1 TCGCAACGCGATTCTGACTTTCGCAACG
2130860 AGATAATACA
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.28
Consensus pattern (40 bp):
TCGCAACGCGATTCTGACTTTCGCAACGCAATACTGACTC
Found at i:2131637 original size:24 final size:24
Alignment explanation
Indices: 2131599--2131652 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
2131589 GTATTCAAAA
* *
2131599 TTTGATCTTGTTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
2131623 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
2131647 TTTGAT
1 TTTGAT
2131653 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.43
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:2131844 original size:12 final size:12
Alignment explanation
Indices: 2131827--2131851 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2131817 ATATAATCCT
2131827 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2131839 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2131851 G
1 G
2131852 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2134192 original size:19 final size:20
Alignment explanation
Indices: 2134150--2134204 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
2134140 CAATCATCTT
*
2134150 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAACGCGGA
2134170 AATGACTATCGCAATC-C-GA
1 AATGACTATCGCAA-CGCGGA
**
2134189 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
2134205 AGAGAATCGC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 1 0.03
19 14 0.47
20 14 0.47
21 1 0.03
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (20 bp):
AATGACTATCGCAACGCGGA
Found at i:2134223 original size:33 final size:33
Alignment explanation
Indices: 2134177--2134303 Score: 209
Period size: 33 Copynumber: 3.8 Consensus size: 33
2134167 GGAAATGACT
*
2134177 ATCGCAATCCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
2134210 ATCGCAATGCGAAATGAAAATCGCAACGACAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
2134243 ATCGTAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
2134276 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
2134304 CGAATTTAGT
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 87 1.00
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2134233 original size:19 final size:18
Alignment explanation
Indices: 2134157--2134307 Score: 83
Period size: 19 Copynumber: 8.7 Consensus size: 18
2134147 CTTAATGTCT
**
2134157 ATCGCAACGCGGAAATGACT
1 ATCGCAA-GC-GAAATGAAA
*
2134177 ATCGCAATCCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
2134196 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
2134210 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
2134229 ATCGCAA-CGACA-G--A
1 ATCGCAAGCGAAATGAAA
*
2134243 ATCGTAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
**
2134262 ATCGCAA-CG--A-GGGA
1 ATCGCAAGCGAAATGAAA
2134276 ATCGCAAAGCGAAATGAAA
1 ATCGC-AAGCGAAATGAAA
2134295 ATCGCAACGCGAA
1 ATCGCAA-GCGAA
2134308 TTTAGTTTCG
Statistics
Matches: 101, Mismatches: 14, Indels: 33
0.68 0.09 0.22
Matches are distributed among these distances:
14 24 0.24
15 4 0.04
16 9 0.09
17 9 0.09
18 4 0.04
19 43 0.43
20 8 0.08
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.13
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:2134325 original size:19 final size:19
Alignment explanation
Indices: 2134303--2134363 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
2134293 AAATCGCAAC
*
2134303 GCGAATTTAGTTTCGTGTT
1 GCGAATTTAGTTTCGCGTT
*
2134322 GCGATTTTAGTTTCGCGTT
1 GCGAATTTAGTTTCGCGTT
* *
2134341 GCGATTTTCA-TTTCGCATT
1 GCGAATTT-AGTTTCGCGTT
2134360 GCGA
1 GCGA
2134364 TTCTCTCGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
19 37 0.97
20 1 0.03
ACGTcount: A:0.15, C:0.16, G:0.25, T:0.44
Consensus pattern (19 bp):
GCGAATTTAGTTTCGCGTT
Found at i:2134364 original size:19 final size:18
Alignment explanation
Indices: 2134320--2134430 Score: 87
Period size: 19 Copynumber: 6.4 Consensus size: 18
2134310 TAGTTTCGTG
2134320 TTGCGATTTT-AGTTTCGC
1 TTGCGATTTTCA-TTTCGC
2134338 GTTGCGATTTTCATTTCGC
1 -TTGCGATTTTCATTTCGC
*
2134357 ATTGCGA--TTC-TCTCG-
1 -TTGCGATTTTCATTTCGC
*
2134372 TTACGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
*
2134390 GTTGCGA--TTC-TCTCG-
1 -TTGCGATTTTCATTTCGC
2134405 TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
2134423 ATTGCGAT
1 -TTGCGAT
2134431 AGTCATTTTT
Statistics
Matches: 74, Mismatches: 7, Indels: 22
0.72 0.07 0.21
Matches are distributed among these distances:
14 11 0.15
16 14 0.19
17 14 0.19
19 34 0.46
20 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.46
Consensus pattern (18 bp):
TTGCGATTTTCATTTCGC
Found at i:2134384 original size:33 final size:33
Alignment explanation
Indices: 2134337--2134430 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
2134327 TTTAGTTTCG
2134337 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* *
2134370 CGTTACGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
2134403 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
2134431 AGTCATTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:2134556 original size:14 final size:14
Alignment explanation
Indices: 2134537--2134573 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2134527 CATCAATTAA
2134537 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2134551 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2134565 ACAAATCAA
1 ACAAATCAA
2134574 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2135999 original size:42 final size:42
Alignment explanation
Indices: 2135914--2136002 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 42
2135904 GTGAATCGGG
* * *
2135914 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGAAGGGACCTCTTCAACGATGACAGGGGC
* *
2135956 CTCTTGAACGGTGGAAGGGGA-CTC-TCAAGGAATGATAGGGGC
1 CTCTTGAACGGTGGAA-GGGACCTCTTCAACG-ATGACAGGGGC
2135998 CTCTT
1 CTCTT
2136003 CACGATAGGA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 5 0.12
42 31 0.77
43 4 0.10
ACGTcount: A:0.22, C:0.20, G:0.34, T:0.24
Consensus pattern (42 bp):
CTCTTGAACGGTGGAAGGGACCTCTTCAACGATGACAGGGGC
Found at i:2136585 original size:94 final size:94
Alignment explanation
Indices: 2136424--2136654 Score: 428
Period size: 94 Copynumber: 2.5 Consensus size: 94
2136414 GAATAGTTTC
* *
2136424 AATTGGCAGCAAACGAACAAATTTACTTTCAACCAAAAGATAAAACAAAGACAAATACTAACTTC
1 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
2136489 ACAGTGTTAAAGAATACACAGTTTAGCAG
66 ACAGTGTTAAAGAATACACAGTTTAGCAG
2136518 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
1 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
2136583 ACAGTGTTAAAGAATACACAGTTTAGCAG
66 ACAGTGTTAAAGAATACACAGTTTAGCAG
*
2136612 AATTGGCAGCAACCGAATAAATTTAC-TTCAACCAAAAGACAAA
1 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAA
2136655 TACTAACTTC
Statistics
Matches: 134, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
93 17 0.13
94 117 0.87
ACGTcount: A:0.48, C:0.19, G:0.13, T:0.20
Consensus pattern (94 bp):
AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
ACAGTGTTAAAGAATACACAGTTTAGCAG
Found at i:2136707 original size:78 final size:79
Alignment explanation
Indices: 2136564--2136716 Score: 254
Period size: 78 Copynumber: 1.9 Consensus size: 79
2136554 AAGACAAAAC
*
2136564 AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
1 AAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGCAGAATTGGCAGCAACCGAA
2136629 TAAATTTACTTCAACCA
63 TAAATTTACTTCAACCA
*
2136646 AAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCAGTATTGGCAGCAACCGAATAA
1 AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGAATTGGCAGCAACCGAATAA
2136710 ATTTACT
66 ATTTACT
2136717 AAGCAATCTA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
78 42 0.61
82 27 0.39
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (79 bp):
AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGAATTGGCAGCAACCGAATAA
ATTTACTTCAACCA
Found at i:2138418 original size:20 final size:20
Alignment explanation
Indices: 2138393--2138550 Score: 108
Period size: 19 Copynumber: 8.9 Consensus size: 20
2138383 TTTTGGTTGA
*
2138393 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGCGAG
2138413 AATGAAAATCGCAACGCG-G
1 AATGAAAATCGCAACGCGAG
**
2138432 AAATGACTATCGCAA--CGAG
1 -AATGAAAATCGCAACGCGAG
2138451 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGCGAG
*
2138466 AATGAAAATTGCAA--CGAG
1 AATGAAAATCGCAACGCGAG
2138484 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGCGAG
2138499 AATGAAAATCGCAA--CGAG
1 AATGAAAATCGCAACGCGAG
2138517 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGCGAG
*
2138532 AATGAAAATCGCAATGCGA
1 AATGAAAATCGCAACGCGA
2138551 TTTTGGTTTC
Statistics
Matches: 109, Mismatches: 7, Indels: 45
0.68 0.04 0.28
Matches are distributed among these distances:
14 22 0.20
16 15 0.14
17 12 0.11
18 2 0.02
19 29 0.27
20 29 0.27
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGCGAG
Done.